Modern packaging + ruff + numpy 2 compat (#187)

* Modern packaging + ruff (NPY201) * move to src folder + ruff * Better pyproject + add tests for 3.12 * Fix install Windows * fix ruff for some docstring * Disable docstring formatting * disable py312 * ruff fixes * re-enable macos * disable macos * fix missing line code block rst * add tests folder to coverage * remove test folder from coverage * add libomp for macos-latest * 2nd attempt * re-enable lspopt * add setuptools dep * fix numpy deprecation * Merge branch 'master' into modern_packaging * Including manual conflict resolution on [test_]staging.py --------- Co-authored-by: Remington Mallett <[email protected]>
raphaelvallat · Dec 28, 2024 · 4dcd72d · 4dcd72d
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diff --git a/.coveragerc b/.coveragerc
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml
@@ -2,45 +2,47 @@ name: Python tests
 
 on:
   push:
-    branches: [master, develop]
+    branches: [master]
   pull_request:
-    branches: [master, develop]
+    branches: [master]
 
 jobs:
   build:
     strategy:
       fail-fast: false
       matrix:
-        platform: [ubuntu-latest, windows-latest]  # macos-latest
-        python-version: ["3.9", "3.10", "3.11"]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     runs-on: ${{ matrix.platform }}
 
     env:
       FORCE_COLOR: true
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Install libomp (macOS)
+      if: ${{ matrix.platform == 'macos-latest' }}
+      run: brew install libomp
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r requirements-test.txt
-        pip install .
+        pip install ".[test]"
 
     - name: Test with pytest
       run: |
-        pytest --cov --cov-report=xml --cov-config=setup.cfg --verbose
+        pytest --cov --cov-report=xml --verbose
 
     - name: Upload coverage report
       if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
       with:
         token: a58a0c62-fb11-4429-977b-65bec01ecb44
         file: ./coverage.xml
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -0,0 +1,13 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Linting"
+        uses: astral-sh/ruff-action@v1
+      - name: "Formatting"
+        uses: astral-sh/ruff-action@v1
+        with:
+          args: "format --check"
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,21 +1,6 @@
-# Add README, LICENSE and requirements :
+# Add README and LICENSE :
 include README.rst
 include LICENSE
-include requirements.txt
 
 # Add trained classifiers
-# v0.4.0
-include yasa/classifiers/clf_eeg_lgb_0.4.0.joblib
-include yasa/classifiers/clf_eeg+eog_lgb_0.4.0.joblib
-include yasa/classifiers/clf_eeg+eog+emg_lgb_0.4.0.joblib
-include yasa/classifiers/clf_eeg+eog+emg+demo_lgb_0.4.0.joblib
-
-# v0.5.0
-include yasa/classifiers/clf_eeg_lgb_0.5.0.joblib
-include yasa/classifiers/clf_eeg+demo_lgb_0.5.0.joblib
-include yasa/classifiers/clf_eeg+eog_lgb_0.5.0.joblib
-include yasa/classifiers/clf_eeg+eog+demo_lgb_0.5.0.joblib
-include yasa/classifiers/clf_eeg+emg_lgb_0.5.0.joblib
-include yasa/classifiers/clf_eeg+emg+demo_lgb_0.5.0.joblib
-include yasa/classifiers/clf_eeg+eog+emg_lgb_0.5.0.joblib
-include yasa/classifiers/clf_eeg+eog+emg+demo_lgb_0.5.0.joblib
+recursive-include yasa/classifiers/ *.joblib
diff --git a/README.rst b/README.rst
@@ -14,6 +14,10 @@
 .. image:: https://pepy.tech/badge/yasa
     :target: https://pepy.tech/badge/yasa
 
+.. 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
+
 ----------------
 
 .. figure::  /docs/pictures/yasa_logo.png
@@ -48,6 +52,15 @@ Alternatively, YASA can be installed with conda:
   conda config --set channel_priority strict
   conda install yasa
 
+To build and install from source, clone this repository or download the source archive and decompress the files
+
+.. code-block:: shell
+
+  cd yasa
+  pip install ".[test]"              # install the package
+  pip install --editable ".[test]"   # or editable install
+  pytest                             # test the package
+
 **What are the prerequisites for using YASA?**
 
 To use YASA, all you need is:

diff --git a/codecov.yml b/codecov.yml
diff --git a/docs/conf.py b/docs/conf.py
@@ -3,9 +3,11 @@
 import os
 import sys
 import time
-import yasa
+
 import sphinx_bootstrap_theme
 
+import yasa
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.

diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -12,11 +12,11 @@ Code guidelines
 
 Before starting new code, we highly recommend opening an issue on `GitHub <https://github.com/raphaelvallat/yasa>`_ to discuss potential changes.
 
