Hopefully RTD works (#36)

* Fixed a bug that caused an error when multiple different types were created

* Updated the backprop example

* Minor changes to prepare for new release

* Minor change

* Version changes

* Minor changes

* Hopefullt fixed version system

* Updated changelog

* Trying to fix RTD errors

* Grrr

* grrrrrr

* Fixed bugs with RTD not allowing RTD to build

dendrify/__init__.py

@@ -3,3 +3,7 @@
                               update_default_params)
 from .equations import library
 from .neuronmodel import NeuronModel, PointNeuronModel
+
+__version__ = '2.1.4'
+__author__ = 'Michalis Pagkalos'
+__email__ = 'mpagkalos93@gmail.com'

dendrify/neuronmodel.py

@@ -284,15 +284,16 @@ def config_dspikes(self, event_name: str,
         for comp in self._compartments:
             if isinstance(comp, Dendrite) and comp._dspike_params:
                 event_id = f"{event_name}_{comp.name}"
-                dt = defaultclock.dt
-                d = {f"Vth_{event_id}": threshold,
-                     f"duration_rise_{event_id}": comp._timestep(duration_rise, dt),
-                     f"duration_fall_{event_id}": comp._timestep(duration_fall, dt),
-                     f"E_rise_{event_name}": comp._ionic_param(reversal_rise),
-                     f"E_fall_{event_name}": comp._ionic_param(reversal_fall),
-                     f"offset_fall_{event_id}": comp._timestep(offset_fall, dt),
-                     f"refractory_{event_id}": comp._timestep(refractory, dt)}
-                comp._dspike_params[event_id].update(d)
+                if event_id in comp._dspike_params:
+                    dt = defaultclock.dt
+                    d = {f"Vth_{event_id}": threshold,
+                        f"duration_rise_{event_id}": comp._timestep(duration_rise, dt),
+                        f"duration_fall_{event_id}": comp._timestep(duration_fall, dt),
+                        f"E_rise_{event_name}": comp._ionic_param(reversal_rise),
+                        f"E_fall_{event_name}": comp._ionic_param(reversal_fall),
+                        f"offset_fall_{event_id}": comp._timestep(offset_fall, dt),
+                        f"refractory_{event_id}": comp._timestep(refractory, dt)}
+                    comp._dspike_params[event_id].update(d)
 
     def make_neurongroup(self,
                          N: int,

docs_sphinx/source/changelog.rst

@@ -1,6 +1,15 @@
 Release notes
 =============
 
+Version 2.1.4
+-------------
+    * Fixed a bug that raised an error when config_dspikes was called multiple times
+      to configure different dSpike types. Thank you Tim Bax for discovering and
+      reporting this issue.
+    * Checked compatibility with Brian 2.7.0.
+    * Added package metadata (e.g. dendrify.__version__ works now).
+    * Minor documentation improvements.
+
 Version 2.1.3
 -------------
     * Changed package requirements to fix installation conflicts with Brian 2.6.0.

docs_sphinx/source/conf.py

@@ -3,17 +3,22 @@
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-import os
-import sys
+import os, sys
 
 sys.path.insert(0, os.path.abspath('../..'))
 sys.path.insert(0, os.path.abspath('../../..'))
 
+
+
 # -- Project information -------------------------------------------------------
 project = 'Dendrify'
 copyright = '2024, Michalis Pagkalos'
 author = 'Michalis Pagkalos'
-release = '2.1.3'
+release = '2.1.4'
+# release = re.search(
+#     r'__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
+#     io.open('dendrify/__init__.py', encoding='utf_8_sig').read()
+#     ).group(1)
 
 
 # -- General configuration -----------------------------------------------------

docs_sphinx/source/examples/comp_backprop.rst

@@ -74,7 +74,7 @@ In this example we show:
     # Run simulation
     net = b.Network(neuron, ap_reset, M)
     net.run(10*ms)
-    neuron.I_ext_soma = 150*pA
+    neuron.I_ext_soma = 115*pA
     net.run(100*ms)
     neuron.I_ext_soma = 0*pA
     net.run(60*ms)

examples_new/comp_backprop.py

@@ -75,7 +75,7 @@
 # Run simulation
 net = b.Network(neuron, ap_reset, M)
 net.run(10*ms)
-neuron.I_ext_soma = 150*pA
+neuron.I_ext_soma = 115*pA
 net.run(100*ms)
 neuron.I_ext_soma = 0*pA
 net.run(60*ms)

setup.py

@@ -1,6 +1,6 @@
 from setuptools import find_packages, setup
+VERSION = '2.1.4'
 
-VERSION = '2.1.3'
 DESCRIPTION = 'A package for adding dendrites to SNNs'
 with open("README.rst") as f:
     LONG_DESCRIPTION = f.read()
@@ -15,7 +15,7 @@
     long_description_content_type="text/x-rst; charset=UTF-8",
     long_description=LONG_DESCRIPTION,
     packages=find_packages(),
-    install_requires=['brian2==2.6.0'],
+    install_requires=['brian2==2.7.0'],
     keywords=['python', 'brian2', 'dendrites', 'SNNs', 'network models'],
     classifiers=[
         "Development Status :: 5 - Production/Stable",