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

.github/workflows/run_precommit.yml

@@ -11,4 +11,4 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
-    - uses: pre-commit/[email protected].0
+    - uses: pre-commit/[email protected].1

.github/workflows/test.yml

@@ -46,7 +46,7 @@ jobs:
     - uses: actions/setup-python@v5
     - name: install tox
       run: pip install tox
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       id: cache
       env:
         cache-name: ds000017
@@ -136,7 +136,7 @@ jobs:
 
     - name: Restore cached data ds000017
       id: cache
-      uses: actions/cache/restore@v3
+      uses: actions/cache/restore@v4
       with:
         path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
         key: ds000017
@@ -155,7 +155,7 @@ jobs:
       if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} || ${{ github.event.pull_request.merged }}
       run: pytest --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome
 
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
       if: ${{ always() }}
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -176,7 +176,7 @@ jobs:
 
       - name: Restore cached data ds000017
         id: cache
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
           key: ds000017

.github/workflows/update_precommit_hooks.yml

@@ -43,7 +43,7 @@ jobs:
         -   name: Update pre-commit hooks
             run: pre-commit autoupdate
         -   name: Create Pull Request
-            uses: peter-evans/create-pull-request@v5
+            uses: peter-evans/create-pull-request@v6
             with:
                 commit-message: pre-commit hooks auto-update
                 base: main

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.3.0
     hooks:
     -   id: black
 -   repo: https://github.com/codespell-project/codespell

giga_connectome/logger.py

@@ -1,4 +1,5 @@
 """General logger for the cohort_creator package."""
+
 from __future__ import annotations
 
 import logging

giga_connectome/methods.py

@@ -39,9 +39,9 @@ def generate_method_section(
         "atlas": atlas,
         "smoothing_fwhm": smoothing_fwhm,
         "strategy": strategy,
-        "standardize": "percent signal change"
-        if standardize == "psc"
-        else standardize,
+        "standardize": (
+            "percent signal change" if standardize == "psc" else standardize
+        ),
         "mni_space": mni_space,
         "average_correlation": average_correlation,
         "analysis_level": analysis_level,

giga_connectome/tests/test_cli.py

@@ -1,6 +1,7 @@
 """
 Simple code to smoke test the functionality.
 """
+
 from pathlib import Path
 from pkg_resources import resource_filename
 from giga_connectome.run import main

giga_connectome/utils.py

@@ -101,9 +101,11 @@ def _filter_pybids_none_any(dct: dict) -> dict:
     import bids
 
     return {
-        k: bids.layout.Query.NONE
-        if v is None
-        else (bids.layout.Query.ANY if v == "*" else v)
+        k: (
+            bids.layout.Query.NONE
+            if v is None
+            else (bids.layout.Query.ANY if v == "*" else v)
+        )
         for k, v in dct.items()
     }
 

giga_connectome/workflow.py

@@ -1,6 +1,7 @@
 """
 Process fMRIPrep outputs to timeseries based on denoising strategy.
 """
+
 from __future__ import annotations
 
 from giga_connectome import (

tools/download_templates.py

@@ -2,6 +2,7 @@
 Set up templateflow with customised altases.
 Download atlases that are relevant.
 """
+
 from pathlib import Path
 
 from giga_connectome.logger import gc_logger