Merge branch 'main' into haplo-stats

alexlancaster · Jan 21, 2025 · cb3c967 · cb3c967
2 parents be8ec39 + 37a34a6
commit cb3c967
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Showing 105 changed files with 13,222 additions and 3,127 deletions.
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -13,6 +13,8 @@ on:
       - 'CITATION.cff'
       - '.zenodo.json'
       - 'website/**'
+      - 'data/**'
+      - 'src/obsolete/**'
       - '.github/dependabot.yml'
       - '.github/release-drafter.yml'
       - '.github/ISSUE_TEMPLATE/**'
@@ -30,6 +32,8 @@ on:
       - 'CITATION.cff'
       - '.zenodo.json'
       - 'website/**'
+      - 'data/**'
+      - 'src/obsolete/**'
       - '.github/dependabot.yml'
       - '.github/release-drafter.yml'
       - '.github/ISSUE_TEMPLATE/**'

diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -59,12 +59,20 @@ jobs:
       - uses: actions/setup-python@v5
       - name: Install dependencies
         run: |
-          pip install setuptools_scm sphinx==8.0.2 piccolo-theme myst_parser rst2pdf sphinx_togglebutton sphinx-argparse sphinx_copybutton sphinxcontrib-bibtex
+          pip install setuptools_scm sphinx==8.0.2 piccolo-theme myst_parser rst2pdf sphinx_togglebutton sphinx-argparse sphinx_copybutton sphinxcontrib-bibtex toml
           sudo apt clean
           sudo apt-get update
           sudo apt-get install --fix-missing -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended texlive-fonts-extra texlive-luatex texlive-xetex
       - name: Sphinx build
         run: |
+
+          # need to generate _metadata.py manually since we are not
+          # doing a `pip install` build
+          PKGNAME=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['project']['name'])")
+          VERSION_SCHEME=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['tool']['setuptools_scm']['version_scheme'])")
+          echo "__pkgname__ = \"${PKGNAME}\"" > src/PyPop/_metadata.py
+          echo "__version_scheme__ = \"${VERSION_SCHEME}\"" >> src/PyPop/_metadata.py
+
           # latex build in separate directory
           # it generates a lot of files we don't need to keep
           sphinx-build -b latex website _latexbuild

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.9.1"
+    rev: "v0.9.2"
     hooks:
       - id: ruff
         args: ["--show-fixes"] # FIXME: add "--exit-zero" to list to commit to ignore ruff fixes
@@ -46,7 +46,7 @@ repos:
 
   # for checking C extension code
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v19.1.6
+    rev: v19.1.7
     hooks:
       - id: clang-format
         args: ['--style=LLVM', '--verbose']

diff --git a/README.rst b/README.rst
@@ -1,4 +1,4 @@
-|PyPI version shields.io| |Build status| |Website pypop.org| |GitHub license| |Citations| |DOI|
+|PyPI version shields.io| |Build status| |Pre-commit| |Website pypop.org| |GitHub license| |Citations| |DOI|
 
 PyPop: Python for Population Genomics
 =====================================
@@ -396,13 +396,13 @@ PyPop is distributed under the terms of GPLv2
    :target: https://github.com/alexlancaster/pypop/releases/
 
 .. |Build status| image:: https://github.com/alexlancaster/pypop/actions/workflows/build_wheels.yml/badge.svg?branch=main
-    :target: https://github.com/alexlancaster/pypop/actions/workflows/build_wheels.yml
+   :target: https://github.com/alexlancaster/pypop/actions/workflows/build_wheels.yml
 
 .. |GitHub license| image:: https://img.shields.io/github/license/alexlancaster/pypop.svg
    :target: https://github.com/alexlancaster/pypop/blob/main/LICENSE
 
 .. |GitHub issues| image:: https://img.shields.io/github/issues/alexlancaster/pypop.svg
-    :target: https://github.com/alexlancaster/pypop/issues
+   :target: https://github.com/alexlancaster/pypop/issues
 
 .. |Citations| image:: https://api.juleskreuer.eu/citation-badge.php?doi=10.1111/j.1399-0039.2006.00769.x
    :target: https://juleskreuer.eu/projekte/citation-badge/
@@ -418,3 +418,7 @@ PyPop is distributed under the terms of GPLv2
 
 .. |Website pypop.org| image:: https://img.shields.io/website-up-down-green-red/http/pypop.org.svg
    :target: http://pypop.org/
+
+.. |Pre-commit| image:: https://results.pre-commit.ci/badge/github/alexlancaster/pypop/main.svg
+   :target: https://results.pre-commit.ci/latest/github/alexlancaster/pypop/main
+   :alt: pre-commit.ci status