From: =?utf-8?q?Brigitta_Sip=C5=91cz?= Date: Tue, 20 Dec 2022 05:34:03 -0800 Subject: [PATCH] MAINT: fix for np 1.24 (#858) * CI: update actions versions * CI: do only weekly cron * MAINT: tox4 compatibility fixes * MAINT: temporarily limit numpy version * CI: update codecov action version, too * MAINT: fix compatibility with np 1.24 * MAINT: remove version pin * MAINT: remove travis CI things --- .github/workflows/publish.yml | 8 ++++---- spectral_cube/_moments.py | 2 +- spectral_cube/dask_spectral_cube.py | 2 +- spectral_cube/spectral_cube.py | 8 ++++---- spectral_cube/tests/test_moments.py | 2 +- spectral_cube/tests/test_spectral_cube.py | 15 +++------------ 6 files changed, 14 insertions(+), 23 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 708072b..3777b04 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -7,8 +7,8 @@ jobs: name: Build source distribution runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 name: Install Python with: python-version: '3.9' @@ -16,7 +16,7 @@ jobs: run: python -m pip install build - name: Build sdist run: python -m build --sdist --wheel --outdir dist/ . - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v3 with: path: dist/* @@ -26,7 +26,7 @@ jobs: runs-on: ubuntu-latest if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') steps: - - uses: actions/download-artifact@v2 + - uses: actions/download-artifact@v3 with: name: artifact path: dist diff --git a/spectral_cube/_moments.py b/spectral_cube/_moments.py index 04ea68c..b19bcbd 100644 --- a/spectral_cube/_moments.py +++ b/spectral_cube/_moments.py @@ -46,7 +46,7 @@ def _slice0(cube, axis): view = [slice(None)] * 3 - valid = np.zeros(shp, dtype=np.bool) + valid = np.zeros(shp, dtype=bool) for i in range(cube.shape[axis]): view[axis] = i plane = cube._get_filled_data(fill=np.nan, view=tuple(view)) diff --git a/spectral_cube/dask_spectral_cube.py b/spectral_cube/dask_spectral_cube.py index e4121f6..d13c1f8 100644 --- a/spectral_cube/dask_spectral_cube.py +++ b/spectral_cube/dask_spectral_cube.py @@ -1528,7 +1528,7 @@ class DaskVaryingResolutionSpectralCube(DaskSpectralCubeMixin, VaryingResolution # We need to pass in the beams to dask, so we hide them inside an object array # that can then be chunked like the data. - beams = da.from_array(np.array(beams, dtype=np.object) + beams = da.from_array(np.array(beams, dtype=object) .reshape((len(beams), 1, 1)), chunks=(-1, -1, -1)) needs_beam_ratio = self.unit.is_equivalent(u.Jy / u.beam) diff --git a/spectral_cube/spectral_cube.py b/spectral_cube/spectral_cube.py index 2efbe3c..7544e38 100644 --- a/spectral_cube/spectral_cube.py +++ b/spectral_cube/spectral_cube.py @@ -2787,7 +2787,7 @@ class BaseSpectralCube(BaseNDClass, MaskableArrayMixinClass, if use_memmap: ntf = tempfile.NamedTemporaryFile(dir=memmap_dir) - outcube = np.memmap(ntf, mode='w+', shape=self.shape, dtype=np.float) + outcube = np.memmap(ntf, mode='w+', shape=self.shape, dtype=float) else: if self._is_huge and not self.allow_huge_operations: raise ValueError("Applying a function without ``use_memmap`` " @@ -2797,7 +2797,7 @@ class BaseSpectralCube(BaseNDClass, MaskableArrayMixinClass, "set ``use_memmap=True`` or set " "``cube.allow_huge_operations=True`` to " "override this restriction.") - outcube = np.empty(shape=self.shape, dtype=np.float) + outcube = np.empty(shape=self.shape, dtype=float) if num_cores == 1 and parallel: warnings.warn("parallel=True was specified but num_cores=1. " @@ -3352,9 +3352,9 @@ class BaseSpectralCube(BaseNDClass, MaskableArrayMixinClass, view_newaxis = tuple(view_newaxis) ntf = tempfile.NamedTemporaryFile() - dsarr = np.memmap(ntf, mode='w+', shape=newshape, dtype=np.float) + dsarr = np.memmap(ntf, mode='w+', shape=newshape, dtype=float) ntf2 = tempfile.NamedTemporaryFile() - mask = np.memmap(ntf2, mode='w+', shape=newshape, dtype=np.bool) + mask = np.memmap(ntf2, mode='w+', shape=newshape, dtype=bool) for ii in progressbar(range(newshape[axis])): view_fulldata = makeslice_local(ii*factor) view_newdata = makeslice_local(ii, nsteps=1) diff --git a/spectral_cube/tests/test_moments.py b/spectral_cube/tests/test_moments.py index 4feb67d..3043dd5 100644 --- a/spectral_cube/tests/test_moments.py +++ b/spectral_cube/tests/test_moments.py @@ -58,7 +58,7 @@ MOMENTSu = MOMENTS def moment_cube(): - cube = np.arange(27).reshape([3, 3, 3]).astype(np.float) + cube = np.arange(27).reshape([3, 3, 3]).astype(float) wcs = WCS(naxis=3) wcs.wcs.ctype = ['RA---TAN', 'DEC--TAN', 'VELO'] # choose values to minimize spherical distortions diff --git a/spectral_cube/tests/test_spectral_cube.py b/spectral_cube/tests/test_spectral_cube.py index 0057a6f..6ce7f4e 100644 --- a/spectral_cube/tests/test_spectral_cube.py +++ b/spectral_cube/tests/test_spectral_cube.py @@ -76,8 +76,6 @@ except ImportError: scipyOK = False import os -# if ON_TRAVIS is set, we're on travis. -on_travis = bool(os.environ.get('ON_TRAVIS')) from radio_beam import Beam, Beams from radio_beam.utils import BeamError @@ -637,14 +635,7 @@ class TestNumpyMethods(BaseTest): # regular median. scmed = self.c.apply_numpy_function(np.median, axis=0) - # this checks whether numpy <=1.9.3 has a bug? - # as far as I can tell, np==1.9.3 no longer has this bug/feature - #if LooseVersion(np.__version__) <= LooseVersion('1.9.3'): - # # print statements added so we get more info in the travis builds - # print("Numpy version is: {0}".format(LooseVersion(np.__version__))) - # assert np.count_nonzero(np.isnan(scmed)) == 5 - #else: - # print("Numpy version is: {0}".format(LooseVersion(np.__version__))) + assert np.count_nonzero(np.isnan(scmed)) == 6 scmed = self.c.apply_numpy_function(np.nanmedian, axis=0) @@ -991,7 +982,7 @@ def test_with_mask_with_boolean_array(use_dask): def test_with_mask_with_good_array_shape(use_dask): cube = _dummy_cube(use_dask) - mask = np.zeros((1, 5), dtype=np.bool) + mask = np.zeros((1, 5), dtype=bool) cube2 = cube.with_mask(mask, inherit_mask=False) assert isinstance(cube2._mask, BooleanArrayMask) np.testing.assert_equal(cube2._mask._mask, mask.reshape((1, 1, 5))) @@ -999,7 +990,7 @@ def test_with_mask_with_good_array_shape(use_dask): def test_with_mask_with_bad_array_shape(use_dask): cube = _dummy_cube(use_dask) - mask = np.zeros((5, 5), dtype=np.bool) + mask = np.zeros((5, 5), dtype=bool) with pytest.raises(ValueError) as exc: cube.with_mask(mask) assert exc.value.args[0] == ("Mask shape is not broadcastable to data shape: "