Sync main to release (#233)

* Incorporate modal tremor power in aggregate function

* Add tolerance for contiguous data to config

* Add pre-commit hooks and add Poetry scripts for simplifying dev process

* Remove segment categorization (set to legacy)

* Adjust pipelines to flexible column names and config updates

* Add info on scale sensitivity and make accelerometer optional

* Clarify installing pre-commit

Author: Erikpostt

.gitattributes

@@ -11,3 +11,9 @@ PPG_segment0001_values.bin filter=lfs diff=lfs merge=lfs -text
 PPG_segment0002_meta.json filter=lfs diff=lfs merge=lfs -text
 PPG_segment0002_time.bin filter=lfs diff=lfs merge=lfs -text
 PPG_segment0002_values.bin filter=lfs diff=lfs merge=lfs -text
+
+# Normalize line endings
+*.py text eol=lf
+*.ipynb text eol=lf
+*.ipynb filter=nb-clean
+*.ipynb filter=nbstripout

.github/workflows/build-and-test.yml

@@ -1,13 +1,10 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Build and test
 
 on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches: [ '**' ]
   workflow_call:
     outputs:
       version:
@@ -16,7 +13,6 @@ on:
 
 jobs:
   build-and-test:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -25,61 +21,62 @@ jobs:
       version: ${{ steps.get_version.outputs.version }}
 
     steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-        lfs: false  # Enable Git LFS support
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Get the version from pyproject.toml
+      # This will be used to tag the release in the publishing workflow
+      - name: Install toml package
+        run: pip install toml
+      - name: Get version from pyproject.toml
+        id: get_version
+        run: |
+          VERSION=$(python -c "import toml; print(toml.load('pyproject.toml')['tool']['poetry']['version'])")
+          echo Version: $VERSION
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+      # Install project dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install poetry
+          poetry install
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
+      # Run pre-commit hooks (formatting, linting, YAML checks, etc.)
+      - name: Run pre-commit hooks
+        run: poetry run pre-commit run --all-files --show-diff-on-failure
 
-    # Get the version from pyproject.toml
-    # This will be used to tag the release in the publishing workflow
-    - name: Install toml package
-      run: pip install toml
-    - name: Get version from pyproject.toml
-      id: get_version
-      run: |
-        VERSION=$(python -c "import toml; print(toml.load('pyproject.toml')['tool']['poetry']['version'])")
-        echo Version: $VERSION
-        echo "version=$VERSION" >> $GITHUB_OUTPUT
+      # Run tests
+      - name: Run pytest
+        run: poetry run pytest --maxfail=1 --disable-warnings -q
 
-    # Install project dependencies
-    - name: Install dependencies
-      run: |
-        python -m pip install poetry
-        poetry install
+      # Static type checks
+      - name: Type check with pytype
+        run: poetry run pytype .
 
-    # Install the Paradigma Jupyter kernel for notebooks
-    - name: Install Paradigma kernel
-      run: |
-        poetry run python -m ipykernel install --user --name=paradigma --display-name "paradigma (Poetry)"
+      # Build the package
+      - name: Build package
+        run: poetry build
 
-    # Testing and checking
-    - name: Test with pytest
-      run: poetry run pytest
-    - name: Type check
-      run: poetry run pytype .
+      - name: Archive build artifacts
+        uses: actions/upload-artifact@v4
+        if: github.ref == 'refs/heads/release'
+        with:
+          name: build-artifacts
+          path: dist/
 
-    # Build the package
-    - name: Build the package
-      run: poetry build
-    - name: Archive build artifacts
-      uses: actions/upload-artifact@v4
-      if: github.ref == 'refs/heads/release'
-      with:
-        name: build-artifacts
-        path: dist/
+      # Build and archive documentation
+      - name: Build documentation
+        run: poetry run make html --directory docs
 
-    # Build the docs
-    - name: Build the docs
-      run: poetry run make html --directory docs
-      
-    - name: Archive documentation
-      uses: actions/upload-artifact@v4
-      if: github.ref == 'refs/heads/release'
-      with:
-        name: docs-html
-        path: docs/build/html/
+      - name: Archive documentation
+        uses: actions/upload-artifact@v4
+        if: github.ref == 'refs/heads/release'
+        with:
+          name: docs-html
+          path: docs/build/html/

.gitignore

@@ -93,6 +93,7 @@ ipython_config.py
 # =========================
 .python-version  # pyenv
 __pypackages__/  # PEP 582
+.ruff*
 
 # =========================
 # Web frameworks

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+repos:
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout
+
+  - repo: https://github.com/srstevenson/nb-clean
+    rev: 4.0.1
+    hooks:
+      - id: nb-clean
+        args:
+          - --remove-empty-cells
+          - --remove-all-notebook-metadata
+
+  - repo: https://github.com/psf/black
+    rev: 25.9.0
+    hooks:
+      - id: black
+        pass_filenames: true
+        types: [python]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 6.1.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+        types: [python]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.0
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-added-large-files
+        args: ["--maxkb=5000"]

CHANGELOG.md

@@ -28,7 +28,7 @@
 - Improved handling of constants in configuration files.
 - Refactored gait configuration files and enhanced constraints.
 - Bumped Python version to 3.10 for compatibility.
-- Tested `Enum` usage for constraints, but reverted to `str` due to the lack of flexibility. 
+- Tested `Enum` usage for constraints, but reverted to `str` due to the lack of flexibility.
 - Fixed typing issues
 - Added project badges and citation file.
 - Updated project naming and authors in citation file.
@@ -45,4 +45,3 @@
 ## v0.1.0 (15/08/2024)
 - First pre-release of `paradigma`!
 - Initial implementation of gait and PPG feature extraction.
-

CITATION.cff

@@ -91,21 +91,21 @@ authors:
 repository-code: 'https://github.com/biomarkersParkinson/paradigma'
 url: 'https://biomarkersparkinson.github.io/paradigma/'
 abstract: >-
-  The Parkinson's disease Digital Markers (ParaDigMa) toolbox is a Python software 
-  package designed for processing and analyzing real-life wrist sensor data to 
-  extract digital measures of motor and non-motor signs of Parkinson's disease (PD).  
+  The Parkinson's disease Digital Markers (ParaDigMa) toolbox is a Python software
+  package designed for processing and analyzing real-life wrist sensor data to
+  extract digital measures of motor and non-motor signs of Parkinson's disease (PD).
 
-  Specifically, the toolbox is designed to process accelerometer, gyroscope and  
-  photoplethysmography signals, collected during passive monitoring in daily life.  
-  It contains three data processing pipelines: (1) arm swing during gait, (2) tremor,  
-  and (3) pulse rate analysis. These pipelines are scientifically validated for their 
-  use in persons with PD. Furthermore, the toolbox contains general functionalities 
-  for signal processing and feature extraction, such as filtering, peak detection, and 
-  spectral analysis. 
+  Specifically, the toolbox is designed to process accelerometer, gyroscope and
+  photoplethysmography signals, collected during passive monitoring in daily life.
+  It contains three data processing pipelines: (1) arm swing during gait, (2) tremor,
+  and (3) pulse rate analysis. These pipelines are scientifically validated for their
+  use in persons with PD. Furthermore, the toolbox contains general functionalities
+  for signal processing and feature extraction, such as filtering, peak detection, and
+  spectral analysis.
 
-  The toolbox is accompanied by a set of example scripts and notebooks for each 
-  processing pipeline that demonstrate how to use the toolbox for extracting digital 
-  measures. In addition, the toolbox is designed to be modular, enabling researchers 
+  The toolbox is accompanied by a set of example scripts and notebooks for each
+  processing pipeline that demonstrate how to use the toolbox for extracting digital
+  measures. In addition, the toolbox is designed to be modular, enabling researchers
   to easily extend the toolbox with new algorithms and functionalities.
 
 keywords:

CONTRIBUTING.md

@@ -9,25 +9,49 @@ helps, and credit will always be given.
 
