Merge remote-tracking branch 'upstream/main' into tasks

* upstream/main: [pre-commit.ci] pre-commit autoupdate (mne-tools#830) [pre-commit.ci] pre-commit autoupdate (mne-tools#829) [pre-commit.ci] pre-commit autoupdate (mne-tools#828) [pre-commit.ci] pre-commit autoupdate (mne-tools#827) [pre-commit.ci] pre-commit autoupdate (mne-tools#826) Switch build backend to hatchling (mne-tools#825)
larsoner · Jan 22, 2024 · 6a46291 · 6a46291
2 parents a3845f8 + 9055e9c
commit 6a46291
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Showing 9 changed files with 117 additions and 81 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -47,7 +47,7 @@ jobs:
       - run:
           name: Get Python running
           command: |
-            pip install --upgrade --progress-bar off pip setuptools
+            pip install --upgrade --progress-bar off pip
             pip install --upgrade --progress-bar off "autoreject @ https://api.github.com/repos/autoreject/autoreject/zipball/master" "mne[hdf5] @ git+https://github.com/mne-tools/mne-python@main" "mne-bids[full] @ https://api.github.com/repos/mne-tools/mne-bids/zipball/main" numba
             pip install -ve .[tests]
             pip install "PyQt6!=6.6.1" "PyQt6-Qt6!=6.6.1"

diff --git a/.git_archival.txt b/.git_archival.txt
@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+.git_archival.txt  export-subst
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -29,8 +29,8 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
-    - run: pip install --upgrade setuptools[toml] pip
-    - run: pip install --no-build-isolation -ve .[tests]
+    - run: pip install --upgrade pip
+    - run: pip install -ve .[tests]
     - run: pytest mne_bids_pipeline -m "not dataset_test"
     - uses: codecov/codecov-action@v3
       if: success()

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,14 +6,14 @@ files: ^(.*\.(py|yaml))$
 exclude: ^(\.[^/]*cache/.*|.*/freesurfer/contrib/.*)$
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 23.12.1
     hooks:
       - id: black
         args:
           - --safe
           - --quiet
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.1.13
     hooks:
       - id: ruff
   - repo: https://github.com/codespell-project/codespell

diff --git a/docs/source/changes.md b/docs/source/changes.md
@@ -1,3 +1,5 @@
+{% include-markdown "./v1.6.md.inc" %}
+
 {% include-markdown "./v1.5.md.inc" %}
 
 {% include-markdown "./v1.4.md.inc" %}

diff --git a/docs/source/v1.6.md.inc b/docs/source/v1.6.md.inc
@@ -0,0 +1,23 @@
+[//]: # (Don't forget to add this to changes.md as an include!)
+
+## vX.Y.0 (unreleased)
+
+[//]: # (### :new: New features & enhancements)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+[//]: # (### :warning: Behavior changes)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+### :package: Requirements
+
+- MNE-BIDS-Pipeline now requires Python 3.9 or newer. (#825 by @hoechenberger)
+
+[//]: # (### :bug: Bug fixes)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+### :medical_symbol: Code health
+
+- The package build backend has been switched from `setuptools` to `hatchling`. (#825 by @hoechenberger)
diff --git a/docs/source/vX.Y.md.inc b/docs/source/vX.Y.md.inc
@@ -10,10 +10,14 @@
 
 [//]: # (- Whatever (#000 by @whoever))
 
-[//]: # (### :medical_symbol: Code health)
+[//]: # (### :package: Requirements)
 
 [//]: # (- Whatever (#000 by @whoever))
 
 [//]: # (### :bug: Bug fixes)
 
