Merge pull request #618 from NeurodataWithoutBorders/fix_yaml_null2

Fix yaml null2

Author: bendichter

src/pynwb/data/nwb.base.yaml

@@ -38,7 +38,7 @@ datasets:
     value: indexes into a list of values for a list of elements
   default_name: vector_index
   shape:
-  -
+  - null
 - neurodata_type_def: ElementIdentifiers
   neurodata_type_inc: NWBData
   dtype: int
@@ -50,7 +50,7 @@ datasets:
     value: unique identifiers for a list of elements
   default_name: element_id
   shape:
-  -
+  - null
 groups:
 - neurodata_type_def: NWBContainer
   doc: The attributes specified here are included in all interfaces.
@@ -98,7 +98,7 @@ groups:
     - num_times
     quantity: '?'
     shape:
-    -
+    - null
   - name: control_description
     dtype: text
     doc: 'Description of each control value. COMMENT: Array length should be as long
@@ -108,7 +108,7 @@ groups:
     - num_control_values
     quantity: '?'
     shape:
-    -
+    - null
   - name: data
     doc: 'Data values. Can also store binary data (eg, image frames) COMMENT: This
       field may be a link to data stored in an external file, especially in the case
@@ -137,7 +137,7 @@ groups:
     dims:
     - num_times
     shape:
-    -
+    - null
   - name: starting_time
     dtype: float64
     doc: 'The timestamp of the first sample. COMMENT: When timestamps are uniformly
@@ -170,7 +170,7 @@ groups:
     - num_times
     quantity: '?'
     shape:
-    -
+    - null
   groups:
   - name: sync
     doc: 'Lab specific time and sync information as provided directly from hardware
@@ -245,7 +245,7 @@ groups:
     doc: The names of the columns in this table. This should be used to specifying
       an order to the columns
     shape:
-    -
+    - null
   - name: description
     dtype: text
     doc: Description of what is in this dynamic table
@@ -255,7 +255,7 @@ groups:
     dtype: int
     doc: The unique identifier for the rows in this dynamic table
     shape:
-    -
+    - null
   - neurodata_type_inc: TableColumn
     doc: The columns in this dynamic table
     quantity: '*'

src/pynwb/data/nwb.behavior.yaml

@@ -24,18 +24,18 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      doc: 'The base unit of measure used to store data. This should be in the SI
-        unit. COMMENT: This is the SI unit (when appropriate) of the stored data,
-        such as Volts. If the actual data is stored in millivolts, the field ''conversion''
-        below describes how to convert the data to the specified SI unit.'
+      doc: "The base unit of measure used to store data. This should be in the SI\
+        \ unit. COMMENT: This is the SI unit (when appropriate) of the stored data,\
+        \ such as Volts. If the actual data is stored in millivolts, the field 'conversion'\
+        \ below describes how to convert the data to the specified SI unit."
       default_value: meter
       required: false
     dims:
     - num_times
     - num_features
     shape:
-    -
-    -
+    - null
+    - null
   - name: reference_frame
     dtype: text
     doc: Description defining what exactly 'straight-ahead' means.

src/pynwb/data/nwb.ecephys.yaml

@@ -84,9 +84,9 @@ groups:
     - - num_times
       - num_channels
     shape:
-    - -
-    - -
-      -
+    - - null
+    - - null
+      - null
   - neurodata_type_inc: ElectrodeTableRegion
     name: electrodes
     doc: the electrodes that this series was generated from
@@ -124,11 +124,11 @@ groups:
       - num_channels
       - num_samples
     shape:
-    - -
-      -
-    - -
-      -
-      -
+    - - null
+      - null
+    - - null
+      - null
+      - null
 - neurodata_type_def: ClusterWaveforms
   neurodata_type_inc: NWBDataInterface
   doc: 'The mean waveform shape, including standard deviation, of the different clusters.
@@ -157,17 +157,17 @@ groups:
     - num_clusters
     - num_samples
     shape:
-    -
-    -
+    - null
+    - null
   - name: waveform_sd
     dtype: float32
     doc: Stdev of waveforms for each cluster, using the same indices as in mean
     dims:
     - num_clusters
     - num_samples
     shape:
-    -
-    -
+    - null
+    - null
   links:
   - name: clustering_interface
     doc: HDF5 link to Clustering interface that was the source of the clustered data
@@ -195,23 +195,23 @@ groups:
     dims:
     - num_events
     shape:
-    -
+    - null
   - name: peak_over_rms
     dtype: float32
     doc: Maximum ratio of waveform peak to RMS on any channel in the cluster (provides
       a basic clustering metric).
     dims:
     - num_clusters
     shape:
-    -
+    - null
   - name: times
     dtype: float64
     doc: Times of clustered events, in seconds. This may be a link to times field
       in associated FeatureExtraction module.
     dims:
     - num_events
     shape:
-    -
+    - null
   default_name: Clustering
 - neurodata_type_def: FeatureExtraction
   neurodata_type_inc: NWBDataInterface
@@ -229,7 +229,7 @@ groups:
     dims:
     - num_features
     shape:
-    -
+    - null
   - name: features
     dtype: float32
     doc: Multi-dimensional array of features extracted from each event.
@@ -238,16 +238,16 @@ groups:
     - num_channels
     - num_features
     shape:
-    -
-    -
-    -
+    - null
+    - null
+    - null
   - name: times
     dtype: float64
     doc: Times of events that features correspond to (can be a link).
     dims:
     - num_events
     shape:
-    -
+    - null
   - neurodata_type_inc: ElectrodeTableRegion
     name: electrodes
     doc: the electrodes that this series was generated from
@@ -274,7 +274,7 @@ groups:
     dims:
     - num_events
     shape:
-    -
+    - null
   - name: times
     dtype: float64
     doc: Timestamps of events, in Seconds
@@ -287,7 +287,7 @@ groups:
     dims:
     - num_events
     shape:
-    -
+    - null
   links:
   - name: source_electricalseries
     doc: HDF5 link to ElectricalSeries that this data was calculated from. Metadata

