Fix tests for numpy 2.0 (#917)

* remove NaNs for numpy 2.0 * More NaNs to fix * Bump python testing versions up (mostly to py311) * add py310 test for newest casa versions * Add casadata fix * Add a py312 min dep test * Fix workflow syntax * '3.10' to avoid 3.1 version check * Remove ptp and nansum methods that were removed in ndarray as methods in numpy 2 * Force numpy<2 for tests with CASA * Don't think we need to set the env variable in setup * Force creation of the data folder? * Missed updating nansum * Attempt to ignore casadata preamble on non-casa builds (esp mac and windows) * Fix yml structure * Fix logic * Try adding manual update cmds for casadata * Add casaconfig install * only pass str to casa tasks * Check on desc dict structure for on-going test failure * try passing dict to beam kwarg in setrestoringbeam * TEMP: print out keys in the desc dict * Extra open/close? * add another temp print line to figure out what's going wrong with setting the beams * setrestoringbeam: hitting a type error? * Clean up unneeded code for ia.setrestoringbeam
radio-astro-tools · Oct 13, 2024 · 9919364 · 9919364
1 parent 8ae6705
commit 9919364
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -15,10 +15,6 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - os: ubuntu-latest
-            python-version: 3.9
-            name: Py3.9 mindeps
-            toxenv: py39-test
           - os: ubuntu-latest
             python-version: '3.10'
             name: Py3.10 mindeps
@@ -28,9 +24,13 @@ jobs:
             name: Py3.11 mindeps
             toxenv: py311-test
           - os: ubuntu-latest
-            python-version: 3.9
-            name: Py3.9 no visualization + coverage
-            toxenv: py39-test-noviz-cov
+            python-version: 3.12
+            name: Py3.12 mindeps
+            toxenv: py312-test
+          - os: ubuntu-latest
+            python-version: 3.11
+            name: Py3.11 no visualization + coverage
+            toxenv: py311-test-noviz-cov
           - os: ubuntu-latest
             python-version: 3.8
             name: Py3.8 mindeps
@@ -44,47 +44,51 @@ jobs:
             name: Py3.9 all
             toxenv: py39-test-viz-noviz
           - os: ubuntu-latest
-            python-version: 3.9
-            name: Py3.9 dev
-            toxenv: py39-test-dev
+            python-version: 3.11
+            name: Py3.11 dev
+            toxenv: py311-test-dev
           - os: ubuntu-latest
-            python-version: 3.9
-            name: Py3.9 viz
-            toxenv: py39-test-viz
+            python-version: 3.11
+            name: Py3.11 viz
+            toxenv: py311-test-viz
               #- os: ubuntu-latest
               #  python-version: 3.9
               #  name: Py3.9 viz w/yt & glue
               #  toxenv: py39-test-viz-viz_extra
           - os: ubuntu-latest
-            python-version: 3.9
-            name: Py3.9 all dev
-            toxenv: py39-test-viz-noviz-dev
+            python-version: 3.11
+            name: Py3.11 all dev
+            toxenv: py311-test-viz-noviz-dev
           - os: ubuntu-latest
             python-version: 3.8
             name: Py3.8 mindeps and CASA
             toxenv: py38-test-casa
           - os: ubuntu-latest
-            python-version: 3.9
-            name: Py3.9, noviz, dev
-            toxenv: py39-test-noviz-dev
+            python-version: '3.10'
+            name: Py3.10 mindeps and CASA
+            toxenv: py310-test-casa
+          - os: ubuntu-latest
+            python-version: 3.11
+            name: Py3.11, noviz, dev
+            toxenv: py311-test-noviz-dev
           - os: ubuntu-latest
             python-version: 3.8
             name: Py3.8 noviz (except CASA)
             toxenv: py38-test-noviz
           - os: macos-latest
-            python-version: 3.9
-            name: Py3.9 noviz (except CASA) MacOS X
+            python-version: 3.11
+            name: Py3.11 noviz (except CASA) MacOS X
             toxenv: py39-test-noviz
           - os: windows-latest
-            python-version: 3.9
-            name: Py3.9, noviz Windows
-            toxenv: py39-test-noviz-dev
+            python-version: 3.11
+            name: Py3.11, noviz Windows
+            toxenv: py311-test-noviz-dev
           - os: windows-latest
-            python-version: 3.9
-            name: Py3.9, noviz, dev; Windows
-            toxenv: py39-test-noviz-dev
+            python-version: 3.11
+            name: Py3.11, noviz, dev; Windows
+            toxenv: py311-test-noviz-dev
           - os: ubuntu-latest
-            python-version: 3.9
+            python-version: 3.11
             name: Documentation
             toxenv: build_docs
 
