several fixes

cpp-lln-lab · Jul 23, 2024 · 2632b20 · 2632b20
1 parent 663cf55
commit 2632b20
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Showing 9 changed files with 31 additions and 32 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -113,7 +113,7 @@ jobs:
                           /bids_dataset \
                           /outputs/ds000001 \
                           subject \
-                          --action default_model \
+                          default_model \
                           --task balloonanalogrisktask \
                           --space MNI152NLin2009cAsym \
                           --verbosity 3
@@ -130,7 +130,7 @@ jobs:
                           /bids_dataset \
                           /outputs/ds000001 \
                           dataset \
-                          --action default_model \
+                          default_model \
                           --task balloonanalogrisktask \
                           --space MNI152NLin2009cAsym \
                           --verbosity 3
@@ -150,7 +150,7 @@ jobs:
                           /outputs/ds000001 \
                           /outputs/ds000001 \
                           dataset \
-                          --action create_roi \
+                          create_roi \
                           --roi_atlas wang \
                           --roi_name V1v V1d \
                           --space IXI549Space \
@@ -190,7 +190,7 @@ jobs:
                           /bids_dataset \
                           /outputs/ds000001 \
                           subject \
-                          --action smooth \
+                          smooth \
                           --task balloonanalogrisktask \
                           --participant_label 01 02 \
                           --space MNI152NLin2009cAsym \
@@ -212,7 +212,7 @@ 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 \
@@ -235,7 +235,7 @@ 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/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/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/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/tests/test_bidspm.py b/tests/test_bidspm.py
@@ -22,7 +22,6 @@
     generate_command_stats,
     new_line,
     preprocess,
-    run_command,
     stats,
 )
 
@@ -59,13 +58,6 @@ def test_append_base_arguments():
     )
 
 
-def test_run_command():
-    """Test run_command."""
-    cmd = "disp('hello'); exit();"
-    return_code = run_command(cmd, platform="octave")
-    assert return_code == 0
-
-
 @pytest.mark.parametrize(
     "action",
     [

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -2,7 +2,7 @@
 
 import pytest
 
-from bidspm.cli import cli
+from bidspm.cli import cli, run_command
 
 
 def test_bidspm_error_dir(caplog):
@@ -15,3 +15,10 @@ def test_bidspm_error_dir(caplog):
     assert ["The 'bids_dir' does not exist:\n\t/foo/bar"] == [
         rec.message for rec in caplog.records
     ]
+
+
+def test_run_command():
+    """Test run_command."""
+    cmd = "disp('hello'); exit();"
+    return_code = run_command(cmd, platform="octave")
+    assert return_code == 0