Cleanup

Author: standage

.gitignore

@@ -3,7 +3,6 @@ __pycache__/
 .pytest_cache/
 .*.swp
 *.swo
-microhapulator.egg-info/
 hg38.fasta
 hg38.fasta.fai
 .coverage.*
@@ -18,7 +17,5 @@ microhapulator/data/hg38.fasta.gz*
 .snakemake/
 .vscode/
 microhapulator/data/hg38.mmi
-
-# pixi environments
 .pixi
 *.egg-info

CHANGELOG.md

@@ -12,6 +12,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Updated working directory organization to provide additional structure (#194).
 - Snakemake is now invoked using its new Python API, requiring a minimum version of 8.0 and Python 3.11+ (#195).
 - FASTQ intake is now handled by a dedicated package ezfastq, which was based on MicroHapulator code (#196).
+- Switched from conda to pixi for project and dependency management (#197).
 
 ### Fixed
 - Bug with handling marker vs. locus identifiers when running `mhpl8r seq` (#190).

docs/devel.md

@@ -6,7 +6,7 @@ The documentation for MicroHapulator's [command line interface](cli.md) and [Pyt
 
 ## Automated test suite
 
-- Invoke test suite with `make test`
+- Invoke test suite with `pixi run test`
 - Most tests reside in `microhapulator/tests/test_*.py`
 - Some tests (doctests) reside in docstrings in module implementations in `microhapulator/*.py`
 

docs/install.md

@@ -20,27 +20,15 @@ pytest --pyargs microhapulator
 ```
 
 
-## Dependencies
-
-MicroHapulator depends on several Python packages.
-These are listed in `setup.py` in the main source code distribution.
-If performing a non-standard installation with `pip`, these dependencies will automatically be installed from the Python Package Index (PyPI).
-
-Preparing Illumina reads for analysis and interpretation with MicroHapulator also depends on several bioinformatics tools, including [FLASH](https://ccb.jhu.edu/software/FLASH/), [Minimap2](https://lh3.github.io/minimap2/minimap2.html) (or an alternative short read aligner), [SAMtools](http://www.htslib.org/), and [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
-These software tools are installed automatically when performing a standard installation with Conda.
-Otherwise, they must be installed manually.
-
-
 ## Development quick start
 
-If you're setting up an environment for developing MicroHapulator, you may want to skip the procedure outlined above and use the following instead.
+If you're setting up an environment for developing MicroHapulator, you probably want to skip the procedure outlined above and use the following instead, after [installing pixi](https://pixi.sh/latest/installation/).
 
 ```bash
-conda create --name microhapulator python=3.11 flash minimap2 samtools fastqc
-conda activate microhapulator
 git clone https://github.com/bioforensics/MicroHapulator.git
 cd MicroHapulator/
-pip install -e .  # Install the package and its Python dependencies
-make devdeps      # Install development packages
-make devhooks     # Register pre-commit hooks for development
+pixi install
+pixi install -e test
+pixi task list
+pixi run hooks
 ```

pixi.lock

@@ -71,16 +71,16 @@ sphinx = "*"
 sphinx-argparse = "*"
 
 [tool.pixi.feature.test.tasks]
-docs = "sphinx-build -b html docs/ docs/_build/"
-hooks = "echo 'set -eo pipefail\npixi run style\npixi run docs' > .git/hooks/pre-commit && chmod 755 .git/hooks/pre-commit"
-format_py = "black --line-length=99 microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py"
-format_smk = "snakefmt --line-length=99 microhapulator/workflows/*.smk"
-format = { depends-on = ["format_py", "format_smk"] }
-style_py = "black --line-length=99 --check microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py"
-style_smk = "snakefmt --line-length=99 --check microhapulator/workflows/*.smk"
-style = { depends-on = ["style_py", "style_smk"] }
-test = "pytest --cov=microhapulator --doctest-modules --pyargs microhapulator"
-test4 = "pytest --cov=microhapulator --doctest-modules --pyargs microhapulator -n 4"
+docs = { cmd = "sphinx-build -b html docs/ docs/_build/", description = "Build documentation" }
+hooks = { cmd = "echo 'set -eo pipefail\npixi run style\npixi run docs' > .git/hooks/pre-commit && chmod 755 .git/hooks/pre-commit", description = "Install development hooks"}
+_format_py = "black --line-length=99 microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py"
+_format_smk = "snakefmt --line-length=99 microhapulator/workflows/*.smk"
+format = { depends-on = ["_format_py", "_format_smk"], description = "Autoformat Python and Snakemake code" }
+_style_py = "black --line-length=99 --check microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py"
+_style_smk = "snakefmt --line-length=99 --check microhapulator/workflows/*.smk"
+style = { depends-on = ["_style_py", "_style_smk"], description = "Check Python and Snakemake code style" }
+test = { cmd = "pytest --cov=microhapulator --doctest-modules --pyargs microhapulator", description = "Run automated test suite" }
+test4 = { cmd = "pytest --cov=microhapulator --doctest-modules --pyargs microhapulator -n 4", description = "Run automated test suite with 4 parallel jobs" }
 
 [tool.pixi.environments]
 test = ["test"]