From 7adb57f565c6f67f352f64e517a7ea8b3d83bd43 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Cl=C3=A9net?= <boris.clenet@inria.fr>
Date: Wed, 10 Jan 2024 14:02:26 +0100
Subject: [PATCH] [DOC] command line tools

---
 INSTALL.md          | 26 ++++++++++++++++++++++----
 docs/data.md        |  2 +-
 docs/description.md |  2 +-
 docs/running.md     |  4 ++--
 docs/status.md      |  2 +-
 5 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/INSTALL.md b/INSTALL.md
index 3d78cd3b..872e0b44 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -74,12 +74,30 @@ cd /home/neuro/code/
 pip install .
 ```
 
-Finally, you are able to run pipelines :
+Finally, you are able to use the scripts of the project :
+
+* `narps_open_runner`: run pipelines
+* `narps_description`: get the textual description made by a team
+* `narps_results`: download the original results from teams
+* `narps_open_status`: get status information about the development process of the pipelines
 
 ```bash
-python narps_open/runner.py
-  usage: runner.py [-h] -t TEAM (-r RSUBJECTS | -s SUBJECTS [SUBJECTS ...] | -n NSUBJECTS) [-g | -f] [-c]
+# Run the pipeline for team 2T6S, with 40 subjects
+narps_open_runner -t 2T6S -n 40
+
+# Get the description of team C88N in markdown formatting
+narps_description -t C88N --md
+
+# Download the results from all teams
+narps_results -a
+
+#  Get the pipeline work status information in json formatting
+narps_open_status --json
 ```
 
 > [!NOTE]  
-> For further information, read this documentation page [docs/running.md](docs/running.md).
+> For further information about these command line tools, read the corresponding documentation pages.
+> * `narps_open_runner` : [docs/running.md](docs/running.md)
+> * `narps_description` : [docs/description.md](docs/description.md)
+> * `narps_results` : [docs/data.md](docs/data.md)
+> * `narps_open_status` : [docs/status.md](docs/status.md)
diff --git a/docs/data.md b/docs/data.md
index 3471729a..3a68b32e 100644
--- a/docs/data.md
+++ b/docs/data.md
@@ -67,7 +67,7 @@ for team in teams:
     collection.rectify() # Rectified versions are created
 ```
 
-> [! TIP]
+> [!TIP]
 > In the following examples, use `narps_results` or `python narps_open/data/results` indifferently to launch the command line tool.
 
 ```bash
diff --git a/docs/description.md b/docs/description.md
index 1723f64f..82f78097 100644
--- a/docs/description.md
+++ b/docs/description.md
@@ -12,7 +12,7 @@ The class `TeamDescription` of module `narps_open.data.description` acts as a pa
 
 You can use the command-line tool as so. Option `-t` is for the team id, option `-d` allows to print only one of the sub parts of the description among : `general`, `exclusions`, `preprocessing`, `analysis`, `categorized_for_analysis`, `derived`, and `comments`. Options `--json` and `--md` allow to choose the export format you prefer between JSON and Markdown.
 
-> [! TIP]
+> [!TIP]
 > In the following examples, use `narps_description` or `python narps_open/data/description` indifferently to launch the command line tool.
 
 ```bash
diff --git a/docs/running.md b/docs/running.md
index edf94171..b2f7da77 100644
--- a/docs/running.md
+++ b/docs/running.md
@@ -4,7 +4,7 @@
 
 The `narps_open.runner` module allows to run pipelines from the command line.
 
-> [! TIP]
+> [!TIP]
 > In the following examples, use `narps_open_runner` or `python narps_open/runner.py` indifferently to launch the command line tool.
 
 ```bash
@@ -28,7 +28,7 @@ narps_open_runner -t 2T6S -r 4 -f
 narps_open_runner -t 2T6S -r 4 -f -c # Check the output files without launching the runner
 ```
 
-> [! NOTE]
+> [!NOTE]
 > In this usecase, the paths where to store the outputs and to the dataset are picked by the runner from the [configuration](docs/configuration.md).
 
 ## Using the `PipelineRunner` object
diff --git a/docs/status.md b/docs/status.md
index 8ffc7beb..d461b1ea 100644
--- a/docs/status.md
+++ b/docs/status.md
@@ -46,7 +46,7 @@ report.markdown() # Returns a string containing the markdown
 
 You can also use the command-line tool as so.
 
-> [! TIP]
+> [!TIP]
 > In the following examples, use `narps_open_status` or `python narps_open/utils/status.py` indifferently to launch the command line tool.
 
 ```bash