[DOC] list of available team ids in command tools documentation

README.md

@@ -50,11 +50,11 @@ This project is supported by Région Bretagne (Boost MIND) and by Inria (Explora
 
 ## Credits
 
-This project is developed in the Empenn team by Boris Clenet, Elodie Germani, Jeremy Lefort-Besnard and Camille Maumet with contributions by Rémi Gau.
+This project is developed in the Empenn team by Boris Clénet, Elodie Germani, Jeremy Lefort-Besnard and Camille Maumet with contributions by Rémi Gau.
 
 In addition, this project was presented and received contributions during the following events:
- - [OHBM Brainhack 2022](https://ohbm.github.io/hackathon2022/) (June 2022): Elodie Germani, Arshitha Basavaraj, Trang Cao, Rémi Gau, Anna Menacher, Camille Maumet.
- - [e-ReproNim FENS NENS Cluster Brainhack](https://repro.school/2023-e-repronim-brainhack/) (June 2023) : Liz Bushby, Boris Clénet, Michael Dayan, Aimee Westbrook.
- - [OHBM Brainhack 2023](https://ohbm.github.io/hackathon2023/) (July 2023): Arshitha Basavaraj, Boris Clénet, Rémi Gau, Élodie Germani, Yaroslav Halchenko, Camille Maumet, Paul Taylor.
- - [ORIGAMI lab](https://neurodatascience.github.io/) hackathon (September 2023): 
  - [Brainhack Marseille 2023](https://brainhack-marseille.github.io/) (December 2023): 
+ - [ORIGAMI lab](https://neurodatascience.github.io/) hackathon (September 2023): 
+ - [OHBM Brainhack 2023](https://ohbm.github.io/hackathon2023/) (July 2023): Arshitha Basavaraj, Boris Clénet, Rémi Gau, Élodie Germani, Yaroslav Halchenko, Camille Maumet, Paul Taylor.
+ - [e-ReproNim FENS NENS Cluster Brainhack](https://repro.school/2023-e-repronim-brainhack/) (June 2023) : Liz Bushby, Boris Clénet, Michael Dayan, Aimee Westbrook.
+ - [OHBM Brainhack 2022](https://ohbm.github.io/hackathon2022/) (June 2022): Elodie Germani, Arshitha Basavaraj, Trang Cao, Rémi Gau, Anna Menacher, Camille Maumet.

narps_open/data/description/__main__.py

@@ -7,14 +7,15 @@
 from json import dumps
 
 from narps_open.data.description import TeamDescription
+from narps_open.pipelines import implemented_pipelines
 
 def main():
     """ Entry-point for the command line tool narps_description """
 
     # Parse arguments
     parser = ArgumentParser(description='Get description of a NARPS pipeline.')
     parser.add_argument('-t', '--team', type=str, required=True,
-        help='the team ID')
+        help='the team ID', choices=implemented_pipelines.keys())
     parser.add_argument('-d', '--dictionary', type=str, required=False,
         choices=[
             'general',

narps_open/data/results/__main__.py

@@ -8,15 +8,14 @@
 from narps_open.data.results import ResultsCollectionFactory
 from narps_open.pipelines import implemented_pipelines
 
-
 def main():
     """ Entry-point for the command line tool narps_results """
 
     # Parse arguments
     parser = ArgumentParser(description='Get Neurovault collection of results from NARPS teams.')
     group = parser.add_mutually_exclusive_group(required = True)
     group.add_argument('-t', '--teams', nargs='+', type=str, action='extend',
-        help='a list of team IDs')
+        help='a list of team IDs', choices=implemented_pipelines.keys())
     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')

narps_open/pipelines/__main__.py

@@ -0,0 +1,30 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Provide a command-line interface for the package narps_open.pipelines """
+
+from argparse import ArgumentParser
+
+from narps_open.pipelines import get_implemented_pipelines
+
+def main():
+    """ Entry-point for the command line tool narps_open_pipeline """
+
+    # Parse arguments
+    parser = ArgumentParser(description='Get description of a NARPS pipeline.')
+    parser.add_argument('-v', '--verbose', action='store_true',
+        help='verbose mode')
+    arguments = parser.parse_args()
+
+    # Print header
+    print('NARPS Open Pipelines')
+
+    # Print general information about NARS Open Pipelines
+    print('A codebase reproducing the 70 pipelines of the NARPS study (Botvinik-Nezer et al., 2020) shared as an open resource for the community.')
+
+    # Print pipelines
+    implemented_pipelines = get_implemented_pipelines()
+    print(f'There are currently {len(implemented_pipelines)} implemented pipelines: {implemented_pipelines}')
+
+if __name__ == '__main__':
+    main()

narps_open/tester.py

@@ -8,13 +8,15 @@
 
 import pytest
 
+from narps_open.pipelines import get_implemented_pipelines
+
 def main():
     """ Entry-point for the command line tool narps_open_tester """
 
     # Parse arguments
     parser = ArgumentParser(description='Test the pipelines from NARPS.')
     parser.add_argument('-t', '--team', type=str, required=True,
-        help='the team ID')
+        help='the team ID', choices=get_implemented_pipelines())
     arguments = parser.parse_args()
 
     sys.exit(pytest.main([