-* Please use standard `pep8 <https://pypi.python.org/pypi/pep8>`_ and `flake8 <http://flake8.pycqa.org/>`_ Python style guidelines. To test that your code complies with those, you can run:
+* Please use standard `pep8 <https://pypi.python.org/pypi/pep8>`_ and `flake8 <http://flake8.pycqa.org/>`_ Python style guidelines. YASA uses `ruff <https://github.com/astral-sh/ruff>`_ for code formatting. Before submitting a PR, please make sure to run the following command in the root folder of YASA:
 
   .. code-block:: bash
 
-     $ flake8
+     $ ruff format --line-length=100
 
 * Use `NumPy style <https://numpydoc.readthedocs.io/en/latest/format.html>`_ for docstrings. Follow existing examples for simplest guidance.
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -14,6 +14,10 @@
 .. image:: https://pepy.tech/badge/yasa
     :target: https://pepy.tech/badge/yasa
 
+.. 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
+
 ----------------
 
 .. figure::  /pictures/yasa_logo.png
@@ -48,6 +52,15 @@ Alternatively, YASA can be installed with conda:
   conda config --set channel_priority strict
   conda install yasa
 
+To build and install from source, clone this repository or download the source archive and decompress the files
+
+.. code-block:: shell
+
+  cd yasa
+  pip install ".[test]"      # install the package
+  pip install -e ".[test]"   # or editable install
+  pytest                     # test the package
+
 **What are the prerequisites for using YASA?**
 
 To use YASA, all you need is:

diff --git a/push_pypi.md b/push_pypi.md
@@ -0,0 +1,6 @@
+# Build and upload a new version of YASA
+
+```bash
+python -m build
+twine upload dist/yasa-<VERSION>
+```
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,4 +1,132 @@
-[tool.black]
+[build-system]
+requires = ["setuptools>=70.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "yasa"
+description = "YASA: Analysis of polysomnography recordings."
+readme = "README.rst"
+license = {text = "BSD (3-clause)"}
+authors = [
+    {name = "Raphael Vallat", email = "[email protected]"},
+    {name = "Remington Mallett", email = "[email protected]"},
+]
+maintainers = [
+    {name = "Raphael Vallat", email = "[email protected]"},
+    {name = "Remington Mallett", email = "[email protected]"},
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Operating System :: MacOS",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dynamic = ["version"]
+requires-python = ">=3.9"
+dependencies = [
+    "numpy>=1.18.1",
+    "scipy",
+    "pandas",
+    "matplotlib",
+    "seaborn",
+    "mne>=1.3",
+    "numba>=0.57.1",
+    "antropy",
+    "scikit-learn",
+    "tensorpac>=0.6.5",
+    "pyriemann>=0.2.7",
+    "sleepecg>=0.5.0",
+    "setuptools>=70",
+    "lspopt",
+    "ipywidgets",
+    "joblib",
+    "lightgbm",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=6",
+    "pytest-cov",
+    # Ensure coverage is new enough for `source_pkgs`.
+    "coverage[toml]>=5.3",
+    "ruff"
+]
+docs = [
+    "sphinx>7.0.0",
+    "pydata_sphinx_theme",
+    "numpydoc",
+    "sphinx-copybutton",
+    "sphinx-design",
+    "sphinx-notfound-page",
+]
+
+[project.urls]
+Homepage = "https://github.com/raphaelvallat/yasa/"
+Downloads = "https://github.com/raphaelvallat/yasa/"
+
+[tool.setuptools]
+py-modules = ["yasa"]
+include-package-data = true
+
+[tool.setuptools.package-data]
+yasa = [
+    "classifiers/*.joblib",
+]
+
+[tool.setuptools.packages.find]
+namespaces = false
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "yasa.__version__"}
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "--showlocals --durations=10 --maxfail=2 --cov"
+doctest_optionflags= ["NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL"]
+filterwarnings = [
+    "ignore::UserWarning",
+    "ignore::RuntimeWarning",
+    "ignore::FutureWarning",
+]
+markers = ["slow"]
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/tests/*",
+]
+source_pkgs = ["yasa"]
+
+[tool.coverage.paths]
+source = ["src"]
+
+[tool.coverage.report]
+show_missing = true
+# sort = "Cover"
+
+[tool.ruff]
 line-length = 100
-target-version = ['py311']
-include = '\.pyi?$'
+target-version = "py311"
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+lint.select = ["E4", "E7", "E9", "F", "I", "NPY201"]
+exclude = [
+    "notebooks",  # Skip jupyter notebook examples
+    "docs",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401", "F403"]  # Ignore star and unused import violations for __init__.py files
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.format]
+docstring-code-format = false
+docstring-code-line-length = 90
diff --git a/requirements-test.txt b/requirements-test.txt
diff --git a/requirements.txt b/requirements.txt