Migrate to pixi for environment management

.gitattributes

@@ -5,3 +5,5 @@ binder/*.html linguist-documentation
 notebook/*/*.ipynb linguist-documentation
 microhapulator/data/template.html linguist-documentation
 microhapulator/data/fancyTable.js linguist-vendored
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/cibuild.yml

@@ -8,30 +8,29 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12"]
       fail-fast: false
     steps:
-    - uses: actions/checkout@v1
+    - name: Check out code
+      uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Set up pixi package manager
+      uses: prefix-dev/setup-pixi@v0.8.10
+      with:
+        pixi-version: v0.48.2
+        cache: true
     - name: Install
       run: |
-        sudo apt-get update
-        sudo apt-get install minimap2 samtools fastqc tabix
-        curl -L -O http://ccb.jhu.edu/software/FLASH/FLASH-1.2.11-Linux-x86_64.tar.gz && tar -xzf FLASH-1.2.11-Linux-x86_64.tar.gz && sudo cp FLASH-1.2.11-Linux-x86_64/flash /usr/local/bin/ && rm -r FLASH-1.2.11*
-        python -m pip install --upgrade pip
-        pip install .
-        mhpl8r getrefr
-        make devdeps
+        pixi install
+        pixi install -e test
+        pixi run mhpl8r getrefr
     - name: Test with pytest
       run: |
-        # Move the source code so the tests run on the *installed* code (which is where the
-        # reference genome index is placed) rather than the source code
-        mv microhapulator mhpl8r_src
-        make test
-        # Move the code back for style check
-        mv mhpl8r_src microhapulator
-    - name: Style check
-      run: make style
+        pixi run test
+    - name: Style and documentation check
+      run: |
+        pixi run style
+        pixi run docs

.gitignore

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

microhapulator/workflows/analysis.smk

@@ -10,11 +10,11 @@
 # Development Center.
 # -------------------------------------------------------------------------------------------------
 
+from importlib.resources import files
 from microhapulator import api as mhapi
 from microhapulator.pipe import OverviewReporter, DetailReporter
 from microhapulator.profile import TypingResult
 from microhapulator.thresholds import ThresholdIndex
-from pkg_resources import resource_filename
 import shutil
 
 
@@ -55,12 +55,12 @@ rule report:
         expand("analysis/{sample}/03typing/{sample}-typing-rate.tsv", sample=config["samples"]),
         expand("analysis/{sample}/03typing/{sample}-discard-rate.tsv", sample=config["samples"]),
         expand("analysis/{sample}/03typing/{sample}-gapped-rate.tsv", sample=config["samples"]),
-        resource_filename("microhapulator", "data/template.html"),
-        resource_filename("microhapulator", "data/marker_details_template.html"),
-        resource_filename("microhapulator", "data/third-party/bootstrap.min.css"),
-        resource_filename("microhapulator", "data/third-party/fancyTable.js"),
-        resource_filename("microhapulator", "data/third-party/jquery-ui.min.js"),
-        resource_filename("microhapulator", "data/third-party/jquery.min.js"),
+        files("microhapulator") / "data" / "template.html",
+        files("microhapulator") / "data" / "marker_details_template.html",
+        files("microhapulator") / "data" / "third-party" / "bootstrap.min.css",
+        files("microhapulator") / "data" / "third-party" / "fancyTable.js",
+        files("microhapulator") / "data" / "third-party" / "jquery-ui.min.js",
+        files("microhapulator") / "data" / "third-party" / "jquery.min.js",
     output:
         main="report/report.html",
         detail="report/marker-detail-report.html",
@@ -82,7 +82,7 @@ rule report:
         reporter = DetailReporter(config["samples"])
         with open(output.detail, "w") as fh:
             print(reporter.render(), file=fh, end="")
-        tpdir = resource_filename("microhapulator", "data/third-party/")
+        tpdir = files("microhapulator") / "data" / "third-party"
         shell("mkdir -p report/img/")
         shell("cp -r {tpdir} report/assets")
         for sample in config["samples"]: