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Bio-Engine Consolidated Pipeline

chore: bump version to 0.8.0 and finalize release notes #42

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chore: bump version to 0.8.0 and finalize release notes

chore: bump version to 0.8.0 and finalize release notes #42

Workflow file for this run

.github/workflows/pipeline.yml at 98ea0b1
name: Bio-Engine Consolidated Pipeline
on:
push:
branches: [ master, main, develop, fix/windows-dll-issues ]
tags: [ 'v*' ]
workflow_dispatch:
paths:
- '**.py'
- 'requirements.txt'
- 'bio-engine.spec'
- '.github/workflows/**'
jobs:
build-linux:
name: Build Linux Binary
runs-on: ubuntu-22.04
permissions:
contents: write
steps:
- name: Checkout Code
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.10'
cache: 'pip'
- name: Install Dependencies
shell: bash
run: |
python -m pip install --upgrade pip
while IFS= read -r line || [ -n "$line" ]; do
line=$(echo "$line" | sed 's/#.*//' | xargs)
[ -z "$line" ] && continue
[[ "$line" =~ ^[[:space:]] ]] && continue
pip install "$line" || echo "WARNING: Failed to install $line (may be platform-specific)"
done < requirements.txt
pip install pyinstaller
- name: Build with PyInstaller
run: pyinstaller bio-engine.spec
- name: Upload Binary
uses: actions/upload-artifact@v4
with:
name: bio-engine-linux
path: dist/bio-engine
if-no-files-found: error
build-windows:
name: Build Windows Binary
runs-on: windows-latest
permissions:
contents: write
steps:
- name: Checkout Code
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.10'
cache: 'pip'
- name: Install Dependencies
shell: bash
run: |
python -m pip install --upgrade pip
while IFS= read -r line || [ -n "$line" ]; do
line=$(echo "$line" | sed 's/#.*//' | xargs)
[ -z "$line" ] && continue
[[ "$line" =~ ^[[:space:]] ]] && continue
pip install "$line" || echo "WARNING: Failed to install $line (may be platform-specific)"
done < requirements.txt
pip install pyinstaller
- name: Build with PyInstaller
run: pyinstaller bio-engine.spec
- name: Upload Binary
uses: actions/upload-artifact@v4
with:
name: bio-engine-windows
path: dist/bio-engine.exe
if-no-files-found: error
test-linux:
name: Verify Linux (pysam)
needs: build-linux
runs-on: ubuntu-latest
continue-on-error: true
permissions:
contents: write
steps:
- name: Checkout Code
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.12'
cache: 'pip'
- name: Install Dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements.txt
pip install pytest pytest-cov
- name: Run Tests with pytest and coverage
run: |
PYTHONPATH=. pytest
- name: Generate Coverage Badge
uses: tj-actions/coverage-badge-py@v2
with:
output: coverage.svg
- name: Verify Changed files
uses: tj-actions/verify-changed-files@v20
id: verify-changed-files
with:
files: coverage.svg
- name: Commit and push coverage badge
if: steps.verify-changed-files.outputs.files_changed == 'true'
run: |
git config --local user.email "github-actions[bot]@users.noreply.github.com"
git config --local user.name "github-actions[bot]"
git add coverage.svg
git commit -m "chore: update coverage badge"
git push
test-windows:
name: Verify Windows (Binaries)
needs: build-windows
runs-on: windows-latest
continue-on-error: true
steps:
- name: Checkout Code
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.10'
cache: 'pip'
- name: Install Dependencies
shell: bash
run: |
python -m pip install --upgrade pip
while IFS= read -r line || [ -n "$line" ]; do
line=$(echo "$line" | sed 's/#.*//' | xargs)
[ -z "$line" ] && continue
[[ "$line" =~ ^[[:space:]] ]] && continue
pip install "$line" || echo "WARNING: Failed to install $line (may be platform-specific)"
done < requirements.txt
pip install h11
- name: Setup MSYS2
uses: msys2/setup-msys2@v2
with:
msystem: MINGW64
update: true
install: mingw-w64-x86_64-samtools mingw-w64-x86_64-htslib
- name: Run Windows Binary Test
shell: msys2 {0}
env:
BIO_BGZIP_PATH: bgzip
BIO_SAMTOOLS_PATH: samtools
TRACY_PATH: echo
run: |
export PATH="/c/hostedtoolcache/windows/Python/3.10.11/x64:$PATH"
python --version
python tests/test_windows_binaries.py
- name: Prep Isolated environment (Diagnostic & Bundling)
shell: msys2 {0}
run: |
mkdir -p isolated_test
cp /mingw64/bin/bgzip.exe isolated_test/bgzip.exe
cp /mingw64/bin/samtools.exe isolated_test/samtools.exe || true
echo "### Diagnostic: Identifying dependencies for bgzip ###"
ldd /mingw64/bin/bgzip.exe
# Copy all DLLs mentioned by ldd that are in /mingw64/bin/
# This is a robust way to ensure we catch everything
ldd /mingw64/bin/bgzip.exe | grep /mingw64/bin/ | awk '{print $3}' | xargs -I {} cp {} isolated_test/
echo "Contents of isolated_test:"
ls -l isolated_test
echo "Isolated environment prepped with dependencies"
- name: Run Windows Isolated Test (to confirm fix)
shell: pwsh
env:
BIO_BGZIP_PATH: isolated_test\bgzip.exe
run: |
python tests/test_isolated_bgzip.py
release:
name: Upload to Release
needs: [test-linux, test-windows]
if: startsWith(github.ref, 'refs/tags/')
runs-on: ubuntu-latest
permissions:
contents: write
steps:
- name: Checkout Code
uses: actions/checkout@v4
- name: Download Linux Binary
uses: actions/download-artifact@v4
with:
name: bio-engine-linux
path: linux-bin
- name: Download Windows Binary
uses: actions/download-artifact@v4
with:
name: bio-engine-windows
path: windows-bin
- name: Prepare Binaries for Release
run: |
mv linux-bin/bio-engine bio-engine-x86_64-unknown-linux-gnu
mv windows-bin/bio-engine.exe bio-engine-x86_64-pc-windows-msvc.exe
ls -l
- name: Upload to GitHub Release
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
gh release create ${{ github.ref_name }} --generate-notes || true
gh release upload ${{ github.ref_name }} \
bio-engine-x86_64-unknown-linux-gnu \
bio-engine-x86_64-pc-windows-msvc.exe \
--clobber