Merge pull request #119 from NeuralEnsemble/development

NeuroML 2.2 release

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [2.7, 3.7, 3.8, 3.9]
+        python-version: ["2.7", "3.7", "3.8", "3.9", "3.10"]
 
     steps:
     - uses: actions/checkout@v2
@@ -27,8 +27,9 @@ jobs:
 
     - name: Install dependencies
       run: |
+        sudo apt-get install libhdf5-serial-dev liblzo2-dev -y
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
     - name: Build package

.github/workflows/regenerate.yml

@@ -0,0 +1,53 @@
+name: Regenerate nml.py
+
+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", "3.10"]
+
+    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: |
+        sudo apt-get install libhdf5-serial-dev liblzo2-dev -y
+        python -m pip install --upgrade pip
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Rebuild nml.py
+      run: |
+        cd neuroml/nml && rm -f nml.py && ./regenerate-nml.sh -a
+
+    - name: Build package
+      run: |
+        pip install .[full]
+
+    - name: Test with pytest
+      run: |
+        pytest
+
+    - name: Run examples
+      run: |
+        cd ./neuroml/examples && python run_all.py
+
+    - 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

@@ -50,3 +50,5 @@ neuroml/test/*.h5
 /mongoo
 
 .venv
+/data
+.mypy_cache/

README.md

@@ -1,6 +1,5 @@
 ## Introduction
 
-[![Travis CI](https://travis-ci.org/NeuralEnsemble/libNeuroML.svg?branch=master)](https://travis-ci.org/NeuralEnsemble/libNeuroML)
 [![GH Build](https://github.com/NeuralEnsemble/libNeuroML/actions/workflows/ci.yml/badge.svg)](https://github.com/NeuralEnsemble/libNeuroML/actions/workflows/ci.yml)
 [![Documentation Status](https://readthedocs.org/projects/libneuroml/badge/?version=latest)](https://libneuroml.readthedocs.io/en/latest/?badge=latest)
 [![PyPI](https://img.shields.io/pypi/v/libNeuroML)](https://pypi.org/project/libNeuroML/)
@@ -10,6 +9,7 @@
 [![GitHub issues](https://img.shields.io/github/issues/NeuralEnsemble/libNeuroML)](https://github.com/NeuralEnsemble/libNeuroML/issues)
 [![GitHub Org's stars](https://img.shields.io/github/stars/NeuralEnsemble?style=social)](https://github.com/NeuralEnsemble)
 [![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)
 
 This package provides Python libNeuroML, for working with neuronal models specified in [NeuroML 2](http://neuroml.org/neuromlv2).
 
@@ -25,7 +25,7 @@ Documentation is available at http://readthedocs.org/docs/libneuroml/en/latest/
 
 For installation instructions, see http://readthedocs.org/docs/libneuroml/en/latest/install.html
 
-For an overview of all NeuroML related libraries/documentation/publications see https://neuroml.org/getneuroml.
+For an overview of all NeuroML related libraries/documentation/publications see https://docs.neuroml.org
 
 ## pyNeuroML
 
@@ -36,50 +36,77 @@ pyNeuroML builds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML)
 
 ## Development process for libNeuroML
 
-Most of the work happens in the [development branch](https://github.com/NeuralEnsemble/libNeuroML/tree/development). That branch is kept up to date with the development branches for [NeuroML 2](https://github.com/NeuroML/NeuroML2/tree/development) and related libraries. See https://neuroml.org/getneuroml for an overview of the various NeuroML libraries.
+Most of the work happens in the [development branch](https://github.com/NeuralEnsemble/libNeuroML/tree/development).
+That branch is kept up to date with the development branches for [NeuroML 2](https://github.com/NeuroML/NeuroML2/tree/development) and related libraries.
+See https://docs.neuroml.org/ for an overview of the various NeuroML libraries.
 
 ## Changelog
+### version 0.2.57 (dev)
+
+- Enable Python 3.10 support
+- Regenerate nml.py with generateDS using Python 3
+- Add generic `add` method to all NeuroML ComponentType classes that allows users to easily construct their NeuroML documents.
+- Improve unit tests
+- DEPRECATION notice: `append_to_element` will be deprecated in future releases, please use the `add` method instead
+
+### version 0.2.56
+
+- Documentation updates for RTD and other minor fixes.
+
+### version 0.2.55
+
+- Patch release with minor changes under the hood.
+- Use PyTest for testing.
+- Enable CI on GitHub Actions
 
 ### version 0.2.54
- - Using Schema for NeuroML v2.1. Better compatibility with Python 3
 
- ### version 0.2.50
-  - Updated to use the final stable Schema for NeuroML v2.0
+- Using Schema for NeuroML v2.1. Better compatibility with Python 3
+
+### version 0.2.50
+
+- Updated to use the final stable Schema for NeuroML v2.0
 
 ### version 0.2.47
- - Updated to use the final stable Schema for NeuroML v2beta5
+
+- Updated to use the final stable Schema for NeuroML v2beta5
 
 ### version 0.2.18
- - Updated to use the final stable Schema for NeuroML v2beta4
- - Tested with Python 3
+
+- Updated to use the final stable Schema for NeuroML v2beta4
+- Tested with Python 3
 
 ### version 0.2.4
- - Updated to use the Schema for NeuroML v2beta4
+
+- Updated to use the Schema for NeuroML v2beta4
 
 ### version 0.2.2
- - Updated to use the Schema for NeuroML v2beta3
- - Ensures numpy & pytables are only required when using non-XML loaders/writers
+
+- Updated to use the Schema for NeuroML v2beta3
+- Ensures numpy & pytables are only required when using non-XML loaders/writers
 
 ### version 0.2.0
- - Updated to use the Schema for NeuroML v2beta2
+
+- Updated to use the Schema for NeuroML v2beta2
 
 ### version 0.1.9
- - Minor release: Update to latest schema
+
+- Minor release: Update to latest schema
 
 ### version 0.1.8
 
- - Several Bug fixes and small enhamcements
- - Support for latest NeuroML schema (see change outline)
- - JSON serialization
- - MongoDB backend
- - HDF5 serialization
- - Improved installation process
- - All usage examples are now run on the Travis-CI continuous integration server to confirm that that they do not error.
- - Schema validation utility
- - Improved documentation and documentation new look
+- Several Bug fixes and small enhamcements
+- Support for latest NeuroML schema (see change outline)
+- JSON serialization
+- MongoDB backend
+- HDF5 serialization
+- Improved installation process
+- All usage examples are now run on the Travis-CI continuous integration server to confirm that that they do not error.
+- Schema validation utility
+- Improved documentation and documentation new look
 
 
-:copyright: Copyright 2020 by the libNeuroML team, see [AUTHORS](AUTHORS). Modified BSD License, see [LICENSE](LICENSE) for details.
+:copyright: Copyright 2021 by the libNeuroML team, see [AUTHORS](AUTHORS). Modified BSD License, see [LICENSE](LICENSE) for details.
 
 
 [![Build Status](https://api.travis-ci.org/NeuralEnsemble/libNeuroML.png)](https://travis-ci.org/NeuralEnsemble/libNeuroML)