magenpy==0.0.1 release

.github/workflows/ci-docs.yml

@@ -0,0 +1,35 @@
+name: ci Docs
+on:
+  push:
+    branches:
+      - master
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+
+      - uses: actions/checkout@v4
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+
+      - run: python -m pip install -r requirements-docs.txt
+      - run: mkdocs gh-deploy --force

.github/workflows/ci-linux.yml

@@ -0,0 +1,39 @@
+name: magenpy Linux-CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up miniconda
+        uses: conda-incubator/[email protected]
+        with:
+          channels: conda-forge
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up Conda environment
+        shell: "bash -l {0}"
+        run: >
+          conda create --name "magenpy_ci" -c conda-forge -c anaconda 
+          python=${{matrix.python-version}} pip wheel compilers openblas -y
+
+      - name: Install magenpy
+        shell: "bash -l {0}"
+        run: |
+          conda activate magenpy_ci
+          python -m pip install -v -e .[test]
+
+      - name: Run tests
+        shell: "bash -l {0}"
+        run: |
+          conda activate magenpy_ci
+          pytest -v

.github/workflows/ci-osx.yml

@@ -0,0 +1,39 @@
+name: magenpy OSX-CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up miniconda
+        uses: conda-incubator/[email protected]
+        with:
+          channels: conda-forge
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up Conda environment
+        shell: "bash -l {0}"
+        run: >
+          conda create --name "magenpy_ci" -c conda-forge -c anaconda 
+          python=${{matrix.python-version}} pip wheel compilers openblas -y
+
+      - name: Install magenpy
+        shell: "bash -l {0}"
+        run: |
+          conda activate magenpy_ci
+          python -m pip install -v -e .[test]
+
+      - name: Run tests
+        shell: "bash -l {0}"
+        run: |
+          conda activate magenpy_ci
+          pytest -v

.github/workflows/ci-windows.yml

@@ -0,0 +1,39 @@
+name: magenpy OSX-CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up miniconda
+        uses: conda-incubator/[email protected]
+        with:
+          channels: conda-forge
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up Conda environment
+        shell: "bash -l {0}"
+        run: >
+          conda create --name "magenpy_ci" -c conda-forge -c anaconda 
+          python=${{matrix.python-version}} pip wheel compilers openblas -y
+
+      - name: Install magenpy
+        shell: "bash -l {0}"
+        run: |
+          conda activate magenpy_ci
+          python -m pip install -v -e .[test]
+
+      - name: Run tests
+        shell: "bash -l {0}"
+        run: |
+          conda activate magenpy_ci
+          pytest -v

.github/workflows/wheels.yml

@@ -0,0 +1,71 @@
+name: Build magenpy and upload to PyPI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - name: test install
+        run: pip install dist/magenpy*.tar.gz
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          # To test: repository-url: https://test.pypi.org/legacy/

.gitignore

@@ -4,6 +4,7 @@
 
 # C extensions
 *.c
+*.cpp
 *.so
 
 # Distribution / packaging
@@ -18,6 +19,7 @@ lib/
 lib64/
 parts/
 sdist/
+site/
 var/
 *.egg-info/
 .installed.cfg
@@ -34,6 +36,9 @@ pip-delete-this-directory.txt
 
 # custom
 .idea/
+.vscode/
+.tox/
+.pytest_cache/
 *.html
 *.zarr
 *.npz

CHANGELOG.md

@@ -5,6 +5,37 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.0] - 2024-04-04
+
+A large scale restructuring of the code base to improve efficiency and usability.
+
+### Changed
+
+- Bug fixes across the entire code base.
+- Simulator classes have been renamed from `GWASimulator` to `PhenotypeSimulator`.
+- Moved plotting script to its own separate module.
+- Updated some method names / commandline flags to be consistent throughout.
+
+### Added
+
+- Basic integration testing with `pytest` and GitHub workflows.
+- Documentation for the entire package using `mkdocs`.
+- Integration testing / automating building with GitHub workflows.
+- New implementation of the LD matrix that uses CSR matrix data structures.
+  - Quantization / float precision specification when storing LD matrices.
+  - Allow user to specify Compressor / Compressor options for Zarr storage.
+- New implementation of `magenpy_simulate` script.
+  - Allow users to set random seed.
+  - Now accept `--prop-causal` instead of specifying full mixing proportions.
+- Tried to incorporate `genome_build` into various data structures. This will be useful in the 
+future to ensure consistent genome builds across different data types.
+- Allow user to pass various metadata to `magenpy_ld` to save information about dataset 
+characteristics.
+- New sumstats parsers:
+  - Saige sumstats format.
+  - plink1.9 sumstats format.
+  - GWAS Catalog sumstats format.
+- Chained transform function for transforming phenotypes.
 
 ## [0.0.12] - 2023-02-12
 

CITATION.md

@@ -0,0 +1,21 @@
+If you use `magenpy` in your research, please cite the following paper(s):
+
+> Zabad, S., Gravel, S., & Li, Y. (2023). **Fast and accurate Bayesian polygenic risk modeling with variational inference.** 
+The American Journal of Human Genetics, 110(5), 741–761. https://doi.org/10.1016/j.ajhg.2023.03.009
+
+## BibTeX records
+
+```bibtex
+@article{ZABAD2023741,
+    title = {Fast and accurate Bayesian polygenic risk modeling with variational inference},
+    journal = {The American Journal of Human Genetics},
+    volume = {110},
+    number = {5},
+    pages = {741-761},
+    year = {2023},
+    issn = {0002-9297},
+    doi = {https://doi.org/10.1016/j.ajhg.2023.03.009},
+    url = {https://www.sciencedirect.com/science/article/pii/S0002929723000939},
+    author = {Shadi Zabad and Simon Gravel and Yue Li}
+}
+```

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Shadi Zabad, McGill University
+Copyright (c) 2024 Shadi Zabad, McGill University.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -2,12 +2,13 @@ include MANIFEST.in
 include requirements*.txt
 include magenpy/config/*.ini
 include LICENSE
-include README.md
+include *.md
 include setup.py
 
 graft magenpy
 
 global-exclude *.c
+global-exclude *.cpp
 global-exclude *.so
 global-exclude *.pyd
 global-exclude *.pyc

Makefile

@@ -1,23 +1,40 @@
-.PHONY: build dist redist install install-from-source clean uninstall
+.PHONY: build build-inplace test test-inplace dist redist install install-from-source clean uninstall publish-test publish
 
 build:
 	python3 setup.py build
 
+build-inplace:
+	python3 setup.py build_ext --inplace
+
+test-inplace:
+	PYTHONPATH=. pytest
+
+test:
+	python -m pytest
+
 dist:
-	python3 setup.py sdist bdist_wheel
+	python setup.py sdist bdist_wheel
 
 redist: clean dist
 
 install:
-	pip install .
+	python -m pip install .
 
 install-from-source: dist
-	pip install dist/magenpy-*.tar.gz
+	python -m pip install dist/magenpy-*.tar.gz
 
 clean:
 	$(RM) -r build dist *.egg-info
-	$(RM) -r magenpy/LDMatrix.c magenpy/utils/c_utils.c
+	$(RM) -r magenpy/stats/ld/*.c magenpy/stats/score/*.cpp
+	$(RM) -r magenpy/stats/ld/*.so magenpy/stats/score/*.so
+	$(RM) -r .pytest_cache .tox temp output
 	find . -name __pycache__ -exec rm -r {} +
 
 uninstall:
-	pip uninstall magenpy
+	python -m pip uninstall magenpy
+
+publish-test:
+	python -m twine upload -r testpypi dist/* --verbose
+
+publish:
+	python -m twine upload dist/* --verbose