MAINT: Migrate to hatchling

.circleci/config.yml

@@ -647,8 +647,7 @@ jobs:
           command: |
             python -m venv /tmp/venv
             source /tmp/venv/bin/activate
-            python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                          setuptools_scm_git_archive pip twine docutils
+            python -m pip install -U build hatch hatchling pip twine docutils
       - run:
           name: Build and check
           command: |
@@ -659,7 +658,7 @@ jobs:
           name: Validate version
           command: |
             source /tmp/venv/bin/activate
-            THISVERSION=$( python3 -m setuptools_scm )
+            THISVERSION=$( python3 -m hatch version | tail -n1 | xargs )
             python -m pip install dist/*.tar.gz
             mkdir empty
             cd empty
@@ -677,15 +676,14 @@ jobs:
           command: |
             python -m venv /tmp/venv
             source /tmp/venv/bin/activate
-            python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                          setuptools_scm_git_archive pip twine docutils
+            python -m pip -U hatch hatchling pip twine docutils
       - run:
           name: Deploy to PyPi
           command: |
             source /tmp/venv/bin/activate
 
             # Set version on stone before editing the bundle
-            export SETUPTOOLS_SCM_PRETEND_VERSION=$( python -m setuptools_scm )
+            export SETUPTOOLS_SCM_PRETEND_VERSION=$( python3 -m hatch version | tail -n1 | xargs )
 
             # Inject MRIQC-WebAPI secret
             if [ "${MRIQC_API_SECRET_TOKEN}" != "" ]; then

.github/workflows/pythonpackage.yml

@@ -16,8 +16,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
-        pip: ["pip==21.2", "pip~=22.0"]
+        python-version: ['3.8', '3.9', '3.11']
+        pip: ["pip==21.2", "pip~=23.0"]
 
     steps:
     - uses: actions/checkout@v2
@@ -38,8 +38,7 @@ 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
+        python -m pip install -U build hatch hatchling pip twine docutils
 
         python -m build -s -w
         python -m twine check dist/mriqc-*
@@ -49,15 +48,15 @@ jobs:
         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}" >> $GITHUB_ENV
     - name: Install in confined environment [pip]
       run: |
         python -m venv /tmp/pip
         source /tmp/pip/bin/activate
-        python -m pip install -U "setuptools >= 45" "setuptools_scm >= 6.2" "${{ matrix.pip }}"
+        python -m pip install -U hatch hatchling "${{ matrix.pip }}"
         python -m pip install .
         INSTALLED_VERSION=$(python -c 'import mriqc as qc; print(qc.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
@@ -67,7 +66,7 @@ jobs:
       run: |
         python -m venv /tmp/install_sdist
         source /tmp/install_sdist/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
+        python -m pip install -U hatch hatchling "${{ matrix.pip }}"
         python -m pip install /tmp/package/mriqc*.tar.gz
         INSTALLED_VERSION=$(python -c 'import mriqc as qc; print(qc.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
@@ -87,9 +86,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.7
+    - name: Set up Python 3.9
       uses: actions/setup-python@v1
       with:
-        python-version: 3.7
-    - run: pip install flake8
+        python-version: 3.9
+    - run: pip install flake8-pyproject 
     - run: flake8 mriqc/

pyproject.toml

@@ -1,15 +1,206 @@
 [build-system]
-requires = [
-    "setuptools >= 45",
-    "setuptools_scm[toml] >= 6.2",
-    "wheel"
-]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools_scm]
-write_to = "mriqc/_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"
+description = "Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain."
+readme = "README.rst"
+authors = [{name = "The NiPreps Developers", email = "nipreps@gmail.com"}]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Image Recognition",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10"
+]
+license = "Apache-2.0"
+requires-python = ">=3.8"
+dependencies = [
+    'importlib_resources; python_version < "3.9"',
+    # jinja2 imports deprecated function removed in 2.1
+    "markupsafe ~= 2.0.1",
+    "matplotlib",
+    "migas",
+    "mriqc-learn",
+    "nibabel >= 3.0.1,<4.0",
+    "nilearn >= 0.5.1",
+    "nipype ~= 1.4",
+    "nitransforms >= 21.0.1",
+    "niworkflows ~= 1.7.1",
+    "nitransforms ~= 21.0.1",
+    "numpy ~=1.20",
+    "pandas ~=1.0",
+    "pybids >= 0.15.6",
+    "PyYAML",
+    "scipy ~=1.8",
+    "statsmodels",
+    "toml",
+    "torch >= 1.10.2",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/nipreps/mriqc"
+NiPreps = "https://www.nipreps.org/"
+Documentation = "https://mriqc.readthedocs.io/"
+Manuscript = "https://doi.org/10.1371/journal.pone.0184661"
+"Sci Dat Paper" = "https://doi.org/10.1038/s41597-019-0035-4"
+"Web API" = "https://mriqc.nimh.nih.gov/"
+"Docker Images" = "https://hub.docker.com/r/nipreps/mriqc/tags/"
+
+[project.optional-dependencies]
+doc = [
+    "nipype",
+    "packaging",
+    "pydot>=1.2.3",
+    "pydotplus",
+    "sphinx-argparse",
+    "sphinx_rtd_theme",
+    "sphinx~=4.0",
+]
+
+full = [
+    "dipy<=1.4.0", # see nipreps/mriqc#969; can be removed if nipype>1.7.0
+    "nitime",
+    "nirodents >= 0.2.8",
+    "scikit-learn ~= 1.0",
+    "seaborn",
+    "templateflow",
+    "xvfbwrapper",
+]
+
+notebook = [
+    "ipython",
+    "jupyter",
+    "nipy",
+]
+
+dev = [
+    "black ~= 22.3.0",
+    "pre-commit",
+    "isort ~= 5.10.1",
+    "flake8-pyproject",
+]
+
+test = [
+    "coverage",
+    "mock",
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+]
+
+other = [
+    "scikit-image",
+]
+
+# Aliases
+docs = ["mriqc[doc]"]
+tests = ["mriqc[test]"]
+others = ["mriqc[other]"]
+all = ["mriqc[doc,full,test,notebook,other]"]
+
+[project.scripts]
+mriqc = "mriqc.cli.run:main"
+synthstrip = "mriqc.synthstrip.cli:main"
+mriqc_plot = "mriqc.bin.mriqc_plot:main"
+abide2bids = "mriqc.bin.abide2bids:main"
+fs2gif = "mriqc.bin.fs2gif:main"
+dfcheck = "mriqc.bin.dfcheck:main"
+nib-hash = "mriqc.bin.nib_hash:main"
+participants = "mriqc.bin.subject_wrangler:main"
+mriqc_labeler = "mriqc.bin.labeler:main"
+mriqcwebapi_test = "mriqc.bin.mriqcwebapi_test: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 = ["mriqc"]
+# exclude = [
+#     "mriqc/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 = "mriqc/_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
+omit = [
+    '*/tests/*',
+    '*/__init__.py',
+    '*/conftest.py',
+    'mriqc/_version.py'
+]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_lines = [
+    'raise NotImplementedError',
+    'warnings\.warn',
+]