cli args for data, methods

src/rsatoolbox/cli.py

@@ -1,4 +1,27 @@
 """Command Line Interface
+
+Usage output:
+```
+Representational Similarity Analysis
+
+positional arguments:
+  file                  One or more files or directories with data
+
+options:
+  -h, --help            show this help message and exit
+  --version             show program's version number and exit
+  --model MODEL         File with RDM models
+  --estimator {auto,euclidean,correlation,mahalanobis,crossnobis,poisson,poisson_cv}
+                        Which dissimilarity measure to generate RDM with
+  --comparator {auto,cosine,spearman,corr,kendall,tau-a,rho-a,corr_cov,cosine_cov,neg_riem_dist,bures,bures_metric}
+                        Which method to use when evaluating models or comparing RDMs
+  --searchlight SEARCHLIGHT
+                        Run a searchlight over the whole space with the given radius. Unit depends on data modality.
+  --window [WINDOW ...]
+                        Boundaries of a temporal window in milliseconds, e.g. "150 200"
+  --roi [ROI ...]       One or more "mask" or "picks" files to specify voxel or channel selection
+```
+
 """
 from argparse import ArgumentParser
 from importlib.metadata import version
@@ -10,13 +33,67 @@
 parser.add_argument(
     'file',
     default='.',
-    help='Data directory or file'
-)  
+    help='One or more files or directories with data',
+    nargs='*',
+)
 parser.add_argument(
     '--version',
     action='version',
     version=f'rsatoolbox {version("rsatoolbox")}'
 )
+parser.add_argument(
+    '--model',
+    help='File with RDM models',
+)
+parser.add_argument(
+    '--estimator',
+    help='Which dissimilarity measure to generate RDM with',
+    choices=[
+        'auto',
+        'euclidean',
+        'correlation',
+        'mahalanobis',
+        'crossnobis',
+        'poisson',
+        'poisson_cv',
+    ],
+    default='auto',
+)
+parser.add_argument(
+    '--comparator',
+    help='Which method to use when evaluating models or comparing RDMs',
+    choices=[
+        'auto',
+        'cosine',
+        'spearman',
+        'corr',
+        'kendall',
+        'tau-a',
+        'rho-a',
+        'corr_cov',
+        'cosine_cov',
+        'neg_riem_dist',
+        'bures',
+        'bures_metric',
+    ],
+    default='auto',
+)
+parser.add_argument(
+    '--searchlight',
+    help='Run a searchlight over the whole space with the given radius. Unit depends on data modality.',
+    type=int,
+    default=0,
+)
+parser.add_argument(
+    '--window',
+    help='Boundaries of a temporal window in milliseconds, e.g. "150 200"',
+    nargs='*',
+)
+parser.add_argument(
+    '--roi',
+    help='One or more "mask" or "picks" files to specify voxel or channel selection',
+    nargs='*',
+)
 
 
 def main():