MAINT: Initate porting to PEP517/8

.circleci/config.yml

@@ -5,7 +5,7 @@ orbs:
 jobs:
   test_package:
     docker:
-      - image: cimg/python:3.8.5
+      - image: cimg/python:3.11
         auth:
           username: $DOCKER_USER
           password: $DOCKER_PAT
@@ -17,9 +17,11 @@ jobs:
           command: |
             python3 -m venv /tmp/buildenv
             source /tmp/buildenv/bin/activate
-            python -m pip install -U "setuptools~=58.0" "setuptools_scm>=6.2" pip wheel twine docutils
-            python setup.py sdist bdist_wheel
-            twine check dist/mriqc_learn*
+            python -m pip install -U build hatch pip twine
+
+            # Build and test package
+            python -m build -s -w
+            python -m twine check dist/mriqc_learn-*
       - store_artifacts:
           path: /tmp/src/mriqc_learn/dist
       - persist_to_workspace:
@@ -30,10 +32,11 @@ jobs:
           command: |
             python3 -m venv /tmp/install_sdist
             source /tmp/install_sdist/bin/activate
-            python -m pip install -U pip "setuptools~=58.0" "setuptools_scm>=6.2"
-            THISVERSION=$( python setup.py --version )
+                    
+            THISVERSION=$( python -m hatch version | tail -n1 | xargs )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
-            python -m pip install dist/mriqc-learn*.tar.gz
+
+            python -m pip install /tmp/src/mriqc_learn/dist/mriqc_learn*.tar.gz
             INSTALLED_VERSION=$(python -c 'import mriqc_learn as ml; print(ml.__version__, end="")')
             echo "VERSION: \"${THISVERSION}\""
             echo "INSTALLED: \"${INSTALLED_VERSION}\""
@@ -43,18 +46,19 @@ jobs:
           command: |
             python3 -m venv /tmp/install_wheel
             source /tmp/install_wheel/bin/activate
-            python -m pip install "setuptools~=58.0" "setuptools_scm>=6.2" wheel "pip>=10.0.1"
-            THISVERSION=$( python setup.py --version )
+
+            THISVERSION=$( python -m hatch version | tail -n1 | xargs )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
-            python -m pip install dist/mriqc_learn*.whl
+
+            python -m pip install /tmp/src/mriqc_learn/dist/mriqc_learn*.whl
             INSTALLED_VERSION=$(python -c 'import mriqc_learn as ml; print(ml.__version__, end="")')
             echo "VERSION: \"${THISVERSION}\""
             echo "INSTALLED: \"${INSTALLED_VERSION}\""
             test "${INSTALLED_VERSION}" = "${THISVERSION}"
 
   deploy_pypi:
     docker:
-      - image: cimg/python:3.8.5
+      - image: cimg/python:3.11
     working_directory: /tmp/src/mriqc_learn
     steps:
       - attach_workspace:

.github/workflows/pythonpackage.yml

@@ -12,87 +12,69 @@ on:
 
 jobs:
   build:
-    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+    if: "!startsWith(github.ref, 'refs/tags/') && !contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         ssh-key: "${{ secrets.NIPREPS_DEPLOY }}"
         fetch-depth: 0
-    - name: Build in confined, updated environment and interpolate version
+    - name: Build in confined environment and interpolate version
       run: |
         python -m venv /tmp/buildenv
         source /tmp/buildenv/bin/activate
-        python -m pip install -U "setuptools~=58.0" "setuptools_scm>=6.2" pip wheel twine docutils
+        python -m pip install -U build hatch pip twine
+
+        python -m build -s -w
+        python -m twine check dist/mriqc_learn-*
+
+        mv dist /tmp/package
 
         # Interpolate version
         if [[ "$GITHUB_REF" == refs/tags/* ]]; then
           TAG=${GITHUB_REF##*/}
         fi
-        THISVERSION=$( python setup.py --version )
+        THISVERSION=$( python -m hatch version | tail -n1 | xargs )
         THISVERSION=${TAG:-$THISVERSION}
         echo "Expected VERSION: \"${THISVERSION}\""
         echo "THISVERSION=${THISVERSION}" >> ${GITHUB_ENV}
 