src/pynwb/data/nwb.file.yaml

@@ -24,7 +24,7 @@ groups:
     dims:
     - '*unlimited*'
     shape:
-    -
+    - null
   - name: identifier
     dtype: text
     doc: 'A unique text identifier for the file. COMMENT: Eg, concatenated lab name,
@@ -255,7 +255,7 @@ groups:
           dims:
           - num_namespaces
           shape:
-          -
+          - null
         quantity: '*'
       quantity: '?'
     - neurodata_type_def: Subject

src/pynwb/data/nwb.icephys.yaml

@@ -18,7 +18,7 @@ groups:
     dims:
     - num_times
     shape:
-    -
+    - null
   - name: gain
     dtype: float
     doc: 'Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)'

src/pynwb/data/nwb.image.yaml

@@ -31,23 +31,23 @@ groups:
       - y
       - x
     shape:
-    - - 
-      - 
-    - - 
-      - 
-      - 
-    - - 
-      - 
-      - 
-      - 
+    - - null
+      - null
+    - - null
+      - null
+      - null
+    - - null
+      - null
+      - null
+      - null
   - name: dimension
     dtype: int32
     doc: Number of pixels on x, y, (and z) axes.
     dims:
     - rank
     quantity: '?'
     shape:
-    - 
+    - null
   - name: external_file
     dtype: text
     doc: 'Path or URL to one or more external file(s). Field only present if format=external.
@@ -64,12 +64,12 @@ groups:
       dims:
       - num_files
       shape:
-      - 
+      - null
     dims:
     - num_files
     quantity: '?'
     shape:
-    - 
+    - null
   - name: format
     dtype: text
     doc: Format of image. If this is 'external' then the field external_file contains
@@ -149,7 +149,7 @@ groups:
     dims:
     - num_times
     shape:
-    - 
+    - null
   links:
   - name: indexed_timeseries
     doc: HDF5 link to TimeSeries containing images that are indexed.

src/pynwb/data/nwb.misc.yaml

@@ -33,23 +33,23 @@ groups:
     - num_times
     - num_features
     shape:
-    -
-    -
+    - null
+    - null
   - name: feature_units
     dtype: text
     doc: Units of each feature.
     dims:
     - num_features
     quantity: '?'
     shape:
-    -
+    - null
   - name: features
     dtype: text
     doc: Description of the features represented in TimeSeries::data.
     dims:
     - num_features
     shape:
-    -
+    - null
 - neurodata_type_def: AnnotationSeries
   neurodata_type_inc: TimeSeries
   doc: Stores, eg, user annotations made during an experiment. The TimeSeries::data[]
@@ -77,7 +77,7 @@ groups:
     dims:
     - num_times
     shape:
-    -
+    - null
 - neurodata_type_def: IntervalSeries
   neurodata_type_inc: TimeSeries
   doc: Stores intervals of data. The timestamps field stores the beginning and end
@@ -108,7 +108,7 @@ groups:
     dims:
     - num_times
     shape:
-    -
+    - null
 - neurodata_type_def: UnitTimes
   neurodata_type_inc: NWBDataInterface
   doc: Event times of observed units (e.g. cell, synapse, etc.). The UnitTimes group

src/pynwb/data/nwb.ogen.yaml

@@ -23,7 +23,7 @@ groups:
     dims:
     - num_times
     shape:
-    -
+    - null
   links:
   - name: site
     doc: link to OptogeneticStimulusSite group that describes the site to which this

src/pynwb/data/nwb.ophys.yaml

@@ -13,9 +13,9 @@ datasets:
   - num_x
   - num_y
   shape:
-  -
-  -
-  -
+  - null
+  - null
+  - null
 - neurodata_type_def: PixelMasks
   neurodata_type_inc: VectorData
   dtype:
@@ -121,8 +121,8 @@ groups:
     - num_times
     - num_ROIs
     shape:
-    -
-    -
+    - null
+    - null
   - neurodata_type_inc: ROITableRegion
     name: rois
     doc: a dataset referencing into an ROITable containing information on the ROIs
@@ -263,8 +263,8 @@ groups:
     - weight
     - x|y|z
     shape:
-    -
-    -
+    - null
+    - null
     - 3
   - name: reference_frame
     dtype: text