migrate to new python packaging

.github/actions/setup-python-env/action.yml

@@ -0,0 +1,30 @@
+name: "Setup Python Environment"
+description: "Set up Python environment for the given Python version"
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+    default: "3.13"
+  uv-version:
+    description: "uv version to use"
+    required: true
+    default: "0.7.14"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: ${{ inputs.uv-version }}
+        enable-cache: 'true'
+        cache-suffix: ${{ matrix.python-version }}
+
+    - name: Install Python dependencies
+      run: uv sync --frozen
+      shell: bash

.github/workflows/python-ci-cd.yml

@@ -0,0 +1,21 @@
+name: Python CI/CD
+permissions:
+  contents: write
+  id-token: write
+
+on:
+  push:
+    branches: ["*"]
+    tags: ["*"]
+
+jobs:
+  python-ci-cd:
+    name: Python CI/CD
+    permissions:
+      contents: write
+      id-token: write
+    uses: biocommons/.github/.github/workflows/python-ci-cd.yml@main
+    with:
+      publish: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') }}
+    secrets:
+      pypi-token: ${{ secrets.UV_PUBLISH_TOKEN }}

.github/workflows/stale.yml

@@ -1,5 +1,3 @@
-# https://github.com/actions/stale
-
 name: 'Close stale issues and PRs'
 on:
   workflow_dispatch:

.github/workflows/validate-codecov-config.yml

@@ -0,0 +1,17 @@
+name: Validate Codecov Config
+
+on:
+  pull_request:
+    paths: [codecov.yaml]
+  push:
+    branches: [main]
+
+jobs:
+  validate-codecov-config:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+      - name: Validate codecov configuration
+        run: curl -sSL --fail-with-body --data-binary @codecov.yaml https://codecov.io/validate

.gitignore

@@ -1,50 +1,111 @@
+*$py.class
 *.bak
-*.cache
+*.cover
 *.egg
-*.egg-info
-*.err
-*.fai
+*.egg-info/
 *.log
+*.manifest
+*.mo
 *.orig
-*.pyc
-*.pylint
-*.pyo
-*.rej
+*.pot
+*.py.cover
+*.py[cod]
+*.py[codz]
+*.sage.py
+*.so
+*.spec
 *.sqlite3
-*.tar.gz
+*.sqlite3-journal
 *~
-.*.conf.mk
 .DS_Store
 .Python
+.abstra/
+.cache
 .coverage
-.eggs/**
+.coverage.*
+.cursorignore
+.cursorindexingignore
+.dmypy.json
+.eggs/
+.env
+.envrc
+.hypothesis/
 .idea
 .installed.cfg
 .ipynb_checkpoints
+.mypy_cache/
+.nox/
+.pdm-build/
+.pdm-python
+.pixi
+.pybuilder/
+.pypirc
+.pyre/
 .pytest_cache
+.pytest_cache/
 .python-version
+.pytype/
+.ropeproject
+.ruff_cache/
+.scrapy
+.spyderproject
+.spyproject
 .tags
 .tags.mk
-.tox
+.tox/
+.venv
 .vscode
-^examples/.+\.rst
+.webassets-cache
+/site
+ENV/
+MANIFEST
+__marimo__/
+__pycache__/
+__pypackages__/
 archive
 bdist
+bioutils/_data/assemblies/pull
 build
-cover
+build/
+celerybeat-schedule
+celerybeat.pid
+cover/
 coverage.xml
-dist
+cython_debug/
+develop-eggs/
+dist/
+dmypy.json
+doc*/changelog/*/.tags
+doc*/changelog/*/.tags.mk
+doc/_build
 doc/build
-examples/*_files
-examples/.ipynb_checkpoints
-hg-git-remap.pl
-hgvs.dot
-hgvs.sfood
-hgvs.svg
+doc/changelog/*/.tags
+doc/changelog/*/.tags.mk
+doc/changelog/*/hg-git-remap.pl
+docs/_build/
+docs/source
+downloads/
+eggs/
+env.bak/
+env/
+htmlcov/
+instance/
+ipython_config.py
+lib/
+lib64/
+local_settings.py
+marimo/_lsp/
+marimo/_static/
 misc
-prof
-sdist
-tests/data/*.out
-tmp
-venv*
-workspace
+nosetests.xml
+parts/
+pip-delete-this-directory.txt
+pip-log.txt
+profile_default/
+sdist/
+share/python-wheels/
+target/
+var/
+venv.bak/
+venv/
+wheels/

.mailmap

@@ -1,11 +1,13 @@
-# This is used by Git to consolidate the users who used multiple accounts
+# This file is used by Git to consolidate the users who used multiple accounts
 # I pick the account with the most modified files in git shortlog -sne
-Reece Hart <reecehart@gmail.com> Reece Hart <reece@biocommons.org>
-Reece Hart <reecehart@gmail.com> Reece Hart <reece@biocmmons.org>
-Rudy Rico <rudy.rico@invitae.com> Rudolph Rico <rudy.rico@invitae.com>
-Meng <wangm0855@gmail.com> Meng Wang <wangm0855@gmail.com>
-Andreas Prlic <andreas.prlic@invitae.com> Andreas Prlic <andreas.prlic@gmail.com>
 Andreas Prlic <andreas.prlic@invitae.com> Andreas Prlic <36012160+andreas-invitae@users.noreply.github.com>
+Andreas Prlic <andreas.prlic@invitae.com> Andreas Prlic <andreas.prlic@gmail.com>
 Caitlin Gong <ccaitlingo@gmail.com> Caitlin Gong <clgong@vassar.edu>
 Katie Stahl <kathryn.stahl@nationwidechildrens.org> katie stahl <kathryn.stahl@nationwidechildrens.org>
 Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de> Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
+Meng <wangm0855@gmail.com> Meng Wang <wangm0855@gmail.com>
+Reece Hart <reecehart@gmail.com> Reece Hart <reece@biocmmons.org>
+Reece Hart <reecehart@gmail.com> Reece Hart <reece@biocommons.org>
+Reece Hart <reecehart@gmail.com> Reece Hart <reecehart@Reeces-MacBook-Pro.local>
+Reece Hart <reecehart@gmail.com> Reece Hart <reece@ip-192-168-0-13.us-west-2.compute.internal>
+Rudy Rico <rudy.rico@invitae.com> Rudolph Rico <rudy.rico@invitae.com>

.pre-commit-config.yaml

@@ -1,7 +1,35 @@
 repos:
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.9.6
-  hooks:
-    - id: ruff
-      args: [ --fix ]
-    - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v6.0.0"
+    hooks:
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-json
+        exclude: ^.devcontainer/.*devcontainer.json
+      - id: check-shebang-scripts-are-executable
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-yaml
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: pretty-format-json
+        exclude: ^.devcontainer/.*devcontainer.json
+        args: [--autofix, --no-sort-keys]
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.12.7"
+    hooks:
+      - id: ruff-check
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: local
+    hooks:
+      - id: canonicalize-gitignore
+        name: Sort unique .gitignore
+        entry: sh -c 'LC_ALL=C sort -u -o .gitignore .gitignore'
+        language: system
+        files: ^\.gitignore$