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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.
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: ***@***.***>
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?
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
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?
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!
There is a stack trace in the linked issue above, i'm not sure why it would be appropriate to bring this up over there unless i'm really misunderstanding the problem. Plus, there is already this issue here.
Sorry for the confusion, scikit-bio was failing to install because it depends on biom-format which is failing to build. Happy to take a stab at a PR for you!
@wasade that wasn't too bad, builds all seemed to work locally, tried to keep configurations as close to the same as i could just focusing on moving to pyproject.toml and getting cibuildtool in there.
Resolved by #996, which restored wheel builds via cibuildwheel. 2.1.17 shipped wheels for CPython 3.9–3.13 on manylinux x86_64/aarch64, macOS x86_64/arm64, and Windows AMD64. Python 3.14 wheels are being added in #1005 for 2.1.18.
Activity
pkirti33 commentedon Jun 7, 2024
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'
packagesconfiguration.Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools'
packagesconfiguration.Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools'
packagesconfiguration.wasade commentedon Jun 7, 2024
pkirti33 commentedon Jun 7, 2024
Sorry for not including that!
wasade commentedon Jun 7, 2024
Thanks. Is this within WSL?
pkirti33 commentedon Jun 7, 2024
No - I'm running my commands directly in Windows Command Prompt
wasade commentedon Jun 7, 2024
We test against
windows-latestwhich 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 fromconda?pkirti33 commentedon Jun 7, 2024
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 commentedon Jun 7, 2024
Any chance you'd be interested in futzing with
setup.pyandpyproject.tomlin your local clone to see if you can find something which works, and issue a pull request?pkirti33 commentedon Jun 7, 2024
Hello,
Thank you for your help, I think I found a workaround.
biom-formatis pre-installed in qiime2 (which I'm using), so I'm just going to perform my operations within that venv. Thank you!wasade commentedon Jun 7, 2024
Sounds good, thanks!
make biom-format install w conda instead of pip (see biocore/biom-for…
Coveralls fix, install biom-format from conda instead of pip (#295)
schlich commentedon Jun 12, 2025
This still seems to be an issue and is causing failures installing scikit-bio, I'm getting very similar error messages + missing gcc
wasade commentedon Jun 12, 2025
Could you open an issue with scikit-bio?
schlich commentedon Jun 12, 2025
I don't think it's an issue with scikit-bio. Do they maintain this repository?
schlich commentedon Jun 12, 2025
There is a stack trace in the linked issue above, i'm not sure why it would be appropriate to bring this up over there unless i'm really misunderstanding the problem. Plus, there is already this issue here.
wasade commentedon Jun 12, 2025
You said you were having an issue installing scikit-bio?
I would welcome a PR to restore wheel builds, but I am currently on leave and cannot do it myself anytime soon
schlich commentedon Jun 12, 2025
Sorry for the confusion, scikit-bio was failing to install because it depends on biom-format which is failing to build. Happy to take a stab at a PR for you!
wasade commentedon Jun 12, 2025
Thanks! The scikit-bio team would value feedback though if their installation instructions are not covering your environment
schlich commentedon Jun 13, 2025
@wasade that wasn't too bad, builds all seemed to work locally, tried to keep configurations as close to the same as i could just focusing on moving to pyproject.toml and getting cibuildtool in there.
#994
wasade commentedon Oct 3, 2026
Resolved by #996, which restored wheel builds via cibuildwheel. 2.1.17 shipped wheels for CPython 3.9–3.13 on manylinux x86_64/aarch64, macOS x86_64/arm64, and Windows AMD64. Python 3.14 wheels are being added in #1005 for 2.1.18.