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‎.github/workflows/test_pytest.yml‎

Lines changed: 96 additions & 96 deletions
Original file line numberDiff line numberDiff line change
@@ -2,101 +2,101 @@ name: tests_pytest
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on: [push, pull_request, workflow_dispatch]
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defaults:
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run:
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shell: bash -l {0}
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run:
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shell: bash -l {0}
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jobs:
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check_versions_matches:
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name: Check deeptools version matches galaxy tools
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runs-on: ubuntu-latest
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if: github.base_ref == 'master'
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steps:
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- uses: actions/checkout@v4
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- name: Check path
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run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml"
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- name: Get Version of Deeptools
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run: echo "deeptools_version=$(grep "version" /home/runner/work/deepTools/deepTools/pyproject.toml | awk '{print substr($NF, 2, length($NF) - 2)}')" >> $GITHUB_ENV
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- name: Get Version of Galaxy tools
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run: echo "galaxy_deeptools_version=$(grep "token.*TOOL_VERSION" /home/runner/work/deepTools/deepTools/galaxy/wrapper/deepTools_macros.xml | awk -F '>|<' '{print $3}')" >> $GITHUB_ENV
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- name: Versions
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run: |
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echo deeptools version=${deeptools_version}
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echo deeptools version in galaxy=${galaxy_deeptools_version}
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- name: Fail PR if versions not matching
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run: |
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if [ -z $galaxy_deeptools_version ]; then
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echo "galaxy_deeptools_version not defined change the github action"
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exit 1
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fi
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if [ -z $deeptools_version ]; then
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echo "deeptools_version not defined change the github action"
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exit 1
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fi
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if [ "$galaxy_deeptools_version" != "$deeptools_version" ]; then
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echo "versions do not match"
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exit 1
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fi
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build-linux:
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name: Test on Linux
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.9','3.10', '3.11', '3.12', '3.13']
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install Rust
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uses: actions-rust-lang/setup-rust-toolchain@v1
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- name: build deeptools
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run: |
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python -m venv venv
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source venv/bin/activate
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pip install maturin
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maturin develop --release --extras actions
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- name: test deeptools
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run: |
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source venv/bin/activate
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pytest -v
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- name: build wheel
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run: |
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source venv/bin/activate
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python -m build
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- name: test wheel
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run: |
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source venv/bin/activate
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pip install dist/*whl
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build-osx:
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name: Test on OSX
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runs-on: macOS-latest
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strategy:
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matrix:
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python-version: ['3.9','3.10', '3.11', '3.12', '3.13']
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install Rust
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uses: actions-rust-lang/setup-rust-toolchain@v1
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- name: build deeptools
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run: |
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python -m venv venv
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source venv/bin/activate
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pip install maturin
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maturin develop --release --extras actions
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- name: test deeptools
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run: |
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source venv/bin/activate
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pytest -v
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- name: build wheel
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run: |
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source venv/bin/activate
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python -m build
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- name: test wheel
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run: |
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source venv/bin/activate
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pip install dist/*whl
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check_versions_matches:
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name: Check deeptools version matches galaxy tools
11+
runs-on: ubuntu-latest
12+
if: github.base_ref == 'master'
13+
steps:
14+
- uses: actions/checkout@v4
15+
- name: Check path
16+
run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml"
17+
- name: Get Version of Deeptools
18+
run: echo "deeptools_version=$(grep "version" /home/runner/work/deepTools/deepTools/pyproject.toml | awk '{print substr($NF, 2, length($NF) - 2)}')" >> $GITHUB_ENV
19+
- name: Get Version of Galaxy tools
20+
run: echo "galaxy_deeptools_version=$(grep "token.*TOOL_VERSION" /home/runner/work/deepTools/deepTools/galaxy/wrapper/deepTools_macros.xml | awk -F '>|<' '{print $3}')" >> $GITHUB_ENV
21+
- name: Versions
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run: |
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echo deeptools version=${deeptools_version}
24+
echo deeptools version in galaxy=${galaxy_deeptools_version}
25+
- name: Fail PR if versions not matching
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run: |
27+
if [ -z $galaxy_deeptools_version ]; then
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echo "galaxy_deeptools_version not defined change the github action"
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exit 1
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fi
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if [ -z $deeptools_version ]; then
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echo "deeptools_version not defined change the github action"
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exit 1
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fi
35+
if [ "$galaxy_deeptools_version" != "$deeptools_version" ]; then
36+
echo "versions do not match"
37+
exit 1
38+
fi
39+
build-linux:
40+
name: Test on Linux
41+
runs-on: ubuntu-latest
42+
strategy:
43+
matrix:
44+
python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
45+
steps:
46+
- uses: actions/checkout@v4
47+
- uses: actions/setup-python@v5
48+
with:
49+
python-version: ${{ matrix.python-version }}
50+
cache: "pip"
51+
- name: Install Rust
52+
uses: actions-rust-lang/setup-rust-toolchain@v1
53+
- name: build deeptools
54+
run: |
55+
python -m venv venv
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source venv/bin/activate
57+
pip install maturin
58+
maturin develop --release --extras actions
59+
- name: test deeptools
60+
run: |
61+
source venv/bin/activate
62+
pytest -v
63+
- name: build wheel
64+
run: |
65+
source venv/bin/activate
66+
python -m build
67+
- name: test wheel
68+
run: |
69+
source venv/bin/activate
70+
pip install dist/*whl
71+
build-osx:
72+
name: Test on OSX
73+
runs-on: macOS-latest
74+
strategy:
75+
matrix:
76+
python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
77+
steps:
78+
- uses: actions/checkout@v4
79+
- uses: actions/setup-python@v5
80+
with:
81+
python-version: ${{ matrix.python-version }}
82+
cache: "pip"
83+
- name: Install Rust
84+
uses: actions-rust-lang/setup-rust-toolchain@v1
85+
- name: build deeptools
86+
run: |
87+
python -m venv venv
88+
source venv/bin/activate
89+
pip install maturin
90+
maturin develop --release --extras actions
91+
- name: test deeptools
92+
run: |
93+
source venv/bin/activate
94+
pytest -v
95+
- name: build wheel
96+
run: |
97+
source venv/bin/activate
98+
python -m build
99+
- name: test wheel
100+
run: |
101+
source venv/bin/activate
102+
pip install dist/*whl

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