Update name and version to 0.0.2

.gitignore

@@ -5,7 +5,7 @@ docs/source/_static
 !docs/source/_static/theme_overrides.css
 
 # copied spec files
-src/pynwb/ndx_novela_namespace/spec/*.yaml
+src/pynwb/ndx_franklab_novela/spec/*.yaml
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

setup.py

@@ -22,7 +22,7 @@
 
 setup_args = {
     'name': 'ndx-franklab-novela',
-    'version': '0.0.1',
+    'version': '0.0.2',
     'description': 'NovelaNeurotechnologies Namespaces',
     'long_description': readme,
     'long_description_content_type': readme_type,
@@ -35,7 +35,7 @@
     ],
     'packages': find_packages('src/pynwb'),
     'package_dir': {'': 'src/pynwb'},
-    'package_data': {'ndx_novela_namespace': [
+    'package_data': {'ndx_franklab_novela': [
         'spec/ndx-franklab-novela.namespace.yaml',
         'spec/ndx-franklab-novela.extensions.yaml',
     ]},
@@ -51,7 +51,7 @@ def _copy_spec_files(project_dir):
     ns_path = os.path.join(project_dir, 'spec', 'ndx-franklab-novela.namespace.yaml')
     ext_path = os.path.join(project_dir, 'spec', 'ndx-franklab-novela.extensions.yaml')
 
-    dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'ndx_novela_namespace', 'spec')
+    dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'ndx_franklab_novela', 'spec')
     if not os.path.exists(dst_dir):
         os.mkdir(dst_dir)
 

src/pynwb/ndx_novela_namespace/__init__.py → src/pynwb/ndx_franklab_novela/__init__.py

@@ -3,21 +3,21 @@
 from pynwb import load_namespaces
 
 # Set path of the namespace.yaml file to the expected install location
-ndx_novela_namespace_specpath = os.path.join(
+ndx_franklab_novela_specpath = os.path.join(
     os.path.dirname(__file__),
     'spec',
     'ndx-franklab-novela.namespace.yaml'
 )
 
 # If the extension has not been installed yet but we are running directly from
 # the git repo
-if not os.path.exists(ndx_novela_namespace_specpath):
-    ndx_novela_namespace_specpath = os.path.abspath(os.path.join(
+if not os.path.exists(ndx_franklab_novela_specpath):
+    ndx_franklab_novela_specpath = os.path.abspath(os.path.join(
         os.path.dirname(__file__),
         '..', '..', '..',
         'spec',
         'ndx-franklab-novela.namespace.yaml'
     ))
 
 # Load the namespace
-load_namespaces(ndx_novela_namespace_specpath)
+load_namespaces(ndx_franklab_novela_specpath)

src/pynwb/ndx_novela_namespace/apparatus.py → src/pynwb/ndx_franklab_novela/apparatus.py

@@ -1,8 +1,8 @@
 from pynwb import register_class
 from pynwb.core import MultiContainerInterface
 
-from src.pynwb.ndx_novela_namespace.edge import Edge
-from src.pynwb.ndx_novela_namespace.node import Node
+from src.pynwb.ndx_franklab_novela.edge import Edge
+from src.pynwb.ndx_franklab_novela.node import Node
 
 
 @register_class('Apparatus', 'ndx-franklab-novela')

