ANOSPP data analysis
Project description
anospp-analysis
Python package for ANOSPP data analysis
Installation
TODO
Documentation
TODO
Development
Setup
Installation is hybrid with conda + poetry:
git clone git@github.com:malariagen/anospp-analysis.git
cd anospp-analysis
mamba env create -f environment.yml
conda activate anospp_analysis
poetry install
Activate development environment:
poetry shell
Usage & testing
The code in this repository can be accessed via wrapper scripts:
python anospp_analysis/qc.py \
--haplotypes test_data/haplotypes.tsv \
--samples test_data/samples.csv \
--stats test_data/stats.tsv \
--outdir test_data/qc
Besides, individual functions are available as an API
TODO testing & CI
Adding Python deps
Introducing python dependencies should be done via poetry:
poetry add package_name
This should update both pyproject.toml and poetry.lock files
If the package should be used in development environment only, use
poetry add package_name --dev
Adding non-Python deps
Introducing non-python dependencies should be done via conda: edit environment.yml,
then re-create the conda environment and poetry deps:
mamba env create -f environment.yml
conda activate anospp_analysis
poetry install
Changes in conda environment might also introduce changes to the python installation, in which case one should update poetry lock file
poetry lock
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