Merge pull request #168 from NeuralEnsemble/development

Changes for NML v2.3 release

.github/workflows/ci.yml

@@ -2,50 +2,56 @@ name: Build
 
 on:
   push:
-    branches: [ master, development ]
+    branches: [ master, development, experimental ]
   pull_request:
-    branches: [ master, development ]
+    branches: [ master, development, experimental ]
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
-    strategy:      
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        runs-on: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
     - uses: actions/checkout@v3
 
-    - name: Start MongoDB
-      uses: supercharge/[email protected]
-
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
-        sudo apt-get install libhdf5-serial-dev liblzo2-dev -y
+        #sudo apt-get install libhdf5-serial-dev liblzo2-dev libgraphviz-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: Build package
       run: |
         pip install .[full]
 
     - name: Test with pytest
+      if: ${{ matrix.runs-on == 'ubuntu-latest' }}
       run: |
-        pytest
+        # Just test on linux for now...
+        pytest -vs 
 
     - name: Run examples
+      if: ${{ matrix.python-version != '3.7' || matrix.runs-on != 'macos-latest' }} # issue with _bz2 module...
+      run: |
+        cd neuroml/examples
+        python run_all.py
+
+    - name: Final version info
       run: |
-        cd ./neuroml/examples && python run_all.py
+          pip list
 
     - name: Lint with flake8
+      if: ${{ matrix.runs-on == 'ubuntu-latest' }}
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

.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@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      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@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/regenerate.yml

@@ -2,32 +2,31 @@ name: Regenerate nml.py
 
 on:
   push:
-    branches: [ master, development ]
+    branches: [ master, development, experimental ]
   pull_request:
-    branches: [ master, development ]
+    branches: [ master, development, experimental ]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
-        sudo apt-get install libhdf5-serial-dev liblzo2-dev -y
+        sudo apt-get install libhdf5-serial-dev liblzo2-dev libgraphviz-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
+        pip install .[dev]
 
     - name: Rebuild nml.py
       run: |

.gitignore

@@ -52,3 +52,6 @@ neuroml/test/*.h5
 .venv
 /data
 .mypy_cache/
+
+sed-script.txt
+/test.sh

.readthedocs.yaml

@@ -0,0 +1,18 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+
+sphinx:
+  configuration: doc/conf.py
+
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

AUTHORS

@@ -2,9 +2,10 @@ Contributions to the Python libNeuroML package:
 
 Andrew Davison [1]
 Michele Mattioni [2]
-Padraig Gleeson [3] 
+Padraig Gleeson [3]
 Mike Vella [4]
 Mike Hull [5]
+Ankur Sinha [3]
 
 [1] UNIC, CNRS, Gif sur Yvette
 [2] EBI
@@ -13,3 +14,8 @@ Mike Hull [5]
 [5] University of Bristol
 
 If you contribute code, please add your name and affiliation to this file.
+
+Please see also:
+
+- https://github.com/NeuralEnsemble/libNeuroML/graphs/contributors
+- https://docs.neuroml.org/NeuroMLOrg/Contributors.html

README.md

@@ -33,15 +33,38 @@ A related package, **[pyNeuroML](https://github.com/NeuroML/pyNeuroML)** builds
 
 pyNeuroML builds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) & [PyLEMS](https://github.com/LEMS/pylems) and wraps functionality from [jNeuroML](https://github.com/NeuroML/jNeuroML).
 
-
 ## 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://docs.neuroml.org/ for an overview of the various NeuroML libraries.
 
 ## Changelog
-### version 0.2.57 (dev)
+
+### version 0.4.1
+
+- add multiple cell builder utility functions
+- performance improvements in generic helper functions
+- documentation fixes/improvements
+- add type annotations to all nml classes to aid users
+- add level 1 validation method
+- add generic component inspection methods
+
+### version 0.4.0
+
+- update to use schema version 2.3
+- drop python 2 support
+
+### version 0.3.1
+
+- include schema documentation in generated `nml.py` API
+- introduce generic methods to add child/children elements to components
+
+### version 0.2.58
+
+- multiple documentation fixes
+
+### version 0.2.57
 
 - Enable Python 3.10 support
 - Regenerate nml.py with generateDS using Python 3
@@ -105,6 +128,4 @@ See https://docs.neuroml.org/ for an overview of the various NeuroML libraries.
 - Schema validation utility
 - Improved documentation and documentation new look
 
-
 :copyright: Copyright 2023 by the libNeuroML team, see [AUTHORS](AUTHORS). Modified BSD License, see [LICENSE](LICENSE) for details.
-