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Tests should collect without optional dependencies #10246
Description
Currently we silence import issues at test collection (see scientific-python/pytest-doctestplus#108 and xrefs therein) which is the same behaviour as doctest would do when doctest_ignore_import_error is opted in.
Some of the offending modules are also picked up at import tests in #7952
Here is a hopefully full list:
$ pytest astropy
================================================= test session starts ==================================================
platform darwin -- Python 3.8.2, pytest-5.4.1, py-1.8.1, pluggy-0.13.1
Running tests with Astropy version 4.1.dev1224+gf3060a1f1.
Running tests in astropy.
Date: 2020-04-30T16:29:49
Platform: macOS-10.13.6-x86_64-i386-64bit
Executable: /Users/bsipocz/miniconda/envs/test_imports/bin/python
Full Python Version:
3.8.2 (default, Mar 26 2020, 10:43:30)
[Clang 4.0.1 (tags/RELEASE_401/final)]
encodings: sys: utf-8, locale: UTF-8, filesystem: utf-8
byteorder: little
float info: dig: 15, mant_dig: 15
Package versions:
Numpy: 1.18.3
Scipy: not available
Matplotlib: not available
h5py: not available
Pandas: not available
Cython: not available
Scikit-image: not available
asdf: not available
Using Astropy options: remote_data: none.
rootdir: /Users/bsipocz/munka/devel/astropy, inifile: setup.cfg
plugins: arraydiff-0.3, remotedata-0.3.2, hypothesis-5.10.4, filter-subpackage-0.1.1, openfiles-0.5.0, astropy-header-0.1.2, cov-2.8.1, doctestplus-0.7.0.dev0
collected 14083 items / 36 errors / 72 skipped / 13975 selected
======================================================== ERRORS ========================================================
___________________________________ ERROR collecting astropy/_erfa/setup_package.py ____________________________________
astropy/_erfa/setup_package.py:9: in <module>
from extension_helpers import import_file
E ModuleNotFoundError: No module named 'extension_helpers'
__________________________________ ERROR collecting astropy/io/fits/setup_package.py ___________________________________
astropy/io/fits/setup_package.py:12: in <module>
from extension_helpers import pkg_config, get_compiler
E ModuleNotFoundError: No module named 'extension_helpers'
_______________________________________ ERROR collecting astropy/io/misc/yaml.py _______________________________________
astropy/io/misc/yaml.py:81: in <module>
import yaml
E ModuleNotFoundError: No module named 'yaml'
During handling of the above exception, another exception occurred:
astropy/io/misc/yaml.py:83: in <module>
raise ImportError('`import yaml` failed, PyYAML package is required for YAML')
E ImportError: `import yaml` failed, PyYAML package is required for YAML
__________________________________ ERROR collecting astropy/io/misc/asdf/extension.py __________________________________
astropy/io/misc/asdf/extension.py:6: in <module>
from asdf.extension import AsdfExtension, BuiltinExtension
E ModuleNotFoundError: No module named 'asdf'
____________________________________ ERROR collecting astropy/io/misc/asdf/types.py ____________________________________
astropy/io/misc/asdf/types.py:4: in <module>
from asdf.types import CustomType, ExtensionTypeMeta
E ModuleNotFoundError: No module named 'asdf'
___________________________ ERROR collecting astropy/io/misc/asdf/tags/coordinates/angle.py ____________________________
astropy/io/misc/asdf/tags/coordinates/angle.py:6: in <module>
from astropy.io.misc.asdf.tags.unit.quantity import QuantityType
astropy/io/misc/asdf/tags/unit/quantity.py:7: in <module>
from asdf.tags.core import NDArrayType
E ModuleNotFoundError: No module named 'asdf'
_______________________ ERROR collecting astropy/io/misc/asdf/tags/coordinates/earthlocation.py ________________________
astropy/io/misc/asdf/tags/coordinates/earthlocation.py:5: in <module>
from ...types import AstropyType
astropy/io/misc/asdf/types.py:4: in <module>
from asdf.types import CustomType, ExtensionTypeMeta
E ModuleNotFoundError: No module named 'asdf'
___________________________ ERROR collecting astropy/io/misc/asdf/tags/coordinates/frames.py ___________________________
astropy/io/misc/asdf/tags/coordinates/frames.py:6: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
_______________________ ERROR collecting astropy/io/misc/asdf/tags/coordinates/representation.py _______________________
astropy/io/misc/asdf/tags/coordinates/representation.py:5: in <module>
from astropy.io.misc.asdf.types import AstropyType
astropy/io/misc/asdf/types.py:4: in <module>
from asdf.types import CustomType, ExtensionTypeMeta
E ModuleNotFoundError: No module named 'asdf'
__________________________ ERROR collecting astropy/io/misc/asdf/tags/coordinates/skycoord.py __________________________
astropy/io/misc/asdf/tags/coordinates/skycoord.py:6: in <module>
from ...types import AstropyType
astropy/io/misc/asdf/types.py:4: in <module>
from asdf.types import CustomType, ExtensionTypeMeta
E ModuleNotFoundError: No module named 'asdf'
