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Merged
DonFreed merged 3 commits into from
Nov 25, 2025
Merged

Use exec instead of the shell to run commands #16

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e2148ab
Use `exec` instead of the shell to run commands
DonFreed Nov 25, 2025
5e70ff4
Pass environment variables directly to bwa in hybrid stage1
DonFreed Nov 25, 2025
474c1b4
Correct pipes in hybrid stage1
DonFreed Nov 25, 2025
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32 changes: 16 additions & 16 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,19 +8,18 @@ jobs:
strategy:
fail-fast: true
matrix:
python-version: ["3.8", "3.13"]
poetry-version: ["1.5.1"]
python-version: ["3.9", "3.13"]
os: [ubuntu-22.04] #, macos-latest, windows-latest]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
- uses: actions/checkout@v5
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Run image
uses: abatilo/actions-poetry@v2
with:
poetry-version: ${{ matrix.poetry-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade poetry
- name: Test build
run: |
poetry config virtualenvs.in-project true
Expand All @@ -32,22 +31,23 @@ jobs:
fail-fast: true
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
- uses: actions/checkout@v5
- uses: actions/setup-python@v5
with:
python-version: "3.11"
- name: Run image
uses: abatilo/actions-poetry@v2
with:
poetry-version: "1.5.1"
python-version: "3.13"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade poetry
poetry install --with dev
- name: Install the project dependencies
run: poetry install
- name: Run black formatter
run: poetry run black --check --exclude '__pycache__|scripts|sentieon_cli/archive.py' --line-length 79 sentieon_cli
- name: Run mypy
run: poetry run mypy sentieon_cli
- name: Run flake8
run: poetry run flake8 . --extend-ignore E231,E221, --exclude .github/scripts/license_message.py,sentieon_cli/scripts/gvcf_combine.py,sentieon_cli/scripts/vcf_mod.py,sentieon_cli/scripts/hybrid_anno.py,sentieon_cli/scripts/hybrid_select.py,sentieon_cli/archive.py,tests # false+ from python 3.12
run: poetry run flake8 . --extend-ignore E231,E221, --exclude .github/scripts/license_message.py,sentieon_cli/scripts/gvcf_combine.py,sentieon_cli/scripts/vcf_mod.py,sentieon_cli/scripts/hybrid_anno.py,sentieon_cli/scripts/hybrid_select.py,sentieon_cli/archive.py,playground,tests # false+ from python 3.12
- name: Run the automated tests
run: poetry run pytest -v
- name: Run doct tests
Expand Down
51 changes: 24 additions & 27 deletions .github/workflows/main.yml
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Expand Up @@ -14,20 +14,19 @@ jobs:
fail-fast: true
max-parallel: 1
matrix:
python-version: ["3.8", "3.13"]
poetry-version: ["1.5.1"]
sentieon-version: ["202503"]
python-version: ["3.9", "3.13"]
sentieon-version: ["202503.01"]
os: [ubuntu-22.04] #, macos-latest, windows-latest]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
- uses: actions/checkout@v5
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Run image
uses: abatilo/actions-poetry@v2
with:
poetry-version: ${{ matrix.poetry-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade poetry
- name: Install the project dependencies
run: |
poetry config virtualenvs.in-project true
Expand Down Expand Up @@ -91,20 +90,19 @@ jobs:
fail-fast: true
max-parallel: 1
matrix:
python-version: ["3.8", "3.13"]
poetry-version: ["1.5.1"]
sentieon-version: ["202503"]
python-version: ["3.9", "3.13"]
sentieon-version: ["202503.01"]
os: [ubuntu-22.04] #, macos-latest, windows-latest]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
- uses: actions/checkout@v5
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Run image
uses: abatilo/actions-poetry@v2
with:
poetry-version: ${{ matrix.poetry-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade poetry
- name: Install the project dependencies
run: |
poetry config virtualenvs.in-project true
Expand Down Expand Up @@ -204,20 +202,19 @@ jobs:
fail-fast: true
max-parallel: 1
matrix:
python-version: ["3.8", "3.13"]
poetry-version: ["1.5.1"]
sentieon-version: ["202503.01.rc1"]
python-version: ["3.9", "3.13"]
sentieon-version: ["202503.01"]
os: [ubuntu-22.04] #, macos-latest, windows-latest]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
- uses: actions/checkout@v5
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Run image
uses: abatilo/actions-poetry@v2
with:
poetry-version: ${{ matrix.poetry-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade poetry
- name: Install the project dependencies
run: |
poetry config virtualenvs.in-project true
Expand Down
10 changes: 5 additions & 5 deletions .github/workflows/release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,11 @@ jobs:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
with:
python-version: "3.12"
- name: Run image
uses: abatilo/actions-poetry@v2
with:
poetry-version: "1.5.1"
python-version: "3.13"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade poetry
- name: Test build
run: |
poetry config virtualenvs.in-project true
Expand Down
41 changes: 33 additions & 8 deletions poetry.lock
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