Merge pull request #61 from NeuroML/development

Changes for NML v2.3 release
NeuroML · Sep 20, 2023 · 7ca95b5 · 7ca95b5
2 parents 924a6ee + ac205ae
commit 7ca95b5
Show file tree

Hide file tree

Showing 86 changed files with 15,001 additions and 14,589 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7,3.9]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     env:
       JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML"
       HDF5_DISABLE_VERSION_CHECK: 1
@@ -58,9 +58,9 @@ jobs:
         cd pyNeuroML
         git checkout $pynml_branch
         pip install pandas==1.3.5
-        pip install NEURON==7.8.2 # Specify version of neuron - 8.2.1 fails
+        pip install NEURON==8.2.2 # Specify version of neuron - 8.2.1 fails
         #pip install -r requirements-dev.txt
-        python setup.py install
+        pip install .
         cd -
 
         # Install latest jnml...

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -0,0 +1,36 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -202,3 +202,11 @@ docs/_build
 /examples/pyr_4_sym.cell.nml
 *_eden.py
 arm64
+/examples/Example4_PyNN.mdf
+*.mdf.json
+*.mdf.yaml
+/examples/Example6_PyNN.mdf
+/examples/Example7_Brunel2000.mdf
+/examples/Example3_Network.yaml
+/examples/SimExample3.yaml
+/examples/Example4_PyNN.mdf.1
diff --git a/docs/NeuroMLlite_specification.json b/docs/NeuroMLlite_specification.json
@@ -1,5 +1,5 @@
 {
-    "version": "NeuroMLlite v0.5.3",
+    "version": "NeuroMLlite v0.5.7",
     "specification": {
         "Network": {
             "definition": "A Network containing multiple Population's, connected by Projection's and receiving Input's",
@@ -237,7 +237,7 @@
                     "description": "Unique identifier for this Population"
                 },
                 "size": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "The size of the population."
                 },
                 "component": {
@@ -366,11 +366,11 @@
                     "description": "type of projection: projection (default; standard chemical, event triggered), electricalProjection\n(for gap junctions) or continuousProjection (for analogue/graded synapses)"
                 },
                 "delay": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Delay to use (default: 0)"
                 },
                 "weight": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Weight to use (default: 1)"
                 },
                 "random_connectivity": {
@@ -395,7 +395,7 @@
                     "description": ""
                 },
                 "probability": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Random probability of connection."
                 }
             }
@@ -442,23 +442,23 @@
                     "description": "Population to target"
                 },
                 "cell_ids": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Specific ids of _Cell_s to apply this input to (cannot be used with percentage"
                 },
                 "percentage": {
-                    "type": "float",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Percentage of Cells to apply input to"
                 },
                 "number_per_cell": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Number of individual inputs per selected Cell (default: 1)"
                 },
                 "segment_ids": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Which segments to target (default: [0])"
                 },
                 "weight": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Weight to use (default: 1)"
                 }
             }

diff --git a/docs/NeuroMLlite_specification.yaml b/docs/NeuroMLlite_specification.yaml
@@ -1,4 +1,4 @@
-version: NeuroMLlite v0.5.3
+version: NeuroMLlite v0.5.7
 specification:
     Network:
         definition: A Network containing multiple Population's, connected by Projection's
@@ -178,7 +178,8 @@ specification:
                 type: str
                 description: Unique identifier for this Population
             size:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: The size of the population.
             component:
                 type: str
@@ -276,10 +277,12 @@ specification:
                     (for gap junctions) or continuousProjection (for analogue/graded
                     synapses)'
             delay:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Delay to use (default: 0)'
             weight:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Weight to use (default: 1)'
             random_connectivity:
                 type: RandomConnectivity
@@ -298,7 +301,8 @@ specification:
                 type: str
                 description: ''
             probability:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: Random probability of connection.
     ConvergentConnectivity:
         definition: A ConvergentConnectivity definition.
@@ -331,19 +335,24 @@ specification:
                 type: str
                 description: Population to target
             cell_ids:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: Specific ids of _Cell_s to apply this input to (cannot
                     be used with percentage
             percentage:
-                type: float
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: Percentage of Cells to apply input to
             number_per_cell:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Number of individual inputs per selected Cell (default:
                     1)'
             segment_ids:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Which segments to target (default: [0])'
             weight:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Weight to use (default: 1)'
diff --git a/docs/README.md b/docs/README.md
@@ -1,4 +1,4 @@
-# Specification of NeuroMLlite v0.5.3
+# Specification of NeuroMLlite v0.5.7
 **Note: the NeuroMLlite specification is still in development! Subject to change...**
 
 ## Network
@@ -404,7 +404,7 @@ A Population definition.
 
   <tr>
     <td><b>size</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>The size of the population.</i></td>
  </tr>
 
@@ -622,14 +622,14 @@ A Projection definition.
 
