Not working under Windows

[ZeweiSong]

I posted this question at BioStars:

I tried to install Biom format from the source under Windows:
@python setup.py install
However, when I typed the following to check the version, I got a error message:
@python -c "from biom import version; print version"
Traceback (most recent call last):
  File "", line 1, in
  File "biom_init_.py", line 65, in
    from .table import Table
  File "biom\table.py", line 194, in
    from ._filter import _filter
ImportError: No module named _filter
Any idea on how can I make it work in Windows?

[wasade]

Hi @ZeweiSong, what I suspect is that the Cython code needs to be regenerated. To do so, you need to make sure Cython is in the environment (e.g., pip install cython). You should then be able to ask biom to regenerate the extensions with python setup.py build_ext, and then a install might work. None of the developers use Windows machines though, so this is an untested platform for us at this time.

[auberginekenobi]

I get the same error using build_ext as build - it doesn't look like that install solution works.

[wasade]

@auberginekenobi it's unfortunate but I'm not very surprised. I don't believe any of the contributors to this project have Windows machines for development use which has presented challenges testing on that platform.

[auberginekenobi]

Potential workarounds for Windows users who visit this page in the future:

• biom-format installs successfully on the Ubuntu shell that comes with the latest update of Windows 10
• use a virtual machine, such as QIIME - already comes with biom-format installed
• biom-format installs successfully on Windows distributions of R (even the python commands work...)

[wasade]

That's useful, thank you for adding those comments and observations!

[wasade]

Closing as it doesn't seem like there is a strong push to support Windows.

[ElDeveloper]

... actually, it looks like the windows build works. See the conda-forge feedstock here, notice how the Windows build is "passing". It would be good if someone could try this and report back. conda install -c conda-forge biom-format.

[wasade]

Oh, accidental support?