[ENH] use sub commands for python CLI (#1292)

* start adding sub commands * preproc subcommand * deal with create roi parser * deal with default_model sub command * deal with bms action * deal with stats actions * start adapting cli * add test for command building * add test for CLI for preproc, smooth... * add test for command building for stats * add test for command building for bms * rename function * start switching CLI * several fixes * more fix * keep switchingµ * fix * fix * linti * fixes * fixes * minor fixes * additional fixes * fix output ROI * visualize output in circle ci
cpp-lln-lab · Jul 24, 2024 · f4b986f · f4b986f
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -113,10 +113,11 @@ jobs:
                           /bids_dataset \
                           /outputs/ds000001 \
                           subject \
-                          --action default_model \
+                          default_model \
                           --task balloonanalogrisktask \
                           --space MNI152NLin2009cAsym \
-                          --verbosity 3
+                          --verbosity 3 \
+                          --skip_validation
 
                     cat /home/circleci/outputs/ds000001/derivatives/models/*.json
 
@@ -130,10 +131,11 @@ jobs:
                           /bids_dataset \
                           /outputs/ds000001 \
                           dataset \
-                          --action default_model \
+                          default_model \
                           --task balloonanalogrisktask \
                           --space MNI152NLin2009cAsym \
-                          --verbosity 3
+                          --verbosity 3 \
+                          --skip_validation
 
                     cat /home/circleci/outputs/ds000001/derivatives/models/*.json
 
@@ -147,15 +149,17 @@ jobs:
                       -v /tmp/workspace/data/ds000001:/bids_dataset \
                       -v /home/circleci/outputs:/outputs \
                         << parameters.dh_orga >>/<< parameters.dh_repo >> \
-                          /outputs/ds000001 \
+                          /bids_dataset \
                           /outputs/ds000001 \
                           dataset \
-                          --action create_roi \
+                          create_roi \
                           --roi_atlas wang \
                           --roi_name V1v V1d \
                           --space IXI549Space \
                           --verbosity 3
 
+                    cat /home/circleci/outputs
+
         -   store_artifacts:
                 path: /home/circleci/outputs
 
@@ -190,7 +194,7 @@ jobs:
                           /bids_dataset \
                           /outputs/ds000001 \
                           subject \
-                          --action smooth \
+                          smooth \
                           --task balloonanalogrisktask \
                           --participant_label 01 02 \
                           --space MNI152NLin2009cAsym \
@@ -212,10 +216,9 @@ jobs:
                           /bids_dataset \
                           /outputs/ds000001 \
                           subject \
-                          --action stats \
+                          stats \
                           --preproc_dir /outputs/ds000001/derivatives/bidspm-preproc \
                           --model_file /models/model-balloonanalogrisktaskDefault_smdl.json \
-                          --ignore slicetiming \
                           --space MNI152NLin2009cAsym \
                           --skip_validation \
                           --fwhm 0 \
@@ -235,7 +238,7 @@ jobs:
                           /bids_dataset \
                           /outputs/ds000001 \
                           dataset \
-                          --action stats \
+                          stats \
                           --preproc_dir /outputs/ds000001/derivatives/bidspm-preproc \
                           --model_file /models/model-balloonanalogrisktaskDefault_smdl.json \
                           --space MNI152NLin2009cAsym \

diff --git a/.flake8 b/.flake8
@@ -1,6 +1,6 @@
 [flake8]
-max-line-length = 110
-max-complexity = 10
+max-line-length = 90
+max-complexity = 11
 ignore = F841, D100, D101, D103, D104
 exclude =
     *build

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -39,13 +39,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - allow inter session contrasts to be computed at the subject level
   - improve naming of contrast to mention bids ses and run
 
+* [ENH] add Bayesian model selection to the python CLI #1292 @Remi-Gau
 
 ### Changed
 
+
 * [ENH] align specification of F contrasts on the BIDS stats model: they should now be specified as a 2D matrix and not a 1D vector. #1276 @Remi-Gau
 * [DOC] change theme and structure of the documentation #1256 @Remi-Gau
 * [REF] Refactor and update CLI in #1096 @Remi-Gau
 * [ENH] {func}`getData` only loads anat data when requested #1257 @Remi-Gau
+* [ENH] the python CLI now uses sub-commands instead of the named parameter `--action` #1292 @Remi-Gau
 
 ### Deprecated
 

diff --git a/demos/MoAE/README.md b/demos/MoAE/README.md
@@ -19,7 +19,7 @@ bidspm \
     $PWD/inputs/raw \
     $PWD/outputs/derivatives \
     subject \
-    --action preprocess \
+    preprocess \
     --participant_label 01 \
     --space individual IXI549Space \
     --task auditory \
@@ -37,7 +37,7 @@ bidspm \
     $PWD/inputs/fmriprep \
     $PWD/outputs/derivatives \
     subject \
-    --action smooth \
+    smooth \
     --participant_label 01 \
     --space '^.*MNI.*$' \
     --task auditory \
@@ -52,7 +52,7 @@ bidspm \
     $PWD/inputs/raw \
     $PWD/outputs/derivatives \
      dataset \
-    --action default_model \
+    default_model \
     --space IXI549Space \
     --task auditory \
     --verbosity 2 \
@@ -66,7 +66,7 @@ bidspm \
     $PWD/inputs/raw \
     $PWD/outputs/derivatives \
     subject \
-    --action stats \
+    stats \
     --preproc_dir $PWD/outputs/derivatives/bidspm-preproc \
     --model_file $PWD/models/model-MoAE_smdl.json \
     --fwhm 6
@@ -77,7 +77,7 @@ bidspm \
     $PWD/inputs/raw \
     $PWD/outputs/derivatives \
     subject \
-    --action stats \
+    stats \
     --preproc_dir $PWD/outputs/derivatives/bidspm-preproc \
     --model_file $PWD/outputs/derivatives/models/model-defaultAuditory_smdl.json \
     --fwhm 6
@@ -96,7 +96,7 @@ docker run -it --rm \
         /derivatives \
         subject \
         --task auditory \
-        --action preprocess \
+        preprocess \
         --fwhm 8
 ```
 
@@ -111,7 +111,7 @@ docker run -it --rm \
         /raw \
         /derivatives \
         subject \
-        --action stats \
+        stats \
         --preproc_dir /derivatives/bidspm-preproc \
         --model_file /models/model-MoAE_smdl.json \
         --fwhm 6

diff --git a/demos/MoAE/test_moae.m b/demos/MoAE/test_moae.m
@@ -31,17 +31,18 @@
 
 optionsFile = fullfile(WD, 'options', 'options_task-auditory.json');
 
-space = {'individual'
+space = {
          'IXI549Space'
+         'individual'
          'IXI549Space'
          'individual'};
-ignore = {{'unwarp'}
-          {'unwarp', 'qa'}
+ignore = {{'unwarp', 'qa'}
+          {'unwarp'}
           {''}
           {''}};
-
-models = {fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')
+models = {
           fullfile(WD, 'models', 'model-MoAE_smdl.json')
+          fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')
           fullfile(WD, 'models', 'model-MoAE_smdl.json')
           fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')};
 
@@ -65,14 +66,16 @@
   %% stats
   preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 
-  % only specify the subject level model
-  bidspm(bids_dir, output_dir, 'subject', ...
-         'participant_label', {'01'}, ...
-         'action', 'stats', ...
-         'preproc_dir', preproc_dir, ...
-         'model_file', models{iOption}, ...
-         'options', optionsFile, ...
-         'design_only', true);
+  if ~bids.internal.is_octave() && ~ispc()
+    % only specify the subject level model
+    bidspm(bids_dir, output_dir, 'subject', ...
+           'participant_label', {'01'}, ...
+           'action', 'stats', ...
+           'preproc_dir', preproc_dir, ...
+           'model_file', models{iOption}, ...
+           'options', optionsFile, ...
+           'design_only', true);
+  end
 
   % specify, estimate model and contrasts, and view results
   bidspm(bids_dir, output_dir, 'subject', ...

diff --git a/demos/face_repetition/README.md b/demos/face_repetition/README.md
@@ -12,7 +12,7 @@ bidspm \
     $PWD/outputs/raw \
     $PWD/outputs/derivatives \
     subject \
-    --action preprocess \
+    preprocess \
     --participant_label 01 \
     --space individual IXI549Space \
     --task facerepetition \
@@ -25,7 +25,7 @@ bidspm \
     $PWD/outputs/raw \
     $PWD/outputs/derivatives \
     subject \
-    --action preprocess \
+    preprocess \
     --space individual IXI549Space \
     --anat_only \
     --skip_validation
@@ -38,7 +38,7 @@ bidspm \
     $PWD/outputs/raw \
     $PWD/outputs/derivatives \
     subject \
-    --action create_roi \
+    create_roi \
     --roi_atlas wang \
     --roi_name MST hMT
 ```
@@ -48,7 +48,7 @@ bidspm \
     $PWD/outputs/raw \
     $PWD/outputs/derivatives \
     subject \
-    --action create_roi \
+    create_roi \
     --roi_atlas hpcex \
     --roi_name MST MT
 ```
@@ -65,7 +65,7 @@ docker run -it --rm \
         /raw \
         /derivatives \
         subject \
-        --action create_roi \
+        create_roi \
         --roi_atlas hcpex \
         --roi_name MST MT
 ```
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -85,11 +85,13 @@
 }
 
 # We recommend adding the following config value.
-# Sphinx defaults to automatically resolve *unresolved* labels using all your Intersphinx mappings.
-# This behavior has unintended side-effects, namely that documentations local references can
+# Sphinx defaults to automatically resolve *unresolved* labels
+# using all your Intersphinx mappings.
+# This behavior has unintended side-effects,
+# namely that documentations local references can
 # suddenly resolve to an external location.
 # See also:
-# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_disabled_reftypes
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_disabled_reftypes # noqa
 # intersphinx_disabled_reftypes = ["*"]
 
 coverage_show_missing_items = True

diff --git a/docs/source/images/mermaid.md b/docs/source/images/mermaid.md
@@ -17,4 +17,4 @@ graph TD
     batch_02 --> E[SPM12]
     end
 
-    CLI -->|--action results\n--participant-label 01 02\n--model_file smdl.json| bidsResults
+    CLI -->|results\n--participant-label 01 02\n--model_file smdl.json| bidsResults
diff --git a/docs/source/installation/containers.md b/docs/source/installation/containers.md
@@ -48,7 +48,7 @@ docker run -it --rm \
         /derivatives \
         subject \
         --task auditory \
-        --action preprocess \
+        preprocess \
         --fwhm 8
 ```
 
@@ -68,7 +68,7 @@ docker run -it --rm \
         /raw \
         /derivatives \
         subject \
-        --action stats \
+        stats \
         --preproc_dir /derivatives/bidspm-preproc \
         --model_file /models/smdl.json \
         --fwhm 8

diff --git a/docs/source/stats/bids_stats_model.md b/docs/source/stats/bids_stats_model.md
@@ -477,7 +477,7 @@ Subject level contrast averaging beta across runs
 
 ```{figure} ./images/gui_contrast_cross_session.png
 ---
-name: contrast_subject
+name: contrast_subject_cross_sessions
 align: center
 ---
 Subject level contrast averaging beta across runs

diff --git a/docs/source/usage_notes.rst b/docs/source/usage_notes.rst
@@ -11,5 +11,5 @@ Command line API
 ================
 
 .. argparse::
-   :ref: src.bidspm.parsers.common_parser
+   :ref: src.bidspm.parsers.sub_command_parser
    :prog: bidspm
diff --git a/pyproject.toml b/pyproject.toml
@@ -61,7 +61,6 @@ test = [
 
 [project.scripts]
 bidspm = "bidspm.cli:cli"
-bidspm_2 = "bidspm.cli:new_cli"
 validate_model = "bidspm.validate:cli"
 
 [project.urls]

diff --git a/src/IO/overwriteDir.m b/src/IO/overwriteDir.m
@@ -7,10 +7,9 @@ function overwriteDir(directory, opt)
 
   % (C) Copyright 2021 bidspm developers
 
-  directory = bids.internal.format_path(directory);
-
   if exist(directory, 'dir') == 7
-    msg = sprintf('\noverwriting directory:\n\t%s\n\n', directory);
+    formatted_directory = bids.internal.format_path(directory);
+    msg = sprintf('\noverwriting directory:\n\t%s\n\n', formatted_directory);
     id = 'overWritingDir';
     logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
     rmdir(directory, 's');