src/pynwb/ndx_franklab_novela/spec/ndx-franklab-novela.extensions.yaml

@@ -0,0 +1,151 @@
+groups:
+- neurodata_type_def: FLElectrodeGroup
+  neurodata_type_inc: ElectrodeGroup
+  doc: A custom ElectrodesGroup interface
+  attributes:
+  - name: id
+    dtype: int
+    doc: id of electrode group
+- neurodata_type_def: NTrode
+  neurodata_type_inc: ElectrodeGroup
+  doc: A custom ntrode ElectrodesGroup interface
+  attributes:
+  - name: ntrode_id
+    dtype: int
+    doc: id of electrode group
+  - name: probe_id
+    dtype: int
+    doc: id of probe
+  datasets:
+  - name: map
+    dtype: int
+    dims:
+    - 2
+    shape:
+    - 32
+    doc: map of ntrodes
+- neurodata_type_def: Probe
+  neurodata_type_inc: Device
+  doc: A custom Probes interface
+  attributes:
+  - name: id
+    dtype: int
+    doc: unique id of the probe
+  - name: contact_size
+    dtype: float
+    doc: value of contact size in float
+  - name: probe_type
+    dtype: text
+    doc: type of the probe
+  - name: num_shanks
+    dtype: int
+    doc: number of shanks in probe
+- neurodata_type_def: Apparatus
+  neurodata_type_inc: NWBDataInterface
+  doc: a graph of nodes and edges
+  quantity: '*'
+  attributes:
+  - name: name
+    dtype: text
+    doc: the name of this apparatus
+  - name: help
+    dtype: text
+    value: Behavioral Apparatus
+    doc: help doc
+  groups:
+  - neurodata_type_def: Node
+    neurodata_type_inc: NWBDataInterface
+    doc: nodes in the graph
+    quantity: '*'
+    attributes:
+    - name: name
+      dtype: text
+      doc: the name of this node
+    - name: value
+      dtype: int
+      doc: the value of this node
+    - name: help
+      dtype: text
+      value: Apparatus Node
+      doc: help doc
+  - neurodata_type_def: Edge
+    neurodata_type_inc: NWBDataInterface
+    doc: edges in the graph
+    quantity: '*'
+    attributes:
+    - name: help
+      dtype: text
+      value: Apparatus Edge
+      doc: help doc
+    datasets:
+    - name: edge_nodes
+      dtype: text
+      dims:
+      - first_node_name|second_node_name
+      shape:
+      - 2
+      doc: names of the nodes this edge connects
+- neurodata_type_def: HeaderDevice
+  neurodata_type_inc: Device
+  doc: metadata from global configuration from header
+  attributes:
+  - name: headstage_serial
+    dtype: text
+    doc: headstage_serial from global configuration
+  - name: headstage_smart_ref_on
+    dtype: text
+    doc: headstage_smart_ref_on from global configuration
+  - name: realtime_mode
+    dtype: text
+    doc: realtime_mode from global configuration
+  - name: headstage_auto_settle_on
+    dtype: text
+    doc: headstage_auto_settle_on from global configuration
+  - name: timestamp_at_creation
+    dtype: text
+    doc: timestamp_at_creation from global configuration
+  - name: controller_firmware_version
+    dtype: text
+    doc: conntroller_firmware_version from global configuration
+  - name: controller_serial
+    dtype: text
+    doc: controller_serial from global configuration
+  - name: save_displayed_chan_only
+    dtype: text
+    doc: save_displayed_chan_only from global configuration
+  - name: headstage_firmware_version
+    dtype: text
+    doc: headstage_firmware_version from global configuration
+  - name: qt_version
+    dtype: text
+    doc: qt_version_version from global configuration
+  - name: compile_date
+    dtype: text
+    doc: compile_date_version from global configuration
+  - name: compile_time
+    dtype: text
+    doc: compile_time_version from global configuration
+  - name: file_prefixn
+    dtype: text
+    doc: file_prefix_version from global configuration
+  - name: headstage_gyro_sensor_on
+    dtype: text
+    doc: headstage_gyro_sensor_on_version from global configuration
+  - name: headstage_mag_sensor_on
+    dtype: text
+    doc: headstage_mag_sensor_on_version from global configuration
+  - name: trodes_version
+    dtype: text
+    doc: trodes_versionversion from global configuration
+  - name: headstage_accel_sensor_on
+    dtype: text
+    doc: headstage_accel_sensor_on from global configuration
+  - name: commit_head
+    dtype: text
+    doc: commit_head from global configuration
+  - name: system_time_at_creation
+    dtype: text
+    doc: system_time_at_creation from global configuration
+  - name: file_path
+    dtype: text
+    doc: file_path from global configuration

src/pynwb/ndx_franklab_novela/spec/ndx-franklab-novela.namespace.yaml

@@ -0,0 +1,15 @@
+namespaces:
+- author:
+  - NovelaDevops
+  contact:
+  - [email protected]
+  doc: NovelaNeurotechnologies Namespaces
+  name: ndx-franklab-novela
+  schema:
+  - namespace: core
+    neurodata_types:
+    - ElectrodeGroup
+    - Device
+    - NWBDataInterface
+  - source: ndx-franklab-novela.extensions.yaml
+  version: 0.0.1

src/pynwb/tests/test_apparatus.py

@@ -1,9 +1,9 @@
 from unittest import TestCase
 from unittest.mock import Mock
 
-from src.pynwb.ndx_novela_namespace.apparatus import Apparatus
-from src.pynwb.ndx_novela_namespace.edge import Edge
-from src.pynwb.ndx_novela_namespace.node import Node
+from src.pynwb.ndx_franklab_novela.apparatus import Apparatus
+from src.pynwb.ndx_franklab_novela.edge import Edge
+from src.pynwb.ndx_franklab_novela.node import Node
 
 
 class TestApparatus(TestCase):

src/pynwb/tests/test_edge.py

@@ -1,8 +1,8 @@
 import unittest
 from unittest.mock import Mock
 
-from src.pynwb.ndx_novela_namespace.edge import Edge
-from src.pynwb.ndx_novela_namespace.node import Node
+from src.pynwb.ndx_franklab_novela.edge import Edge
+from src.pynwb.ndx_franklab_novela.node import Node
 
 
 class TestEdge(unittest.TestCase):

src/pynwb/tests/test_fl_electrode_group.py

@@ -3,7 +3,7 @@
 
 from pynwb.device import Device
 
-from src.pynwb.ndx_novela_namespace.fl_electrode_group import FLElectrodeGroup
+from src.pynwb.ndx_franklab_novela.fl_electrode_group import FLElectrodeGroup
 
 
 class TestFLElectrodeGroup(unittest.TestCase):

src/pynwb/tests/test_header_device.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from src.pynwb.ndx_novela_namespace.header_device import HeaderDevice
+from src.pynwb.ndx_franklab_novela.header_device import HeaderDevice
 
 
 class TestHeaderDevice(TestCase):

src/pynwb/tests/test_node.py

@@ -1,6 +1,6 @@
 import unittest
 
-from src.pynwb.ndx_novela_namespace.node import Node
+from src.pynwb.ndx_franklab_novela.node import Node
 
 
 class TestNode(unittest.TestCase):

src/pynwb/tests/test_ntrode.py

@@ -3,7 +3,7 @@
 
 from pynwb.device import Device
 
-from src.pynwb.ndx_novela_namespace.ntrode import NTrode
+from src.pynwb.ndx_franklab_novela.ntrode import NTrode
 
 
 class TestNTrode(unittest.TestCase):

src/pynwb/tests/test_probe.py

@@ -1,6 +1,6 @@
 import unittest
 
-from src.pynwb.ndx_novela_namespace.probe import Probe
+from src.pynwb.ndx_franklab_novela.probe import Probe
 
 
 class TestProbe(unittest.TestCase):