Add annsel

[srivarra]

Checklist for adding packages

Mandatory

Name of the tool: annsel

Short description: Annsel is a user-friendly library that brings familiar dataframe-style operations to AnnData objects such as filter, select, and group by's.

How does the package use scverse data structures (please describe in a few sentences):

It uses AnnData's obs, var, X, obs_names. and var_names attributes to filter, select and run "group bys" in order to partition and subset the AnnData object as a whole. For example, a user can filter their AnnData object based on a "Cell Type" column in obs.

• The code is publicly available under an OSI-approved license
• The package provides versioned releases
• The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
• Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1]
• Continuous integration (CI) automatically executes these tests on each push or pull request [^2]
• The package provides API documentation via a website or README[^3]
• The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
• I am an author or maintainer of the tool and agree on listing the package on the scverse website

Recommended

• Please announce this package on scverse communication channels (zulip, discourse, twitter)

Zulip link

• Please tag the author(s) these announcements. Handles (e.g. @scverse_team) to include are:
  • Zulip:
  • Discourse:
  • Mastodon:
  • Bluesky:
  • Twitter:
• The package provides tutorials (or "vignettes") that help getting users started quickly
• The package uses the scverse cookiecutter template.

[ilan-gold]

Looks good to me other than the comment, but not sure about that

[ilan-gold]

@grst This won't work out-of-the-box since there is no env created - how do we handle this command? By contrast, pip install xxxx will work because you don't need a virtual env for that

[grst]

uv run pytest should work without pip install?
This test command is anyway more to prove there are tests, as we don't execute it (for now).

[ilan-gold]

uv pip install won't work though, no?

[ilan-gold]

@srivarra so perhaps just use pip here for now?

[srivarra]

@ilan-gold Just replaced it with only pip!

[flying-sheep]

pip install xxxx will work because you don't need a virtual env for that

not on modern systems:

$ pip install httpx
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try 'pacman -S
    python-xyz', where xyz is the package you are trying to
    install.
    
    If you wish to install a non-Arch-packaged Python package,
    create a virtual environment using 'python -m venv path/to/venv'.
    Then use path/to/venv/bin/python and path/to/venv/bin/pip.
    
    If you wish to install a non-Arch packaged Python application,
    it may be easiest to use 'pipx install xyz', which will manage a
    virtual environment for you. Make sure you have python-pipx
    installed via pacman.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.

But hatch test (or uvx hatch test or pipx hatch test) will work if the respective tools are installed.

[grst]

but it should work in a CI context with sudo rights?

[flying-sheep]

probably, yeah. uv pip install --system too.

(sorry @srivarra for using your PR as a discussion platform for this, but we should probably improve our guidance on what the test command should be)

[grst]

Thanks @srivarra!