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
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for anospp_analysis-0.1.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a660edcc576d1008a8282310e5f18983a05c1afef0fd14410da96469fcacc2a6 |
|
MD5 | 108bf3d9fdcd1bf65df064e6df9a3ccc |
|
BLAKE2b-256 | 211925a75d45cf2e96fdaa366a13a6397a3fdbbe227597a44c1f4d2ce579b4dc |