Release 0.2.0: repo modernization

.github/workflows/python_tests.yml

@@ -3,42 +3,141 @@ name: Python tests
 on:
   push:
     branches: [master]
+    paths: ['src/**', 'tests/**', 'pyproject.toml']
   pull_request:
     branches: [master]
+    paths: ['src/**', 'tests/**', 'pyproject.toml']
 
 jobs:
-  build:
+  test-core:
+    name: ${{ matrix.platform }} / Python ${{ matrix.python-version }}
     strategy:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     runs-on: ${{ matrix.platform }}
 
     env:
       FORCE_COLOR: true
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install ".[test]"
-
-    - name: Test with pytest
-      run: |
-        pytest --cov --cov-report=xml --verbose
-
-    - name: Upload coverage report
-      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
-      uses: codecov/codecov-action@v4
-      with:
-        token: d5ef1de8-d1c4-4d89-b304-4d8fffdf9906
-        file: ./coverage.xml
+      - uses: actions/checkout@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Install dependencies
+        run: uv pip install --group=test . --system
+
+      - name: Test with pytest
+        run: pytest --verbose --no-cov
+
+  test-dependency-combinations:
+    name: Dep combo / ${{ matrix.platform }} / ${{ matrix.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, windows-latest]
+        include:
+          - label: minimum-versions
+            python-version: "3.10"
+            numpy: "1.22.4"
+            scipy: "1.8.0"
+            scikit-learn: "1.2.0"
+            numba: "0.57.0"
+          - label: old-versions
+            python-version: "3.11"
+            numpy: "1.25.2"
+            scipy: "1.11.4"
+            scikit-learn: "1.4.2"
+            numba: "0.59.0"
+          - label: mid-versions
+            python-version: "3.12"
+            numpy: "2.0.2"
+            scipy: "1.14.1"
+            scikit-learn: "1.5.2"
+            numba: "0.60.0"
+
+    runs-on: ${{ matrix.platform }}
+
+    env:
+      FORCE_COLOR: true
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Install numpy (pinned)
+        if: matrix.numpy != ''
+        run: uv pip install "numpy==${{ matrix.numpy }}" --system
+
+      - name: Install numpy (latest)
+        if: matrix.numpy == ''
+        run: uv pip install numpy --system
+
+      - name: Install pinned dependencies
+        if: matrix.label != 'latest-versions'
+        run: uv pip install "scipy==${{ matrix.scipy }}" "scikit-learn==${{ matrix.scikit-learn }}" "numba==${{ matrix.numba }}" --system
+
+      - name: Install latest dependencies
+        if: matrix.label == 'latest-versions'
+        run: uv pip install scipy scikit-learn numba --system
+
+      - name: Install antropy (no deps, already pinned above)
+        run: uv pip install . --no-deps --system
+
+      - name: Install test dependencies
+        run: uv pip install --group=test --system
+
+      - name: Print installed versions
+        run: |
+          python -c "import numpy, scipy, sklearn, numba; print(f'numpy={numpy.__version__}, scipy={scipy.__version__}, sklearn={sklearn.__version__}, numba={numba.__version__}')"
+
+      - name: Test with pytest
+        run: pytest --verbose --no-cov
+
+  coverage:
+    name: Coverage (Ubuntu)
+    runs-on: ubuntu-latest
+
+    env:
+      FORCE_COLOR: true
+      NUMBA_DISABLE_JIT: "1"
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Install dependencies
+        run: uv pip install --group=test . --system
+
+      - name: Test with pytest and coverage
+        run: pytest --cov --cov-report=xml --verbose
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          fail_ci_if_error: true

.github/workflows/ruff.yml

@@ -4,10 +4,9 @@ jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
       - name: "Linting"
-        uses: astral-sh/ruff-action@v1
+        run: uvx ruff check
       - name: "Formatting"
-        uses: astral-sh/ruff-action@v1
-        with:
-          args: "format --check"
+        run: uvx ruff format --check

README.rst

@@ -2,6 +2,12 @@
 
 |
 
+.. image:: https://badge.fury.io/py/antropy.svg
+  :target: https://badge.fury.io/py/antropy
+
+.. image:: https://img.shields.io/conda/vn/conda-forge/antropy.svg
+  :target: https://anaconda.org/conda-forge/antropy
+
 .. image:: https://img.shields.io/github/license/raphaelvallat/antropy.svg
   :target: https://github.com/raphaelvallat/antropy/blob/master/LICENSE
 
