[MAINT] Replace setup.py with pyproject.toml (#160)

* Add new toml files --------- Signed-off-by: Adam Li <[email protected]>
mne-tools · Dec 6, 2023 · 52c3824 · 52c3824
1 parent 241b6ff
commit 52c3824
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Showing 22 changed files with 868 additions and 774 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
diff --git a/.codespellignore b/.codespellignore
@@ -0,0 +1,3 @@
+raison
+fro
+nd
diff --git a/.flake8 b/.flake8
@@ -0,0 +1,28 @@
+[flake8]
+max-line-length = 100
+
+ignore =
+    # these rules don't play well with black
+    # whitespace before ':'
+    E203
+    # line break before binary operator
+    W503
+    E241,E305,W504,W605,E731
+
+exclude =
+    .git
+    .github
+    .venv
+    .mypy_cache
+    .pytest_cache
+    .circleci
+    paper
+    setup.py
+    doc
+    benchmarks
+    build
+
+per-file-ignores =
+    # __init__.py files are allowed to have unused imports
+    */__init__.py:F401
+    */**/__init__.py:F401
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
diff --git a/.github/workflows/cffconvert.yml b/.github/workflows/cffconvert.yml
@@ -6,7 +6,7 @@ on:
       - CITATION.cff
   pull_request:
     paths:
-      - CITATION.cff        
+      - CITATION.cff
 
 jobs:
   validate:
@@ -19,4 +19,4 @@ jobs:
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/[email protected]
         with:
-          args: "--validate"
+          args: "--validate"
diff --git a/.github/workflows/code-style.yaml b/.github/workflows/code-style.yaml
@@ -0,0 +1,47 @@
+name: code-style
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+  push:
+    branches: [main, maint/0.2, maint/0.3, maint/0.4]
+  workflow_dispatch:
+
+jobs:
+  style:
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools
+          python -m pip install --progress-bar off .[style]
+      - name: Run isort
+        uses: isort/isort-action@master
+      - name: Run black
+        uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+      - name: Run Ruff
+        run: ruff check .
+      - name: Run codespell
+        uses: codespell-project/actions-codespell@master
+        with:
+          check_filenames: true
+          check_hidden: true
+          skip: './.git,./build,./.mypy_cache,./.pytest_cache,./mne_icalabel/iclabel/network/assets'
+          ignore_words_file: ./.codespellignore
+      # - name: Run pydocstyle
+      #   run: pydocstyle .
+      - name: Run toml-sort
+        run: toml-sort pyproject.toml --check
+      - name: Run yamllint
+        run: yamllint . -c .yamllint.yaml --strict
diff --git a/.github/workflows/linux_conda.yml b/.github/workflows/linux_conda.yml
@@ -41,7 +41,7 @@ jobs:
           curl https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/get_minimal_commands.sh -o get_minimal_commands.sh
           chmod +x get_minimal_commands.sh
           source ./get_minimal_commands.sh
-          pip install -r requirements_testing.txt
+          pip install .[test]
         name: 'Install dependencies'
       - run: pip install git+https://github.com/mne-tools/mne-python@main
       - run: pip install -e .
@@ -51,5 +51,5 @@ jobs:
           python -c "import numpy; numpy.show_config()"
         name: 'Show infos'
       - name: Run pytest
-        run: python -m pytest . --cov=mne_connectivity --cov-report=xml --cov-config=setup.cfg --verbose --ignore mne-python
+        run: python -m pytest . --cov=mne_connectivity --cov-report=xml --cov-config=pyproject.toml --verbose --ignore mne-python
       - uses: codecov/codecov-action@v3
diff --git a/.github/workflows/publish_release.yml b/.github/workflows/publish_release.yml
@@ -8,25 +8,25 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    
+
     steps:
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.10
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.10
 
-    - name: Checkout code
-      uses: actions/checkout@v2
+      - name: Checkout code
+        uses: actions/checkout@v2
 
-    - name: Install dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install twine wheel
+      - name: Install dependencies
+        run: |
+          pip install .[build]
+          pip install twine wheel
 
-    - name: Build and publish to PyPi
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        python -m twine upload --repository pypi dist/*
+      - name: Build and publish to PyPi
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python setup.py sdist bdist_wheel
+          python -m twine upload --repository pypi dist/*
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -1,46 +1,24 @@
-name: 'unit_tests'
+name: "unit_tests"
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.type }}
   cancel-in-progress: true
 on:
   push:
     branches:
-      - 'main'
+      - "main"
   pull_request:
     branches:
-      - '*'
+      - "*"
 
 jobs:
-  # Run style tests
-  style:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ 3.9 ]
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install pip
-        run: |
-          pip install --upgrade pip setuptools wheel
-          pip install --upgrade --upgrade-strategy eager -r requirements.txt
-          pip install --upgrade --upgrade-strategy eager -r requirements_testing.txt
-      - name: Run style & documentation tests
-        run: make pep
-
   # Run installation tests
   install:
-    runs-on: ${{ matrix.os }}
+    runs-on: install-${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ "3.11" ]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.11"]
         include:
           # An old one
           - os: ubuntu-latest
@@ -57,8 +35,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install --upgrade pip setuptools wheel
-          pip install --upgrade --upgrade-strategy eager -r requirements.txt
-          pip install --upgrade --upgrade-strategy eager -r requirements_testing.txt
+          pip install --upgrade .[test]
       - run: mne sys_info
       - name: Build sdist
         run: python setup.py sdist
@@ -117,10 +94,10 @@ jobs:
     env:
       TZ: Europe/Berlin
       FORCE_COLOR: true
-      DISPLAY: ':99.0'
-      MNE_LOGGING_LEVEL: 'info'
-      OPENBLAS_NUM_THREADS: '1'
-      PYTHONUNBUFFERED: '1'
+      DISPLAY: ":99.0"
+      MNE_LOGGING_LEVEL: "info"
+      OPENBLAS_NUM_THREADS: "1"
+      PYTHONUNBUFFERED: "1"
     steps:
       - uses: actions/setup-python@v4
         with:
@@ -133,7 +110,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install --upgrade pip setuptools wheel
-          pip install --upgrade --upgrade-strategy eager -r requirements.txt -r requirements_testing.txt
+          pip install --upgrade --upgrade-strategy eager .[test]
       - if: matrix.mne-version == 'mne-stable'
         run: pip install --upgrade mne
       - name: Install MNE (main)
@@ -149,5 +126,5 @@ jobs:
           which python
       - run: pip install -e .
       - run: mne sys_info
-      - run: python -m pytest . --cov=mne_connectivity --cov-report=xml --cov-config=setup.cfg --verbose --ignore mne-python
+      - run: python -m pytest . --cov=mne_connectivity --cov-report=xml --cov-config=pyproject.toml --verbose --ignore mne-python
       - uses: codecov/codecov-action@v3
diff --git a/.yamllint.yaml b/.yamllint.yaml
@@ -0,0 +1,6 @@
+extends: default
+
+rules:
+  line-length: disable
+  document-start: disable
+  truthy: disable
diff --git a/Makefile b/Makefile
@@ -1,12 +1,12 @@
-# simple makefile to simplify repetetive build env management tasks under posix
+# simple makefile to simplify repetitive build env management tasks under posix
 
 # caution: testing won't work on windows, see README
 
 PYTHON ?= python
 PYTESTS ?= pytest
 CTAGS ?= ctags
 CODESPELL_SKIPS ?= "*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,plot_*.rst,*.rst.txt,*.html,gdf_encodes.txt"
-CODESPELL_DIRS ?= mne_connectivity/ doc/ examples/
+CODESPELL_DIRS ?= mne_connectivity/ doc/ examples/ benchmarks/
 all: clean inplace test test-doc
 
 clean-pyc:
@@ -65,7 +65,7 @@ test-doc: sample_data testing_data
 test-coverage: testing_data
 	rm -rf coverage .coverage
 	$(PYTESTS) --cov=mne_connectivity --cov-report html:coverage
-# whats the difference with test-no-sample-with-coverage?
+# what's the difference with test-no-sample-with-coverage?
 
 test-mem: in testing_data
 	ulimit -v 1097152 && $(PYTESTS) mne
@@ -91,11 +91,31 @@ flake:
 	fi;
 	@echo "flake8 passed"
 
+black:
+	@if command -v black > /dev/null; then \
+		echo "Running black"; \
+		black mne_connectivity examples; \
+	else \
+		echo "black not found, please install it!"; \
+		exit 1; \
+	fi;
+	@echo "black passed"
+
+isort:
+	@if command -v isort > /dev/null; then \
+		echo "Running isort"; \
+		isort mne_connectivity examples doc; \
+	else \
+		echo "isort not found, please install it!"; \
+		exit 1; \
+	fi;
+	@echo "isort passed"
+
 codespell:  # running manually
-	@codespell -w -i 3 -q 3 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt $(CODESPELL_DIRS)
+	@codespell -w -i 3 -q 3 -S $(CODESPELL_SKIPS) --ignore-words=.codespellignore $(CODESPELL_DIRS)
 
 codespell-error:  # running on travis
-	@codespell -i 0 -q 7 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt $(CODESPELL_DIRS)
+	@codespell -i 0 -q 7 -S $(CODESPELL_SKIPS) --ignore-words=.codespellignore $(CODESPELL_DIRS)
 
 pydocstyle:
 	@echo "Running pydocstyle"
@@ -116,4 +136,12 @@ build-doc:
 	@echo "Building documentation"
 	make -C doc/ clean
 	make -C doc/ html-noplot
-	cd doc/ && make view
+	cd doc/ && make view
+
+run-checks:
+	isort --check .
+	black --check mne_connectivity examples
+	flake8 .
+	mypy ./mne_connectivity
+	@$(MAKE) pydocstyle
+	@$(MAKE) codespell-error
-Original file line number
+Diff line change
@@ -0,0 +1,3 @@
+    raison
+    fro
+    nd