1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 2243 2244 2245 2246 2247 2248 2249 2250 2251 2252 2253 2254 2255 2256 2257 2258 2259 2260 2261 2262 2263 2264 2265 2266 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 2280 2281 2282 2283 2284 2285 2286 2287 2288 2289 2290 2291 2292 2293 2294 2295 2296 2297 2298 2299 2300 2301 2302 2303 2304 2305 2306 2307 2308 2309 2310 2311 2312 2313 2314 2315 2316 2317 2318 2319 2320 2321 2322 2323 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 2335 2336 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355 2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385 2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400 2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415 2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460 2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 2685 2686 2687 2688 2689 2690 2691 2692 2693 2694 2695 2696 2697 2698 2699 2700 2701 2702 2703 2704 2705 2706 2707 2708 2709 2710 2711 2712 2713 2714 2715 2716 2717 2718 2719 2720 2721 2722 2723 2724 2725 2726 2727 2728 2729 2730 2731 2732 2733 2734 2735 2736 2737 2738 2739 2740 2741 2742 2743 2744 2745 2746 2747 2748 2749 2750 2751 2752 2753 2754 2755 2756 2757 2758 2759 2760 2761 2762 2763 2764 2765 2766 2767 2768 2769 2770 2771 2772 2773 2774 2775 2776 2777 2778 2779 2780 2781 2782 2783 2784 2785 2786 2787 2788 2789 2790 2791 2792 2793 2794 2795 2796 2797 2798 2799 2800 2801 2802 2803 2804 2805 2806 2807 2808 2809 2810 2811 2812 2813 2814 2815 2816 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827 2828 2829 2830 2831 2832 2833 2834 2835 2836 2837 2838 2839 2840 2841 2842 2843 2844 2845 2846 2847 2848 2849 2850 2851 2852 2853 2854 2855 2856 2857 2858 2859 2860 2861 2862 2863 2864 2865 2866 2867 2868 2869 2870 2871 2872 2873 2874 2875 2876 2877 2878 2879 2880 2881 2882 2883 2884 2885 2886 2887 2888 2889 2890 2891 2892 2893 2894 2895 2896 2897 2898 2899 2900 2901 2902 2903 2904 2905 2906 2907 2908 2909 2910 2911 2912 2913 2914 2915 2916 2917 2918 2919 2920 2921 2922 2923 2924 2925 2926 2927 2928 2929 2930 2931 2932 2933 2934 2935 2936 2937 2938 2939 2940 2941 2942 2943 2944 2945 2946 2947 2948 2949 2950 2951 2952 2953 2954 2955 2956 2957 2958 2959 2960 2961 2962 2963 2964 2965 2966 2967 2968 2969 2970 2971 2972 2973 2974 2975 2976 2977 2978 2979 2980 2981 2982 2983 2984 2985 2986 2987 2988 2989 2990 2991 2992 2993 2994 2995 2996 2997 2998 2999 3000 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3011 3012 3013 3014 3015 3016 3017 3018 3019 3020 3021 3022 3023 3024 3025 3026 3027 3028 3029 3030 3031 3032 3033 3034 3035 3036 3037 3038 3039 3040 3041 3042 3043 3044 3045 3046 3047 3048 3049 3050 3051 3052 3053 3054 3055 3056 3057 3058 3059 3060 3061 3062 3063 3064 3065 3066 3067 3068 3069 3070 3071 3072 3073 3074 3075 3076 3077 3078 3079 3080 3081 3082 3083 3084 3085 3086 3087 3088 3089 3090 3091 3092 3093 3094 3095 3096 3097 3098 3099 3100 3101 3102 3103 3104 3105 3106 3107 3108 3109 3110 3111 3112 3113 3114 3115 3116 3117 3118 3119 3120 3121 3122 3123 3124 3125 3126 3127 3128 3129 3130 3131 3132 3133 3134 3135 3136 3137 3138 3139 3140 3141 3142 3143 3144 3145 3146 3147 3148 3149 3150 3151 3152 3153 3154 3155 3156 3157 3158 3159 3160 3161 3162 3163 3164 3165 3166 3167 3168 3169 3170 3171 3172 3173 3174 3175 3176 3177 3178 3179 3180 3181 3182 3183 3184 3185 3186 3187 3188 3189 3190 3191 3192 3193 3194 3195 3196 3197 3198 3199 3200 3201 3202 3203 3204 3205 3206 3207 3208 3209 3210 3211 3212 3213 3214 3215 3216 3217 3218 3219 3220 3221 3222 3223 3224 3225 3226 3227 3228 3229 3230 3231 3232 3233 3234 3235 3236 3237 3238 3239 3240 3241 3242 3243 3244 3245 3246 3247 3248 3249 3250 3251 3252 3253 3254 3255 3256 3257 3258 3259 3260 3261 3262 3263 3264 3265 3266 3267 3268 3269 3270 3271 3272 3273 3274 3275 3276 3277 3278 3279 3280 3281 3282 3283 3284 3285 3286 3287 3288 3289 3290 3291 3292 3293 3294 3295 3296 3297 3298 3299 3300 3301 3302 3303 3304 3305 3306 3307 3308 3309 3310 3311 3312 3313 3314 3315 3316 3317 3318 3319 3320 3321 3322 3323 3324 3325 3326 3327 3328 3329 3330 3331 3332 3333 3334 3335 3336 3337 3338 3339 3340 3341 3342 3343 3344 3345 3346 3347 3348 3349 3350 3351 3352 3353 3354 3355 3356 3357 3358 3359 3360 3361 3362 3363 3364 3365 3366 3367 3368 3369 3370 3371 3372 3373 3374 3375 3376 3377 3378 3379 3380 3381 3382 3383 3384 3385 3386 3387 3388 3389 3390 3391 3392 3393 3394 3395 3396 3397 3398 3399 3400 3401 3402 3403 3404 3405 3406 3407 3408 3409 3410 3411 3412 3413 3414 3415 3416 3417 3418 3419 3420 3421 3422 3423 3424 3425 3426 3427 3428 3429 3430 3431 3432 3433 3434 3435 3436 3437 3438 3439 3440 3441 3442 3443 3444 3445 3446 3447 3448 3449 3450 3451 3452 3453 3454 3455 3456 3457 3458 3459 3460 3461 3462 3463 3464 3465 3466 3467 3468 3469 3470 3471 3472 3473 3474 3475 3476 3477 3478 3479 3480 3481 3482 3483 3484 3485 3486 3487 3488 3489 3490 3491 3492 3493 3494 3495 3496 3497 3498 3499 3500 3501 3502 3503 3504 3505 3506 3507 3508 3509 3510 3511 3512 3513 3514 3515 3516 3517 3518 3519 3520 3521 3522 3523 3524 3525 3526 3527 3528 3529 3530 3531 3532 3533 3534 3535 3536 3537 3538 3539 3540 3541 3542 3543 3544 3545 3546 3547 3548 3549 3550 3551 3552 3553 3554 3555 3556 3557 3558 3559 3560 3561 3562 3563 3564 3565 3566 3567 3568 3569 3570 3571 3572 3573 3574 3575 3576 3577 3578 3579 3580 3581 3582 3583 3584 3585 3586 3587 3588 3589 3590 3591 3592 3593 3594 3595 3596 3597 3598 3599 3600 3601 3602 3603 3604 3605 3606 3607 3608 3609 3610 3611 3612 3613 3614 3615 3616 3617 3618 3619 3620 3621 3622 3623 3624 3625 3626 3627 3628 3629 3630 3631 3632 3633 3634 3635 3636 3637 3638 3639 3640 3641 3642 3643 3644 3645 3646 3647 3648 3649 3650 3651 3652 3653 3654 3655 3656 3657 3658 3659 3660 3661 3662 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 3673 3674 3675 3676 3677 3678 3679 3680 3681 3682 3683 3684 3685 3686 3687 3688 3689 3690 3691 3692 3693 3694 3695 3696 3697 3698 3699 3700 3701 3702 3703 3704 3705 3706 3707 3708 3709 3710 3711 3712 3713 3714 3715 3716 3717 3718 3719 3720 3721 3722 3723 3724 3725 3726 3727 3728 3729 3730 3731 3732 3733 3734 3735 3736 3737 3738 3739 3740 3741 3742 3743 3744 3745 3746 3747 3748 3749 3750 3751 3752 3753 3754 3755 3756 3757 3758 3759 3760 3761 3762 3763 3764 3765 3766 3767 3768 3769 3770 3771 3772 3773 3774 3775 3776 3777 3778 3779 3780 3781 3782 3783 3784 3785 3786 3787 3788 3789 3790 3791 3792 3793 3794 3795 3796 3797 3798 3799 3800 3801 3802 3803 3804 3805 3806 3807 3808 3809 3810 3811 3812 3813 3814 3815 3816 3817 3818 3819 3820 3821 3822 3823 3824 3825 3826 3827 3828 3829 3830 3831 3832 3833 3834 3835 3836 3837 3838 3839 3840 3841 3842 3843 3844 3845 3846 3847 3848 3849 3850 3851 3852 3853 3854 3855 3856 3857 3858 3859 3860 3861 3862 3863 3864 3865 3866 3867 3868 3869 3870 3871 3872 3873 3874 3875 3876 3877 3878 3879 3880 3881 3882 3883 3884 3885 3886 3887 3888 3889 3890 3891 3892 3893 3894 3895 3896 3897 3898 3899 3900 3901 3902 3903 3904 3905 3906 3907 3908 3909 3910 3911 3912 3913 3914 3915 3916 3917 3918 3919 3920 3921 3922 3923 3924 3925 3926 3927 3928 3929 3930 3931 3932 3933 3934 3935 3936 3937 3938 3939 3940 3941 3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956 3957 3958 3959 3960 3961 3962 3963 3964 3965 3966 3967 3968 3969 3970 3971 3972 3973 3974 3975 3976 3977 3978 3979 3980 3981 3982 3983 3984 3985 3986 3987 3988 3989 3990 3991 3992 3993 3994 3995 3996 3997 3998 3999 4000 4001 4002 4003 4004 4005 4006 4007 4008 4009 4010 4011 4012 4013 4014 4015 4016 4017 4018 4019 4020 4021 4022 4023 4024 4025 4026 4027 4028 4029 4030 4031 4032 4033 4034 4035 4036 4037 4038 4039 4040 4041 4042 4043 4044 4045 4046 4047 4048 4049 4050 4051 4052 4053 4054 4055 4056 4057 4058 4059 4060 4061 4062 4063 4064 4065 4066 4067 4068 4069 4070 4071 4072 4073 4074 4075 4076 4077 4078 4079 4080 4081 4082 4083 4084 4085 4086 4087 4088 4089 4090 4091 4092 4093 4094 4095 4096 4097 4098 4099 4100 4101 4102 4103 4104 4105 4106 4107 4108 4109 4110 4111 4112 4113 4114 4115 4116 4117 4118 4119 4120 4121 4122 4123 4124 4125 4126 4127 4128 4129 4130 4131 4132 4133 4134 4135 4136 4137 4138 4139 4140 4141 4142 4143 4144 4145 4146 4147 4148 4149 4150 4151 4152 4153 4154 4155 4156 4157 4158 4159 4160 4161 4162 4163 4164 4165 4166 4167 4168 4169 4170 4171 4172 4173 4174 4175 4176 4177 4178 4179 4180 4181 4182 4183 4184 4185 4186 4187 4188 4189 4190 4191 4192 4193 4194 4195 4196 4197 4198 4199 4200 4201 4202 4203 4204 4205 4206 4207 4208 4209 4210 4211 4212 4213 4214 4215 4216 4217 4218 4219 4220 4221 4222 4223 4224 4225 4226 4227 4228 4229 4230 4231 4232 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 4243 4244 4245 4246 4247 4248 4249 4250 4251 4252 4253 4254 4255 4256 4257 4258 4259 4260 4261 4262 4263 4264 4265 4266 4267 4268 4269 4270 4271 4272 4273 4274 4275 4276 4277 4278 4279 4280 4281 4282 4283 4284 4285 4286 4287 4288 4289 4290 4291 4292 4293 4294 4295 4296 4297 4298 4299 4300 4301 4302 4303 4304 4305 4306 4307 4308 4309 4310 4311 4312 4313 4314 4315 4316 4317 4318 4319 4320 4321 4322 4323 4324 4325 4326 4327 4328 4329 4330 4331 4332 4333 4334 4335 4336 4337 4338 4339 4340 4341 4342 4343 4344 4345 4346 4347 4348 4349 4350 4351 4352 4353 4354 4355 4356 4357 4358 4359 4360 4361 4362 4363 4364 4365 4366 4367 4368 4369 4370 4371 4372 4373 4374 4375 4376 4377 4378 4379 4380 4381 4382 4383 4384 4385 4386 4387 4388 4389 4390 4391 4392 4393 4394 4395 4396 4397 4398 4399 4400 4401 4402 4403 4404 4405 4406 4407 4408 4409 4410 4411 4412 4413 4414 4415 4416 4417 4418 4419 4420 4421 4422 4423 4424 4425 4426 4427 4428 4429 4430 4431 4432 4433 4434 4435 4436 4437 4438 4439 4440 4441 4442 4443 4444 4445 4446 4447 4448 4449 4450 4451 4452 4453 4454 4455 4456 4457 4458 4459 4460 4461 4462 4463 4464 4465 4466 4467 4468 4469 4470 4471 4472 4473 4474 4475 4476 4477 4478 4479 4480 4481 4482 4483 4484 4485 4486 4487 4488 4489 4490 4491 4492 4493 4494 4495 4496 4497 4498 4499 4500 4501 4502 4503 4504 4505 4506 4507 4508 4509 4510 4511 4512 4513 4514 4515 4516 4517 4518 4519 4520 4521 4522 4523 4524 4525 4526 4527 4528 4529 4530 4531 4532 4533 4534 4535 4536 4537 4538 4539 4540 4541 4542 4543 4544 4545 4546 4547 4548 4549 4550 4551 4552 4553 4554 4555 4556 4557 4558 4559 4560 4561 4562 4563 4564 4565 4566 4567 4568 4569 4570 4571 4572 4573 4574 4575 4576 4577 4578 4579 4580 4581 4582 4583 4584 4585 4586 4587 4588 4589 4590 4591 4592 4593 4594 4595 4596 4597 4598 4599 4600 4601 4602 4603 4604 4605 4606 4607 4608 4609 4610 4611 4612 4613 4614 4615 4616 4617 4618 4619 4620 4621 4622 4623 4624 4625 4626 4627 4628 4629 4630 4631 4632 4633 4634 4635 4636 4637 4638 4639 4640 4641 4642 4643 4644 4645 4646 4647 4648 4649 4650 4651 4652 4653 4654 4655 4656 4657 4658 4659 4660 4661 4662 4663 4664 4665 4666 4667 4668 4669 4670 4671 4672 4673 4674 4675 4676 4677 4678 4679 4680 4681 4682 4683 4684 4685 4686 4687 4688 4689 4690 4691 4692 4693 4694 4695 4696 4697 4698 4699 4700 4701 4702 4703 4704 4705 4706 4707 4708 4709 4710 4711 4712 4713 4714 4715 4716 4717 4718 4719 4720 4721 4722 4723 4724 4725 4726 4727 4728 4729 4730 4731 4732 4733 4734 4735 4736 4737 4738 4739 4740 4741 4742 4743 4744 4745 4746 4747 4748 4749 4750 4751 4752 4753 4754 4755 4756 4757 4758 4759 4760 4761 4762 4763 4764 4765 4766 4767 4768 4769 4770 4771 4772 4773 4774 4775 4776 4777 4778 4779 4780 4781 4782 4783 4784 4785 4786 4787 4788 4789 4790 4791 4792 4793 4794 4795 4796 4797 4798 4799 4800 4801 4802 4803 4804 4805 4806 4807 4808 4809 4810 4811 4812 4813 4814 4815 4816 4817 4818 4819 4820 4821 4822 4823 4824 4825 4826 4827 4828 4829 4830 4831 4832 4833 4834 4835 4836 4837 4838 4839 4840 4841 4842 4843 4844 4845 4846 4847 4848 4849 4850 4851 4852 4853 4854 4855 4856 4857 4858 4859 4860 4861 4862 4863 4864 4865 4866 4867 4868 4869 4870 4871 4872 4873 4874 4875 4876 4877 4878 4879 4880 4881 4882 4883 4884 4885 4886 4887 4888 4889 4890 4891 4892 4893 4894 4895 4896 4897 4898 4899 4900 4901 4902 4903 4904 4905 4906 4907 4908 4909 4910 4911 4912 4913 4914 4915 4916 4917 4918 4919 4920 4921 4922 4923 4924 4925 4926 4927 4928 4929 4930 4931 4932 4933 4934 4935 4936 4937 4938 4939 4940 4941 4942 4943 4944 4945 4946 4947 4948 4949 4950 4951 4952 4953 4954 4955 4956 4957 4958 4959 4960 4961 4962 4963 4964 4965 4966 4967 4968 4969 4970 4971 4972 4973 4974 4975 4976 4977 4978 4979 4980 4981 4982 4983 4984 4985 4986 4987 4988 4989 4990 4991 4992 4993 4994 4995 4996 4997 4998 4999 5000 5001 5002 5003 5004 5005 5006 5007 5008 5009 5010 5011 5012 5013 5014 5015 5016 5017 5018 5019 5020 5021 5022 5023 5024 5025 5026 5027 5028 5029 5030 5031 5032 5033 5034 5035 5036 5037 5038 5039 5040 5041 5042 5043 5044 5045 5046 5047 5048 5049 5050 5051 5052 5053 5054 5055 5056 5057 5058 5059 5060 5061 5062 5063 5064 5065 5066 5067 5068 5069 5070 5071 5072 5073 5074 5075 5076 5077 5078 5079 5080 5081 5082 5083 5084 5085 5086 5087 5088 5089 5090 5091 5092 5093 5094 5095 5096 5097 5098 5099 5100 5101 5102 5103 5104 5105 5106 5107 5108 5109 5110 5111 5112 5113 5114 5115 5116 5117 5118 5119 5120 5121 5122 5123 5124 5125 5126 5127 5128 5129 5130 5131 5132 5133 5134 5135 5136 5137 5138 5139 5140 5141 5142 5143 5144 5145 5146 5147 5148 5149 5150 5151 5152 5153 5154 5155 5156 5157 5158 5159 5160 5161 5162 5163 5164 5165 5166 5167 5168 5169 5170 5171 5172 5173 5174 5175 5176 5177 5178 5179 5180 5181 5182 5183 5184 5185 5186 5187 5188 5189 5190 5191 5192 5193 5194 5195 5196 5197 5198 5199 5200 5201 5202 5203 5204 5205 5206 5207 5208 5209 5210 5211 5212 5213 5214 5215 5216 5217 5218 5219 5220 5221 5222 5223 5224 5225 5226 5227 5228 5229 5230 5231 5232 5233 5234 5235 5236 5237 5238 5239 5240 5241 5242 5243 5244 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257 5258 5259 5260 5261 5262 5263 5264 5265 5266 5267 5268 5269 5270 5271 5272 5273 5274 5275 5276 5277 5278 5279 5280 5281 5282 5283 5284 5285 5286 5287 5288 5289 5290 5291 5292 5293 5294 5295 5296 5297 5298 5299 5300 5301 5302 5303 5304 5305 5306 5307 5308 5309 5310 5311 5312 5313 5314 5315 5316 5317 5318 5319 5320 5321 5322 5323 5324 5325 5326 5327 5328 5329 5330 5331 5332 5333 5334 5335 5336 5337 5338 5339 5340 5341 5342 5343 5344 5345 5346 5347 5348 5349 5350 5351 5352 5353 5354 5355 5356 5357 5358 5359 5360 5361 5362 5363 5364 5365 5366 5367 5368 5369 5370 5371 5372 5373 5374 5375 5376 5377 5378 5379 5380 5381 5382 5383 5384 5385 5386 5387 5388 5389 5390 5391 5392 5393 5394 5395 5396 5397 5398 5399 5400 5401 5402 5403 5404 5405 5406 5407 5408 5409 5410 5411 5412 5413 5414 5415 5416 5417 5418 5419 5420 5421 5422 5423 5424 5425 5426 5427 5428 5429 5430 5431 5432 5433 5434 5435 5436 5437 5438 5439 5440 5441 5442 5443 5444 5445 5446 5447 5448 5449 5450 5451 5452 5453 5454 5455 5456 5457 5458 5459 5460 5461 5462 5463 5464 5465 5466 5467 5468 5469 5470 5471 5472 5473 5474 5475 5476 5477 5478 5479 5480 5481 5482 5483 5484 5485 5486 5487 5488 5489 5490 5491 5492 5493 5494 5495 5496 5497 5498 5499 5500 5501 5502 5503 5504 5505 5506 5507 5508 5509 5510 5511 5512 5513 5514 5515 5516 5517 5518 5519 5520 5521 5522 5523 5524 5525 5526 5527 5528 5529 5530 5531 5532 5533 5534 5535 5536 5537 5538 5539 5540 5541 5542 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 5553 5554 5555 5556 5557 5558 5559 5560 5561 5562 5563 5564 5565 5566 5567 5568 5569 5570 5571 5572 5573 5574 5575 5576 5577 5578 5579 5580 5581 5582 5583 5584 5585 5586 5587 5588 5589 5590 5591 5592 5593 5594 5595 5596 5597 5598 5599 5600 5601 5602 5603 5604 5605 5606 5607 5608 5609 5610 5611 5612 5613 5614 5615 5616 5617 5618 5619 5620 5621 5622 5623 5624 5625 5626 5627 5628 5629 5630 5631 5632 5633 5634 5635 5636 5637 5638 5639 5640 5641 5642 5643 5644 5645 5646 5647 5648 5649 5650 5651 5652 5653 5654 5655 5656 5657 5658 5659 5660 5661 5662 5663 5664 5665 5666 5667 5668 5669 5670 5671 5672 5673 5674 5675 5676 5677 5678 5679 5680 5681 5682 5683 5684 5685 5686 5687 5688 5689 5690 5691 5692 5693 5694 5695 5696 5697 5698 5699 5700 5701 5702 5703 5704 5705 5706 5707 5708 5709 5710 5711 5712 5713 5714 5715 5716 5717 5718 5719 5720 5721 5722 5723 5724 5725 5726 5727 5728 5729 5730 5731 5732 5733 5734 5735 5736 5737 5738 5739 5740 5741 5742 5743 5744 5745 5746 5747 5748 5749 5750 5751 5752 5753 5754 5755 5756 5757 5758 5759 5760 5761 5762 5763 5764 5765 5766 5767 5768 5769 5770 5771 5772 5773 5774 5775 5776 5777 5778 5779 5780 5781 5782 5783 5784 5785 5786 5787 5788 5789 5790 5791 5792 5793 5794 5795 5796 5797 5798 5799 5800 5801 5802 5803 5804 5805 5806 5807 5808 5809 5810 5811 5812 5813 5814 5815 5816 5817 5818 5819 5820 5821 5822 5823 5824 5825 5826 5827 5828 5829 5830 5831 5832 5833 5834 5835 5836 5837 5838 5839 5840 5841 5842 5843 5844 5845 5846 5847 5848 5849 5850 5851 5852 5853 5854 5855 5856 5857 5858 5859 5860 5861 5862 5863 5864 5865 5866 5867 5868 5869 5870 5871 5872 5873 5874 5875 5876 5877 5878 5879 5880 5881 5882 5883 5884 5885 5886 5887 5888 5889 5890 5891 5892 5893 5894 5895 5896 5897 5898 5899 5900 5901 5902 5903 5904 5905 5906 5907 5908 5909 5910 5911 5912 5913 5914 5915 5916 5917 5918 5919 5920 5921 5922 5923 5924 5925 5926 5927 5928 5929 5930 5931 5932 5933 5934 5935 5936 5937 5938 5939 5940 5941 5942 5943 5944 5945 5946 5947 5948 5949 5950 5951 5952 5953 5954 5955 5956 5957 5958 5959 5960 5961 5962 5963 5964 5965 5966 5967 5968 5969 5970 5971 5972 5973 5974 5975 5976 5977 5978 5979 5980 5981 5982 5983 5984 5985 5986 5987 5988 5989 5990 5991 5992 5993 5994 5995 5996 5997 5998 5999 6000 6001 6002 6003 6004 6005 6006 6007 6008 6009 6010 6011 6012 6013 6014 6015 6016 6017 6018 6019 6020 6021 6022 6023 6024 6025 6026 6027 6028 6029 6030 6031 6032 6033 6034 6035 6036 6037 6038 6039 6040 6041 6042 6043 6044 6045 6046 6047 6048 6049 6050 6051 6052 6053 6054 6055 6056 6057 6058 6059 6060 6061 6062 6063 6064 6065 6066 6067 6068 6069 6070 6071 6072 6073 6074 6075 6076 6077 6078 6079 6080 6081 6082 6083 6084 6085 6086 6087 6088 6089 6090 6091 6092 6093 6094 6095 6096 6097 6098 6099 6100 6101 6102 6103 6104 6105 6106 6107 6108 6109 6110 6111 6112 6113 6114 6115 6116 6117 6118 6119 6120 6121 6122 6123 6124 6125 6126 6127 6128 6129 6130 6131 6132 6133 6134 6135 6136 6137 6138 6139 6140 6141 6142 6143 6144 6145 6146 6147 6148 6149 6150 6151 6152 6153 6154 6155 6156 6157 6158 6159 6160 6161 6162 6163 6164 6165 6166 6167 6168 6169 6170 6171 6172 6173 6174 6175 6176 6177 6178 6179 6180 6181 6182 6183 6184 6185 6186 6187 6188 6189 6190 6191 6192 6193 6194 6195 6196 6197 6198 6199 6200 6201 6202 6203 6204 6205 6206 6207 6208 6209 6210 6211 6212 6213 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 6224 6225 6226 6227 6228 6229 6230 6231 6232 6233 6234 6235 6236 6237 6238 6239 6240 6241 6242 6243 6244 6245 6246 6247 6248 6249 6250 6251 6252 6253 6254 6255 6256 6257 6258 6259 6260 6261 6262 6263 6264 6265 6266 6267 6268 6269 6270 6271 6272 6273 6274 6275 6276 6277 6278 6279 6280 6281 6282 6283 6284 6285 6286 6287 6288 6289 6290 6291 6292 6293 6294 6295 6296 6297 6298 6299 6300 6301 6302 6303 6304 6305 6306 6307 6308 6309 6310 6311 6312 6313 6314 6315 6316 6317 6318 6319 6320 6321 6322 6323 6324 6325 6326 6327 6328 6329 6330 6331 6332 6333 6334 6335 6336 6337 6338 6339 6340 6341 6342 6343 6344 6345 6346 6347 6348 6349 6350 6351 6352 6353 6354 6355 6356 6357 6358 6359 6360 6361 6362 6363 6364 6365 6366 6367 6368 6369 6370 6371 6372 6373 6374 6375 6376 6377 6378 6379 6380 6381 6382 6383 6384 6385 6386 6387 6388 6389 6390 6391 6392 6393 6394 6395 6396 6397 6398 6399 6400 6401 6402 6403 6404 6405 6406 6407 6408 6409 6410 6411 6412 6413 6414 6415 6416 6417 6418 6419 6420 6421 6422 6423 6424 6425 6426 6427 6428 6429 6430 6431 6432 6433 6434 6435 6436 6437 6438 6439 6440 6441 6442 6443 6444 6445 6446 6447 6448 6449 6450 6451 6452 6453 6454 6455 6456 6457 6458 6459 6460 6461 6462 6463 6464 6465 6466 6467 6468 6469 6470 6471 6472 6473 6474 6475 6476 6477 6478 6479 6480 6481 6482 6483 6484 6485 6486 6487 6488 6489 6490 6491 6492 6493 6494 6495 6496 6497 6498 6499 6500 6501 6502 6503 6504 6505 6506 6507 6508 6509 6510 6511 6512 6513 6514 6515 6516 6517 6518 6519 6520 6521 6522 6523 6524 6525 6526 6527 6528 6529 6530 6531 6532 6533 6534 6535 6536 6537 6538 6539 6540 6541 6542 6543 6544 6545 6546 6547 6548 6549 6550 6551 6552 6553 6554 6555 6556 6557 6558 6559 6560 6561 6562 6563 6564 6565 6566 6567 6568 6569 6570 6571 6572 6573 6574 6575 6576 6577 6578 6579 6580 6581 6582 6583 6584 6585 6586 6587 6588 6589 6590 6591 6592 6593 6594 6595 6596 6597 6598 6599 6600 6601 6602 6603 6604 6605 6606 6607 6608 6609 6610 6611 6612 6613 6614 6615 6616 6617 6618 6619 6620 6621 6622 6623 6624 6625 6626 6627 6628 6629 6630 6631 6632 6633 6634 6635 6636 6637 6638 6639 6640 6641 6642 6643 6644 6645 6646 6647 6648 6649 6650 6651 6652 6653 6654 6655 6656 6657 6658 6659 6660 6661 6662 6663 6664 6665 6666 6667 6668 6669 6670 6671 6672 6673 6674 6675 6676 6677 6678 6679 6680 6681 6682 6683 6684 6685 6686 6687 6688 6689 6690 6691 6692 6693 6694 6695 6696 6697 6698 6699 6700 6701 6702 6703 6704 6705 6706 6707 6708 6709 6710 6711 6712 6713 6714 6715 6716 6717 6718 6719 6720 6721 6722 6723 6724 6725 6726 6727 6728 6729 6730 6731 6732 6733 6734 6735 6736 6737 6738 6739 6740 6741 6742 6743 6744 6745 6746 6747 6748 6749 6750 6751 6752 6753 6754 6755 6756 6757 6758 6759 6760 6761 6762 6763 6764 6765 6766 6767 6768 6769 6770 6771 6772 6773 6774 6775 6776 6777 6778 6779 6780 6781 6782 6783 6784 6785 6786 6787 6788 6789 6790 6791 6792 6793 6794 6795 6796 6797 6798 6799 6800 6801 6802 6803 6804 6805 6806 6807 6808 6809 6810 6811 6812 6813 6814 6815 6816 6817 6818 6819 6820 6821 6822 6823 6824 6825 6826 6827 6828 6829 6830 6831 6832 6833 6834 6835 6836 6837 6838 6839 6840 6841 6842 6843 6844 6845 6846 6847 6848 6849 6850 6851 6852 6853 6854 6855 6856 6857 6858 6859 6860 6861 6862 6863 6864 6865 6866 6867 6868 6869 6870 6871 6872 6873 6874 6875 6876 6877 6878 6879 6880 6881 6882 6883 6884 6885 6886 6887 6888 6889 6890 6891 6892 6893 6894 6895 6896 6897 6898 6899 6900 6901 6902 6903 6904 6905 6906 6907 6908 6909 6910 6911 6912 6913 6914 6915 6916 6917 6918 6919 6920 6921 6922 6923 6924 6925 6926 6927 6928 6929 6930 6931 6932 6933 6934 6935 6936 6937 6938 6939 6940 6941 6942 6943 6944 6945 6946 6947 6948 6949 6950 6951 6952 6953 6954 6955 6956 6957 6958 6959 6960 6961 6962 6963 6964 6965 6966 6967 6968 6969 6970 6971 6972 6973 6974 6975 6976 6977 6978 6979 6980 6981 6982 6983 6984 6985 6986 6987 6988 6989 6990 6991 6992 6993 6994 6995 6996 6997 6998 6999 7000 7001 7002 7003 7004 7005 7006 7007 7008 7009 7010 7011 7012 7013 7014 7015 7016 7017 7018 7019 7020 7021 7022 7023 7024 7025 7026 7027 7028 7029 7030 7031 7032 7033 7034 7035 7036 7037 7038 7039 7040 7041 7042 7043 7044 7045 7046 7047 7048 7049 7050 7051 7052 7053 7054 7055 7056 7057 7058 7059 7060 7061 7062 7063 7064 7065 7066 7067 7068 7069 7070 7071 7072 7073 7074 7075 7076 7077 7078 7079 7080 7081 7082 7083 7084 7085 7086 7087 7088 7089 7090 7091 7092 7093 7094 7095 7096 7097 7098 7099 7100 7101 7102 7103 7104 7105 7106 7107 7108 7109 7110 7111 7112 7113 7114 7115 7116 7117 7118 7119 7120 7121 7122 7123 7124 7125 7126 7127 7128 7129 7130 7131 7132 7133 7134 7135 7136 7137 7138 7139 7140 7141 7142 7143 7144 7145 7146 7147 7148 7149 7150 7151 7152 7153 7154 7155 7156 7157 7158 7159 7160 7161 7162 7163 7164 7165 7166 7167 7168 7169 7170 7171 7172 7173 7174 7175 7176 7177 7178 7179 7180 7181 7182 7183 7184 7185 7186 7187 7188 7189 7190 7191 7192 7193 7194 7195 7196 7197 7198 7199 7200 7201 7202 7203 7204 7205 7206 7207 7208 7209 7210 7211 7212 7213 7214 7215 7216 7217 7218 7219 7220 7221 7222 7223 7224 7225 7226 7227 7228 7229 7230 7231 7232 7233 7234 7235 7236 7237 7238 7239 7240 7241 7242 7243 7244 7245 7246 7247 7248 7249 7250 7251 7252 7253 7254 7255 7256 7257 7258 7259 7260 7261 7262 7263 7264 7265 7266 7267 7268 7269 7270 7271 7272 7273 7274 7275 7276 7277 7278 7279 7280 7281 7282 7283 7284 7285 7286 7287 7288 7289 7290 7291 7292 7293 7294 7295 7296 7297 7298 7299 7300 7301 7302 7303 7304 7305 7306 7307 7308 7309 7310 7311 7312 7313 7314 7315 7316 7317 7318 7319 7320 7321 7322 7323 7324 7325 7326 7327 7328 7329 7330 7331 7332 7333 7334 7335 7336 7337 7338 7339 7340 7341 7342 7343 7344 7345 7346 7347 7348 7349 7350 7351 7352 7353 7354 7355 7356 7357 7358 7359 7360 7361 7362 7363 7364 7365 7366 7367 7368 7369 7370 7371 7372 7373 7374 7375 7376 7377 7378 7379 7380 7381 7382 7383 7384 7385 7386 7387 7388 7389 7390 7391 7392 7393 7394 7395 7396 7397 7398 7399 7400 7401 7402 7403 7404 7405 7406 7407 7408 7409 7410 7411 7412 7413 7414 7415 7416 7417 7418 7419 7420 7421 7422 7423 7424 7425 7426 7427 7428 7429 7430 7431 7432 7433 7434 7435 7436 7437 7438 7439 7440 7441 7442 7443 7444 7445 7446 7447 7448 7449 7450 7451 7452 7453 7454 7455 7456 7457 7458 7459 7460 7461 7462 7463 7464 7465 7466 7467 7468 7469 7470 7471 7472 7473 7474 7475 7476 7477 7478 7479 7480 7481 7482 7483 7484 7485 7486 7487 7488 7489 7490 7491 7492 7493 7494 7495 7496 7497 7498 7499 7500 7501 7502 7503 7504 7505 7506 7507 7508 7509 7510 7511 7512 7513 7514 7515 7516 7517 7518 7519 7520 7521 7522 7523 7524 7525 7526 7527 7528 7529 7530 7531 7532 7533 7534 7535 7536 7537 7538 7539 7540 7541 7542 7543 7544 7545 7546 7547 7548 7549 7550 7551 7552 7553 7554 7555 7556 7557 7558 7559 7560 7561 7562 7563 7564 7565 7566 7567 7568 7569 7570 7571 7572 7573 7574 7575 7576 7577 7578 7579 7580 7581 7582 7583 7584 7585 7586 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 7597 7598 7599
|
from __future__ import annotations
import asyncio
import contextlib
import gzip
import itertools
import math
import os.path
import pickle
import platform
import re
import shutil
import sys
import tempfile
import uuid
import warnings
from collections import ChainMap
from collections.abc import Generator, Iterator, Mapping
from contextlib import ExitStack
from importlib import import_module
from io import BytesIO
from pathlib import Path
from typing import TYPE_CHECKING, Any, Final, Literal, cast
from unittest.mock import patch
import numpy as np
import pandas as pd
import pytest
from packaging.version import Version
from pandas.errors import OutOfBoundsDatetime
import xarray as xr
import xarray.testing as xrt
from xarray import (
DataArray,
Dataset,
backends,
load_dataarray,
load_dataset,
open_dataarray,
open_dataset,
open_mfdataset,
save_mfdataset,
)
from xarray.backends.common import robust_getitem
from xarray.backends.h5netcdf_ import H5netcdfBackendEntrypoint
from xarray.backends.netcdf3 import _nc3_dtype_coercions
from xarray.backends.netCDF4_ import (
NetCDF4BackendEntrypoint,
_extract_nc4_variable_encoding,
)
from xarray.backends.pydap_ import PydapDataStore
from xarray.backends.scipy_ import ScipyBackendEntrypoint
from xarray.backends.zarr import ZarrStore
from xarray.coders import CFDatetimeCoder, CFTimedeltaCoder
from xarray.coding.cftime_offsets import date_range
from xarray.coding.strings import check_vlen_dtype, create_vlen_dtype
from xarray.coding.variables import SerializationWarning
from xarray.conventions import encode_dataset_coordinates
from xarray.core import indexing
from xarray.core.indexes import PandasIndex
from xarray.core.options import set_options
from xarray.core.types import PDDatetimeUnitOptions
from xarray.core.utils import module_available
from xarray.namedarray.pycompat import array_type
from xarray.structure.alignment import AlignmentError
from xarray.tests import (
assert_allclose,
assert_array_equal,
assert_equal,
assert_identical,
assert_no_warnings,
has_dask,
has_h5netcdf_1_4_0_or_above,
has_netCDF4,
has_numpy_2,
has_scipy,
has_zarr,
has_zarr_v3,
has_zarr_v3_async_oindex,
has_zarr_v3_dtypes,
mock,
network,
parametrize_zarr_format,
requires_cftime,
requires_dask,
requires_fsspec,
requires_h5netcdf,
requires_h5netcdf_1_4_0_or_above,
requires_h5netcdf_ros3,
requires_iris,
requires_netcdf,
requires_netCDF4,
requires_netCDF4_1_6_2_or_above,
requires_netCDF4_1_7_0_or_above,
requires_pydap,
requires_scipy,
requires_scipy_or_netCDF4,
requires_zarr,
requires_zarr_v3,
)
from xarray.tests.test_coding_times import (
_ALL_CALENDARS,
_NON_STANDARD_CALENDARS,
_STANDARD_CALENDARS,
)
from xarray.tests.test_dataset import (
create_append_string_length_mismatch_test_data,
create_append_test_data,
create_test_data,
)
with contextlib.suppress(ImportError):
import netCDF4 as nc4
try:
import dask
import dask.array as da
except ImportError:
pass
if has_zarr:
import zarr
import zarr.codecs
if has_zarr_v3:
from zarr.storage import MemoryStore as KVStore
from zarr.storage import WrapperStore
ZARR_FORMATS = [2, 3]
else:
ZARR_FORMATS = [2]
try:
from zarr import ( # type: ignore[attr-defined,no-redef,unused-ignore]
KVStoreV3 as KVStore,
)
except ImportError:
KVStore = None # type: ignore[assignment,misc,unused-ignore]
WrapperStore = object # type: ignore[assignment,misc,unused-ignore]
else:
KVStore = None # type: ignore[assignment,misc,unused-ignore]
WrapperStore = object # type: ignore[assignment,misc,unused-ignore]
ZARR_FORMATS = []
@pytest.fixture(scope="module", params=ZARR_FORMATS)
def default_zarr_format(request) -> Generator[None, None]:
if has_zarr_v3:
with zarr.config.set(default_zarr_format=request.param):
yield
else:
yield
def skip_if_zarr_format_3(reason: str):
if has_zarr_v3 and zarr.config["default_zarr_format"] == 3:
pytest.skip(reason=f"Unsupported with zarr_format=3: {reason}")
def skip_if_zarr_format_2(reason: str):
if not has_zarr_v3 or (zarr.config["default_zarr_format"] == 2):
pytest.skip(reason=f"Unsupported with zarr_format=2: {reason}")
ON_WINDOWS = sys.platform == "win32"
default_value = object()
dask_array_type = array_type("dask")
if TYPE_CHECKING:
from xarray.backends.api import T_NetcdfEngine, T_NetcdfTypes
def open_example_dataset(name, *args, **kwargs) -> Dataset:
return open_dataset(
os.path.join(os.path.dirname(__file__), "data", name), *args, **kwargs
)
def open_example_mfdataset(names, *args, **kwargs) -> Dataset:
return open_mfdataset(
[os.path.join(os.path.dirname(__file__), "data", name) for name in names],
*args,
**kwargs,
)
def create_masked_and_scaled_data(dtype: np.dtype) -> Dataset:
x = np.array([np.nan, np.nan, 10, 10.1, 10.2], dtype=dtype)
encoding = {
"_FillValue": -1,
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
"dtype": "i2",
}
return Dataset({"x": ("t", x, {}, encoding)})
def create_encoded_masked_and_scaled_data(dtype: np.dtype) -> Dataset:
attributes = {
"_FillValue": -1,
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
return Dataset(
{"x": ("t", np.array([-1, -1, 0, 1, 2], dtype=np.int16), attributes)}
)
def create_unsigned_masked_scaled_data(dtype: np.dtype) -> Dataset:
encoding = {
"_FillValue": -1,
"_Unsigned": "true",
"dtype": "i1",
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
x = np.array([10.0, 10.1, 22.7, 22.8, np.nan], dtype=dtype)
return Dataset({"x": ("t", x, {}, encoding)})
def create_encoded_unsigned_masked_scaled_data(dtype: np.dtype) -> Dataset:
# These are values as written to the file: the _FillValue will
# be represented in the signed form.
attributes = {
"_FillValue": -1,
"_Unsigned": "true",
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
# Create unsigned data corresponding to [0, 1, 127, 128, 255] unsigned
sb = np.asarray([0, 1, 127, -128, -1], dtype="i1")
return Dataset({"x": ("t", sb, attributes)})
def create_bad_unsigned_masked_scaled_data(dtype: np.dtype) -> Dataset:
encoding = {
"_FillValue": 255,
"_Unsigned": True,
"dtype": "i1",
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
x = np.array([10.0, 10.1, 22.7, 22.8, np.nan], dtype=dtype)
return Dataset({"x": ("t", x, {}, encoding)})
def create_bad_encoded_unsigned_masked_scaled_data(dtype: np.dtype) -> Dataset:
# These are values as written to the file: the _FillValue will
# be represented in the signed form.
attributes = {
"_FillValue": -1,
"_Unsigned": True,
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
# Create signed data corresponding to [0, 1, 127, 128, 255] unsigned
sb = np.asarray([0, 1, 127, -128, -1], dtype="i1")
return Dataset({"x": ("t", sb, attributes)})
def create_signed_masked_scaled_data(dtype: np.dtype) -> Dataset:
encoding = {
"_FillValue": -127,
"_Unsigned": "false",
"dtype": "i1",
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
x = np.array([-1.0, 10.1, 22.7, np.nan], dtype=dtype)
return Dataset({"x": ("t", x, {}, encoding)})
def create_encoded_signed_masked_scaled_data(dtype: np.dtype) -> Dataset:
# These are values as written to the file: the _FillValue will
# be represented in the signed form.
attributes = {
"_FillValue": -127,
"_Unsigned": "false",
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
# Create signed data corresponding to [0, 1, 127, 128, 255] unsigned
sb = np.asarray([-110, 1, 127, -127], dtype="i1")
return Dataset({"x": ("t", sb, attributes)})
def create_unsigned_false_masked_scaled_data(dtype: np.dtype) -> Dataset:
encoding = {
"_FillValue": 255,
"_Unsigned": "false",
"dtype": "u1",
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
x = np.array([-1.0, 10.1, 22.7, np.nan], dtype=dtype)
return Dataset({"x": ("t", x, {}, encoding)})
def create_encoded_unsigned_false_masked_scaled_data(dtype: np.dtype) -> Dataset:
# These are values as written to the file: the _FillValue will
# be represented in the unsigned form.
attributes = {
"_FillValue": 255,
"_Unsigned": "false",
"add_offset": dtype.type(10),
"scale_factor": dtype.type(0.1),
}
# Create unsigned data corresponding to [-110, 1, 127, 255] signed
sb = np.asarray([146, 1, 127, 255], dtype="u1")
return Dataset({"x": ("t", sb, attributes)})
def create_boolean_data() -> Dataset:
attributes = {"units": "-"}
return Dataset(
{
"x": (
("t", "x"),
[[False, True, False, True], [True, False, False, True]],
attributes,
)
}
)
class TestCommon:
def test_robust_getitem(self) -> None:
class UnreliableArrayFailure(Exception):
pass
class UnreliableArray:
def __init__(self, array, failures=1):
self.array = array
self.failures = failures
def __getitem__(self, key):
if self.failures > 0:
self.failures -= 1
raise UnreliableArrayFailure
return self.array[key]
array = UnreliableArray([0])
with pytest.raises(UnreliableArrayFailure):
array[0]
assert array[0] == 0
actual = robust_getitem(array, 0, catch=UnreliableArrayFailure, initial_delay=0)
assert actual == 0
class NetCDF3Only:
netcdf3_formats: tuple[T_NetcdfTypes, ...] = ("NETCDF3_CLASSIC", "NETCDF3_64BIT")
@pytest.mark.asyncio
@pytest.mark.skip(reason="NetCDF backends don't support async loading")
async def test_load_async(self) -> None:
pass
@requires_scipy
def test_dtype_coercion_error(self) -> None:
"""Failing dtype coercion should lead to an error"""
for dtype, format in itertools.product(
_nc3_dtype_coercions, self.netcdf3_formats
):
if dtype == "bool":
# coerced upcast (bool to int8) ==> can never fail
continue
# Using the largest representable value, create some data that will
# no longer compare equal after the coerced downcast
maxval = np.iinfo(dtype).max
x = np.array([0, 1, 2, maxval], dtype=dtype)
ds = Dataset({"x": ("t", x, {})})
with create_tmp_file(allow_cleanup_failure=False) as path:
with pytest.raises(ValueError, match="could not safely cast"):
ds.to_netcdf(path, format=format)
class DatasetIOBase:
engine: T_NetcdfEngine | None = None
file_format: T_NetcdfTypes | None = None
def create_store(self):
raise NotImplementedError()
@contextlib.contextmanager
def roundtrip(
self, data, save_kwargs=None, open_kwargs=None, allow_cleanup_failure=False
):
if save_kwargs is None:
save_kwargs = {}
if open_kwargs is None:
open_kwargs = {}
with create_tmp_file(allow_cleanup_failure=allow_cleanup_failure) as path:
self.save(data, path, **save_kwargs)
with self.open(path, **open_kwargs) as ds:
yield ds
@contextlib.contextmanager
def roundtrip_append(
self, data, save_kwargs=None, open_kwargs=None, allow_cleanup_failure=False
):
if save_kwargs is None:
save_kwargs = {}
if open_kwargs is None:
open_kwargs = {}
with create_tmp_file(allow_cleanup_failure=allow_cleanup_failure) as path:
for i, key in enumerate(data.variables):
mode = "a" if i > 0 else "w"
self.save(data[[key]], path, mode=mode, **save_kwargs)
with self.open(path, **open_kwargs) as ds:
yield ds
# The save/open methods may be overwritten below
def save(self, dataset, path, **kwargs):
return dataset.to_netcdf(
path, engine=self.engine, format=self.file_format, **kwargs
)
@contextlib.contextmanager
def open(self, path, **kwargs):
with open_dataset(path, engine=self.engine, **kwargs) as ds:
yield ds
def test_zero_dimensional_variable(self) -> None:
expected = create_test_data()
expected["float_var"] = ([], 1.0e9, {"units": "units of awesome"})
expected["bytes_var"] = ([], b"foobar")
expected["string_var"] = ([], "foobar")
with self.roundtrip(expected) as actual:
assert_identical(expected, actual)
def test_write_store(self) -> None:
expected = create_test_data()
with self.create_store() as store:
expected.dump_to_store(store)
# we need to cf decode the store because it has time and
# non-dimension coordinates
with xr.decode_cf(store) as actual:
assert_allclose(expected, actual)
def check_dtypes_roundtripped(self, expected, actual):
for k in expected.variables:
expected_dtype = expected.variables[k].dtype
# For NetCDF3, the backend should perform dtype coercion
if (
isinstance(self, NetCDF3Only)
and str(expected_dtype) in _nc3_dtype_coercions
):
expected_dtype = np.dtype(_nc3_dtype_coercions[str(expected_dtype)])
actual_dtype = actual.variables[k].dtype
# TODO: check expected behavior for string dtypes more carefully
string_kinds = {"O", "S", "U"}
assert expected_dtype == actual_dtype or (
expected_dtype.kind in string_kinds
and actual_dtype.kind in string_kinds
)
def test_roundtrip_test_data(self) -> None:
expected = create_test_data()
with self.roundtrip(expected) as actual:
self.check_dtypes_roundtripped(expected, actual)
assert_identical(expected, actual)
def test_load(self) -> None:
# Note: please keep this in sync with test_load_async below as much as possible!
expected = create_test_data()
@contextlib.contextmanager
def assert_loads(vars=None):
if vars is None:
vars = expected
with self.roundtrip(expected) as actual:
for k, v in actual.variables.items():
# IndexVariables are eagerly loaded into memory
assert v._in_memory == (k in actual.dims)
yield actual
for k, v in actual.variables.items():
if k in vars:
assert v._in_memory
assert_identical(expected, actual)
with pytest.raises(AssertionError):
# make sure the contextmanager works!
with assert_loads() as ds:
pass
with assert_loads() as ds:
ds.load()
with assert_loads(["var1", "dim1", "dim2"]) as ds:
ds["var1"].load()
# verify we can read data even after closing the file
with self.roundtrip(expected) as ds:
actual = ds.load()
assert_identical(expected, actual)
@pytest.mark.asyncio
async def test_load_async(self) -> None:
# Note: please keep this in sync with test_load above as much as possible!
# Copied from `test_load` on the base test class, but won't work for netcdf
expected = create_test_data()
@contextlib.contextmanager
def assert_loads(vars=None):
if vars is None:
vars = expected
with self.roundtrip(expected) as actual:
for k, v in actual.variables.items():
# IndexVariables are eagerly loaded into memory
assert v._in_memory == (k in actual.dims)
yield actual
for k, v in actual.variables.items():
if k in vars:
assert v._in_memory
assert_identical(expected, actual)
with pytest.raises(AssertionError):
# make sure the contextmanager works!
with assert_loads() as ds:
pass
with assert_loads() as ds:
await ds.load_async()
with assert_loads(["var1", "dim1", "dim2"]) as ds:
await ds["var1"].load_async()
# verify we can read data even after closing the file
with self.roundtrip(expected) as ds:
actual = await ds.load_async()
assert_identical(expected, actual)
def test_dataset_compute(self) -> None:
expected = create_test_data()
with self.roundtrip(expected) as actual:
# Test Dataset.compute()
for k, v in actual.variables.items():
# IndexVariables are eagerly cached
assert v._in_memory == (k in actual.dims)
computed = actual.compute()
for k, v in actual.variables.items():
assert v._in_memory == (k in actual.dims)
for v in computed.variables.values():
assert v._in_memory
assert_identical(expected, actual)
assert_identical(expected, computed)
def test_pickle(self) -> None:
expected = Dataset({"foo": ("x", [42])})
with self.roundtrip(expected, allow_cleanup_failure=ON_WINDOWS) as roundtripped:
with roundtripped:
# Windows doesn't like reopening an already open file
raw_pickle = pickle.dumps(roundtripped)
with pickle.loads(raw_pickle) as unpickled_ds:
assert_identical(expected, unpickled_ds)
@pytest.mark.filterwarnings("ignore:deallocating CachingFileManager")
def test_pickle_dataarray(self) -> None:
expected = Dataset({"foo": ("x", [42])})
with self.roundtrip(expected, allow_cleanup_failure=ON_WINDOWS) as roundtripped:
with roundtripped:
raw_pickle = pickle.dumps(roundtripped["foo"])
# TODO: figure out how to explicitly close the file for the
# unpickled DataArray?
unpickled = pickle.loads(raw_pickle)
assert_identical(expected["foo"], unpickled)
def test_dataset_caching(self) -> None:
expected = Dataset({"foo": ("x", [5, 6, 7])})
with self.roundtrip(expected) as actual:
assert isinstance(actual.foo.variable._data, indexing.MemoryCachedArray)
assert not actual.foo.variable._in_memory
_ = actual.foo.values # cache
assert actual.foo.variable._in_memory
with self.roundtrip(expected, open_kwargs={"cache": False}) as actual:
assert isinstance(actual.foo.variable._data, indexing.CopyOnWriteArray)
assert not actual.foo.variable._in_memory
_ = actual.foo.values # no caching
assert not actual.foo.variable._in_memory
@pytest.mark.filterwarnings("ignore:deallocating CachingFileManager")
def test_roundtrip_None_variable(self) -> None:
expected = Dataset({None: (("x", "y"), [[0, 1], [2, 3]])})
with self.roundtrip(expected) as actual:
assert_identical(expected, actual)
def test_roundtrip_object_dtype(self) -> None:
floats = np.array([0.0, 0.0, 1.0, 2.0, 3.0], dtype=object)
floats_nans = np.array([np.nan, np.nan, 1.0, 2.0, 3.0], dtype=object)
bytes_ = np.array([b"ab", b"cdef", b"g"], dtype=object)
bytes_nans = np.array([b"ab", b"cdef", np.nan], dtype=object)
strings = np.array(["ab", "cdef", "g"], dtype=object)
strings_nans = np.array(["ab", "cdef", np.nan], dtype=object)
all_nans = np.array([np.nan, np.nan], dtype=object)
original = Dataset(
{
"floats": ("a", floats),
"floats_nans": ("a", floats_nans),
"bytes": ("b", bytes_),
"bytes_nans": ("b", bytes_nans),
"strings": ("b", strings),
"strings_nans": ("b", strings_nans),
"all_nans": ("c", all_nans),
"nan": ([], np.nan),
}
)
expected = original.copy(deep=True)
with self.roundtrip(original) as actual:
try:
assert_identical(expected, actual)
except AssertionError:
# Most stores use '' for nans in strings, but some don't.
# First try the ideal case (where the store returns exactly)
# the original Dataset), then try a more realistic case.
# This currently includes all netCDF files when encoding is not
# explicitly set.
# https://github.com/pydata/xarray/issues/1647
# Also Zarr
expected["bytes_nans"][-1] = b""
expected["strings_nans"][-1] = ""
assert_identical(expected, actual)
def test_roundtrip_string_data(self) -> None:
expected = Dataset({"x": ("t", ["ab", "cdef"])})
with self.roundtrip(expected) as actual:
assert_identical(expected, actual)
def test_roundtrip_string_encoded_characters(self) -> None:
expected = Dataset({"x": ("t", ["ab", "cdef"])})
expected["x"].encoding["dtype"] = "S1"
with self.roundtrip(expected) as actual:
assert_identical(expected, actual)
assert actual["x"].encoding["_Encoding"] == "utf-8"
expected["x"].encoding["_Encoding"] = "ascii"
with self.roundtrip(expected) as actual:
assert_identical(expected, actual)
assert actual["x"].encoding["_Encoding"] == "ascii"
def test_roundtrip_numpy_datetime_data(self) -> None:
times = pd.to_datetime(["2000-01-01", "2000-01-02", "NaT"], unit="ns")
expected = Dataset({"t": ("t", times), "t0": times[0]})
kwargs = {"encoding": {"t0": {"units": "days since 1950-01-01"}}}
with self.roundtrip(expected, save_kwargs=kwargs) as actual:
assert_identical(expected, actual)
assert actual.t0.encoding["units"] == "days since 1950-01-01"
@requires_cftime
def test_roundtrip_cftime_datetime_data(self) -> None:
from xarray.tests.test_coding_times import _all_cftime_date_types
date_types = _all_cftime_date_types()
for date_type in date_types.values():
times = [date_type(1, 1, 1), date_type(1, 1, 2)]
expected = Dataset({"t": ("t", times), "t0": times[0]})
kwargs = {"encoding": {"t0": {"units": "days since 0001-01-01"}}}
expected_decoded_t = np.array(times)
expected_decoded_t0 = np.array([date_type(1, 1, 1)])
expected_calendar = times[0].calendar
with warnings.catch_warnings():
if expected_calendar in {"proleptic_gregorian", "standard"}:
warnings.filterwarnings("ignore", "Unable to decode time axis")
with self.roundtrip(expected, save_kwargs=kwargs) as actual:
# proleptic gregorian will be decoded into numpy datetime64
# fixing to expectations
if actual.t.dtype.kind == "M":
dtype = actual.t.dtype
expected_decoded_t = expected_decoded_t.astype(dtype)
expected_decoded_t0 = expected_decoded_t0.astype(dtype)
assert_array_equal(actual.t.values, expected_decoded_t)
assert (
actual.t.encoding["units"]
== "days since 0001-01-01 00:00:00.000000"
)
assert actual.t.encoding["calendar"] == expected_calendar
assert_array_equal(actual.t0.values, expected_decoded_t0)
assert actual.t0.encoding["units"] == "days since 0001-01-01"
assert actual.t.encoding["calendar"] == expected_calendar
def test_roundtrip_timedelta_data(self) -> None:
# todo: suggestion from review:
# roundtrip large microsecond or coarser resolution timedeltas,
# though we cannot test that until we fix the timedelta decoding
# to support large ranges
time_deltas = pd.to_timedelta(["1h", "2h", "NaT"]).as_unit("s") # type: ignore[arg-type, unused-ignore]
encoding = {"units": "seconds"}
expected = Dataset({"td": ("td", time_deltas), "td0": time_deltas[0]})
expected["td"].encoding = encoding
expected["td0"].encoding = encoding
with self.roundtrip(
expected, open_kwargs={"decode_timedelta": CFTimedeltaCoder(time_unit="ns")}
) as actual:
assert_identical(expected, actual)
def test_roundtrip_timedelta_data_via_dtype(
self, time_unit: PDDatetimeUnitOptions
) -> None:
time_deltas = pd.to_timedelta(["1h", "2h", "NaT"]).as_unit(time_unit) # type: ignore[arg-type, unused-ignore]
expected = Dataset(
{"td": ("td", time_deltas), "td0": time_deltas[0].to_numpy()}
)
with self.roundtrip(expected) as actual:
assert_identical(expected, actual)
def test_roundtrip_float64_data(self) -> None:
expected = Dataset({"x": ("y", np.array([1.0, 2.0, np.pi], dtype="float64"))})
with self.roundtrip(expected) as actual:
assert_identical(expected, actual)
@requires_netcdf
def test_roundtrip_example_1_netcdf(self) -> None:
with open_example_dataset("example_1.nc") as expected:
with self.roundtrip(expected) as actual:
# we allow the attributes to differ since that
# will depend on the encoding used. For example,
# without CF encoding 'actual' will end up with
# a dtype attribute.
assert_equal(expected, actual)
def test_roundtrip_coordinates(self) -> None:
original = Dataset(
{"foo": ("x", [0, 1])}, {"x": [2, 3], "y": ("a", [42]), "z": ("x", [4, 5])}
)
with self.roundtrip(original) as actual:
assert_identical(original, actual)
original["foo"].encoding["coordinates"] = "y"
with self.roundtrip(original, open_kwargs={"decode_coords": False}) as expected:
# check roundtripping when decode_coords=False
with self.roundtrip(
expected, open_kwargs={"decode_coords": False}
) as actual:
assert_identical(expected, actual)
def test_roundtrip_global_coordinates(self) -> None:
original = Dataset(
{"foo": ("x", [0, 1])}, {"x": [2, 3], "y": ("a", [42]), "z": ("x", [4, 5])}
)
with self.roundtrip(original) as actual:
assert_identical(original, actual)
# test that global "coordinates" is as expected
_, attrs = encode_dataset_coordinates(original)
assert attrs["coordinates"] == "y"
# test warning when global "coordinates" is already set
original.attrs["coordinates"] = "foo"
with pytest.warns(SerializationWarning):
_, attrs = encode_dataset_coordinates(original)
assert attrs["coordinates"] == "foo"
def test_roundtrip_coordinates_with_space(self) -> None:
original = Dataset(coords={"x": 0, "y z": 1})
expected = Dataset({"y z": 1}, {"x": 0})
with pytest.warns(SerializationWarning):
with self.roundtrip(original) as actual:
assert_identical(expected, actual)
def test_roundtrip_boolean_dtype(self) -> None:
original = create_boolean_data()
assert original["x"].dtype == "bool"
with self.roundtrip(original) as actual:
assert_identical(original, actual)
assert actual["x"].dtype == "bool"
# this checks for preserving dtype during second roundtrip
# see https://github.com/pydata/xarray/issues/7652#issuecomment-1476956975
with self.roundtrip(actual) as actual2:
assert_identical(original, actual2)
assert actual2["x"].dtype == "bool"
with self.roundtrip(actual) as actual3:
# GH10536
assert_identical(original.transpose(), actual3.transpose())
def test_orthogonal_indexing(self) -> None:
in_memory = create_test_data()
with self.roundtrip(in_memory) as on_disk:
indexers = {"dim1": [1, 2, 0], "dim2": [3, 2, 0, 3], "dim3": np.arange(5)}
expected = in_memory.isel(indexers)
actual = on_disk.isel(**indexers)
# make sure the array is not yet loaded into memory
assert not actual["var1"].variable._in_memory
assert_identical(expected, actual)
# do it twice, to make sure we're switched from orthogonal -> numpy
# when we cached the values
actual = on_disk.isel(**indexers)
assert_identical(expected, actual)
def test_vectorized_indexing(self) -> None:
in_memory = create_test_data()
with self.roundtrip(in_memory) as on_disk:
indexers = {
"dim1": DataArray([0, 2, 0], dims="a"),
"dim2": DataArray([0, 2, 3], dims="a"),
}
expected = in_memory.isel(indexers)
actual = on_disk.isel(**indexers)
# make sure the array is not yet loaded into memory
assert not actual["var1"].variable._in_memory
assert_identical(expected, actual.load())
# do it twice, to make sure we're switched from
# vectorized -> numpy when we cached the values
actual = on_disk.isel(**indexers)
assert_identical(expected, actual)
def multiple_indexing(indexers):
# make sure a sequence of lazy indexings certainly works.
with self.roundtrip(in_memory) as on_disk:
actual = on_disk["var3"]
expected = in_memory["var3"]
for ind in indexers:
actual = actual.isel(ind)
expected = expected.isel(ind)
# make sure the array is not yet loaded into memory
assert not actual.variable._in_memory
assert_identical(expected, actual.load())
# two-staged vectorized-indexing
indexers2 = [
{
"dim1": DataArray([[0, 7], [2, 6], [3, 5]], dims=["a", "b"]),
"dim3": DataArray([[0, 4], [1, 3], [2, 2]], dims=["a", "b"]),
},
{"a": DataArray([0, 1], dims=["c"]), "b": DataArray([0, 1], dims=["c"])},
]
multiple_indexing(indexers2)
# vectorized-slice mixed
indexers3 = [
{
"dim1": DataArray([[0, 7], [2, 6], [3, 5]], dims=["a", "b"]),
"dim3": slice(None, 10),
}
]
multiple_indexing(indexers3)
# vectorized-integer mixed
indexers4 = [
{"dim3": 0},
{"dim1": DataArray([[0, 7], [2, 6], [3, 5]], dims=["a", "b"])},
{"a": slice(None, None, 2)},
]
multiple_indexing(indexers4)
# vectorized-integer mixed
indexers5 = [
{"dim3": 0},
{"dim1": DataArray([[0, 7], [2, 6], [3, 5]], dims=["a", "b"])},
{"a": 1, "b": 0},
]
multiple_indexing(indexers5)
def test_vectorized_indexing_negative_step(self) -> None:
# use dask explicitly when present
open_kwargs: dict[str, Any] | None
if has_dask:
open_kwargs = {"chunks": {}}
else:
open_kwargs = None
in_memory = create_test_data()
def multiple_indexing(indexers):
# make sure a sequence of lazy indexings certainly works.
with self.roundtrip(in_memory, open_kwargs=open_kwargs) as on_disk:
actual = on_disk["var3"]
expected = in_memory["var3"]
for ind in indexers:
actual = actual.isel(ind)
expected = expected.isel(ind)
# make sure the array is not yet loaded into memory
assert not actual.variable._in_memory
assert_identical(expected, actual.load())
# with negative step slice.
indexers = [
{
"dim1": DataArray([[0, 7], [2, 6], [3, 5]], dims=["a", "b"]),
"dim3": slice(-1, 1, -1),
}
]
multiple_indexing(indexers)
# with negative step slice.
indexers = [
{
"dim1": DataArray([[0, 7], [2, 6], [3, 5]], dims=["a", "b"]),
"dim3": slice(-1, 1, -2),
}
]
multiple_indexing(indexers)
def test_outer_indexing_reversed(self) -> None:
# regression test for GH6560
ds = xr.Dataset(
{"z": (("t", "p", "y", "x"), np.ones((1, 1, 31, 40)))},
)
with self.roundtrip(ds) as on_disk:
subset = on_disk.isel(t=[0], p=0).z[:, ::10, ::10][:, ::-1, :]
assert subset.sizes == subset.load().sizes
def test_isel_dataarray(self) -> None:
# Make sure isel works lazily. GH:issue:1688
in_memory = create_test_data()
with self.roundtrip(in_memory) as on_disk:
expected = in_memory.isel(dim2=in_memory["dim2"] < 3)
actual = on_disk.isel(dim2=on_disk["dim2"] < 3)
assert_identical(expected, actual)
def validate_array_type(self, ds):
# Make sure that only NumpyIndexingAdapter stores a bare np.ndarray.
def find_and_validate_array(obj):
# recursively called function. obj: array or array wrapper.
if hasattr(obj, "array"):
if isinstance(obj.array, indexing.ExplicitlyIndexed):
find_and_validate_array(obj.array)
elif isinstance(obj.array, np.ndarray):
assert isinstance(obj, indexing.NumpyIndexingAdapter)
elif isinstance(obj.array, dask_array_type):
assert isinstance(obj, indexing.DaskIndexingAdapter)
elif isinstance(obj.array, pd.Index):
assert isinstance(obj, indexing.PandasIndexingAdapter)
else:
raise TypeError(f"{type(obj.array)} is wrapped by {type(obj)}")
for v in ds.variables.values():
find_and_validate_array(v._data)
def test_array_type_after_indexing(self) -> None:
in_memory = create_test_data()
with self.roundtrip(in_memory) as on_disk:
self.validate_array_type(on_disk)
indexers = {"dim1": [1, 2, 0], "dim2": [3, 2, 0, 3], "dim3": np.arange(5)}
expected = in_memory.isel(indexers)
actual = on_disk.isel(**indexers)
assert_identical(expected, actual)
self.validate_array_type(actual)
# do it twice, to make sure we're switched from orthogonal -> numpy
# when we cached the values
actual = on_disk.isel(**indexers)
assert_identical(expected, actual)
self.validate_array_type(actual)
def test_dropna(self) -> None:
# regression test for GH:issue:1694
a = np.random.randn(4, 3)
a[1, 1] = np.nan
in_memory = xr.Dataset(
{"a": (("y", "x"), a)}, coords={"y": np.arange(4), "x": np.arange(3)}
)
assert_identical(
in_memory.dropna(dim="x"), in_memory.isel(x=slice(None, None, 2))
)
with self.roundtrip(in_memory) as on_disk:
self.validate_array_type(on_disk)
expected = in_memory.dropna(dim="x")
actual = on_disk.dropna(dim="x")
assert_identical(expected, actual)
def test_ondisk_after_print(self) -> None:
"""Make sure print does not load file into memory"""
in_memory = create_test_data()
with self.roundtrip(in_memory) as on_disk:
repr(on_disk)
assert not on_disk["var1"]._in_memory
class CFEncodedBase(DatasetIOBase):
def test_roundtrip_bytes_with_fill_value(self) -> None:
values = np.array([b"ab", b"cdef", np.nan], dtype=object)
encoding = {"_FillValue": b"X", "dtype": "S1"}
original = Dataset({"x": ("t", values, {}, encoding)})
expected = original.copy(deep=True)
with self.roundtrip(original) as actual:
assert_identical(expected, actual)
original = Dataset({"x": ("t", values, {}, {"_FillValue": b""})})
with self.roundtrip(original) as actual:
assert_identical(expected, actual)
def test_roundtrip_string_with_fill_value_nchar(self) -> None:
values = np.array(["ab", "cdef", np.nan], dtype=object)
expected = Dataset({"x": ("t", values)})
encoding = {"dtype": "S1", "_FillValue": b"X"}
original = Dataset({"x": ("t", values, {}, encoding)})
# Not supported yet.
with pytest.raises(NotImplementedError):
with self.roundtrip(original) as actual:
assert_identical(expected, actual)
def test_roundtrip_empty_vlen_string_array(self) -> None:
# checks preserving vlen dtype for empty arrays GH7862
dtype = create_vlen_dtype(str)
original = Dataset({"a": np.array([], dtype=dtype)})
assert check_vlen_dtype(original["a"].dtype) is str
with self.roundtrip(original) as actual:
assert_identical(original, actual)
if np.issubdtype(actual["a"].dtype, object):
# only check metadata for capable backends
# eg. NETCDF3 based backends do not roundtrip metadata
if actual["a"].dtype.metadata is not None:
assert check_vlen_dtype(actual["a"].dtype) is str
else:
# zarr v3 sends back "<U1"
assert np.issubdtype(actual["a"].dtype, np.dtype("=U1"))
@pytest.mark.parametrize(
"decoded_fn, encoded_fn",
[
(
create_unsigned_masked_scaled_data,
create_encoded_unsigned_masked_scaled_data,
),
pytest.param(
create_bad_unsigned_masked_scaled_data,
create_bad_encoded_unsigned_masked_scaled_data,
marks=pytest.mark.xfail(reason="Bad _Unsigned attribute."),
),
(
create_signed_masked_scaled_data,
create_encoded_signed_masked_scaled_data,
),
(
create_unsigned_false_masked_scaled_data,
create_encoded_unsigned_false_masked_scaled_data,
),
(create_masked_and_scaled_data, create_encoded_masked_and_scaled_data),
],
)
@pytest.mark.parametrize("dtype", [np.dtype("float64"), np.dtype("float32")])
def test_roundtrip_mask_and_scale(self, decoded_fn, encoded_fn, dtype) -> None:
if hasattr(self, "zarr_version") and dtype == np.float32:
pytest.skip("float32 will be treated as float64 in zarr")
decoded = decoded_fn(dtype)
encoded = encoded_fn(dtype)
if decoded["x"].encoding["dtype"] == "u1" and not (
(self.engine == "netcdf4" and self.file_format is None)
or self.file_format == "NETCDF4"
):
pytest.skip("uint8 data can't be written to non-NetCDF4 data")
with self.roundtrip(decoded) as actual:
for k in decoded.variables:
assert decoded.variables[k].dtype == actual.variables[k].dtype
# CF _FillValue is always on-disk type
assert (
decoded.variables[k].encoding["_FillValue"]
== actual.variables[k].encoding["_FillValue"]
)
assert_allclose(decoded, actual, decode_bytes=False)
with self.roundtrip(decoded, open_kwargs=dict(decode_cf=False)) as actual:
# TODO: this assumes that all roundtrips will first
# encode. Is that something we want to test for?
for k in encoded.variables:
assert encoded.variables[k].dtype == actual.variables[k].dtype
# CF _FillValue is always on-disk type
assert (
decoded.variables[k].encoding["_FillValue"]
== actual.variables[k].attrs["_FillValue"]
)
assert_allclose(encoded, actual, decode_bytes=False)
with self.roundtrip(encoded, open_kwargs=dict(decode_cf=False)) as actual:
for k in encoded.variables:
assert encoded.variables[k].dtype == actual.variables[k].dtype
# CF _FillValue is always on-disk type
assert (
encoded.variables[k].attrs["_FillValue"]
== actual.variables[k].attrs["_FillValue"]
)
assert_allclose(encoded, actual, decode_bytes=False)
# make sure roundtrip encoding didn't change the
# original dataset.
assert_allclose(encoded, encoded_fn(dtype), decode_bytes=False)
with self.roundtrip(encoded) as actual:
for k in decoded.variables:
assert decoded.variables[k].dtype == actual.variables[k].dtype
assert_allclose(decoded, actual, decode_bytes=False)
@pytest.mark.parametrize(
("fill_value", "exp_fill_warning"),
[
(np.int8(-1), False),
(np.uint8(255), True),
(-1, False),
(255, True),
],
)
def test_roundtrip_unsigned(self, fill_value, exp_fill_warning):
@contextlib.contextmanager
def _roundtrip_with_warnings(*args, **kwargs):
is_np2 = module_available("numpy", minversion="2.0.0.dev0")
if exp_fill_warning and is_np2:
warn_checker: contextlib.AbstractContextManager = pytest.warns(
SerializationWarning,
match="_FillValue attribute can't be represented",
)
else:
warn_checker = contextlib.nullcontext()
with warn_checker:
with self.roundtrip(*args, **kwargs) as actual:
yield actual
# regression/numpy2 test for
encoding = {
"_FillValue": fill_value,
"_Unsigned": "true",
"dtype": "i1",
}
x = np.array([0, 1, 127, 128, 254, np.nan], dtype=np.float32)
decoded = Dataset({"x": ("t", x, {}, encoding)})
attributes = {
"_FillValue": fill_value,
"_Unsigned": "true",
}
# Create unsigned data corresponding to [0, 1, 127, 128, 255] unsigned
sb = np.asarray([0, 1, 127, -128, -2, -1], dtype="i1")
encoded = Dataset({"x": ("t", sb, attributes)})
unsigned_dtype = np.dtype(f"u{sb.dtype.itemsize}")
with _roundtrip_with_warnings(decoded) as actual:
for k in decoded.variables:
assert decoded.variables[k].dtype == actual.variables[k].dtype
exp_fv = decoded.variables[k].encoding["_FillValue"]
if exp_fill_warning:
exp_fv = np.array(exp_fv, dtype=unsigned_dtype).view(sb.dtype)
assert exp_fv == actual.variables[k].encoding["_FillValue"]
assert_allclose(decoded, actual, decode_bytes=False)
with _roundtrip_with_warnings(
decoded, open_kwargs=dict(decode_cf=False)
) as actual:
for k in encoded.variables:
assert encoded.variables[k].dtype == actual.variables[k].dtype
exp_fv = encoded.variables[k].attrs["_FillValue"]
if exp_fill_warning:
exp_fv = np.array(exp_fv, dtype=unsigned_dtype).view(sb.dtype)
assert exp_fv == actual.variables[k].attrs["_FillValue"]
assert_allclose(encoded, actual, decode_bytes=False)
@staticmethod
def _create_cf_dataset():
original = Dataset(
dict(
variable=(
("ln_p", "latitude", "longitude"),
np.arange(8, dtype="f4").reshape(2, 2, 2),
{"ancillary_variables": "std_devs det_lim"},
),
std_devs=(
("ln_p", "latitude", "longitude"),
np.arange(0.1, 0.9, 0.1).reshape(2, 2, 2),
{"standard_name": "standard_error"},
),
det_lim=(
(),
0.1,
{"standard_name": "detection_minimum"},
),
),
dict(
latitude=("latitude", [0, 1], {"units": "degrees_north"}),
longitude=("longitude", [0, 1], {"units": "degrees_east"}),
latlon=((), -1, {"grid_mapping_name": "latitude_longitude"}),
latitude_bnds=(("latitude", "bnds2"), [[0, 1], [1, 2]]),
longitude_bnds=(("longitude", "bnds2"), [[0, 1], [1, 2]]),
areas=(
("latitude", "longitude"),
[[1, 1], [1, 1]],
{"units": "degree^2"},
),
ln_p=(
"ln_p",
[1.0, 0.5],
{
"standard_name": "atmosphere_ln_pressure_coordinate",
"computed_standard_name": "air_pressure",
},
),
P0=((), 1013.25, {"units": "hPa"}),
),
)
original["variable"].encoding.update(
{"cell_measures": "area: areas", "grid_mapping": "latlon"},
)
original.coords["latitude"].encoding.update(
dict(grid_mapping="latlon", bounds="latitude_bnds")
)
original.coords["longitude"].encoding.update(
dict(grid_mapping="latlon", bounds="longitude_bnds")
)
original.coords["ln_p"].encoding.update({"formula_terms": "p0: P0 lev : ln_p"})
return original
def test_grid_mapping_and_bounds_are_not_coordinates_in_file(self) -> None:
original = self._create_cf_dataset()
with self.roundtrip(original, open_kwargs={"decode_coords": False}) as ds:
assert ds.coords["latitude"].attrs["bounds"] == "latitude_bnds"
assert ds.coords["longitude"].attrs["bounds"] == "longitude_bnds"
assert "coordinates" not in ds["variable"].attrs
assert "coordinates" not in ds.attrs
def test_coordinate_variables_after_dataset_roundtrip(self) -> None:
original = self._create_cf_dataset()
with self.roundtrip(original, open_kwargs={"decode_coords": "all"}) as actual:
assert_identical(actual, original)
with self.roundtrip(original) as actual:
expected = original.reset_coords(
["latitude_bnds", "longitude_bnds", "areas", "P0", "latlon"]
)
# equal checks that coords and data_vars are equal which
# should be enough
# identical would require resetting a number of attributes
# skip that.
assert_equal(actual, expected)
def test_grid_mapping_and_bounds_are_coordinates_after_dataarray_roundtrip(
self,
) -> None:
original = self._create_cf_dataset()