-        python setup.py sdist
-        python -m twine check dist/mriqc-learn-${THISVERSION}.tar.gz
-
-        python setup.py bdist_wheel
-        python -m twine check dist/mriqc_learn-${THISVERSION}-py3-none-any.whl
-
+    - name: Install in confined environment [pip]
+      run: |
+        python -m venv /tmp/pip
+        source /tmp/pip/bin/activate
+        pip install -U pip
+        python -m pip install .
+        INSTALLED_VERSION=$(python -c 'import mriqc_learn as em; print(em.__version__, end="")')
+        echo "VERSION: \"${THISVERSION}\""
+        echo "INSTALLED: \"${INSTALLED_VERSION}\""
+        test "${INSTALLED_VERSION}" = "${THISVERSION}"
+
     - name: Install in confined environment [sdist]
       run: |
         python -m venv /tmp/install_sdist
         source /tmp/install_sdist/bin/activate
-        python -m pip install --upgrade pip wheel
-        python -m pip install dist/mriqc-learn-${THISVERSION}.tar.gz
-        INSTALLED_VERSION=$(python -c 'import mriqc_learn; print(mriqc_learn.__version__, end="")')
+        pip install -U pip
+        python -m pip install /tmp/package/mriqc_learn*.tar.gz
+        INSTALLED_VERSION=$(python -c 'import mriqc_learn as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
         echo "INSTALLED: \"${INSTALLED_VERSION}\""
         test "${INSTALLED_VERSION}" = "${THISVERSION}"
+
     - name: Install in confined environment [wheel]
       run: |
         python -m venv /tmp/install_wheel
         source /tmp/install_wheel/bin/activate
-        python -m pip install --upgrade pip wheel
-        python -m pip install dist/mriqc_learn-${THISVERSION}-py3-none-any.whl
-        INSTALLED_VERSION=$(python -c 'import mriqc_learn; print(mriqc_learn.__version__, end="")')
+        pip install -U pip
+        python -m pip install /tmp/package/mriqc_learn*.whl
+        INSTALLED_VERSION=$(python -c 'import mriqc_learn as em; print(em.__version__, end="")')
         echo "INSTALLED: \"${INSTALLED_VERSION}\""
         test "${INSTALLED_VERSION}" = "${THISVERSION}"
-    - name: Install in confined environment [pip install .]
-      run: |
-        python -m venv /tmp/setup_install
-        source /tmp/setup_install/bin/activate
-        python -m pip install --upgrade pip wheel
-        python -m pip install .
-        INSTALLED_VERSION=$(python -c 'import mriqc_learn; print(mriqc_learn.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-    - name: Install in confined environment [pip install -e .]
-      run: |
-        python -m venv /tmp/setup_develop
-        source /tmp/setup_develop/bin/activate
-        python -m pip install pip
-        python -m pip install --upgrade pip wheel
-        python -m pip install -e .
-        INSTALLED_VERSION=$(python -c 'import mriqc_learn; print(mriqc_learn.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-  flake8:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.7
-    - run: pip install flake8
-    - run: flake8 mriqc_learn/

pyproject.toml

@@ -1,10 +1,157 @@
 [build-system]
-requires = ["setuptools>=45, <58", "wheel", "setuptools_scm>=6.2"]
-
-[tool.setuptools_scm]
-write_to = "mriqc_learn/_version.py"
-write_to_template = """\
-\"\"\"Version file, automatically generated by setuptools_scm.\"\"\"
-__version__ = "{version}"
-"""
-fallback_version = "0.0"
+requires = ["hatchling", "hatch-vcs", "nipreps-versions"]
+build-backend = "hatchling.build"
+
+[project]
+name = "mriqc-learn"
+description = "Learning on MRIQC-generated image quality metrics (IQMs)."
+readme = "README.md"
+authors = [{name = "The NiPreps Developers", email = "[email protected]"}]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Image Recognition",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+license = "Apache-2.0"
+requires-python = ">=3.8"
+dependencies = [
+    "numpy",
+    "joblib",
+    "pandas",
+    "scikit-learn",
+]
+dynamic = ["version"]
+
+[project.urls]
+Home = "https://github.com/nipreps/mriqc-learn"
+
+[project.optional-dependencies]
+doc = [
+    "furo >= 2024.01.29",
+    "pydot >= 1.2.3",
+    "pydotplus",
+    "sphinx >= 4.5",
+    "sphinxcontrib-apidoc",
+    "sphinxcontrib-napoleon",
+]
+
+mem = [
+    "psutil",
+]
+
+test = [
+    "codecov",
+    "coverage",
+    "pytest",
+    "pytest-cov",
+    "pytest-env",
+    "pytest-xdist",
+]
+
+# Aliases
+docs = ["mriqc-learn[doc]"]
+tests = ["mriqc-learn[test]"]
+all = ["mriqc-learn[doc,test,mem]"]
+
+#
+# Hatch configurations
+#
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.sdist]
+exclude = [".git_archival.txt"]  # No longer needed in sdist
+
+[tool.hatch.build.targets.wheel]
+packages = ["mriqc_learn"]
+# exclude = [
+#     "mriqc_learn/tests/largedata",  # Large test data directory
+# ]
+
+
+[tool.hatch.version]
+validate-bump = true
+source = "vcs"
+raw-options = { version_scheme = "nipreps-calver" }
+
+[tool.hatch.build.hooks.vcs]
+version-file = "mriqc_learn/_version.py"
+
+#
+# Developer tool configurations
+#
+
+[tool.black]
+line-length = 99
+target-version = ['py39']
+skip-string-normalization = true
+exclude = '''
+# Directories
+/(
+    \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | venv
+  | _build
+  | build
+  | dist
+)/
+'''
+
+[tool.isort]
+profile = 'black'
+skip_gitignore = true
+
+[tool.flake8]
+max-line-length = 99
+doctests = false
+exclude = ["*build/", "docs/"]
+select = "C,E,F,W,B,B950"
+ignore = "N802,N806,W503,E203"
+per-file-ignores = [
+    "*/__init__.py: F401",
+    "docs/conf.py: E265",
+    "/^\\s*\\.\\. _.*?: http/: E501"
+]
+
+[tool.pytest.ini_options]
+norecursedirs = [".*", "_*"]
+addopts = "-vsx --doctest-modules"
+doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE NUMBER"
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
+
+
+[tool.coverage.run]
+branch = true
+concurrency = 'multiprocessing'
+omit = [
+    '*/tests/*',
+    '*/__init__.py',
+    '*/conftest.py',
+    'mriqc_learn/_version.py'
+]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_lines = [
+    'raise NotImplementedError',
+    'warnings\.warn',
+]
+
+[tool.codespell]
+# nd - import scipy.ndimage as nd
+# mapp, reson -- Mapp. and Reson. abbreviations in citation
+ignore-words-list = 'nd,mapp,reson'
+skip = """
+./.git,*.pdf,*.svg,*.min.js,*.ipynb,ORIGINAL_LICENSE,\
+./docs/source/_static/example_anatreport.html"""