Merge pull request #65 from LEMS/development

NeuroML 2.2 release

Author: pgleeson

.github/workflows/examples.yml

@@ -0,0 +1,38 @@
+# Check that examples are same in pylems and in jlems
+name: Check LEMS examples
+
+on:
+  push:
+    branches:  [ master, development, experimental ]
+
+jobs:
+  verify:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: nelonoel/[email protected]
+
+    # https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
+    - name: Extract branch name
+      shell: bash
+      run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+      id: extract_branch
+
+    - name: Checkout jlems
+      uses: actions/checkout@v2
+      with:
+        repository: LEMS/jLEMS
+        ref: ${{ steps.extract_branch.outputs.branch }}
+        path: jlems
+
+    - name: check examples
+      run: |
+        for ex in "example1.xml" "example2.xml" "example3.xml" "example4.xml" "example5.xml" "example6.xml" "example7.xml" "example8.xml" "bounce-conditional.xml" ; do
+
+          if ! diff -ur "examples/$ex" "jlems/src/test/resources/$ex" ; then
+            echo "Example file $ex is not identical"
+            exit -1
+          fi
+        done

.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@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      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@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

README.md

@@ -1,6 +1,6 @@
-## PyLEMS 
+## PyLEMS
 
-[![Documentation Status](https://readthedocs.org/projects/pylems/badge/?version=latest)](https://pylems.readthedocs.io/en/latest/?badge=latest)
+[![Build](https://github.com/LEMS/pylems/actions/workflows/ci.yml/badge.svg)](https://github.com/LEMS/pylems/actions/workflows/ci.yml) [![Documentation Status](https://readthedocs.org/projects/pylems/badge/?version=latest)](https://pylems.readthedocs.io/en/latest/?badge=latest)
 
 
 A LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2 (http://neuroml.org/neuroml2.php) models.
@@ -13,10 +13,10 @@ Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapa
 
 _**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_
 
-For more details on LEMS see: 
+For more details on LEMS see:
 
-Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver, 
-**LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2**, 
+Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver,
+**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
 
 
@@ -33,7 +33,7 @@ To install as root:
 Alternatively, you can obtain the latest version with
 
     git clone https://github.com/LEMS/pylems.git
-    cd pylems 
+    cd pylems
     git checkout development   # optional
     sudo python setup.py install
 
@@ -81,9 +81,9 @@ Alternatively, you can obtain the latest version with
 - 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 
+   i.e. use `<Simulation...>` not `<SimulationSet...>`, to work in PyLEMS
+
 
-      
 **LEMS elements that do not work**
 
 - KSChannel
@@ -105,5 +105,3 @@ pylems is integrated with the the [Travis Continuous Integration service](http:/
 [![Build Status](https://travis-ci.com/LEMS/pylems.png?branch=master)](https://travis-ci.com/LEMS/pylems)
 
 This code is distributed under the terms of the GNU Lesser General Public License.
-
-

ci/run-examples-ghactions.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Copyright 2021 LEMS contributors
-# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com> 
+# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
 # File : run-examples-ghactions.sh
 #
 # Run tests on GitHub actions
@@ -16,6 +16,7 @@ echo "Running standard LEMS examples"
 #./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