Merge branch 'Inria-Empenn:main' into O21U_repro_2

Author: bclenet

.github/workflows/code_quality.yml

@@ -25,14 +25,14 @@ jobs:
     # Steps that define the job
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}
@@ -50,7 +50,7 @@ jobs:
         pylint --fail-under 8 tests > pylint_report_tests.txt
 
     - name: Archive pylint results
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: failure() # Only if previous step failed
       with:
         name: pylint-reports-python

.github/workflows/codespell.yml

@@ -17,6 +17,6 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2

.github/workflows/pipeline_status.yml

@@ -22,22 +22,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout main branch
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: main
 
     - name: Checkout wiki
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: ${{github.repository}}.wiki
         path: wiki
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}

.github/workflows/pipeline_tests.yml

@@ -20,7 +20,7 @@ jobs:
       tests: ${{ steps.identify.outputs.tests }}
     steps:
     - name: Checkout current branch
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -54,7 +54,7 @@ jobs:
     timeout-minutes: 2880 # 48h
     steps:
     - name: Checkout PR branch
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Load configuration for self-hosted runner
       run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
@@ -75,7 +75,7 @@ jobs:
 
     - name: Archive pipeline execution failures
       if: ${{ failure() }} # Run only if previous job fails
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: pipeline_tests-reports
         path: |

.github/workflows/test_changes.yml

@@ -19,7 +19,7 @@ jobs:
       tests: ${{ steps.identify.outputs.tests }}
     steps:
     - name: Checkout main branch for comparison
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -45,7 +45,7 @@ jobs:
     timeout-minutes: 2880 # 48h
     steps:
     - name: Checkout PR branch
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Load configuration for self-hosted runner
       run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml

.github/workflows/unit_tests.yml

@@ -30,7 +30,7 @@ jobs:
     # Steps that define the job
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Load configuration for self-hosted runner
       run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
@@ -48,7 +48,7 @@ jobs:
 
     - name: Archive pytest results
       if: ${{ failure() }} # Run only if previous job fails
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: unit_tests-reports
         path: |

docs/core.md

@@ -124,6 +124,17 @@ This module contains a set of functions dedicated to computations on images.
 # Get dimensions of voxels along x, y, and z in mm (returns e.g.: [1.0, 1.0, 1.0]).
 get_voxel_dimensions('/path/to/the/image.nii.gz')
 ```
+
+ * `get_image_timepoint` : extracts the 3D volume in a given time point range from a 4D Nifti image
+
+```python
+# Create a nifti 3D file containing time point 5 of the input image (returns a path to the generated 3D image)
+get_image_timepoints('/path/to/the/image.nii.gz', 5, 5):
+
+# Create a nifti 3D file containing time points 5 to 10 of the input image (returns a path to the generated 3D image)
+get_image_timepoints('/path/to/the/image.nii.gz', 5, 10):
+```
+
 ## narps_open.core.interfaces
 
 This module contains a set of interface creators inheriting form the `narps_open.core.interfaces.InterfaceCreator` abstract class.

docs/data.md

@@ -88,6 +88,7 @@ narps_results -h
                             a list of team IDs
       -a, --all             download results from all teams
       -r, --rectify         rectify the results
+      --config CONFIG       custom configuration file to be used
 
 # Either download all collections
 narps_results -a

docs/description.md

@@ -28,6 +28,7 @@ narps_description -h
 #                         the sub dictionary of team description
 #  --json                output team description as JSON
 #  --md                  output team description as Markdown
+#  --config CONFIG       custom configuration file to be used
 
 narps_description -t 2T6S --json
 # {

docs/running.md

@@ -30,6 +30,7 @@ narps_open_runner -h
 	                        the analysis levels to run (p=preprocessing, r=run, s=subject, g=group)
 	  -c, --check           check pipeline outputs (runner is not launched)
 	  -e, --exclusions      run the analyses without the excluded subjects
+	  --config CONFIG       custom configuration file to be used
 
 narps_open_runner -t 2T6S -s 001 006 020 100 # Launches the full pipeline on the given subjects
 narps_open_runner -t 2T6S -r 4 # Launches the full pipeline on 4 random subjects