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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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Wheels are not being built properly #970

Open wasade opened 3 months ago

wasade commented 3 months ago

This has been holding up a 2.1.16 release. No time to do it right now, and this would represent at least 1.5 week delay. Deferring a fix to later.

pkirti33 commented 2 months ago

I am having this issue when using "pip install biom-format" into my virtual environment. I am getting several error messages, which include:

Building wheel for biom-format (pyproject.toml) did not run successfully. Python recognizes 'biom.assets' as an importable package[^1], but it is absent from setuptools' packages configuration. Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools' packages configuration. Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools' packages configuration.

wasade commented 2 months ago

Thanks, good catch. What operating system, and version of python?On Jun 7, 2024, at 10:00, pkirti33 @.***> wrote: I am having this issue when using "pip install biom-format" into my virtual environment. I am getting several error messages, which include: Building wheel for biom-format (pyproject.toml) did not run successfully. Python recognizes 'biom.assets' as an importable package[^1], but it is absent from setuptools' packages configuration. Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools' packages configuration. Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools' packages configuration.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

pkirti33 commented 2 months ago

Sorry for not including that!

wasade commented 2 months ago

Thanks. Is this within WSL?

pkirti33 commented 2 months ago

No - I'm running my commands directly in Windows Command Prompt

wasade commented 2 months ago

We test against windows-latest which is Windows 2022. However, we don't have any Windows systems locally.

We are not instrumented to assert wheels build correctly, and as noted in this issue, we did not push wheels for this latest release. Could you attempt installing natively as done in the CI action and see if that works (e.g., git clone https://github.com/biocore/biom-format.git; cd biom-format; pip install .)? Alternatively, can you install from conda?

pkirti33 commented 2 months ago

Hi, Thanks for your prompt replies! Installing it natively didn't work - I ran into the same issues. One thing that might be noteworthy is that my project uses a pyproject.toml file. The last line of my error message states:

ERROR: Could not build wheels for biom-format, which is required to install pyproject.toml-based projects

wasade commented 2 months ago

Any chance you'd be interested in futzing with setup.py and pyproject.toml in your local clone to see if you can find something which works, and issue a pull request?

pkirti33 commented 2 months ago

Hello, Thank you for your help, I think I found a workaround. biom-format is pre-installed in qiime2 (which I'm using), so I'm just going to perform my operations within that venv. Thank you!

wasade commented 2 months ago

Sounds good, thanks!