[DOC] Adding automatic pages with --help of scripts

docs/.readthedocs.yaml

@@ -6,11 +6,19 @@
 version: 2
 
 # Set the version of Python and other tools you might need
+# Note. pre-build jobs requires dwi_ml to be installed but ok; the python
+# install section is launched before the pre-build.
 build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
 
+  jobs:
+    pre_build:
+      - pip install --upgrade pip setuptools wheel
+      - pip install .
+      - bash docs/build_automatic_help_docs.sh
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py

docs/automatic_doc/index_automatic.rst

@@ -0,0 +1,31 @@
+Scripts
+=======
+
+.. toctree::
+    :caption: Scripts (--help)
+
+    ae_train_model_help
+    dwiml_compute_connectivity_matrix_from_blocs_help
+    dwiml_compute_connectivity_matrix_from_labels_help
+    dwiml_compute_connectivity_score_help
+    dwiml_create_hdf5_dataset_help
+    dwiml_divide_volume_into_blocs_help
+    dwiml_hdf5_extract_data_help
+    dwiml_hdf5_print_architecture_help
+    dwiml_send_value_to_comet_from_log_help
+    dwiml_send_value_to_comet_manually_help
+    dwiml_visualize_logs_correlation_help
+    dwiml_visualize_logs_help
+    dwiml_visualize_noise_on_streamlines_help
+    l2t_resume_training_from_checkpoint_help
+    l2t_track_from_model_help
+    l2t_train_model_help
+    l2t_update_deprecated_exp_help
+    l2t_visualize_loss_help
+    l2t_visualize_weights_evolution_help
+    tt_resume_training_from_checkpoint_help
+    tt_track_from_model_help
+    tt_train_model_help
+    tt_update_deprecated_exp_help
+    tt_visualize_loss_help
+    tt_visualize_weights_help

docs/build_automatic_help_docs.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+# This generates the automatic pages with the --help
+# This is added in
+
+index_page=docs/automatic_doc/index_automatic.rst
+
+# Preparing the toctree
+if [ -f $index_page ]
+then
+    rm $index_page
+fi
+{
+  echo "Scripts"
+  echo "======="
+  echo " "
+  echo ".. toctree::"
+  echo "    :caption: Scripts (--help)"
+  echo " "
+} > $index_page
+
+
+for script in src/dwi_ml/cli/*.py;
+do
+    script_name=$(basename $script)
+    script_name=${script_name%.py}
+
+    if [ $script_name != '__init__' ]
+    then
+      echo "Preparing help page for script $script_name"
+
+      # Prepare help file
+      outfile="docs/automatic_doc/${script_name}_help.rst"
+      if [ -f $outfile ]
+      then
+          rm $outfile
+      fi
+      {
+        echo $script_name
+        echo "========================================================="
+        echo ""
+        echo ".. code-block:: text"
+        echo ""
+        $script_name --help | sed 's/^/    /'
+      } > $outfile
+
+      # Add file to toctree
+      echo "    ${script_name}_help" >> $index_page
+    fi
+done

docs/index.rst

@@ -113,6 +113,8 @@ Page in this section explain more in details how the code is implemented in pyth
     - :ref:`tracking`
 
 
+.. --------------------Hidden toctree: For developers---------------
+
 .. toctree::
     :maxdepth: 3
     :caption: Explanations for developers
@@ -122,4 +124,14 @@ Page in this section explain more in details how the code is implemented in pyth
     for_developers/hdf5/advanced_hdf5_organization
     for_developers/training/training
     for_developers/data_management/index
-    for_developers/testing/tracking_objects
+    for_developers/testing/tracking_objects
+
+
+.. --------------------Hidden toctree: scripts ---------------
+
+.. toctree::
+    :maxdepth: 2
+    :caption: Scripts (--help)
+    :hidden:
+
+    automatic_doc/index_automatic.rst