Merge branch 'master' into master

Author: effigies

.flake8

@@ -0,0 +1,9 @@
+[flake8]
+max-line-length = 100
+extend-ignore = E203,E266,E402,E731
+exclude =
+    *test*
+    *sphinx*
+    nibabel/externals/*
+per-file-ignores =
+    */__init__.py: F401

.git-blame-ignore-revs

@@ -0,0 +1,14 @@
+# Sun Jan 1 12:38:02 2023 -0500 - [email protected] - STY: Run pre-commit config on all files
+d14c1cf282a9c3b19189f490f10c35f5739e24d1
+# Thu Dec 29 22:53:17 2022 -0500 - [email protected] - STY: Reduce array().astype() and similar constructs
+bf298113da99079c9c7b5e1690e41879828cd472
+# Thu Dec 29 22:32:46 2022 -0500 - [email protected] - STY: pyupgrade --py37-plus
+4481a4c2640bd4be6e9c468e550d01aae448ab99
+# Fri Dec 30 11:01:19 2022 -0500 - [email protected] - STY: Run vanilla blue
+6b0ddd23b1da1df7ca9ae275673f82bfa20a754c
+# Thu Dec 29 21:46:13 2022 -0500 - [email protected] - STY: Manual, blue-compatible touchups
+263fca9bf6d4ca314a5a322b4824d6f53d0589df
+# Thu Dec 29 21:32:00 2022 -0500 - [email protected] - STY: isort
+0ab2856cac4d4baae7ab3e2f6d58421db55d807f
+# Thu Dec 29 21:30:29 2022 -0500 - [email protected] - STY: blue
+1a8dd302ff85b1136c81d492509b80e7748339f0

.git_archival.txt

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

.gitattributes

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

.github/workflows/misc.yml

@@ -24,7 +24,7 @@ jobs:
       matrix:
         python-version: ["3.10"]
         install: ['pip']
-        check: ['style', 'doc']
+        check: ['style', 'doctest', 'typing']
         pip-flags: ['']
         depends: ['REQUIREMENTS']
     env:
@@ -59,9 +59,6 @@ jobs:
       - name: Run tests
         run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - name: Submit coverage
-        run: tools/ci/submit_coverage.sh
-        if: ${{ always() }}
       - name: Upload pytest test results
         uses: actions/upload-artifact@v3
         with:

.github/workflows/pre-release.yml

@@ -18,6 +18,13 @@ defaults:
   run:
     shell: bash
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
 jobs:
   pre-release:
     # Check pre-releases of dependencies on stable Python
@@ -26,7 +33,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         architecture: ['x64', 'x86']
         install: ['pip']
         check: ['test']
@@ -36,7 +43,7 @@ jobs:
         include:
           # Pydicom master
           - os: ubuntu-latest
-            python-version: "3.10"
+            python-version: "3.11"
             install: pip
             check: test
             pip-flags: ''
@@ -80,9 +87,10 @@ jobs:
       - name: Run tests
         run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - name: Submit coverage
-        run: tools/ci/submit_coverage.sh
+      - uses: codecov/codecov-action@v3
         if: ${{ always() }}
+        with:
+          files: cov.xml
       - name: Upload pytest test results
         uses: actions/upload-artifact@v3
         with:

.github/workflows/stable.yml

@@ -24,6 +24,13 @@ defaults:
   run:
     shell: bash
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -39,11 +46,17 @@ jobs:
         run: python -m build
       - run: twine check dist/*
       - name: Build git archive
-        run: git archive -v -o dist/nibabel-archive.tgz HEAD
-      - uses: actions/upload-artifact@v3
+        run: mkdir archive && git archive -v -o archive/nibabel-archive.tgz HEAD
+      - name: Upload sdist and wheel artifacts
+        uses: actions/upload-artifact@v3
         with:
           name: dist
           path: dist/
+      - name: Upload git archive artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: archive
+          path: archive/
 
