Merge pull request #90 from NeuroML/development

For NML v2.1 release

Author: pgleeson

.github/workflows/ci.yml

@@ -0,0 +1,34 @@
+name: Continuous builds
+
+on:
+  push:
+    branches: [ master, development ]
+  pull_request:
+    branches: [ master, development ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [2.7, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version:  ${{ matrix.python-version }}
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8
+        pip install .
+    - name: Lint with flake8
+      run: |
+        flake8 . --count --exit-zero --show-source --max-line-length=127 --statistics
+    - name: Run tests
+      run: |
+        pynml -h
+        ./test-ghactions.sh

README.md

@@ -1,22 +1,53 @@
 pyNeuroML
 =========
 
+[![GitHub CI](https://github.com/NeuroML/pyNeuroML/actions/workflows/ci.yml/badge.svg)](https://github.com/NeuroML/pyNeuroML/actions/workflows/ci.yml)
+[![Travis CI](https://travis-ci.com/NeuroML/pyNeuroML.svg?branch=master)](https://travis-ci.com/NeuroML/pyNeuroML)
+[![PyPI](https://img.shields.io/pypi/v/pyNeuroML)](https://pypi.org/project/pyNeuroML/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyNeuroML)](https://pypi.org/project/pyNeuroML/)
+[![GitHub](https://img.shields.io/github/license/NeuroML/pyNeuroML)](https://github.com/NeuroML/pyNeuroML/blob/master/LICENSE.lesser)
+[![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuroML/pyNeuroML)](https://github.com/NeuroML/pyNeuroML/pulls)
+[![GitHub issues](https://img.shields.io/github/issues/NeuroML/pyNeuroML)](https://github.com/NeuroML/pyNeuroML/issues)
+[![GitHub Org's stars](https://img.shields.io/github/stars/NeuroML?style=social)](https://github.com/NeuroML)
+[![Twitter Follow](https://img.shields.io/twitter/follow/NeuroML?style=social)](https://twitter.com/NeuroML)
+
 A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.
 
 Builds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) & [PyLEMS](https://github.com/LEMS/pylems) and wraps functionality from [jNeuroML](https://github.com/NeuroML/jNeuroML).
 
 Installation
 ------------
 
+### Dependencies
+
+pyNeuroML relies on additional software to carry out its functions:
+
+- Java Runtime environment (JRE)
+- dot (from [Graphviz](http://graphviz.org/))
+- lxml
+
+On most Linux systems, these can be installed using the default package manager.
+On Ubuntu based distributions:
+
+    sudo apt-get install python-lxml graphviz openjdk-11-jdk
+
+
 ### Pip
 
-pyNeuroML can be installed with pip:
+pyNeuroML can be installed with pip (preferably in a [virtual environment](https://docs.python.org/3/tutorial/venv.html)):
+
+    pip install pyneuroml
+
+### Fedora
 
-    sudo pip install pyneuroml
+The [NeuroFedora](https://neuro.fedoraproject.org) community initiative provides pyNeuroML for use on the [Fedora Linux Distribution](https://getfedora.org).
+Fedora users can install pyNeuroML using the following commands:
 
-You may need to install lxml on Linux with:
+    sudo dnf copr enable @neurofedora/neurofedora-extra
+    sudo dnf install python3-pyneuroml
 
-    sudo apt-get install python-lxml
+This will also pull in all the necessary dependencies (Java, lxml, graphviz).
+Please see the [project documentation](https://docs.fedoraproject.org/en-US/neurofedora/copr/) for more information.
 
 ### Installation from source
 

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  v1.7.1
-         org.neuroml.model   v1.7.1
-         jLEMS               v0.10.3
+         org.neuroml.export  v1.7.2
+         org.neuroml.model   v1.7.2
+         jLEMS               v0.10.4
 
 ENDCOMMENT
 

pyneuroml/__init__.py

@@ -1,5 +1,5 @@
 
 
-__version__ = '0.5.9'
+__version__ = '0.5.11'
 
-JNEUROML_VERSION = '0.10.1'
+JNEUROML_VERSION = '0.10.3'