First version of FieldTrip Python

.github/workflows/create-tag.yml

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+name: Create tag from new version
+
+on:
+  workflow_dispatch:
+  workflow_call:
+  push:
+    branches:
+      - main
+    paths: 
+      - fieldtrip/_version.py
+
+permissions: 
+  contents: write
+
+jobs:
+  setup-tag:
+    runs-on: "ubuntu-latest"
+    steps: 
+      - name: Check out FieldTrip Python
+        uses: actions/checkout@v4
+
+      - name: Get package version
+        run: |
+           VERSION=$(sed -n 's/^__version__ = "\(.*\)"/\1/p' fieldtrip/_version.py)
+           echo "pyproject.toml version: $VERSION" 
+           git config user.name github-actions
+           git config user.email [email protected]
+           MSG=$(git log $(git describe --tags --abbrev=0)..HEAD --oneline)
+           echo "Creating tag $VERSION with message:"
+           echo "$MSG"
+           git tag -a "$VERSION" -m "$MSG"
+
+      - name: Publish tags
+        run: git push --tags 

.github/workflows/publish-release.yml

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+name: Upload and Publish Python Package
+on:
+  workflow_run:
+    workflows: ["run_unit_tests"]
+    types:
+      - completed
+  workflow_dispatch:
+
+env: 
+  PYTHON_VERSION: "3.13"
+
+jobs:
+  check-tag:
+    name: Check if commit is a tag
+    if: >
+      github.event_name == 'workflow_dispatch' ||
+      github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    outputs:
+      is_tagged: ${{ steps.check-tag.outputs.is_tagged }}
+      tag_name: ${{ steps.check-tag.outputs.tag_name }}
+      is_prerelease: ${{ steps.check-tag.outputs.is_prerelease }}
+    steps:
+      - name: Checkout full history
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Determine tagged commit and pre-release
+        id: check-tag
+        run: |
+          TAG=$(git tag --points-at HEAD | head -n 1)
+          echo "Found tag: $TAG"
+          if [[ "$TAG" =~ ^[0-9]+\.[0-9]+\.[0-9]+.*$ ]]; then
+            echo "is_tagged=true" >> $GITHUB_OUTPUT
+            echo "tag_name=$TAG" >> $GITHUB_OUTPUT
+
+            if [[ "$TAG" =~ ^[0-9]+\.[0-9]+\.[0-9]+[a-zA-Z].*$ ]]; then
+              echo "is_prerelease=true" >> $GITHUB_OUTPUT
+            else
+              echo "is_prerelease=false" >> $GITHUB_OUTPUT
+            fi
+          else
+            echo "is_tagged=false" >> $GITHUB_OUTPUT
+          fi
+
+  build:
+    name: Build Package
+    needs: check-tag
+    if: needs.check-tag.outputs.is_tagged == 'true'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Upload built packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  test-install:
+    name: Test Install from TestPyPI
+    needs: publish-to-testpypi
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Test install from TestPyPI
+        run: |
+          python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple fieldtrip-python
+          python -c "import fieldtrip"  
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: test-install
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/fieldtrip-python/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  sign-and-release:
+    name: Sign and Create GitHub Release
+    needs: [check-tag, publish-to-pypi]
+    if: needs.check-tag.outputs.is_tagged == 'true'
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Sign with Sigstore
+        uses: sigstore/[email protected]
+        with:
+          inputs: >-
+            dist/*.tar.gz
+            dist/*.whl
+
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh release create "${{ needs.check-tag.outputs.tag_name }}" \
+            --repo "$GITHUB_REPOSITORY" \
+            --generate-notes \
+            $([[ "${{ needs.check-tag.outputs.is_prerelease }}" == "true" ]] && echo "--prerelease") \
+            dist/*