# The DataArray roundtrip should have the same warnings as the
# Dataset, but we already tested for those, so just go for the
# new warnings. It would appear that there is no way to tell
# pytest "This warning and also this warning should both be
# present".
# xarray/tests/test_conventions.py::TestCFEncodedDataStore
# needs the to_dataset. The other backends should be fine
# without it.
with pytest.warns(
UserWarning,
match=(
r"Variable\(s\) referenced in bounds not in variables: "
r"\['l(at|ong)itude_bnds'\]"
),
):
with self.roundtrip(
original["variable"].to_dataset(), open_kwargs={"decode_coords": "all"}
) as actual:
assert_identical(actual, original["variable"].to_dataset())
@requires_iris
@requires_netcdf
def test_coordinate_variables_after_iris_roundtrip(self) -> None:
original = self._create_cf_dataset()
iris_cube = original["variable"].to_iris()
actual = DataArray.from_iris(iris_cube)
# Bounds will be missing (xfail)
del original.coords["latitude_bnds"], original.coords["longitude_bnds"]
# Ancillary vars will be missing
# Those are data_vars, and will be dropped when grabbing the variable
assert_identical(actual, original["variable"])
def test_coordinates_encoding(self) -> None:
def equals_latlon(obj):
return obj in {"lat lon", "lon lat"}
original = Dataset(
{"temp": ("x", [0, 1]), "precip": ("x", [0, -1])},
{"lat": ("x", [2, 3]), "lon": ("x", [4, 5])},
)
with self.roundtrip(original) as actual:
assert_identical(actual, original)
with self.roundtrip(original, open_kwargs=dict(decode_coords=False)) as ds:
assert equals_latlon(ds["temp"].attrs["coordinates"])
assert equals_latlon(ds["precip"].attrs["coordinates"])
assert "coordinates" not in ds.attrs
assert "coordinates" not in ds["lat"].attrs
assert "coordinates" not in ds["lon"].attrs
modified = original.drop_vars(["temp", "precip"])
with self.roundtrip(modified) as actual:
assert_identical(actual, modified)
with self.roundtrip(modified, open_kwargs=dict(decode_coords=False)) as ds:
assert equals_latlon(ds.attrs["coordinates"])
assert "coordinates" not in ds["lat"].attrs
assert "coordinates" not in ds["lon"].attrs
original["temp"].encoding["coordinates"] = "lat"
with self.roundtrip(original) as actual:
assert_identical(actual, original)
original["precip"].encoding["coordinates"] = "lat"
with self.roundtrip(original, open_kwargs=dict(decode_coords=True)) as ds:
assert "lon" not in ds["temp"].encoding["coordinates"]
assert "lon" not in ds["precip"].encoding["coordinates"]
assert "coordinates" not in ds["lat"].encoding
assert "coordinates" not in ds["lon"].encoding
def test_roundtrip_endian(self) -> None:
skip_if_zarr_format_3("zarr v3 has not implemented endian support yet")
ds = Dataset(
{
"x": np.arange(3, 10, dtype=">i2"),
"y": np.arange(3, 20, dtype="<i4"),
"z": np.arange(3, 30, dtype="=i8"),
"w": ("x", np.arange(3, 10, dtype=float)),
}
)
with self.roundtrip(ds) as actual:
# technically these datasets are slightly different,
# one hold mixed endian data (ds) the other should be
# all big endian (actual). assertDatasetIdentical
# should still pass though.
assert_identical(ds, actual)
if self.engine == "netcdf4":
ds["z"].encoding["endian"] = "big"
with pytest.raises(NotImplementedError):
with self.roundtrip(ds) as actual:
pass
def test_invalid_dataarray_names_raise(self) -> None:
te = (TypeError, "string or None")
ve = (ValueError, "string must be length 1 or")
data = np.random.random((2, 2))
da = xr.DataArray(data)
for name, (error, msg) in zip(
[0, (4, 5), True, ""], [te, te, te, ve], strict=True
):
ds = Dataset({name: da})
with pytest.raises(error) as excinfo:
with self.roundtrip(ds):
pass
excinfo.match(msg)
excinfo.match(repr(name))
def test_encoding_kwarg(self) -> None:
ds = Dataset({"x": ("y", np.arange(10.0))})
kwargs: dict[str, Any] = dict(encoding={"x": {"dtype": "f4"}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
encoded_dtype = actual.x.encoding["dtype"]
# On OS X, dtype sometimes switches endianness for unclear reasons
assert encoded_dtype.kind == "f" and encoded_dtype.itemsize == 4
assert ds.x.encoding == {}
kwargs = dict(encoding={"x": {"foo": "bar"}})
with pytest.raises(ValueError, match=r"unexpected encoding"):
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
pass
kwargs = dict(encoding={"x": "foo"})
with pytest.raises(ValueError, match=r"must be castable"):
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
pass
kwargs = dict(encoding={"invalid": {}})
with pytest.raises(KeyError):
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
pass
def test_encoding_unlimited_dims(self) -> None:
if isinstance(self, ZarrBase):
pytest.skip("No unlimited_dims handled in zarr.")
ds = Dataset({"x": ("y", np.arange(10.0))})
with self.roundtrip(ds, save_kwargs=dict(unlimited_dims=["y"])) as actual:
assert actual.encoding["unlimited_dims"] == set("y")
assert_equal(ds, actual)
# Regression test for https://github.com/pydata/xarray/issues/2134
with self.roundtrip(ds, save_kwargs=dict(unlimited_dims="y")) as actual:
assert actual.encoding["unlimited_dims"] == set("y")
assert_equal(ds, actual)
ds.encoding = {"unlimited_dims": ["y"]}
with self.roundtrip(ds) as actual:
assert actual.encoding["unlimited_dims"] == set("y")
assert_equal(ds, actual)
# Regression test for https://github.com/pydata/xarray/issues/2134
ds.encoding = {"unlimited_dims": "y"}
with self.roundtrip(ds) as actual:
assert actual.encoding["unlimited_dims"] == set("y")
assert_equal(ds, actual)
# test unlimited_dims validation
# https://github.com/pydata/xarray/issues/10549
ds.encoding = {"unlimited_dims": "z"}
with pytest.raises(
ValueError,
match=r"Unlimited dimension\(s\) .* declared in 'dataset.encoding'",
):
with self.roundtrip(ds) as _:
pass
ds.encoding = {}
with pytest.raises(
ValueError,
match=r"Unlimited dimension\(s\) .* declared in 'unlimited_dims-kwarg'",
):
with self.roundtrip(ds, save_kwargs=dict(unlimited_dims=["z"])) as _:
pass
def test_encoding_kwarg_dates(self) -> None:
ds = Dataset({"t": pd.date_range("2000-01-01", periods=3)})
units = "days since 1900-01-01"
kwargs = dict(encoding={"t": {"units": units}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert actual.t.encoding["units"] == units
assert_identical(actual, ds)
def test_encoding_kwarg_fixed_width_string(self) -> None:
# regression test for GH2149
for strings in [[b"foo", b"bar", b"baz"], ["foo", "bar", "baz"]]:
ds = Dataset({"x": strings})
kwargs = dict(encoding={"x": {"dtype": "S1"}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert actual["x"].encoding["dtype"] == "S1"
assert_identical(actual, ds)
def test_default_fill_value(self) -> None:
# Test default encoding for float:
ds = Dataset({"x": ("y", np.arange(10.0))})
kwargs = dict(encoding={"x": {"dtype": "f4"}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert math.isnan(actual.x.encoding["_FillValue"])
assert ds.x.encoding == {}
# Test default encoding for int:
ds = Dataset({"x": ("y", np.arange(10.0))})
kwargs = dict(encoding={"x": {"dtype": "int16"}})
with warnings.catch_warnings():
warnings.filterwarnings("ignore", ".*floating point data as an integer")
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert "_FillValue" not in actual.x.encoding
assert ds.x.encoding == {}
# Test default encoding for implicit int:
ds = Dataset({"x": ("y", np.arange(10, dtype="int16"))})
with self.roundtrip(ds) as actual:
assert "_FillValue" not in actual.x.encoding
assert ds.x.encoding == {}
def test_explicitly_omit_fill_value(self) -> None:
ds = Dataset({"x": ("y", [np.pi, -np.pi])})
ds.x.encoding["_FillValue"] = None
with self.roundtrip(ds) as actual:
assert "_FillValue" not in actual.x.encoding
def test_explicitly_omit_fill_value_via_encoding_kwarg(self) -> None:
ds = Dataset({"x": ("y", [np.pi, -np.pi])})
kwargs = dict(encoding={"x": {"_FillValue": None}})
# _FillValue is not a valid encoding for Zarr
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert "_FillValue" not in actual.x.encoding
assert ds.y.encoding == {}
def test_explicitly_omit_fill_value_in_coord(self) -> None:
ds = Dataset({"x": ("y", [np.pi, -np.pi])}, coords={"y": [0.0, 1.0]})
ds.y.encoding["_FillValue"] = None
with self.roundtrip(ds) as actual:
assert "_FillValue" not in actual.y.encoding
def test_explicitly_omit_fill_value_in_coord_via_encoding_kwarg(self) -> None:
ds = Dataset({"x": ("y", [np.pi, -np.pi])}, coords={"y": [0.0, 1.0]})
kwargs = dict(encoding={"y": {"_FillValue": None}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert "_FillValue" not in actual.y.encoding
assert ds.y.encoding == {}
def test_encoding_same_dtype(self) -> None:
ds = Dataset({"x": ("y", np.arange(10.0, dtype="f4"))})
kwargs = dict(encoding={"x": {"dtype": "f4"}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
encoded_dtype = actual.x.encoding["dtype"]
# On OS X, dtype sometimes switches endianness for unclear reasons
assert encoded_dtype.kind == "f" and encoded_dtype.itemsize == 4
assert ds.x.encoding == {}
def test_append_write(self) -> None:
# regression for GH1215
data = create_test_data()
with self.roundtrip_append(data) as actual:
assert_identical(data, actual)
def test_append_overwrite_values(self) -> None:
# regression for GH1215
data = create_test_data()
with create_tmp_file(allow_cleanup_failure=False) as tmp_file:
self.save(data, tmp_file, mode="w")
data["var2"][:] = -999
data["var9"] = data["var2"] * 3
self.save(data[["var2", "var9"]], tmp_file, mode="a")
with self.open(tmp_file) as actual:
assert_identical(data, actual)
def test_append_with_invalid_dim_raises(self) -> None:
data = create_test_data()
with create_tmp_file(allow_cleanup_failure=False) as tmp_file:
self.save(data, tmp_file, mode="w")
data["var9"] = data["var2"] * 3
data = data.isel(dim1=slice(2, 6)) # modify one dimension
with pytest.raises(
ValueError, match=r"Unable to update size for existing dimension"
):
self.save(data, tmp_file, mode="a")
def test_multiindex_not_implemented(self) -> None:
ds = Dataset(coords={"y": ("x", [1, 2]), "z": ("x", ["a", "b"])}).set_index(
x=["y", "z"]
)
with pytest.raises(NotImplementedError, match=r"MultiIndex"):
with self.roundtrip(ds):
pass
# regression GH8628 (can serialize reset multi-index level coordinates)
ds_reset = ds.reset_index("x")
with self.roundtrip(ds_reset) as actual:
assert_identical(actual, ds_reset)
@requires_dask
def test_string_object_warning(self) -> None:
original = Dataset(
{
"x": (
[
"y",
],
np.array(["foo", "bar"], dtype=object),
)
}
).chunk()
with pytest.warns(SerializationWarning, match="dask array with dtype=object"):
with self.roundtrip(original) as actual:
assert_identical(original, actual)
@pytest.mark.parametrize(
"indexer",
(
{"y": [1]},
{"y": slice(2)},
{"y": 1},
{"x": [1], "y": [1]},
{"x": ("x0", [0, 1]), "y": ("x0", [0, 1])},
),
)
def test_indexing_roundtrip(self, indexer) -> None:
# regression test for GH8909
ds = xr.Dataset()
ds["A"] = xr.DataArray([[1, "a"], [2, "b"]], dims=["x", "y"])
with self.roundtrip(ds) as ds2:
expected = ds2.sel(indexer)
with self.roundtrip(expected) as actual:
assert_identical(actual, expected)
class NetCDFBase(CFEncodedBase):
"""Tests for all netCDF3 and netCDF4 backends."""
@pytest.mark.asyncio
@pytest.mark.skip(reason="NetCDF backends don't support async loading")
async def test_load_async(self) -> None:
await super().test_load_async()
@pytest.mark.skipif(
ON_WINDOWS, reason="Windows does not allow modifying open files"
)
def test_refresh_from_disk(self) -> None:
# regression test for https://github.com/pydata/xarray/issues/4862
with create_tmp_file() as example_1_path:
with create_tmp_file() as example_1_modified_path:
with open_example_dataset("example_1.nc") as example_1:
self.save(example_1, example_1_path)
example_1.rh.values += 100
self.save(example_1, example_1_modified_path)
a = open_dataset(example_1_path, engine=self.engine).load()
# Simulate external process modifying example_1.nc while this script is running
shutil.copy(example_1_modified_path, example_1_path)
# Reopen example_1.nc (modified) as `b`; note that `a` has NOT been closed
b = open_dataset(example_1_path, engine=self.engine).load()
try:
assert not np.array_equal(a.rh.values, b.rh.values)
finally:
a.close()
b.close()
def test_byte_attrs(self, byte_attrs_dataset: dict[str, Any]) -> None:
# test for issue #9407
input = byte_attrs_dataset["input"]
expected = byte_attrs_dataset["expected"]
with self.roundtrip(input) as actual:
assert_identical(actual, expected)
_counter = itertools.count()
@contextlib.contextmanager
def create_tmp_file(
suffix: str = ".nc", allow_cleanup_failure: bool = False
) -> Iterator[str]:
temp_dir = tempfile.mkdtemp()
path = os.path.join(temp_dir, f"temp-{next(_counter)}{suffix}")
try:
yield path
finally:
try:
shutil.rmtree(temp_dir)
except OSError:
if not allow_cleanup_failure:
raise
@contextlib.contextmanager
def create_tmp_files(
nfiles: int, suffix: str = ".nc", allow_cleanup_failure: bool = False
) -> Iterator[list[str]]:
with ExitStack() as stack:
files = [
stack.enter_context(create_tmp_file(suffix, allow_cleanup_failure))
for _ in range(nfiles)
]
yield files
class NetCDF4Base(NetCDFBase):
"""Tests for both netCDF4-python and h5netcdf."""
engine: T_NetcdfEngine = "netcdf4"
def test_open_group(self) -> None:
# Create a netCDF file with a dataset stored within a group
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, "w") as rootgrp:
foogrp = rootgrp.createGroup("foo")
ds = foogrp
ds.createDimension("time", size=10)
x = np.arange(10)
ds.createVariable("x", np.int32, dimensions=("time",))
ds.variables["x"][:] = x
expected = Dataset()
expected["x"] = ("time", x)
# check equivalent ways to specify group
for group in "foo", "/foo", "foo/", "/foo/":
with self.open(tmp_file, group=group) as actual:
assert_equal(actual["x"], expected["x"])
# check that missing group raises appropriate exception
with pytest.raises(OSError):
open_dataset(tmp_file, group="bar")
with pytest.raises(ValueError, match=r"must be a string"):
open_dataset(tmp_file, group=(1, 2, 3))
def test_open_subgroup(self) -> None:
# Create a netCDF file with a dataset stored within a group within a
# group
with create_tmp_file() as tmp_file:
rootgrp = nc4.Dataset(tmp_file, "w")
foogrp = rootgrp.createGroup("foo")
bargrp = foogrp.createGroup("bar")
ds = bargrp
ds.createDimension("time", size=10)
x = np.arange(10)
ds.createVariable("x", np.int32, dimensions=("time",))
ds.variables["x"][:] = x
rootgrp.close()
expected = Dataset()
expected["x"] = ("time", x)
# check equivalent ways to specify group
for group in "foo/bar", "/foo/bar", "foo/bar/", "/foo/bar/":
with self.open(tmp_file, group=group) as actual:
assert_equal(actual["x"], expected["x"])
def test_write_groups(self) -> None:
data1 = create_test_data()
data2 = data1 * 2
with create_tmp_file() as tmp_file:
self.save(data1, tmp_file, group="data/1")
self.save(data2, tmp_file, group="data/2", mode="a")
with self.open(tmp_file, group="data/1") as actual1:
assert_identical(data1, actual1)
with self.open(tmp_file, group="data/2") as actual2:
assert_identical(data2, actual2)
def test_child_group_with_inconsistent_dimensions(self) -> None:
base = Dataset(coords={"x": [1, 2]})
child = Dataset(coords={"x": [1, 2, 3]})
with create_tmp_file() as tmp_file:
self.save(base, tmp_file)
self.save(child, tmp_file, group="child", mode="a")
with self.open(tmp_file) as actual_base:
assert_identical(base, actual_base)
with self.open(tmp_file, group="child") as actual_child:
assert_identical(child, actual_child)
@pytest.mark.parametrize(
"input_strings, is_bytes",
[
([b"foo", b"bar", b"baz"], True),
(["foo", "bar", "baz"], False),
(["foó", "bár", "baź"], False),
],
)
def test_encoding_kwarg_vlen_string(
self, input_strings: list[str], is_bytes: bool
) -> None:
original = Dataset({"x": input_strings})
expected_string = ["foo", "bar", "baz"] if is_bytes else input_strings
expected = Dataset({"x": expected_string})
kwargs = dict(encoding={"x": {"dtype": str}})
with self.roundtrip(original, save_kwargs=kwargs) as actual:
assert actual["x"].encoding["dtype"] == "=U3"
assert actual["x"].dtype == "=U3"
assert_identical(actual, expected)
@pytest.mark.parametrize("fill_value", ["XXX", "", "bár"])
def test_roundtrip_string_with_fill_value_vlen(self, fill_value: str) -> None:
values = np.array(["ab", "cdef", np.nan], dtype=object)
expected = Dataset({"x": ("t", values)})
original = Dataset({"x": ("t", values, {}, {"_FillValue": fill_value})})
with self.roundtrip(original) as actual:
assert_identical(expected, actual)
original = Dataset({"x": ("t", values, {}, {"_FillValue": ""})})
with self.roundtrip(original) as actual:
assert_identical(expected, actual)
def test_roundtrip_character_array(self) -> None:
with create_tmp_file() as tmp_file:
values = np.array([["a", "b", "c"], ["d", "e", "f"]], dtype="S")
with nc4.Dataset(tmp_file, mode="w") as nc:
nc.createDimension("x", 2)
nc.createDimension("string3", 3)
v = nc.createVariable("x", np.dtype("S1"), ("x", "string3"))
v[:] = values
values = np.array(["abc", "def"], dtype="S")
expected = Dataset({"x": ("x", values)})
with open_dataset(tmp_file) as actual:
assert_identical(expected, actual)
# regression test for #157
with self.roundtrip(actual) as roundtripped:
assert_identical(expected, roundtripped)
def test_default_to_char_arrays(self) -> None:
data = Dataset({"x": np.array(["foo", "zzzz"], dtype="S")})
with self.roundtrip(data) as actual:
assert_identical(data, actual)
assert actual["x"].dtype == np.dtype("S4")
def test_open_encodings(self) -> None:
# Create a netCDF file with explicit time units
# and make sure it makes it into the encodings
# and survives a round trip
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, "w") as ds:
ds.createDimension("time", size=10)
ds.createVariable("time", np.int32, dimensions=("time",))
units = "days since 1999-01-01"
ds.variables["time"].setncattr("units", units)
ds.variables["time"][:] = np.arange(10) + 4
expected = Dataset()
time = pd.date_range("1999-01-05", periods=10, unit="ns")
encoding = {"units": units, "dtype": np.dtype("int32")}
expected["time"] = ("time", time, {}, encoding)
with open_dataset(tmp_file) as actual:
assert_equal(actual["time"], expected["time"])
actual_encoding = {
k: v
for k, v in actual["time"].encoding.items()
if k in expected["time"].encoding
}
assert actual_encoding == expected["time"].encoding
def test_dump_encodings(self) -> None:
# regression test for #709
ds = Dataset({"x": ("y", np.arange(10.0))})
kwargs = dict(encoding={"x": {"zlib": True}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert actual.x.encoding["zlib"]
def test_dump_and_open_encodings(self) -> None:
# Create a netCDF file with explicit time units
# and make sure it makes it into the encodings
# and survives a round trip
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, "w") as ds:
ds.createDimension("time", size=10)
ds.createVariable("time", np.int32, dimensions=("time",))
units = "days since 1999-01-01"
ds.variables["time"].setncattr("units", units)
ds.variables["time"][:] = np.arange(10) + 4
with open_dataset(tmp_file) as xarray_dataset:
with create_tmp_file() as tmp_file2:
xarray_dataset.to_netcdf(tmp_file2)
with nc4.Dataset(tmp_file2, "r") as ds:
assert ds.variables["time"].getncattr("units") == units
assert_array_equal(ds.variables["time"], np.arange(10) + 4)
def test_compression_encoding_legacy(self) -> None:
data = create_test_data()
data["var2"].encoding.update(
{
"zlib": True,
"chunksizes": (5, 5),
"fletcher32": True,
"shuffle": True,
"original_shape": data.var2.shape,
}
)
with self.roundtrip(data) as actual:
for k, v in data["var2"].encoding.items():
assert v == actual["var2"].encoding[k]
# regression test for #156
expected = data.isel(dim1=0)
with self.roundtrip(expected) as actual:
assert_equal(expected, actual)
def test_encoding_kwarg_compression(self) -> None:
ds = Dataset({"x": np.arange(10.0)})
encoding = dict(
dtype="f4",
zlib=True,
complevel=9,
fletcher32=True,
chunksizes=(5,),
shuffle=True,
)
kwargs = dict(encoding=dict(x=encoding))
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert_equal(actual, ds)
assert actual.x.encoding["dtype"] == "f4"
assert actual.x.encoding["zlib"]
assert actual.x.encoding["complevel"] == 9
assert actual.x.encoding["fletcher32"]
assert actual.x.encoding["chunksizes"] == (5,)
assert actual.x.encoding["shuffle"]
assert ds.x.encoding == {}
def test_keep_chunksizes_if_no_original_shape(self) -> None:
ds = Dataset({"x": [1, 2, 3]})
chunksizes = (2,)
ds.variables["x"].encoding = {"chunksizes": chunksizes}
with self.roundtrip(ds) as actual:
assert_identical(ds, actual)
assert_array_equal(
ds["x"].encoding["chunksizes"], actual["x"].encoding["chunksizes"]
)
def test_preferred_chunks_is_present(self) -> None:
ds = Dataset({"x": [1, 2, 3]})
chunksizes = (2,)
ds.variables["x"].encoding = {"chunksizes": chunksizes}
with self.roundtrip(ds) as actual:
assert actual["x"].encoding["preferred_chunks"] == {"x": 2}
@requires_dask
def test_auto_chunking_is_based_on_disk_chunk_sizes(self) -> None:
x_size = y_size = 1000
y_chunksize = y_size
x_chunksize = 10
with dask.config.set({"array.chunk-size": "100KiB"}):
with self.chunked_roundtrip(
(1, y_size, x_size),
(1, y_chunksize, x_chunksize),
open_kwargs={"chunks": "auto"},
) as ds:
t_chunks, y_chunks, x_chunks = ds["image"].data.chunks
assert all(np.asanyarray(y_chunks) == y_chunksize)
# Check that the chunk size is a multiple of the file chunk size
assert all(np.asanyarray(x_chunks) % x_chunksize == 0)
@requires_dask
def test_base_chunking_uses_disk_chunk_sizes(self) -> None:
x_size = y_size = 1000
y_chunksize = y_size
x_chunksize = 10
with self.chunked_roundtrip(
(1, y_size, x_size),
(1, y_chunksize, x_chunksize),
open_kwargs={"chunks": {}},
) as ds:
for chunksizes, expected in zip(
ds["image"].data.chunks, (1, y_chunksize, x_chunksize), strict=True
):
assert all(np.asanyarray(chunksizes) == expected)
@contextlib.contextmanager
def chunked_roundtrip(
self,
array_shape: tuple[int, int, int],
chunk_sizes: tuple[int, int, int],
open_kwargs: dict[str, Any] | None = None,
) -> Generator[Dataset, None, None]:
t_size, y_size, x_size = array_shape
t_chunksize, y_chunksize, x_chunksize = chunk_sizes
image = xr.DataArray(
np.arange(t_size * x_size * y_size, dtype=np.int16).reshape(
(t_size, y_size, x_size)
),
dims=["t", "y", "x"],
)
image.encoding = {"chunksizes": (t_chunksize, y_chunksize, x_chunksize)}
dataset = xr.Dataset(dict(image=image))
with self.roundtrip(dataset, open_kwargs=open_kwargs) as ds:
yield ds
def test_preferred_chunks_are_disk_chunk_sizes(self) -> None:
x_size = y_size = 1000
y_chunksize = y_size
x_chunksize = 10
with self.chunked_roundtrip(
(1, y_size, x_size), (1, y_chunksize, x_chunksize)
) as ds:
assert ds["image"].encoding["preferred_chunks"] == {
"t": 1,
"y": y_chunksize,
"x": x_chunksize,
}
def test_encoding_chunksizes_unlimited(self) -> None:
# regression test for GH1225
ds = Dataset({"x": [1, 2, 3], "y": ("x", [2, 3, 4])})
ds.variables["x"].encoding = {
"zlib": False,
"shuffle": False,
"complevel": 0,
"fletcher32": False,
"contiguous": False,
"chunksizes": (2**20,),
"original_shape": (3,),
}
with self.roundtrip(ds) as actual:
assert_equal(ds, actual)
def test_mask_and_scale(self) -> None:
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, mode="w") as nc:
nc.createDimension("t", 5)
nc.createVariable("x", "int16", ("t",), fill_value=-1)
v = nc.variables["x"]
v.set_auto_maskandscale(False)
v.add_offset = 10
v.scale_factor = 0.1
v[:] = np.array([-1, -1, 0, 1, 2])
dtype = type(v.scale_factor)
# first make sure netCDF4 reads the masked and scaled data
# correctly
with nc4.Dataset(tmp_file, mode="r") as nc:
expected = np.ma.array(
[-1, -1, 10, 10.1, 10.2], mask=[True, True, False, False, False]
)
actual = nc.variables["x"][:]
assert_array_equal(expected, actual)
# now check xarray
with open_dataset(tmp_file) as ds:
expected = create_masked_and_scaled_data(np.dtype(dtype))
assert_identical(expected, ds)
def test_0dimensional_variable(self) -> None:
# This fix verifies our work-around to this netCDF4-python bug:
# https://github.com/Unidata/netcdf4-python/pull/220
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, mode="w") as nc:
v = nc.createVariable("x", "int16")
v[...] = 123
with open_dataset(tmp_file) as ds:
expected = Dataset({"x": ((), 123)})
assert_identical(expected, ds)
def test_read_variable_len_strings(self) -> None:
with create_tmp_file() as tmp_file:
values = np.array(["foo", "bar", "baz"], dtype=object)
with nc4.Dataset(tmp_file, mode="w") as nc:
nc.createDimension("x", 3)
v = nc.createVariable("x", str, ("x",))
v[:] = values
expected = Dataset({"x": ("x", values)})
for kwargs in [{}, {"decode_cf": True}]:
with open_dataset(tmp_file, **cast(dict, kwargs)) as actual:
assert_identical(expected, actual)
def test_raise_on_forward_slashes_in_names(self) -> None:
# test for forward slash in variable names and dimensions
# see GH 7943
data_vars: list[dict[str, Any]] = [
{"PASS/FAIL": (["PASSFAIL"], np.array([0]))},
{"PASS/FAIL": np.array([0])},
{"PASSFAIL": (["PASS/FAIL"], np.array([0]))},
]
for dv in data_vars:
ds = Dataset(data_vars=dv)
with pytest.raises(ValueError, match="Forward slashes '/' are not allowed"):
with self.roundtrip(ds):
pass
@requires_netCDF4
def test_encoding_enum__no_fill_value(self, recwarn):
with create_tmp_file() as tmp_file:
cloud_type_dict = {"clear": 0, "cloudy": 1}
with nc4.Dataset(tmp_file, mode="w") as nc:
nc.createDimension("time", size=2)
cloud_type = nc.createEnumType(np.uint8, "cloud_type", cloud_type_dict)
v = nc.createVariable(
"clouds",
cloud_type,
"time",
fill_value=None,
)
v[:] = 1
with open_dataset(tmp_file) as original:
save_kwargs = {}
# We don't expect any errors.
# This is effectively a void context manager
expected_warnings = 0
if self.engine == "h5netcdf":
if not has_h5netcdf_1_4_0_or_above:
save_kwargs["invalid_netcdf"] = True
expected_warnings = 1
expected_msg = "You are writing invalid netcdf features to file"
else:
expected_warnings = 1
expected_msg = "Creating variable with default fill_value 0 which IS defined in enum type"
with self.roundtrip(original, save_kwargs=save_kwargs) as actual:
assert len(recwarn) == expected_warnings
if expected_warnings:
assert issubclass(recwarn[0].category, UserWarning)
assert str(recwarn[0].message).startswith(expected_msg)
assert_equal(original, actual)
assert (
actual.clouds.encoding["dtype"].metadata["enum"]
== cloud_type_dict
)
if not (
self.engine == "h5netcdf" and not has_h5netcdf_1_4_0_or_above
):
# not implemented in h5netcdf yet
assert (
actual.clouds.encoding["dtype"].metadata["enum_name"]
== "cloud_type"
)
@requires_netCDF4
def test_encoding_enum__multiple_variable_with_enum(self):
with create_tmp_file() as tmp_file:
cloud_type_dict = {"clear": 0, "cloudy": 1, "missing": 255}
with nc4.Dataset(tmp_file, mode="w") as nc:
nc.createDimension("time", size=2)
cloud_type = nc.createEnumType(np.uint8, "cloud_type", cloud_type_dict)
nc.createVariable(
"clouds",
cloud_type,
"time",
fill_value=255,
)
nc.createVariable(
"tifa",
cloud_type,
"time",
fill_value=255,
)
with open_dataset(tmp_file) as original:
save_kwargs = {}
if self.engine == "h5netcdf" and not has_h5netcdf_1_4_0_or_above:
save_kwargs["invalid_netcdf"] = True
with self.roundtrip(original, save_kwargs=save_kwargs) as actual:
assert_equal(original, actual)
assert (
actual.clouds.encoding["dtype"] == actual.tifa.encoding["dtype"]
)
assert (
actual.clouds.encoding["dtype"].metadata
== actual.tifa.encoding["dtype"].metadata
)
assert (
actual.clouds.encoding["dtype"].metadata["enum"]
== cloud_type_dict
)
if not (
self.engine == "h5netcdf" and not has_h5netcdf_1_4_0_or_above
):
# not implemented in h5netcdf yet
assert (
actual.clouds.encoding["dtype"].metadata["enum_name"]
== "cloud_type"
)
@requires_netCDF4
def test_encoding_enum__error_multiple_variable_with_changing_enum(self):
"""
Given 2 variables, if they share the same enum type,
the 2 enum definition should be identical.
"""
with create_tmp_file() as tmp_file:
cloud_type_dict = {"clear": 0, "cloudy": 1, "missing": 255}
with nc4.Dataset(tmp_file, mode="w") as nc:
nc.createDimension("time", size=2)
cloud_type = nc.createEnumType(np.uint8, "cloud_type", cloud_type_dict)
nc.createVariable(
"clouds",
cloud_type,
"time",
fill_value=255,
)
nc.createVariable(
"tifa",
cloud_type,
"time",
fill_value=255,
)
with open_dataset(tmp_file) as original:
assert (
original.clouds.encoding["dtype"].metadata
== original.tifa.encoding["dtype"].metadata
)
modified_enum = original.clouds.encoding["dtype"].metadata["enum"]
modified_enum.update({"neblig": 2})
original.clouds.encoding["dtype"] = np.dtype(
"u1",
metadata={"enum": modified_enum, "enum_name": "cloud_type"},
)
if not (self.engine == "h5netcdf" and not has_h5netcdf_1_4_0_or_above):
# not implemented yet in h5netcdf
with pytest.raises(
ValueError,
match=(
"Cannot save variable .*"
" because an enum `cloud_type` already exists in the Dataset .*"
),
):
with self.roundtrip(original):
pass
@pytest.mark.parametrize("create_default_indexes", [True, False])
def test_create_default_indexes(self, tmp_path, create_default_indexes) -> None:
store_path = tmp_path / "tmp.nc"
original_ds = xr.Dataset(
{"data": ("x", np.arange(3))}, coords={"x": [-1, 0, 1]}
)
original_ds.to_netcdf(store_path, engine=self.engine, mode="w")
with open_dataset(
store_path,
engine=self.engine,
create_default_indexes=create_default_indexes,
) as loaded_ds:
if create_default_indexes:
assert list(loaded_ds.xindexes) == ["x"] and isinstance(
loaded_ds.xindexes["x"], PandasIndex
)
else:
assert len(loaded_ds.xindexes) == 0
@requires_netCDF4
class TestNetCDF4Data(NetCDF4Base):
@contextlib.contextmanager
def create_store(self):
with create_tmp_file() as tmp_file:
with backends.NetCDF4DataStore.open(tmp_file, mode="w") as store:
yield store
def test_variable_order(self) -> None:
# doesn't work with scipy or h5py :(
ds = Dataset()
ds["a"] = 1
ds["z"] = 2
ds["b"] = 3
ds.coords["c"] = 4
with self.roundtrip(ds) as actual:
assert list(ds.variables) == list(actual.variables)
def test_unsorted_index_raises(self) -> None:
# should be fixed in netcdf4 v1.2.1
random_data = np.random.random(size=(4, 6))
dim0 = [0, 1, 2, 3]
dim1 = [0, 2, 1, 3, 5, 4] # We will sort this in a later step
da = xr.DataArray(
data=random_data,
dims=("dim0", "dim1"),
coords={"dim0": dim0, "dim1": dim1},
name="randovar",
)
ds = da.to_dataset()
with self.roundtrip(ds) as ondisk:
inds = np.argsort(dim1)
ds2 = ondisk.isel(dim1=inds)
# Older versions of NetCDF4 raise an exception here, and if so we
# want to ensure we improve (that is, replace) the error message
try:
_ = ds2.randovar.values
except IndexError as err:
assert "first by calling .load" in str(err)
def test_setncattr_string(self) -> None:
list_of_strings = ["list", "of", "strings"]
one_element_list_of_strings = ["one element"]
one_string = "one string"
attrs = {
"foo": list_of_strings,
"bar": one_element_list_of_strings,
"baz": one_string,
}
ds = Dataset({"x": ("y", [1, 2, 3], attrs)}, attrs=attrs)
with self.roundtrip(ds) as actual:
for totest in [actual, actual["x"]]:
assert_array_equal(list_of_strings, totest.attrs["foo"])
assert_array_equal(one_element_list_of_strings, totest.attrs["bar"])
assert one_string == totest.attrs["baz"]
@pytest.mark.parametrize(
"compression",
[
None,
"zlib",
"szip",
"zstd",
"blosc_lz",
"blosc_lz4",
"blosc_lz4hc",
"blosc_zlib",
"blosc_zstd",
],
)
@requires_netCDF4_1_6_2_or_above
@pytest.mark.xfail(ON_WINDOWS, reason="new compression not yet implemented")
def test_compression_encoding(self, compression: str | None) -> None:
data = create_test_data(dim_sizes=(20, 80, 10))
encoding_params: dict[str, Any] = dict(compression=compression, blosc_shuffle=1)
data["var2"].encoding.update(encoding_params)
data["var2"].encoding.update(
{
"chunksizes": (20, 40),
"original_shape": data.var2.shape,
"blosc_shuffle": 1,
"fletcher32": False,
}
)
with self.roundtrip(data) as actual:
expected_encoding = data["var2"].encoding.copy()
# compression does not appear in the retrieved encoding, that differs
# from the input encoding. shuffle also chantges. Here we modify the
# expected encoding to account for this
compression = expected_encoding.pop("compression")
blosc_shuffle = expected_encoding.pop("blosc_shuffle")
if compression is not None:
if "blosc" in compression and blosc_shuffle:
expected_encoding["blosc"] = {
"compressor": compression,
"shuffle": blosc_shuffle,
}
expected_encoding["shuffle"] = False
elif compression == "szip":
expected_encoding["szip"] = {
"coding": "nn",
"pixels_per_block": 8,
}
expected_encoding["shuffle"] = False
else:
# This will set a key like zlib=true which is what appears in
# the encoding when we read it.
expected_encoding[compression] = True
if compression == "zstd":
expected_encoding["shuffle"] = False
else:
expected_encoding["shuffle"] = False
actual_encoding = actual["var2"].encoding
assert expected_encoding.items() <= actual_encoding.items()
if (
encoding_params["compression"] is not None
and "blosc" not in encoding_params["compression"]
):
# regression test for #156
expected = data.isel(dim1=0)
with self.roundtrip(expected) as actual:
assert_equal(expected, actual)
@pytest.mark.skip(reason="https://github.com/Unidata/netcdf4-python/issues/1195")
def test_refresh_from_disk(self) -> None:
super().test_refresh_from_disk()
@requires_netCDF4_1_7_0_or_above
def test_roundtrip_complex(self):
expected = Dataset({"x": ("y", np.ones(5) + 1j * np.ones(5))})
skwargs = dict(auto_complex=True)
okwargs = dict(auto_complex=True)
with self.roundtrip(
expected, save_kwargs=skwargs, open_kwargs=okwargs
) as actual:
assert_equal(expected, actual)
@requires_netCDF4
class TestNetCDF4AlreadyOpen:
def test_base_case(self) -> None:
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, mode="w") as nc:
v = nc.createVariable("x", "int")
v[...] = 42
nc = nc4.Dataset(tmp_file, mode="r")
store = backends.NetCDF4DataStore(nc)
with open_dataset(store) as ds:
expected = Dataset({"x": ((), 42)})
assert_identical(expected, ds)
def test_group(self) -> None:
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, mode="w") as nc:
group = nc.createGroup("g")
v = group.createVariable("x", "int")
v[...] = 42
nc = nc4.Dataset(tmp_file, mode="r")
store = backends.NetCDF4DataStore(nc.groups["g"])
with open_dataset(store) as ds:
expected = Dataset({"x": ((), 42)})
assert_identical(expected, ds)
nc = nc4.Dataset(tmp_file, mode="r")
store = backends.NetCDF4DataStore(nc, group="g")
with open_dataset(store) as ds:
expected = Dataset({"x": ((), 42)})
assert_identical(expected, ds)
with nc4.Dataset(tmp_file, mode="r") as nc:
with pytest.raises(ValueError, match="must supply a root"):
backends.NetCDF4DataStore(nc.groups["g"], group="g")
def test_deepcopy(self) -> None:
# regression test for https://github.com/pydata/xarray/issues/4425
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, mode="w") as nc:
nc.createDimension("x", 10)
v = nc.createVariable("y", np.int32, ("x",))
v[:] = np.arange(10)
h5 = nc4.Dataset(tmp_file, mode="r")
store = backends.NetCDF4DataStore(h5)
with open_dataset(store) as ds:
copied = ds.copy(deep=True)
expected = Dataset({"y": ("x", np.arange(10))})
assert_identical(expected, copied)
@requires_netCDF4
@requires_dask
@pytest.mark.filterwarnings("ignore:deallocating CachingFileManager")
class TestNetCDF4ViaDaskData(TestNetCDF4Data):
@contextlib.contextmanager
def roundtrip(
self, data, save_kwargs=None, open_kwargs=None, allow_cleanup_failure=False
):
if open_kwargs is None:
open_kwargs = {}
if save_kwargs is None:
save_kwargs = {}
open_kwargs.setdefault("chunks", -1)
with TestNetCDF4Data.roundtrip(
self, data, save_kwargs, open_kwargs, allow_cleanup_failure
) as ds:
yield ds
def test_unsorted_index_raises(self) -> None:
# Skip when using dask because dask rewrites indexers to getitem,
# dask first pulls items by block.
pass
@pytest.mark.skip(reason="caching behavior differs for dask")
def test_dataset_caching(self) -> None:
pass
def test_write_inconsistent_chunks(self) -> None:
# Construct two variables with the same dimensions, but different
# chunk sizes.
x = da.zeros((100, 100), dtype="f4", chunks=(50, 100))
x = DataArray(data=x, dims=("lat", "lon"), name="x")
x.encoding["chunksizes"] = (50, 100)
x.encoding["original_shape"] = (100, 100)
y = da.ones((100, 100), dtype="f4", chunks=(100, 50))
y = DataArray(data=y, dims=("lat", "lon"), name="y")
y.encoding["chunksizes"] = (100, 50)
y.encoding["original_shape"] = (100, 100)
# Put them both into the same dataset
ds = Dataset({"x": x, "y": y})
with self.roundtrip(ds) as actual:
assert actual["x"].encoding["chunksizes"] == (50, 100)
assert actual["y"].encoding["chunksizes"] == (100, 50)
# Flaky test. Very open to contributions on fixing this
@pytest.mark.flaky
def test_roundtrip_coordinates(self) -> None:
super().test_roundtrip_coordinates()
@requires_cftime
def test_roundtrip_cftime_bnds(self):
# Regression test for issue #7794
import cftime
original = xr.Dataset(
{
"foo": ("time", [0.0]),
"time_bnds": (
("time", "bnds"),
[
[
cftime.Datetime360Day(2005, 12, 1, 0, 0, 0, 0),
cftime.Datetime360Day(2005, 12, 2, 0, 0, 0, 0),
]
],
),
},
{"time": [cftime.Datetime360Day(2005, 12, 1, 12, 0, 0, 0)]},
)
with create_tmp_file() as tmp_file:
original.to_netcdf(tmp_file)
with open_dataset(tmp_file) as actual:
# Operation to load actual time_bnds into memory
assert_array_equal(actual.time_bnds.values, original.time_bnds.values)
chunked = actual.chunk(time=1)
with create_tmp_file() as tmp_file_chunked:
chunked.to_netcdf(tmp_file_chunked)
@requires_zarr
@pytest.mark.usefixtures("default_zarr_format")
class ZarrBase(CFEncodedBase):
DIMENSION_KEY = "_ARRAY_DIMENSIONS"
zarr_version = 2
version_kwargs: dict[str, Any] = {}
def create_zarr_target(self):
raise NotImplementedError
@contextlib.contextmanager
def create_store(self, cache_members: bool = False):
with self.create_zarr_target() as store_target:
yield backends.ZarrStore.open_group(
store_target,
mode="w",
cache_members=cache_members,
**self.version_kwargs,
)
def save(self, dataset, store_target, **kwargs): # type: ignore[override]
return dataset.to_zarr(store=store_target, **kwargs, **self.version_kwargs)
@contextlib.contextmanager
def open(self, path, **kwargs):
with xr.open_dataset(
path, engine="zarr", mode="r", **kwargs, **self.version_kwargs
) as ds:
yield ds
@contextlib.contextmanager
def roundtrip(
self, data, save_kwargs=None, open_kwargs=None, allow_cleanup_failure=False
):
if save_kwargs is None:
save_kwargs = {}
if open_kwargs is None:
open_kwargs = {}
with self.create_zarr_target() as store_target:
self.save(data, store_target, **save_kwargs)
with self.open(store_target, **open_kwargs) as ds:
yield ds
@pytest.mark.asyncio
@pytest.mark.skipif(
not has_zarr_v3,
reason="zarr-python <3 did not support async loading",
)
async def test_load_async(self) -> None:
await super().test_load_async()
def test_roundtrip_bytes_with_fill_value(self):
pytest.xfail("Broken by Zarr 3.0.7")
@pytest.mark.parametrize("consolidated", [False, True, None])
def test_roundtrip_consolidated(self, consolidated) -> None:
expected = create_test_data()
with self.roundtrip(
expected,
save_kwargs={"consolidated": consolidated},
open_kwargs={"backend_kwargs": {"consolidated": consolidated}},
) as actual:
self.check_dtypes_roundtripped(expected, actual)
assert_identical(expected, actual)
def test_read_non_consolidated_warning(self) -> None:
expected = create_test_data()
with self.create_zarr_target() as store:
self.save(
expected, store_target=store, consolidated=False, **self.version_kwargs
)
if getattr(store, "supports_consolidated_metadata", True):
with pytest.warns(
RuntimeWarning,
match="Failed to open Zarr store with consolidated",
):
with xr.open_zarr(store, **self.version_kwargs) as ds:
assert_identical(ds, expected)
def test_non_existent_store(self) -> None:
with pytest.raises(
FileNotFoundError,
match="(No such file or directory|Unable to find group|No group found in store)",
):
xr.open_zarr(f"{uuid.uuid4()}")
@pytest.mark.skipif(has_zarr_v3, reason="chunk_store not implemented in zarr v3")
def test_with_chunkstore(self) -> None:
expected = create_test_data()
with (
self.create_zarr_target() as store_target,
self.create_zarr_target() as chunk_store,
):
save_kwargs = {"chunk_store": chunk_store}
self.save(expected, store_target, **save_kwargs)
# the chunk store must have been populated with some entries
assert len(chunk_store) > 0
open_kwargs = {"backend_kwargs": {"chunk_store": chunk_store}}
with self.open(store_target, **open_kwargs) as ds:
assert_equal(ds, expected)
@requires_dask
def test_auto_chunk(self) -> None:
original = create_test_data().chunk()
with self.roundtrip(original, open_kwargs={"chunks": None}) as actual:
for k, v in actual.variables.items():
# only index variables should be in memory
assert v._in_memory == (k in actual.dims)
# there should be no chunks
assert v.chunks is None
with self.roundtrip(original, open_kwargs={"chunks": {}}) as actual:
for k, v in actual.variables.items():
# only index variables should be in memory
assert v._in_memory == (k in actual.dims)
# chunk size should be the same as original
assert v.chunks == original[k].chunks
@requires_dask
@pytest.mark.filterwarnings("ignore:The specified chunks separate:UserWarning")
def test_manual_chunk(self) -> None:
original = create_test_data().chunk({"dim1": 3, "dim2": 4, "dim3": 3})
# Using chunks = None should return non-chunked arrays
open_kwargs: dict[str, Any] = {"chunks": None}
with self.roundtrip(original, open_kwargs=open_kwargs) as actual:
for k, v in actual.variables.items():
# only index variables should be in memory
assert v._in_memory == (k in actual.dims)
# there should be no chunks
assert v.chunks is None
# uniform arrays
for i in range(2, 6):
rechunked = original.chunk(chunks=i)
open_kwargs = {"chunks": i}
with self.roundtrip(original, open_kwargs=open_kwargs) as actual:
for k, v in actual.variables.items():
# only index variables should be in memory
assert v._in_memory == (k in actual.dims)
# chunk size should be the same as rechunked
assert v.chunks == rechunked[k].chunks
chunks = {"dim1": 2, "dim2": 3, "dim3": 5}
rechunked = original.chunk(chunks=chunks)
open_kwargs = {
"chunks": chunks,
"backend_kwargs": {"overwrite_encoded_chunks": True},
}
with self.roundtrip(original, open_kwargs=open_kwargs) as actual:
for k, v in actual.variables.items():
assert v.chunks == rechunked[k].chunks
with self.roundtrip(actual) as auto:
# encoding should have changed
for k, v in actual.variables.items():
assert v.chunks == rechunked[k].chunks
assert_identical(actual, auto)
assert_identical(actual.load(), auto.load())
@requires_dask
@pytest.mark.filterwarnings("ignore:.*does not have a Zarr V3 specification.*")
def test_warning_on_bad_chunks(self) -> None:
original = create_test_data().chunk({"dim1": 4, "dim2": 3, "dim3": 3})
bad_chunks = (2, {"dim2": (3, 3, 2, 1)})
for chunks in bad_chunks:
kwargs = {"chunks": chunks}
with pytest.warns(UserWarning):
with self.roundtrip(original, open_kwargs=kwargs) as actual:
for k, v in actual.variables.items():
# only index variables should be in memory
assert v._in_memory == (k in actual.dims)
good_chunks: tuple[dict[str, Any], ...] = ({"dim2": 3}, {"dim3": (6, 4)}, {})
for chunks in good_chunks:
kwargs = {"chunks": chunks}
with assert_no_warnings():
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
message=".*Zarr format 3 specification.*",
category=UserWarning,
)
with self.roundtrip(original, open_kwargs=kwargs) as actual:
for k, v in actual.variables.items():
# only index variables should be in memory
assert v._in_memory == (k in actual.dims)
@requires_dask
def test_deprecate_auto_chunk(self) -> None:
original = create_test_data().chunk()
with pytest.raises(TypeError):
with self.roundtrip(original, open_kwargs={"auto_chunk": True}) as actual:
for k, v in actual.variables.items():
# only index variables should be in memory
assert v._in_memory == (k in actual.dims)
# chunk size should be the same as original
assert v.chunks == original[k].chunks
with pytest.raises(TypeError):
with self.roundtrip(original, open_kwargs={"auto_chunk": False}) as actual:
for k, v in actual.variables.items():
# only index variables should be in memory
assert v._in_memory == (k in actual.dims)
# there should be no chunks
assert v.chunks is None
@requires_dask
def test_write_uneven_dask_chunks(self) -> None:
# regression for GH#2225
original = create_test_data().chunk({"dim1": 3, "dim2": 4, "dim3": 3})
with self.roundtrip(original, open_kwargs={"chunks": {}}) as actual:
for k, v in actual.data_vars.items():
assert v.chunks == actual[k].chunks
def test_chunk_encoding(self) -> None:
# These datasets have no dask chunks. All chunking specified in
# encoding
data = create_test_data()
chunks = (5, 5)
data["var2"].encoding.update({"chunks": chunks})
with self.roundtrip(data) as actual:
assert chunks == actual["var2"].encoding["chunks"]
# expect an error with non-integer chunks
data["var2"].encoding.update({"chunks": (5, 4.5)})
with pytest.raises(TypeError):
with self.roundtrip(data) as actual:
pass
def test_shard_encoding(self) -> None:
# These datasets have no dask chunks. All chunking/sharding specified in
# encoding
if has_zarr_v3 and zarr.config.config["default_zarr_format"] == 3:
data = create_test_data()
chunks = (1, 1)
shards = (5, 5)
data["var2"].encoding.update({"chunks": chunks})
data["var2"].encoding.update({"shards": shards})
with self.roundtrip(data) as actual:
assert shards == actual["var2"].encoding["shards"]
# expect an error with shards not divisible by chunks
data["var2"].encoding.update({"chunks": (2, 2)})
with pytest.raises(ValueError):
with self.roundtrip(data) as actual:
pass
@requires_dask
@pytest.mark.skipif(
ON_WINDOWS,
reason="Very flaky on Windows CI. Can re-enable assuming it starts consistently passing.",
)
def test_chunk_encoding_with_dask(self) -> None:
# These datasets DO have dask chunks. Need to check for various
# interactions between dask and zarr chunks
ds = xr.DataArray((np.arange(12)), dims="x", name="var1").to_dataset()
# - no encoding specified -
# zarr automatically gets chunk information from dask chunks
ds_chunk4 = ds.chunk({"x": 4})
with self.roundtrip(ds_chunk4) as actual:
assert (4,) == actual["var1"].encoding["chunks"]
# should fail if dask_chunks are irregular...
ds_chunk_irreg = ds.chunk({"x": (5, 4, 3)})
with pytest.raises(ValueError, match=r"uniform chunk sizes."):
with self.roundtrip(ds_chunk_irreg) as actual:
pass
# should fail if encoding["chunks"] clashes with dask_chunks
badenc = ds.chunk({"x": 4})
badenc.var1.encoding["chunks"] = (6,)
with pytest.raises(ValueError, match=r"named 'var1' would overlap"):
with self.roundtrip(badenc) as actual:
pass
# unless...
with self.roundtrip(badenc, save_kwargs={"safe_chunks": False}) as actual:
# don't actually check equality because the data could be corrupted
pass
# if dask chunks (4) are an integer multiple of zarr chunks (2) it should not fail...
goodenc = ds.chunk({"x": 4})
goodenc.var1.encoding["chunks"] = (2,)
with self.roundtrip(goodenc) as actual:
pass
# if initial dask chunks are aligned, size of last dask chunk doesn't matter
goodenc = ds.chunk({"x": (3, 3, 6)})
goodenc.var1.encoding["chunks"] = (3,)
with self.roundtrip(goodenc) as actual:
pass
goodenc = ds.chunk({"x": (3, 6, 3)})
goodenc.var1.encoding["chunks"] = (3,)
with self.roundtrip(goodenc) as actual:
pass
# ... also if the last chunk is irregular
ds_chunk_irreg = ds.chunk({"x": (5, 5, 2)})
with self.roundtrip(ds_chunk_irreg) as actual:
assert (5,) == actual["var1"].encoding["chunks"]
# re-save Zarr arrays
with self.roundtrip(ds_chunk_irreg) as original:
with self.roundtrip(original) as actual:
assert_identical(original, actual)
# but intermediate unaligned chunks are bad
badenc = ds.chunk({"x": (3, 5, 3, 1)})
badenc.var1.encoding["chunks"] = (3,)
with pytest.raises(ValueError, match=r"would overlap multiple Dask chunks"):
with self.roundtrip(badenc) as actual:
pass
# - encoding specified -
# specify compatible encodings
for chunk_enc in 4, (4,):
ds_chunk4["var1"].encoding.update({"chunks": chunk_enc})
with self.roundtrip(ds_chunk4) as actual:
assert (4,) == actual["var1"].encoding["chunks"]
# TODO: remove this failure once synchronized overlapping writes are
# supported by xarray
ds_chunk4["var1"].encoding.update({"chunks": 5})
with pytest.raises(ValueError, match=r"named 'var1' would overlap"):
with self.roundtrip(ds_chunk4) as actual:
pass
# override option
with self.roundtrip(ds_chunk4, save_kwargs={"safe_chunks": False}) as actual:
# don't actually check equality because the data could be corrupted
pass
@requires_netcdf
def test_drop_encoding(self):
with open_example_dataset("example_1.nc") as ds:
encodings = {v: {**ds[v].encoding} for v in ds.data_vars}
with self.create_zarr_target() as store:
ds.to_zarr(store, encoding=encodings)
def test_hidden_zarr_keys(self) -> None:
skip_if_zarr_format_3("This test is unnecessary; no hidden Zarr keys")
expected = create_test_data()
with self.create_store() as store:
expected.dump_to_store(store)
zarr_group = store.ds
# check that a variable hidden attribute is present and correct
# JSON only has a single array type, which maps to list in Python.
# In contrast, dims in xarray is always a tuple.
for var in expected.variables.keys():
dims = zarr_group[var].attrs[self.DIMENSION_KEY]
assert dims == list(expected[var].dims)
with xr.decode_cf(store):
# make sure it is hidden
for var in expected.variables.keys():
assert self.DIMENSION_KEY not in expected[var].attrs
# put it back and try removing from a variable
attrs = dict(zarr_group["var2"].attrs)
del attrs[self.DIMENSION_KEY]
zarr_group["var2"].attrs.put(attrs)
with pytest.raises(KeyError):
with xr.decode_cf(store):
pass
def test_dimension_names(self) -> None:
skip_if_zarr_format_2("No dimension names in V2")
expected = create_test_data()
with self.create_store() as store:
expected.dump_to_store(store)
zarr_group = store.ds
for var in zarr_group:
assert expected[var].dims == zarr_group[var].metadata.dimension_names
@pytest.mark.parametrize("group", [None, "group1"])
def test_write_persistence_modes(self, group) -> None:
original = create_test_data()
# overwrite mode
with self.roundtrip(
original,
save_kwargs={"mode": "w", "group": group},
open_kwargs={"group": group},
) as actual:
assert_identical(original, actual)
# don't overwrite mode
with self.roundtrip(
original,
save_kwargs={"mode": "w-", "group": group},
open_kwargs={"group": group},
) as actual:
assert_identical(original, actual)
# make sure overwriting works as expected
with self.create_zarr_target() as store:
self.save(original, store)
# should overwrite with no error
self.save(original, store, mode="w", group=group)
with self.open(store, group=group) as actual:
assert_identical(original, actual)
with pytest.raises((ValueError, FileExistsError)):
self.save(original, store, mode="w-")
# check append mode for normal write
with self.roundtrip(
original,
save_kwargs={"mode": "a", "group": group},
open_kwargs={"group": group},
) as actual:
assert_identical(original, actual)
# check append mode for append write
ds, ds_to_append, _ = create_append_test_data()
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, mode="w", group=group, **self.version_kwargs)
ds_to_append.to_zarr(
store_target, append_dim="time", group=group, **self.version_kwargs
)
original = xr.concat([ds, ds_to_append], dim="time")
actual = xr.open_dataset(
store_target, group=group, engine="zarr", **self.version_kwargs
)
assert_identical(original, actual)
def test_compressor_encoding(self) -> None:
# specify a custom compressor
original = create_test_data()
if has_zarr_v3 and zarr.config.config["default_zarr_format"] == 3:
encoding_key = "compressors"
# all parameters need to be explicitly specified in order for the comparison to pass below
encoding = {
"serializer": zarr.codecs.BytesCodec(endian="little"),
encoding_key: (
zarr.codecs.BloscCodec(
cname="zstd",
clevel=3,
shuffle="shuffle",
typesize=8,
blocksize=0,
),
),
}
else:
from numcodecs.blosc import Blosc
encoding_key = "compressors" if has_zarr_v3 else "compressor"
comp = Blosc(cname="zstd", clevel=3, shuffle=2)
encoding = {encoding_key: (comp,) if has_zarr_v3 else comp}
save_kwargs = dict(encoding={"var1": encoding})
with self.roundtrip(original, save_kwargs=save_kwargs) as ds:
enc = ds["var1"].encoding[encoding_key]
assert enc == encoding[encoding_key]
def test_group(self) -> None:
original = create_test_data()
group = "some/random/path"
with self.roundtrip(
original, save_kwargs={"group": group}, open_kwargs={"group": group}
) as actual:
assert_identical(original, actual)
def test_zarr_mode_w_overwrites_encoding(self) -> None:
data = Dataset({"foo": ("x", [1.0, 1.0, 1.0])})
with self.create_zarr_target() as store:
data.to_zarr(
store, **self.version_kwargs, encoding={"foo": {"add_offset": 1}}
)
np.testing.assert_equal(
zarr.open_group(store, **self.version_kwargs)["foo"], data.foo.data - 1
)
data.to_zarr(
store,
**self.version_kwargs,
encoding={"foo": {"add_offset": 0}},
mode="w",
)
np.testing.assert_equal(
zarr.open_group(store, **self.version_kwargs)["foo"], data.foo.data
)
def test_encoding_kwarg_fixed_width_string(self) -> None:
# not relevant for zarr, since we don't use EncodedStringCoder
pass
def test_dataset_caching(self) -> None:
super().test_dataset_caching()
def test_append_write(self) -> None:
super().test_append_write()
def test_append_with_mode_rplus_success(self) -> None:
original = Dataset({"foo": ("x", [1])})
modified = Dataset({"foo": ("x", [2])})
with self.create_zarr_target() as store:
original.to_zarr(store, **self.version_kwargs)
modified.to_zarr(store, mode="r+", **self.version_kwargs)
with self.open(store) as actual:
assert_identical(actual, modified)
def test_append_with_mode_rplus_fails(self) -> None:
original = Dataset({"foo": ("x", [1])})
modified = Dataset({"bar": ("x", [2])})
with self.create_zarr_target() as store:
original.to_zarr(store, **self.version_kwargs)
with pytest.raises(
ValueError, match="dataset contains non-pre-existing variables"
):
modified.to_zarr(store, mode="r+", **self.version_kwargs)
def test_append_with_invalid_dim_raises(self) -> None:
ds, ds_to_append, _ = create_append_test_data()
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, mode="w", **self.version_kwargs)
with pytest.raises(
ValueError, match="does not match any existing dataset dimensions"
):
ds_to_append.to_zarr(
store_target, append_dim="notvalid", **self.version_kwargs
)
def test_append_with_no_dims_raises(self) -> None:
with self.create_zarr_target() as store_target:
Dataset({"foo": ("x", [1])}).to_zarr(
store_target, mode="w", **self.version_kwargs
)
with pytest.raises(ValueError, match="different dimension names"):
Dataset({"foo": ("y", [2])}).to_zarr(
store_target, mode="a", **self.version_kwargs
)
def test_append_with_append_dim_not_set_raises(self) -> None:
ds, ds_to_append, _ = create_append_test_data()
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, mode="w", **self.version_kwargs)
with pytest.raises(ValueError, match="different dimension sizes"):
ds_to_append.to_zarr(store_target, mode="a", **self.version_kwargs)
def test_append_with_mode_not_a_raises(self) -> None:
ds, ds_to_append, _ = create_append_test_data()
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, mode="w", **self.version_kwargs)
with pytest.raises(ValueError, match="cannot set append_dim unless"):
ds_to_append.to_zarr(
store_target, mode="w", append_dim="time", **self.version_kwargs
)
def test_append_with_existing_encoding_raises(self) -> None:
ds, ds_to_append, _ = create_append_test_data()
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, mode="w", **self.version_kwargs)
with pytest.raises(ValueError, match="but encoding was provided"):
ds_to_append.to_zarr(
store_target,
append_dim="time",
encoding={"da": {"compressor": None}},
**self.version_kwargs,
)
@pytest.mark.parametrize("dtype", ["U", "S"])
def test_append_string_length_mismatch_raises(self, dtype) -> None:
if has_zarr_v3 and not has_zarr_v3_dtypes:
skip_if_zarr_format_3("This actually works fine with Zarr format 3")
ds, ds_to_append = create_append_string_length_mismatch_test_data(dtype)
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, mode="w", **self.version_kwargs)
with pytest.raises(ValueError, match="Mismatched dtypes for variable"):
ds_to_append.to_zarr(
store_target, append_dim="time", **self.version_kwargs
)
@pytest.mark.parametrize("dtype", ["U", "S"])
def test_append_string_length_mismatch_works(self, dtype) -> None:
skip_if_zarr_format_2("This doesn't work with Zarr format 2")
# ...but it probably would if we used object dtype
if has_zarr_v3_dtypes:
pytest.skip("This works on pre ZDtype Zarr-Python, but fails after.")
ds, ds_to_append = create_append_string_length_mismatch_test_data(dtype)
expected = xr.concat([ds, ds_to_append], dim="time")
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, mode="w", **self.version_kwargs)
ds_to_append.to_zarr(store_target, append_dim="time", **self.version_kwargs)
actual = xr.open_dataset(store_target, engine="zarr")
xr.testing.assert_identical(expected, actual)
def test_check_encoding_is_consistent_after_append(self) -> None:
ds, ds_to_append, _ = create_append_test_data()
# check encoding consistency
with self.create_zarr_target() as store_target:
import numcodecs
encoding_value: Any
if has_zarr_v3 and zarr.config.config["default_zarr_format"] == 3:
compressor = zarr.codecs.BloscCodec()
else:
compressor = numcodecs.Blosc()
encoding_key = "compressors" if has_zarr_v3 else "compressor"
encoding_value = (compressor,) if has_zarr_v3 else compressor
encoding = {"da": {encoding_key: encoding_value}}
ds.to_zarr(store_target, mode="w", encoding=encoding, **self.version_kwargs)
original_ds = xr.open_dataset(
store_target, engine="zarr", **self.version_kwargs
)
original_encoding = original_ds["da"].encoding[encoding_key]
ds_to_append.to_zarr(store_target, append_dim="time", **self.version_kwargs)
actual_ds = xr.open_dataset(
store_target, engine="zarr", **self.version_kwargs
)
actual_encoding = actual_ds["da"].encoding[encoding_key]
assert original_encoding == actual_encoding
assert_identical(
xr.open_dataset(
store_target, engine="zarr", **self.version_kwargs
).compute(),
xr.concat([ds, ds_to_append], dim="time"),
)
def test_append_with_new_variable(self) -> None:
ds, ds_to_append, ds_with_new_var = create_append_test_data()
# check append mode for new variable
with self.create_zarr_target() as store_target:
combined = xr.concat([ds, ds_to_append], dim="time")
combined.to_zarr(store_target, mode="w", **self.version_kwargs)
assert_identical(
combined,
xr.open_dataset(store_target, engine="zarr", **self.version_kwargs),
)
ds_with_new_var.to_zarr(store_target, mode="a", **self.version_kwargs)
combined = xr.concat([ds, ds_to_append], dim="time")
combined["new_var"] = ds_with_new_var["new_var"]
assert_identical(
combined,
xr.open_dataset(store_target, engine="zarr", **self.version_kwargs),
)
def test_append_with_append_dim_no_overwrite(self) -> None:
ds, ds_to_append, _ = create_append_test_data()
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, mode="w", **self.version_kwargs)
original = xr.concat([ds, ds_to_append], dim="time")
original2 = xr.concat([original, ds_to_append], dim="time")
# overwrite a coordinate;
# for mode='a-', this will not get written to the store
# because it does not have the append_dim as a dim
lon = ds_to_append.lon.to_numpy().copy()
lon[:] = -999
ds_to_append["lon"] = lon
ds_to_append.to_zarr(
store_target, mode="a-", append_dim="time", **self.version_kwargs
)
actual = xr.open_dataset(store_target, engine="zarr", **self.version_kwargs)
assert_identical(original, actual)
# by default, mode="a" will overwrite all coordinates.
ds_to_append.to_zarr(store_target, append_dim="time", **self.version_kwargs)
actual = xr.open_dataset(store_target, engine="zarr", **self.version_kwargs)
lon = original2.lon.to_numpy().copy()
lon[:] = -999
original2["lon"] = lon
assert_identical(original2, actual)
@requires_dask
def test_to_zarr_compute_false_roundtrip(self) -> None:
from dask.delayed import Delayed
original = create_test_data().chunk()
with self.create_zarr_target() as store:
delayed_obj = self.save(original, store, compute=False)
assert isinstance(delayed_obj, Delayed)
# make sure target store has not been written to yet
with pytest.raises(AssertionError):
with self.open(store) as actual:
assert_identical(original, actual)
delayed_obj.compute()
with self.open(store) as actual:
assert_identical(original, actual)
@requires_dask
def test_to_zarr_append_compute_false_roundtrip(self) -> None:
from dask.delayed import Delayed
ds, ds_to_append, _ = create_append_test_data()
ds, ds_to_append = ds.chunk(), ds_to_append.chunk()
with pytest.warns(SerializationWarning):
with self.create_zarr_target() as store:
delayed_obj = self.save(ds, store, compute=False, mode="w")
assert isinstance(delayed_obj, Delayed)
with pytest.raises(AssertionError):
with self.open(store) as actual:
assert_identical(ds, actual)
delayed_obj.compute()
with self.open(store) as actual:
assert_identical(ds, actual)
delayed_obj = self.save(
ds_to_append, store, compute=False, append_dim="time"
)
assert isinstance(delayed_obj, Delayed)
with pytest.raises(AssertionError):
with self.open(store) as actual:
assert_identical(
xr.concat([ds, ds_to_append], dim="time"), actual
)
delayed_obj.compute()
with self.open(store) as actual:
assert_identical(xr.concat([ds, ds_to_append], dim="time"), actual)
@pytest.mark.parametrize("chunk", [False, True])
def test_save_emptydim(self, chunk) -> None:
if chunk and not has_dask:
pytest.skip("requires dask")
ds = Dataset({"x": (("a", "b"), np.empty((5, 0))), "y": ("a", [1, 2, 5, 8, 9])})
if chunk:
ds = ds.chunk({}) # chunk dataset to save dask array
with self.roundtrip(ds) as ds_reload:
assert_identical(ds, ds_reload)
@requires_dask
def test_no_warning_from_open_emptydim_with_chunks(self) -> None:
ds = Dataset({"x": (("a", "b"), np.empty((5, 0)))}).chunk({"a": 1})
with assert_no_warnings():
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
message=".*Zarr format 3 specification.*",
category=UserWarning,
)
with self.roundtrip(ds, open_kwargs=dict(chunks={"a": 1})) as ds_reload:
assert_identical(ds, ds_reload)
@pytest.mark.parametrize("consolidated", [False, True, None])
@pytest.mark.parametrize("compute", [False, True])
@pytest.mark.parametrize("use_dask", [False, True])
@pytest.mark.parametrize("write_empty", [False, True, None])
def test_write_region(self, consolidated, compute, use_dask, write_empty) -> None:
if (use_dask or not compute) and not has_dask:
pytest.skip("requires dask")
zeros = Dataset({"u": (("x",), np.zeros(10))})
nonzeros = Dataset({"u": (("x",), np.arange(1, 11))})
if use_dask:
zeros = zeros.chunk(2)
nonzeros = nonzeros.chunk(2)
with self.create_zarr_target() as store:
zeros.to_zarr(
store,
consolidated=consolidated,
compute=compute,
encoding={"u": dict(chunks=2)},
**self.version_kwargs,
)
if compute:
with xr.open_zarr(
store, consolidated=consolidated, **self.version_kwargs
) as actual:
assert_identical(actual, zeros)
for i in range(0, 10, 2):
region = {"x": slice(i, i + 2)}
nonzeros.isel(region).to_zarr(
store,
region=region,
consolidated=consolidated,
write_empty_chunks=write_empty,
**self.version_kwargs,
)
with xr.open_zarr(
store, consolidated=consolidated, **self.version_kwargs
) as actual:
assert_identical(actual, nonzeros)
@pytest.mark.parametrize("mode", [None, "r+", "a"])
def test_write_region_mode(self, mode) -> None:
zeros = Dataset({"u": (("x",), np.zeros(10))})
nonzeros = Dataset({"u": (("x",), np.arange(1, 11))})
with self.create_zarr_target() as store:
zeros.to_zarr(store, **self.version_kwargs)
for region in [{"x": slice(5)}, {"x": slice(5, 10)}]:
nonzeros.isel(region).to_zarr(
store, region=region, mode=mode, **self.version_kwargs
)
with xr.open_zarr(store, **self.version_kwargs) as actual:
assert_identical(actual, nonzeros)
@requires_dask
def test_write_preexisting_override_metadata(self) -> None:
"""Metadata should be overridden if mode="a" but not in mode="r+"."""
original = Dataset(
{"u": (("x",), np.zeros(10), {"variable": "original"})},
attrs={"global": "original"},
)
both_modified = Dataset(
{"u": (("x",), np.ones(10), {"variable": "modified"})},
attrs={"global": "modified"},
)
global_modified = Dataset(
{"u": (("x",), np.ones(10), {"variable": "original"})},
attrs={"global": "modified"},
)
only_new_data = Dataset(
{"u": (("x",), np.ones(10), {"variable": "original"})},
attrs={"global": "original"},
)
with self.create_zarr_target() as store:
original.to_zarr(store, compute=False, **self.version_kwargs)
both_modified.to_zarr(store, mode="a", **self.version_kwargs)
with self.open(store) as actual:
# NOTE: this arguably incorrect -- we should probably be
# overriding the variable metadata, too. See the TODO note in
# ZarrStore.set_variables.
assert_identical(actual, global_modified)
with self.create_zarr_target() as store:
original.to_zarr(store, compute=False, **self.version_kwargs)
both_modified.to_zarr(store, mode="r+", **self.version_kwargs)
with self.open(store) as actual:
assert_identical(actual, only_new_data)
with self.create_zarr_target() as store:
original.to_zarr(store, compute=False, **self.version_kwargs)
# with region, the default mode becomes r+
both_modified.to_zarr(
store, region={"x": slice(None)}, **self.version_kwargs
)
with self.open(store) as actual:
assert_identical(actual, only_new_data)
def test_write_region_errors(self) -> None:
data = Dataset({"u": (("x",), np.arange(5))})
data2 = Dataset({"u": (("x",), np.array([10, 11]))})
@contextlib.contextmanager
def setup_and_verify_store(expected=data):
with self.create_zarr_target() as store:
data.to_zarr(store, **self.version_kwargs)
yield store
with self.open(store) as actual:
assert_identical(actual, expected)
# verify the base case works
expected = Dataset({"u": (("x",), np.array([10, 11, 2, 3, 4]))})
with setup_and_verify_store(expected) as store:
data2.to_zarr(store, region={"x": slice(2)}, **self.version_kwargs)
with setup_and_verify_store() as store:
with pytest.raises(
ValueError,
match=re.escape(
"cannot set region unless mode='a', mode='a-', mode='r+' or mode=None"
),
):
data.to_zarr(
store, region={"x": slice(None)}, mode="w", **self.version_kwargs
)
with setup_and_verify_store() as store:
with pytest.raises(TypeError, match=r"must be a dict"):
data.to_zarr(store, region=slice(None), **self.version_kwargs) # type: ignore[call-overload]
with setup_and_verify_store() as store:
with pytest.raises(TypeError, match=r"must be slice objects"):
data2.to_zarr(store, region={"x": [0, 1]}, **self.version_kwargs) # type: ignore[dict-item]
with setup_and_verify_store() as store:
with pytest.raises(ValueError, match=r"step on all slices"):
data2.to_zarr(
store, region={"x": slice(None, None, 2)}, **self.version_kwargs
)
with setup_and_verify_store() as store:
with pytest.raises(
ValueError,
match=r"all keys in ``region`` are not in Dataset dimensions",
):
data.to_zarr(store, region={"y": slice(None)}, **self.version_kwargs)
with setup_and_verify_store() as store:
with pytest.raises(
ValueError,
match=r"all variables in the dataset to write must have at least one dimension in common",
):
data2.assign(v=2).to_zarr(
store, region={"x": slice(2)}, **self.version_kwargs
)
with setup_and_verify_store() as store:
with pytest.raises(
ValueError, match=r"cannot list the same dimension in both"
):
data.to_zarr(
store,
region={"x": slice(None)},
append_dim="x",
**self.version_kwargs,
)
with setup_and_verify_store() as store:
with pytest.raises(
ValueError,
match=r"variable 'u' already exists with different dimension sizes",
):
data2.to_zarr(store, region={"x": slice(3)}, **self.version_kwargs)
@requires_dask
def test_encoding_chunksizes(self) -> None:
# regression test for GH2278
# see also test_encoding_chunksizes_unlimited
nx, ny, nt = 4, 4, 5
original = xr.Dataset(
{},
coords={
"x": np.arange(nx),
"y": np.arange(ny),
"t": np.arange(nt),
},
)
original["v"] = xr.Variable(("x", "y", "t"), np.zeros((nx, ny, nt)))
original = original.chunk({"t": 1, "x": 2, "y": 2})
with self.roundtrip(original) as ds1:
assert_equal(ds1, original)
with self.roundtrip(ds1.isel(t=0)) as ds2:
assert_equal(ds2, original.isel(t=0))
@requires_dask
def test_chunk_encoding_with_partial_dask_chunks(self) -> None:
original = xr.Dataset(
{"x": xr.DataArray(np.random.random(size=(6, 8)), dims=("a", "b"))}
).chunk({"a": 3})
with self.roundtrip(
original, save_kwargs={"encoding": {"x": {"chunks": [3, 2]}}}
) as ds1:
assert_equal(ds1, original)
@requires_dask
def test_chunk_encoding_with_larger_dask_chunks(self) -> None:
original = xr.Dataset({"a": ("x", [1, 2, 3, 4])}).chunk({"x": 2})
with self.roundtrip(
original, save_kwargs={"encoding": {"a": {"chunks": [1]}}}
) as ds1:
assert_equal(ds1, original)
@requires_cftime
def test_open_zarr_use_cftime(self) -> None:
ds = create_test_data()
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, **self.version_kwargs)
ds_a = xr.open_zarr(store_target, **self.version_kwargs)
assert_identical(ds, ds_a)
decoder = CFDatetimeCoder(use_cftime=True)
ds_b = xr.open_zarr(
store_target, decode_times=decoder, **self.version_kwargs
)
assert xr.coding.times.contains_cftime_datetimes(ds_b.time.variable)
def test_write_read_select_write(self) -> None:
# Test for https://github.com/pydata/xarray/issues/4084
ds = create_test_data()
# NOTE: using self.roundtrip, which uses open_dataset, will not trigger the bug.
with self.create_zarr_target() as initial_store:
ds.to_zarr(initial_store, mode="w", **self.version_kwargs)
ds1 = xr.open_zarr(initial_store, **self.version_kwargs)
# Combination of where+squeeze triggers error on write.
ds_sel = ds1.where(ds1.coords["dim3"] == "a", drop=True).squeeze("dim3")
with self.create_zarr_target() as final_store:
ds_sel.to_zarr(final_store, mode="w", **self.version_kwargs)
@pytest.mark.parametrize("obj", [Dataset(), DataArray(name="foo")])
def test_attributes(self, obj) -> None:
obj = obj.copy()
obj.attrs["good"] = {"key": "value"}
ds = obj if isinstance(obj, Dataset) else obj.to_dataset()
with self.create_zarr_target() as store_target:
ds.to_zarr(store_target, **self.version_kwargs)
assert_identical(ds, xr.open_zarr(store_target, **self.version_kwargs))
obj.attrs["bad"] = DataArray()
ds = obj if isinstance(obj, Dataset) else obj.to_dataset()
with self.create_zarr_target() as store_target:
with pytest.raises(TypeError, match=r"Invalid attribute in Dataset.attrs."):
ds.to_zarr(store_target, **self.version_kwargs)
@requires_dask
@pytest.mark.parametrize("dtype", ["datetime64[ns]", "timedelta64[ns]"])
def test_chunked_datetime64_or_timedelta64(self, dtype) -> None:
# Generalized from @malmans2's test in PR #8253
original = create_test_data().astype(dtype).chunk(1)
with self.roundtrip(
original,
open_kwargs={
"chunks": {},
"decode_timedelta": CFTimedeltaCoder(time_unit="ns"),
},
) as actual:
for name, actual_var in actual.variables.items():
assert original[name].chunks == actual_var.chunks
assert original.chunks == actual.chunks
@requires_cftime
@requires_dask
def test_chunked_cftime_datetime(self) -> None:
# Based on @malmans2's test in PR #8253
times = date_range("2000", freq="D", periods=3, use_cftime=True)
original = xr.Dataset(data_vars={"chunked_times": (["time"], times)})
original = original.chunk({"time": 1})
with self.roundtrip(original, open_kwargs={"chunks": {}}) as actual:
for name, actual_var in actual.variables.items():
assert original[name].chunks == actual_var.chunks
assert original.chunks == actual.chunks
def test_cache_members(self) -> None:
"""
Ensure that if `ZarrStore` is created with `cache_members` set to `True`,
a `ZarrStore` only inspects the underlying zarr group once,
and that the results of that inspection are cached.
Otherwise, `ZarrStore.members` should inspect the underlying zarr group each time it is
invoked
"""
with self.create_zarr_target() as store_target:
zstore_mut = backends.ZarrStore.open_group(
store_target, mode="w", cache_members=False
)
# ensure that the keys are sorted
array_keys = sorted(("foo", "bar"))
# create some arrays
for ak in array_keys:
zstore_mut.zarr_group.create(name=ak, shape=(1,), dtype="uint8")
zstore_stat = backends.ZarrStore.open_group(
store_target, mode="r", cache_members=True
)
observed_keys_0 = sorted(zstore_stat.array_keys())
assert observed_keys_0 == array_keys
# create a new array
new_key = "baz"
zstore_mut.zarr_group.create(name=new_key, shape=(1,), dtype="uint8")
observed_keys_1 = sorted(zstore_stat.array_keys())
assert observed_keys_1 == array_keys
observed_keys_2 = sorted(zstore_mut.array_keys())
assert observed_keys_2 == sorted(array_keys + [new_key])
@requires_dask
@pytest.mark.parametrize("dtype", [int, float])
def test_zarr_fill_value_setting(self, dtype):
# When zarr_format=2, _FillValue sets fill_value
# When zarr_format=3, fill_value is set independently
# We test this by writing a dask array with compute=False,
# on read we should receive chunks filled with `fill_value`
fv = -1
ds = xr.Dataset(
{"foo": ("x", dask.array.from_array(np.array([0, 0, 0], dtype=dtype)))}
)
expected = xr.Dataset({"foo": ("x", [fv] * 3)})
zarr_format_2 = (
has_zarr_v3 and zarr.config.get("default_zarr_format") == 2
) or not has_zarr_v3
if zarr_format_2:
attr = "_FillValue"
expected.foo.attrs[attr] = fv
else:
attr = "fill_value"
if dtype is float:
# for floats, Xarray inserts a default `np.nan`
expected.foo.attrs["_FillValue"] = np.nan
# turn off all decoding so we see what Zarr returns to us.
# Since chunks, are not written, we should receive on `fill_value`
open_kwargs = {
"mask_and_scale": False,
"consolidated": False,
"use_zarr_fill_value_as_mask": False,
}
save_kwargs = dict(compute=False, consolidated=False)
with self.roundtrip(
ds,
save_kwargs=ChainMap(save_kwargs, dict(encoding={"foo": {attr: fv}})),
open_kwargs=open_kwargs,
) as actual:
assert_identical(actual, expected)
ds.foo.encoding[attr] = fv
with self.roundtrip(
ds, save_kwargs=save_kwargs, open_kwargs=open_kwargs
) as actual:
assert_identical(actual, expected)
if zarr_format_2:
ds = ds.drop_encoding()
with pytest.raises(ValueError, match="_FillValue"):
with self.roundtrip(
ds,
save_kwargs=ChainMap(
save_kwargs, dict(encoding={"foo": {"fill_value": fv}})
),
open_kwargs=open_kwargs,
):
pass
# TODO: this doesn't fail because of the
# ``raise_on_invalid=vn in check_encoding_set`` line in zarr.py
# ds.foo.encoding["fill_value"] = fv
@requires_zarr
@pytest.mark.skipif(
KVStore is None, reason="zarr-python 2.x or ZARR_V3_EXPERIMENTAL_API is unset."
)
class TestInstrumentedZarrStore:
if has_zarr_v3:
methods = [
"get",
"set",
"list_dir",
"list_prefix",
]
else:
methods = [
"__iter__",
"__contains__",
"__setitem__",
"__getitem__",
"listdir",
"list_prefix",
]
@contextlib.contextmanager
def create_zarr_target(self):
if Version(zarr.__version__) < Version("2.18.0"):
pytest.skip("Instrumented tests only work on latest Zarr.")
if has_zarr_v3:
kwargs = {"read_only": False}
else:
kwargs = {} # type: ignore[arg-type,unused-ignore]
store = KVStore({}, **kwargs) # type: ignore[arg-type,unused-ignore]
yield store
def make_patches(self, store):
from unittest.mock import MagicMock
return {
method: MagicMock(
f"KVStore.{method}",
side_effect=getattr(store, method),
autospec=True,
)
for method in self.methods
}
def summarize(self, patches):
summary = {}
for name, patch_ in patches.items():
count = 0
for call in patch_.mock_calls:
if "zarr.json" not in call.args:
count += 1
summary[name.strip("_")] = count
return summary
def check_requests(self, expected, patches):
summary = self.summarize(patches)
for k in summary:
assert summary[k] <= expected[k], (k, summary)
def test_append(self) -> None:
original = Dataset({"foo": ("x", [1])}, coords={"x": [0]})
modified = Dataset({"foo": ("x", [2])}, coords={"x": [1]})
with self.create_zarr_target() as store:
if has_zarr_v3:
# TODO: verify these
expected = {
"set": 5,
"get": 4,
"list_dir": 2,
"list_prefix": 1,
}
else:
expected = {
"iter": 1,
"contains": 18,
"setitem": 10,
"getitem": 13,
"listdir": 0,
"list_prefix": 3,
}
patches = self.make_patches(store)
with patch.multiple(KVStore, **patches):
original.to_zarr(store)
self.check_requests(expected, patches)
patches = self.make_patches(store)
# v2024.03.0: {'iter': 6, 'contains': 2, 'setitem': 5, 'getitem': 10, 'listdir': 6, 'list_prefix': 0}
# 6057128b: {'iter': 5, 'contains': 2, 'setitem': 5, 'getitem': 10, "listdir": 5, "list_prefix": 0}
if has_zarr_v3:
expected = {
"set": 4,
"get": 9, # TODO: fixme upstream (should be 8)
"list_dir": 2, # TODO: fixme upstream (should be 2)
"list_prefix": 0,
}
else:
expected = {
"iter": 1,
"contains": 11,
"setitem": 6,
"getitem": 15,
"listdir": 0,
"list_prefix": 1,
}
with patch.multiple(KVStore, **patches):
modified.to_zarr(store, mode="a", append_dim="x")
self.check_requests(expected, patches)
patches = self.make_patches(store)
if has_zarr_v3:
expected = {
"set": 4,
"get": 9, # TODO: fixme upstream (should be 8)
"list_dir": 2, # TODO: fixme upstream (should be 2)
"list_prefix": 0,
}
else:
expected = {
"iter": 1,
"contains": 11,
"setitem": 6,
"getitem": 15,
"listdir": 0,
"list_prefix": 1,
}
with patch.multiple(KVStore, **patches):
modified.to_zarr(store, mode="a-", append_dim="x")
self.check_requests(expected, patches)
with open_dataset(store, engine="zarr") as actual:
assert_identical(
actual, xr.concat([original, modified, modified], dim="x")
)
@requires_dask
def test_region_write(self) -> None:
ds = Dataset({"foo": ("x", [1, 2, 3])}, coords={"x": [1, 2, 3]}).chunk()
with self.create_zarr_target() as store:
if has_zarr_v3:
expected = {
"set": 5,
"get": 2,
"list_dir": 2,
"list_prefix": 4,
}
else:
expected = {
"iter": 1,
"contains": 16,
"setitem": 9,
"getitem": 13,
"listdir": 0,
"list_prefix": 5,
}
patches = self.make_patches(store)
with patch.multiple(KVStore, **patches):
ds.to_zarr(store, mode="w", compute=False)
self.check_requests(expected, patches)
# v2024.03.0: {'iter': 5, 'contains': 2, 'setitem': 1, 'getitem': 6, 'listdir': 5, 'list_prefix': 0}
# 6057128b: {'iter': 4, 'contains': 2, 'setitem': 1, 'getitem': 5, 'listdir': 4, 'list_prefix': 0}
if has_zarr_v3:
expected = {
"set": 1,
"get": 3,
"list_dir": 0,
"list_prefix": 0,
}
else:
expected = {
"iter": 1,
"contains": 6,
"setitem": 1,
"getitem": 7,
"listdir": 0,
"list_prefix": 0,
}
patches = self.make_patches(store)
with patch.multiple(KVStore, **patches):
ds.to_zarr(store, region={"x": slice(None)})
self.check_requests(expected, patches)
# v2024.03.0: {'iter': 6, 'contains': 4, 'setitem': 1, 'getitem': 11, 'listdir': 6, 'list_prefix': 0}
# 6057128b: {'iter': 4, 'contains': 2, 'setitem': 1, 'getitem': 7, 'listdir': 4, 'list_prefix': 0}
if has_zarr_v3:
expected = {
"set": 1,
"get": 4,
"list_dir": 0,
"list_prefix": 0,
}
else:
expected = {
"iter": 1,
"contains": 6,
"setitem": 1,
"getitem": 8,
"listdir": 0,
"list_prefix": 0,
}
patches = self.make_patches(store)
with patch.multiple(KVStore, **patches):
ds.to_zarr(store, region="auto")
self.check_requests(expected, patches)
if has_zarr_v3:
expected = {
"set": 0,
"get": 5,
"list_dir": 0,
"list_prefix": 0,
}
else:
expected = {
"iter": 1,
"contains": 6,
"setitem": 0,
"getitem": 8,
"listdir": 0,
"list_prefix": 0,
}
patches = self.make_patches(store)
with patch.multiple(KVStore, **patches):
with open_dataset(store, engine="zarr") as actual:
assert_identical(actual, ds)
self.check_requests(expected, patches)
@requires_zarr
class TestZarrDictStore(ZarrBase):
@contextlib.contextmanager
def create_zarr_target(self):
if has_zarr_v3:
yield zarr.storage.MemoryStore({}, read_only=False)
else:
yield {}
def test_chunk_key_encoding_v2(self) -> None:
encoding = {"name": "v2", "configuration": {"separator": "/"}}
# Create a dataset with a variable name containing a period
data = np.ones((4, 4))
original = Dataset({"var1": (("x", "y"), data)})
# Set up chunk key encoding with slash separator
encoding = {
"var1": {
"chunk_key_encoding": encoding,
"chunks": (2, 2),
}
}
# Write to store with custom encoding
with self.create_zarr_target() as store:
original.to_zarr(store, encoding=encoding)
# Verify the chunk keys in store use the slash separator
if not has_zarr_v3:
chunk_keys = [k for k in store.keys() if k.startswith("var1/")]
assert len(chunk_keys) > 0
for key in chunk_keys:
assert "/" in key
assert "." not in key.split("/")[1:] # No dots in chunk coordinates
# Read back and verify data
with xr.open_zarr(store) as actual:
assert_identical(original, actual)
# Verify chunks are preserved
assert actual["var1"].encoding["chunks"] == (2, 2)
@pytest.mark.asyncio
@requires_zarr_v3
async def test_async_load_multiple_variables(self) -> None:
target_class = zarr.AsyncArray
method_name = "getitem"
original_method = getattr(target_class, method_name)
# the indexed coordinate variables is not lazy, so the create_test_dataset has 4 lazy variables in total
N_LAZY_VARS = 4
original = create_test_data()
with self.create_zarr_target() as store:
original.to_zarr(store, zarr_format=3, consolidated=False)
with patch.object(
target_class, method_name, wraps=original_method, autospec=True
) as mocked_meth:
# blocks upon loading the coordinate variables here
ds = xr.open_zarr(store, consolidated=False, chunks=None)
# TODO we're not actually testing that these indexing methods are not blocking...
result_ds = await ds.load_async()
mocked_meth.assert_called()
assert mocked_meth.call_count == N_LAZY_VARS
mocked_meth.assert_awaited()
xrt.assert_identical(result_ds, ds.load())
@pytest.mark.asyncio
@requires_zarr_v3
@pytest.mark.parametrize("cls_name", ["Variable", "DataArray", "Dataset"])
async def test_concurrent_load_multiple_objects(
self,
cls_name,
) -> None:
N_OBJECTS = 5
N_LAZY_VARS = {
"Variable": 1,
"DataArray": 1,
"Dataset": 4,
} # specific to the create_test_data() used
target_class = zarr.AsyncArray
method_name = "getitem"
original_method = getattr(target_class, method_name)
original = create_test_data()
with self.create_zarr_target() as store:
original.to_zarr(store, consolidated=False, zarr_format=3)
with patch.object(
target_class, method_name, wraps=original_method, autospec=True
) as mocked_meth:
xr_obj = get_xr_obj(store, cls_name)
# TODO we're not actually testing that these indexing methods are not blocking...
coros = [xr_obj.load_async() for _ in range(N_OBJECTS)]
results = await asyncio.gather(*coros)
mocked_meth.assert_called()
assert mocked_meth.call_count == N_OBJECTS * N_LAZY_VARS[cls_name]
mocked_meth.assert_awaited()
for result in results:
xrt.assert_identical(result, xr_obj.load())
@pytest.mark.asyncio
@requires_zarr_v3
@pytest.mark.parametrize("cls_name", ["Variable", "DataArray", "Dataset"])
@pytest.mark.parametrize(
"indexer, method, target_zarr_class",
[
pytest.param({}, "sel", "zarr.AsyncArray", id="no-indexing-sel"),
pytest.param({}, "isel", "zarr.AsyncArray", id="no-indexing-isel"),
pytest.param({"dim2": 1.0}, "sel", "zarr.AsyncArray", id="basic-int-sel"),
pytest.param({"dim2": 2}, "isel", "zarr.AsyncArray", id="basic-int-isel"),
pytest.param(
{"dim2": slice(1.0, 3.0)},
"sel",
"zarr.AsyncArray",
id="basic-slice-sel",
),
pytest.param(
{"dim2": slice(1, 3)}, "isel", "zarr.AsyncArray", id="basic-slice-isel"
),
pytest.param(
{"dim2": [1.0, 3.0]},
"sel",
"zarr.core.indexing.AsyncOIndex",
id="outer-sel",
),
pytest.param(
{"dim2": [1, 3]},
"isel",
"zarr.core.indexing.AsyncOIndex",
id="outer-isel",
),
pytest.param(
{
"dim1": xr.Variable(data=[2, 3], dims="points"),
"dim2": xr.Variable(data=[1.0, 2.0], dims="points"),
},
"sel",
"zarr.core.indexing.AsyncVIndex",
id="vectorized-sel",
),
pytest.param(
{
"dim1": xr.Variable(data=[2, 3], dims="points"),
"dim2": xr.Variable(data=[1, 3], dims="points"),
},
"isel",
"zarr.core.indexing.AsyncVIndex",
id="vectorized-isel",
),
],
)
async def test_indexing(
self,
cls_name,
method,
indexer,
target_zarr_class,
) -> None:
if not has_zarr_v3_async_oindex and target_zarr_class in (
"zarr.core.indexing.AsyncOIndex",
"zarr.core.indexing.AsyncVIndex",
):
pytest.skip(
"current version of zarr does not support orthogonal or vectorized async indexing"
)
if cls_name == "Variable" and method == "sel":
pytest.skip("Variable doesn't have a .sel method")
# Each type of indexing ends up calling a different zarr indexing method
# They all use a method named .getitem, but on a different internal zarr class
def _resolve_class_from_string(class_path: str) -> type[Any]:
"""Resolve a string class path like 'zarr.AsyncArray' to the actual class."""
module_path, class_name = class_path.rsplit(".", 1)
module = import_module(module_path)
return getattr(module, class_name)
target_class = _resolve_class_from_string(target_zarr_class)
method_name = "getitem"
original_method = getattr(target_class, method_name)
original = create_test_data()
with self.create_zarr_target() as store:
original.to_zarr(store, consolidated=False, zarr_format=3)
with patch.object(
target_class, method_name, wraps=original_method, autospec=True
) as mocked_meth:
xr_obj = get_xr_obj(store, cls_name)
# TODO we're not actually testing that these indexing methods are not blocking...
result = await getattr(xr_obj, method)(**indexer).load_async()
mocked_meth.assert_called()
mocked_meth.assert_awaited()
assert mocked_meth.call_count > 0
expected = getattr(xr_obj, method)(**indexer).load()
xrt.assert_identical(result, expected)
@pytest.mark.asyncio
@pytest.mark.parametrize(
("indexer", "expected_err_msg"),
[
pytest.param(
{"dim2": 2},
"basic async indexing",
marks=pytest.mark.skipif(
has_zarr_v3,
reason="current version of zarr has basic async indexing",
),
), # tests basic indexing
pytest.param(
{"dim2": [1, 3]},
"orthogonal async indexing",
marks=pytest.mark.skipif(
has_zarr_v3_async_oindex,
reason="current version of zarr has async orthogonal indexing",
),
), # tests oindexing
pytest.param(
{
"dim1": xr.Variable(data=[2, 3], dims="points"),
"dim2": xr.Variable(data=[1, 3], dims="points"),
},
"vectorized async indexing",
marks=pytest.mark.skipif(
has_zarr_v3_async_oindex,
reason="current version of zarr has async vectorized indexing",
),
), # tests vindexing
],
)
@parametrize_zarr_format
async def test_raise_on_older_zarr_version(
self,
indexer,
expected_err_msg,
zarr_format,
):
"""Test that trying to use async load with insufficiently new version of zarr raises a clear error"""
original = create_test_data()
with self.create_zarr_target() as store:
original.to_zarr(store, consolidated=False, zarr_format=zarr_format)
ds = xr.open_zarr(store, consolidated=False, chunks=None)
var = ds["var1"].variable
with pytest.raises(NotImplementedError, match=expected_err_msg):
await var.isel(**indexer).load_async()
def get_xr_obj(
store: zarr.abc.store.Store, cls_name: Literal["Variable", "DataArray", "Dataset"]
):
ds = xr.open_zarr(store, consolidated=False, chunks=None)
match cls_name:
case "Variable":
return ds["var1"].variable
case "DataArray":
return ds["var1"]
case "Dataset":
return ds
class NoConsolidatedMetadataSupportStore(WrapperStore):
"""
Store that explicitly does not support consolidated metadata.
Useful as a proxy for stores like Icechunk, see https://github.com/zarr-developers/zarr-python/pull/3119.
"""
supports_consolidated_metadata = False
def __init__(
self,
store,
*,
read_only: bool = False,
) -> None:
self._store = store.with_read_only(read_only=read_only)
def with_read_only(
self, read_only: bool = False
) -> NoConsolidatedMetadataSupportStore:
return type(self)(
store=self._store,
read_only=read_only,
)
@requires_zarr_v3
class TestZarrNoConsolidatedMetadataSupport(ZarrBase):
@contextlib.contextmanager
def create_zarr_target(self):
# TODO the zarr version would need to be >3.08 for the supports_consolidated_metadata property to have any effect
yield NoConsolidatedMetadataSupportStore(
zarr.storage.MemoryStore({}, read_only=False)
)
@requires_zarr
@pytest.mark.skipif(
ON_WINDOWS,
reason="Very flaky on Windows CI. Can re-enable assuming it starts consistently passing.",
)
class TestZarrDirectoryStore(ZarrBase):
@contextlib.contextmanager
def create_zarr_target(self):
with create_tmp_file(suffix=".zarr") as tmp:
yield tmp
@requires_zarr
class TestZarrWriteEmpty(TestZarrDirectoryStore):
@contextlib.contextmanager
def temp_dir(self) -> Iterator[tuple[str, str]]:
with tempfile.TemporaryDirectory() as d:
store = os.path.join(d, "test.zarr")
yield d, store
@contextlib.contextmanager
def roundtrip_dir(
self,
data,
store,
save_kwargs=None,
open_kwargs=None,
allow_cleanup_failure=False,
) -> Iterator[Dataset]:
if save_kwargs is None:
save_kwargs = {}
if open_kwargs is None:
open_kwargs = {}
data.to_zarr(store, **save_kwargs, **self.version_kwargs)
with xr.open_dataset(
store, engine="zarr", **open_kwargs, **self.version_kwargs
) as ds:
yield ds
@pytest.mark.parametrize("consolidated", [True, False, None])
@pytest.mark.parametrize("write_empty", [True, False, None])
def test_write_empty(
self,
consolidated: bool | None,
write_empty: bool | None,
) -> None:
def assert_expected_files(expected: list[str], store: str) -> None:
"""Convenience for comparing with actual files written"""
ls = []
test_root = os.path.join(store, "test")
for root, _, files in os.walk(test_root):
ls.extend(
[
os.path.join(root, f).removeprefix(test_root).lstrip("/")
for f in files
]
)
assert set(expected) == {
file.lstrip("c/")
for file in ls
if (file not in (".zattrs", ".zarray", "zarr.json"))
}
# The zarr format is set by the `default_zarr_format`
# pytest fixture that acts on a superclass
zarr_format_3 = has_zarr_v3 and zarr.config.config["default_zarr_format"] == 3
if (write_empty is False) or (write_empty is None and has_zarr_v3):
expected = ["0.1.0"]
else:
expected = [
"0.0.0",
"0.0.1",
"0.1.0",
"0.1.1",
]
if zarr_format_3:
data = np.array([0.0, 0, 1.0, 0]).reshape((1, 2, 2))
# transform to the path style of zarr 3
# e.g. 0/0/1
expected = [e.replace(".", "/") for e in expected]
else:
# use nan for default fill_value behaviour
data = np.array([np.nan, np.nan, 1.0, np.nan]).reshape((1, 2, 2))
ds = xr.Dataset(data_vars={"test": (("Z", "Y", "X"), data)})
if has_dask:
ds["test"] = ds["test"].chunk(1)
encoding = None
else:
encoding = {"test": {"chunks": (1, 1, 1)}}
with self.temp_dir() as (d, store):
ds.to_zarr(
store,
mode="w",
encoding=encoding,
write_empty_chunks=write_empty,
)
# check expected files after a write
assert_expected_files(expected, store)
with self.roundtrip_dir(
ds,
store,
save_kwargs={
"mode": "a",
"append_dim": "Z",
"write_empty_chunks": write_empty,
},
) as a_ds:
expected_ds = xr.concat([ds, ds], dim="Z")
assert_identical(a_ds, expected_ds.compute())
# add the new files we expect to be created by the append
# that was performed by the roundtrip_dir
if (write_empty is False) or (write_empty is None and has_zarr_v3):
expected.append("1.1.0")
elif not has_zarr_v3:
# TODO: remove zarr3 if once zarr issue is fixed
# https://github.com/zarr-developers/zarr-python/issues/2931
expected.extend(
[
"1.1.0",
"1.0.0",
"1.0.1",
"1.1.1",
]
)
else:
expected.append("1.1.0")
if zarr_format_3:
expected = [e.replace(".", "/") for e in expected]
assert_expected_files(expected, store)
def test_avoid_excess_metadata_calls(self) -> None:
"""Test that chunk requests do not trigger redundant metadata requests.
