maint: migrate to PEP517/518 packaging

.circleci/config.yml

@@ -229,10 +229,10 @@ jobs:
           command: |
             export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
             pyenv local $PY3
-            python3 -m pip install --upgrade setuptools setuptools_scm pip
+            python3 -m pip install -U build hatch hatchling pip twine docutils
 
             # Get version, update files.
-            THISVERSION=$( python3 -m setuptools_scm )
+            THISVERSION=$( python3 -m hatch version | tail -n1 | xargs )
             if [[ ${THISVERSION:0:1} == "0" ]] ; then
               echo "WARNING: latest git tag could not be found"
               echo "Please, make sure you fetch all tags from upstream with"
@@ -255,7 +255,7 @@ jobs:
             export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
             pyenv local $PY3
             # Get version, update files.
-            THISVERSION=$( python3 -m setuptools_scm )
+            THISVERSION=$( python3 -m hatch version | tail -n1 | xargs )
             BUILT_VERSION=$( docker run --rm --entrypoint=python nipreps/sdcflows:latest -c "import sdcflows; print(sdcflows.__version__)" )
             BUILT_VERSION=${BUILT_VERSION%$'\r'}
             echo "VERSION: \"$THISVERSION\""
@@ -376,13 +376,13 @@ jobs:
           command: |
             python -m venv /tmp/venv
             source /tmp/venv/bin/activate
-            python -m pip install -U pip setuptools setuptools_scm
-            pip install --no-cache-dir -r docs/requirements.txt
+            python -m pip install -U build hatch hatchling pip twine docutils
+            python -m pip install --no-cache-dir -r docs/requirements.txt
       - run:
           name: Build only this commit
           command: |
             source /tmp/venv/bin/activate
-            python -m setuptools_scm
+            python -m hatch version | tail -n1 | xargs
             BRANCH=$( echo $CIRCLE_BRANCH | sed 's+/+_+g' )
             make -C docs SPHINXOPTS="-W" BUILDDIR="$HOME/docs" OUTDIR=${CIRCLE_TAG:-$BRANCH} html
       - store_artifacts:
@@ -422,7 +422,7 @@ jobs:
           command: |
             python -m venv /tmp/buildenv
             source /tmp/buildenv/bin/activate
-            python -m pip install -U build twine setuptools_scm
+            python3 -m pip install -U build hatch hatchling pip twine docutils
             python3 -m build
             twine check dist/sdcflows*
       - store_artifacts:
@@ -435,7 +435,7 @@ jobs:
           name: Validate version
           command: |
             source /tmp/buildenv/bin/activate
-            THISVERSION=$( python -m setuptools_scm )
+            THISVERSION=$( python -m hatch version | tail -n1 | xargs )
             python -m pip install dist/*.whl
             mkdir empty
             cd empty

.git_archival.txt

@@ -1 +1,4 @@
-ref-names: $Format:%D$
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1,2 +1 @@
-sdcflows/_version.py export-subst
 .git_archival.txt  export-subst

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

@@ -46,9 +46,9 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install -r docs/requirements.txt
-        pip install --no-cache-dir "setuptools ~= 45.0" "setuptools_scm[toml] >= 3.4"
-        python setup.py --version
+        python -m pip install -U build hatch hatchling pip docutils
+        python -m pip install -r docs/requirements.txt
+        python -m hatch version | tail -n1 | xargs
 
     - name: Build docs
       run: |

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

@@ -46,9 +46,9 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install -r docs/requirements.txt
-        pip install --no-cache-dir "setuptools ~= 45.0" "setuptools_scm[toml] >= 3.4"
-        python setup.py --version
+        python -m pip install -U build hatch hatchling pip docutils
+        python -m pip install -r docs/requirements.txt
+        python -m hatch version | tail -n1 | xargs
 
     - name: Build docs
       run: |

.github/workflows/pythonpackage.yml

@@ -45,8 +45,8 @@ jobs:
           if [[ "$GITHUB_REF" == refs/tags/* ]]; then
             VERSION=${GITHUB_REF##*/}
           else
-            pip install setuptools_scm
-            VERSION=$( python -m setuptools_scm )
+            pip install -U build hatch hatchling pip twine docutils
+            VERSION=$( python -m hatch version | tail -n1 | xargs )
           fi
           echo version=$VERSION | tee -a $GITHUB_OUTPUT
 
@@ -78,7 +78,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.12"]
+        python-version: ["3.10", "3.12"]
         install: [repo, sdist, wheel, editable]
 
     env:

.github/workflows/unittests.yml

@@ -35,10 +35,10 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         deps: ["requirements"]
         include:
-          - python-version: "3.8"
+          - python-version: "3.10"
             deps: "min-requirements"
 
     steps:

.gitignore

@@ -1,5 +1,5 @@
 # setuptools-scm
-sdcflows/_version.py
+_version.py
 
 # Byte-compiled / optimized / DLL files
 pip-wheel-metadata

pyproject.toml

@@ -1,10 +1,184 @@
 [build-system]
-requires = ["setuptools >= 42.0", "wheel", "setuptools_scm[toml] >= 3.4"]
-
-[tool.setuptools_scm]
-write_to = "sdcflows/_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 = "sdcflows"
+description = "Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes."
+readme = "README.rst"
+authors = [{name = "The NiPreps Developers", email = "[email protected]"}]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Image Recognition",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+license = "Apache-2.0"
+requires-python = ">=3.10"
+dependencies = [
+    "attrs >= 20.1.0",
+    "nibabel >=3.1.0",
+    "nipype >=1.8.5,<2.0",
+    "traits <6.4",
+    "niworkflows >= 1.7.0",
+    "nitransforms >= 23.0.1",
+    "numpy >= 1.21.0",
+    "pybids >= 0.15.1",
+    "scikit-image >= 0.18",
+    "scipy >= 1.8.1",
+    "templateflow",
+]
+dynamic = ["version"]
+
+[project.urls]
+Documentation = "https://www.nipreps.org/sdcflows"
+Home = "https://github.com/nipreps/sdcflows"
+NiPreps = "https://www.nipreps.org/"
+
+[project.optional-dependencies]
+doc = [
+    "attrs >= 20.1.0",
+    "furo",
+    "importlib_resources",
+    "matplotlib >= 2.2.0",
+    "nibabel",
+    "nipype >= 1.5.1",
+    "traits < 6.4",
+    "niworkflows ~= 1.6.3",
+    "numpy",
+    "packaging",
+    "pydot >= 1.2.3",
+    "pydotplus",
+    "sphinx >= 7.2.2",
+    "sphinxcontrib-apidoc",
+    "templateflow"
+]
+
+mem = [
+    "psutil"
+]
+
+dev = [
+    "black",
+    "pre-commit",
+    "isort",
+    "flake8-pyproject",
+]
+
+test = [
+    "coverage",
+    "pytest",
+    "pytest-cov",
+    "pytest-env",
+    "pytest-xdist"
+]
+
+# Aliases
+docs = ["sdcflows[doc]"]
+tests = ["sdcflows[test]"]
+all = ["sdcflows[doc,test,mem,dev,test]"]
+
+[project.scripts]
+sdcflows-find-estimators = "sdcflows.cli.find_estimators:main"
+
+#
+# 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 = ["sdcflows"]
+# exclude = [
+#     "sdcflows/tests/data",  # Large test data directory
+# ]
+
+##  The following two sections configure setuptools_scm in the hatch way
+
+[tool.hatch.version]
+validate-bump = true
+source = "vcs"
+raw-options = { version_scheme = "nipreps-calver" }
+
+[tool.hatch.build.hooks.vcs]
+version-file = "sdcflows/_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/"
+ignore = ["W503", "E203"]
+per-file-ignores = [
+    "**/__init__.py : F401",
+    "docs/conf.py : E265",
+]
+
+[tool.pytest.ini_options]
+norecursedirs = [".git"]
+addopts = "-svx --doctest-modules"
+doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
+junit_family = "xunit2"
+
+
+[tool.coverage.run]
+branch = true
+concurrency = 'multiprocessing'
+omit = [
+    '*/tests/*',
+    '*/__init__.py',
+    '*/conftest.py',
+    'sdcflows/_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"""