From 815a9507921fe2c54d158d92990d36faaec768a6 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Mon, 16 Jun 2025 15:40:54 -0400 Subject: [PATCH 1/7] Trying pixi --- .gitattributes | 2 + .github/workflows/cibuild.yml | 21 +- .gitignore | 4 + Makefile | 44 - microhapulator/workflows/analysis.smk | 16 +- pixi.lock | 5618 +++++++++++++++++++++++++ pyproject.toml | 86 + setup.py | 80 - 8 files changed, 5728 insertions(+), 143 deletions(-) delete mode 100644 Makefile create mode 100644 pixi.lock create mode 100644 pyproject.toml delete mode 100644 setup.py diff --git a/.gitattributes b/.gitattributes index 32fcfee..73d1162 100644 --- a/.gitattributes +++ b/.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 diff --git a/.github/workflows/cibuild.yml b/.github/workflows/cibuild.yml index 1f40095..4f911a9 100644 --- a/.github/workflows/cibuild.yml +++ b/.github/workflows/cibuild.yml @@ -8,7 +8,7 @@ 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 @@ -18,20 +18,19 @@ jobs: python-version: ${{ matrix.python-version }} - 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 + curl -fsSL https://pixi.sh/install.sh | sh + 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 + pixi run test # Move the code back for style check mv mhpl8r_src microhapulator - - name: Style check - run: make style + - name: Style and documentation check + run: | + pixi run style + pixi run docs diff --git a/.gitignore b/.gitignore index 4036f69..fff13a5 100644 --- a/.gitignore +++ b/.gitignore @@ -18,3 +18,7 @@ microhapulator/data/hg38.fasta.gz* .snakemake/ .vscode/ microhapulator/data/hg38.mmi + +# pixi environments +.pixi +*.egg-info diff --git a/Makefile b/Makefile deleted file mode 100644 index 60dd4d7..0000000 --- a/Makefile +++ /dev/null @@ -1,44 +0,0 @@ -## help: print this help message and exit -help: Makefile - @echo '' - @sed -n 's/^## //p' Makefile - @echo '' - -## test: execute the automated test suite -test: - pytest -m "not known_failing" --cov=microhapulator --doctest-modules --pyargs microhapulator - -## test4: execute the automated test suite in multithreaded mode -test4: - pytest -m "not known_failing" -n 4 --cov=microhapulator --doctest-modules --pyargs microhapulator - -## devdeps: install development dependencies -devdeps: - pip install --upgrade pip setuptools - pip install wheel twine - pip install 'black<25.0.0,>=24.1.1' 'snakefmt>=0.10.0' 'pytest>=6.0' pytest-cov pytest-xdist myst-parser sphinx sphinx-argparse - -## doc: build HTML documentation -doc: - sphinx-build -b html docs/ docs/_build/ - -## devhooks: install development hooks -devhooks: - echo 'set -eo pipefail' > .git/hooks/pre-commit - echo 'make style' >> .git/hooks/pre-commit - echo 'make doc' >> .git/hooks/pre-commit - chmod 755 .git/hooks/pre-commit - -## clean: remove development artifacts -clean: - rm -rf __pycache__/ microhapulator/__pycache__/ microhapulator/*/__pycache__ build/ dist/ *.egg-info/ - -## style: check code style vs Black -style: - black --line-length=99 --check microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py setup.py - snakefmt --line-length=99 --check microhapulator/workflows/*.smk - -## format: autoformat Python code -format: - black --line-length=99 microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py setup.py - snakefmt --line-length=99 microhapulator/workflows/*.smk diff --git a/microhapulator/workflows/analysis.smk b/microhapulator/workflows/analysis.smk index 7c7fd1c..9cfb1a1 100644 --- a/microhapulator/workflows/analysis.smk +++ b/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"]: diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..d707ddd --- /dev/null +++ b/pixi.lock @@ -0,0 +1,5618 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/bioconda/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda + - 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-from setuptools import setup -import versioneer - -with open("README.md", "r") as infile: - longdesc = infile.read() - -setup( - name="microhapulator", - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), - description="Software package for simulating and analyzing microhaplotype sequence data", - long_description=longdesc, - long_description_content_type="text/markdown", - url="https://github.com/bioforensics/microhapulator", - author="Daniel Standage", - author_email="daniel.standage@nbacc.dhs.gov", - packages=[ - "microhapulator", - "microhapulator.cli", - "microhapulator.happer", - "microhapulator.pipe", - "microhapulator.tests", - ], - package_data={ - "microhapulator": [ - "microhapulator/Snakefile", - "microhapulator/data/*", - "microhapulator/tests/data/*", - "microhapulator/tests/data/*/*", - ] - }, - include_package_data=True, - install_requires=[ - "biopython", - "ezfastq", - "insilicoseq>=1.5.4,<2.0", - "jsonschema>=4.0", - "matplotlib>=3.0", - "microhapdb>=0.12", - "multiqc>=1.14", - "nbformat>=5.0,<5.6", - "numpy>=1.19", - "pandas>1.0", - "pulp==2.3.1", - "scipy>=1.7", - "seaborn>=0.13.2", - "snakemake>=8", - "termgraph>=0.5", - "tqdm>=4.0", - ], - entry_points={ - "console_scripts": [ - "mhpl8r = microhapulator.cli:main", - "happer = microhapulator.happer.