.github/workflows/run_unit_tests.yml

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+name: Unit tests
+on:
+  workflow_dispatch:
+  workflow_call:
+  push:
+    paths:
+      - tests/**
+      - fieldtrip/**
+      - setup.py
+      - pyproject.toml
+  pull_request:
+
+env:
+  MLM_LICENSE_TOKEN: ${{ secrets.MATLAB_BATCH_TOKEN }}
+
+jobs:
+  run-unit-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: False
+      matrix:
+        matlab: ["R2025b"]
+        os: [ubuntu-latest, macos-13, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        include:
+          - os: ubuntu-latest
+            os_name: Linux
+            platform: Linux
+          - os: macos-13
+            os_name: macOS_Intel
+            platform: Mac
+          - os: macos-latest
+            os_name: macOS_Apple_Silicon
+            platform: Mac
+          - os: windows-latest
+            os_name: Windows
+            platform: Windows
+
+    steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install FieldTrip Python from latest Release (to get CTF file) 
+        run: |
+          python -m pip install https://github.com/johmedr/fieldtrip-python/releases/latest/download/fieldtrip_python-20241219b1-py3-none-any.whl
+
+      - name: Check out FieldTrip Python
+        uses: actions/checkout@v4
+
+      # Setup MATLAB and Runtime
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v2
+        with:
+          release: ${{matrix.matlab}}
+          cache: True
+          products: |
+            MATLAB_Compiler
+            MATLAB_Compiler_SDK
+
+      - name: Extract MATLAB path to file
+        uses: matlab-actions/run-command@v2
+        with:
+          command: |
+            fileID = fopen('matlab_path.txt', 'w');
+            matlabpath = matlabroot;
+            matlabpath = strrep(matlabpath, filesep, '/');
+            matlabpath = strrep(matlabpath, '\', '\\');
+            matlabpath = strrep(matlabpath, 'C:', '/c/');
+            matlabpath = strrep(matlabpath, 'D:', '/d/');
+            fprintf(fileID, matlabpath);
+            fclose(fileID);
+        # sometimes this step hangs when closing matlab, automatically terminating after 2 minutes solves the issue
+        timeout-minutes: 2
+        continue-on-error: true
+
+      - name: Set environment variable with MATLAB path
+        shell: bash # Works on Windows as well because of shell: bash
+        run: |
+          matlab_path=$(cat matlab_path.txt)
+          echo "MATLAB_PATH=$matlab_path" >> $GITHUB_ENV
+
+      - name: Run tests (Mac Apple Silicon)
+        if: matrix.os_name == 'macOS_Apple_Silicon'
+        run: |
+          export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH:+${DYLD_LIBRARY_PATH}:}\
+          ${{ env.MATLAB_PATH }}/runtime/maca64:\
+          ${{ env.MATLAB_PATH }}/bin/maca64:\
+          ${{ env.MATLAB_PATH }}/sys/os/maca64:\
+          ${{ env.MATLAB_PATH }}/extern/bin/maca64"
+          export PYTHONHOME=${{ env.pythonLocation }}
+          mwpython -m unittest discover tests -v
+
+      - name: Run tests (Mac Intel)
+        if: matrix.os_name == 'macOS_Intel'
+        run: |
+          export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH:+${DYLD_LIBRARY_PATH}:}\
+          ${{ env.MATLAB_PATH }}/runtime/maci64:\
+          ${{ env.MATLAB_PATH }}/bin/maci64:\
+          ${{ env.MATLAB_PATH }}/sys/os/maci64:\
+          ${{ env.MATLAB_PATH }}/extern/bin/maci64"
+          export PYTHONHOME=${{ env.pythonLocation }}
+          mwpython -m unittest discover tests -v
+
+      - name: Run tests (Windows)
+        if: matrix.os_name == 'Windows'
+        shell: bash
+        run: |
+          export PATH="${{ env.MATLAB_PATH }}/runtime/win64:\
+          ${{ env.MATLAB_PATH }}/bin/win64:\
+          ${{ env.MATLAB_PATH }}/sys/os/win64:\
+          ${{ env.MATLAB_PATH }}/extern/bin/win64\
+          ${{ env.MATLAB_PATH }}/runtime/win32:\
+          ${{ env.MATLAB_PATH }}/bin/win32:\
+          ${{ env.MATLAB_PATH }}/sys/os/win32:\
+          ${{ env.MATLAB_PATH }}/extern/bin/win32:${PATH}"
+          python -m unittest discover tests -v
+
+      - name: Run tests (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          export LD_LIBRARY_PATH="${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}\
+          ${{ env.MATLAB_PATH }}/runtime/glnxa64:\
+          ${{ env.MATLAB_PATH }}/bin/glnxa64:\
+          ${{ env.MATLAB_PATH }}/sys/os/glnxa64:\
+          ${{ env.MATLAB_PATH }}/extern/bin/glnxa64"
+          python -m unittest discover tests -v

.gitignore

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+# Python cache files
+**/__pycache__/
+
+# Virtual environment
+**/venv/
+**/.env/
+**/env/
+**/.venv/
+
+# Distribution files
+**/dist/
+**/build/
+**/*.egg-info/
+
+# Jupyter Notebook checkpoints
+**/.ipynb_checkpoints/
+
+# IDE and editor files
+**/.vscode/
+**/.idea/
+**/*.swp
+
+# Pytest cache
+.cache/
+
+# OS-specific files
+**/.DS_Store
+**/Thumbs.db
+
+*.nii
+
+# MPython Hashmaps
+**/.mpython_hashmap.csv
+.mpython/build
+.mpython/external
+**/*.asv
+examples/data/
+
+# CTF file
+**/*.ctf

.mpython/templates/class_header.py

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+from mpython import MatlabClass
+from fieldtrip._runtime import Runtime, RuntimeMixin
+
+
+class <classname>(RuntimeMixin, MatlabClass):
+    def __init__(self, *args, **kwargs):
+        <docstring>
+        super().__init__()

.mpython/templates/docstring.py

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+"""
+<matlabhelp>
+
+This file was automatically converted from Matlab to Python using
+[MPython](https://github.com/MPython-Package-Factory/mpython), please
+refer to the original matlab file for the most accurate documentation.
+
+[Matlab code]( https://github.com/fieldtrip/fieldtrip/blob/master/<rfilepath> )
+
+Copyright (C) 2011-2021, Robert Oostenveld
+Copyright (C) 2022-, Jan-Mathijs Schoffelen and Robert Oostenveld
+
+This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
+for the documentation and details.
+
+FieldTrip is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+FieldTrip is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
+"""