Use PyNWB autogen classes instead of handwritten classes (#3)

Author: rly

README.md

@@ -1,7 +1,18 @@
 # ndx-franklab-novela Extension for NWB
 
 # About
-ndx-franklab-novela is a python package containing NWB custom extensions.
+ndx-franklab-novela is a python package containing NWB custom extensions for Loren Frank's Lab.
+
+# How to install
+
+Add ndx-franklab-novela to your conda environment
+
+`pip install git+git://github.com/LorenFrankLab/ndx-franklab-novela`
+
+The original published extension maintained by NovelaNeuro can be installed using:
+
+`conda install -c conda-forge -c novelakrk ndx-franklab-novela`
+
 
 # How to install
 
@@ -14,75 +25,83 @@ The original published extension maintained by NovelaNeuro can be installed usin
 
 # Extensions
 
-### AssociatedFiles
-Representation of associated files in NWB <br>
-**Attributes:** <br>
-    **description**  `string`: description of associated file <br>
-    **content**  `string`: content of associated file <br>
-    **task_epochs**  `string`: id of epochs with task that is descripted by associated files <br>
-
-#### HeaderDevice
-Representation of HeaderDevice in NWB. <br>
-**Attributes:** <br>
-    **headstage_serial**  `string`: headstage_serial from header global configuration <br>
-    **headstage_smart_ref_on**  `string`: headstage_smart_ref_on from header global configuration <br>
-    **realtime_mode**  `string`: realtime_mode from header global configuration <br>
-    **headstage_auto_settle_on**  `string`: headstage_auto_settle_on from header global configuration <br>
-    **timestamp_at_creation**  `string`: timestamp_at_creation from header global configuration <br>
-    **controller_firmware_version**  `string`: conntroller_firmware_version from header global configuration <br>
-    **controller_serial**  `string`: conntroller_serial from header global configuration <br>
-    **save_displayed_chan_only**  `string`: save_displayed_chan_only from header global configuration <br>
-    **headstage_firmware_version**  `string`: headstage_firmware_version from header global configuration <br>
-    **qt_version**  `string`: qt_version from header global configuration <br>
-    **compile_date**  `string`: compile_date from header global configuration <br>
-    **compile_time**  `string`: compile_time from header global configuration <br>
-    **file_prefix**  `string`: file_prefix from header global configuration <br>
-    **headstage_gyro_sensor_on**  `string`: headstage_gyro_sensor_on from header global configuration <br>
-    **headstage_mag_sensor_on**  `string`: headstage_mag_sensor_on from header global configuration <br>
-    **trodes_version**  `string`: trodes_version from header global configuration <br>
-    **headstage_accel_sensor_on**  `string`: headstage_accel_sensor_on from header global configuration <br>
-    **commit_head**  `string`: commit_head from header global configuration <br>
-    **system_time_at_creation**  `string`: system_time_at_creation from header global configuration <br>
-    **file_path**  `string`: file_path from header global configuration <br>
-
-#### ShanksElectrode
-Representation of ShanksElectrode object in NWB <br>
-**Attributes:** <br>
-    **name**  `string`: name of the shank <br>
-    **rel_x**  `float`: the rel_x value of this electrode <br>
-    **rel_y**  `float`: the rel_y value of this electrode <br>
-    **rel_z**  `float`: the rel_z value of this electrode of p
-
-#### Shank
-Representation of Shank object in NWB <br>
-**Attributes:** <br>
-    **name**  `string`: name of the shank <br>
-    **shanks_electrodes**  `list`,`tuple`:  'electrodes in shank', 'default': list() <br>
-
-#### Probe
-Representation of Probe object in NWB <br>
-**Attributes:** <br>
-    **id**  `int`: unique id of the probe <br>
-    **probe_type**  `string`: type of probe <br>
-    **units**  `string`: units in device <br>
-    **probe_description**  `string`: probe_description of probe <br>
-    **contact_side_numbering**  `bool`: is contact_side_numbering enabled <br>
-    **contact_size**  `float`: value of contact size as float <br>
-    **shanks**  `object`: shanks in the probe <br>
-
-#### DataAcqDevice
-Representation of DataAcqDevice object in NWB <br>
-**Attributes:** <br>
-    **system**  `string`: system of device <br>
-    **amplifier**  `string`: amplifier (default: '') <br>
-    **adc_circuit**  `string`: adc_circuit (default: '') <br>
-
-#### CameraDevice
-Representation of CameraDevice object in NWB <br>
-**Attributes:** <br>
-    **meters_per_pixel**  `float`: meter per pixel <br>
-    **model**  `string`: model of this camera device <br>
-    **lens**  `string`: info about lens in this camera <br>
-    **camera_name**  `string`: name of this camera <br>
+## AssociatedFiles
+Representation of associated files in NWB.
+
+**Attributes:**
+- **description**  `string`: description of associated file
+- **content**  `string`: content of associated file
+- **task_epochs**  `string`: id of epochs with task that is descripted by associated files
+
+## HeaderDevice
+Representation of HeaderDevice in NWB.
+
+**Attributes:**
+- **headstage_serial**  `string`: headstage_serial from header global configuration
+- **headstage_smart_ref_on**  `string`: headstage_smart_ref_on from header global configuration
+- **realtime_mode**  `string`: realtime_mode from header global configuration
+- **headstage_auto_settle_on**  `string`: headstage_auto_settle_on from header global configuration
+- **timestamp_at_creation**  `string`: timestamp_at_creation from header global configuration
+- **controller_firmware_version**  `string`: conntroller_firmware_version from header global configuration
+- **controller_serial**  `string`: conntroller_serial from header global configuration
+- **save_displayed_chan_only**  `string`: save_displayed_chan_only from header global configuration
+- **headstage_firmware_version**  `string`: headstage_firmware_version from header global configuration
+- **qt_version**  `string`: qt_version from header global configuration
+- **compile_date**  `string`: compile_date from header global configuration
+- **compile_time**  `string`: compile_time from header global configuration
+- **file_prefix**  `string`: file_prefix from header global configuration
+- **headstage_gyro_sensor_on**  `string`: headstage_gyro_sensor_on from header global configuration
+- **headstage_mag_sensor_on**  `string`: headstage_mag_sensor_on from header global configuration
+- **trodes_version**  `string`: trodes_version from header global configuration
+- **headstage_accel_sensor_on**  `string`: headstage_accel_sensor_on from header global configuration
+- **commit_head**  `string`: commit_head from header global configuration
+- **system_time_at_creation**  `string`: system_time_at_creation from header global configuration
+- **file_path**  `string`: file_path from header global configuration
+
+## ShanksElectrode
+Representation of electrodes of a shank in NWB.
+
+**Attributes:**
+- **name**  `string`: name of the shank
+- **rel_x**  `float`: the rel_x value of this electrode
+- **rel_y**  `float`: the rel_y value of this electrode
+- **rel_z**  `float`: the rel_z value of this electrode
+
+## Shank
+Representation of a shank in NWB.
+
+**Attributes:**
+- **name**  `string`: name of the shank
+- **shanks_electrodes**  `dict`: electrodes in the shank
+
+## Probe
+Representation of a probe in NWB.
+
+**Attributes:**
+- **id**  `int`: unique id of the probe
+- **probe_type**  `string`: type of probe
+- **units**  `string`: units in device
+- **probe_description**  `string`: description of probe
+- **contact_side_numbering**  `bool`: is contact_side_numbering enabled
+- **contact_size**  `float`: value of contact size as float
+- **shanks**  `dict`: shanks in the probe
+
+## DataAcqDevice
+Representation of data acquisition device in NWB.
+
+**Attributes:**
+- **system**  `string`: system of device
+- **amplifier**  `string`: amplifier (optional)
+- **adc_circuit**  `string`: adc_circuit (optional)
+
+## CameraDevice
+Representation of a camera device in NWB.
+
+**Attributes:**
+- **meters_per_pixel**  `float`: meters per pixel
+- **model**  `string`: model of this camera device
+- **lens**  `string`: info about lens in this camera
+- **camera_name**  `string`: name of this camera
 