 If you are reporting a bug, please include:
 
-* Your operating system name and version.
-* Any details about your local setup that might be helpful in troubleshooting.
-* Detailed steps to reproduce the bug.
+* Your operating system name and version
+* Python version
+* Any details about your local setup that might be helpful in troubleshooting
+* Detailed steps to reproduce the bug
 
 ### Fix Bugs
 
-Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
-wanted" is open to whoever wants to implement it.
+Look through the [GitHub issues](https://github.com/biomarkersParkinson/paradigma/issues) for bugs.
+Anything tagged with `bug` or `help wanted` is open to whoever wants to implement it.
 
 ### Implement Features
 
-Look through the GitHub issues for features. Anything tagged with "enhancement"
-and "help wanted" is open to whoever wants to implement it.
+Look through the [GitHub issues](https://github.com/biomarkersParkinson/paradigma/issues) for features.
+Anything tagged with `enhancement` or `help wanted` is open to whoever wants to implement it.
 
 ### Write Documentation
 
-You can never have enough documentation! Please feel free to contribute to any
-part of the documentation, such as the official docs, docstrings, or even
-on the web in blog posts, articles, and such.
+Documentation contributions are always welcome! You can contribute to:
+* Official docs: Located in `docs/`
+* Tutorial notebooks: `docs/tutorials/`
+* Docstrings: In Python modules
+* Articles or blog posts
+
+#### Workflow for notebooks and docs:
+1. Run and export notebooks:
+
+```bash
+poetry run build-docs
+```
+
+This will:
+* Execute all notebooks in `docs/tutorials/`
+* Export them to Markdown in `docs/tutorials/_static/`
+* Strip outputs
+* Build the HTML documentation
+
+2. Serve documentation locally:
+
+```bash
+poetry run serve-docs
+```
+
+This will serve the built HTML at `http://localhost:8000`.
 
 ### Submit Feedback
 
@@ -36,28 +60,49 @@ If you are proposing a feature:
 * Explain in detail how it would work.
 * Keep the scope as narrow as possible, to make it easier to implement.
 * Remember that this is a volunteer-driven project, and that contributions
-  are welcome :)
+  are welcome!
 
 ## Get Started!
 
-Ready to contribute? Here's how to set up `paradigma` for local development.
+Ready to contribute? Here's how to set up `paradigma` locally:
+1. Clone the repository:
+
+```bash
+git clone https://github.com/biomarkersParkinson/paradigma.git
+cd paradigma
+```
+
+2. Install dependencies via Poetry:
+
+```bash
+poetry install
+```
+
+3. Create a new branch for your work:
+
+```bash
+git checkout -b name-of-your-bugfix-or-feature
+```
 
-1. Download a copy of `paradigma` locally.
-2. Install `paradigma` using `poetry`:
+4. Make your changes and run the pre-commit hooks:
 
-    ```console
-    $ poetry install
-    ```
+```bash
+pip install pre-commit
+pre-commit install
+pre-commit run --all-files
+```
 
-3. Use `git` (or similar) to create a branch for local development and make your changes:
+This ensures code formatting (`black`), import sorting (`isort`), stripping notebook outputs, and other checks.
+These pre-commit hooks also run for changed and staged files when committing.
 
-    ```console
-    $ git checkout -b name-of-your-bugfix-or-feature
-    ```
+5. If contributing to docs, build and serve them locally to verify:
 
-4. When you're done making changes, check that your changes conform to any code formatting requirements and pass any tests.
+```bash
+poetry run build-docs
+poetry run serve-docs
+```
 
-5. Commit your changes and open a pull request.
+6. Commit your changes and open a pull request.
 
 ## Pull Request Guidelines
 
@@ -70,4 +115,5 @@ Before you submit a pull request, check that it meets these guidelines:
 ## Code of Conduct
 
 Please note that the `paradigma` project is released with a
-Code of Conduct. By contributing to this project you agree to abide by its terms.
+[Code of Conduct](https://biomarkersparkinson.github.io/paradigma/conduct.html).
+By contributing to this project you agree to abide by its terms.

LICENSE

@@ -189,4 +189,3 @@ distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
-