__main__:main", - ] - }, - classifiers=[ - "Environment :: Console", - "Framework :: IPython", - "Framework :: Jupyter", - "Intended Audience :: Science/Research", - "Intended Audience :: Legal Industry", - "License :: OSI Approved :: BSD License", - "Programming Language :: Python :: 3", - "Topic :: Scientific/Engineering :: Bio-Informatics", - ], - zip_safe=True, -) From bee78e7f3d8c4e3e0badfb3406573d65a16499c3 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Mon, 16 Jun 2025 15:42:53 -0400 Subject: [PATCH 2/7] Troubleshooting CI --- .github/workflows/cibuild.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/cibuild.yml b/.github/workflows/cibuild.yml index 4f911a9..017183e 100644 --- a/.github/workflows/cibuild.yml +++ b/.github/workflows/cibuild.yml @@ -19,6 +19,7 @@ jobs: - name: Install run: | curl -fsSL https://pixi.sh/install.sh | sh + source $HOME/.bashrc pixi install pixi install -e test pixi run mhpl8r getrefr From 2a93c1e8f5c84011bed3a533c1beaa5faea296b3 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Mon, 16 Jun 2025 15:45:45 -0400 Subject: [PATCH 3/7] Troubleshooting CI --- .github/workflows/cibuild.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/cibuild.yml b/.github/workflows/cibuild.yml index 017183e..c163331 100644 --- a/.github/workflows/cibuild.yml +++ b/.github/workflows/cibuild.yml @@ -20,6 +20,8 @@ jobs: run: | curl -fsSL https://pixi.sh/install.sh | sh source $HOME/.bashrc + cat $HOME/.bashrc + which pixi pixi install pixi install -e test pixi run mhpl8r getrefr From 92fa431aa327228968cbb33fff727f6b062079a0 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Mon, 16 Jun 2025 15:52:31 -0400 Subject: [PATCH 4/7] Troubleshooting CI --- .github/workflows/cibuild.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/cibuild.yml b/.github/workflows/cibuild.yml index c163331..47f6cb9 100644 --- a/.github/workflows/cibuild.yml +++ b/.github/workflows/cibuild.yml @@ -11,16 +11,21 @@ jobs: 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: | curl -fsSL https://pixi.sh/install.sh | sh source $HOME/.bashrc - cat $HOME/.bashrc which pixi pixi install pixi install -e test From a6f34fe2ba0e71123558a48771dd0ac809891292 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Mon, 16 Jun 2025 15:56:10 -0400 Subject: [PATCH 5/7] Troubleshooting CI --- .github/workflows/cibuild.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.github/workflows/cibuild.yml b/.github/workflows/cibuild.yml index 47f6cb9..e5cb4eb 100644 --- a/.github/workflows/cibuild.yml +++ b/.github/workflows/cibuild.yml @@ -24,20 +24,12 @@ jobs: cache: true - name: Install run: | - curl -fsSL https://pixi.sh/install.sh | sh - source $HOME/.bashrc - which pixi 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 pixi run test - # Move the code back for style check - mv mhpl8r_src microhapulator - name: Style and documentation check run: | pixi run style From ab458cb687e339901701f65c831efe3ecebc1cf1 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Mon, 16 Jun 2025 16:18:00 -0400 Subject: [PATCH 6/7] Cleanup --- .gitignore | 3 --- CHANGELOG.md | 1 + docs/devel.md | 2 +- docs/install.md | 22 +++++----------------- pixi.lock | 2 +- pyproject.toml | 20 ++++++++++---------- 6 files changed, 18 insertions(+), 32 deletions(-) diff --git a/.gitignore b/.gitignore index fff13a5..9b2072b 100644 --- a/.gitignore +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index a27a69e..2114be8 100644 --- a/CHANGELOG.md +++ b/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). diff --git a/docs/devel.md b/docs/devel.md index 1cbe621..fae74f7 100644 --- a/docs/devel.md +++ b/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` diff --git a/docs/install.md b/docs/install.md index 0b622c1..faad62a 100644 --- a/docs/install.md +++ b/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 ``` diff --git a/pixi.lock b/pixi.lock index d707ddd..8c2c9bf 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3018,7 +3018,7 @@ packages: - pypi: ./ name: microhapulator version: 0.8.4 - sha256: 226712d603c219b9993534447e632ef4add0361340df85095c1eb385d37bdd90 + sha256: d7a5c54dcfda0a23a413ac80a80f52a200fcbd2f30b69d76f2bab89c452a74c2 requires_python: '>=3.11,<3.14' editable: true - conda: https://conda.anaconda.org/bioconda/linux-64/minimap2-2.30-h577a1d6_0.tar.bz2 diff --git a/pyproject.toml b/pyproject.toml index 74b8041..4c74ada 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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"] From 22e2f1395e359d1faf7977fd9e76898f0bb63845 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Mon, 16 Jun 2025 16:20:40 -0400 Subject: [PATCH 7/7] update pixi lock :shrug: --- pixi.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index 8c2c9bf..3c810f1 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3018,7 +3018,7 @@ packages: - pypi: ./ name: microhapulator version: 0.8.4 - sha256: d7a5c54dcfda0a23a413ac80a80f52a200fcbd2f30b69d76f2bab89c452a74c2 + sha256: eeaafffe3dcfdd89f47dfcf545fff65b6b1944f5e17e58e72526e390cc056743 requires_python: '>=3.11,<3.14' editable: true - conda: https://conda.anaconda.org/bioconda/linux-64/minimap2-2.30-h577a1d6_0.tar.bz2