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python3Packages.astropy: unbreak multiple modules #120874

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merged 6 commits into from
May 5, 2021
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rmcgibbo
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Motivation for this change

I noticed that a few astropy packages were broken since a recent mass update: https://rmcgibbo.github.io/mydra/post/nixpkgs-fdce3b59/

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

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@rmcgibbo
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rmcgibbo commented Apr 27, 2021

The spectral-cube error looks to be caused by the radio-beam update (radio-astro-tools/spectral-cube#708) from 5446c0c / #117452


Build report after a86a447a87f3c93cf187e8432da5f32226a3d784:

Result of nixpkgs-review run on x86_64-linux 1

26 packages built:
  • python38Packages.aplpy
  • python38Packages.asdf
  • python38Packages.astropy-healpix
  • python38Packages.drms
  • python38Packages.glymur
  • python38Packages.pyregion
  • python38Packages.pytest-astropy
  • python38Packages.pytest-doctestplus
  • python38Packages.pytest-filter-subpackage
  • python38Packages.radio_beam
  • python38Packages.reproject
  • python38Packages.spectral-cube
  • python38Packages.sunpy
  • python39Packages.aplpy
  • python39Packages.asdf
  • python39Packages.astropy-healpix
  • python39Packages.drms
  • python39Packages.glymur
  • python39Packages.pyregion
  • python39Packages.pytest-astropy
  • python39Packages.pytest-doctestplus
  • python39Packages.pytest-filter-subpackage
  • python39Packages.radio_beam
  • python39Packages.reproject
  • python39Packages.spectral-cube
  • python39Packages.sunpy

@rmcgibbo rmcgibbo force-pushed the astropy branch 2 times, most recently from 68ae1a5 to a86a447 Compare April 27, 2021 17:47
@smaret
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smaret commented Apr 28, 2021

Built and tested on macOS. It looks go to me.
Thanks for the fix!

@fabaff
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fabaff commented May 4, 2021

Result of nixpkgs-review pr 120874 run on x86_64-linux 1

4 packages failed to build:
  • python38Packages.glymur
  • python38Packages.sunpy
  • python39Packages.glymur
  • python39Packages.sunpy
22 packages built:
  • python38Packages.aplpy
  • python38Packages.asdf
  • python38Packages.astropy-healpix
  • python38Packages.drms
  • python38Packages.pyregion
  • python38Packages.pytest-astropy
  • python38Packages.pytest-doctestplus
  • python38Packages.pytest-filter-subpackage
  • python38Packages.radio_beam
  • python38Packages.reproject
  • python38Packages.spectral-cube
  • python39Packages.aplpy
  • python39Packages.asdf
  • python39Packages.astropy-healpix
  • python39Packages.drms
  • python39Packages.pyregion
  • python39Packages.pytest-astropy
  • python39Packages.pytest-doctestplus
  • python39Packages.pytest-filter-subpackage
  • python39Packages.radio_beam
  • python39Packages.reproject
  • python39Packages.spectral-cube
builder for '/nix/store/j2m7r8zkzbbzw4m9dsajmsmbkx5czwn9-python3.8-glymur-0.9.3.drv' failed with exit code 1; last 10 log lines:
  tests/test_jp2k.py: 59 warnings
  tests/test_printing.py: 1 warning
    /build/source/glymur/jp2k.py:1084: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
    Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
      rlevel = np.int(np.round(np.log2(step)))
  
  -- Docs: https://docs.pytest.org/en/stable/warnings.html
  =========================== short test summary info ============================
  FAILED tests/test_jp2k.py::TestJp2k::test_thread_support - AssertionError: Fa...
  ======= 1 failed, 450 passed, 1 skipped, 61 warnings in 86.65s (0:01:26) =======

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rmcgibbo commented May 4, 2021

@fabaff: Unfortunately I cannot reproduce the glymur failure. It builds fine for me from this PR. It might be flaky?

@fabaff
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fabaff commented May 4, 2021

It might be flaky?

Could be. Local build of glymur is fine for me.

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fabaff commented May 5, 2021

Result of nixpkgs-review pr 120874 run on x86_64-linux 1

26 packages built:
  • python38Packages.aplpy
  • python38Packages.asdf
  • python38Packages.astropy-healpix
  • python38Packages.drms
  • python38Packages.glymur
  • python38Packages.pyregion
  • python38Packages.pytest-astropy
  • python38Packages.pytest-doctestplus
  • python38Packages.pytest-filter-subpackage
  • python38Packages.radio_beam
  • python38Packages.reproject
  • python38Packages.spectral-cube
  • python38Packages.sunpy
  • python39Packages.aplpy
  • python39Packages.asdf
  • python39Packages.astropy-healpix
  • python39Packages.drms
  • python39Packages.glymur
  • python39Packages.pyregion
  • python39Packages.pytest-astropy
  • python39Packages.pytest-doctestplus
  • python39Packages.pytest-filter-subpackage
  • python39Packages.radio_beam
  • python39Packages.reproject
  • python39Packages.spectral-cube
  • python39Packages.sunpy

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Changes look good to me.

@fabaff fabaff merged commit 37c75aa into NixOS:master May 5, 2021
@rmcgibbo rmcgibbo deleted the astropy branch May 5, 2021 20:14
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5 participants