Merge pull request #68 from LEMS/development

For NML2.3 release

.github/workflows/ci.yml

@@ -2,35 +2,35 @@ name: Build
 
 on:
   push:
-    branches: [ master, development, test* ]
+    branches: [ master, development, experimental, test* ]
   pull_request:
-    branches: [ master, development, test* ]
+    branches: [ master, development, experimental, test* ]
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.runs-on }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.7", "3.9", "3.10", "3.11"]
+        runs-on: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install pytest pytest-cov
 
     - name: Checkout NeuroML2
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: NeuroML/NeuroML2
         ref: development
@@ -42,7 +42,7 @@ jobs:
 
     - name: Test with pytest
       run: |
-        pytest
+        pytest --cov=lems
 
     - name: Test examples
       run: |
@@ -52,6 +52,10 @@ jobs:
       run: |
         ./ci/run-apitest.sh
 
+    - name: Final version info
+      run: |
+          pip list
+
     - name: Lint with flake8
       run: |
         # Install flake

.github/workflows/examples.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: nelonoel/[email protected]
 
     # https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
@@ -21,7 +21,7 @@ jobs:
       id: extract_branch
 
     - name: Checkout jlems
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: LEMS/jLEMS
         ref: ${{ steps.extract_branch.outputs.branch }}

.github/workflows/python-publish.yml

@@ -18,9 +18,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

.gitignore

@@ -14,5 +14,7 @@ doc/_build
 comp_*
 /lems/test/hhcell_resaved3.xml
 /lems/__init__$py.class
-/PyLEMS.egg-info
+*PyLEMS.egg-info
 /dist
+*ken.sh
+*.whl

MANIFEST.in

@@ -2,3 +2,4 @@ include README.md
 include examples/*.xml
 include examples/*.py
 include LICENSE.lesser
+recursive-include man *.1

Makefile

@@ -18,46 +18,46 @@ clean:
 	rm -rf doc/epydoc/*
 
 example1:
-	./pylems examples/example1.xml
+	pylems examples/example1.xml
 
 example2:
-	./pylems examples/example2.xml
+	pylems examples/example2.xml
 
 example3:
-	./pylems examples/example3.xml
+	pylems examples/example3.xml
 
 example4:
-	./pylems examples/example4.xml
+	pylems examples/example4.xml
 
 example5:
-	./pylems examples/example5.xml
+	pylems examples/example5.xml
 
 example6:
-	./pylems examples/example6.xml
+	pylems examples/example6.xml
 
 example7:
-	./pylems examples/example7.xml
+	pylems examples/example7.xml
 
 example8:
-	./pylems examples/example8.xml
+	pylems examples/example8.xml
 
 example9:
-	./pylems examples/example9.xml
+	pylems examples/example9.xml
 
 ex0:
-	./pylems examples/LEMS_NML2_Ex0.xml
+	pylems examples/LEMS_NML2_Ex0.xml
 
 nmlex0:
-	./pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex0_IaF.xml
+	pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex0_IaF.xml
 
 nmlex1:
-	./pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex1_HH.xml
+	pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex1_HH.xml
 
 nmlex2:
-	./pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex2_Izh.xml
+	pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex2_Izh.xml
 
 nmlex3:
-	./pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex3_Net.xml
+	pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex3_Net.xml
 
 run:	example1
 

README.md

@@ -5,8 +5,7 @@
 [![Documentation Status](https://readthedocs.org/projects/pylems/badge/?version=latest)](https://pylems.readthedocs.io/en/latest/?badge=latest)
 [![PyPI](https://img.shields.io/pypi/v/pylems)](https://pypi.org/project/pylems/)
 
-
-A LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2 (http://neuroml.org/neuroml2.php) models.
+A LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2  models (see [here](https://docs.neuroml.org/Userdocs/Software/pyLEMS.html)).
 