_______________________________ ERROR collecting astropy/io/misc/asdf/tags/fits/fits.py ________________________________
astropy/io/misc/asdf/tags/fits/fits.py:9: in <module>
from astropy.io.misc.asdf.types import AstropyType, AstropyAsdfType
astropy/io/misc/asdf/types.py:4: in <module>
from asdf.types import CustomType, ExtensionTypeMeta
E ModuleNotFoundError: No module named 'asdf'
______________________________ ERROR collecting astropy/io/misc/asdf/tags/table/table.py _______________________________
astropy/io/misc/asdf/tags/table/table.py:5: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
_______________________________ ERROR collecting astropy/io/misc/asdf/tags/time/time.py ________________________________
astropy/io/misc/asdf/tags/time/time.py:7: in <module>
from asdf.versioning import AsdfSpec
E ModuleNotFoundError: No module named 'asdf'
_____________________________ ERROR collecting astropy/io/misc/asdf/tags/time/timedelta.py _____________________________
astropy/io/misc/asdf/tags/time/timedelta.py:9: in <module>
from ...types import AstropyType
astropy/io/misc/asdf/types.py:4: in <module>
from asdf.types import CustomType, ExtensionTypeMeta
E ModuleNotFoundError: No module named 'asdf'
____________________________ ERROR collecting astropy/io/misc/asdf/tags/transform/basic.py _____________________________
astropy/io/misc/asdf/tags/transform/basic.py:4: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
___________________________ ERROR collecting astropy/io/misc/asdf/tags/transform/compound.py ___________________________
astropy/io/misc/asdf/tags/transform/compound.py:3: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
______________________ ERROR collecting astropy/io/misc/asdf/tags/transform/functional_models.py _______________________
astropy/io/misc/asdf/tags/transform/functional_models.py:7: in <module>
from .basic import TransformType
astropy/io/misc/asdf/tags/transform/basic.py:4: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
_____________________________ ERROR collecting astropy/io/misc/asdf/tags/transform/math.py _____________________________
astropy/io/misc/asdf/tags/transform/math.py:10: in <module>
from .basic import TransformType
astropy/io/misc/asdf/tags/transform/basic.py:4: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
_______________________ ERROR collecting astropy/io/misc/asdf/tags/transform/physical_models.py ________________________
astropy/io/misc/asdf/tags/transform/physical_models.py:8: in <module>
from .basic import TransformType
astropy/io/misc/asdf/tags/transform/basic.py:4: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
__________________________ ERROR collecting astropy/io/misc/asdf/tags/transform/polynomial.py __________________________
astropy/io/misc/asdf/tags/transform/polynomial.py:7: in <module>
from asdf.versioning import AsdfVersion
E ModuleNotFoundError: No module named 'asdf'
__________________________ ERROR collecting astropy/io/misc/asdf/tags/transform/powerlaws.py ___________________________
astropy/io/misc/asdf/tags/transform/powerlaws.py:7: in <module>
from .basic import TransformType
astropy/io/misc/asdf/tags/transform/basic.py:4: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
_________________________ ERROR collecting astropy/io/misc/asdf/tags/transform/projections.py __________________________
astropy/io/misc/asdf/tags/transform/projections.py:7: in <module>
from .basic import TransformType
astropy/io/misc/asdf/tags/transform/basic.py:4: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
___________________________ ERROR collecting astropy/io/misc/asdf/tags/transform/tabular.py ____________________________
astropy/io/misc/asdf/tags/transform/tabular.py:9: in <module>
from .basic import TransformType
astropy/io/misc/asdf/tags/transform/basic.py:4: in <module>
from asdf import tagged
E ModuleNotFoundError: No module named 'asdf'
____________________________ ERROR collecting astropy/io/misc/asdf/tags/unit/equivalency.py ____________________________
astropy/io/misc/asdf/tags/unit/equivalency.py:8: in <module>
from astropy.io.misc.asdf.types import AstropyType
astropy/io/misc/asdf/types.py:4: in <module>
from asdf.types import CustomType, ExtensionTypeMeta
E ModuleNotFoundError: No module named 'asdf'
_____________________________ ERROR collecting astropy/io/misc/asdf/tags/unit/quantity.py ______________________________
astropy/io/misc/asdf/tags/unit/quantity.py:7: in <module>
from asdf.tags.core import NDArrayType
E ModuleNotFoundError: No module named 'asdf'
_______________________________ ERROR collecting astropy/io/misc/asdf/tags/unit/unit.py ________________________________
astropy/io/misc/asdf/tags/unit/unit.py:7: in <module>
from astropy.io.misc.asdf.types import AstropyAsdfType
astropy/io/misc/asdf/types.py:4: in <module>
from asdf.types import CustomType, ExtensionTypeMeta
E ModuleNotFoundError: No module named 'asdf'
__________________________________ ERROR collecting astropy/modeling/setup_package.py __________________________________
astropy/modeling/setup_package.py:9: in <module>
from extension_helpers import import_file
E ModuleNotFoundError: No module named 'extension_helpers'
____________________________________ ERROR collecting astropy/tests/image_tests.py _____________________________________
astropy/tests/image_tests.py:1: in <module>
import matplotlib
E ModuleNotFoundError: No module named 'matplotlib'
_________________ ERROR collecting astropy/timeseries/periodograms/lombscargle/fix-parents-astropy.py __________________
astropy/timeseries/periodograms/lombscargle/fix-parents-astropy.py:7: in <module>
commit = os.environ['GIT_COMMIT']
../../../miniconda/envs/test_imports/lib/python3.8/os.py:675: in __getitem__
raise KeyError(key) from None
E KeyError: 'GIT_COMMIT'
________ ERROR collecting astropy/timeseries/periodograms/lombscargle/implementations/lomb_scargle_multiband.py ________
astropy/timeseries/periodograms/lombscargle/implementations/lomb_scargle_multiband.py:11: in <module>
from .modeler import PeriodicModelerMultiband
astropy/timeseries/periodograms/lombscargle/implementations/modeler.py:5: in <module>
from .optimizer import LinearScanOptimizer
E ModuleNotFoundError: No module named 'astropy.timeseries.periodograms.lombscargle.implementations.optimizer'
_______________ ERROR collecting astropy/timeseries/periodograms/lombscargle/implementations/modeler.py ________________
astropy/timeseries/periodograms/lombscargle/implementations/modeler.py:5: in <module>
from .optimizer import LinearScanOptimizer
E ModuleNotFoundError: No module named 'astropy.timeseries.periodograms.lombscargle.implementations.optimizer'
___________ ERROR collecting astropy/timeseries/periodograms/lombscargle/implementations/naive_multiband.py ____________
astropy/timeseries/periodograms/lombscargle/implementations/naive_multiband.py:12: in <module>
from scipy.stats import mode
E ModuleNotFoundError: No module named 'scipy'
__ ERROR collecting astropy/timeseries/periodograms/lombscargle/implementations/tests/test_lomb_scargle_multiband.py ___
astropy/timeseries/periodograms/lombscargle/implementations/tests/test_lomb_scargle_multiband.py:5: in <module>
from nose import SkipTest
E ModuleNotFoundError: No module named 'nose'
__ ERROR collecting astropy/timeseries/periodograms/lombscargle/implementations/tests/test_lomb_scargle_multiband.py ___
ImportError while importing test module '/Users/bsipocz/munka/devel/astropy/astropy/timeseries/periodograms/lombscargle/implementations/tests/test_lomb_scargle_multiband.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
astropy/timeseries/periodograms/lombscargle/implementations/tests/test_lomb_scargle_multiband.py:5: in <module>
from nose import SkipTest
E ModuleNotFoundError: No module named 'nose'
_________________________________ ERROR collecting astropy/utils/xml/setup_package.py __________________________________
astropy/utils/xml/setup_package.py:10: in <module>
from extension_helpers import pkg_config
E ModuleNotFoundError: No module named 'extension_helpers'
____________________________________ ERROR collecting astropy/wcs/setup_package.py _____________________________________
astropy/wcs/setup_package.py:16: in <module>
from extension_helpers import import_file, write_if_different, get_compiler, pkg_config
E ModuleNotFoundError: No module named 'extension_helpers'
=============================================== short test summary info ================================================
Activity
bsipocz commentedon May 1, 2020
(ignore the timeseries ones, that's due to some local only files I haven't noticed in time)
astrofrog commentedon May 1, 2020
Fundamentally the issue is that pytest-doctestplus shouldn't be trying to import all files in the first place, I think it should be possible to extract docstrings/doctests without importing. I think it's ok to have imports in
setup_package.pythat are build-time requirements only, and don't have to be available at testing time, so I don't consider it a bug in astropy core as such.bsipocz commentedon May 1, 2020
Ok, that indeed makes sense for the setup_package/extension helpers case. But asdf and pyyaml are different beasts, and ideally should behave similarly to e.g h5py or pandas which are patched around to check for availability first
astrofrog commentedon May 1, 2020
I agree in general, although in the case of asdf I think it's reasonable to expect that importing astropy.io.misc.asdf would require asdf?
bsipocz commentedon May 1, 2020
I agree that it seems reasonable, but some other modules don't have the issue (though one can argue they are much more simple, e.g.
astropy.io.mist.hdf5)pllim commentedon May 1, 2020
I'll have a look... see below
but no promises.yaml-- MNT: Make yaml import truly optional in io.misc.yaml #10257matplotlib-- MNT: Make matplotlib import truly optional in image_tests.py #10259asdf-- MNT: Make asdf import truly optional in io.misc.asdf #10260 (closed without merge)vvasuki commentedon Sep 21, 2020
This probably downs our downstream tests - https://github.com/sanskrit-coders/jyotisha/runs/1142973750?check_suite_focus=true
EDIT - Opened separate issue - #10752 .
Limit astropy version to prevent docs breaking