Merge pull request #51 from SilverLabUCL/update-extension-yamls

update extension yamls (+ therefore signatures)
adapt to newer `tifffile`

Author: alessandrofelder

setup.py

@@ -60,7 +60,7 @@ def read(*names, **kwargs):
         'numpy',
         'pandas>=0.20',
         'ruamel.yaml',
-        'tifffile',
+        'tifffile[all]',  # [all] needed in newer versions of tifffile to ensure imagecodecs is included.
     ],
     extras_require={
         'test': ['pytest', 'tox'],

src/silverlabnwb/generate_extended_schema.py

@@ -41,6 +41,7 @@ def generate_extended_schema():
                                            'normalised Z, '
                                            '\'Pockels\' i.e. laser power in %, '
                                            'and z offset for drive motors',
+                                       name='pockels',
                                        shape=(None, 4),
                                        attributes=[pockels_column_names_attr],
                                        neurodata_type_def='ZplanePockelsDataset')

src/silverlabnwb/silverlab.metadata.yaml

@@ -1,7 +1,7 @@
 groups:
 - neurodata_type_def: SilverLabMetaData
   neurodata_type_inc: LabMetaData
-  doc: A place to store silverlab specific metadata
+  doc: A place to store Silver lab specific metadata
   attributes:
   - name: silverlab_api_version
     dtype: text

src/silverlabnwb/silverlab.namespace.yaml

@@ -1,6 +1,6 @@
 namespaces:
 - doc: Extensions for acousto-optic lens data
-  full_name: Silverlab data extension to NWB format for acousto-optic lens experiments
+  full_name: Silver lab data extension to NWB format for acousto-optic lens experiments
   name: silverlab_extended_schema
   schema:
   - namespace: core

src/silverlabnwb/silverlab.ophys.yaml

@@ -1,7 +1,7 @@
 groups:
 - neurodata_type_def: SilverLabOptophysiology
   neurodata_type_inc: LabMetaData
-  doc: Silverlab optophysiology specifications
+  doc: A place to store Silver lab specific optophysiology data
   attributes:
   - name: cycle_time
     dtype: float
@@ -14,7 +14,7 @@ groups:
     dtype: int
     shape:
     - 2
-    doc: ' the 2d imaging frame size in voxels'
+    doc: the 2d imaging frame size in voxels
   - name: imaging_mode
     dtype: text
     doc: the acquisition mode for the experiment; pointing = single-voxel ROIs, miniscan
@@ -25,8 +25,8 @@ groups:
     shape:
     - null
     - 4
-    doc: "pockels data set, recording calibration data for focusing at different z-planesin\
-      \ four columns: Z offset from focal plane (micrometres), normalised Z,'Pockels'\
+    doc: "pockels data set, recording calibration data for focusing at different z-planes\
+      \ in four columns: Z offset from focal plane (micrometres), normalised Z, 'Pockels'\
       \ i.e. laser power in %, and z offset for drive motors"
     attributes:
     - name: columns