This test targets logic in backends.zarr.ZarrArrayWrapper, asserting that calls
to retrieve chunk data after initialization do not trigger additional
metadata requests.
https://github.com/pydata/xarray/issues/8290
"""
ds = xr.Dataset(data_vars={"test": (("Z",), np.array([123]).reshape(1))})
# The call to retrieve metadata performs a group lookup. We patch Group.__getitem__
# so that we can inspect calls to this method - specifically count of calls.
# Use of side_effect means that calls are passed through to the original method
# rather than a mocked method.
Group: Any
if has_zarr_v3:
Group = zarr.AsyncGroup
patched = patch.object(
Group, "getitem", side_effect=Group.getitem, autospec=True
)
else:
Group = zarr.Group
patched = patch.object(
Group, "__getitem__", side_effect=Group.__getitem__, autospec=True
)
with self.create_zarr_target() as store, patched as mock:
ds.to_zarr(store, mode="w")
# We expect this to request array metadata information, so call_count should be == 1,
xrds = xr.open_zarr(store)
call_count = mock.call_count
assert call_count == 1
# compute() requests array data, which should not trigger additional metadata requests
# we assert that the number of calls has not increased after fetchhing the array
xrds.test.compute(scheduler="sync")
assert mock.call_count == call_count
@requires_zarr
@requires_fsspec
@pytest.mark.skipif(has_zarr_v3, reason="Difficult to test.")
def test_zarr_storage_options() -> None:
pytest.importorskip("aiobotocore")
ds = create_test_data()
store_target = "memory://test.zarr"
ds.to_zarr(store_target, storage_options={"test": "zarr_write"})
ds_a = xr.open_zarr(store_target, storage_options={"test": "zarr_read"})
assert_identical(ds, ds_a)
@requires_zarr
def test_zarr_version_deprecated() -> None:
ds = create_test_data()
store: Any
if has_zarr_v3:
store = KVStore()
else:
store = {}
with pytest.warns(FutureWarning, match="zarr_version"):
ds.to_zarr(store=store, zarr_version=2)
with pytest.warns(FutureWarning, match="zarr_version"):
xr.open_zarr(store=store, zarr_version=2)
with pytest.raises(ValueError, match="zarr_format"):
xr.open_zarr(store=store, zarr_version=2, zarr_format=3)
@requires_scipy
class TestScipyInMemoryData(NetCDF3Only, CFEncodedBase):
engine: T_NetcdfEngine = "scipy"
@contextlib.contextmanager
def create_store(self):
fobj = BytesIO()
yield backends.ScipyDataStore(fobj, "w")
@pytest.mark.asyncio
@pytest.mark.skip(reason="NetCDF backends don't support async loading")
async def test_load_async(self) -> None:
await super().test_load_async()
def test_to_netcdf_explicit_engine(self) -> None:
with pytest.warns(
FutureWarning,
match=re.escape("return value of to_netcdf() without a target"),
):
Dataset({"foo": 42}).to_netcdf(engine="scipy")
def test_roundtrip_via_bytes(self) -> None:
original = create_test_data()
with pytest.warns(
FutureWarning,
match=re.escape("return value of to_netcdf() without a target"),
):
netcdf_bytes = original.to_netcdf(engine="scipy")
roundtrip = open_dataset(netcdf_bytes, engine="scipy")
assert_identical(roundtrip, original)
def test_bytes_pickle(self) -> None:
data = Dataset({"foo": ("x", [1, 2, 3])})
with pytest.warns(
FutureWarning,
match=re.escape("return value of to_netcdf() without a target"),
):
fobj = data.to_netcdf()
with self.open(fobj) as ds:
unpickled = pickle.loads(pickle.dumps(ds))
assert_identical(unpickled, data)
@requires_scipy
class TestScipyFileObject(NetCDF3Only, CFEncodedBase):
# TODO: Consider consolidating some of these cases (e.g.,
# test_file_remains_open) with TestH5NetCDFFileObject
engine: T_NetcdfEngine = "scipy"
@contextlib.contextmanager
def create_store(self):
fobj = BytesIO()
yield backends.ScipyDataStore(fobj, "w")
@contextlib.contextmanager
def roundtrip(
self, data, save_kwargs=None, open_kwargs=None, allow_cleanup_failure=False
):
if save_kwargs is None:
save_kwargs = {}
if open_kwargs is None:
open_kwargs = {}
with create_tmp_file() as tmp_file:
with open(tmp_file, "wb") as f:
self.save(data, f, **save_kwargs)
with open(tmp_file, "rb") as f:
with self.open(f, **open_kwargs) as ds:
yield ds
@pytest.mark.xfail(
reason="scipy.io.netcdf_file closes files upon garbage collection"
)
def test_file_remains_open(self) -> None:
data = Dataset({"foo": ("x", [1, 2, 3])})
f = BytesIO()
data.to_netcdf(f, engine="scipy")
assert not f.closed
restored = open_dataset(f, engine="scipy")
assert not f.closed
assert_identical(restored, data)
restored.close()
assert not f.closed
@pytest.mark.skip(reason="cannot pickle file objects")
def test_pickle(self) -> None:
pass
@pytest.mark.skip(reason="cannot pickle file objects")
def test_pickle_dataarray(self) -> None:
pass
@pytest.mark.parametrize("create_default_indexes", [True, False])
def test_create_default_indexes(self, tmp_path, create_default_indexes) -> None:
store_path = tmp_path / "tmp.nc"
original_ds = xr.Dataset(
{"data": ("x", np.arange(3))}, coords={"x": [-1, 0, 1]}
)
original_ds.to_netcdf(store_path, engine=self.engine, mode="w")
with open_dataset(
store_path,
engine=self.engine,
create_default_indexes=create_default_indexes,
) as loaded_ds:
if create_default_indexes:
assert list(loaded_ds.xindexes) == ["x"] and isinstance(
loaded_ds.xindexes["x"], PandasIndex
)
else:
assert len(loaded_ds.xindexes) == 0
@requires_scipy
class TestScipyFilePath(NetCDF3Only, CFEncodedBase):
engine: T_NetcdfEngine = "scipy"
@contextlib.contextmanager
def create_store(self):
with create_tmp_file() as tmp_file:
with backends.ScipyDataStore(tmp_file, mode="w") as store:
yield store
def test_array_attrs(self) -> None:
ds = Dataset(attrs={"foo": [[1, 2], [3, 4]]})
with pytest.raises(ValueError, match=r"must be 1-dimensional"):
with self.roundtrip(ds):
pass
def test_roundtrip_example_1_netcdf_gz(self) -> None:
with open_example_dataset("example_1.nc.gz") as expected:
with open_example_dataset("example_1.nc") as actual:
assert_identical(expected, actual)
def test_netcdf3_endianness(self) -> None:
# regression test for GH416
with open_example_dataset("bears.nc", engine="scipy") as expected:
for var in expected.variables.values():
assert var.dtype.isnative
@requires_netCDF4
def test_nc4_scipy(self) -> None:
with create_tmp_file(allow_cleanup_failure=True) as tmp_file:
with nc4.Dataset(tmp_file, "w", format="NETCDF4") as rootgrp:
rootgrp.createGroup("foo")
with pytest.raises(TypeError, match=r"pip install netcdf4"):
open_dataset(tmp_file, engine="scipy")
@requires_netCDF4
class TestNetCDF3ViaNetCDF4Data(NetCDF3Only, CFEncodedBase):
engine: T_NetcdfEngine = "netcdf4"
file_format: T_NetcdfTypes = "NETCDF3_CLASSIC"
@contextlib.contextmanager
def create_store(self):
with create_tmp_file() as tmp_file:
with backends.NetCDF4DataStore.open(
tmp_file, mode="w", format="NETCDF3_CLASSIC"
) as store:
yield store
def test_encoding_kwarg_vlen_string(self) -> None:
original = Dataset({"x": ["foo", "bar", "baz"]})
kwargs = dict(encoding={"x": {"dtype": str}})
with pytest.raises(ValueError, match=r"encoding dtype=str for vlen"):
with self.roundtrip(original, save_kwargs=kwargs):
pass
@requires_netCDF4
class TestNetCDF4ClassicViaNetCDF4Data(NetCDF3Only, CFEncodedBase):
engine: T_NetcdfEngine = "netcdf4"
file_format: T_NetcdfTypes = "NETCDF4_CLASSIC"
@contextlib.contextmanager
def create_store(self):
with create_tmp_file() as tmp_file:
with backends.NetCDF4DataStore.open(
tmp_file, mode="w", format="NETCDF4_CLASSIC"
) as store:
yield store
@requires_scipy_or_netCDF4
class TestGenericNetCDFData(NetCDF3Only, CFEncodedBase):
# verify that we can read and write netCDF3 files as long as we have scipy
# or netCDF4-python installed
file_format: T_NetcdfTypes = "NETCDF3_64BIT"
def test_write_store(self) -> None:
# there's no specific store to test here
pass
@requires_scipy
def test_engine(self) -> None:
data = create_test_data()
with pytest.raises(ValueError, match=r"unrecognized engine"):
data.to_netcdf("foo.nc", engine="foobar") # type: ignore[call-overload]
with pytest.raises(ValueError, match=r"invalid engine"):
data.to_netcdf(engine="netcdf4")
with create_tmp_file() as tmp_file:
data.to_netcdf(tmp_file)
with pytest.raises(ValueError, match=r"unrecognized engine"):
open_dataset(tmp_file, engine="foobar")
bytes_io = BytesIO()
data.to_netcdf(bytes_io, engine="scipy")
with pytest.raises(ValueError, match=r"unrecognized engine"):
open_dataset(bytes_io, engine="foobar")
def test_cross_engine_read_write_netcdf3(self) -> None:
data = create_test_data()
valid_engines: set[T_NetcdfEngine] = set()
if has_netCDF4:
valid_engines.add("netcdf4")
if has_scipy:
valid_engines.add("scipy")
for write_engine in valid_engines:
for format in self.netcdf3_formats:
with create_tmp_file() as tmp_file:
data.to_netcdf(tmp_file, format=format, engine=write_engine)
for read_engine in valid_engines:
with open_dataset(tmp_file, engine=read_engine) as actual:
# hack to allow test to work:
# coord comes back as DataArray rather than coord,
# and so need to loop through here rather than in
# the test function (or we get recursion)
[
assert_allclose(data[k].variable, actual[k].variable)
for k in data.variables
]
def test_encoding_unlimited_dims(self) -> None:
ds = Dataset({"x": ("y", np.arange(10.0))})
with self.roundtrip(ds, save_kwargs=dict(unlimited_dims=["y"])) as actual:
assert actual.encoding["unlimited_dims"] == set("y")
assert_equal(ds, actual)
# Regression test for https://github.com/pydata/xarray/issues/2134
with self.roundtrip(ds, save_kwargs=dict(unlimited_dims="y")) as actual:
assert actual.encoding["unlimited_dims"] == set("y")
assert_equal(ds, actual)
ds.encoding = {"unlimited_dims": ["y"]}
with self.roundtrip(ds) as actual:
assert actual.encoding["unlimited_dims"] == set("y")
assert_equal(ds, actual)
# Regression test for https://github.com/pydata/xarray/issues/2134
ds.encoding = {"unlimited_dims": "y"}
with self.roundtrip(ds) as actual:
assert actual.encoding["unlimited_dims"] == set("y")
assert_equal(ds, actual)
@requires_scipy
def test_roundtrip_via_bytes(self) -> None:
original = create_test_data()
with pytest.warns(
FutureWarning,
match=re.escape("return value of to_netcdf() without a target"),
):
netcdf_bytes = original.to_netcdf()
roundtrip = open_dataset(netcdf_bytes)
assert_identical(roundtrip, original)
@pytest.mark.xfail(
reason="scipy.io.netcdf_file closes files upon garbage collection"
)
@requires_scipy
def test_roundtrip_via_file_object(self) -> None:
original = create_test_data()
f = BytesIO()
original.to_netcdf(f)
assert not f.closed
restored = open_dataset(f)
assert not f.closed
assert_identical(restored, original)
restored.close()
assert not f.closed
@requires_h5netcdf
@requires_netCDF4
@pytest.mark.filterwarnings("ignore:use make_scale(name) instead")
class TestH5NetCDFData(NetCDF4Base):
engine: T_NetcdfEngine = "h5netcdf"
@contextlib.contextmanager
def create_store(self):
with create_tmp_file() as tmp_file:
yield backends.H5NetCDFStore.open(tmp_file, "w")
@pytest.mark.skipif(
has_h5netcdf_1_4_0_or_above, reason="only valid for h5netcdf < 1.4.0"
)
def test_complex(self) -> None:
expected = Dataset({"x": ("y", np.ones(5) + 1j * np.ones(5))})
save_kwargs = {"invalid_netcdf": True}
with pytest.warns(UserWarning, match="You are writing invalid netcdf features"):
with self.roundtrip(expected, save_kwargs=save_kwargs) as actual:
assert_equal(expected, actual)
@pytest.mark.skipif(
has_h5netcdf_1_4_0_or_above, reason="only valid for h5netcdf < 1.4.0"
)
@pytest.mark.parametrize("invalid_netcdf", [None, False])
def test_complex_error(self, invalid_netcdf) -> None:
import h5netcdf
expected = Dataset({"x": ("y", np.ones(5) + 1j * np.ones(5))})
save_kwargs = {"invalid_netcdf": invalid_netcdf}
with pytest.raises(
h5netcdf.CompatibilityError, match="are not a supported NetCDF feature"
):
with self.roundtrip(expected, save_kwargs=save_kwargs) as actual:
assert_equal(expected, actual)
def test_numpy_bool_(self) -> None:
# h5netcdf loads booleans as numpy.bool_, this type needs to be supported
# when writing invalid_netcdf datasets in order to support a roundtrip
expected = Dataset({"x": ("y", np.ones(5), {"numpy_bool": np.bool_(True)})})
save_kwargs = {"invalid_netcdf": True}
with pytest.warns(UserWarning, match="You are writing invalid netcdf features"):
with self.roundtrip(expected, save_kwargs=save_kwargs) as actual:
assert_identical(expected, actual)
def test_cross_engine_read_write_netcdf4(self) -> None:
# Drop dim3, because its labels include strings. These appear to be
# not properly read with python-netCDF4, which converts them into
# unicode instead of leaving them as bytes.
data = create_test_data().drop_vars("dim3")
data.attrs["foo"] = "bar"
valid_engines: list[T_NetcdfEngine] = ["netcdf4", "h5netcdf"]
for write_engine in valid_engines:
with create_tmp_file() as tmp_file:
data.to_netcdf(tmp_file, engine=write_engine)
for read_engine in valid_engines:
with open_dataset(tmp_file, engine=read_engine) as actual:
assert_identical(data, actual)
def test_read_byte_attrs_as_unicode(self) -> None:
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, "w") as nc:
nc.foo = b"bar"
with open_dataset(tmp_file) as actual:
expected = Dataset(attrs={"foo": "bar"})
assert_identical(expected, actual)
def test_compression_encoding_h5py(self) -> None:
ENCODINGS: tuple[tuple[dict[str, Any], dict[str, Any]], ...] = (
# h5py style compression with gzip codec will be converted to
# NetCDF4-Python style on round-trip
(
{"compression": "gzip", "compression_opts": 9},
{"zlib": True, "complevel": 9},
),
# What can't be expressed in NetCDF4-Python style is
# round-tripped unaltered
(
{"compression": "lzf", "compression_opts": None},
{"compression": "lzf", "compression_opts": None},
),
# If both styles are used together, h5py format takes precedence
(
{
"compression": "lzf",
"compression_opts": None,
"zlib": True,
"complevel": 9,
},
{"compression": "lzf", "compression_opts": None},
),
)
for compr_in, compr_out in ENCODINGS:
data = create_test_data()
compr_common = {
"chunksizes": (5, 5),
"fletcher32": True,
"shuffle": True,
"original_shape": data.var2.shape,
}
data["var2"].encoding.update(compr_in)
data["var2"].encoding.update(compr_common)
compr_out.update(compr_common)
data["scalar"] = ("scalar_dim", np.array([2.0]))
data["scalar"] = data["scalar"][0]
with self.roundtrip(data) as actual:
for k, v in compr_out.items():
assert v == actual["var2"].encoding[k]
def test_compression_check_encoding_h5py(self) -> None:
"""When mismatched h5py and NetCDF4-Python encodings are expressed
in to_netcdf(encoding=...), must raise ValueError
"""
data = Dataset({"x": ("y", np.arange(10.0))})
# Compatible encodings are graciously supported
with create_tmp_file() as tmp_file:
data.to_netcdf(
tmp_file,
engine="h5netcdf",
encoding={
"x": {
"compression": "gzip",
"zlib": True,
"compression_opts": 6,
"complevel": 6,
}
},
)
with open_dataset(tmp_file, engine="h5netcdf") as actual:
assert actual.x.encoding["zlib"] is True
assert actual.x.encoding["complevel"] == 6
# Incompatible encodings cause a crash
with create_tmp_file() as tmp_file:
with pytest.raises(
ValueError, match=r"'zlib' and 'compression' encodings mismatch"
):
data.to_netcdf(
tmp_file,
engine="h5netcdf",
encoding={"x": {"compression": "lzf", "zlib": True}},
)
with create_tmp_file() as tmp_file:
with pytest.raises(
ValueError,
match=r"'complevel' and 'compression_opts' encodings mismatch",
):
data.to_netcdf(
tmp_file,
engine="h5netcdf",
encoding={
"x": {
"compression": "gzip",
"compression_opts": 5,
"complevel": 6,
}
},
)
def test_dump_encodings_h5py(self) -> None:
# regression test for #709
ds = Dataset({"x": ("y", np.arange(10.0))})
kwargs = {"encoding": {"x": {"compression": "gzip", "compression_opts": 9}}}
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert actual.x.encoding["zlib"]
assert actual.x.encoding["complevel"] == 9
kwargs = {"encoding": {"x": {"compression": "lzf", "compression_opts": None}}}
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert actual.x.encoding["compression"] == "lzf"
assert actual.x.encoding["compression_opts"] is None
def test_decode_utf8_warning(self) -> None:
title = b"\xc3"
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, "w") as f:
f.title = title
with pytest.warns(UnicodeWarning, match="returning bytes undecoded") as w:
ds = xr.load_dataset(tmp_file, engine="h5netcdf")
assert ds.title == title
assert "attribute 'title' of h5netcdf object '/'" in str(w[0].message)
def test_byte_attrs(self, byte_attrs_dataset: dict[str, Any]) -> None:
with pytest.raises(ValueError, match=byte_attrs_dataset["h5netcdf_error"]):
super().test_byte_attrs(byte_attrs_dataset)
@requires_h5netcdf_1_4_0_or_above
def test_roundtrip_complex(self):
expected = Dataset({"x": ("y", np.ones(5) + 1j * np.ones(5))})
with self.roundtrip(expected) as actual:
assert_equal(expected, actual)
def test_phony_dims_warning(self) -> None:
import h5py
foo_data = np.arange(125).reshape(5, 5, 5)
bar_data = np.arange(625).reshape(25, 5, 5)
var = {"foo1": foo_data, "foo2": bar_data, "foo3": foo_data, "foo4": bar_data}
with create_tmp_file() as tmp_file:
with h5py.File(tmp_file, "w") as f:
grps = ["bar", "baz"]
for grp in grps:
fx = f.create_group(grp)
for k, v in var.items():
fx.create_dataset(k, data=v)
with pytest.warns(UserWarning, match="The 'phony_dims' kwarg"):
with xr.open_dataset(tmp_file, engine="h5netcdf", group="bar") as ds:
assert ds.sizes == {
"phony_dim_0": 5,
"phony_dim_1": 5,
"phony_dim_2": 5,
"phony_dim_3": 25,
}
@requires_h5netcdf
@requires_netCDF4
class TestH5NetCDFAlreadyOpen:
def test_open_dataset_group(self) -> None:
import h5netcdf
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, mode="w") as nc:
group = nc.createGroup("g")
v = group.createVariable("x", "int")
v[...] = 42
kwargs = {"decode_vlen_strings": True}
h5 = h5netcdf.File(tmp_file, mode="r", **kwargs)
store = backends.H5NetCDFStore(h5["g"])
with open_dataset(store) as ds:
expected = Dataset({"x": ((), 42)})
assert_identical(expected, ds)
h5 = h5netcdf.File(tmp_file, mode="r", **kwargs)
store = backends.H5NetCDFStore(h5, group="g")
with open_dataset(store) as ds:
expected = Dataset({"x": ((), 42)})
assert_identical(expected, ds)
def test_deepcopy(self) -> None:
import h5netcdf
with create_tmp_file() as tmp_file:
with nc4.Dataset(tmp_file, mode="w") as nc:
nc.createDimension("x", 10)
v = nc.createVariable("y", np.int32, ("x",))
v[:] = np.arange(10)
kwargs = {"decode_vlen_strings": True}
h5 = h5netcdf.File(tmp_file, mode="r", **kwargs)
store = backends.H5NetCDFStore(h5)
with open_dataset(store) as ds:
copied = ds.copy(deep=True)
expected = Dataset({"y": ("x", np.arange(10))})
assert_identical(expected, copied)
@requires_h5netcdf
class TestH5NetCDFFileObject(TestH5NetCDFData):
engine: T_NetcdfEngine = "h5netcdf"
def test_open_badbytes(self) -> None:
with pytest.raises(
ValueError, match=r"match in any of xarray's currently installed IO"
):
with open_dataset(b"garbage"):
pass
with pytest.raises(ValueError, match=r"can only read bytes"):
with open_dataset(b"garbage", engine="netcdf4"):
pass
with pytest.raises(
ValueError, match=r"not the signature of a valid netCDF4 file"
):
with open_dataset(BytesIO(b"garbage"), engine="h5netcdf"):
pass
def test_open_twice(self) -> None:
expected = create_test_data()
expected.attrs["foo"] = "bar"
with create_tmp_file() as tmp_file:
expected.to_netcdf(tmp_file, engine="h5netcdf")
with open(tmp_file, "rb") as f:
with open_dataset(f, engine="h5netcdf"):
with open_dataset(f, engine="h5netcdf"):
pass
@requires_scipy
def test_open_fileobj(self) -> None:
# open in-memory datasets instead of local file paths
expected = create_test_data().drop_vars("dim3")
expected.attrs["foo"] = "bar"
with create_tmp_file() as tmp_file:
expected.to_netcdf(tmp_file, engine="h5netcdf")
with open(tmp_file, "rb") as f:
with open_dataset(f, engine="h5netcdf") as actual:
assert_identical(expected, actual)
f.seek(0)
with open_dataset(f) as actual:
assert_identical(expected, actual)
f.seek(0)
with BytesIO(f.read()) as bio:
with open_dataset(bio, engine="h5netcdf") as actual:
assert_identical(expected, actual)
f.seek(0)
with pytest.raises(TypeError, match="not a valid NetCDF 3"):
open_dataset(f, engine="scipy")
# TODO: this additional open is required since scipy seems to close the file
# when it fails on the TypeError (though didn't when we used
# `raises_regex`?). Ref https://github.com/pydata/xarray/pull/5191
with open(tmp_file, "rb") as f:
f.seek(8)
with open_dataset(f): # ensure file gets closed
pass
def test_file_remains_open(self) -> None:
data = Dataset({"foo": ("x", [1, 2, 3])})
f = BytesIO()
data.to_netcdf(f, engine="h5netcdf")
assert not f.closed
restored = open_dataset(f, engine="h5netcdf")
assert not f.closed
assert_identical(restored, data)
restored.close()
assert not f.closed
@requires_h5netcdf
class TestH5NetCDFInMemoryData:
def test_roundtrip_via_bytes(self) -> None:
original = create_test_data()
netcdf_bytes = original.to_netcdf(engine="h5netcdf")
roundtrip = open_dataset(netcdf_bytes, engine="h5netcdf")
assert_identical(roundtrip, original)
def test_roundtrip_group_via_bytes(self) -> None:
original = create_test_data()
netcdf_bytes = original.to_netcdf(group="sub", engine="h5netcdf")
roundtrip = open_dataset(netcdf_bytes, group="sub", engine="h5netcdf")
assert_identical(roundtrip, original)
@requires_h5netcdf
@requires_dask
@pytest.mark.filterwarnings("ignore:deallocating CachingFileManager")
class TestH5NetCDFViaDaskData(TestH5NetCDFData):
@contextlib.contextmanager
def roundtrip(
self, data, save_kwargs=None, open_kwargs=None, allow_cleanup_failure=False
):
if save_kwargs is None:
save_kwargs = {}
if open_kwargs is None:
open_kwargs = {}
open_kwargs.setdefault("chunks", -1)
with TestH5NetCDFData.roundtrip(
self, data, save_kwargs, open_kwargs, allow_cleanup_failure
) as ds:
yield ds
@pytest.mark.skip(reason="caching behavior differs for dask")
def test_dataset_caching(self) -> None:
pass
def test_write_inconsistent_chunks(self) -> None:
# Construct two variables with the same dimensions, but different
# chunk sizes.
x = da.zeros((100, 100), dtype="f4", chunks=(50, 100))
x = DataArray(data=x, dims=("lat", "lon"), name="x")
x.encoding["chunksizes"] = (50, 100)
x.encoding["original_shape"] = (100, 100)
y = da.ones((100, 100), dtype="f4", chunks=(100, 50))
y = DataArray(data=y, dims=("lat", "lon"), name="y")
y.encoding["chunksizes"] = (100, 50)
y.encoding["original_shape"] = (100, 100)
# Put them both into the same dataset
ds = Dataset({"x": x, "y": y})
with self.roundtrip(ds) as actual:
assert actual["x"].encoding["chunksizes"] == (50, 100)
assert actual["y"].encoding["chunksizes"] == (100, 50)
@requires_h5netcdf_ros3
class TestH5NetCDFDataRos3Driver(TestCommon):
engine: T_NetcdfEngine = "h5netcdf"
test_remote_dataset: str = (
"https://www.unidata.ucar.edu/software/netcdf/examples/OMI-Aura_L2-example.nc"
)
@pytest.mark.filterwarnings("ignore:Duplicate dimension names")
def test_get_variable_list(self) -> None:
with open_dataset(
self.test_remote_dataset,
engine="h5netcdf",
backend_kwargs={"driver": "ros3"},
) as actual:
assert "Temperature" in list(actual)
@pytest.mark.filterwarnings("ignore:Duplicate dimension names")
def test_get_variable_list_empty_driver_kwds(self) -> None:
driver_kwds = {
"secret_id": b"",
"secret_key": b"",
}
backend_kwargs = {"driver": "ros3", "driver_kwds": driver_kwds}
with open_dataset(
self.test_remote_dataset, engine="h5netcdf", backend_kwargs=backend_kwargs
) as actual:
assert "Temperature" in list(actual)
@pytest.fixture(params=["scipy", "netcdf4", "h5netcdf", "zarr"])
def readengine(request):
return request.param
@pytest.fixture(params=[1, 20])
def nfiles(request):
return request.param
@pytest.fixture(params=[5, None])
def file_cache_maxsize(request):
maxsize = request.param
if maxsize is not None:
with set_options(file_cache_maxsize=maxsize):
yield maxsize
else:
yield maxsize
@pytest.fixture(params=[True, False])
def parallel(request):
return request.param
@pytest.fixture(params=[None, 5])
def chunks(request):
return request.param
@pytest.fixture(params=["tmp_path", "ZipStore", "Dict"])
def tmp_store(request, tmp_path):
if request.param == "tmp_path":
return tmp_path
elif request.param == "ZipStore":
from zarr.storage import ZipStore
path = tmp_path / "store.zip"
return ZipStore(path)
elif request.param == "Dict":
return dict()
else:
raise ValueError("not supported")
# using pytest.mark.skipif does not work so this a work around
def skip_if_not_engine(engine):
if engine == "netcdf4":
pytest.importorskip("netCDF4")
else:
pytest.importorskip(engine)
@requires_dask
@pytest.mark.filterwarnings("ignore:use make_scale(name) instead")
@pytest.mark.skip(
reason="Flaky test which can cause the worker to crash (so don't xfail). Very open to contributions fixing this"
)
def test_open_mfdataset_manyfiles(
readengine, nfiles, parallel, chunks, file_cache_maxsize
):
# skip certain combinations
skip_if_not_engine(readengine)
randdata = np.random.randn(nfiles)
original = Dataset({"foo": ("x", randdata)})
# test standard open_mfdataset approach with too many files
with create_tmp_files(nfiles) as tmpfiles:
# split into multiple sets of temp files
for ii in original.x.values:
subds = original.isel(x=slice(ii, ii + 1))
if readengine != "zarr":
subds.to_netcdf(tmpfiles[ii], engine=readengine)
else: # if writeengine == "zarr":
subds.to_zarr(store=tmpfiles[ii])
# check that calculation on opened datasets works properly
with open_mfdataset(
tmpfiles,
combine="nested",
concat_dim="x",
engine=readengine,
parallel=parallel,
chunks=chunks if (not chunks and readengine != "zarr") else "auto",
) as actual:
# check that using open_mfdataset returns dask arrays for variables
assert isinstance(actual["foo"].data, dask_array_type)
assert_identical(original, actual)
@requires_netCDF4
@requires_dask
def test_open_mfdataset_can_open_path_objects() -> None:
dataset = os.path.join(os.path.dirname(__file__), "data", "example_1.nc")
with open_mfdataset(Path(dataset)) as actual:
assert isinstance(actual, Dataset)
@requires_netCDF4
@requires_dask
def test_open_mfdataset_list_attr() -> None:
"""
Case when an attribute of type list differs across the multiple files
"""
from netCDF4 import Dataset
with create_tmp_files(2) as nfiles:
for i in range(2):
with Dataset(nfiles[i], "w") as f:
f.createDimension("x", 3)
vlvar = f.createVariable("test_var", np.int32, ("x"))
# here create an attribute as a list
vlvar.test_attr = [f"string a {i}", f"string b {i}"]
vlvar[:] = np.arange(3)
with open_dataset(nfiles[0]) as ds1:
with open_dataset(nfiles[1]) as ds2:
original = xr.concat([ds1, ds2], dim="x")
with xr.open_mfdataset(
[nfiles[0], nfiles[1]], combine="nested", concat_dim="x"
) as actual:
assert_identical(actual, original)
@requires_scipy_or_netCDF4
@requires_dask
class TestOpenMFDatasetWithDataVarsAndCoordsKw:
coord_name = "lon"
var_name = "v1"
@contextlib.contextmanager
def setup_files_and_datasets(self, *, fuzz=0, new_combine_kwargs: bool = False):
ds1, ds2 = self.gen_datasets_with_common_coord_and_time()
# to test join='exact'
ds1["x"] = ds1.x + fuzz
with create_tmp_file() as tmpfile1:
with create_tmp_file() as tmpfile2:
# save data to the temporary files
ds1.to_netcdf(tmpfile1)
ds2.to_netcdf(tmpfile2)
with set_options(use_new_combine_kwarg_defaults=new_combine_kwargs):
yield [tmpfile1, tmpfile2], [ds1, ds2]
def gen_datasets_with_common_coord_and_time(self):
# create coordinate data
nx = 10
nt = 10
x = np.arange(nx)
t1 = np.arange(nt)
t2 = np.arange(nt, 2 * nt, 1)
v1 = np.random.randn(nt, nx)
v2 = np.random.randn(nt, nx)
ds1 = Dataset(
data_vars={self.var_name: (["t", "x"], v1), self.coord_name: ("x", 2 * x)},
coords={"t": (["t"], t1), "x": (["x"], x)},
)
ds2 = Dataset(
data_vars={self.var_name: (["t", "x"], v2), self.coord_name: ("x", 2 * x)},
coords={"t": (["t"], t2), "x": (["x"], x)},
)
return ds1, ds2
@pytest.mark.parametrize(
"combine, concat_dim", [("nested", "t"), ("by_coords", None)]
)
@pytest.mark.parametrize("opt", ["all", "minimal", "different"])
@pytest.mark.parametrize("join", ["outer", "inner", "left", "right"])
def test_open_mfdataset_does_same_as_concat(
self, combine, concat_dim, opt, join
) -> None:
with self.setup_files_and_datasets() as (files, [ds1, ds2]):
if combine == "by_coords":
files.reverse()
with open_mfdataset(
files,
data_vars=opt,
combine=combine,
concat_dim=concat_dim,
join=join,
compat="equals",
) as ds:
ds_expect = xr.concat(
[ds1, ds2], data_vars=opt, dim="t", join=join, compat="equals"
)
assert_identical(ds, ds_expect)
@pytest.mark.parametrize("use_new_combine_kwarg_defaults", [True, False])
@pytest.mark.parametrize(
["combine_attrs", "attrs", "expected", "expect_error"],
(
pytest.param("drop", [{"a": 1}, {"a": 2}], {}, False, id="drop"),
pytest.param(
"override", [{"a": 1}, {"a": 2}], {"a": 1}, False, id="override"
),
pytest.param(
"no_conflicts", [{"a": 1}, {"a": 2}], None, True, id="no_conflicts"
),
pytest.param(
"identical",
[{"a": 1, "b": 2}, {"a": 1, "c": 3}],
None,
True,
id="identical",
),
pytest.param(
"drop_conflicts",
[{"a": 1, "b": 2}, {"b": -1, "c": 3}],
{"a": 1, "c": 3},
False,
id="drop_conflicts",
),
),
)
def test_open_mfdataset_dataset_combine_attrs(
self,
use_new_combine_kwarg_defaults,
combine_attrs,
attrs,
expected,
expect_error,
):
with self.setup_files_and_datasets() as (files, [ds1, ds2]):
# Give the files an inconsistent attribute
for i, f in enumerate(files):
ds = open_dataset(f).load()
ds.attrs = attrs[i]
ds.close()
ds.to_netcdf(f)
with set_options(
use_new_combine_kwarg_defaults=use_new_combine_kwarg_defaults
):
warning: contextlib.AbstractContextManager = (
pytest.warns(FutureWarning)
if not use_new_combine_kwarg_defaults
else contextlib.nullcontext()
)
error: contextlib.AbstractContextManager = (
pytest.raises(xr.MergeError)
if expect_error
else contextlib.nullcontext()
)
with warning:
with error:
with xr.open_mfdataset(
files,
combine="nested",
concat_dim="t",
combine_attrs=combine_attrs,
) as ds:
assert ds.attrs == expected
def test_open_mfdataset_dataset_attr_by_coords(self) -> None:
"""
Case when an attribute differs across the multiple files
"""
with self.setup_files_and_datasets() as (files, [ds1, ds2]):
# Give the files an inconsistent attribute
for i, f in enumerate(files):
ds = open_dataset(f).load()
ds.attrs["test_dataset_attr"] = 10 + i
ds.close()
ds.to_netcdf(f)
with set_options(use_new_combine_kwarg_defaults=True):
with xr.open_mfdataset(files, combine="nested", concat_dim="t") as ds:
assert ds.test_dataset_attr == 10
def test_open_mfdataset_dataarray_attr_by_coords(self) -> None:
"""
Case when an attribute of a member DataArray differs across the multiple files
"""
with self.setup_files_and_datasets(new_combine_kwargs=True) as (
files,
[ds1, ds2],
):
# Give the files an inconsistent attribute
for i, f in enumerate(files):
ds = open_dataset(f).load()
ds["v1"].attrs["test_dataarray_attr"] = i
ds.close()
ds.to_netcdf(f)
with xr.open_mfdataset(
files, data_vars=None, combine="nested", concat_dim="t"
) as ds:
assert ds["v1"].test_dataarray_attr == 0
@pytest.mark.parametrize(
"combine, concat_dim", [("nested", "t"), ("by_coords", None)]
)
@pytest.mark.parametrize(
"kwargs",
[
{"data_vars": "all"},
{"data_vars": "minimal"},
{
"data_vars": "all",
"coords": "different",
"compat": "no_conflicts",
}, # old defaults
{
"data_vars": None,
"coords": "minimal",
"compat": "override",
}, # new defaults
{"data_vars": "different", "compat": "no_conflicts"},
{},
],
)
def test_open_mfdataset_exact_join_raises_error(
self, combine, concat_dim, kwargs
) -> None:
with self.setup_files_and_datasets(fuzz=0.1, new_combine_kwargs=True) as (
files,
_,
):
if combine == "by_coords":
files.reverse()
with pytest.raises(
ValueError, match="cannot align objects with join='exact'"
):
open_mfdataset(
files,
**kwargs,
combine=combine,
concat_dim=concat_dim,
join="exact",
)
def test_open_mfdataset_defaults_with_exact_join_warns_as_well_as_raising(
self,
) -> None:
with self.setup_files_and_datasets(fuzz=0.1, new_combine_kwargs=True) as (
files,
_,
):
files.reverse()
with pytest.raises(
ValueError, match="cannot align objects with join='exact'"
):
open_mfdataset(files, combine="by_coords")
def test_common_coord_when_datavars_all(self) -> None:
opt: Final = "all"
with self.setup_files_and_datasets() as (files, [ds1, ds2]):