   <tr>
     <td><b>delay</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Delay to use (default: 0)</i></td>
  </tr>
 
 
   <tr>
     <td><b>weight</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Weight to use (default: 1)</i></td>
  </tr>
 
@@ -671,7 +671,7 @@ A RandomConnectivity definition.
 
   <tr>
     <td><b>probability</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Random probability of connection.</i></td>
  </tr>
 
@@ -748,35 +748,35 @@ An Input definition.
 
   <tr>
     <td><b>cell_ids</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Specific ids of <a href="#cell">Cell</a>s to apply this input to (cannot be used with percentage</i></td>
  </tr>
 
 
   <tr>
     <td><b>percentage</b></td>
-    <td>float</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Percentage of Cells to apply input to</i></td>
  </tr>
 
 
   <tr>
     <td><b>number_per_cell</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Number of individual inputs per selected Cell (default: 1)</i></td>
  </tr>
 
 
   <tr>
     <td><b>segment_ids</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Which segments to target (default: [0])</i></td>
  </tr>
 
 
   <tr>
     <td><b>weight</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Weight to use (default: 1)</i></td>
  </tr>
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -53,7 +53,7 @@
     # space here is important since __version__ is used in generation of
     # version_info also
     if "__version__ =" in aline:
-        version = aline.split("\"")[1]
+        version = aline.split('"')[1]
 # The full version, including alpha/beta/rc tags.
 release = version
 

diff --git a/docs/generate.py b/docs/generate.py
@@ -2,7 +2,6 @@
 
 
 if __name__ == "__main__":
-
     net = neuromllite.Network(id="net")
     doc = net.generate_documentation(format="markdown")
     print(doc)

diff --git a/examples/Example10_Lorenz.json b/examples/Example10_Lorenz.json
@@ -1,6 +1,6 @@
 {
     "Example10_Lorenz": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 10: Lorenz",
         "parameters": {
             "N": 1,

diff --git a/examples/Example10_Lorenz.mdf.yaml b/examples/Example10_Lorenz.mdf.yaml
@@ -1,25 +1,32 @@
 Example10_Lorenz:
-    format: ModECI MDF v0.3
+    format: ModECI MDF v0.4
     graphs:
         Example10_Lorenz:
             notes: 'Example 10: Lorenz'
             nodes:
-                lorenzPop_0:
+                lorenzPop:
                     parameters:
                         sigma:
-                            value: 10.0
+                            value:
+                            - 10.0
                         b:
-                            value: 2.67
+                            value:
+                            - 2.67
                         r:
-                            value: 28.0
+                            value:
+                            - 28.0
                         x0:
-                            value: 1.0
+                            value:
+                            - 1.0
                         y0:
-                            value: 1.0
+                            value:
+                            - 1.0
                         z0:
-                            value: 1.0
+                            value:
+                            - 1.0
                         sec:
-                            value: 1.0
+                            value:
+                            - 1.0
                         x:
                             default_initial_value: x0
                             time_derivative: ( sigma * (y - x) ) / sec

diff --git a/examples/Example11_Synapses.json b/examples/Example11_Synapses.json
@@ -1,6 +1,6 @@
 {
     "Example11_Synapses": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 11: synaptic properties",
         "parameters": {
             "input_amp": 0.23,
@@ -87,7 +87,7 @@
             "stim": {
                 "input_source": "i_clamp",
                 "population": "pop0",
-                "percentage": 100.0
+                "percentage": 100
             }
         }
     }

diff --git a/examples/Example11_Synapses.net.nml b/examples/Example11_Synapses.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example11_Synapses">
-    <notes>Generated by NeuroMLlite v0.5.3
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Example11_Synapses
     Generation seed: 1234
     NeuroMLlite parameters: