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ci: switch to uv + tox, add GitHub Actions workflows (#1)
* ci: switch to uv + tox, add GitHub Actions workflows - Replace setuptools with hatchling; declare runtime deps explicitly - Add uv dependency-groups (dev/test/lint) and tox envs via tox-uv - Configure ruff (format + lint) and mypy under tox - Add GitHub Actions: CI (3.12 + 3.14 matrix), PR title lint, publish, release-please - Slim environment-dev.yml to python + uv - Generate uv.lock - Reformat sources with ruff format; minor mypy type annotation - Stop tracking .devcontainer * style: preserve multi-line method chains with fmt: skip
1 parent 030d2ff commit 9f49cc7

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‎.github/workflows/check-pr.yml‎

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name: PR Title Lint
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on:
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pull_request:
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types:
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- opened
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- edited
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- synchronize
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- reopened
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permissions:
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pull-requests: read
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statuses: write
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jobs:
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conventional-title:
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name: Validate PR title (Conventional Commits)
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runs-on: ubuntu-latest
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steps:
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- uses: amannn/action-semantic-pull-request@48f256284bd46cdaab1048c3721360e808335d50 # v6.1.1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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types: |
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feat
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fix
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chore
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docs
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refactor
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test
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ci
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build
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perf
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style
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revert
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requireScope: false
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subjectPattern: ^[a-z].+[^.]$
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subjectPatternError: |
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Subject must start with lowercase letter and not end with a period.
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Got: "{subject}"
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wip: true

‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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workflow_dispatch:
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env:
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UV_VERSION: "0.11.6"
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UV_PYTHON_PREFERENCE: "managed"
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jobs:
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quality-checks:
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name: Quality Checks
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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version: ${{ env.UV_VERSION }}
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.14
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- name: Ensure uv lockfile is up-to-date
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run: uv lock --check
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- name: Install project dependencies
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run: uv sync --all-groups
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- name: Check formatting
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run: uv run tox -e format-check
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- name: Linting
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run: uv run tox -e lints
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- name: Run type checking
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run: uv run tox -e typecheck
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test:
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name: Test (Python ${{ matrix.python-version }})
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needs: [quality-checks]
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.12", "3.14"]
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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version: ${{ env.UV_VERSION }}
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enable-cache: true
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- name: Set up Python ${{ matrix.python-version }}
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run: uv python install ${{ matrix.python-version }}
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- name: Install project dependencies
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run: uv sync --all-groups
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- name: Run tests
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run: uv run tox -e py${{ matrix.python-version }}

‎.github/workflows/publish.yml‎

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name: Publish to PyPI
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on:
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workflow_dispatch:
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push:
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tags:
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- "v[0-9]+.[0-9]+.[0-9]+*"
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env:
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UV_VERSION: "0.11.6"
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jobs:
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build-and-publish:
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name: Build & Publish to PyPI
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/nmd_scanner
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permissions:
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id-token: write
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contents: read
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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with:
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ref: ${{ github.ref }}
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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version: ${{ env.UV_VERSION }}
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.14
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- name: Build package
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run: uv build --sdist --wheel --out-dir dist
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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packages-dir: dist

‎.github/workflows/release-please.yml‎

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name: Release Please
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on:
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push:
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branches: [main]
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workflow_dispatch:
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permissions:
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contents: write
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pull-requests: write
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env:
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UV_VERSION: "0.11.6"
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UV_PYTHON_PREFERENCE: "managed"
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jobs:
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release-please:
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name: Release Please
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runs-on: ubuntu-latest
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outputs:
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release_created: ${{ steps.release.outputs.release_created }}
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tag_name: ${{ steps.release.outputs.tag_name }}
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prs: ${{ steps.release.outputs.prs }}
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steps:
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- uses: googleapis/release-please-action@v4
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id: release
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with:
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config-file: release-please-config.json
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manifest-file: .release-please-manifest.json
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refresh-lock:
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name: Refresh uv.lock on release PR
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needs: release-please
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if: ${{ needs.release-please.outputs.prs != '' && needs.release-please.outputs.prs != '[]' }}
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Determine release PR branch
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id: branch
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run: |
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BRANCH=$(echo '${{ needs.release-please.outputs.prs }}' | jq -r '.[0].headBranchName')
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echo "name=$BRANCH" >> "$GITHUB_OUTPUT"
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- name: Checkout release PR branch
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uses: actions/checkout@v4
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with:
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ref: ${{ steps.branch.outputs.name }}
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token: ${{ secrets.GITHUB_TOKEN }}
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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version: ${{ env.UV_VERSION }}
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.14
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- name: Refresh uv.lock
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run: |
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uv lock
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if git diff --quiet uv.lock; then
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echo "uv.lock already in sync — nothing to commit."
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exit 0
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fi
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git config user.name "github-actions[bot]"
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git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
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git add uv.lock
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git commit -m "chore: refresh uv.lock for release"
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git push

