Comments (10)
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.
from biom-format.
from biom-format.
Sorry for not including that!
- Operating system: Windows 10 Enterprise
- Python version: 3.11.9
from biom-format.
Thanks. Is this within WSL?
from biom-format.
No - I'm running my commands directly in Windows Command Prompt
from biom-format.
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
?
from biom-format.
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
from biom-format.
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?
from biom-format.
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!
from biom-format.
Sounds good, thanks!
from biom-format.
Related Issues (20)
- Add wheel testing
- Expand partiton API HOT 2
- Trouble with installation using pip HOT 8
- Issue adding biom-format support for aarch64 conda HOT 9
- update_ids strict=False is not necessarily working as expected HOT 1
- `add-metadata` is not representing floats correctly HOT 1
- `add-metadata` is representing Taxonomy as np array of byte strings HOT 1
- `add-metadata` help messages need clarity
- Possible to represent relative abundance of taxonomy rather than OTUs? HOT 4
- align_tree cannot handle features with 0 counts HOT 3
- Edge case for biom.Table subsample with replacement HOT 7
- DOC: changelog
- NumPy 2.0 compatibility issue HOT 2
- NumPy compatibility issue (further) HOT 12
- update_ids can silently truncate IDs
- Expose the _subsample method
- TypeError: the JSON object must be str, bytes or bytearray, not File HOT 9
- Adding table metadata HOT 3
- From dataframe
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from biom-format.