Merge pull request Remi-Gau#41 from Remi-Gau/maint

[MAINT] general maintencance updates

.github/dependabot.yml

@@ -1,13 +1,14 @@
+---
 # Documentation
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
 updates:
-  - package-ecosystem: 'github-actions'
-    directory: '/'
+-   package-ecosystem: github-actions
+    directory: /
     schedule:
-      interval: 'monthly'
+        interval: monthly
 
-  - package-ecosystem: 'gitsubmodule'
-    directory: '/'
+-   package-ecosystem: gitsubmodule
+    directory: /
     schedule:
-      interval: 'monthly'
+        interval: monthly

.github/workflows/test_and_coverage.yml

@@ -1,43 +1,46 @@
+---
 name: Test and coverage
 
 on:
-  push:
-    branches: [ master, main, dev ]
-  pull_request:
-    branches: [ master, main, dev ]
+    push:
+        branches: [master, main, dev]
+    pull_request:
+        branches: [master, main, dev]
 
 jobs:
-  build:
-
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [macos-latest, ubuntu-20.04]
-        python-version: ['3.8', '3.9', '3.10']
-
-    steps:
-
-    - name: Clone repo
-      uses: actions/checkout@v4
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools
-        pip install -r requirements.txt
-
-    - name: Run tests and generate coverage report
-      run: pytest --cov=./ --cov-report=xml
-
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-umbrella
-        fail_ci_if_error: true
-        verbose: true
+    build:
+
+        runs-on: ${{ matrix.os }}
+        strategy:
+            matrix:
+                os: [macos-latest, ubuntu-latest]
+                python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+            fail-fast: false # Don't cancel all jobs if one fails
+
+        steps:
+
+        -   name: Clone repo
+            uses: actions/checkout@v4
+
+        -   name: Set up Python ${{ matrix.python-version }}
+            uses: actions/setup-python@v5
+            with:
+                python-version: ${{ matrix.python-version }}
+
+        -   name: Install dependencies
+            run: |
+                python -m pip install --upgrade pip setuptools
+                pip install -r requirements.txt
+
+        -   name: Run tests and generate coverage report
+            run: pytest --cov=./ --cov-report=xml
+
+        -   name: Upload coverage to Codecov
+            uses: codecov/codecov-action@v4
+            with:
+                file: ./coverage.xml
+                flags: unittests
+                name: codecov-umbrella
+                token: ${{ secrets.CODECOV_TOKEN }}
+                fail_ci_if_error: false
+                verbose: true

.pre-commit-config.yaml

@@ -1,26 +1,33 @@
+---
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0pre-commit.ci] pre-commit autoupdate)
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
     hooks:
-      - id: trailing-whitespace
-      - id: check-yaml
-      - id: check-added-large-files
-      - id: end-of-file-fixer
+    -   id: trailing-whitespace
+    -   id: check-yaml
+    -   id: check-added-large-files
+    -   id: end-of-file-fixer
 
-  - repo: https://github.com/psf/black
+-   repo: https://github.com/psf/black
 
-    rev: 22.10.0[pre-commit.ci] pre-commit autoupdate)
+    rev: 24.1.1
     hooks:
-      - id: black
+    -   id: black
 
-  - repo: https://github.com/ikamensh/flynt/
-    rev: "0.76"
+-   repo: https://github.com/ikamensh/flynt/
+    rev: 1.0.1
     hooks:
-      - id: flynt
+    -   id: flynt
 
-  - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.9.0
+-   repo: https://github.com/asottile/reorder_python_imports
+    rev: v3.12.0
     hooks:
-      - id: reorder-python-imports
+    -   id: reorder-python-imports
+
+-   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+    rev: 0.2.3
+    hooks:
+    -   id: yamlfmt
+        args: [--mapping, '4', --sequence, '4', --offset, '0']

bidsNighres/segment.py

@@ -70,7 +70,6 @@ def skullstrip(layout_in, layout_out, this_participant, bids_filter: dict):
             output_dir=output_dir,
         )
 
-
         bidsify_skullstrip_output(
             skullstrip_output,
             layout_in=layout_in,