 For more about PyLEMS see:
 
@@ -22,36 +21,35 @@ Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin,
 **LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2**,
 [Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00079/abstract), doi: 10.3389/fninf.2014.00079
 
-
 ### Installation
 
 A stable version of PyLEMS is [available on PyPI](https://pypi.python.org/pypi/PyLEMS) using [pip](https://pip.pypa.io/en/latest/installing.html):
 
-    pip install pylems
-
-To install as root:
-
-    sudo pip install pylems
+```
+pip install pylems
+```
 
 Alternatively, you can obtain the latest version with
 
-    git clone https://github.com/LEMS/pylems.git
-    cd pylems
-    git checkout development   # optional
-    sudo python setup.py install
+```
+git clone https://github.com/LEMS/pylems.git
+cd pylems
+git checkout development   # optional
+pip install .
+```
 
 ### Usage as a LEMS model simulator
 
-    pylems [options] LEMS_file
+```
+pylems [options] LEMS_file
+```
 
 **Options**
 
 - -I/-include path - Adds a directory to the model file include search path
 
-
 ### Examples
 
-
 **NeuroML examples (from https://github.com/NeuroML/NeuroML2/tree/development/NeuroML2CoreTypes)**
 
 - Example 0 --  Working
@@ -74,7 +72,6 @@ Alternatively, you can obtain the latest version with
 - Example 17 -- Working
 - Example 18 -- Working
 
-
 **LEMS examples (in directory examples)**
 
 - example1.xml --  Working
@@ -83,9 +80,8 @@ Alternatively, you can obtain the latest version with
 - example4.xml --  Not working (Unsupported in PyLEMS: KSChannel)
 - example5.xml --  Not working (Unsupported in PyLEMS: KSChannel)
 - example6.xml --  Working
--- TODO: Rest of examples require an update to the `<Simulation>` element,
-   i.e. use `<Simulation...>` not `<SimulationSet...>`, to work in PyLEMS
 
+TODO: Rest of examples require an update to the `<Simulation>` element, i.e. use `<Simulation...>` not `<SimulationSet...>`, to work in PyLEMS
 
 **LEMS elements that do not work**
 

ci/run-apitest.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2021 LEMS contributors
+# Copyright 2023 LEMS contributors
 # Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com> 
 # File : run-apitest.sh
 #
@@ -12,6 +12,10 @@ python examples/loadtest.py
 
 # Update NeuroML2 path for CI
 if [ "$CI" = "true" ]; then
-    sed -i 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py
+    if [ "$RUNNER_OS" = "macOS" ]; then
+        sed -i '' 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py;
+    else
+        sed -i 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py;
+    fi
 fi
-python lems/dlems/exportdlems.py
+python lems/dlems/exportdlems.py

ci/run-examples-ghactions.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2021 LEMS contributors
+# Copyright 2023 LEMS contributors
 # Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
 # File : run-examples-ghactions.sh
 #
@@ -10,33 +10,33 @@ mkdir results
 
 ###      Try running "standard" LEMS examples
 echo "Running standard LEMS examples"
-./pylems examples/example1.xml -nogui
-./pylems examples/example2.xml -nogui
-./pylems examples/example3.xml -nogui
-#./pylems examples/example4.xml -nogui     # Not working (Unsupported in PyLEMS: KSChannel)
-#./pylems examples/example5.xml -nogui     # Not working (Unsupported in PyLEMS: KSChannel)
-./pylems examples/example6.xml -nogui
-./pylems examples/bounce-conditional.xml -nogui
+pylems examples/example1.xml -nogui
+pylems examples/example2.xml -nogui
+pylems examples/example3.xml -nogui
+#pylems examples/example4.xml -nogui     # Not working (Unsupported in PyLEMS: KSChannel)
+#pylems examples/example5.xml -nogui     # Not working (Unsupported in PyLEMS: KSChannel)
+pylems examples/example6.xml -nogui
+pylems examples/bounce-conditional.xml -nogui
 # Rest of examples require an update to the <Simulation> element, i.e. use <Simulation...> not <SimulationSet...>, to work in PyLEMS
 
 ###      Try running NeuroML 2 examples
 echo "Running NeuroML2 examples"
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex1_HH.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex2_Izh.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex3_Net.xml -nogui
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex4_KS.xml -nogui  # Not working (Unsupported in PyLEMS: KSChannel)
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex6_NMDA.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex7_STP.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex8_AdEx.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -nogui
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex10_Q10.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex11_STDP.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex1_HH.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex2_Izh.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex3_Net.xml -nogui
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex4_KS.xml -nogui  # Not working (Unsupported in PyLEMS: KSChannel)
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex6_NMDA.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex7_STP.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex8_AdEx.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -nogui
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex10_Q10.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex11_STDP.xml -nogui
 
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex13_Instances.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex13_Instances.xml -nogui
 
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml -nogui
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml -nogui
 
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex17_Tissue.xml -nogui
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex18_GHK.xml -nogui  # Mismatch...
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex17_Tissue.xml -nogui
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex18_GHK.xml -nogui  # Mismatch...