File: test_execute.py

package info (click to toggle)
python-papermill 2.6.0-3.1
  • links: PTS, VCS
  • area: main
  • in suites: trixie
  • size: 2,216 kB
  • sloc: python: 4,977; makefile: 17; sh: 5
file content (463 lines) | stat: -rw-r--r-- 20,998 bytes parent folder | download | duplicates (2)
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
import os
import shutil
import tempfile
import unittest
from copy import deepcopy
from functools import partial
from pathlib import Path
from unittest.mock import ANY, patch

import nbformat
from colors import strip_color
from nbformat import validate

from papermill import engines, translators
from papermill.exceptions import PapermillExecutionError
from papermill.execute import execute_notebook
from papermill.iorw import load_notebook_node
from papermill.log import logger
from papermill.utils import chdir
from . import get_notebook_path, kernel_name

execute_notebook = partial(execute_notebook, kernel_name=kernel_name)


class TestNotebookHelpers(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()
        self.notebook_name = 'simple_execute.ipynb'
        self.notebook_path = get_notebook_path(self.notebook_name)
        self.nb_test_executed_fname = os.path.join(self.test_dir, f'output_{self.notebook_name}')

    def tearDown(self):
        shutil.rmtree(self.test_dir)

    @patch(f"{engines.__name__}.PapermillNotebookClient")
    def test_start_timeout(self, preproc_mock):
        execute_notebook(self.notebook_path, self.nb_test_executed_fname, start_timeout=123)
        args, kwargs = preproc_mock.call_args
        expected = [
            ('timeout', None),
            ('startup_timeout', 123),
            ('kernel_name', kernel_name),
            ('log', logger),
        ]
        actual = {(key, kwargs[key]) for key in kwargs}
        self.assertTrue(
            set(expected).issubset(actual),
            msg=f'Expected arguments {expected} are not a subset of actual {actual}',
        )

    @patch(f"{engines.__name__}.PapermillNotebookClient")
    def test_default_start_timeout(self, preproc_mock):
        execute_notebook(self.notebook_path, self.nb_test_executed_fname)
        args, kwargs = preproc_mock.call_args
        expected = [
            ('timeout', None),
            ('startup_timeout', 60),
            ('kernel_name', kernel_name),
            ('log', logger),
        ]
        actual = {(key, kwargs[key]) for key in kwargs}
        self.assertTrue(
            set(expected).issubset(actual),
            msg=f'Expected arguments {expected} are not a subset of actual {actual}',
        )

    def test_cell_insertion(self):
        execute_notebook(self.notebook_path, self.nb_test_executed_fname, {'msg': 'Hello'})
        test_nb = load_notebook_node(self.nb_test_executed_fname)
        self.assertListEqual(test_nb.cells[1].get('source').split('\n'), ['# Parameters', 'msg = "Hello"', ''])
        self.assertEqual(test_nb.metadata.papermill.parameters, {'msg': 'Hello'})

    def test_no_tags(self):
        notebook_name = 'no_parameters.ipynb'
        nb_test_executed_fname = os.path.join(self.test_dir, f'output_{notebook_name}')
        execute_notebook(get_notebook_path(notebook_name), nb_test_executed_fname, {'msg': 'Hello'})
        test_nb = load_notebook_node(nb_test_executed_fname)
        self.assertListEqual(test_nb.cells[0].get('source').split('\n'), ['# Parameters', 'msg = "Hello"', ''])
        self.assertEqual(test_nb.metadata.papermill.parameters, {'msg': 'Hello'})

    def test_quoted_params(self):
        execute_notebook(self.notebook_path, self.nb_test_executed_fname, {'msg': '"Hello"'})
        test_nb = load_notebook_node(self.nb_test_executed_fname)
        self.assertListEqual(test_nb.cells[1].get('source').split('\n'), ['# Parameters', r'msg = "\"Hello\""', ''])
        self.assertEqual(test_nb.metadata.papermill.parameters, {'msg': '"Hello"'})

    def test_backslash_params(self):
        execute_notebook(self.notebook_path, self.nb_test_executed_fname, {'foo': r'do\ not\ crash'})
        test_nb = load_notebook_node(self.nb_test_executed_fname)
        self.assertListEqual(
            test_nb.cells[1].get('source').split('\n'),
            ['# Parameters', r'foo = "do\\ not\\ crash"', ''],
        )
        self.assertEqual(test_nb.metadata.papermill.parameters, {'foo': r'do\ not\ crash'})

    def test_backslash_quote_params(self):
        execute_notebook(self.notebook_path, self.nb_test_executed_fname, {'foo': r'bar=\"baz\"'})
        test_nb = load_notebook_node(self.nb_test_executed_fname)
        self.assertListEqual(
            test_nb.cells[1].get('source').split('\n'),
            ['# Parameters', r'foo = "bar=\\\"baz\\\""', ''],
        )
        self.assertEqual(test_nb.metadata.papermill.parameters, {'foo': r'bar=\"baz\"'})

    def test_double_backslash_quote_params(self):
        execute_notebook(self.notebook_path, self.nb_test_executed_fname, {'foo': r'\\"bar\\"'})
        test_nb = load_notebook_node(self.nb_test_executed_fname)
        self.assertListEqual(
            test_nb.cells[1].get('source').split('\n'),
            ['# Parameters', r'foo = "\\\\\"bar\\\\\""', ''],
        )
        self.assertEqual(test_nb.metadata.papermill.parameters, {'foo': r'\\"bar\\"'})

    def test_prepare_only(self):
        for example in ['broken1.ipynb', 'keyboard_interrupt.ipynb']:
            path = get_notebook_path(example)
            result_path = os.path.join(self.test_dir, example)
            # Should not raise as we don't execute the notebook at all
            execute_notebook(path, result_path, {'foo': r'do\ not\ crash'}, prepare_only=True)
            nb = load_notebook_node(result_path)
            self.assertEqual(nb.cells[0].cell_type, "code")
            self.assertEqual(
                nb.cells[0].get('source').split('\n'),
                ['# Parameters', r'foo = "do\\ not\\ crash"', ''],
            )


class TestBrokenNotebook1(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()

    def tearDown(self):
        shutil.rmtree(self.test_dir)

    def test(self):
        path = get_notebook_path('broken1.ipynb')

        # check that the notebook has two existing marker cells, so that this test is sure to be
        # validating the removal logic (the markers are simulatin an error in the first code cell
        # that has since been fixed)
        original_nb = load_notebook_node(path)
        self.assertEqual(original_nb.cells[0].metadata["tags"], ["papermill-error-cell-tag"])
        self.assertIn("In [1]", original_nb.cells[0].source)
        self.assertEqual(original_nb.cells[2].metadata["tags"], ["papermill-error-cell-tag"])

        result_path = os.path.join(self.test_dir, 'broken1.ipynb')
        with self.assertRaises(PapermillExecutionError):
            execute_notebook(path, result_path)
        nb = load_notebook_node(result_path)
        self.assertEqual(nb.cells[0].cell_type, "markdown")
        self.assertRegex(nb.cells[0].source, r'^<span .*<a href="#papermill-error-cell".*In \[2\].*</span>$')
        self.assertEqual(nb.cells[0].metadata["tags"], ["papermill-error-cell-tag"])

        self.assertEqual(nb.cells[1].cell_type, "markdown")
        self.assertEqual(nb.cells[2].execution_count, 1)
        self.assertEqual(nb.cells[3].cell_type, "markdown")
        self.assertEqual(nb.cells[4].cell_type, "markdown")

        self.assertEqual(nb.cells[5].cell_type, "markdown")
        self.assertRegex(nb.cells[5].source, '<span id="papermill-error-cell" .*</span>')
        self.assertEqual(nb.cells[5].metadata["tags"], ["papermill-error-cell-tag"])
        self.assertEqual(nb.cells[6].execution_count, 2)
        self.assertEqual(nb.cells[6].outputs[0].output_type, 'error')

        self.assertEqual(nb.cells[7].execution_count, None)