# open the files with the data_var option
with open_mfdataset(
files, data_vars=opt, combine="nested", concat_dim="t"
) as ds:
coord_shape = ds[self.coord_name].shape
coord_shape1 = ds1[self.coord_name].shape
coord_shape2 = ds2[self.coord_name].shape
var_shape = ds[self.var_name].shape
assert var_shape == coord_shape
assert coord_shape1 != coord_shape
assert coord_shape2 != coord_shape
def test_common_coord_when_datavars_minimal(self) -> None:
opt: Final = "minimal"
with self.setup_files_and_datasets(new_combine_kwargs=True) as (
files,
[ds1, ds2],
):
# open the files using data_vars option
with open_mfdataset(
files, data_vars=opt, combine="nested", concat_dim="t"
) as ds:
coord_shape = ds[self.coord_name].shape
coord_shape1 = ds1[self.coord_name].shape
coord_shape2 = ds2[self.coord_name].shape
var_shape = ds[self.var_name].shape
assert var_shape != coord_shape
assert coord_shape1 == coord_shape
assert coord_shape2 == coord_shape
def test_invalid_data_vars_value_should_fail(self) -> None:
with self.setup_files_and_datasets() as (files, _):
with pytest.raises(ValueError):
with open_mfdataset(files, data_vars="minimum", combine="by_coords"): # type: ignore[arg-type]
pass
# test invalid coord parameter
with pytest.raises(ValueError):
with open_mfdataset(files, coords="minimum", combine="by_coords"):
pass
@pytest.mark.parametrize(
"combine, concat_dim", [("nested", "t"), ("by_coords", None)]
)
@pytest.mark.parametrize(
"kwargs", [{"data_vars": "different"}, {"coords": "different"}]
)
def test_open_mfdataset_warns_when_kwargs_set_to_different(
self, combine, concat_dim, kwargs
) -> None:
with self.setup_files_and_datasets(new_combine_kwargs=True) as (
files,
[ds1, ds2],
):
if combine == "by_coords":
files.reverse()
with pytest.raises(
ValueError, match="Previously the default was `compat='no_conflicts'`"
):
open_mfdataset(files, combine=combine, concat_dim=concat_dim, **kwargs)
with pytest.raises(
ValueError, match="Previously the default was `compat='equals'`"
):
xr.concat([ds1, ds2], dim="t", **kwargs)
with set_options(use_new_combine_kwarg_defaults=False):
expectation: contextlib.AbstractContextManager = (
pytest.warns(
FutureWarning,
match="will change from data_vars='all'",
)
if "data_vars" not in kwargs
else contextlib.nullcontext()
)
with pytest.warns(
FutureWarning,
match="will change from compat='equals'",
):
with expectation:
ds_expect = xr.concat([ds1, ds2], dim="t", **kwargs)
with pytest.warns(
FutureWarning, match="will change from compat='no_conflicts'"
):
with expectation:
with open_mfdataset(
files, combine=combine, concat_dim=concat_dim, **kwargs
) as ds:
assert_identical(ds, ds_expect)
@requires_dask
@requires_scipy
@requires_netCDF4
class TestDask(DatasetIOBase):
@contextlib.contextmanager
def create_store(self):
yield Dataset()
@contextlib.contextmanager
def roundtrip(
self, data, save_kwargs=None, open_kwargs=None, allow_cleanup_failure=False
):
yield data.chunk()
# Override methods in DatasetIOBase - not applicable to dask
def test_roundtrip_string_encoded_characters(self) -> None:
pass
def test_roundtrip_coordinates_with_space(self) -> None:
pass
def test_roundtrip_numpy_datetime_data(self) -> None:
# Override method in DatasetIOBase - remove not applicable
# save_kwargs
times = pd.to_datetime(["2000-01-01", "2000-01-02", "NaT"], unit="ns")
expected = Dataset({"t": ("t", times), "t0": times[0]})
with self.roundtrip(expected) as actual:
assert_identical(expected, actual)
def test_roundtrip_cftime_datetime_data(self) -> None:
# Override method in DatasetIOBase - remove not applicable
# save_kwargs
from xarray.tests.test_coding_times import _all_cftime_date_types
date_types = _all_cftime_date_types()
for date_type in date_types.values():
times = [date_type(1, 1, 1), date_type(1, 1, 2)]
expected = Dataset({"t": ("t", times), "t0": times[0]})
expected_decoded_t = np.array(times)
expected_decoded_t0 = np.array([date_type(1, 1, 1)])
with self.roundtrip(expected) as actual:
assert_array_equal(actual.t.values, expected_decoded_t)
assert_array_equal(actual.t0.values, expected_decoded_t0)
def test_write_store(self) -> None:
# Override method in DatasetIOBase - not applicable to dask
pass
def test_dataset_caching(self) -> None:
expected = Dataset({"foo": ("x", [5, 6, 7])})
with self.roundtrip(expected) as actual:
assert not actual.foo.variable._in_memory
_ = actual.foo.values # no caching
assert not actual.foo.variable._in_memory
def test_open_mfdataset(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
original.isel(x=slice(5)).to_netcdf(tmp1)
original.isel(x=slice(5, 10)).to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested"
) as actual:
assert isinstance(actual.foo.variable.data, da.Array)
assert actual.foo.variable.data.chunks == ((5, 5),)
assert_identical(original, actual)
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested", chunks={"x": 3}
) as actual:
assert actual.foo.variable.data.chunks == ((3, 2, 3, 2),)
with pytest.raises(OSError, match=r"no files to open"):
open_mfdataset("foo-bar-baz-*.nc")
with pytest.raises(ValueError, match=r"wild-card"):
open_mfdataset("http://some/remote/uri")
@requires_fsspec
def test_open_mfdataset_no_files(self) -> None:
pytest.importorskip("aiobotocore")
# glob is attempted as of #4823, but finds no files
with pytest.raises(OSError, match=r"no files"):
open_mfdataset("http://some/remote/uri", engine="zarr")
def test_open_mfdataset_2d(self) -> None:
original = Dataset({"foo": (["x", "y"], np.random.randn(10, 8))})
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
with create_tmp_file() as tmp3:
with create_tmp_file() as tmp4:
original.isel(x=slice(5), y=slice(4)).to_netcdf(tmp1)
original.isel(x=slice(5, 10), y=slice(4)).to_netcdf(tmp2)
original.isel(x=slice(5), y=slice(4, 8)).to_netcdf(tmp3)
original.isel(x=slice(5, 10), y=slice(4, 8)).to_netcdf(tmp4)
with open_mfdataset(
[[tmp1, tmp2], [tmp3, tmp4]],
combine="nested",
concat_dim=["y", "x"],
) as actual:
assert isinstance(actual.foo.variable.data, da.Array)
assert actual.foo.variable.data.chunks == ((5, 5), (4, 4))
assert_identical(original, actual)
with open_mfdataset(
[[tmp1, tmp2], [tmp3, tmp4]],
combine="nested",
concat_dim=["y", "x"],
chunks={"x": 3, "y": 2},
) as actual:
assert actual.foo.variable.data.chunks == (
(3, 2, 3, 2),
(2, 2, 2, 2),
)
def test_open_mfdataset_pathlib(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_file() as tmps1:
with create_tmp_file() as tmps2:
tmp1 = Path(tmps1)
tmp2 = Path(tmps2)
original.isel(x=slice(5)).to_netcdf(tmp1)
original.isel(x=slice(5, 10)).to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested"
) as actual:
assert_identical(original, actual)
def test_open_mfdataset_2d_pathlib(self) -> None:
original = Dataset({"foo": (["x", "y"], np.random.randn(10, 8))})
with create_tmp_file() as tmps1:
with create_tmp_file() as tmps2:
with create_tmp_file() as tmps3:
with create_tmp_file() as tmps4:
tmp1 = Path(tmps1)
tmp2 = Path(tmps2)
tmp3 = Path(tmps3)
tmp4 = Path(tmps4)
original.isel(x=slice(5), y=slice(4)).to_netcdf(tmp1)
original.isel(x=slice(5, 10), y=slice(4)).to_netcdf(tmp2)
original.isel(x=slice(5), y=slice(4, 8)).to_netcdf(tmp3)
original.isel(x=slice(5, 10), y=slice(4, 8)).to_netcdf(tmp4)
with open_mfdataset(
[[tmp1, tmp2], [tmp3, tmp4]],
combine="nested",
concat_dim=["y", "x"],
) as actual:
assert_identical(original, actual)
def test_open_mfdataset_2(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
original.isel(x=slice(5)).to_netcdf(tmp1)
original.isel(x=slice(5, 10)).to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested"
) as actual:
assert_identical(original, actual)
def test_open_mfdataset_with_ignore(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_files(2) as (tmp1, tmp2):
ds1 = original.isel(x=slice(5))
ds2 = original.isel(x=slice(5, 10))
ds1.to_netcdf(tmp1)
ds2.to_netcdf(tmp2)
with open_mfdataset(
[tmp1, "non-existent-file.nc", tmp2],
concat_dim="x",
combine="nested",
errors="ignore",
) as actual:
assert_identical(original, actual)
def test_open_mfdataset_with_warn(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with pytest.warns(UserWarning, match="Ignoring."):
with create_tmp_files(2) as (tmp1, tmp2):
ds1 = original.isel(x=slice(5))
ds2 = original.isel(x=slice(5, 10))
ds1.to_netcdf(tmp1)
ds2.to_netcdf(tmp2)
with open_mfdataset(
[tmp1, "non-existent-file.nc", tmp2],
concat_dim="x",
combine="nested",
errors="warn",
) as actual:
assert_identical(original, actual)
def test_open_mfdataset_2d_with_ignore(self) -> None:
original = Dataset({"foo": (["x", "y"], np.random.randn(10, 8))})
with create_tmp_files(4) as (tmp1, tmp2, tmp3, tmp4):
original.isel(x=slice(5), y=slice(4)).to_netcdf(tmp1)
original.isel(x=slice(5, 10), y=slice(4)).to_netcdf(tmp2)
original.isel(x=slice(5), y=slice(4, 8)).to_netcdf(tmp3)
original.isel(x=slice(5, 10), y=slice(4, 8)).to_netcdf(tmp4)
with open_mfdataset(
[[tmp1, tmp2], ["non-existent-file.nc", tmp3, tmp4]],
combine="nested",
concat_dim=["y", "x"],
errors="ignore",
) as actual:
assert_identical(original, actual)
def test_open_mfdataset_2d_with_warn(self) -> None:
original = Dataset({"foo": (["x", "y"], np.random.randn(10, 8))})
with pytest.warns(UserWarning, match="Ignoring."):
with create_tmp_files(4) as (tmp1, tmp2, tmp3, tmp4):
original.isel(x=slice(5), y=slice(4)).to_netcdf(tmp1)
original.isel(x=slice(5, 10), y=slice(4)).to_netcdf(tmp2)
original.isel(x=slice(5), y=slice(4, 8)).to_netcdf(tmp3)
original.isel(x=slice(5, 10), y=slice(4, 8)).to_netcdf(tmp4)
with open_mfdataset(
[[tmp1, tmp2, "non-existent-file.nc"], [tmp3, tmp4]],
combine="nested",
concat_dim=["y", "x"],
errors="warn",
) as actual:
assert_identical(original, actual)
def test_attrs_mfdataset(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
ds1 = original.isel(x=slice(5))
ds2 = original.isel(x=slice(5, 10))
ds1.attrs["test1"] = "foo"
ds2.attrs["test2"] = "bar"
ds1.to_netcdf(tmp1)
ds2.to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested"
) as actual:
# presumes that attributes inherited from
# first dataset loaded
assert actual.test1 == ds1.test1
# attributes from ds2 are not retained, e.g.,
with pytest.raises(AttributeError, match=r"no attribute"):
_ = actual.test2
def test_open_mfdataset_attrs_file(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_files(2) as (tmp1, tmp2):
ds1 = original.isel(x=slice(5))
ds2 = original.isel(x=slice(5, 10))
ds1.attrs["test1"] = "foo"
ds2.attrs["test2"] = "bar"
ds1.to_netcdf(tmp1)
ds2.to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested", attrs_file=tmp2
) as actual:
# attributes are inherited from the master file
assert actual.attrs["test2"] == ds2.attrs["test2"]
# attributes from ds1 are not retained, e.g.,
assert "test1" not in actual.attrs
def test_open_mfdataset_attrs_file_path(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_files(2) as (tmps1, tmps2):
tmp1 = Path(tmps1)
tmp2 = Path(tmps2)
ds1 = original.isel(x=slice(5))
ds2 = original.isel(x=slice(5, 10))
ds1.attrs["test1"] = "foo"
ds2.attrs["test2"] = "bar"
ds1.to_netcdf(tmp1)
ds2.to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested", attrs_file=tmp2
) as actual:
# attributes are inherited from the master file
assert actual.attrs["test2"] == ds2.attrs["test2"]
# attributes from ds1 are not retained, e.g.,
assert "test1" not in actual.attrs
def test_open_mfdataset_auto_combine(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10)), "x": np.arange(10)})
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
original.isel(x=slice(5)).to_netcdf(tmp1)
original.isel(x=slice(5, 10)).to_netcdf(tmp2)
with open_mfdataset([tmp2, tmp1], combine="by_coords") as actual:
assert_identical(original, actual)
def test_open_mfdataset_raise_on_bad_combine_args(self) -> None:
# Regression test for unhelpful error shown in #5230
original = Dataset({"foo": ("x", np.random.randn(10)), "x": np.arange(10)})
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
original.isel(x=slice(5)).to_netcdf(tmp1)
original.isel(x=slice(5, 10)).to_netcdf(tmp2)
with pytest.raises(ValueError, match="`concat_dim` has no effect"):
open_mfdataset([tmp1, tmp2], concat_dim="x")
def test_encoding_mfdataset(self) -> None:
original = Dataset(
{
"foo": ("t", np.random.randn(10)),
"t": ("t", pd.date_range(start="2010-01-01", periods=10, freq="1D")),
}
)
original.t.encoding["units"] = "days since 2010-01-01"
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
ds1 = original.isel(t=slice(5))
ds2 = original.isel(t=slice(5, 10))
ds1.t.encoding["units"] = "days since 2010-01-01"
ds2.t.encoding["units"] = "days since 2000-01-01"
ds1.to_netcdf(tmp1)
ds2.to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], combine="nested", concat_dim="t"
) as actual:
assert actual.t.encoding["units"] == original.t.encoding["units"]
assert actual.t.encoding["units"] == ds1.t.encoding["units"]
assert actual.t.encoding["units"] != ds2.t.encoding["units"]
def test_encoding_mfdataset_new_defaults(self) -> None:
original = Dataset(
{
"foo": ("t", np.random.randn(10)),
"t": ("t", pd.date_range(start="2010-01-01", periods=10, freq="1D")),
}
)
original.t.encoding["units"] = "days since 2010-01-01"
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
ds1 = original.isel(t=slice(5))
ds2 = original.isel(t=slice(5, 10))
ds1.t.encoding["units"] = "days since 2010-01-01"
ds2.t.encoding["units"] = "days since 2000-01-01"
ds1.to_netcdf(tmp1)
ds2.to_netcdf(tmp2)
for setting in [True, False]:
with set_options(use_new_combine_kwarg_defaults=setting):
with open_mfdataset(
[tmp1, tmp2], combine="nested", concat_dim="t"
) as old:
assert (
old.t.encoding["units"] == original.t.encoding["units"]
)
assert old.t.encoding["units"] == ds1.t.encoding["units"]
assert old.t.encoding["units"] != ds2.t.encoding["units"]
with set_options(use_new_combine_kwarg_defaults=True):
with pytest.raises(
AlignmentError, match="If you are intending to concatenate"
):
open_mfdataset([tmp1, tmp2], combine="nested")
def test_preprocess_mfdataset(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_file() as tmp:
original.to_netcdf(tmp)
def preprocess(ds):
return ds.assign_coords(z=0)
expected = preprocess(original)
with open_mfdataset(
tmp, preprocess=preprocess, combine="by_coords"
) as actual:
assert_identical(expected, actual)
def test_save_mfdataset_roundtrip(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
datasets = [original.isel(x=slice(5)), original.isel(x=slice(5, 10))]
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
save_mfdataset(datasets, [tmp1, tmp2])
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested"
) as actual:
assert_identical(actual, original)
def test_save_mfdataset_invalid(self) -> None:
ds = Dataset()
with pytest.raises(ValueError, match=r"cannot use mode"):
save_mfdataset([ds, ds], ["same", "same"])
with pytest.raises(ValueError, match=r"same length"):
save_mfdataset([ds, ds], ["only one path"])
def test_save_mfdataset_invalid_dataarray(self) -> None:
# regression test for GH1555
da = DataArray([1, 2])
with pytest.raises(TypeError, match=r"supports writing Dataset"):
save_mfdataset([da], ["dataarray"])
def test_save_mfdataset_pathlib_roundtrip(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
datasets = [original.isel(x=slice(5)), original.isel(x=slice(5, 10))]
with create_tmp_file() as tmps1:
with create_tmp_file() as tmps2:
tmp1 = Path(tmps1)
tmp2 = Path(tmps2)
save_mfdataset(datasets, [tmp1, tmp2])
with open_mfdataset(
[tmp1, tmp2], concat_dim="x", combine="nested"
) as actual:
assert_identical(actual, original)
def test_save_mfdataset_pass_kwargs(self) -> None:
# create a timeseries to store in a netCDF file
times = [0, 1]
time = xr.DataArray(times, dims=("time",))
# create a simple dataset to write using save_mfdataset
test_ds = xr.Dataset()
test_ds["time"] = time
# make sure the times are written as double and
# turn off fill values
encoding = dict(time=dict(dtype="double"))
unlimited_dims = ["time"]
# set the output file name
output_path = "test.nc"
# attempt to write the dataset with the encoding and unlimited args
# passed through
xr.save_mfdataset(
[test_ds], [output_path], encoding=encoding, unlimited_dims=unlimited_dims
)
def test_open_and_do_math(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_file() as tmp:
original.to_netcdf(tmp)
with open_mfdataset(tmp, combine="by_coords") as ds:
actual = 1.0 * ds
assert_allclose(original, actual, decode_bytes=False)
@pytest.mark.parametrize(
"kwargs",
[pytest.param({"concat_dim": None}, id="none"), pytest.param({}, id="default")],
)
def test_open_mfdataset_concat_dim(self, kwargs) -> None:
with set_options(use_new_combine_kwarg_defaults=True):
with create_tmp_file() as tmp1:
with create_tmp_file() as tmp2:
data = Dataset({"x": 0})
data.to_netcdf(tmp1)
Dataset({"x": np.nan}).to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], **kwargs, combine="nested"
) as actual:
assert_identical(data, actual)
def test_open_dataset(self) -> None:
original = Dataset({"foo": ("x", np.random.randn(10))})
with create_tmp_file() as tmp:
original.to_netcdf(tmp)
with open_dataset(tmp, chunks={"x": 5}) as actual:
assert isinstance(actual.foo.variable.data, da.Array)
assert actual.foo.variable.data.chunks == ((5, 5),)
assert_identical(original, actual)
with open_dataset(tmp, chunks=5) as actual:
assert_identical(original, actual)
with open_dataset(tmp) as actual:
assert isinstance(actual.foo.variable.data, np.ndarray)
assert_identical(original, actual)
def test_open_single_dataset(self) -> None:
# Test for issue GH #1988. This makes sure that the
# concat_dim is utilized when specified in open_mfdataset().
rnddata = np.random.randn(10)
original = Dataset({"foo": ("x", rnddata)})
dim = DataArray([100], name="baz", dims="baz")
expected = Dataset(
{"foo": (("baz", "x"), rnddata[np.newaxis, :])}, {"baz": [100]}
)
with create_tmp_file() as tmp:
original.to_netcdf(tmp)
with open_mfdataset(
[tmp], concat_dim=dim, data_vars="all", combine="nested"
) as actual:
assert_identical(expected, actual)
def test_open_multi_dataset(self) -> None:
# Test for issue GH #1988 and #2647. This makes sure that the
# concat_dim is utilized when specified in open_mfdataset().
# The additional wrinkle is to ensure that a length greater
# than one is tested as well due to numpy's implicit casting
# of 1-length arrays to booleans in tests, which allowed
# #2647 to still pass the test_open_single_dataset(),
# which is itself still needed as-is because the original
# bug caused one-length arrays to not be used correctly
# in concatenation.
rnddata = np.random.randn(10)
original = Dataset({"foo": ("x", rnddata)})
dim = DataArray([100, 150], name="baz", dims="baz")
expected = Dataset(
{"foo": (("baz", "x"), np.tile(rnddata[np.newaxis, :], (2, 1)))},
{"baz": [100, 150]},
)
with create_tmp_file() as tmp1, create_tmp_file() as tmp2:
original.to_netcdf(tmp1)
original.to_netcdf(tmp2)
with open_mfdataset(
[tmp1, tmp2], concat_dim=dim, data_vars="all", combine="nested"
) as actual:
assert_identical(expected, actual)
# Flaky test. Very open to contributions on fixing this
@pytest.mark.flaky
def test_dask_roundtrip(self) -> None:
with create_tmp_file() as tmp:
data = create_test_data()
data.to_netcdf(tmp)
chunks = {"dim1": 4, "dim2": 4, "dim3": 4, "time": 10}
with open_dataset(tmp, chunks=chunks) as dask_ds:
assert_identical(data, dask_ds)
with create_tmp_file() as tmp2:
dask_ds.to_netcdf(tmp2)
with open_dataset(tmp2) as on_disk:
assert_identical(data, on_disk)
def test_deterministic_names(self) -> None:
with create_tmp_file() as tmp:
data = create_test_data()
data.to_netcdf(tmp)
with open_mfdataset(tmp, combine="by_coords") as ds:
original_names = {k: v.data.name for k, v in ds.data_vars.items()}
with open_mfdataset(tmp, combine="by_coords") as ds:
repeat_names = {k: v.data.name for k, v in ds.data_vars.items()}
for var_name, dask_name in original_names.items():
assert var_name in dask_name
assert dask_name[:13] == "open_dataset-"
assert original_names == repeat_names
def test_dataarray_compute(self) -> None:
# Test DataArray.compute() on dask backend.
# The test for Dataset.compute() is already in DatasetIOBase;
# however dask is the only tested backend which supports DataArrays
actual = DataArray([1, 2]).chunk()
computed = actual.compute()
assert not actual._in_memory
assert computed._in_memory
assert_allclose(actual, computed, decode_bytes=False)
def test_save_mfdataset_compute_false_roundtrip(self) -> None:
from dask.delayed import Delayed
original = Dataset({"foo": ("x", np.random.randn(10))}).chunk()
datasets = [original.isel(x=slice(5)), original.isel(x=slice(5, 10))]
with create_tmp_file(allow_cleanup_failure=ON_WINDOWS) as tmp1:
with create_tmp_file(allow_cleanup_failure=ON_WINDOWS) as tmp2:
delayed_obj = save_mfdataset(
datasets, [tmp1, tmp2], engine=self.engine, compute=False
)
assert isinstance(delayed_obj, Delayed)
delayed_obj.compute()
with open_mfdataset(
[tmp1, tmp2], combine="nested", concat_dim="x"
) as actual:
assert_identical(actual, original)
def test_load_dataset(self) -> None:
with create_tmp_file() as tmp:
original = Dataset({"foo": ("x", np.random.randn(10))})
original.to_netcdf(tmp)
ds = load_dataset(tmp)
# this would fail if we used open_dataset instead of load_dataset
ds.to_netcdf(tmp)
def test_load_dataarray(self) -> None:
with create_tmp_file() as tmp:
original = Dataset({"foo": ("x", np.random.randn(10))})
original.to_netcdf(tmp)
ds = load_dataarray(tmp)
# this would fail if we used open_dataarray instead of
# load_dataarray
ds.to_netcdf(tmp)
@pytest.mark.skipif(
ON_WINDOWS,
reason="counting number of tasks in graph fails on windows for some reason",
)
def test_inline_array(self) -> None:
with create_tmp_file() as tmp:
original = Dataset({"foo": ("x", np.random.randn(10))})
original.to_netcdf(tmp)
chunks = {"time": 10}
def num_graph_nodes(obj):
return len(obj.__dask_graph__())
with (
open_dataset(tmp, inline_array=False, chunks=chunks) as not_inlined_ds,
open_dataset(tmp, inline_array=True, chunks=chunks) as inlined_ds,
):
assert num_graph_nodes(inlined_ds) < num_graph_nodes(not_inlined_ds)
with (
open_dataarray(
tmp, inline_array=False, chunks=chunks
) as not_inlined_da,
open_dataarray(tmp, inline_array=True, chunks=chunks) as inlined_da,
):
assert num_graph_nodes(inlined_da) < num_graph_nodes(not_inlined_da)
@requires_scipy_or_netCDF4
@requires_pydap
@pytest.mark.filterwarnings("ignore:The binary mode of fromstring is deprecated")
class TestPydap:
def convert_to_pydap_dataset(self, original):
from pydap.model import BaseType, DatasetType
ds = DatasetType("bears", **original.attrs)
for key, var in original.data_vars.items():
ds[key] = BaseType(
key, var.values, dtype=var.values.dtype.kind, dims=var.dims, **var.attrs
)
# check all dims are stored in ds
for d in original.coords:
ds[d] = BaseType(d, original[d].values, dims=(d,), **original[d].attrs)
return ds
@contextlib.contextmanager
def create_datasets(self, **kwargs):
with open_example_dataset("bears.nc") as expected:
# print("QQ0:", expected["bears"].load())
pydap_ds = self.convert_to_pydap_dataset(expected)
actual = open_dataset(PydapDataStore(pydap_ds))
# netcdf converts string to byte not unicode
# fixed in pydap 3.5.6. https://github.com/pydap/pydap/issues/510
actual["bears"].values = actual["bears"].values.astype("S")
yield actual, expected
def test_cmp_local_file(self) -> None:
with self.create_datasets() as (actual, expected):
assert_equal(actual, expected)
# global attributes should be global attributes on the dataset
assert "NC_GLOBAL" not in actual.attrs
assert "history" in actual.attrs
# we don't check attributes exactly with assertDatasetIdentical()
# because the test DAP server seems to insert some extra
# attributes not found in the netCDF file.
assert actual.attrs.keys() == expected.attrs.keys()
with self.create_datasets() as (actual, expected):
assert_equal(actual[{"l": 2}], expected[{"l": 2}])
with self.create_datasets() as (actual, expected):
# always return arrays and not scalars
# scalars will be promoted to unicode for numpy >= 2.3.0
assert_equal(actual.isel(i=[0], j=[-1]), expected.isel(i=[0], j=[-1]))
with self.create_datasets() as (actual, expected):
assert_equal(actual.isel(j=slice(1, 2)), expected.isel(j=slice(1, 2)))
with self.create_datasets() as (actual, expected):
indexers = {"i": [1, 0, 0], "j": [1, 2, 0, 1]}
assert_equal(actual.isel(**indexers), expected.isel(**indexers))
with self.create_datasets() as (actual, expected):
indexers2 = {
"i": DataArray([0, 1, 0], dims="a"),
"j": DataArray([0, 2, 1], dims="a"),
}
assert_equal(actual.isel(**indexers2), expected.isel(**indexers2))
def test_compatible_to_netcdf(self) -> None:
# make sure it can be saved as a netcdf
with self.create_datasets() as (actual, expected):
with create_tmp_file() as tmp_file:
actual.to_netcdf(tmp_file)
with open_dataset(tmp_file) as actual2:
assert_equal(actual2, expected)
@requires_dask
def test_dask(self) -> None:
with self.create_datasets(chunks={"j": 2}) as (actual, expected):
assert_equal(actual, expected)
@network
@requires_scipy_or_netCDF4
@requires_pydap
class TestPydapOnline(TestPydap):
@contextlib.contextmanager
def create_dap2_datasets(self, **kwargs):
# in pydap 3.5.0, urls defaults to dap2.
url = "http://test.opendap.org/opendap/data/nc/bears.nc"
actual = open_dataset(url, engine="pydap", **kwargs)
# pydap <3.5.6 converts to unicode dtype=|U. Not what
# xarray expects. Thus force to bytes dtype. pydap >=3.5.6
# does not convert to unicode. https://github.com/pydap/pydap/issues/510
actual["bears"].values = actual["bears"].values.astype("S")
with open_example_dataset("bears.nc") as expected:
yield actual, expected
def output_grid_deprecation_warning_dap2dataset(self):
with pytest.warns(DeprecationWarning, match="`output_grid` is deprecated"):
with self.create_dap2_datasets(output_grid=True) as (actual, expected):
assert_equal(actual, expected)
def create_dap4_dataset(self, **kwargs):
url = "dap4://test.opendap.org/opendap/data/nc/bears.nc"
actual = open_dataset(url, engine="pydap", **kwargs)
with open_example_dataset("bears.nc") as expected:
# workaround to restore string which is converted to byte
# only needed for pydap <3.5.6 https://github.com/pydap/pydap/issues/510
expected["bears"].values = expected["bears"].values.astype("S")
yield actual, expected
def test_session(self) -> None:
from requests import Session
session = Session() # blank requests.Session object
with mock.patch("pydap.client.open_url") as mock_func:
xr.backends.PydapDataStore.open("http://test.url", session=session)
mock_func.assert_called_with(
url="http://test.url",
application=None,
session=session,
output_grid=False,
timeout=120,
verify=True,
user_charset=None,
)
class TestEncodingInvalid:
def test_extract_nc4_variable_encoding(self) -> None:
var = xr.Variable(("x",), [1, 2, 3], {}, {"foo": "bar"})
with pytest.raises(ValueError, match=r"unexpected encoding"):
_extract_nc4_variable_encoding(var, raise_on_invalid=True)
var = xr.Variable(("x",), [1, 2, 3], {}, {"chunking": (2, 1)})
encoding = _extract_nc4_variable_encoding(var)
assert {} == encoding
# regression test
var = xr.Variable(("x",), [1, 2, 3], {}, {"shuffle": True})
encoding = _extract_nc4_variable_encoding(var, raise_on_invalid=True)
assert {"shuffle": True} == encoding
# Variables with unlim dims must be chunked on output.
var = xr.Variable(("x",), [1, 2, 3], {}, {"contiguous": True})
encoding = _extract_nc4_variable_encoding(var, unlimited_dims=("x",))
assert {} == encoding
@requires_netCDF4
def test_extract_nc4_variable_encoding_netcdf4(self):
# New netCDF4 1.6.0 compression argument.
var = xr.Variable(("x",), [1, 2, 3], {}, {"compression": "szlib"})
_extract_nc4_variable_encoding(var, backend="netCDF4", raise_on_invalid=True)
@pytest.mark.xfail
def test_extract_h5nc_encoding(self) -> None:
# not supported with h5netcdf (yet)
var = xr.Variable(("x",), [1, 2, 3], {}, {"least_significant_digit": 2})
with pytest.raises(ValueError, match=r"unexpected encoding"):
_extract_nc4_variable_encoding(var, raise_on_invalid=True)
class MiscObject:
pass
@requires_netCDF4
class TestValidateAttrs:
def test_validating_attrs(self) -> None:
def new_dataset():
return Dataset({"data": ("y", np.arange(10.0))}, {"y": np.arange(10)})
def new_dataset_and_dataset_attrs():
ds = new_dataset()
return ds, ds.attrs
def new_dataset_and_data_attrs():
ds = new_dataset()
return ds, ds.data.attrs
def new_dataset_and_coord_attrs():
ds = new_dataset()
return ds, ds.coords["y"].attrs
for new_dataset_and_attrs in [
new_dataset_and_dataset_attrs,
new_dataset_and_data_attrs,
new_dataset_and_coord_attrs,
]:
ds, attrs = new_dataset_and_attrs()
attrs[123] = "test"
with pytest.raises(TypeError, match=r"Invalid name for attr: 123"):
ds.to_netcdf("test.nc")
ds, attrs = new_dataset_and_attrs()
attrs[MiscObject()] = "test"
with pytest.raises(TypeError, match=r"Invalid name for attr: "):
ds.to_netcdf("test.nc")
ds, attrs = new_dataset_and_attrs()
attrs[""] = "test"
with pytest.raises(ValueError, match=r"Invalid name for attr '':"):
ds.to_netcdf("test.nc")
# This one should work
ds, attrs = new_dataset_and_attrs()
attrs["test"] = "test"
with create_tmp_file() as tmp_file:
ds.to_netcdf(tmp_file)
ds, attrs = new_dataset_and_attrs()
attrs["test"] = {"a": 5}
with pytest.raises(TypeError, match=r"Invalid value for attr 'test'"):
ds.to_netcdf("test.nc")
ds, attrs = new_dataset_and_attrs()
attrs["test"] = MiscObject()
with pytest.raises(TypeError, match=r"Invalid value for attr 'test'"):
ds.to_netcdf("test.nc")
ds, attrs = new_dataset_and_attrs()
attrs["test"] = 5
with create_tmp_file() as tmp_file:
ds.to_netcdf(tmp_file)
ds, attrs = new_dataset_and_attrs()
attrs["test"] = 3.14
with create_tmp_file() as tmp_file:
ds.to_netcdf(tmp_file)
ds, attrs = new_dataset_and_attrs()
attrs["test"] = [1, 2, 3, 4]
with create_tmp_file() as tmp_file:
ds.to_netcdf(tmp_file)
ds, attrs = new_dataset_and_attrs()
attrs["test"] = (1.9, 2.5)
with create_tmp_file() as tmp_file:
ds.to_netcdf(tmp_file)
ds, attrs = new_dataset_and_attrs()
attrs["test"] = np.arange(5)
with create_tmp_file() as tmp_file:
ds.to_netcdf(tmp_file)
ds, attrs = new_dataset_and_attrs()
attrs["test"] = "This is a string"
with create_tmp_file() as tmp_file:
ds.to_netcdf(tmp_file)
ds, attrs = new_dataset_and_attrs()
attrs["test"] = ""
with create_tmp_file() as tmp_file:
ds.to_netcdf(tmp_file)
@requires_scipy_or_netCDF4
class TestDataArrayToNetCDF:
def test_dataarray_to_netcdf_no_name(self) -> None:
original_da = DataArray(np.arange(12).reshape((3, 4)))
with create_tmp_file() as tmp:
original_da.to_netcdf(tmp)
with open_dataarray(tmp) as loaded_da:
assert_identical(original_da, loaded_da)
def test_dataarray_to_netcdf_with_name(self) -> None:
original_da = DataArray(np.arange(12).reshape((3, 4)), name="test")
with create_tmp_file() as tmp:
original_da.to_netcdf(tmp)
with open_dataarray(tmp) as loaded_da:
assert_identical(original_da, loaded_da)
def test_dataarray_to_netcdf_coord_name_clash(self) -> None:
original_da = DataArray(
np.arange(12).reshape((3, 4)), dims=["x", "y"], name="x"
)
with create_tmp_file() as tmp:
original_da.to_netcdf(tmp)
with open_dataarray(tmp) as loaded_da:
assert_identical(original_da, loaded_da)
def test_open_dataarray_options(self) -> None:
data = DataArray(np.arange(5), coords={"y": ("x", range(5))}, dims=["x"])
with create_tmp_file() as tmp:
data.to_netcdf(tmp)
expected = data.drop_vars("y")
with open_dataarray(tmp, drop_variables=["y"]) as loaded:
assert_identical(expected, loaded)
@requires_scipy
def test_dataarray_to_netcdf_return_bytes(self) -> None:
# regression test for GH1410
data = xr.DataArray([1, 2, 3])
with pytest.warns(
FutureWarning,
match=re.escape("return value of to_netcdf() without a target"),
):
output = data.to_netcdf(engine="scipy")
assert isinstance(output, bytes)
def test_dataarray_to_netcdf_no_name_pathlib(self) -> None:
original_da = DataArray(np.arange(12).reshape((3, 4)))
with create_tmp_file() as tmps:
tmp = Path(tmps)
original_da.to_netcdf(tmp)
with open_dataarray(tmp) as loaded_da:
assert_identical(original_da, loaded_da)
@requires_zarr
class TestDataArrayToZarr:
def skip_if_zarr_python_3_and_zip_store(self, store) -> None:
if has_zarr_v3 and isinstance(store, zarr.storage.ZipStore):
pytest.skip(
reason="zarr-python 3.x doesn't support reopening ZipStore with a new mode."
