Entry points accept configuration files at runtime (Inria-Empenn#240)

* Runner allows for configuration at runtime

* Other scripts allow for configuration at runtime

* Documentation update

* New actions versions

Author: bclenet

.github/workflows/code_quality.yml

@@ -25,10 +25,10 @@ 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
 
@@ -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

@@ -22,18 +22,18 @@ 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
 

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

docs/status.md

@@ -59,6 +59,7 @@ narps_open_status -h
 #   -h, --help  show this help message and exit
 #   --json      output the report as JSON
 #   --md        output the report as Markdown
+#   --config CONFIG  custom configuration file to be used
 
 narps_open_status --json
 # {

narps_open/data/description/__main__.py

@@ -30,8 +30,14 @@ def main():
     formats = parser.add_mutually_exclusive_group(required = False)
     formats.add_argument('--json', action='store_true', help='output team description as JSON')
     formats.add_argument('--md', action='store_true', help='output team description as Markdown')
+    parser.add_argument('--config', type=str, required=False,
+        help='custom configuration file to be used')
     arguments = parser.parse_args()
 
+    # Init configuration
+    if arguments.config:
+        Configuration('custom').config_file = arguments.config
+
     # Initialize a TeamDescription
     information = TeamDescription(team_id = arguments.team)
 

narps_open/data/results/__main__.py

@@ -19,8 +19,15 @@ def main():
     group.add_argument('-a', '--all', action='store_true', help='download results from all teams')
     parser.add_argument('-r', '--rectify', action='store_true', default = False, required = False,
         help='rectify the results')
+    parser.add_argument('--config', type=str, required=False,
+        help='custom configuration file to be used')
     arguments = parser.parse_args()
 
+    # Init configuration
+    if arguments.config:
+        Configuration('custom').config_file = arguments.config
+
+    # Start collecting result data
     factory = ResultsCollectionFactory()
 
     if arguments.all:

narps_open/runner.py

@@ -226,13 +226,19 @@ def main():
         help='check pipeline outputs (runner is not launched)')
     parser.add_argument('-e', '--exclusions', action='store_true', required=False,
         help='run the analyses without the excluded subjects')
+    parser.add_argument('--config', type=str, required=False,
+        help='custom configuration file to be used')
     arguments = parser.parse_args()
 
     # Check arguments
     if arguments.exclusions and not arguments.nsubjects:
         print('Argument -e/--exclusions only works with -n/--nsubjects')
         return
 
+    # Init configuration
+    if arguments.config:
+        Configuration('custom').config_file = arguments.config
+
     # Initialize a PipelineRunner
     runner = PipelineRunner(team_id = arguments.team)
     runner.pipeline.directories.dataset_dir = Configuration()['directories']['dataset']