Documentation updates (Inria-Empenn#141)

* [BUG] inside unit_tests workflow

* [DOC] fix some broken links

* [DOC] adding template for pipeline testing

* [DOC] adding template for pipeline testing

* About implemented_pipelines

* Deal with test template

* [DOC] new readme for the doc

* Changes in README.md

* [DOC] slight changes to docs/README.md

* Add links to past events

* Changes in readme.md

* fMRI trail

* Adding trail description in contribution guide

* Separate trails in contribution guide

* [TEST] Solving pytest issues with template test

* Changing docker image in use

* FSL template correction

* [DOC] writing test files

* Codespell

* First step in writing documentation about NARPS

* [DOC] completing doc about narps

* [DOC] completing doc about narps

* [DOC] completing doc about narps

* [DATALAD] change results url

* [DOC] reference to the github project for reproduction mgmt

* [DOC] adding team id choices for narps open runner

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

* [DOC] configuration info inside INSTALL.md

* [DOC] configuration info inside INSTALL.md

* NARPS Exclusion comments

CONTRIBUTING.md

@@ -9,7 +9,7 @@ In the following, read the instruction sections where the badge corresponding to
 ## 1 - Choose a pipeline
 `🧠 fMRI soft` `🐍 Python`
 
-Not sure which pipeline to start with :thinking:? The [pipeline dashboard](https://github.com/Inria-Empenn/narps_open_pipelines/wiki/pipeline_status) provides the progress status for each pipeline. You can pick any pipeline that is not fully reproduced, i.e.: not started :red_circle: or in progress :orange_circle: .
+Not sure which pipeline to start with :thinking:? The [pipeline dashboard](https://github.com/Inria-Empenn/narps_open_pipelines/wiki/pipeline_status) provides the progress status for each pipeline. You can pick a pipeline that is not fully reproduced, i.e.: not started :red_circle: or in progress :orange_circle: . Also have a look to the [pipeline reproduction management page](https://github.com/orgs/Inria-Empenn/projects/1/views/1) in order to get in touch with contributors working on the same pipeline.
 
 > [!NOTE]
 > Need more information to make a decision? The `narps_open.utils.description` module of the project, as described [in the documentation](/docs/description.md) provides easy access to all the info we have on each pipeline.

INSTALL.md

@@ -66,6 +66,22 @@ Start a Docker container from the Docker image :
 docker run -it -v PATH_TO_THE_REPOSITORY:/home/neuro/code/ nipype/nipype
 ```
 
+Optionally edit the configuration file `narps_open/utils/default_config.toml` so that the referred paths match the ones inside the container. E.g.: if using the previous command line, the `directories` part of the configuration file should be :
+```toml
+# default_config.toml
+# ...
+
+[directories]
+dataset = "/home/neuro/code/data/original/ds001734/"
+reproduced_results = "/home/neuro/code/data/reproduced/"
+narps_results = "/home/neuro/code/data/results/"
+
+# ...
+```
+
+> [!NOTE]  
+> Further information about configuration files can be found on the page [docs/configuration.md](docs/configuration.md).
+
 Install NARPS Open Pipelines inside the container :
 
 ```bash

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/description/analysis_pipelines_comments.tsv