        # double check the removal (the new cells above should be the only two tagged ones)
        self.assertEqual(sum("papermill-error-cell-tag" in cell.metadata.get("tags", []) for cell in nb.cells), 2)


class TestBrokenNotebook2(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()

    def tearDown(self):
        shutil.rmtree(self.test_dir)

    def test(self):
        path = get_notebook_path('broken2.ipynb')
        result_path = os.path.join(self.test_dir, 'broken2.ipynb')
        with self.assertRaises(PapermillExecutionError):
            execute_notebook(path, result_path)
        nb = load_notebook_node(result_path)
        self.assertEqual(nb.cells[0].cell_type, "markdown")
        self.assertRegex(nb.cells[0].source, r'^<span .*<a href="#papermill-error-cell">.*In \[2\].*</span>$')
        self.assertEqual(nb.cells[1].execution_count, 1)

        self.assertEqual(nb.cells[2].cell_type, "markdown")
        self.assertRegex(nb.cells[2].source, '<span id="papermill-error-cell" .*</span>')
        self.assertEqual(nb.cells[3].execution_count, 2)
        self.assertEqual(nb.cells[3].outputs[0].output_type, 'display_data')
        self.assertEqual(nb.cells[3].outputs[1].output_type, 'error')

        self.assertEqual(nb.cells[4].execution_count, None)


class TestReportMode(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()
        self.notebook_name = 'report_mode_test.ipynb'
        self.notebook_path = get_notebook_path(self.notebook_name)
        self.nb_test_executed_fname = os.path.join(self.test_dir, f'output_{self.notebook_name}')

    def tearDown(self):
        shutil.rmtree(self.test_dir)

    def test_report_mode(self):
        nb = execute_notebook(self.notebook_path, self.nb_test_executed_fname, {'a': 0}, report_mode=True)
        for cell in nb.cells:
            if cell.cell_type == 'code':
                self.assertEqual(cell.metadata.get('jupyter', {}).get('source_hidden'), True)


class TestOutputPathNone(unittest.TestCase):
    def test_output_path_of_none(self):
        """Output path of None should return notebook node obj but not write an ipynb"""
        nb = execute_notebook(get_notebook_path('simple_execute.ipynb'), None, {'msg': 'Hello'})
        self.assertEqual(nb.metadata.papermill.parameters, {'msg': 'Hello'})


class TestCWD(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()
        self.base_test_dir = tempfile.mkdtemp()

        self.check_notebook_name = 'read_check.ipynb'
        self.check_notebook_path = os.path.join(self.base_test_dir, 'read_check.ipynb')
        # Setup read paths so base_test_dir has check_notebook_name
        shutil.copyfile(get_notebook_path(self.check_notebook_name), self.check_notebook_path)
        with open(os.path.join(self.test_dir, 'check.txt'), 'w', encoding='utf-8') as f:
            # Needed for read_check to pass
            f.write('exists')

        self.simple_notebook_name = 'simple_execute.ipynb'
        self.simple_notebook_path = os.path.join(self.base_test_dir, 'simple_execute.ipynb')
        # Setup read paths so base_test_dir has simple_notebook_name
        shutil.copyfile(get_notebook_path(self.simple_notebook_name), self.simple_notebook_path)

        self.nb_test_executed_fname = 'test_output.ipynb'

    def tearDown(self):
        shutil.rmtree(self.test_dir)
        shutil.rmtree(self.base_test_dir)

    def test_local_save_ignores_cwd_assignment(self):
        with chdir(self.base_test_dir):
            # Both paths are relative
            execute_notebook(self.simple_notebook_name, self.nb_test_executed_fname, cwd=self.test_dir)
        self.assertTrue(os.path.isfile(os.path.join(self.base_test_dir, self.nb_test_executed_fname)))

    def test_execution_respects_cwd_assignment(self):
        with chdir(self.base_test_dir):
            # Both paths are relative
            execute_notebook(self.check_notebook_name, self.nb_test_executed_fname, cwd=self.test_dir)
        self.assertTrue(os.path.isfile(os.path.join(self.base_test_dir, self.nb_test_executed_fname)))

    def test_pathlib_paths(self):
        # Copy of test_execution_respects_cwd_assignment but with `Path`s
        with chdir(self.base_test_dir):
            execute_notebook(
                Path(self.check_notebook_name),
                Path(self.nb_test_executed_fname),
                cwd=Path(self.test_dir),
            )
        self.assertTrue(Path(self.base_test_dir).joinpath(self.nb_test_executed_fname).exists())


class TestSysExit(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()

    def tearDown(self):
        shutil.rmtree(self.test_dir)

    def test_sys_exit(self):
        notebook_name = 'sysexit.ipynb'
        result_path = os.path.join(self.test_dir, f'output_{notebook_name}')
        execute_notebook(get_notebook_path(notebook_name), result_path)
        nb = load_notebook_node(result_path)
        self.assertEqual(nb.cells[0].cell_type, "code")
        self.assertEqual(nb.cells[0].execution_count, 1)
        self.assertEqual(nb.cells[1].execution_count, 2)
        self.assertEqual(nb.cells[1].outputs[0].output_type, 'error')
        self.assertEqual(nb.cells[1].outputs[0].ename, 'SystemExit')
        self.assertEqual(nb.cells[1].outputs[0].evalue, '')
        self.assertEqual(nb.cells[2].execution_count, None)

    def test_sys_exit0(self):
        notebook_name = 'sysexit0.ipynb'
        result_path = os.path.join(self.test_dir, f'output_{notebook_name}')
        execute_notebook(get_notebook_path(notebook_name), result_path)
        nb = load_notebook_node(result_path)
        self.assertEqual(nb.cells[0].cell_type, "code")
        self.assertEqual(nb.cells[0].execution_count, 1)
        self.assertEqual(nb.cells[1].execution_count, 2)
        self.assertEqual(nb.cells[1].outputs[0].output_type, 'error')
        self.assertEqual(nb.cells[1].outputs[0].ename, 'SystemExit')
        self.assertEqual(nb.cells[1].outputs[0].evalue, '0')
        self.assertEqual(nb.cells[2].execution_count, None)

    def test_sys_exit1(self):
        notebook_name = 'sysexit1.ipynb'
        result_path = os.path.join(self.test_dir, f'output_{notebook_name}')
        with self.assertRaises(PapermillExecutionError):
            execute_notebook(get_notebook_path(notebook_name), result_path)
        nb = load_notebook_node(result_path)
        self.assertEqual(nb.cells[0].cell_type, "markdown")
        self.assertRegex(nb.cells[0].source, r'^<span .*<a href="#papermill-error-cell".*In \[2\].*</span>$')
        self.assertEqual(nb.cells[1].execution_count, 1)

        self.assertEqual(nb.cells[2].cell_type, "markdown")
        self.assertRegex(nb.cells[2].source, '<span id="papermill-error-cell" .*</span>')
        self.assertEqual(nb.cells[3].execution_count, 2)
        self.assertEqual(nb.cells[3].outputs[0].output_type, 'error')

        self.assertEqual(nb.cells[4].execution_count, None)

    def test_system_exit(self):
        notebook_name = 'systemexit.ipynb'
        result_path = os.path.join(self.test_dir, f'output_{notebook_name}')
        execute_notebook(get_notebook_path(notebook_name), result_path)
        nb = load_notebook_node(result_path)
        self.assertEqual(nb.cells[0].cell_type, "code")
        self.assertEqual(nb.cells[0].execution_count, 1)
        self.assertEqual(nb.cells[1].execution_count, 2)
        self.assertEqual(nb.cells[1].outputs[0].output_type, 'error')
        self.assertEqual(nb.cells[1].outputs[0].ename, 'SystemExit')
        self.assertEqual(nb.cells[1].outputs[0].evalue, '')
        self.assertEqual(nb.cells[2].execution_count, None)

    def test_line_magic_error(self):
        notebook_name = 'line_magic_error.ipynb'
        result_path = os.path.join(self.test_dir, f'output_{notebook_name}')
        with self.assertRaises(PapermillExecutionError):
            execute_notebook(get_notebook_path(notebook_name), result_path)
        nb = load_notebook_node(result_path)
        self.assertEqual(nb.cells[0].cell_type, "markdown")
        self.assertRegex(nb.cells[0].source, r'^<span .*<a href="#papermill-error-cell".*In \[1\].*</span>$')
        self.assertEqual(nb.cells[0].metadata["tags"], ["papermill-error-cell-tag"])
        self.assertEqual(nb.cells[2].cell_type, "code")
        self.assertEqual(nb.cells[2].execution_count, 1)
        self.assertEqual(nb.cells[3].execution_count, None)


class TestNotebookValidation(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()

    def tearDown(self):
        shutil.rmtree(self.test_dir)

    def test_from_version_4_4_upgrades(self):
        notebook_name = 'nb_version_4.4.ipynb'
        result_path = os.path.join(self.test_dir, f'output_{notebook_name}')
        execute_notebook(get_notebook_path(notebook_name), result_path, {'var': 'It works'})
        nb = load_notebook_node(result_path)
        validate(nb)


class TestMinimalNotebook(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()

    def tearDown(self):
        shutil.rmtree(self.test_dir)

    def test_no_v3_language_backport(self):
        notebook_name = 'blank-vscode.ipynb'
        result_path = os.path.join(self.test_dir, f'output_{notebook_name}')
        execute_notebook(get_notebook_path(notebook_name), result_path, {'var': 'It works'})
        nb = load_notebook_node(result_path)
        validate(nb)


class TestExecuteWithCustomEngine(unittest.TestCase):
    class CustomEngine(engines.Engine):
        @classmethod
        def execute_managed_notebook(cls, nb_man, kernel_name, **kwargs):
            pass

        @classmethod
        def nb_kernel_name(cls, nb, name=None):
            return "my_custom_kernel"

        @classmethod
        def nb_language(cls, nb, language=None):
            return "my_custom_language"

    def setUp(self):
        self.test_dir = tempfile.mkdtemp()
        self.notebook_path = get_notebook_path('simple_execute.ipynb')
        self.nb_test_executed_fname = os.path.join(self.test_dir, 'output_simple_execute.ipynb')

        self._orig_papermill_engines = deepcopy(engines.papermill_engines)
        self._orig_translators = deepcopy(translators.papermill_translators)
        engines.papermill_engines.register("custom_engine", self.CustomEngine)
        translators.papermill_translators.register("my_custom_language", translators.PythonTranslator())

    def tearDown(self):
        shutil.rmtree(self.test_dir)
        engines.papermill_engines = self._orig_papermill_engines
        translators.papermill_translators = self._orig_translators

    @patch.object(CustomEngine, "execute_managed_notebook", wraps=CustomEngine.execute_managed_notebook)
    @patch("papermill.parameterize.translate_parameters", wraps=translators.translate_parameters)
    def test_custom_kernel_name_and_language(self, translate_parameters, execute_managed_notebook):
        """Tests execute against engine with custom implementations to fetch
        kernel name and language from the notebook object
        """
        execute_notebook(
            self.notebook_path,
            self.nb_test_executed_fname,
            engine_name="custom_engine",
            parameters={"msg": "fake msg"},
        )
        self.assertEqual(execute_managed_notebook.call_args[0], (ANY, "my_custom_kernel"))
        self.assertEqual(translate_parameters.call_args[0], (ANY, 'my_custom_language', {"msg": "fake msg"}, ANY))


class TestNotebookNodeInput(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.TemporaryDirectory()
        self.result_path = os.path.join(self.test_dir.name, 'output.ipynb')

    def tearDown(self):
        self.test_dir.cleanup()

    def test_notebook_node_input(self):
        input_nb = nbformat.read(get_notebook_path('simple_execute.ipynb'), as_version=4)
        execute_notebook(input_nb, self.result_path, {'msg': 'Hello'})
        test_nb = nbformat.read(self.result_path, as_version=4)
        self.assertEqual(test_nb.metadata.papermill.parameters, {'msg': 'Hello'})


class TestOutputFormatting(unittest.TestCase):
    def setUp(self):
        self.test_dir = tempfile.mkdtemp()

    def tearDown(self):
        shutil.rmtree(self.test_dir)

    def test_output_formatting(self):
        notebook_name = 'sysexit1.ipynb'
        result_path = os.path.join(self.test_dir, f'output_{notebook_name}')
        try:
            execute_notebook(get_notebook_path(notebook_name), result_path)
            # exception should be thrown by now
            self.assertFalse(True)
        except PapermillExecutionError as ex:
            self.assertEqual(ex.traceback[1], "\x1b[0;31mSystemExit\x1b[0m\x1b[0;31m:\x1b[0m 1\n")
            self.assertEqual(strip_color(ex.traceback[1]), "SystemExit: 1\n")

        nb = load_notebook_node(result_path)
        self.assertEqual(nb.cells[0].cell_type, "markdown")
        self.assertRegex(nb.cells[0].source, r'^<span .*<a href="#papermill-error-cell".*In \[2\].*</span>$')
        self.assertEqual(nb.cells[1].execution_count, 1)

        self.assertEqual(nb.cells[2].cell_type, "markdown")
        self.assertRegex(nb.cells[2].source, '<span id="papermill-error-cell" .*</span>')
        self.assertEqual(nb.cells[3].execution_count, 2)
        self.assertEqual(nb.cells[3].outputs[0].output_type, 'error')

        self.assertEqual(nb.cells[4].execution_count, None)