)
def test_dataarray_to_zarr_no_name(self, tmp_store) -> None:
self.skip_if_zarr_python_3_and_zip_store(tmp_store)
original_da = DataArray(np.arange(12).reshape((3, 4)))
original_da.to_zarr(tmp_store)
with open_dataarray(tmp_store, engine="zarr") as loaded_da:
assert_identical(original_da, loaded_da)
def test_dataarray_to_zarr_with_name(self, tmp_store) -> None:
self.skip_if_zarr_python_3_and_zip_store(tmp_store)
original_da = DataArray(np.arange(12).reshape((3, 4)), name="test")
original_da.to_zarr(tmp_store)
with open_dataarray(tmp_store, engine="zarr") as loaded_da:
assert_identical(original_da, loaded_da)
def test_dataarray_to_zarr_coord_name_clash(self, tmp_store) -> None:
self.skip_if_zarr_python_3_and_zip_store(tmp_store)
original_da = DataArray(
np.arange(12).reshape((3, 4)), dims=["x", "y"], name="x"
)
original_da.to_zarr(tmp_store)
with open_dataarray(tmp_store, engine="zarr") as loaded_da:
assert_identical(original_da, loaded_da)
def test_open_dataarray_options(self, tmp_store) -> None:
self.skip_if_zarr_python_3_and_zip_store(tmp_store)
data = DataArray(np.arange(5), coords={"y": ("x", range(1, 6))}, dims=["x"])
data.to_zarr(tmp_store)
expected = data.drop_vars("y")
with open_dataarray(tmp_store, engine="zarr", drop_variables=["y"]) as loaded:
assert_identical(expected, loaded)
@requires_dask
def test_dataarray_to_zarr_compute_false(self, tmp_store) -> None:
from dask.delayed import Delayed
skip_if_zarr_format_3(tmp_store)
original_da = DataArray(np.arange(12).reshape((3, 4)))
output = original_da.to_zarr(tmp_store, compute=False)
assert isinstance(output, Delayed)
output.compute()
with open_dataarray(tmp_store, engine="zarr") as loaded_da:
assert_identical(original_da, loaded_da)
@requires_dask
def test_dataarray_to_zarr_align_chunks_true(self, tmp_store) -> None:
# TODO: Improve data integrity checks when using Dask.
# Detecting automatic alignment issues in Dask can be tricky,
# as unintended misalignment might lead to subtle data corruption.
# For now, ensure that the parameter is present, but explore
# more robust verification methods to confirm data consistency.
skip_if_zarr_format_3(tmp_store)
arr = DataArray(
np.arange(4), dims=["a"], coords={"a": np.arange(4)}, name="foo"
).chunk(a=(2, 1, 1))
arr.to_zarr(
tmp_store,
align_chunks=True,
encoding={"foo": {"chunks": (3,)}},
)
with open_dataarray(tmp_store, engine="zarr") as loaded_da:
assert_identical(arr, loaded_da)
@requires_scipy_or_netCDF4
def test_no_warning_from_dask_effective_get() -> None:
with create_tmp_file() as tmpfile:
with assert_no_warnings():
ds = Dataset()
ds.to_netcdf(tmpfile)
@requires_scipy_or_netCDF4
def test_source_encoding_always_present() -> None:
# Test for GH issue #2550.
rnddata = np.random.randn(10)
original = Dataset({"foo": ("x", rnddata)})
with create_tmp_file() as tmp:
original.to_netcdf(tmp)
with open_dataset(tmp) as ds:
assert ds.encoding["source"] == tmp
@requires_scipy_or_netCDF4
def test_source_encoding_always_present_with_pathlib() -> None:
# Test for GH issue #5888.
rnddata = np.random.randn(10)
original = Dataset({"foo": ("x", rnddata)})
with create_tmp_file() as tmp:
original.to_netcdf(tmp)
with open_dataset(Path(tmp)) as ds:
assert ds.encoding["source"] == tmp
@requires_h5netcdf
@requires_fsspec
def test_source_encoding_always_present_with_fsspec() -> None:
import fsspec
rnddata = np.random.randn(10)
original = Dataset({"foo": ("x", rnddata)})
with create_tmp_file() as tmp:
original.to_netcdf(tmp)
fs = fsspec.filesystem("file")
with fs.open(tmp) as f, open_dataset(f) as ds:
assert ds.encoding["source"] == tmp
with fs.open(tmp) as f, open_mfdataset([f]) as ds:
assert "foo" in ds
def _assert_no_dates_out_of_range_warning(record):
undesired_message = "dates out of range"
for warning in record:
assert undesired_message not in str(warning.message)
@requires_scipy_or_netCDF4
@pytest.mark.parametrize("calendar", _STANDARD_CALENDARS)
def test_use_cftime_standard_calendar_default_in_range(calendar) -> None:
x = [0, 1]
time = [0, 720]
units_date = "2000-01-01"
units = "days since 2000-01-01"
original = DataArray(x, [("time", time)], name="x").to_dataset()
for v in ["x", "time"]:
original[v].attrs["units"] = units
original[v].attrs["calendar"] = calendar
x_timedeltas = np.array(x).astype("timedelta64[D]")
time_timedeltas = np.array(time).astype("timedelta64[D]")
decoded_x = np.datetime64(units_date, "ns") + x_timedeltas
decoded_time = np.datetime64(units_date, "ns") + time_timedeltas
expected_x = DataArray(decoded_x, [("time", decoded_time)], name="x")
expected_time = DataArray(decoded_time, [("time", decoded_time)], name="time")
with create_tmp_file() as tmp_file:
original.to_netcdf(tmp_file)
with warnings.catch_warnings(record=True) as record:
with open_dataset(tmp_file) as ds:
assert_identical(expected_x, ds.x)
assert_identical(expected_time, ds.time)
_assert_no_dates_out_of_range_warning(record)
@requires_cftime
@requires_scipy_or_netCDF4
@pytest.mark.parametrize("calendar", ["standard", "gregorian"])
def test_use_cftime_standard_calendar_default_out_of_range(calendar) -> None:
# todo: check, if we still need to test for two dates
import cftime
x = [0, 1]
time = [0, 720]
units = "days since 1582-01-01"
original = DataArray(x, [("time", time)], name="x").to_dataset()
for v in ["x", "time"]:
original[v].attrs["units"] = units
original[v].attrs["calendar"] = calendar
decoded_x = cftime.num2date(x, units, calendar, only_use_cftime_datetimes=True)
decoded_time = cftime.num2date(
time, units, calendar, only_use_cftime_datetimes=True
)
expected_x = DataArray(decoded_x, [("time", decoded_time)], name="x")
expected_time = DataArray(decoded_time, [("time", decoded_time)], name="time")
with create_tmp_file() as tmp_file:
original.to_netcdf(tmp_file)
with pytest.warns(SerializationWarning):
with open_dataset(tmp_file) as ds:
assert_identical(expected_x, ds.x)
assert_identical(expected_time, ds.time)
@requires_cftime
@requires_scipy_or_netCDF4
@pytest.mark.parametrize("calendar", _ALL_CALENDARS)
@pytest.mark.parametrize("units_year", [1500, 2000, 2500])
def test_use_cftime_true(calendar, units_year) -> None:
import cftime
x = [0, 1]
time = [0, 720]
units = f"days since {units_year}-01-01"
original = DataArray(x, [("time", time)], name="x").to_dataset()
for v in ["x", "time"]:
original[v].attrs["units"] = units
original[v].attrs["calendar"] = calendar
decoded_x = cftime.num2date(x, units, calendar, only_use_cftime_datetimes=True)
decoded_time = cftime.num2date(
time, units, calendar, only_use_cftime_datetimes=True
)
expected_x = DataArray(decoded_x, [("time", decoded_time)], name="x")
expected_time = DataArray(decoded_time, [("time", decoded_time)], name="time")
with create_tmp_file() as tmp_file:
original.to_netcdf(tmp_file)
with warnings.catch_warnings(record=True) as record:
decoder = CFDatetimeCoder(use_cftime=True)
with open_dataset(tmp_file, decode_times=decoder) as ds:
assert_identical(expected_x, ds.x)
assert_identical(expected_time, ds.time)
_assert_no_dates_out_of_range_warning(record)
@requires_scipy_or_netCDF4
@pytest.mark.parametrize("calendar", _STANDARD_CALENDARS)
@pytest.mark.xfail(
has_numpy_2, reason="https://github.com/pandas-dev/pandas/issues/56996"
)
def test_use_cftime_false_standard_calendar_in_range(calendar) -> None:
x = [0, 1]
time = [0, 720]
units_date = "2000-01-01"
units = "days since 2000-01-01"
original = DataArray(x, [("time", time)], name="x").to_dataset()
for v in ["x", "time"]:
original[v].attrs["units"] = units
original[v].attrs["calendar"] = calendar
x_timedeltas = np.array(x).astype("timedelta64[D]")
time_timedeltas = np.array(time).astype("timedelta64[D]")
decoded_x = np.datetime64(units_date, "ns") + x_timedeltas
decoded_time = np.datetime64(units_date, "ns") + time_timedeltas
expected_x = DataArray(decoded_x, [("time", decoded_time)], name="x")
expected_time = DataArray(decoded_time, [("time", decoded_time)], name="time")
with create_tmp_file() as tmp_file:
original.to_netcdf(tmp_file)
with warnings.catch_warnings(record=True) as record:
coder = xr.coders.CFDatetimeCoder(use_cftime=False)
with open_dataset(tmp_file, decode_times=coder) as ds:
assert_identical(expected_x, ds.x)
assert_identical(expected_time, ds.time)
_assert_no_dates_out_of_range_warning(record)
@requires_scipy_or_netCDF4
@pytest.mark.parametrize("calendar", ["standard", "gregorian"])
def test_use_cftime_false_standard_calendar_out_of_range(calendar) -> None:
x = [0, 1]
time = [0, 720]
units = "days since 1582-01-01"
original = DataArray(x, [("time", time)], name="x").to_dataset()
for v in ["x", "time"]:
original[v].attrs["units"] = units
original[v].attrs["calendar"] = calendar
with create_tmp_file() as tmp_file:
original.to_netcdf(tmp_file)
with pytest.raises((OutOfBoundsDatetime, ValueError)):
decoder = CFDatetimeCoder(use_cftime=False)
open_dataset(tmp_file, decode_times=decoder)
@requires_scipy_or_netCDF4
@pytest.mark.parametrize("calendar", _NON_STANDARD_CALENDARS)
@pytest.mark.parametrize("units_year", [1500, 2000, 2500])
def test_use_cftime_false_nonstandard_calendar(calendar, units_year) -> None:
x = [0, 1]
time = [0, 720]
units = f"days since {units_year}"
original = DataArray(x, [("time", time)], name="x").to_dataset()
for v in ["x", "time"]:
original[v].attrs["units"] = units
original[v].attrs["calendar"] = calendar
with create_tmp_file() as tmp_file:
original.to_netcdf(tmp_file)
with pytest.raises((OutOfBoundsDatetime, ValueError)):
decoder = CFDatetimeCoder(use_cftime=False)
open_dataset(tmp_file, decode_times=decoder)
@pytest.mark.parametrize("engine", ["netcdf4", "scipy"])
def test_invalid_netcdf_raises(engine) -> None:
data = create_test_data()
with pytest.raises(ValueError, match=r"unrecognized option 'invalid_netcdf'"):
data.to_netcdf("foo.nc", engine=engine, invalid_netcdf=True)
@requires_zarr
def test_encode_zarr_attr_value() -> None:
# array -> list
arr = np.array([1, 2, 3])
expected1 = [1, 2, 3]
actual1 = backends.zarr.encode_zarr_attr_value(arr)
assert isinstance(actual1, list)
assert actual1 == expected1
# scalar array -> scalar
sarr = np.array(1)[()]
expected2 = 1
actual2 = backends.zarr.encode_zarr_attr_value(sarr)
assert isinstance(actual2, int)
assert actual2 == expected2
# string -> string (no change)
expected3 = "foo"
actual3 = backends.zarr.encode_zarr_attr_value(expected3)
assert isinstance(actual3, str)
assert actual3 == expected3
@requires_zarr
def test_extract_zarr_variable_encoding() -> None:
var = xr.Variable("x", [1, 2])
actual = backends.zarr.extract_zarr_variable_encoding(var, zarr_format=3)
assert "chunks" in actual
assert actual["chunks"] == ("auto" if has_zarr_v3 else None)
var = xr.Variable("x", [1, 2], encoding={"chunks": (1,)})
actual = backends.zarr.extract_zarr_variable_encoding(var, zarr_format=3)
assert actual["chunks"] == (1,)
# does not raise on invalid
var = xr.Variable("x", [1, 2], encoding={"foo": (1,)})
actual = backends.zarr.extract_zarr_variable_encoding(var, zarr_format=3)
# raises on invalid
var = xr.Variable("x", [1, 2], encoding={"foo": (1,)})
with pytest.raises(ValueError, match=r"unexpected encoding parameters"):
actual = backends.zarr.extract_zarr_variable_encoding(
var, raise_on_invalid=True, zarr_format=3
)
@requires_zarr
@requires_fsspec
@pytest.mark.filterwarnings("ignore:deallocating CachingFileManager")
def test_open_fsspec() -> None:
import fsspec
if not hasattr(zarr.storage, "FSStore") or not hasattr(
zarr.storage.FSStore, "getitems"
):
pytest.skip("zarr too old")
ds = open_dataset(os.path.join(os.path.dirname(__file__), "data", "example_1.nc"))
m = fsspec.filesystem("memory")
mm = m.get_mapper("out1.zarr")
ds.to_zarr(mm) # old interface
ds0 = ds.copy()
# pd.to_timedelta returns ns-precision, but the example data is in second precision
# so we need to fix this
ds0["time"] = ds.time + np.timedelta64(1, "D")
mm = m.get_mapper("out2.zarr")
ds0.to_zarr(mm) # old interface
# single dataset
url = "memory://out2.zarr"
ds2 = open_dataset(url, engine="zarr")
xr.testing.assert_equal(ds0, ds2)
# single dataset with caching
url = "simplecache::memory://out2.zarr"
ds2 = open_dataset(url, engine="zarr")
xr.testing.assert_equal(ds0, ds2)
# open_mfdataset requires dask
if has_dask:
# multi dataset
url = "memory://out*.zarr"
ds2 = open_mfdataset(url, engine="zarr")
xr.testing.assert_equal(xr.concat([ds, ds0], dim="time"), ds2)
# multi dataset with caching
url = "simplecache::memory://out*.zarr"
ds2 = open_mfdataset(url, engine="zarr")
xr.testing.assert_equal(xr.concat([ds, ds0], dim="time"), ds2)
@requires_h5netcdf
@requires_netCDF4
def test_load_single_value_h5netcdf(tmp_path: Path) -> None:
"""Test that numeric single-element vector attributes are handled fine.
At present (h5netcdf v0.8.1), the h5netcdf exposes single-valued numeric variable
attributes as arrays of length 1, as opposed to scalars for the NetCDF4
backend. This was leading to a ValueError upon loading a single value from
a file, see #4471. Test that loading causes no failure.
"""
ds = xr.Dataset(
{
"test": xr.DataArray(
np.array([0]), dims=("x",), attrs={"scale_factor": 1, "add_offset": 0}
)
}
)
ds.to_netcdf(tmp_path / "test.nc")
with xr.open_dataset(tmp_path / "test.nc", engine="h5netcdf") as ds2:
ds2["test"][0].load()
@requires_zarr
@requires_dask
@pytest.mark.parametrize(
"chunks", ["auto", -1, {}, {"x": "auto"}, {"x": -1}, {"x": "auto", "y": -1}]
)
def test_open_dataset_chunking_zarr(chunks, tmp_path: Path) -> None:
encoded_chunks = 100
dask_arr = da.from_array(
np.ones((500, 500), dtype="float64"), chunks=encoded_chunks
)
ds = xr.Dataset(
{
"test": xr.DataArray(
dask_arr,
dims=("x", "y"),
)
}
)
ds["test"].encoding["chunks"] = encoded_chunks
ds.to_zarr(tmp_path / "test.zarr")
with dask.config.set({"array.chunk-size": "1MiB"}):
expected = ds.chunk(chunks)
with open_dataset(
tmp_path / "test.zarr", engine="zarr", chunks=chunks
) as actual:
xr.testing.assert_chunks_equal(actual, expected)
@requires_zarr
@requires_dask
@pytest.mark.parametrize(
"chunks", ["auto", -1, {}, {"x": "auto"}, {"x": -1}, {"x": "auto", "y": -1}]
)
@pytest.mark.filterwarnings("ignore:The specified chunks separate")
def test_chunking_consintency(chunks, tmp_path: Path) -> None:
encoded_chunks: dict[str, Any] = {}
dask_arr = da.from_array(
np.ones((500, 500), dtype="float64"), chunks=encoded_chunks
)
ds = xr.Dataset(
{
"test": xr.DataArray(
dask_arr,
dims=("x", "y"),
)
}
)
ds["test"].encoding["chunks"] = encoded_chunks
ds.to_zarr(tmp_path / "test.zarr")
ds.to_netcdf(tmp_path / "test.nc")
with dask.config.set({"array.chunk-size": "1MiB"}):
expected = ds.chunk(chunks)
with xr.open_dataset(
tmp_path / "test.zarr", engine="zarr", chunks=chunks
) as actual:
xr.testing.assert_chunks_equal(actual, expected)
with xr.open_dataset(tmp_path / "test.nc", chunks=chunks) as actual:
xr.testing.assert_chunks_equal(actual, expected)
def _check_guess_can_open_and_open(entrypoint, obj, engine, expected):
assert entrypoint.guess_can_open(obj)
with open_dataset(obj, engine=engine) as actual:
assert_identical(expected, actual)
@requires_netCDF4
def test_netcdf4_entrypoint(tmp_path: Path) -> None:
entrypoint = NetCDF4BackendEntrypoint()
ds = create_test_data()
path = tmp_path / "foo"
ds.to_netcdf(path, format="NETCDF3_CLASSIC")
_check_guess_can_open_and_open(entrypoint, path, engine="netcdf4", expected=ds)
_check_guess_can_open_and_open(entrypoint, str(path), engine="netcdf4", expected=ds)
path = tmp_path / "bar"
ds.to_netcdf(path, format="NETCDF4_CLASSIC")
_check_guess_can_open_and_open(entrypoint, path, engine="netcdf4", expected=ds)
_check_guess_can_open_and_open(entrypoint, str(path), engine="netcdf4", expected=ds)
assert entrypoint.guess_can_open("http://something/remote")
assert entrypoint.guess_can_open("something-local.nc")
assert entrypoint.guess_can_open("something-local.nc4")
assert entrypoint.guess_can_open("something-local.cdf")
assert not entrypoint.guess_can_open("not-found-and-no-extension")
path = tmp_path / "baz"
with open(path, "wb") as f:
f.write(b"not-a-netcdf-file")
assert not entrypoint.guess_can_open(path)
@requires_scipy
def test_scipy_entrypoint(tmp_path: Path) -> None:
entrypoint = ScipyBackendEntrypoint()
ds = create_test_data()
path = tmp_path / "foo"
ds.to_netcdf(path, engine="scipy")
_check_guess_can_open_and_open(entrypoint, path, engine="scipy", expected=ds)
_check_guess_can_open_and_open(entrypoint, str(path), engine="scipy", expected=ds)
with open(path, "rb") as f:
_check_guess_can_open_and_open(entrypoint, f, engine="scipy", expected=ds)
with pytest.warns(
FutureWarning, match=re.escape("return value of to_netcdf() without a target")
):
contents = ds.to_netcdf(engine="scipy")
_check_guess_can_open_and_open(entrypoint, contents, engine="scipy", expected=ds)
_check_guess_can_open_and_open(
entrypoint, BytesIO(contents), engine="scipy", expected=ds
)
path = tmp_path / "foo.nc.gz"
with gzip.open(path, mode="wb") as f:
f.write(contents)
_check_guess_can_open_and_open(entrypoint, path, engine="scipy", expected=ds)
_check_guess_can_open_and_open(entrypoint, str(path), engine="scipy", expected=ds)
assert entrypoint.guess_can_open("something-local.nc")
assert entrypoint.guess_can_open("something-local.nc.gz")
assert not entrypoint.guess_can_open("not-found-and-no-extension")
assert not entrypoint.guess_can_open(b"not-a-netcdf-file")
@requires_h5netcdf
def test_h5netcdf_entrypoint(tmp_path: Path) -> None:
entrypoint = H5netcdfBackendEntrypoint()
ds = create_test_data()
path = tmp_path / "foo"
ds.to_netcdf(path, engine="h5netcdf")
_check_guess_can_open_and_open(entrypoint, path, engine="h5netcdf", expected=ds)
_check_guess_can_open_and_open(
entrypoint, str(path), engine="h5netcdf", expected=ds
)
with open(path, "rb") as f:
_check_guess_can_open_and_open(entrypoint, f, engine="h5netcdf", expected=ds)
assert entrypoint.guess_can_open("something-local.nc")
assert entrypoint.guess_can_open("something-local.nc4")
assert entrypoint.guess_can_open("something-local.cdf")
assert not entrypoint.guess_can_open("not-found-and-no-extension")
@requires_netCDF4
@pytest.mark.parametrize("str_type", (str, np.str_))
def test_write_file_from_np_str(str_type: type[str | np.str_], tmpdir: str) -> None:
# https://github.com/pydata/xarray/pull/5264
scenarios = [str_type(v) for v in ["scenario_a", "scenario_b", "scenario_c"]]
years = range(2015, 2100 + 1)
tdf = pd.DataFrame(
data=np.random.random((len(scenarios), len(years))),
columns=years,
index=scenarios,
)
tdf.index.name = "scenario"
tdf.columns.name = "year"
tdf = cast(pd.DataFrame, tdf.stack())
tdf.name = "tas"
txr = tdf.to_xarray()
txr.to_netcdf(tmpdir.join("test.nc"))
@requires_zarr
@requires_netCDF4
class TestNCZarr:
@property
def netcdfc_version(self):
return Version(nc4.getlibversion().split()[0].split("-development")[0])
def _create_nczarr(self, filename):
if self.netcdfc_version < Version("4.8.1"):
pytest.skip("requires netcdf-c>=4.8.1")
if platform.system() == "Windows" and self.netcdfc_version == Version("4.8.1"):
# Bug in netcdf-c==4.8.1 (typo: Nan instead of NaN)
# https://github.com/Unidata/netcdf-c/issues/2265
pytest.skip("netcdf-c==4.8.1 has issues on Windows")
ds = create_test_data()
# Drop dim3: netcdf-c does not support dtype='<U1'
# https://github.com/Unidata/netcdf-c/issues/2259
ds = ds.drop_vars("dim3")
ds.to_netcdf(f"file://{filename}#mode=nczarr")
return ds
def test_open_nczarr(self) -> None:
with create_tmp_file(suffix=".zarr") as tmp:
expected = self._create_nczarr(tmp)
actual = xr.open_zarr(tmp, consolidated=False)
assert_identical(expected, actual)
def test_overwriting_nczarr(self) -> None:
with create_tmp_file(suffix=".zarr") as tmp:
ds = self._create_nczarr(tmp)
expected = ds[["var1"]]
expected.to_zarr(tmp, mode="w")
actual = xr.open_zarr(tmp, consolidated=False)
assert_identical(expected, actual)
@pytest.mark.parametrize("mode", ["a", "r+"])
@pytest.mark.filterwarnings("ignore:.*non-consolidated metadata.*")
def test_raise_writing_to_nczarr(self, mode) -> None:
if self.netcdfc_version > Version("4.8.1"):
pytest.skip("netcdf-c>4.8.1 adds the _ARRAY_DIMENSIONS attribute")
with create_tmp_file(suffix=".zarr") as tmp:
ds = self._create_nczarr(tmp)
with pytest.raises(
KeyError, match="missing the attribute `_ARRAY_DIMENSIONS`,"
):
ds.to_zarr(tmp, mode=mode)
@requires_netCDF4
@requires_dask
@pytest.mark.usefixtures("default_zarr_format")
def test_pickle_open_mfdataset_dataset():
with open_example_mfdataset(["bears.nc"]) as ds:
assert_identical(ds, pickle.loads(pickle.dumps(ds)))
@requires_zarr
@pytest.mark.usefixtures("default_zarr_format")
def test_zarr_closing_internal_zip_store():
store_name = "tmp.zarr.zip"
original_da = DataArray(np.arange(12).reshape((3, 4)))
original_da.to_zarr(store_name, mode="w")
with open_dataarray(store_name, engine="zarr") as loaded_da:
assert_identical(original_da, loaded_da)
@requires_zarr
@pytest.mark.parametrize("create_default_indexes", [True, False])
def test_zarr_create_default_indexes(tmp_path, create_default_indexes) -> None:
from xarray.core.indexes import PandasIndex
store_path = tmp_path / "tmp.zarr"
original_ds = xr.Dataset({"data": ("x", np.arange(3))}, coords={"x": [-1, 0, 1]})
original_ds.to_zarr(store_path, mode="w")
with open_dataset(
store_path, engine="zarr", create_default_indexes=create_default_indexes
) as loaded_ds:
if create_default_indexes:
assert list(loaded_ds.xindexes) == ["x"] and isinstance(
loaded_ds.xindexes["x"], PandasIndex
)
else:
assert len(loaded_ds.xindexes) == 0
@requires_zarr
@pytest.mark.usefixtures("default_zarr_format")
def test_raises_key_error_on_invalid_zarr_store(tmp_path):
root = zarr.open_group(tmp_path / "tmp.zarr")
if Version(zarr.__version__) < Version("3.0.0"):
root.create_dataset("bar", shape=(3, 5), dtype=np.float32)
else:
root.create_array("bar", shape=(3, 5), dtype=np.float32)
with pytest.raises(KeyError, match=r"xarray to determine variable dimensions"):
xr.open_zarr(tmp_path / "tmp.zarr", consolidated=False)
@requires_zarr
@pytest.mark.usefixtures("default_zarr_format")
class TestZarrRegionAuto:
"""These are separated out since we should not need to test this logic with every store."""
@contextlib.contextmanager
def create_zarr_target(self):
with create_tmp_file(suffix=".zarr") as tmp:
yield tmp
@contextlib.contextmanager
def create(self):
x = np.arange(0, 50, 10)
y = np.arange(0, 20, 2)
data = np.ones((5, 10))
ds = xr.Dataset(
{"test": xr.DataArray(data, dims=("x", "y"), coords={"x": x, "y": y})}
)
with self.create_zarr_target() as target:
self.save(target, ds)
yield target, ds
def save(self, target, ds, **kwargs):
ds.to_zarr(target, **kwargs)
@pytest.mark.parametrize(
"region",
[
pytest.param("auto", id="full-auto"),
pytest.param({"x": "auto", "y": slice(6, 8)}, id="mixed-auto"),
],
)
def test_zarr_region_auto(self, region):
with self.create() as (target, ds):
ds_region = 1 + ds.isel(x=slice(2, 4), y=slice(6, 8))
self.save(target, ds_region, region=region)
ds_updated = xr.open_zarr(target)
expected = ds.copy()
expected["test"][2:4, 6:8] += 1
assert_identical(ds_updated, expected)
def test_zarr_region_auto_noncontiguous(self):
with self.create() as (target, ds):
with pytest.raises(ValueError):
self.save(target, ds.isel(x=[0, 2, 3], y=[5, 6]), region="auto")
dsnew = ds.copy()
dsnew["x"] = dsnew.x + 5
with pytest.raises(KeyError):
self.save(target, dsnew, region="auto")
def test_zarr_region_index_write(self, tmp_path):
region: Mapping[str, slice] | Literal["auto"]
region_slice = dict(x=slice(2, 4), y=slice(6, 8))
with self.create() as (target, ds):
ds_region = 1 + ds.isel(region_slice)
for region in [region_slice, "auto"]: # type: ignore[assignment]
with patch.object(
ZarrStore,
"set_variables",
side_effect=ZarrStore.set_variables,
autospec=True,
) as mock:
self.save(target, ds_region, region=region, mode="r+")
# should write the data vars but never the index vars with auto mode
for call in mock.call_args_list:
written_variables = call.args[1].keys()
assert "test" in written_variables
assert "x" not in written_variables
assert "y" not in written_variables
def test_zarr_region_append(self):
with self.create() as (target, ds):
x_new = np.arange(40, 70, 10)
data_new = np.ones((3, 10))
ds_new = xr.Dataset(
{
"test": xr.DataArray(
data_new,
dims=("x", "y"),
coords={"x": x_new, "y": ds.y},
)
}
)
# Now it is valid to use auto region detection with the append mode,
# but it is still unsafe to modify dimensions or metadata using the region
# parameter.
with pytest.raises(KeyError):
self.save(target, ds_new, mode="a", append_dim="x", region="auto")
def test_zarr_region(self):
with self.create() as (target, ds):
ds_transposed = ds.transpose("y", "x")
ds_region = 1 + ds_transposed.isel(x=[0], y=[0])
self.save(target, ds_region, region={"x": slice(0, 1), "y": slice(0, 1)})
# Write without region
self.save(target, ds_transposed, mode="r+")
@requires_dask
def test_zarr_region_chunk_partial(self):
"""
Check that writing to partial chunks with `region` fails, assuming `safe_chunks=False`.
"""
ds = (
xr.DataArray(np.arange(120).reshape(4, 3, -1), dims=list("abc"))
.rename("var1")
.to_dataset()
)
with self.create_zarr_target() as target:
self.save(target, ds.chunk(5), compute=False, mode="w")
with pytest.raises(ValueError):
for r in range(ds.sizes["a"]):
self.save(
target, ds.chunk(3).isel(a=[r]), region=dict(a=slice(r, r + 1))
)
@requires_dask
def test_zarr_append_chunk_partial(self):
t_coords = np.array([np.datetime64("2020-01-01").astype("datetime64[ns]")])
data = np.ones((10, 10))
da = xr.DataArray(
data.reshape((-1, 10, 10)),
dims=["time", "x", "y"],
coords={"time": t_coords},
name="foo",
)
new_time = np.array([np.datetime64("2021-01-01").astype("datetime64[ns]")])
da2 = xr.DataArray(
data.reshape((-1, 10, 10)),
dims=["time", "x", "y"],
coords={"time": new_time},
name="foo",
)
with self.create_zarr_target() as target:
self.save(target, da, mode="w", encoding={"foo": {"chunks": (5, 5, 1)}})
with pytest.raises(ValueError, match="encoding was provided"):
self.save(
target,
da2,
append_dim="time",
mode="a",
encoding={"foo": {"chunks": (1, 1, 1)}},
)
# chunking with dask sidesteps the encoding check, so we need a different check
with pytest.raises(ValueError, match="Specified Zarr chunks"):
self.save(
target,
da2.chunk({"x": 1, "y": 1, "time": 1}),
append_dim="time",
mode="a",
)
@requires_dask
def test_zarr_region_chunk_partial_offset(self):
# https://github.com/pydata/xarray/pull/8459#issuecomment-1819417545
with self.create_zarr_target() as store:
data = np.ones((30,))
da = xr.DataArray(
data, dims=["x"], coords={"x": range(30)}, name="foo"
).chunk(x=10)
self.save(store, da, compute=False)
self.save(store, da.isel(x=slice(10)).chunk(x=(10,)), region="auto")
self.save(
store,
da.isel(x=slice(5, 25)).chunk(x=(10, 10)),
safe_chunks=False,
region="auto",
)
with pytest.raises(ValueError):
self.save(
store, da.isel(x=slice(5, 25)).chunk(x=(10, 10)), region="auto"
)
@requires_dask
def test_zarr_safe_chunk_append_dim(self):
with self.create_zarr_target() as store:
data = np.ones((20,))
da = xr.DataArray(
data, dims=["x"], coords={"x": range(20)}, name="foo"
).chunk(x=5)
self.save(store, da.isel(x=slice(0, 7)), safe_chunks=True, mode="w")
with pytest.raises(ValueError):
# If the first chunk is smaller than the border size then raise an error
self.save(
store,
da.isel(x=slice(7, 11)).chunk(x=(2, 2)),
append_dim="x",
safe_chunks=True,
)
self.save(store, da.isel(x=slice(0, 7)), safe_chunks=True, mode="w")
# If the first chunk is of the size of the border size then it is valid
self.save(
store,
da.isel(x=slice(7, 11)).chunk(x=(3, 1)),
safe_chunks=True,
append_dim="x",
)
assert xr.open_zarr(store)["foo"].equals(da.isel(x=slice(0, 11)))
self.save(store, da.isel(x=slice(0, 7)), safe_chunks=True, mode="w")
# If the first chunk is of the size of the border size + N * zchunk then it is valid
self.save(
store,
da.isel(x=slice(7, 17)).chunk(x=(8, 2)),
safe_chunks=True,
append_dim="x",
)
assert xr.open_zarr(store)["foo"].equals(da.isel(x=slice(0, 17)))
self.save(store, da.isel(x=slice(0, 7)), safe_chunks=True, mode="w")
with pytest.raises(ValueError):
# If the first chunk is valid but the other are not then raise an error
self.save(
store,
da.isel(x=slice(7, 14)).chunk(x=(3, 3, 1)),
append_dim="x",
safe_chunks=True,
)
self.save(store, da.isel(x=slice(0, 7)), safe_chunks=True, mode="w")
with pytest.raises(ValueError):
# If the first chunk have a size bigger than the border size but not enough
# to complete the size of the next chunk then an error must be raised
self.save(
store,
da.isel(x=slice(7, 14)).chunk(x=(4, 3)),
append_dim="x",
safe_chunks=True,
)
self.save(store, da.isel(x=slice(0, 7)), safe_chunks=True, mode="w")
# Append with a single chunk it's totally valid,
# and it does not matter the size of the chunk
self.save(
store,
da.isel(x=slice(7, 19)).chunk(x=-1),
append_dim="x",
safe_chunks=True,
)
assert xr.open_zarr(store)["foo"].equals(da.isel(x=slice(0, 19)))
@requires_dask
@pytest.mark.parametrize("mode", ["r+", "a"])
def test_zarr_safe_chunk_region(self, mode: Literal["r+", "a"]):
with self.create_zarr_target() as store:
arr = xr.DataArray(
list(range(11)), dims=["a"], coords={"a": list(range(11))}, name="foo"
).chunk(a=3)
self.save(store, arr, mode="w")
with pytest.raises(ValueError):
# There are two Dask chunks on the same Zarr chunk,
# which means that it is unsafe in any mode
self.save(
store,
arr.isel(a=slice(0, 3)).chunk(a=(2, 1)),
region="auto",
mode=mode,
)
with pytest.raises(ValueError):
# the first chunk is covering the border size, but it is not
# completely covering the second chunk, which means that it is
# unsafe in any mode
self.save(
store,
arr.isel(a=slice(1, 5)).chunk(a=(3, 1)),
region="auto",
mode=mode,
)
with pytest.raises(ValueError):
# The first chunk is safe but the other two chunks are overlapping with
# the same Zarr chunk
self.save(
store,
arr.isel(a=slice(0, 5)).chunk(a=(3, 1, 1)),
region="auto",
mode=mode,
)
# Fully update two contiguous chunks is safe in any mode
self.save(store, arr.isel(a=slice(3, 9)), region="auto", mode=mode)
# The last chunk is considered full based on their current size (2)
self.save(store, arr.isel(a=slice(9, 11)), region="auto", mode=mode)
self.save(
store, arr.isel(a=slice(6, None)).chunk(a=-1), region="auto", mode=mode
)
# Write the last chunk of a region partially is safe in "a" mode
self.save(store, arr.isel(a=slice(3, 8)), region="auto", mode="a")
with pytest.raises(ValueError):
# with "r+" mode it is invalid to write partial chunk
self.save(store, arr.isel(a=slice(3, 8)), region="auto", mode="r+")
# This is safe with mode "a", the border size is covered by the first chunk of Dask
self.save(
store, arr.isel(a=slice(1, 4)).chunk(a=(2, 1)), region="auto", mode="a"
)
with pytest.raises(ValueError):
# This is considered unsafe in mode "r+" because it is writing in a partial chunk
self.save(
store,
arr.isel(a=slice(1, 4)).chunk(a=(2, 1)),
region="auto",
mode="r+",
)
# This is safe on mode "a" because there is a single dask chunk
self.save(
store, arr.isel(a=slice(1, 5)).chunk(a=(4,)), region="auto", mode="a"
)
with pytest.raises(ValueError):
# This is unsafe on mode "r+", because the Dask chunk is partially writing
# in the first chunk of Zarr
self.save(
store,
arr.isel(a=slice(1, 5)).chunk(a=(4,)),
region="auto",
mode="r+",
)
# The first chunk is completely covering the first Zarr chunk
# and the last chunk is a partial one
self.save(
store, arr.isel(a=slice(0, 5)).chunk(a=(3, 2)), region="auto", mode="a"
)
with pytest.raises(ValueError):
# The last chunk is partial, so it is considered unsafe on mode "r+"
self.save(
store,
arr.isel(a=slice(0, 5)).chunk(a=(3, 2)),
region="auto",
mode="r+",
)
# The first chunk is covering the border size (2 elements)
# and also the second chunk (3 elements), so it is valid
self.save(
store, arr.isel(a=slice(1, 8)).chunk(a=(5, 2)), region="auto", mode="a"
)
with pytest.raises(ValueError):
# The first chunk is not fully covering the first zarr chunk
self.save(
store,
arr.isel(a=slice(1, 8)).chunk(a=(5, 2)),
region="auto",
mode="r+",
)
with pytest.raises(ValueError):
# Validate that the border condition is not affecting the "r+" mode
self.save(store, arr.isel(a=slice(1, 9)), region="auto", mode="r+")
self.save(store, arr.isel(a=slice(10, 11)), region="auto", mode="a")
with pytest.raises(ValueError):
# Validate that even if we write with a single Dask chunk on the last Zarr
# chunk it is still unsafe if it is not fully covering it
# (the last Zarr chunk has size 2)
self.save(store, arr.isel(a=slice(10, 11)), region="auto", mode="r+")
# Validate the same as the above test but in the beginning of the last chunk
self.save(store, arr.isel(a=slice(9, 10)), region="auto", mode="a")
with pytest.raises(ValueError):
self.save(store, arr.isel(a=slice(9, 10)), region="auto", mode="r+")
self.save(
store, arr.isel(a=slice(7, None)).chunk(a=-1), region="auto", mode="a"
)
with pytest.raises(ValueError):
# Test that even a Dask chunk that covers the last Zarr chunk can be unsafe
# if it is partial covering other Zarr chunks
self.save(
store,
arr.isel(a=slice(7, None)).chunk(a=-1),
region="auto",
mode="r+",
)
with pytest.raises(ValueError):
# If the chunk is of size equal to the one in the Zarr encoding, but
# it is partially writing in the first chunk then raise an error
self.save(
store,
arr.isel(a=slice(8, None)).chunk(a=3),
region="auto",
mode="r+",
)
with pytest.raises(ValueError):
self.save(
store, arr.isel(a=slice(5, -1)).chunk(a=5), region="auto", mode="r+"
)
# Test if the code is detecting the last chunk correctly
data = np.random.default_rng(0).random((2920, 25, 53))
ds = xr.Dataset({"temperature": (("time", "lat", "lon"), data)})
chunks = {"time": 1000, "lat": 25, "lon": 53}
self.save(store, ds.chunk(chunks), compute=False, mode="w")
region = {"time": slice(1000, 2000, 1)}
chunk = ds.isel(region)
chunk = chunk.chunk()
self.save(store, chunk.chunk(), region=region)
@requires_h5netcdf
@requires_fsspec
def test_h5netcdf_storage_options() -> None:
with create_tmp_files(2, allow_cleanup_failure=ON_WINDOWS) as (f1, f2):
ds1 = create_test_data()
ds1.to_netcdf(f1, engine="h5netcdf")
ds2 = create_test_data()
ds2.to_netcdf(f2, engine="h5netcdf")
files = [f"file://{f}" for f in [f1, f2]]
with xr.open_mfdataset(
files,
engine="h5netcdf",
concat_dim="time",
data_vars="all",
combine="nested",
storage_options={"skip_instance_cache": False},
) as ds:
assert_identical(xr.concat([ds1, ds2], dim="time", data_vars="all"), ds)
|