sourmash-plugin-tables 1.0.0

sourmash plugin to do tables.

tables

Tables! We all love them and couldn't function without them in our daily lives. Now sourmash has tables too!

Installation

For regular install:

pip install sourmash_plugin_tables

For conda environment:

conda activate <env-name>

python -m pip install sourmash_plugin_tables

Or, use a conda environment yaml file:

name: stable
channels:
channels:
    - conda-forge
    - bioconda
    - defaults
dependencies:
    - python>=3.10,<3.12
    - sourmash>=4.8.11,<5
    - polars
    - pip
    - pip:
        - sourmash_plugin_tables

Sanity check

sourmash info -v

Expected output:

== This is sourmash version 4.9.4. ==
== Please cite Irber et. al (2024), doi:10.21105/joss.06830. ==

sourmash version 4.9.4
- loaded from path: /home/colton/miniconda3/envs/smash/lib/python3.14/site-packages/sourmash/cli

khmer version: None (internal Nodegraph)

screed version 1.1.3
- loaded from path: /home/colton/miniconda3/envs/smash/lib/python3.14/site-packages/screed

the following plugins are installed:

plugin type          from python module             v     entry point name    
-------------------- ------------------------------ ----- --------------------
sourmash.cli_script  sourmash_plugin_tables         0.7   compare_rows        
sourmash.cli_script  sourmash_plugin_tables         0.7   gather_tables       
sourmash.cli_script  sourmash_plugin_tables         0.7   hash_tables         
sourmash.cli_script  sourmash_plugin_tables         0.7   prefetch_tables     

Usage

Support

We suggest filing issues in the main sourmash issue tracker as that receives more attention!

Dev docs

tables was developed from https://github.com/sourmash-bio/sourmash_plugin_template.

Testing

Run:

pytest tests

Example/test data located in tests/test-data (shocking, I know)

Generating a release

Bump version number in pyproject.toml and push.

Make a new release on github.

Then pull, and:

make dist

followed by twine upload dist/....