Merge pull request #217 from jhlegarreta/sty/misc-cleanup

STY: Miscellaneous cleanup

Author: jhlegarreta

.github/workflows/test.yml

@@ -51,14 +51,14 @@ jobs:
         uses: actions/cache@v4
         id: test-data
         with:
-          path: /home/runner/nifreeze-tests/
+          path: ${{ env.TEST_DATA_HOME }}
           key: data-v2-${{ steps.test-head.outputs.SHA }}
           lookup-only: true
       - name: Create data-v2-${{ steps.test-head.outputs.SHA }}
         uses: actions/cache@v4
         if: steps.test-data.outputs.cache-hit != 'true'
         with:
-          path: /home/runner/nifreeze-tests/
+          path: ${{ env.TEST_DATA_HOME }}
           key: data-v2-${{ steps.test-head.outputs.SHA }}
           restore-keys: |
             data-v2
@@ -123,7 +123,7 @@ jobs:
           antsRegistration --version
       - uses: actions/cache/restore@v4
         with:
-          path: /home/runner/nifreeze-tests/
+          path: ${{ env.TEST_DATA_HOME }}
           key: data-v2-${{ needs.cache-test-data.outputs.SHA }}
       - name: Install TeX Live
         run: |

pyproject.toml

@@ -9,29 +9,29 @@ description = "A flexible framework for volume-to-volume artifact estimation and
 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 :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering :: Image Recognition",
+  "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",
-    "dipy>=1.5.0",
-    "joblib",
-    "nipype>= 1.5.1,<2.0",
-    "nitransforms>=22.0.0,<24",
-    "nireports",
-    "numpy>=1.21.3",
-    "nest-asyncio>=1.5.1",
-    "scikit-image>=0.15.0",
-    "scikit_learn>=1.3.0",
-    "scipy>=1.8.0",
-    "typing_extensions >=4.12",
+  "attrs",
+  "dipy>=1.5.0",
+  "joblib",
+  "nipype>= 1.5.1,<2.0",
+  "nitransforms>=22.0.0,<24",
+  "nireports",
+  "numpy>=1.21.3",
+  "nest-asyncio>=1.5.1",
+  "scikit-image>=0.15.0",
+  "scikit_learn>=1.3.0",
+  "scipy>=1.8.0",
+  "typing_extensions >=4.12",
 ]
 dynamic = ["version"]
 
@@ -42,41 +42,37 @@ 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, <8",
-    "sphinx-argparse",
-    "sphinx_rtd_theme",
-    "sphinxcontrib-apidoc",
-    "sphinxcontrib-napoleon",
-    "sphinxcontrib-versioning",
-    "sphinx-argparse",
-    "sphinxcontrib-bibtex",
+  "attrs >= 20.1.0",
+  "furo >= 2024.01.29",
+  "matplotlib >= 2.2.0",
+  "nbsphinx",
+  "packaging",
+  "pydot >= 1.2.3",
+  "pydotplus",
+  "sphinx >= 4.5, <8",
+  "sphinx-argparse",
+  "sphinx_rtd_theme",
+  "sphinxcontrib-apidoc",
+  "sphinxcontrib-napoleon",
+  "sphinxcontrib-versioning",
+  "sphinx-argparse",
+  "sphinxcontrib-bibtex",
 ]
-
 dev = [
-    "ruff",
-    "pre-commit",
-    "pre-commit-hooks",
+  "ruff",
+  "pre-commit",
+  "pre-commit-hooks",
 ]
-
 plotting = ["nilearn"]
-
 resmon = ["psutil >=5.4"]
-
 test = [
-    "coverage",
-    "ipykernel",
-    "mriqc-learn",
-    "pytest >= 4.4",
-    "pytest-cov",
-    "pytest-env",
-    "pytest-xdist >= 1.28"
+  "coverage",
+  "ipykernel",
+  "mriqc-learn",
+  "pytest >= 4.4",
+  "pytest-cov",
+  "pytest-env",
+  "pytest-xdist >= 1.28"
 ]
 types = [
   "pandas-stubs",
@@ -87,26 +83,23 @@ types = [
   "types-tqdm",
   "pytest",
 ]
-
 notebooks = [
-    "jupyter",
-    "nbclient",
-    "nbmake",
-    "mriqc_learn",
-    "nipreps-synthstrip",
+  "jupyter",
+  "nbclient",
+  "nbmake",
+  "mriqc_learn",
+  "nipreps-synthstrip",
 ]
-
 antsopt = [
-    "ConfigSpace",
-    "nipreps",
-    "scikit-image",
-    "smac",
+  "ConfigSpace",
+  "nipreps",
+  "scikit-image",
+  "smac",
 ]
-
 benchmark = [
-    "asv",
-    "pyperf",
-    "virtualenv==20.30",
+  "asv",
+  "pyperf",
+  "virtualenv==20.30",
 ]
 