 [//]: # (- Whatever (#000 by @whoever))
+
+[//]: # (### :medical_symbol: Code health)
+
+[//]: # (- Whatever (#000 by @whoever))
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,79 +1,80 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
 [project]
 name = "mne-bids-pipeline"
 # Keep in sync with README.md:
 description = "A full-flegded processing pipeline for your MEG and EEG data"
 readme = "README.md"
-requires-python = ">=3.8"
-license = {file = "LICENSE.txt"}
+requires-python = ">=3.9"
+license = { file = "LICENSE.txt" }
 keywords = ["science", "neuroscience", "psychology"]
 authors = [
-  {name = "Eric Larson"},
-  {name = "Alexandre Gramfort"},
-  {name = "Mainak Jas"},
-  {name = "Richard Höchenberger", email = "richard.hoechenberger@gmail.com"},
+  { name = "Eric Larson" },
+  { name = "Alexandre Gramfort" },
+  { name = "Mainak Jas" },
+  { name = "Richard Höchenberger", email = "richard.hoechenberger@gmail.com" },
 ]
 classifiers = [
   "Intended Audience :: Science/Research",
-  "Programming Language :: Python"
+  "Programming Language :: Python",
 ]
 dependencies = [
-    "typing_extensions; python_version < '3.8'",
-    "importlib_metadata; python_version < '3.8'",
-    "psutil",  # for joblib
-    "packaging",
-    "numpy",
-    "scipy",
-    "matplotlib",
-    "nibabel",
-    "joblib >= 0.14",
-    "threadpoolctl",
-    "dask[distributed]",
-    "bokeh < 3",  # for distributed dashboard
-    "jupyter-server-proxy",  # to have dask and jupyter working together
-    "scikit-learn",
-    "pandas",
-    "pyarrow",  # from pandas
-    "seaborn",
-    "json_tricks",
-    "pydantic >= 2.0.0",
-    "rich",
-    "python-picard",
-    "qtpy",
-    "pyvista",
-    "pyvistaqt",
-    "openpyxl",
-    "autoreject",
-    "mne[hdf5] >=1.2",
-    "mne-bids[full]",
-    "filelock",
-    "setuptools >=65",
+  "psutil",               # for joblib
+  "packaging",
+  "numpy",
+  "scipy",
+  "matplotlib",
+  "nibabel",
+  "joblib >= 0.14",
+  "threadpoolctl",
+  "dask[distributed]",
+  "bokeh < 3",            # for distributed dashboard
+  "jupyter-server-proxy", # to have dask and jupyter working together
+  "scikit-learn",
+  "pandas",
+  "pyarrow",  # from pandas
+  "seaborn",
+  "json_tricks",
+  "pydantic >= 2.0.0",
+  "rich",
+  "python-picard",
+  "qtpy",
+  "pyvista",
+  "pyvistaqt",
+  "openpyxl",
+  "autoreject",
+  "mne[hdf5] >=1.2",
+  "mne-bids[full]",
+  "filelock",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 tests = [
-    "pytest",
-    "pytest-cov",
-    "pooch",
-    "psutil",
-    "datalad",
-    "ruff",
-    "mkdocs",
-    "mkdocs-material >= 9.0.4",
-    "mkdocs-material-extensions",
-    "mkdocs-macros-plugin",
-    "mkdocs-include-markdown-plugin",
-    "mkdocs-exclude",
-    "mkdocstrings-python",
-    "mike",
-    "jinja2",
-    "black",  # function signature formatting
-    "livereload",
-    "openneuro-py >= 2022.2.0",
-    "httpx >= 0.20",
-    "tqdm",
-    "Pygments",
-    "pyyaml",
+  "pytest",
+  "pytest-cov",
+  "pooch",
+  "psutil",
+  "datalad",
+  "ruff",
+  "mkdocs",
+  "mkdocs-material >= 9.0.4",
+  "mkdocs-material-extensions",
+  "mkdocs-macros-plugin",
+  "mkdocs-include-markdown-plugin",
+  "mkdocs-exclude",
+  "mkdocstrings-python",
+  "mike",
+  "jinja2",
+  "black",                          # function signature formatting
+  "livereload",
+  "openneuro-py >= 2022.2.0",
+  "httpx >= 0.20",
+  "tqdm",
+  "Pygments",
+  "pyyaml",
 ]
 
 [project.scripts]
@@ -84,19 +85,22 @@ homepage = "https://mne.tools/mne-bids-pipeline"
 repository = "https://github.com/mne-tools/mne-bids-pipeline"
 changelog = "http://mne.tools/mne-bids-pipeline/changes.html"
 
-[build-system]
-requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools_scm]
-tag_regex = "^(?P<prefix>v)?(?P<version>[0-9.]+)(?P<suffix>.*)?$"
-version_scheme = "release-branch-semver"
+[tool.hatch.version]
+source = "vcs"
+raw-options = { version_scheme = "release-branch-semver" }
 
-[tool.setuptools.packages.find]
-exclude = ["false"]  # on CircleCI this folder appears during pip install -ve. for an unknown reason
-
-[tool.setuptools.package-data]
-"mne_bids_pipeline.steps.freesurfer.contrib" = ["version"]
+[tool.hatch.build]
+exclude = [
+  "/.*",
+  "/codecov.yml",
+  "**/tests",
+  "/docs",
+  "/docs/source/examples/gen_examples.py", # specify explicitly because its exclusion is negated in .gitignore
+  "/Makefile",
+  "/BUILDING.md",
+  "/CONTRIBUTING.md",
+  "ignore_words.txt",
+]
 
 [tool.codespell]
 skip = "docs/site/*,*.html,steps/freesurfer/contrib/*"
@@ -109,13 +113,11 @@ count = ""
 
 [tool.pytest.ini_options]
 addopts = "-ra -vv --tb=short --cov=mne_bids_pipeline --cov-report= --junit-xml=junit-results.xml --durations=10"
-testpaths = [
-    "mne_bids_pipeline",
-]
+testpaths = ["mne_bids_pipeline"]
 junit_family = "xunit2"
 
 [tool.ruff]
-exclude = ["**/freesurfer/contrib", "dist/" , "build/"]
+exclude = ["**/freesurfer/contrib", "dist/", "build/"]
 
 [tool.black]
 exclude = "(.*/freesurfer/contrib/.*)|(dist/)|(build/)"