Dev

.github/workflows/ci.yml

@@ -14,13 +14,29 @@ permissions:
 
 jobs:
   test:
+    name: Test (${{ matrix.python-version }}, pandas ${{ matrix.pandas-label }})
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.9', '3.12']
+        include:
+          - python-version: '3.10'
+            pandas-label: '2.2.3'
+            pandas-spec: 'pandas==2.2.3'
+          - python-version: '3.12'
+            pandas-label: '2.2.3'
+            pandas-spec: 'pandas==2.2.3'
+          - python-version: '3.12'
+            pandas-label: '3.x'
+            pandas-spec: 'pandas>=3,<4'
+          - python-version: '3.14'
+            pandas-label: '3.x'
+            pandas-spec: 'pandas>=3,<4'
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
@@ -30,6 +46,10 @@ jobs:
     - name: Upgrade pip, setuptools, and packaging
       run: |
         python -m pip install --upgrade pip setuptools packaging
+
+    - name: Pin pandas ${{ matrix.pandas-label }}
+      run: |
+        python -m pip install --upgrade "${{ matrix.pandas-spec }}"
 
     - name: Cache src directory
       uses: actions/cache@v4
@@ -62,11 +82,13 @@ jobs:
         python3 test.py -t GRCh37
 
     - name: Build and push Docker image
-      if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.python-version == '3.12'
+      if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.python-version == '3.12' && matrix.pandas-label == '3.x'
       run: |
         echo "Starting Docker deployment to GHCR for sigprofilersuite..."
 
-        VERSION_TAG=$(grep "VERSION = " setup.py | cut -d'"' -f2)
+        python -m pip install --upgrade setuptools_scm
+        VERSION_TAG=$(python -m setuptools_scm)
+        VERSION_TAG=${VERSION_TAG//+/-}
 
         # Get the repository name and convert it to lowercase
         REPO_NAME=$(basename ${{ github.repository }} | tr '[:upper:]' '[:lower:]')

.github/workflows/release.yml

@@ -0,0 +1,92 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v6
+      with:
+        python-version: "3.12"
+
+    - name: Install build tooling
+      run: |
+        python -m pip install --upgrade pip build twine
+
+    - name: Build distributions
+      run: |
+        python -m build
+
+    - name: Check distributions
+      run: |
+        python -m twine check dist/*
+
+    - name: Verify package version
+      run: |
+        python -m pip install dist/*.whl
+        python -c "import SigProfilerMatrixGenerator; print(SigProfilerMatrixGenerator.__version__)"
+
+    - name: Upload distributions
+      uses: actions/upload-artifact@v7
+      with:
+        name: python-package-distributions
+        path: dist/
+        if-no-files-found: error
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/SigProfilerMatrixGenerator
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distributions
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish package distributions to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    if: github.event_name == 'release' && github.event.action == 'published'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/SigProfilerMatrixGenerator
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distributions
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -16,7 +16,7 @@
 
 # MkDocs build output
 /site/
-SigProfilerMatrixGenerator/version.py
+SigProfilerMatrixGenerator/_version.py
 SigProfilerMatrixGenerator/references/chromosomes/tsb/
 SigProfilerMatrixGenerator/references/vcf_files/*_bench/input/
 SigProfilerMatrixGenerator/references/vcf_files/*_bench/output/

RELEASE_ADMIN.md

@@ -0,0 +1,145 @@
+# SigProfilerMatrixGenerator Release Administration
+
+This repository publishes Python distributions through GitHub Actions and PyPI
+Trusted Publishing. The release process intentionally has two publish steps:
+
+1. Push a version tag such as `v1.3.7` to publish to TestPyPI.
+2. Publish a GitHub Release for that same tag to publish to PyPI.
+
+Merging into `master` does not publish a Python package by itself.
+
+## Required GitHub Setup
+
+Create these GitHub environments:
+
+```text
+testpypi
+pypi
+```
+
+The environment names must exactly match `.github/workflows/release.yml`.
+The `pypi` environment should require reviewer approval before deployment.
+
+## Required TestPyPI Trusted Publisher
+
+Configure this from TestPyPI:
+
+```text
+PyPI Project Name: SigProfilerMatrixGenerator
+Owner: SigProfilerSuite
+Repository name: SigProfilerMatrixGenerator
+Workflow name: release.yml
+Environment name: testpypi
+```
+
+If the project does not exist on TestPyPI yet, use the pending trusted
+publisher flow to create it on first publish.
+
+## Required PyPI Trusted Publisher
+
+Configure this from the existing PyPI project:
+
+```text
+PyPI Project Name: SigProfilerMatrixGenerator
+Owner: SigProfilerSuite
+Repository name: SigProfilerMatrixGenerator
+Workflow name: release.yml
+Environment name: pypi
+```
+
+For an existing PyPI project, configure this from:
+
+```text
+PyPI -> Your projects -> SigProfilerMatrixGenerator -> Manage -> Publishing
+```
+
+If `Manage` is disabled, ask a current project owner to add your PyPI account
+as an owner or maintainer with publishing permissions.
+
+## Versioning
+
+Package versions are derived from Git tags by `setuptools_scm`.
+
+Release tags must start with `v`, for example:
+
+```text
+v1.3.7
+```
+
+The package version for that tag becomes:
+
+```text
+1.3.7
+```
+
+Untagged commits produce development versions, for example:
+
+```text
+1.3.7.dev2+gabcdef0.d20260524
+```
+
+The generated file `SigProfilerMatrixGenerator/_version.py` is ignored and
+must not be committed.
+
+## Release Flow
+
+First merge the release-ready branch into `master` through the repository's
+normal review process.
+
+Then create and push the tag:
+
+```bash
+git checkout master
+git pull origin master
+git tag -a v1.3.7 -m "v1.3.7"
+git push origin v1.3.7
+```
+
+The pushed tag triggers `.github/workflows/release.yml` and publishes to
+TestPyPI.
+
+After TestPyPI is verified, publish a GitHub Release for the same tag. That
+release event triggers the PyPI publish job.
+
+## Verification
+
+After the tag push, verify the GitHub Actions run:
+
+- build job passed
+- `twine check` passed
+- package version printed correctly
+- TestPyPI publish job passed
+
+Optional TestPyPI install check:
+
+```bash
+python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple SigProfilerMatrixGenerator==1.3.7
+python -c "import SigProfilerMatrixGenerator; print(SigProfilerMatrixGenerator.__version__)"
+```
+
+After publishing the GitHub Release, verify the PyPI job and package page:
+
+```text
+https://pypi.org/project/SigProfilerMatrixGenerator/
+```
+
+Optional PyPI install check:
+
+```bash
+python -m pip install SigProfilerMatrixGenerator==1.3.7
+python -c "import SigProfilerMatrixGenerator; print(SigProfilerMatrixGenerator.__version__)"
+```
+
+## Troubleshooting
+
+If the package version is `0+unknown`, check that:
+
+- the release workflow checkout uses `fetch-depth: 0`
+- the tag exists locally and remotely
+- the tag starts with `v`
+
+If Trusted Publishing fails, check that:
+
+- the TestPyPI/PyPI trusted publisher values exactly match this repository
+- the GitHub environment name is `testpypi` or `pypi`
+- the publish job has `id-token: write`

SigProfilerMatrixGenerator/scripts/SVMatrixGenerator.py

@@ -920,9 +920,9 @@ def annotateBedpe(sv_bedpe):
 
     check_exist_list = sample_bps["id"][sample_bps["is_clustered"]]
     sample_bps["is_clustered"][
-        np.in1d(sample_bps["id"].values, check_exist_list.values)
+        np.isin(sample_bps["id"].values, check_exist_list.values)
     ] = True
-    sv_bedpe["is_clustered"] = np.in1d(
+    sv_bedpe["is_clustered"] = np.isin(
         sv_bedpe["id"], sample_bps["id"][sample_bps["is_clustered"]]
     )
     sv_bedpe = processBEDPE(sv_bedpe)