+---
 This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).

setup.py

@@ -1,13 +1,12 @@
 # -*- coding: utf-8 -*-
-
-version = "0.0.011.36"
-print(version)
-
 import os
 from shutil import copy2
 
 from setuptools import find_packages, setup
 
+version = "0.1.0"
+print(version)
+
 # load README.md/README.rst file
 try:
     if os.path.exists('README.md'):
@@ -20,7 +19,7 @@
             readme_type = 'text/x-rst; charset=UTF-8'
     else:
         readme = ""
-except:
+except Exception:
     readme = ""
 
 setup_args = {

spec/ndx-franklab-novela.extensions.yaml

@@ -62,9 +62,11 @@ groups:
   - name: amplifier
     dtype: text
     doc: amplifier
+    required: false
   - name: adc_circuit
     dtype: text
     doc: adc_circuit
+    required: false
 - neurodata_type_def: CameraDevice
   neurodata_type_inc: Device
   doc: A custom Device interface

spec/ndx-franklab-novela.namespace.yaml

@@ -6,7 +6,7 @@ namespaces:
   - Ryan Ly
   contact:
   - [email protected]
-  - loren@cin.ucsf.edu
+  - loren.frank@ucsf.edu
   - [email protected]
   - [email protected]
   doc: NWB extension to store additional metadata and data types for Loren Frank's

src/pynwb/ndx_franklab_novela/__init__.py

@@ -1,6 +1,6 @@
 import os
 
-from pynwb import load_namespaces
+from pynwb import load_namespaces, get_class
 
 # Set path of the namespace.yaml file to the expected install location
 
@@ -23,9 +23,17 @@
 # Load the namespace
 load_namespaces(ndx_franklab_novela_specpath)
 
-from .associated_files import AssociatedFiles
-from .camera_device import CameraDevice
-from .data_acq_device import DataAcqDevice
-from .header_device import HeaderDevice
-from .nwb_electrode_group import NwbElectrodeGroup
-from .probe import Probe, Shank, ShanksElectrode
+AssociatedFiles = get_class('AssociatedFiles', 'ndx-franklab-novela')
+CameraDevice = get_class('CameraDevice', 'ndx-franklab-novela')
+DataAcqDevice = get_class('DataAcqDevice', 'ndx-franklab-novela')
+HeaderDevice = get_class('HeaderDevice', 'ndx-franklab-novela')
+NwbElectrodeGroup = get_class('NwbElectrodeGroup', 'ndx-franklab-novela')
+Probe = get_class('Probe', 'ndx-franklab-novela')
+Shank = get_class('Shank', 'ndx-franklab-novela')
+ShanksElectrode = get_class('ShanksElectrode', 'ndx-franklab-novela')
+
+# define aliases to maintain backward compatibility
+Probe.add_shank = Probe.add_shanks
+Probe.get_shank = Probe.get_shanks
+Shank.add_shanks_electrode = Shank.add_shanks_electrodes
+Shank.get_shanks_electrode = Shank.get_shanks_electrodes