Testing issue: astropy@7.0.1 install with test dependencies fails.

[Sinan81]

Steps to reproduce the failure(s) or link(s) to test output(s)

I tried installing test dependencies of astropy via spack install --test=root astropy which somehow ends up running the install test. Afterwards, install test fails since it can't find astropy package.

More details to be provided soon. Will ping maintainers after looking into the issue a bit further.

Error message

python can't import astropy module (since it's not installed yet?), hence can't even run pytest, although I'm not sure if it should be running pytests during install phase.

Information on your system or the test runner

$ spack debug report

• Spack: 1.0.2
• Builtin repo: /mnt/local/sbulut/spack-1.0.2/dot.spack.user_cache/package_repos/fncqgg4/repos/spack_repo/builtin (32c54f0)
• Python: 3.9.21
• Platform: linux-rhel9-haswell

Additional information

No response

General information

• I have reported the version of Spack/Python/Platform/Runner
• I have run spack maintainers <name-of-the-package> and @mentioned any maintainers
• I have uploaded any available logs
• I have searched the issues of this repo and believe this is not a duplicate

[Sinan81]

managed to workaround the glitch by replacing type="test" with type=("build","run"). Now spack testing works:

$ spack test run /gz2yr25g                                                                                                                                                                                                                                                   ==> Spack test d3tmdpsmqxyvsyigzhdlzayacexwqv66                                                                                                                                                                                                                              ==> Testing package py-astropy-7.0.1-gz2yr25                                                                                                                                                                                                                                 ============================== 1 passed of 1 spec ==============================

However, when I run astropy.test() manually, I get some errors some of which due to missing optional dependencies, which should have been skipped.

...
>>> astropy.test()                                                                                                                                                                                                                                                           /mnt/local/sbulut/spack-1.0.2/opt/spack/linux-x86_64_v3/py-pytest-8.2.1-ehldd3bn4ouc3ik3jahyx2ngeh6tuvbt/lib/python3.11/site-packages/_pytest/assertion/rewrite.py:178: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.                                                                                                                                   exec(co, module.__dict__)                                                                                                                                                                                                                                                  =================================================================================== test session starts ====================================================================================                                                                                 platform linux -- Python 3.11.11, pytest-8.2.1, pluggy-1.5.0                                                                                                                                                                                                                 
Running tests with Astropy version 7.0.1.
Running tests in /mnt/local/sbulut/spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy.

Date: 2025-10-10T14:20:59

Platform: Linux-5.14.0-503.29.1.el9_5.x86_64-x86_64-with-glibc2.34

Executable: /mnt/local/sbulut/spack-1.0.2/opt/spack/linux-x86_64_v3/python-venv-1.0-cdzzlzep7muajjrszpyw2w7bgejs4idv/bin/python

Full Python Version:
3.11.11 (main, Oct 10 2025, 14:08:02) [GCC 11.5.0 20240719 (Red Hat 11.5.0-5)]

encodings: sys: utf-8, locale: UTF-8, filesystem: utf-8
byteorder: little
float info: dig: 15, mant_dig: 15

Package versions:
Numpy: 1.26.4
Scipy: not available
Matplotlib: 3.10.3
h5py: not available
Pandas: not available
PyERFA: 2.0.1.1
Cython: not available
Scikit-image: not available
asdf-astropy: not available

Using Astropy options: remote_data: none.

rootdir: /mnt/local/sbulut/spack-1.0.2
configfile: pytest.ini
plugins: astropy-0.10.0, arraydiff-0.3, astropy-header-0.2.2, openfiles-0.5.0, mock-3.10.0, cov-4.0.0, remotedata-0.4.0, filter-subpackage-0.1.2, xdist-3.2.0, doctestplus-0.13.0, hypothesis-6.96.2
collected 28981 items / 9 errors / 8 skipped
....
================================================================================= short test summary info ==================================================================================
SKIPPED [1] spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/coordinates/tests/test_matching.py:32: Coordinate matching requires scipy
SKIPPED [1] spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/io/fits/hdu/compressed/tests/test_fitsio.py:26: could not import 'fitsio': No module named 'fitsio'
SKIPPED [1] spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/io/fits/tests/test_image_dask.py:9: could not import 'dask.array': No module named 'dask'
SKIPPED [1] spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/io/misc/tests/test_pandas.py:16: could not import 'pandas': No module named 'pandas'
SKIPPED [1] spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/io/misc/tests/test_parquet.py:28: could not import 'pyarrow': No module named 'pyarrow'
SKIPPED [1] spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/io/misc/tests/test_parquet_votable.py:14: could not import 'pyarrow': No module named 'pyarrow'
SKIPPED [1] spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/modeling/tests/test_fitting_parallel.py:8: could not import 'dask': No module named 'dask'
SKIPPED [1] spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/table/mixins/tests/test_dask.py:7: could not import 'dask.array': No module named 'dask'
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/table/mixins/dask.py
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/utils/iers/tests/test_leap_second.py
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/utils/xml/setup_package.py
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/visualization/wcsaxes/tests/test_display_world_coordinates.py - Failed: 'mpl_image_compare' not found in `markers` configuration option
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/visualization/wcsaxes/tests/test_frame.py - Failed: 'mpl_image_compare' not found in `markers` configuration option
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/visualization/wcsaxes/tests/test_images.py - Failed: 'mpl_image_compare' not found in `markers` configuration option
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/visualization/wcsaxes/tests/test_transform_coord_meta.py - Failed: 'mpl_image_compare' not found in `markers` configuration option
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/visualization/wcsaxes/tests/test_wcsapi.py - Failed: 'mpl_image_compare' not found in `markers` configuration option
ERROR spack-1.0.2/opt/spack/linux-x86_64_v3/py-astropy-7.0.1-gz2yr25gz2tou63uqntkrr6aj6lllkp7/lib/python3.11/site-packages/astropy/wcs/setup_package.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 9 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 

[Sinan81]

mpl_image_compare pytest marker is provided in pyproject.toml

[Sinan81]

These require extension_helpers

ERROR astropy/utils/xml/setup_package.py
ERROR astropy/wcs/setup_package.py