[ENH] use python based CLI to run bidspm with octave

.all-contributorsrc

@@ -170,7 +170,7 @@
     },
     {
       "login": "yyang1234",
-      "name": "YingYang",
+      "name": "Ying Yang",
       "avatar_url": "https://avatars.githubusercontent.com/u/59220868?v=4",
       "profile": "https://github.com/yyang1234",
       "contributions": [

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -40,7 +40,6 @@ body:
   - type: textarea
     attributes:
       label: Operating system version
-      render: markdown
       value: |
         - Linux Ubuntu 18.04 "bionic beaver"
         - Mac OS Version 12 "monterey"
@@ -68,8 +67,7 @@ body:
   - type: textarea
     attributes:
       label: Platform version
-      render: markdown
-      placeholder: |
+      value: |
         - MATLAB 2017a
         - Octave 4.2.2
 
@@ -85,6 +83,7 @@ body:
 
         Or check the content of CITATION.cff.
       options:
+        - v2.3.0
         - v2.2.0
         - v2.1.0
         - v2.0.0
@@ -134,7 +133,7 @@ body:
         Describe what you got instead.
         If possible paste below the error message you encountered.
         Also add the error.log that might have been generated.
-      placeholder: |
+      value: |
         ```matlab
         % this is the error I got
 

.gitignore

@@ -16,7 +16,7 @@ tmp
 error_logs
 *_report.md
 src/batches/cfg
-options_task*[0-9][0-9].json
+options_*[0-9][0-9].json
 skipped_roi_*.tsv
 
 # created by tests

bidspm.m

@@ -381,6 +381,7 @@ function initBidspm(dev)
 
     for i = 1:numel(libList)
       BIDSPM_PATHS = cat(2, BIDSPM_PATHS, ...
+                         pathSep, ...
                          genpath(fullfile(thisDirectory, 'lib', libList{i})));
     end
 

demos/MoAE/README.md

@@ -9,3 +9,48 @@ In the `models` shows the BIDS statistical model used to run the GLM of this
 demo.
 
 You can use the makefile to run all the main scripts with `make all`
+
+## CLI commands
+
+### Create model
+
+```bash
+bidspm \
+    /home/remi/github/bidspm/demos/MoAE/inputs/raw \
+    /home/remi/github/bidspm/demos/MoAE/outputs/derivatives \
+     dataset \
+    --action default_model \
+    --space IXI549Space \
+    --task auditory \
+    --verbosity 0 \
+    --ignore transformations
+```
+
+### Preprocessing
+
+```bash
+bidspm \
+    /home/remi/github/bidspm/demos/MoAE/inputs/raw \
+    /home/remi/github/bidspm/demos/MoAE/outputs/derivatives \
+    subject \
+    --action preprocess \
+    --participant_label 01 \
+    --space individual IXI549Space \
+    --task auditory \
+    --verbosity 2 \
+    --fwhm 6 \
+    --ignore unwarp slicetiming
+```
+
+### GLM
+
+```bash
+bidspm \
+    /home/remi/github/bidspm/demos/MoAE/inputs/raw \
+    /home/remi/github/bidspm/demos/MoAE/outputs/derivatives \
+    subject \
+    --action stats \
+    --preproc_dir /home/remi/github/bidspm/demos/MoAE/outputs/derivatives/bidspm-preproc \
+    --model_file /home/remi/github/bidspm/demos/MoAE/models/model-MoAE_smdl.json \
+    --fwhm 6
+```

demos/face_repetition/README.md

@@ -0,0 +1,29 @@
+# Face repetition demo
+
+## CLI commands
+
+### Preprocessing
+
+```bash
+bidspm \
+    /home/remi/github/bidspm/demos/face_repetition/outputs/raw \
+    /home/remi/github/bidspm/demos/face_repetition/outputs/derivatives \
+    subject \
+    --action preprocess \
+    --participant_label 01 \
+    --space individual IXI549Space \
+    --task facerepetition \
+    --skip_validation \
+    --dummy_scans 5
+```
+
+```bash
+bidspm \
+    /home/remi/github/bidspm/demos/face_repetition/outputs/raw \
+    /home/remi/github/bidspm/demos/face_repetition/outputs/derivatives \
+    subject \
+    --action preprocess \
+    --space individual IXI549Space \
+    --anat_only \
+    --skip_validation
+```

demos/face_repetition/face_rep_01_anat_only.m

@@ -42,4 +42,5 @@
 bidspm(bids_dir, output_dir, 'subject', ...
        'action', 'preprocess', ...
        'space', {'individual', 'IXI549Space'}, ...
-       'anat_only', true);
+       'anat_only', true, ...
+       'skip_validation', true);

demos/openneuro/Makefile

@@ -17,21 +17,21 @@ data: data_ds000001 data_ds000114 data_ds001168
 data_ds000001:
 	mkdir -p inputs
 	cd inputs && datalad install ///openneuro/ds000001
-	datalad -d inputs/ds000001 get inputs/ds000001/sub-0[12]
+	cd inputs/ds000001 && datalad get sub-0[12]
 
 data_ds000114:
 	mkdir -p inputs
 	cd inputs && datalad install ///openneuro/ds000114
-	datalad -d inputs/ds000114 get inputs/ds000114/sub-0[12]
+	cd inputs/ds000114 && datalad get sub-0[12]
 
 data_ds001168:
 	datalad install ///openneuro/ds001168 inputs/ds001168
-	datalad -d inputs/ds001168 get inputs/ds001168/sub-0[12]
+	cd inputs/ds001168 && datalad get ds001168/sub-0[12]
 
 data_ds002799:
 	datalad install ///openneuro/ds002799 inputs/ds002799
 	cd inputs/ds002799/derivatives/fmriprep
-	datalad -d get sub-292/*/func/*MNI152NLin2009cAsym*
+	datalad get sub-292/*/func/*MNI152NLin2009cAsym*
 	datalad get sub-292/*/func/*tsv
 	datalad get sub-30[27]/*/func/*MNI152NLin2009cAsym*
 	datalad get sub-30[27]/*/func/*tsv

setup.cfg

@@ -31,11 +31,7 @@ zip_safe = False
 
 [options.entry_points]
 console_scripts =
-    bidspm = src.cli:main
-    bidspm_low = src.cli:low
-    bidspm_preproc = src.cli:preproc
-    bidspm_stats = src.cli:stats
-    bidspm_default_model = src.cli:default_model
+    bidspm = src.bidspm:cli
     validate_model = src.validate:main
 
 [options.extras_require]

src/QA/anatomicalQA.m

@@ -18,7 +18,8 @@ function anatomicalQA(opt)
   % (C) Copyright 2020 bidspm developers
 
   if isOctave()
-    warning('\nanatomicalQA is not yet supported on Octave. This step will be skipped.');
+    fprintf('\n');
+    warning('anatomicalQA is not yet supported on Octave. This step will be skipped.');
     opt.QA.anat.do = false;
   end
 

src/bids/validate.m

@@ -15,8 +15,8 @@ function validate(args)
                         pathToPrint(args.Results.bids_dir)));
 
   [sts_data, msg_data] = bids.validate(args.Results.bids_dir);
-  if sts_data == 1 && ~startsWith(msg_data, 'Require')
-    msg_data = sprintf('\nBIDS validation of %s failed:\n\n%s\n\nCheck with\n: %s\n\n', ...
+  if sts_data == 1 && ~bids.internal.starts_with(msg_data, 'Require')
+    msg_data = sprintf('\nBIDS validation of %s failed:\n\n%s\n\nCheck with:\n %s\n\n', ...
                        args.Results.bids_dir, ...
                        msg_data, ...
                        'https://bids-standard.github.io/bids-validator/');