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selmanozleyenselmanozleyen
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try out this setting
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‎.github/workflows/test.yml‎

Lines changed: 105 additions & 61 deletions
Original file line numberDiff line numberDiff line change
@@ -1,92 +1,136 @@
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name: Test
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name: CI
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on:
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schedule:
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- cron: 00 00 * * 1 # every Monday at 00:00
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push:
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branches: [main]
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branches:
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- main
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- "[0-9]+.[0-9]+.x"
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pull_request:
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branches: [main]
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workflow_dispatch:
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inputs:
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reason:
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description: Reason for the workflow dispatch. Only "release" is valid.
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required: true
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default: release
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env:
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PYTEST_ADDOPTS: "-v --color=yes -n auto --internet-tests --junitxml=test-data/test-results.xml"
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FORCE_COLOR: "1"
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MPLBACKEND: agg
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# It's impossible to ignore SyntaxWarnings for a single module,
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# so because leidenalg 0.10.0 has them, we pre-compile things: https://github.com/vtraag/leidenalg/issues/173
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UV_COMPILE_BYTECODE: "1"
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defaults:
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run:
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shell: bash -e {0} # -e to fail on error
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jobs:
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get-environments:
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runs-on: ubuntu-latest
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outputs:
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envs: ${{ steps.get-envs.outputs.envs }}
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steps:
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- uses: actions/checkout@v4
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with:
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filter: blob:none
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fetch-depth: 0
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- uses: astral-sh/setup-uv@v5
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with:
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enable-cache: false
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- id: get-envs
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run: |
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ENVS_JSON=$(NO_COLOR=1 uvx hatch env show --json | jq -c 'to_entries
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| map(
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select(.key | startswith("hatch-test"))
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| {
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name: .key,
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"test-type": (if (.key | test("pre|min")) then "coverage" else null end),
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python: .value.python | sub("3[.]13"; "3.13.3"), # https://github.com/numba/numba/issues/10101
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}
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)')
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echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
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test:
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runs-on: ${{ matrix.os }}
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needs: get-environments
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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: ["3.10", "3.11", "3.12"]
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os: [ubuntu-latest]
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include:
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- python: "3.12"
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os: macos-latest
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env:
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OS: ${{ matrix.os }}
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PYTHON: ${{ matrix.python }}
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env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
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env: # environment variable for use in codecov's env_vars tagging
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ENV_NAME: ${{ matrix.env.name }}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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filter: blob:none
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- name: Set up Python ${{ matrix.python }}
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uses: astral-sh/setup-uv@v6
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- uses: astral-sh/setup-uv@v5
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with:
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python-version: ${{ matrix.python }}
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enable-cache: true
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python-version: ${{ matrix.env.python }}
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cache-dependency-glob: pyproject.toml
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- name: Install dependencies
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run: |
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./.scripts/ci/install_dependencies.sh
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- name: Restore data cache
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id: data-cache
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- name: Cache downloaded data
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uses: actions/cache@v4
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with:
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path: |
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~/.cache/squidpy/*.h5ad
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key: data-${{ hashFiles('**/download_data.py') }}
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path: .pytest_cache/d/squidpy-data
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key: pytest
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- name: Download datasets
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if: steps.data-cache.outputs.cache-hit != 'true'
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run: |
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uvx hatch run data:download
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- name: Install dependencies
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run: uvx hatch -v env create ${{ matrix.env.name }}
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- name: Test
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timeout-minutes: 60
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env:
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MPLBACKEND: agg
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PLATFORM: ${{ matrix.os }}
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DISPLAY: :42
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PYTEST_ADDOPTS: "-n auto"
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run: |
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uvx hatch test --python ${{ matrix.python }} --randomize --parallel --cover --all
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- name: Run tests
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if: matrix.env.test-type == null
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run: uvx hatch run ${{ matrix.env.name }}:run
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- name: Run tests (coverage)
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if: matrix.env.test-type == 'coverage'
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run: uvx hatch run ${{ matrix.env.name }}:run-cov --cov --cov-report=xml
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- name: Archive figures generated during testing
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if: always()
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uses: actions/upload-artifact@v4
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- name: Upload coverage data
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uses: codecov/codecov-action@v5
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if: matrix.env.test-type == 'coverage'
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with:
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name: visual_test_results_${{ matrix.os }}-python${{ matrix.python }}
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path: tests/figures/*
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token: ${{ secrets.CODECOV_TOKEN }}
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env_vars: ENV_NAME
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fail_ci_if_error: true
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files: test-data/coverage.xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v5
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- name: Upload test results
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# yaml strings can't start with "!", so using explicit substitution
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if: ${{ !cancelled() }}
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uses: codecov/test-results-action@v1
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with:
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name: coverage
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verbose: true
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token: ${{ secrets.CODECOV_TOKEN }}
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env_vars: ENV_NAME
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fail_ci_if_error: true
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file: test-data/test-results.xml
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- name: Publish debug artifacts
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if: ${{ !cancelled() }}
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uses: actions/upload-artifact@v4
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with:
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name: debug-data-${{ matrix.env.name }}
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path: .pytest_cache/d/debug
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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filter: blob:none
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- uses: actions/setup-python@v5
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with:
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python-version: "3.12" # Changed from 3.13 to match squidpy's Python support
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- uses: astral-sh/setup-uv@v5
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with:
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enable-cache: false
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- run: uvx --from build pyproject-build --sdist --wheel .
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- run: uvx twine check dist/*
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check:
86127
if: always()
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needs: [test]
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needs:
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- get-environments
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- test
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- build
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runs-on: ubuntu-latest
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steps:
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- uses: re-actors/alls-green@release/v1
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with:
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jobs: ${{ toJSON(needs) }}
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- uses: re-actors/alls-green@release/v1
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with:
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jobs: ${{ toJSON(needs) }}

‎hatch.toml‎

Lines changed: 26 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -48,4 +48,29 @@ check = "make -C docs linkcheck {args}"
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# Data environment - for downloading data
4949
[envs.data]
5050
[envs.data.scripts]
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download = "python ./.scripts/ci/download_data.py {args}"
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download = "python ./.scripts/ci/download_data.py {args}"
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# Matrix-based test environments (like scanpy)
55+
[envs.hatch-test]
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features = ["test"]
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extra-dependencies = [
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"pytest",
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"pytest-xdist",
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"pytest-cov",
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"pytest-mock",
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"pytest-timeout",
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]
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[[envs.hatch-test.matrix]]
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python = ["3.10", "3.11", "3.12"]
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deps = ["stable"]
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[envs.hatch-test.overrides]
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matrix.deps.python = [
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{ if = ["stable"], value = "3.12" },
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]
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[envs.hatch-test.scripts]
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run = "python -m pytest --color=yes --cov --cov-append --cov-report=xml --cov-config=pyproject.toml --ignore docs/ {args:-vv}"
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run-cov = "python -m pytest --color=yes --cov --cov-append --cov-report=xml --cov-config=pyproject.toml --ignore docs/ {args:-vv}"

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