use reference-based calculation for Q-on to T-off (#4)

* use reference-based calculation for Q-on to T-off

* Update dependencies, add test cases, migrate to GHA

---------

Co-authored-by: l-bick <43580954+l-bick@users.noreply.github.com>

Author: lucasplagwitz

.github/workflows/gitlab-mirror-actions.yml

@@ -0,0 +1,100 @@
+name: CI/CD Pipeline
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install dependencies
+        run: |
+          pip install pytest
+          pip install . 
+
+      - name: Run Tests
+        run: |
+          pytest -W ignore::DeprecationWarning test/
+
+  build-and-publish:
+    needs: test
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install build tools
+        run: pip install twine build --upgrade
+
+      - name: Build Wheel
+        run: python3 -m build
+
+      - name: Upload to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: python3 -m twine upload --skip-existing dist/*
+
+  deploy-docs:
+    needs: test
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install System Dependencies (Pandoc)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Install Python Dependencies
+        run: |
+          pip install sphinx nbsphinx nbsphinx-link ipython sphinx-rtd-theme
+          pip install -r requirements.txt
+
+      - name: Build Sphinx Documentation
+        run: |
+          sphinx-build -M html docs/source/ docs/build/
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/pipeline.yml

@@ -1,3 +1,5 @@
+publication
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.gitignore

@@ -84,7 +84,7 @@ ecg_aligned_80bpm = normalizer.transform(ecg)
     Also works with a lambda function, such as 'np.std'. Default is 'none'.
 
 * `detrend`: Detrend each beat individually using the robust median of slopes.
-    This is only computed if using `agg_beat`. Default is True.
+    This is only computed if using `agg_beat`. Default is False.
 
 * `silent`: Disable all warnings. Default is True.
 

.gitlab-ci.yml

@@ -1,37 +1,39 @@
 [build-system]
 build-backend = "flit_core.buildapi"
 requires = [
-    'flit_core >=3.8.0,<4',
-    'neurokit2>=0.2.7',
-    'numpy>=1.24.2',
-    'scipy>=1.12.0',
-    'pandas>=2.2.0',
-    'scikit-learn>=1.4.0'
+    'flit_core >=3.12,<4',
+    'neurokit2>=0.2.12',
+    'numpy>=2.0',
+    'scipy>=1.17, <2',
+    'pandas>=2.0',
+    'scikit-learn>=1.8'
 ]
 
 [project]
 name='rlign'
-version='1.1'
+version='1.2'
 description='Beat normalization for ECG data.'
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 authors=[
     {name="Lucas Bickmann"},
     {name="Lucas Plagwitz"}
 ]
 dependencies = [
-    'neurokit2>=0.2.10',
-    'numpy>=1.24.2',
-    'scipy>=1.12.0',
-    'pandas>=2.2.0',
-    'scikit-learn>=1.4.0'
+    'neurokit2>=0.2.12',
+    'numpy>=2.0',
+    'scipy>=1.17, <2',
+    'pandas>=2.0',
+    'scikit-learn>=1.8'
 ]
 classifiers=[
     'Intended Audience :: Science/Research',
     'License :: OSI Approved :: MIT License',  
     'Operating System :: POSIX :: Linux',        
     'Programming Language :: Python :: 3',
     'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+    'Programming Language :: Python :: 3.13',
     'Development Status :: 5 - Production/Stable'
 ]
 

README.md

@@ -1,5 +1,5 @@
-numpy>=1.24.2
-neurokit2>=0.2.7
-scikit-learn>=1.4.0
-pandas>=2.2.0
-scipy>=1.12.0
+numpy>=2.2
+neurokit2>=0.2.10
+scikit-learn>=1.8
+pandas>=2.2
+scipy>=1.17<2