refactor: seqrepo rest service to follow python package template (#1)

addresses [biocommons hackathon issue #32](biocommons/hackathon#32)

---------

Co-authored-by: Kori Kuzma <korikuzma@gmail.com>
Co-authored-by: Anastasia Bratulin <bratulin.1@osu.edu>
Co-authored-by: Jennifer Bowser <jduffbowser@gmail.com>

Author: 4 people

.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/build-and-push-image.yml

@@ -26,4 +26,4 @@ jobs:
             https://raw.githubusercontent.com/biocommons/.github/main/etc/labels.yml
             .github/labels.yml
 
-          delete-other-labels: false
+          delete-other-labels: false

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

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

.github/workflows/python-package.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

.github/workflows/stale.yml

@@ -1,22 +1,92 @@
-*.bak
+*$py.class
+*.cover
 *.egg
-*.egg-info
+*.egg-info/
 *.log
 *.manifest
-*.orig
+*.mo
+*.pot
+*.py.cover
+*.py[codz]
+*.sage.py
+*.so
+*.spec
 *.sqlite3
+*.sqlite3-journal
 *~
+.DS_Store
+.Python
+.abstra/
 .cache
 .coverage
-.eggs
-.idea
+.coverage.*
+.cursorignore
+.cursorindexingignore
+.dmypy.json
+.eggs/
+.env
+.envrc
+.hypothesis/
+.installed.cfg
 .ipynb_checkpoints
-.tox
+.mypy_cache/
+.nox/
+.pdm-build/
+.pdm-python
+.pixi
+.pybuilder/
+.pypirc
+.pyre/
+.pytest_cache/
+.pytype/
+.ropeproject
+.ruff_cache/
+.scrapy
+.spyderproject
+.spyproject
+.tox/
+.venv
 .vscode
-__pycache__
+.webassets-cache
+/site
+ENV/
+MANIFEST
+__marimo__/
+__pycache__/
+__pypackages__/
 archive
-build
-dist
-docs/_build
+build/
+celerybeat-schedule
+celerybeat.pid
+cover/
+coverage.xml
+cython_debug/
+develop-eggs/
+dist/
+dmypy.json
+docs/_build/
+docs/source
+downloads/
+eggs/
+env.bak/
+env/
+htmlcov/
+instance/
+ipython_config.py
+lib/
+lib64/
+local_settings.py
+marimo/_lsp/
+marimo/_static/
 nosetests.xml
-venv
+parts/
+pip-delete-this-directory.txt
+pip-log.txt
+profile_default/
+sdist/
+share/python-wheels/
+target/
+var/
+venv.bak/
+venv/
+wheels/

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

@@ -0,0 +1,12 @@
+# I pick the account with the most modified files in git shortlog -sne
+# This is used by Git to consolidate the users who used multiple accounts
+Reece Hart <reecehart@gmail.com>
+Reece Hart <reece@biocmmons.org>
+James Stevenson <james.sharpsteen@gmail.com>
+Kyle Ferriter <kferrite@broadinstitute.org>
+Andreas Prlic <andreas.prlic@invitae.com>
+Ben Robinson <ben.robinson@invitae.com>
+Blake Peterman <blake@peterman.io>
+James Stevenson <james.stevenson@nationwidechildrens.org>
+Kori Kuzma <korikuzma@gmail.com>
+melissacline <melissa.s.cline@gmail.com>

.gitignore

@@ -1,6 +1,43 @@
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.4
-  hooks:
-    - id: ruff-format
-      args: [ --check ]
+repos:
+  - 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$
+
+  - repo: local
+    hooks:
+      - id: canonicalize-pyproject
+        name: Ensure pyproject.toml in canonical order and format
+        entry: uvx toml-sort --in-place --all pyproject.toml
+        language: system
+        files: ^pyproject.toml$