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Merge pull request #20 from aaronmussig/dev
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Release
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@aaronmussig
aaronmussig authored Jul 16, 2024
2 parents 9741f34 + bed49be commit b01d2b1
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Showing 22 changed files with 5,520 additions and 4,674 deletions.
0 .cargo/config → .cargo/config.toml
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257 changes: 193 additions & 64 deletions .github/workflows/build-publish.yml
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Expand Up @@ -11,112 +11,239 @@ jobs:
name: Next version
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-node@v3
- uses: actions/checkout@v4
- uses: actions/setup-node@v4
with:
cache: npm
node-version: 16
node-version: lts/Iron
- run: npm install
- run: npx semantic-release --dry-run
id: semantic_release
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
name: semantic-release
path: |
Cargo.toml
pyproject.toml
CITATION.cff
retention-days: 1
outputs:
version: ${{ steps.semantic_release.outputs.version }}

test_rust:
name: Build Rust
name: Test Rust
needs: semantic_release_next_version
if: needs.semantic_release_next_version.outputs.version != ''
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions-rs/toolchain@v1
- uses: actions/checkout@v4
- uses: actions-rust-lang/setup-rust-toolchain@v1
with:
toolchain: stable
- uses: actions-rs/cargo@v1
- run:
cargo test --release --all-features

build_linux:
needs: test_rust
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: ubuntu-latest
target: x86_64
python-version:
- '3.8'
- '3.9'
- '3.10'
- '3.11'
- '3.12'
steps:
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
name: semantic-release
- uses: actions/setup-python@v5
with:
command: test
args: --release --all-features
python-version: ${{ matrix.python-version }}
- name: Build wheel
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }}
sccache: 'true'
manylinux: auto
- name: Test wheel
run: |
echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree
python -m pip install dendropy
python -m pip install dist/*.whl --force-reinstall
python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')"
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
name: wheels-linux-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }}
path: dist
retention-days: 1

build_python_wheels:
name: Python ${{ matrix.pyver }}@${{ matrix.os }}.whl
needs: semantic_release_next_version
if: needs.semantic_release_next_version.outputs.version != ''
runs-on: ${{ matrix.os }}
musllinux:
needs: test_rust
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
os: [ubuntu-20.04, macos-11]
pyver: [cp37, cp38, cp39, cp310, cp311]
platform:
- runner: ubuntu-latest
target: x86_64
python-version:
- '3.8'
- '3.9'
- '3.10'
- '3.11'
- '3.12'
steps:
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
name: semantic-release
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Build wheel
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }}
sccache: 'true'
manylinux: musllinux_1_2
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
name: wheels-musllinux-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }}
path: dist
retention-days: 1


windows:
needs: test_rust
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: windows-latest
target: x64
python-version:
- '3.8'
- '3.9'
- '3.10'
- '3.11'
- '3.12'
steps:
- uses: actions/checkout@v3
- uses: actions/download-artifact@v3
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
name: semantic-release
- uses: pypa/[email protected]
env:
CIBW_BUILD: ${{matrix.pyver}}-*
- uses: actions/upload-artifact@v3
- uses: actions/setup-python@v5
with:
name: pypi
path: wheelhouse/*.whl
python-version: ${{ matrix.python-version }}
- name: Build wheel
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }}
sccache: 'true'
- name: Test wheel
run: |
echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree
python -m pip install dendropy
python -m pip install (get-item .\dist\*.whl) --force-reinstall
python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')"
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
name: wheels-windows-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }}
path: dist
retention-days: 1

build_python_dist:
name: Python build *.tar.gz
runs-on: ubuntu-latest
needs: semantic_release_next_version
if: needs.semantic_release_next_version.outputs.version != ''
osx:
needs: test_rust
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: macos-12
target: x86_64
- runner: macos-14
target: aarch64
python-version:
- '3.8'
- '3.9'
- '3.10'
- '3.11'
- '3.12'
steps:
- uses: actions/checkout@v3
- uses: actions/download-artifact@v3
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
name: semantic-release
- name: Build sdist
run: pipx run build --sdist
- uses: actions/upload-artifact@v3
- uses: actions/setup-python@v5
with:
name: pypi
path: dist/*.tar.gz
python-version: ${{ matrix.python-version }}
- name: Build wheel
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }}
sccache: 'true'
- name: Test wheel
run: |
echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree
python -m pip install dendropy
python -m pip install dist/*.whl --force-reinstall
python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')"
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
name: wheels-osx-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }}
path: dist
retention-days: 1

test_python_dist:
name: Python test *.tar.gz
sdist:
needs: test_rust
runs-on: ubuntu-latest
needs: build_python_dist
steps:
- uses: actions-rs/toolchain@v1
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
toolchain: stable
- uses: actions/download-artifact@v3
name: semantic-release
- name: Build wheel
uses: PyO3/maturin-action@v1
with:
name: pypi
path: dist
- uses: actions/setup-python@v4
command: sdist
args: --out dist
- name: Test dist
run: |
echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree
python -m pip install dendropy
python -m pip install dist/*.tar.gz --force-reinstall
python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')"
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
python-version: '3.10'
- run: echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree
- run: python -m pip install dendropy
- run: python -m pip install dist/*.tar.gz
- run: python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')"
name: wheels-sdist
path: dist
retention-days: 1

semantic_release_publish:
name: Publish to GitHub
needs: [test_rust, test_python_dist, build_python_wheels]
needs: [build_linux, musllinux, windows, osx, sdist]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-node@v3
- uses: actions/checkout@v4
- uses: actions/setup-node@v4
with:
cache: npm
node-version: 16
node-version: lts/Iron
- run: npm install
- run: npx semantic-release
env:
Expand All @@ -126,27 +253,29 @@ jobs:
name: Publish to PyPI
needs: [semantic_release_publish]
runs-on: ubuntu-latest
environment:
name: pypi
url: https://pypi.org/p/phylodm
permissions:
id-token: write
steps:
- uses: actions/download-artifact@v3
- uses: actions/download-artifact@v4
with:
name: pypi
path: dist

pattern: wheels-*
merge-multiple: true
- uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.PYPI_TOKEN }}

upload_crates:
name: Publish to crates.io
needs: [semantic_release_publish]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/download-artifact@v3
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
name: semantic-release
- uses: actions-rs/toolchain@v1
- uses: actions-rust-lang/setup-rust-toolchain@v1
with:
toolchain: stable
- run: cargo publish --allow-dirty --token ${CRATES_TOKEN}
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4 changes: 4 additions & 0 deletions .gitignore
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Expand Up @@ -145,3 +145,7 @@ wheelhouse/

# Node modules
node_modules/

# venv
bin/*
pyvenv.cfg
5 changes: 3 additions & 2 deletions .releaserc
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@@ -1,15 +1,16 @@
{
"tagFormat": "v${version}",
"branches": [
"main"
"main",
{"name": "dev", "prerelease": true}
],
"plugins": [
"@semantic-release/commit-analyzer",
"@semantic-release/release-notes-generator",
[
"@semantic-release/exec",
{
"verifyReleaseCmd": "./version.sh ${nextRelease.version} && echo ::set-output name=version::${nextRelease.version}"
"verifyReleaseCmd": "./version.sh ${nextRelease.version} && echo version=${nextRelease.version} >> $GITHUB_OUTPUT"
}
],
[
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