@@ -11,23 +17,48 @@
 .. image:: https://codecov.io/gh/raphaelvallat/antropy/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/raphaelvallat/antropy
 
-----------------
+.. image:: https://static.pepy.tech/badge/antropy
+  :target: https://pepy.tech/projects/antropy
 
-.. figure::  https://github.com/raphaelvallat/antropy/blob/master/docs/pictures/logo.png?raw=true
-   :align:   center
+.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+  :target: https://github.com/astral-sh/ruff
+  :alt: Ruff
+
+----------------
 
-AntroPy is a Python 3 package providing several time-efficient algorithms for computing the complexity of time-series.
-It can be used for example to extract features from EEG signals.
+.. figure:: https://raw.githubusercontent.com/raphaelvallat/antropy/master/docs/pictures/logo.png
+   :align: center
 
-Documentation
-=============
+**AntroPy** is a Python 3 package providing several time-efficient algorithms for computing
+the complexity of time-series. It can be used for example to extract features from EEG signals.
 
-- `Link to documentation <https://raphaelvallat.com/antropy/build/html/index.html>`_
+- `Link to documentation <https://raphaelvallat.com/antropy/>`_
 
 Installation
 ============
 
-AntroPy can be installed with pip
+Dependencies
+------------
+
+AntroPy is a Python 3 package and is currently tested for Python 3.10+.
+
+The main dependencies of AntroPy are:
+
+* `NumPy <https://numpy.org/>`_ >= 1.22.4
+* `SciPy <https://scipy.org/>`_ >= 1.8.0
+* `scikit-learn <https://scikit-learn.org/>`_ >= 1.2.0
+* `Numba <https://numba.readthedocs.io/>`_ >= 0.57
+
+User installation
+-----------------
+
+AntroPy can be easily installed using `uv <https://docs.astral.sh/uv/>`_
+
+.. code-block:: shell
+
+  uv pip install antropy
+
+pip
 
 .. code-block:: shell
 
@@ -37,25 +68,21 @@ or conda
 
 .. code-block:: shell
 
-  conda config --add channels conda-forge
-  conda config --set channel_priority strict
-  conda install antropy
+  conda install -c conda-forge antropy
+
+Development
+-----------
 
-To build and install from source, clone this repository or download the source archive and decompress the files
+To build and install from source, clone this repository and install in editable mode with `uv <https://docs.astral.sh/uv/>`_
 
 .. code-block:: shell
 
+  git clone https://github.com/raphaelvallat/antropy.git
   cd antropy
-  pip install ".[test]"     # install the package
-  pip install -e ".[test]"  # or editable install
-  pytest
-
-**Dependencies**
+  uv pip install --group=test --editable .
 
-- `numpy <https://numpy.org/>`_
-- `scipy <https://www.scipy.org/>`_
-- `scikit-learn <https://scikit-learn.org/>`_
-- `numba <http://numba.pydata.org/>`_
+  # test the package
+  pytest --verbose
 
 Functions
 =========
@@ -117,7 +144,7 @@ Functions
     0.47903505674073327
 
 Execution time
-~~~~~~~~~~~~~~
+--------------
 
 Here are some benchmarks computed on a MacBook Pro (2020).
 
@@ -165,9 +192,9 @@ Acknowledgement
 
 Several functions of AntroPy were adapted from:
 
-- MNE-features: https://github.com/mne-tools/mne-features
-- pyEntropy: https://github.com/nikdon/pyEntropy
-- pyrem: https://github.com/gilestrolab/pyrem
-- nolds: https://github.com/CSchoel/nolds
+- `MNE-features <https://github.com/mne-tools/mne-features>`_
+- `pyEntropy <https://github.com/nikdon/pyEntropy>`_
+- `pyrem <https://github.com/gilestrolab/pyrem>`_
+- `nolds <https://github.com/CSchoel/nolds>`_
 
-All the credit goes to the author of these excellent packages.
+All the credit goes to the authors of these excellent packages.

docs/api.rst

@@ -5,6 +5,8 @@
 API reference
 =============
 
+Full list of available functions in AntroPy. Click on any function name to see its detailed documentation.
+
 Entropy
 -------
 

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 7b2edb81324a2cee77846b2cbbcd2de8
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: b957fa437c4655d4207b5c46f99d8ce5
 tags: 645f666f9bcd5a90fca523b33c5a78b7