Update with siibra v1.0a04

Needs further testing and examples

requirements.txt

@@ -1,4 +1,4 @@
-siibra>=0.3a16
+siibra>=1.0a04
 click>=8.0
 click_plugins>=1.0
 simple-term-menu>=1.4

setup.py

@@ -41,7 +41,7 @@ def find_version():
     """,
     python_requires=">=3.7",
     install_requires=[
-        "siibra>=0.3a16",
+        "siibra>=1.0a04",
         "click>=8.0",
         "click-plugins>=1.0",
         "simple-term-menu>=1.4",

siibra_cli/__init__.py

@@ -15,4 +15,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-__version__ = "0.2a2"
+__version__ = "1.0a1"

siibra_cli/cli.py

@@ -25,24 +25,28 @@
 
 # ---- Autocompletion
 
+
 class SpaceName(click.ParamType):
     name = "space"
+
     def shell_complete(self, ctx, param, incomplete):
         print(incomplete)
         return [
             click.CompletionItem(s.key)
-            for s in siibra.spaces 
+            for s in siibra.spaces
             if s.key.startswith(incomplete)
-            ]
+        ]
+
 
 class ParcellationName(click.ParamType):
     name = "parcellation"
+
     def shell_complete(self, ctx, param, incomplete):
         return [
             click.CompletionItem(s.key)
-            for s in siibra.parcellations 
+            for s in siibra.parcellations
             if s.key.startswith(incomplete)
-            ]
+        ]
 
 
 # ---- Main command
@@ -87,7 +91,6 @@ def get(ctx, outfile):
 @click.pass_context
 def map(ctx, parcellation, space):
     """Retrieve a parcellation map in the given space"""
-
     import siibra as siibra
 
     atlas = siibra.atlases[ctx.obj["species"]]
@@ -186,11 +189,11 @@ def find(ctx):
     default=None,
 )
 @click.option(
-    "--tree/--no-tree",
+    "--showtree/--no-tree",
     default=False,
 )
 @click.pass_context
-def region(ctx, region, parcellation, tree):
+def region(ctx, region: str, parcellation: str = None, showtree: bool = False):
     """Find brain regions by name"""
     import siibra
 
@@ -203,13 +206,13 @@ def region(ctx, region, parcellation, tree):
     else:
         parcobj = atlas.get_parcellation(parcellation)
         click.echo(f"Searching for region '{regionspec}' in {parcobj.name}.")
-        matches = parcobj.find_regions(regionspec)
+        matches = parcobj.find(regionspec)
 
     if len(matches) == 0:
         click.echo(f"No region found using the specification {regionspec}.")
         exit(1)
     for i, m in enumerate(matches):
-        txt = m.__repr__() if tree else m.name
+        txt = m.tree2str() if showtree else m.name
         if parcellation is None:
             click.echo(f"{i:5} | {m.parcellation.name:30.30} | {txt}")
         else:
@@ -316,7 +319,7 @@ def coordinate(ctx, coordinate, space, parcellation, labelled, sigma_mm):
     atlas = siibra.atlases[ctx.obj["species"]]
     siibra.logger.info(f"Using atlas '{atlas.name}'.")
     parcobj = atlas.get_parcellation(parcellation)
-    maptype = siibra.MapType.LABELLED if labelled else siibra.MapType.CONTINUOUS
+    maptype = siibra.MapType.LABELLED if labelled else siibra.MapType.STATISTICAL
     requested_space = atlas.get_space(space)
     location = siibra.Point(coordinate, space=requested_space)
 
@@ -347,5 +350,3 @@ def coordinate(ctx, coordinate, space, parcellation, labelled, sigma_mm):
             click.echo(f"{region.name:40.40} {values}")
         else:
             click.echo(region.name)
-
-