Version 0.5.4

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+exclude = NeuroML2

.github/workflows/ci.yml

@@ -0,0 +1,59 @@
+name: Build
+
+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 dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Checkout NeuroML2
+      uses: actions/checkout@v2
+      with:
+        repository: NeuroML/NeuroML2
+        ref: development
+        path: NeuroML2
+
+    - name: Build package
+      run: |
+        pip install .
+
+    - name: Test with pytest
+      run: |
+        pytest
+
+    - name: Test examples
+      run: |
+        ./ci/run-examples-ghactions.sh
+
+    - name: Test API tests
+      run: |
+        ./ci/run-apitest.sh
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

.gitignore

@@ -5,7 +5,7 @@ results
 test*.sh
 build
 *~
-doc
+doc/_build
 *.pyc
 *.pyo
 .project

.travis.yml

@@ -9,6 +9,7 @@ python:
 # command to install dependencies
 install:
   - "pip install ."
+  - "pip install pytest"
   - git clone https://github.com/NeuroML/NeuroML2
   - cd NeuroML2
   # Use the development branch of NeuroML2
@@ -20,7 +21,7 @@ install:
 script:
   ###       Run main python unit tests (not many yet...)
 
-  - nosetests -vs
+  - pytest -v
 
   ###      Try running "standard" LEMS examples
   - ./pylems examples/example1.xml -nogui

README.md

@@ -1,5 +1,8 @@
 ## PyLEMS 
 
+[![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.
 
 For more about PyLEMS see:

ci/run-apitest.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Copyright 2021 LEMS contributors
+# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com> 
+# File : run-apitest.sh
+#
+# Run api tests on GitHub actions
+
+python examples/apitest.py
+python examples/apitest2.py
+python examples/loadtest.py
+
+# Update NeuroML2 path for CI
+if [ "$CI" = "true" ]; then
+    sed -i 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py
+fi
+python lems/dlems/exportdlems.py

ci/run-examples-ghactions.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+
+# Copyright 2021 LEMS contributors
+# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com> 
+# File : run-examples-ghactions.sh
+#
+# Run tests on GitHub actions
+
+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
+# 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_Ex13_Instances.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...

doc/Makefile

@@ -0,0 +1,153 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PyLEMS.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PyLEMS.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/PyLEMS"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PyLEMS"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."