   test-package:
     runs-on: ubuntu-latest
@@ -52,10 +65,18 @@ jobs:
       matrix:
         package: ['wheel', 'sdist', 'archive']
     steps:
-      - uses: actions/download-artifact@v3
+      - name: Download sdist and wheel artifacts
+        if: matrix.package != 'archive'
+        uses: actions/download-artifact@v3
         with:
           name: dist
           path: dist/
+      - name: Download git archive artifact
+        if: matrix.package == 'archive'
+        uses: actions/download-artifact@v3
+        with:
+          name: archive
+          path: archive/
       - uses: actions/setup-python@v4
         with:
           python-version: 3
@@ -64,14 +85,14 @@ jobs:
       - name: Update pip
         run: pip install --upgrade pip
       - name: Install wheel
-        run: pip install dist/nibabel-*.whl
         if: matrix.package == 'wheel'
+        run: pip install dist/nibabel-*.whl
       - name: Install sdist
-        run: pip install dist/nibabel-*.tar.gz
         if: matrix.package == 'sdist'
+        run: pip install dist/nibabel-*.tar.gz
       - name: Install archive
-        run: pip install dist/nibabel-archive.tgz
         if: matrix.package == 'archive'
+        run: pip install archive/nibabel-archive.tgz
       - run: python -c 'import nibabel; print(nibabel.__version__)'
       - name: Install test extras
         run: pip install nibabel[test]
@@ -84,7 +105,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
         architecture: ['x64', 'x86']
         install: ['pip']
         check: ['test']
@@ -94,31 +115,31 @@ jobs:
         include:
           # Basic dependencies only
           - os: ubuntu-latest
-            python-version: 3.7
+            python-version: 3.8
             install: pip
             check: test
             pip-flags: ''
             depends: REQUIREMENTS
             optional-depends: ''
           # Absolute minimum dependencies
           - os: ubuntu-latest
-            python-version: 3.7
+            python-version: 3.8
             install: pip
             check: test
             pip-flags: ''
             depends: MIN_REQUIREMENTS
             optional-depends: ''
           # Absolute minimum dependencies plus old MPL, Pydicom, Pillow
           - os: ubuntu-latest
-            python-version: 3.7
+            python-version: 3.8
             install: pip
             check: test
             pip-flags: ''
             depends: MIN_REQUIREMENTS
             optional-depends: MIN_OPT_DEPENDS
           # Clean install imports only with package-declared dependencies
           - os: ubuntu-latest
-            python-version: 3.7
+            python-version: 3.8
             install: pip
             check: skiptests
             pip-flags: ''
@@ -158,17 +179,18 @@ jobs:
       - name: Install NiBabel
         run: tools/ci/install.sh
       - name: Run tests
-        run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - name: Submit coverage
-        run: tools/ci/submit_coverage.sh
+        run: tools/ci/check.sh
+      - uses: codecov/codecov-action@v3
         if: ${{ always() }}
+        with:
+          files: cov.xml
       - name: Upload pytest test results
+        if: ${{ always() && matrix.check == 'test' }}
         uses: actions/upload-artifact@v3
         with:
           name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
           path: for_testing/test-results.xml
-        if: ${{ always() && matrix.check == 'test' }}
 
   publish:
     runs-on: ubuntu-latest

.gitignore

@@ -1,3 +1,6 @@
+# See also nibabel/.gitignore for test data rules that
+# are meant to make you think before you `git add --force`
+
 # Editor temporary/working/backup files #
 #########################################
 .#*
@@ -36,23 +39,6 @@
 *.py[oc]
 *.so
 
-# Packages #
-############
-# it's better to unpack these files and commit the raw source
-# git has its own built in compression methods
-*.7z
-*.bz2
-*.bzip2
-*.dmg
-*.gz
-*.iso
-*.jar
-*.rar
-*.tar
-*.tbz2
-*.tgz
-*.zip
-
 # Python files #
 ################
 build/
@@ -65,12 +51,14 @@ dist/
 .coverage
 .ropeproject/
 htmlcov/
+.*_cache/
 
 # Logs and databases #
 ######################
 *.log
 *.sql
 *.sqlite
+*.sqlite3
 
 # OS generated files #
 ######################
@@ -83,7 +71,12 @@ Thumbs.db
 # Things specific to this project #
 ###################################
 doc/source/reference
+doc/source/generated
 venv/
 .buildbot.patch
 .vscode
 for_testing/
+
+# Generated by setuptools_scm #
+###############################
+_version.py

.mailmap

@@ -30,6 +30,7 @@ Dimitri Papadopoulos Orfanos <[email protected]> <DimitriPapadopoulos@
 Dimitri Papadopoulos Orfanos <[email protected]> <[email protected]>
 Eric Larson <[email protected]> Eric89GXL <[email protected]>
 Eric Larson <[email protected]> larsoner <[email protected]>
+Fabian Perez <[email protected]>
 Fernando Pérez-García <[email protected]> Fernando <[email protected]>
 Félix C. Morency <[email protected]> Felix C. Morency <[email protected]>
 Félix C. Morency <[email protected]> Félix C. Morency <[email protected]>

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+exclude: ".*/data/.*"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-vcs-permalinks
+  - repo: https://github.com/grantjenks/blue
+    rev: v0.9.1
+    hooks:
+      - id: blue
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        exclude: "^(doc|nisext|tools)/"
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.991
+    hooks:
+      - id: mypy
+        # Sync with project.optional-dependencies.typing
+        additional_dependencies:
+          - pytest
+          - types-setuptools
+          - types-Pillow
+          - pydicom
+          - numpy
+          - pyzstd
+          - importlib_resources
+        args: ["nibabel"]
+        pass_filenames: false