Merge pull request #152 from NeuroML/development

NeuroML 2.2 release

Author: pgleeson

.github/workflows/ci.yml

@@ -2,9 +2,9 @@ name: Continuous builds
 
 on:
   push:
-    branches: [ master, development ]
+    branches: [ master, development, experimental, test* ]
   pull_request:
-    branches: [ master, development ]
+    branches: [ master, development, experimental, test* ]
 
 jobs:
   build:
@@ -13,22 +13,52 @@ jobs:
     strategy:
       matrix:
         python-version: [2.7, 3.7, 3.8, 3.9]
+      fail-fast: false
 
     steps:
+
     - uses: actions/checkout@v2
     - name: Set up Python  ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version:  ${{ matrix.python-version }}
+
+    - name: Print refs
+      run: |
+        echo "github.ref is: ${{ github.ref }}"
+        echo "github.base_ref is: ${{ github.base_ref }}"
+
+    - name: Install deps from development
+      if: ${{ github.ref == 'refs/heads/development' || github.base_ref == 'development' }}
+      run: |
+        echo "Using deps from development for our repos"
+        sed -E -i 's/((libNeuroML|NeuroMLlite|pylems|pyelectro|neurotune).git)@master/\1@development/' requirements-dev.txt
+        sed -E -i 's/((modelspec).git)@main/\1@development/' requirements-dev.txt
+
+    - name: Install deps from experimental
+      if: ${{ github.ref == 'refs/heads/experimental' || github.base_ref == 'experimental' }}
+      run: |
+        echo "Using deps from experimental - assuming development in others"
+        sed -E -i 's/((libNeuroML|NeuroMLlite|pylems|pyelectro|neurotune).git)@master/\1@development/' requirements-dev.txt
+        sed -E -i 's/((modelspec).git)@main/\1@development/' requirements-dev.txt
+
     - name: Install package
       run: |
         python -m pip install --upgrade pip
-        pip install flake8
+        pip install -r requirements-dev.txt
+        pip install pytest
         pip install .
-    - name: Lint with flake8
-      run: |
-        flake8 . --count --exit-zero --show-source --max-line-length=127 --statistics
+
     - name: Run tests
       run: |
+        pytest .
         pynml -h
-        ./test-ghactions.sh
+
+        # For now, only test neuron related examples on py3
+        if [[  ${{ matrix.python-version }} == "3."* ]]; then argnrn=-neuron ; fi
+        ./test-ghactions.sh $argnrn
+
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        flake8 . --count --exit-zero --show-source --max-line-length=127 --statistics

.gitignore

@@ -121,3 +121,4 @@ examples/results/*.dat
 /examples/test_data/ca1/*.mod
 /examples/test_data/ca1/*.hoc
 .venv/
+/examples/LEMS_NML2_Ex5_DetCell_brian2.py

.mypy.ini

@@ -0,0 +1,2 @@
+[mypy]
+ignore_missing_imports = True

CONTRIBUTING.md

@@ -11,6 +11,10 @@ pyNeuroML. Pull requests with enhancements and bug fixes are welcome.
 
 2. The source code uses spaces, and each tab is equivalent to 4 spaces.
 
+3. We use the [reStructuredText (reST)
+   format](https://stackoverflow.com/a/24385103/375067) for Python docstrings.
+   Please document your code when opening pull requests.
+
 ## Pull Request Process
 
 1. Please ensure that the automated build for your pull request passes.

README.md

@@ -2,14 +2,15 @@ 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)
+[![Documentation Status](https://readthedocs.org/projects/pyneuroml/badge/?version=latest)](https://pyneuroml.readthedocs.io/en/latest/?badge=latest)
 [![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)
+[![Gitter](https://badges.gitter.im/NeuroML/community.svg)](https://gitter.im/NeuroML/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
 A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/extras/Readme.md

@@ -0,0 +1,3 @@
+# Extras
+
+These make the doc generation fail, so we leave them out for the moment.

docs/extras/pyneuroml.neuron.analysis.rst

@@ -0,0 +1,21 @@
+pyneuroml.neuron.analysis package
+=================================
+
+Submodules
+----------
+
+pyneuroml.neuron.analysis.HHanalyse module
+------------------------------------------
+
+.. automodule:: pyneuroml.neuron.analysis.HHanalyse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pyneuroml.neuron.analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/extras/pyneuroml.neuron.rst

@@ -0,0 +1,29 @@
+pyneuroml.neuron package
+========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pyneuroml.neuron.analysis
+
+Submodules
+----------
+
+pyneuroml.neuron.nrn\_export\_utils module
+------------------------------------------
+
+.. automodule:: pyneuroml.neuron.nrn_export_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pyneuroml.neuron
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd