numcodecs v0.13.0

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Analysis by source code inspection shows a discrepancy between it and the the package's stated requirements in the meta.yaml.

Packages found by source code inspection but not in the meta.yaml:

• matplotlib
• cython
• py-cpuinfo
• arm_pyart

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[conda-forge-webservices]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

[joshmoore]

  [numcodecs] setting up vlen extension
  Traceback (most recent call last):
    File "/home/conda/feedstock_root/build_artifacts/numcodecs_1720822307230/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/home/conda/feedstock_root/build_artifacts/numcodecs_1720822307230/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/home/conda/feedstock_root/build_artifacts/numcodecs_1720822307230/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
      return hook(metadata_directory, config_settings)
    File "/home/conda/feedstock_root/build_artifacts/numcodecs_1720822307230/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.10/site-packages/setuptools/build_meta.py", line 368, in prepare_metadata_for_build_wheel
      self.run_setup()
    File "/home/conda/feedstock_root/build_artifacts/numcodecs_1720822307230/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.10/site-packages/setuptools/build_meta.py", line 313, in run_setup
      exec(code, locals())
    File "<string>", line 383, in <module>
    File "<string>", line 364, in run_setup
    File "<string>", line 199, in vlen_extension
  ModuleNotFoundError: No module named 'numpy'

[dstansby]

I guess this might be because numpy needs adding to the build requirements?

[conda-forge-webservices]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe/meta.yaml) and found it was in an excellent condition.

[joshmoore]

Looks like adding numpy got us a bit farther:

  error: command 'cc' failed: No such file or directory

[dstansby]

I think some of the errros (which are to do with numpy installations) can be fixed by following https://conda-forge.org/docs/maintainer/knowledge_base/#building-against-numpy

[joshmoore]

Back to a cc fail.

[jakirkham]

Am curious about why NumPy is needed to build. Will follow up in that PR: zarr-developers/numcodecs#515

However as that has already been done. Think we need to re-render

@conda-forge-admin , please re-render

[jakirkham]

@conda-forge-admin , please re-render

[jakirkham]

@conda-forge-admin , please re-render

[jakirkham]

Am curious about why NumPy is needed to build. Will follow up in that PR: zarr-developers/numcodecs#515

After discussing with Isaac in that PR, came up with an approach that should solve the same issue without the NumPy dependency in PR: zarr-developers/numcodecs#555

[rabernat]

Hi @jakirkham - thanks for helping sort this out. We did our best to move zarr-developers/numcodecs#515 forward, but it's great to have your expertise here.

[jakirkham]

Unfortunately after looking at this issue. Think fixing this will entail a full rewrite of vlen. Additionally most of the codecs in there have the same problem, but that PR only fixed one. Sadly I won't have time to do this in the near term

If we are able to identify someone who can finish fixing the bug, I may be able to carve out some time to review

For now, would recommend that we...

1. Revert that PR
2. Reopen the issue
3. Do a 0.13.1 release

[rabernat]

@jakirkham - before we go down the path of reverting, can you explain why adding the numpy dependency is such a bad idea?

[jakirkham]

It's not about whether it is a good/bad idea

It is about the fact that this is the most notable change we made to the build requirements and the result is we don't seem to be able to build Numcodecs here any more

Reverting would at least return us to something we know use to work

That said, if someone has bandwidth to spend fixing the builds here, that would also be a welcome path forward

[jakirkham]

@conda-forge-admin , please re-render

[jakirkham]

Thanks Ryan! 🙏

Have used the reversion patch PR: zarr-developers/numcodecs#557

Let's see if this helps

[jakirkham]

Converting to draft for the moment while we decide on next steps

[dstansby]

Some progress: I did some debugging over at #108, and the issue with the linux builds is not having to build with numpy. That is all working fine.

The issue is some new files that were included in numcodecs 1.21.5, which was introduced with zarr-developers/numcodecs#500. The conda-forge build on linux fails when trying to compile one of these new files.

[dstansby]

The linux native build is failing on the command

  cc -c c-blosc/internal-complibs/zstd-1.5.5/decompress/huf_decompress_amd64.S -o c-blosc/internal-complibs/zstd-1.5.5/decompress/huf_decompress_amd64.o

In a similar passing job the start of the similar command is /home/conda/feedstock_root/build_artifacts/numcodecs_1723464425174/_build_env/bin/aarch64-conda-linux-gnu-cc, which is an explicit path to the c compiler, so I think for some reason the native linux build isn't setting the path to the compiler correctly, or it isn't being picked up.

[rabernat]

It is about the fact that this is the most notable change we made to the build requirements and the result is we don't seem to be able to build Numcodecs here any more

Ok that is helpful--I hadn't quite realized that!

[dstansby]

For a bit more info, I think this might be a bug with either:

• distutils using cc directly to compile the new files, instead of taking the compiler executable from the CC environment variable
• conda-build not setting the CC environment variable correctly (but I'm pretty sure this wouldn't be the issue)

Either way the issue is this step in setup.py of numcodecs: https://github.com/zarr-developers/numcodecs/blob/8b53fc135373d526338399c2dc582673cd560f87/setup.py#L329

Unless anyone has any good ideas for other options, I'm not sure how this can be fixed without downgrading the bundled version of blosc, which is not ideal...

In the meantime I'll ask in the conda-forge gitter to see if anyone can help.

[dstansby]

Thanks to a kind soul in the conda-forge chat, I've got a fix for this that I've patched in #108 and PR'd in zarr-developers/numcodecs#562. So I think this can be closed in favour of #108 now.