‎.gitignore‎

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.devcontainer/
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.DS_Store
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*.egg-info/
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*.pyc

‎.release-please-manifest.json‎

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{
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".": "0.1.0"
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}

‎environment-dev.yaml‎

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‎environment-dev.yml‎

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name: nmd_scanner
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channels:
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- conda-forge
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- bioconda
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- nodefaults
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dependencies:
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- python >=3.13
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- uv =0.11

‎pyproject.toml‎

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[build-system]
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requires = ["hatchling"]
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build-backend = "hatchling.build"
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[project]
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name = "nmd_scanner"
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version = "0.1.0"
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description = "A simple scanner package for NMD"
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authors = [
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{ name = "Your Name", email = "your.email@example.com" }
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{ name = "Carina Hui Schröder", email = "Carina2504@users.noreply.github.com" },
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{ name = "Florian R. Hölzlwimmer", email = "git.ich@frhoelzlwimmer.de" },
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]
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readme = "README.md"
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license = { text = "MIT" }
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license = "MIT"
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requires-python = ">=3.12"
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dependencies = [
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# Add your runtime dependencies here, e.g.
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# "requests >=2.25.1",
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"pandas",
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"numpy",
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"pyfaidx",
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"biopython",
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"pyranges",
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"pysam",
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"tqdm>=4.66.5,<5",
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"importlib-metadata",
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]
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[build-system]
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requires = ["setuptools>=61.0", "wheel"]
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build-backend = "setuptools.build_meta"
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[project.urls]
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"Homepage" = "https://github.com/gagneurlab/NMD-Scanner"
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[tool.setuptools.packages.find]
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where = ["src"]
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[dependency-groups]
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dev = [
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"tox>=4",
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"tox-uv",
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]
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test = [
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"pytest>=8,<9",
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"pytest-xdist",
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"pytest-mock",
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"pytest-cov",
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"pytest-sugar",
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]
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lint = [
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"ruff",
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"mypy",
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"pandas-stubs",
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]
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[project.optional-dependencies]
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dev = ["pytest >=7.0"]
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[tool.hatch.build.targets.wheel]
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packages = ["src/nmd_scanner"]
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[tool.pytest.ini_options]
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testpaths = [
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"tests"
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]
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addopts = [
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"--import-mode=importlib",
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[tool.ruff]
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target-version = "py312"
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line-length = 120
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extend-exclude = ["scripts", "resources", "testdir"]
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[tool.ruff.lint]
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select = ["E", "F", "W", "I"]
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ignore = [
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"E501", # line-too-long
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"E712", # comparison-to-true (pandas idiom: df[col == True])
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"F403", # star imports used intentionally in package
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"F405", # may-be-undefined-from-star-import
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"F841", # local-variable-assigned-but-never-used
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]
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[tool.ruff.lint.per-file-ignores]
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"tests/*" = ["S", "SIM", "PLR", "F811", "F841"]
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"__init__.py" = ["F401"]
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[tool.tox]
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requires = ["tox>=4", "tox-uv"]
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env_list = ["format-check", "lints", "typecheck", "py3.12", "py3.14"]
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isolated_build = true
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[tool.tox.env_run_base]
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runner = "uv-venv-lock-runner"
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description = "run unit tests"
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dependency_groups = ["test"]
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commands = [["pytest", { replace = "posargs", default = ["tests"], extend = true }]]
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[tool.tox.env."format-check"]
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runner = "uv-venv-lock-runner"
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skip_install = true
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dependency_groups = ["lint"]
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commands = [["ruff", "format", "--check", "."]]
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[tool.tox.env."lints"]
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runner = "uv-venv-lock-runner"
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skip_install = true
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dependency_groups = ["lint"]
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commands = [["ruff", "check", "."]]
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[tool.tox.env."typecheck"]
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runner = "uv-venv-lock-runner"
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dependency_groups = ["lint"]
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commands = [["mypy", "src/nmd_scanner"]]
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[tool.mypy]
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python_version = "3.12"
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ignore_missing_imports = true
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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addopts = ["--import-mode=importlib"]

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