@@ -5,7 +5,7 @@ O21U	No	N/A	3
 U26C	No	N/A	4	Link to shared analysis code : https://github.com/gladomat/narps
 43FJ	No	N/A	2	
 C88N	No	N/A	3	
-4TQ6	Yes	Resampled image offset and too large compared to template.	3	
+4TQ6	No	Resampled image offset and too large compared to template.	3	
 T54A	No	N/A	3	
 2T6S	No	N/A	3	
 L7J7	No	N/A	3	
@@ -17,17 +17,17 @@ O6R6	No	N/A	3
 C22U	No	N/A	1	Custom Matlab script for white matter PCA confounds
 3PQ2	No	N/A	2	
 UK24	No	N/A	2	
-4SZ2	Yes	Resampled image offset from template brain.	3	
+4SZ2	No	Resampled image offset from template brain.	3	
 9T8E	No	N/A	3	
 94GU	No	N/A	1	Multiple software dependencies : SPM + ART + TAPAS + Matlab.
 I52Y	No	N/A	2	
 5G9K	Yes	Values in the unthresholded images are not z / t stats	3	
-2T7P	Yes	Missing thresholded images.	2	Link to shared analysis code : https://osf.io/3b57r
+2T7P	No	Missing thresholded images.	2	Link to shared analysis code : https://osf.io/3b57r
 UI76	No	N/A	3	
 B5I6	No	N/A	3	
-V55J	Yes	Bad histogram : very small values.	2	
+V55J	No	Bad histogram : very small values.	2	
 X19V	No	N/A	3	
-0C7Q	Yes	Appears to be a p-value distribution, with slight excursions below and above zero.	2	
+0C7Q	No	Appears to be a p-value distribution, with slight excursions below and above zero.	2	
 R5K7	No	N/A	2	
 0I4U	No	N/A	2	
 3C6G	No	N/A	2	
@@ -37,20 +37,20 @@ O03M	No	N/A	3
 80GC	No	N/A	3	
 J7F9	No	N/A	3	
 R7D1	No	N/A	3	Link to shared analysis code : https://github.com/IMTAltiStudiLucca/NARPS_R7D1
-Q58J	Yes	Bad histogram : bimodal, zero-inflated with a second distribution centered around 5.	3	Link to shared analysis code : https://github.com/amrka/NARPS_Q58J
-L3V8	Yes	Rejected due to large amount of missing brain in center.	2	
+Q58J	No	Bad histogram : bimodal, zero-inflated with a second distribution centered around 5.	3	Link to shared analysis code : https://github.com/amrka/NARPS_Q58J
+L3V8	No	Rejected due to large amount of missing brain in center.	2	
 SM54	No	N/A	3	
 1KB2	No	N/A	2	
-0H5E	Yes	Rejected due to large amount of missing brain in center.	2	
-P5F3	Yes	Rejected due to large amounts of missing data across brain.	2	
+0H5E	No	Rejected due to large amount of missing brain in center.	2	
+P5F3	No	Rejected due to large amounts of missing data across brain.	2	
 Q6O0	No	N/A	3	
 R42Q	No	N/A	2	Uses fMRIflows, a custom software based on NiPype. Code available here : https://github.com/ilkayisik/narps_R42Q
 L9G5	No	N/A	2	
 DC61	No	N/A	3	
-E3B6	Yes	Bad histogram : very long tail, with substantial inflation at a value just below zero.	4	Link to shared analysis code : doi.org/10.5281/zenodo.3518407
+E3B6	No	Bad histogram : very long tail, with substantial inflation at a value just below zero.	4	Link to shared analysis code : doi.org/10.5281/zenodo.3518407
 16IN	Yes	Values in the unthresholded images are not z / t stats	2	Multiple software dependencies : matlab + SPM + FSL + R + TExPosition + neuroim. Link to shared analysis code : https://github.com/jennyrieck/NARPS
 46CD	No	N/A	1	
-6FH5	Yes	Missing much of the central brain.	2	
+6FH5	No	Missing much of the central brain.	2	
 K9P0	No	N/A	3	
 9U7M	No	N/A	2	
 VG39	Yes	Performed small volume corrected instead of whole-brain analysis	3	
@@ -64,8 +64,8 @@ AO86	No	N/A	2
 L1A8	Yes	Not in MNI standard space.	2	
 IZ20	No	N/A	1	
 3TR7	No	N/A	3	
-98BT	Yes	Rejected due to very bad normalization.	2	
+98BT	No	Rejected due to very bad normalization.	2	
 XU70	No	N/A	1	Uses custom software : FSL + 4drealign
 0ED6	No	N/A	2	
-I07H	Yes	Bad histogram : bimodal, with second distribution centered around 2.5.	2	
+I07H	No	Bad histogram : bimodal, with second distribution centered around 2.5.	2	
 1P0Y	No	N/A	2	

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/runner.py

@@ -17,6 +17,7 @@
     get_participants_subset
     )
 from narps_open.utils.configuration import Configuration
+from narps_open.pipelines import get_implemented_pipelines
 
 class PipelineRunner():
     """ A class that allows to run a NARPS pipeline. """
@@ -158,7 +159,7 @@ def main():
     # Parse arguments
     parser = ArgumentParser(description='Run 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())
     subjects = parser.add_mutually_exclusive_group(required=True)
     subjects.add_argument('-s', '--subjects', nargs='+', type=str, action='extend',
         help='a list of subjects to be selected')

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([