Merge pull request #128 from esavary/maint/migrate-to-pep517-8

MAINT: Migrate to PEP517/518 packaging

.circleci/config.yml

@@ -74,8 +74,7 @@ jobs:
       - run:
           name: Initiate versioning
           command: |
-            python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                                  setuptools_scm_git_archive pip twine docutils
+            python3 -m pip install -U build hatch hatchling pip twine docutils
 
             pip install /tmp/src/eddymotion[all]
 

.github/workflows/contrib.yml

@@ -11,15 +11,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
           fetch-depth: 0
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-      - name: Install flake8
-        run: python -m pip install flake8
-      - name: Check EddyMotion
-        run: python -m flake8 src
+          python-version: 3
+      - name: Lint EddyMotion
+        run: pipx run flake8-pyproject

.github/workflows/docs-build-pr.yml

@@ -7,11 +7,11 @@ on:
 
 jobs:
   build:
-    if: "(github.repository_owner != 'nipreps') && !contains(github.event.head_commit.message, '[skip ci]')"
+    if: "!contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -39,10 +39,11 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --no-cache-dir "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2"
+        pip install -U build hatch pip
         pip install -r docs/requirements.txt
+        python -m hatch version | tail -n1
 
     - name: Build docs
       run: |
-          python -m setuptools_scm  # Generate _version.py file
+          python -m hatch build --hooks-only
           make -C docs/ SPHINXOPTS="-W" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html

.github/workflows/docs-build-update.yml

@@ -42,12 +42,13 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --no-cache-dir "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2"
+        pip install -U build hatch pip
         pip install -r docs/requirements.txt
+        python -m hatch version | tail -n1
 
     - name: Build docs
       run: |
-          python -m setuptools_scm  # Generate _version.py file
+          python -m hatch build --hooks-only
           make -C docs/ SPHINXOPTS="-W" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html
 
     - name: Push created tag to gh-pages

.github/workflows/pythonpackage.yml

@@ -16,19 +16,18 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-        pip: ["pip==21.2", "pip~=22.0"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Fetch all tags (for setuptools_scm to work)
-      run: |
-        /usr/bin/git -c protocol.version=2 fetch --tags --prune --unshallow origin
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+        fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/cache@v1
+    - uses: actions/cache@v4
       with:
         path: $HOME/.cache/pip
         key: pip-cache-v1
@@ -39,20 +38,18 @@ jobs:
       run: |
         python -m venv /tmp/buildenv
         source /tmp/buildenv/bin/activate
-        python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                              setuptools_scm_git_archive pip twine docutils
+        pip install -U build hatch pip twine
         
         python -m build -s -w
         python -m twine check dist/eddymotion-*
 
         mv dist /tmp/package
-        rm -rf eddymotion.egg-info/
 
         # Interpolate version
         if [[ "$GITHUB_REF" == refs/tags/* ]]; then
           TAG=${GITHUB_REF##*/}
         fi
-        THISVERSION=$( python -m setuptools_scm )
+        THISVERSION=$( python -m hatch version | tail -n1 | xargs )
         THISVERSION=${TAG:-$THISVERSION}
         echo "Expected VERSION: \"${THISVERSION}\""
         echo "THISVERSION=${THISVERSION}" >> $GITHUB_ENV
@@ -61,7 +58,7 @@ jobs:
       run: |
         python -m venv /tmp/pip
         source /tmp/pip/bin/activate
-        python -m pip install -U "setuptools >= 45" "setuptools_scm >= 6.2" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install .
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
@@ -72,7 +69,7 @@ jobs:
       run: |
         python -m venv /tmp/install_sdist
         source /tmp/install_sdist/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install /tmp/package/eddymotion*.tar.gz
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
@@ -83,7 +80,7 @@ jobs:
       run: |
         python -m venv /tmp/install_wheel
         source /tmp/install_wheel/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install /tmp/package/eddymotion*.whl
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "INSTALLED: \"${INSTALLED_VERSION}\""

docs/index.rst

@@ -1,6 +1,8 @@
 .. include:: links.rst
 .. include:: ../README.rst
    :end-line: 29
+.. include:: ../README.rst
+   :start-line: 34
 
 
 .. image:: _static/eddymotion-flowchart.svg

docs/requirements.txt

@@ -1,6 +1,7 @@
 attrs >= 20.1.0
-furo ~= 2021.10.09
+furo >= 2024.01.29
 matplotlib >= 2.2.0
 packaging
-sphinx ~= 4.2
+sphinx >= 4.5
 sphinxcontrib-apidoc
+nireports

pyproject.toml

@@ -1,15 +1,183 @@
 [build-system]
-requires = [
-    "setuptools >= 45",
-    "setuptools_scm[toml] >= 6.2",
-    "wheel"
-]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools_scm]
-write_to = "src/eddymotion/_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 = "eddymotion"
+description = "Pure python eddy-current and head-motion correction for dMRI, an extension of QSIprep's SHOREline algorithm (Cieslak, 2020) to multiple diffusion models."
+readme = "README.rst"
+authors = [{name = "The NiPreps Developers", email = "[email protected]"}]
+classifiers = [
+    "Development Status :: 3 - 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 = [
+    "dipy>=1.3.0",
+    "joblib",
+    "nipype>= 1.5.1, < 2.0",
+    "nitransforms>=21.0.0",
+    "nireports",
+    "numpy>=1.17.3",
+    "nest-asyncio>=1.5.1",
+    "scikit-image>=0.14.2",
+    "scipy>=1.8.0",
+]
+dynamic = ["version"]
+
+[project.urls]
+Documentation = "https://www.nipreps.org/eddymotion"
+Home = "https://github.com/nipreps/eddymotion"
+NiPreps = "https://www.nipreps.org/"
+
+[project.optional-dependencies]
+doc = [
+    "attrs >= 20.1.0",
+    "furo >= 2024.01.29",
+    "matplotlib >= 2.2.0",
+    "nbsphinx",
+    "packaging",
+    "pydot >= 1.2.3",
+    "pydotplus",
+    "sphinx >= 4.5",
+    "sphinx-argparse",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-apidoc ~= 0.3.0",
+    "sphinxcontrib-napoleon",
+    "sphinxcontrib-versioning"
+]
+
+dev = [
+    "black",
+    "flake8",
+    "flake8-pyproject",
+    "isort",
+    "pre-commit",
+    "pre-commit-hooks",
+]
+
+plotting = ["nilearn"]
+
+resmon = ["psutil >=5.4"]
+
+popylar = ["popylar >= 0.2"]
+
+test = [
+    "coverage",
+    "pytest >= 4.4",
+    "pytest-cov",
+    "pytest-env",
+    "pytest-xdist >= 1.28"
+]
+
+# Aliases
+docs = ["eddymotion[doc]"]
+tests = ["eddymotion[test]"]
+all = ["eddymotion[doc,test,dev,plotting,resmon,popylar]"]
+
+#
+# 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 = ["src/eddymotion"]
+# exclude = [
+#     "eddymotion/tests/data",  # 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 = "src/eddymotion/_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]
+pythonpath = "src/ test/"
+norecursedirs = [".*", "_*"]
+addopts = "-v --doctest-modules"
+doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE"
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
+
+
+[tool.coverage.run]
+branch = true
+concurrency = 'multiprocessing'
+omit = [
+    '*/tests/*',
+    '*/__init__.py',
+    '*/conftest.py',
+    'src/eddymotion/_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"""