Issue adding biom-format support for aarch64 conda

[constellation99]

When trying to add biom-format support for aarch64 conda, I encountered the following error here, which caused the build to fail. The error message I received was "PackagesNotFoundError: The following packages are not available from current channels: biom-format". This occurred after including biom-format in the aarch64 conda requirements file for scikit-bio.

Would it be possible to add support for aarch64 for biom?

[masa-yoshizawa]

I think I have the same issue as constellation99 has. I could not install biom-format via conda install -c bioconda -c conda-forge biom-format under Platform: osx-arm64, because of an error: PackagesNotFoundError: The following packages are not available from current channels:

• biom-format

I tried via 'pip install biom-format' as well but the installed program was not recognized well (no error during installation) since when I run biom, it returned an error: NameError: name 'biom' is not defined

Any advice on this issue would be great!

[wasade]

Hi @masa-yoshizawa,

What version of Python is being used? And could you share the full output from the pip install, which should have worked?

Best, Daniel

[masa-yoshizawa]

Hi Daniel, thank you for responding to my issue. I am using Python 3.11.7 here is the full output of pip install. Again thank you so much for your help for looking into!

====================================

In [4]: pip install biom-format Requirement already satisfied: biom-format in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (2.1.15) Requirement already satisfied: click in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (8.1.7) Requirement already satisfied: numpy>=1.9.2 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (1.26.3) Requirement already satisfied: scipy>=1.3.1 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (1.12.0) Requirement already satisfied: pandas>=0.20.0 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (2.2.0) Requirement already satisfied: h5py in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (3.10.0) Requirement already satisfied: python-dateutil>=2.8.2 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format) (2023.3.post1) Requirement already satisfied: tzdata>=2022.7 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format) (2023.4) Requirement already satisfied: six>=1.5 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas>=0.20.0->biom-format) (1.16.0)

Note: you may need to restart the kernel to use updated packages.

[after restarting the kernel]

in [1]: biom Traceback (most recent call last):

Cell In[1], line 1 biom

NameError: name 'biom' is not defined

====================================

[wasade]

Thanks, @masa-yoshizawa. Could you try import biom? There is a program called biom but it is intended to be run on the command line, whereas the output above suggests the use may be within a Python interpreter

[masa-yoshizawa]

Dear Daniel, thank you so much for this advise! I imported biom and it seemed to work In [2]: import biom as bio In [3]: that is great! However, in the same Python environment, the command line could not call biom (singleCell) user@MacBook-Pro- ~ % biom zsh: command not found: biom The issue is that I cannot install picrust2 due to this issue. Thank you for your thoughts!!!

[wasade]

It's odd that the biom program is not accessible yet the library appears installed. My guess is an environment issue, where either pip installed the program in an unusual location, or the install was done outside of the conda environment? If the general problem is with picrust2, would it be possible to open a help request with them?

[masa-yoshizawa]

I totally agree with you. It is so wired. I have installed biom-format by using pip of this version pip --version pip 23.3.1 from /Users/masato/anaconda3/envs/picrust2/lib/python3.11/site-packages/pip (python 3.11)

Thus, pip is under the same environment where I'd like to install biom-format... I will pose a question in the picrust2 site too. Thank you so much, Daniel!

[wasade]

Thanks, @masa-yoshizawa! Is there an associated issue with the picrust2 tracker to reference?

[wasade]

Closing as I believe conda-forge has now provided support