NeuroML · pgleeson · Jan 4, 2022 · Jan 4, 2022 · Jan 4, 2022 · Jan 4, 2022
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -2,17 +2,25 @@ name: Continuous builds
 
 on:
   push:
-    branches: [ master, development, experimental, test* ]
+    branches:
+      - master
+      - development
+      - experimental
+      - 'test*'
   pull_request:
-    branches: [ master, development, experimental, test* ]
+    branches:
+      - master
+      - development
+      - experimental
+      - 'test*'
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [2.7, 3.7, 3.8, 3.9]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
       fail-fast: false
 
     steps:
@@ -51,12 +59,10 @@ jobs:
 
     - name: Run tests
       run: |
-        pytest .
+        pytest --cov=pyneuroml .
         pynml -h
 
-        # For now, only test neuron related examples on py3
-        if [[  ${{ matrix.python-version }} == "3."* ]]; then argnrn=-neuron ; fi
-        ./test-ghactions.sh $argnrn
+        ./test-ghactions.sh -neuron
 
     - name: Lint with flake8
       run: |

diff --git a/.gitignore b/.gitignore
@@ -122,3 +122,11 @@ examples/results/*.dat
 /examples/test_data/ca1/*.hoc
 .venv/
 /examples/LEMS_NML2_Ex5_DetCell_brian2.py
+/examples/*.gen.so
+*_eden.py
+/examples/test_data/Purk2M9s.nml.png
+/examples/test_data/*.pov
+/examples/test_data/ca1/*.pov
+/examples/test_data/ca1/TestOLMNet.net.nml.png
+/examples/LEMS_NML2_Ex5_DetCell_moose.py
+/examples/NET_NML2_Ex5_DetCell.net.nml
diff --git a/README.md b/README.md
@@ -143,6 +143,3 @@ Builds on [Neurotune](https://github.com/NeuralEnsemble/neurotune) and [pyelectr
 
 Built in viewer of cells in 3D? Mayavi?
 More closely tied to PyNN?
-
-
-[![Build Status](https://travis-ci.com/NeuroML/pyNeuroML.svg?branch=master)](https://travis-ci.com/NeuroML/pyNeuroML)
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -13,3 +13,4 @@ neuromllite
 git+https://github.com/NeuralEnsemble/neurotune.git#egg=neurotune
 git+https://github.com/NeuralEnsemble/pyelectro.git@master#egg=pyelectro
 git+https://github.com/aarongarrett/inspyred.git@master#egg=inspyred
+neuron
diff --git a/docs/source/pyneuroml.neuron.rst b/docs/source/pyneuroml.neuron.rst
@@ -0,0 +1,16 @@
+pyneuroml.neuron package
+==========================
+
+.. automodule:: pyneuroml.neuron
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyneuroml.neuron.analysis module
+--------------------------------
+
+.. automodule:: pyneuroml.neuron.analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
diff --git a/docs/source/pyneuroml.rst b/docs/source/pyneuroml.rst
@@ -18,8 +18,8 @@ Subpackages
    pyneuroml.povray
    pyneuroml.swc
    pyneuroml.tune
+   pyneuroml.neuron
 
-.. pyneuroml.neuron
 
 pyneuroml.pynml module
 ----------------------

diff --git a/examples/LeakConductance.mod b/examples/LeakConductance.mod
@@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=LeakConductance type=ionChannelHH)
 COMMENT
 
     This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
-         org.neuroml.export  v1.8.1
-         org.neuroml.model   v1.8.1
-         jLEMS               v0.10.6
+         org.neuroml.export  v1.9.0
+         org.neuroml.model   v1.9.0
+         jLEMS               v0.10.7
 
 ENDCOMMENT
 

diff --git a/examples/generate_povray.py b/examples/generate_povray.py
@@ -0,0 +1,6 @@
+
+from pyneuroml.povray.NeuroML2ToPOVRay import generate_povray
+
+#generate_povray(neuroml_file='test_data/ca1/TestOLMNet.net.nml')
+
+generate_povray(neuroml_file='test_data/Purk2M9s.nml', scalez=3)
diff --git a/examples/run_jneuroml_plot_matplotlib.py b/examples/run_jneuroml_plot_matplotlib.py
@@ -34,6 +34,17 @@
     )
 
 
+####################################################################
+#   Run LEMS in EDEN
+
+
+if "-eden" in sys.argv:  # To allow skipping of this for ease of testing
+    print("Running with EDEN...")
+    results4 = pynml.run_lems_with_eden(
+        example_lems_file, load_saved_data=True, verbose=True
+    )
+
+
 ####################################################################
 #   Reload & plot results
 
@@ -51,6 +62,8 @@
                 plt.plot(results2["t"], results2[key], label="jNeuroML_NEURON: " + key)
             if "-brian2" in sys.argv:
                 plt.plot(results3["t"], results3[key], label="jNeuroML_Brian2: " + key)
+            if "-eden" in sys.argv:
+                plt.plot(results4["t"], results4[key], label="EDEN: " + key)
         plt.legend(loc=2, fontsize="x-small")
 
     plt.show()
Original file line number	Diff line number	Diff line change
Expand Up		@@ -143,6 +143,3 @@ Builds on [Neurotune](https://github.com/NeuralEnsemble/neurotune) and [pyelectr

		Built in viewer of cells in 3D? Mayavi?
		More closely tied to PyNN?


		[![Build Status](https://travis-ci.com/NeuroML/pyNeuroML.svg?branch=master)](https://travis-ci.com/NeuroML/pyNeuroML)