 # Aliases
@@ -130,10 +123,9 @@ exclude = [".git_archival.txt"]  # No longer needed in sdist
 [tool.hatch.build.targets.wheel]
 packages = ["src/nifreeze"]
 # exclude = [
-#     "nifreeze/tests/data",  # Large test data directory
+#   "nifreeze/tests/data",  # Large test data directory
 # ]
 
-
 [tool.hatch.version]
 validate-bump = true
 source = "vcs"
@@ -142,7 +134,6 @@ source = "vcs"
 version_scheme = "nipreps-calver"
 local_scheme = "no-local-version"
 
-
 [tool.hatch.build.hooks.vcs]
 version-file = "src/nifreeze/_version.py"
 
@@ -180,7 +171,6 @@ exclude = [
   "build",
   "dist",
 ]
-extend-exclude = ["docs/notebooks/PET_example.ipynb"]
 
 [tool.ruff.lint]
 select = [
@@ -221,10 +211,10 @@ addopts = "-v --doctest-modules"
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 markers = [
-    "random_gtab_data: Custom marker for random gtab data tests",
-    "random_dwi_data: Custom marker for random dwi data tests",
-    "random_uniform_ndim_data: Custom marker for random multi-dimensional data tests",
-    "random_uniform_spatial_data: Custom marker for random spatial data tests",
+  "random_gtab_data: Custom marker for random gtab data tests",
+  "random_dwi_data: Custom marker for random dwi data tests",
+  "random_uniform_ndim_data: Custom marker for random multi-dimensional data tests",
+  "random_uniform_spatial_data: Custom marker for random spatial data tests",
 ]
 filterwarnings = [
   "ignore::DeprecationWarning",
@@ -234,31 +224,29 @@ filterwarnings = [
   "ignore:The optimal value found for dimension.*:sklearn.exceptions.ConvergenceWarning",
 ]
 
-
 [tool.coverage.run]
 branch = true
 parallel = true
-concurrency = ['multiprocessing']
+concurrency = ["multiprocessing"]
 omit = [
-    '*/tests/*',
-    '*/testing/*',
-    '*/viz/*',
-    '*/__init__.py',
-    '*/conftest.py',
-    'src/nifreeze/_version.py'
+  "*/tests/*",
+  "*/testing/*",
+  "*/viz/*",
+  "*/__init__.py",
+  "*/conftest.py",
+  "src/nifreeze/_version.py"
 ]
 
 [tool.coverage.report]
 # Regexes for lines to exclude from consideration
 exclude_lines = [
-    'raise NotImplementedError',
-    'warnings\.warn',
+  "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'
+ignore-words-list = "nd,mapp,reson"
 skip = """
-./.git,*.pdf,*.svg,*.min.js,*.ipynb,ORIGINAL_LICENSE,\
-./docs/source/_static/example_anatreport.html"""
+./.git,*.pdf,*.svg,*.min.js,*.ipynb"""