Merge branch 'test_neuroml' into test_sbml

Author: pgleeson

.github/workflows/ci.yml

@@ -60,11 +60,7 @@ jobs:
         cd ../neuroml2
         python neuroml2_spec.py
 
-        pip install pyneuroml
-
-        # Requires: pip install pyneuroml
-        pynml -validate hello_world_neuroml.net.nml
-        pynml -validate TestNeuroML.xml
+        # Note: NeuroML files will be validated with OMV below
 
     - name: Run pytest
       run: |
@@ -78,7 +74,6 @@ jobs:
           cd examples
           python Example1.py
 
-
     - name: Install MDF
       run: |
 
@@ -100,6 +95,20 @@ jobs:
         make clean
         make html
 
+    - name: Install and test with OMV
+      if: ${{ matrix.runs-on != 'windows-latest' }}
+      run: |
+        # Note: OMV not well tested on Windows...
+
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+        pip install scipy sympy matplotlib cython pandas tables
+
+        # Run OMV tests on all engines
+        cd examples
+        omv all -V
+
+        omv list -V # list installed engines
+
     - name: Final version info
       run: |
           pip list

.github/workflows/static.yml

@@ -0,0 +1,71 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[dev]
+
+    - name: List packages so far
+      run: |
+        pip list
+
+    - name: Build Documentation
+      run: |
+
+        pip install .[docs]
+        cd docs
+        python generate.py
+        python contributors.py
+        cd sphinx
+        make clean
+        make html
+
+    - name: Setup Pages
+      uses: actions/configure-pages@v3
+
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v2
+      with:
+        # Upload just docs
+        path: 'docs/sphinx/build/html'
+
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v2

docs/sphinx/source/api/Contributors.md

@@ -3,7 +3,7 @@
 # Modelspec contributors
 
 This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
-This page is generated periodically, most recently on 2023-08-23.
+This page is generated periodically, most recently on 2023-09-13.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
 - Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))

examples/neuroml2/.test.validate.omt

@@ -0,0 +1,5 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+# This test will validate NeuroML 2 files in the current directory using: jnml -validate *.nml
+target: "*.nml TestNeuroML.xml"
+engine: jNeuroML_validate

src/modelspec/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.2"
+__version__ = "0.3.3"
 
 from .base_types import Base, define, has, field, fields, optional, instance_of, in_
 

test_all.sh

@@ -31,6 +31,11 @@ cd ../..
 
 pytest tests -v
 
+## Run OMV tests
+
+# See https://github.com/OpenSourceBrain/osb-model-validation
+omv all -V
+
 
 ## Generate the docs
 
@@ -42,4 +47,6 @@ make clean
 make html
 cd ..
 
+## Format all file
+
 pre-commit run --all-files