@@ -95,9 +99,25 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install testing dependencies
-      run: python -m pip install tox
-    - name: Run tests with ${{ matrix.name }}
+      run: python -m pip install tox codecov
+
+
+    - name: Run tests with ${{ matrix.name }} (optionally with CASA)
+      if: ${{ !contains(matrix.toxenv,'-casa') }}
       run: tox -v -e ${{ matrix.toxenv }}
+    - name: Run tests with ${{ matrix.name }} (no CASA)
+      if: ${{ contains(matrix.toxenv,'-casa') }}
+      run: |
+          pip install casaconfig
+          mkdir ${GITHUB_WORKSPACE}/.casa
+          mkdir ${GITHUB_WORKSPACE}/.casa/data
+          chmod 777 -R ${GITHUB_WORKSPACE}/.casa
+          echo "datapath=['${GITHUB_WORKSPACE}/.casa/data']; measurespath=datapath[0]; measures_auto_update=True; data_auto_update=True" > $GITHUB_WORKSPACE/config.py
+          pip install casadata
+          # https://casadocs.readthedocs.io/en/stable/notebooks/external-data.html#Populating-the-Data-Directory-Manually
+          python -m casaconfig --update-all
+          python -m casaconfig --current-data
+          CASASITECONFIG=$GITHUB_WORKSPACE/config.py tox -v -e ${{ matrix.toxenv }}
     - name: Upload coverage to codecov
       if: ${{ contains(matrix.toxenv,'-cov') }}
       uses: codecov/codecov-action@v4

diff --git a/spectral_cube/analysis_utilities.py b/spectral_cube/analysis_utilities.py
@@ -70,12 +70,12 @@ def fourier_shift(x, shift, axis=0, add_pad=False, pad_size=None):
 
     # Check if there are all NaNs before shifting
     if nanmask.all():
-        return np.array([np.NaN] * pad_mask.size)
+        return np.array([np.nan] * pad_mask.size)
 
     nonan_shift = _fourier_shifter(pad_nonan, shift, axis)
     if shift_mask:
         mask_shift = _fourier_shifter(pad_mask, shift, axis) > 0.5
-        nonan_shift[mask_shift] = np.NaN
+        nonan_shift[mask_shift] = np.nan
 
     return nonan_shift
 

diff --git a/spectral_cube/conftest.py b/spectral_cube/conftest.py
@@ -396,15 +396,15 @@ def data_vda_beams_image(tmp_path):
     hdul.writeto(tmp_path / 'vda_beams.fits')
     from casatools import image
     ia = image()
-    ia.fromfits(infile=tmp_path / 'vda_beams.fits',
-                outfile=tmp_path / 'vda_beams.image',
+    ia.fromfits(infile=str(tmp_path / 'vda_beams.fits'),
+                outfile=str(tmp_path / 'vda_beams.image'),
                 overwrite=True)
     for (bmaj, bmin, bpa, chan, pol) in beams.data:
-        ia.setrestoringbeam(major={'unit': 'arcsec', 'value': bmaj},
-                            minor={'unit': 'arcsec', 'value': bmin},
-                            pa={'unit': 'deg', 'value': bpa},
-                            channel=chan,
-                            polarization=pol)
+        ia.setrestoringbeam(beam={'major': {'unit': 'arcsec', 'value': float(bmaj)},
+                                  'minor': {'unit': 'arcsec', 'value': float(bmin)},
+                                  'positionangle': {'unit': 'deg', 'value': float(bpa)}},
+                            channel=int(chan),
+                            polarization=int(pol))
     ia.close()
     return tmp_path / 'vda_beams.image'
 

diff --git a/spectral_cube/io/casa_image.py b/spectral_cube/io/casa_image.py
@@ -105,6 +105,11 @@ def load_casa_image(filename, skipdata=False, memmap=True,
     elif 'beams' in beam_:
         bdict = beam_['beams']
 
+        # NOTE: temp to check failing test
+        print(desc['_keywords_']['coords'])
+        print(list(desc['_keywords_']['coords'].keys()))
+
+
         stokes_params = desc['_keywords_']['coords']['stokes1']['stokes']
 
         nbeams = len(bdict)

diff --git a/spectral_cube/lower_dimensional_structures.py b/spectral_cube/lower_dimensional_structures.py
@@ -815,7 +815,7 @@ def __getattribute__(self, attrname):
         # `Quantity`, but for now this approach works.... we just have
         # to add more functions to this list.
         if attrname in ('min', 'max', 'std', 'mean', 'sum', 'cumsum',
-                        'nansum', 'ptp', 'var'):
+                        'var'):
             return getattr(self.quantity, attrname)
         else:
             return super(BaseOneDSpectrum, self).__getattribute__(attrname)

diff --git a/spectral_cube/spectral_cube.py b/spectral_cube/spectral_cube.py
@@ -835,7 +835,7 @@ def _argmaxmin_world(self, axis, method, **kwargs):
 
         # Compute whether the mask has any valid data along `axis`
         collapsed_mask = self.mask.include().any(axis=axis)
-        out[~collapsed_mask] = np.NaN
+        out[~collapsed_mask] = np.nan
 
         # Return a Projection.
         new_wcs = wcs_utils.drop_axis(self._wcs, np2wcs[axis])
@@ -3274,7 +3274,7 @@ def spectral_interpolate(self, spectral_grid,
                     newmask[outslice,iy,ix] = interped
             else:
                 newmask[:, iy, ix] = False
-                newcube[:, iy, ix] = np.NaN
+                newcube[:, iy, ix] = np.nan
 
             update_function()
 

diff --git a/spectral_cube/tests/test_analysis_functions.py b/spectral_cube/tests/test_analysis_functions.py
@@ -31,11 +31,11 @@ def test_shift():
     # With part masked
     masked_spectrum = true_spectrum.copy()
     mask = np.abs(spectral_axis.value) <= 30
-    masked_spectrum[~mask] = np.NaN
+    masked_spectrum[~mask] = np.nan
 
     rolled_mask = np.roll(mask, 10)
     rolled_masked_spectrum = rolled_spectrum.copy()
-    rolled_masked_spectrum[~rolled_mask] = np.NaN
+    rolled_masked_spectrum[~rolled_mask] = np.nan
 
     shift_spectrum = fourier_shift(masked_spectrum, 10)
 
@@ -413,7 +413,7 @@ def test_stacking_noisy(use_dask):
 
 #     cov = fit_g.fit_info['param_cov']
 #     if cov is None:
-#         cov = np.zeros((3, 3)) * np.NaN
+#         cov = np.zeros((3, 3)) * np.nan
 #     parvals = g_fit.parameters
 
 #     parerrs = np.sqrt(np.diag(cov))

diff --git a/spectral_cube/tests/test_projection.py b/spectral_cube/tests/test_projection.py
@@ -635,7 +635,7 @@ def test_spectral_interpolate_with_mask(data_522_delta, use_dask):
     # The output makes CDELT3 > 0 (reversed spectral axis) so the masked
     # portion are the final 2 channels.
     np.testing.assert_almost_equal(result.filled_data[:].value,
-                                   [0.0, 0.5, np.NaN, np.NaN])
+                                   [0.0, 0.5, np.nan, np.nan])
 
 
 def test_spectral_interpolate_reversed(data_522_delta, use_dask):
@@ -718,7 +718,7 @@ def test_1d_slices(data_255_delta, use_dask):
                     reason='https://github.com/numpy/numpy/issues/20699')
 @pytest.mark.parametrize('method',
                          ('min', 'max', 'std', 'mean', 'sum', 'cumsum',
-                          'nansum', 'ptp', 'var'),
+                          'var'),
                         )
 def test_1d_slice_reductions(method, data_255_delta, use_dask):
 

diff --git a/spectral_cube/tests/test_regrid.py b/spectral_cube/tests/test_regrid.py
@@ -129,7 +129,7 @@ def test_reproject(use_memmap, data_adv, use_dask):
     result = cube.reproject(header_out, use_memmap=use_memmap)
 
     assert result.shape == (cube.shape[0], 5, 4)
-    
+
     # empirically, this is how close we can get after https://github.com/astropy/astropy/pull/14508
     tolerance = 1e-12
 
@@ -346,7 +346,7 @@ def test_spectral_interpolate_with_mask(data_522_delta, use_dask):
     # The output makes CDELT3 > 0 (reversed spectral axis) so the masked
     # portion are the final 2 channels.
     np.testing.assert_almost_equal(result[:, 0, 0].value,
-                                   [0.0, 0.5, np.NaN, np.NaN])
+                                   [0.0, 0.5, np.nan, np.nan])
 
     assert cube.wcs.wcs.compare(orig_wcs.wcs)
 

diff --git a/tox.ini b/tox.ini
@@ -1,6 +1,6 @@
 [tox]
 envlist =
-    py{38,39,310,311}-test{,-dev,-noviz,-viz,-viz_extra,-cov,-noopenfiles}
+    py{38,39,310,311,312}-test{,-dev,-noviz,-viz,-viz_extra,-cov,-noopenfiles}
     build_docs
     codestyle
 requires =
@@ -14,7 +14,7 @@ passenv = HOME,DISPLAY,LC_ALL,LC_CTYPE,ON_TRAVIS
 changedir = .tmp/{envname}
 description = run tests with pytest
 deps =
-    casa: numpy
+    casa: numpy<2.0.0
     casa: scipy
     casa: matplotlib
     casa: casatools