Merge pull request #257 from NeuroML/development

 Changes for NML v2.3 release

.all-contributorsrc

@@ -0,0 +1,178 @@
+{
+  "projectName": "pyNeuroML",
+  "projectOwner": "NeuroML",
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "files": [
+    "README.md"
+  ],
+  "imageSize": 100,
+  "commit": true,
+  "commitConvention": "angular",
+  "contributors": [
+    {
+      "login": "pgleeson",
+      "name": "Padraig Gleeson",
+      "avatar_url": "https://avatars.githubusercontent.com/u/1556687?v=4",
+      "profile": "http://www.opensourcebrain.org/",
+      "contributions": [
+        "bug",
+        "code",
+        "content",
+        "data",
+        "doc",
+        "design",
+        "eventOrganizing",
+        "ideas",
+        "infra",
+        "maintenance",
+        "mentoring",
+        "platform",
+        "projectManagement",
+        "question",
+        "research",
+        "review",
+        "tool",
+        "tutorial",
+        "talk",
+        "userTesting"
+      ]
+    },
+    {
+      "login": "sanjayankur31",
+      "name": "Ankur Sinha",
+      "avatar_url": "https://avatars.githubusercontent.com/u/102575?v=4",
+      "profile": "https://ankursinha.in/",
+      "contributions": [
+        "bug",
+        "code",
+        "content",
+        "data",
+        "doc",
+        "design",
+        "eventOrganizing",
+        "ideas",
+        "mentoring",
+        "platform",
+        "question",
+        "research"
+      ]
+    },
+    {
+      "login": "borismarin",
+      "name": "Boris Marin",
+      "avatar_url": "https://avatars.githubusercontent.com/u/3452783?v=4",
+      "profile": "https://github.com/borismarin",
+      "contributions": [
+        "bug",
+        "code",
+        "content",
+        "data",
+        "doc",
+        "design",
+        "eventOrganizing",
+        "ideas",
+        "infra",
+        "maintenance",
+        "platform",
+        "question",
+        "research",
+        "review",
+        "tool",
+        "userTesting"
+      ]
+    },
+    {
+      "login": "rgerkin",
+      "name": "Richard C Gerkin",
+      "avatar_url": "https://avatars.githubusercontent.com/u/549787?v=4",
+      "profile": "http://rick.gerk.in/",
+      "contributions": [
+        "bug",
+        "code",
+        "ideas",
+        "maintenance",
+        "platform",
+        "research",
+        "review",
+        "tool",
+        "userTesting"
+      ]
+    },
+    {
+      "login": "lungd",
+      "name": "David Lung",
+      "avatar_url": "https://avatars.githubusercontent.com/u/5890526?v=4",
+      "profile": "https://github.com/lungd",
+      "contributions": [
+        "bug",
+        "code",
+        "maintenance",
+        "tool",
+        "userTesting"
+      ]
+    },
+    {
+      "login": "mwatts15",
+      "name": "Mark Watts",
+      "avatar_url": "https://avatars.githubusercontent.com/u/1487560?v=4",
+      "profile": "https://www.thispersondoesnotexist.com/",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "ccluri",
+      "name": "Chaitanya Chintaluri ",
+      "avatar_url": "https://avatars.githubusercontent.com/u/546703?v=4",
+      "profile": "https://chchaitanya.wordpress.com/",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "34383c",
+      "name": "34383c",
+      "avatar_url": "https://avatars.githubusercontent.com/u/17238193?v=4",
+      "profile": "https://github.com/34383c",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "jrieke",
+      "name": "Johannes Rieke",
+      "avatar_url": "https://avatars.githubusercontent.com/u/5103165?v=4",
+      "profile": "https://github.com/jrieke",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "andrisecker",
+      "name": "András Ecker",
+      "avatar_url": "https://avatars.githubusercontent.com/u/13274870?v=4",
+      "profile": "https://github.com/andrisecker",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "RokasSt",
+      "name": "Rokas Stanislovas",
+      "avatar_url": "https://avatars.githubusercontent.com/u/12904422?v=4",
+      "profile": "https://github.com/RokasSt",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    }
+  ],
+  "contributorsPerLine": 7,
+  "linkToUsage": true
+}

.github/workflows/ci.yml

@@ -2,24 +2,32 @@ name: Continuous builds
 
 on:
   push:
-    branches: [ master, development, experimental, test* ]
+    branches:
+      - master
+      - development
+      - experimental
+      - 'test*'
   pull_request:
-    branches: [ master, development, experimental, test* ]
+    branches:
+      - master
+      - development
+      - experimental
+      - 'test*'
 
 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"]
       fail-fast: false
 
     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 }}
 
@@ -28,35 +36,21 @@ jobs:
         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' }}
+    - name: Upgrade pip, install inspyred
       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
+        python -m pip install --upgrade pip
+        pip install git+https://github.com/aarongarrett/inspyred.git@master#egg=inspyred
+        pip install .[dev]
 
-    - name: Install package
+    - name: List packages so far
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements-dev.txt
-        pip install pytest
-        pip install .
+        pip list
 
     - name: Run tests
       run: |
-        pytest .
         pynml -h
 
-        # For now, only test neuron related examples on py3
-        if [[  ${{ matrix.python-version }} == "3."* ]]; then argnrn=-neuron ; fi
-        ./test-ghactions.sh $argnrn
+        ./test-ghactions.sh -neuron
 
     - name: Lint with flake8
       run: |

.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 }}

.gitignore

@@ -122,3 +122,46 @@ examples/results/*.dat
 /examples/test_data/ca1/*.hoc
 .venv/
 /examples/LEMS_NML2_Ex5_DetCell_brian2.py
+/examples/*.gen.so
+*_eden.py
+/examples/test_data/Purk2M9s.nml.png
+/examples/test_data/*.pov
+/examples/test_data/ca1/*.pov
+/examples/test_data/ca1/TestOLMNet.net.nml.png
+/examples/test_data/complex_cell.cell.png
+/examples/test_data/simple_cell.cell.png
+/examples/test_data/complex_cell.morph.png
+/examples/test_data/simple_cell.morph.png
+/examples/LEMS_NML2_Ex5_DetCell_moose.py
+/examples/NET_NML2_Ex5_DetCell.net.nml
+
+.mypy_cache/
+/examples/test_data/TwoCell.net.png
+/examples/test_data/Purk2M9s.png
+/.coverage
+/Nav.channel.nml
+/iv_izh2007RS0.net.nml
+/leak_chan.channel.nml
+/test_analysis_if.png
+/test_analysis_iv.png
+/test_analysis_traces.png
+/test_cell_analysis.cell.nml
+/tests/DoubExpSyn.channel.nml
+/tests/Nav.channel.nml
+/tests/iv_izh2007RS0.net.nml
+/tests/leak_chan.channel.nml
+/tests/test_cell_analysis.cell.nml
+arm64
+*.neux
+/test_*plot*png
+/examples/plot.py
+/tests/utils/test_rotation.net.nml
+/tests/utils/test_rotation.net.png
+/tests/analysis/test_analysis_if.png
+/tests/analysis/test_analysis_iv.png
+/tests/analysis/test_analysis_traces.png
+/tests/analysis/test_cell_analysis.cell.nml
+/tests/plot/test_schematic_plot_2d_test_cell_nml_xy.png
+/tests/plot/test_schematic_plot_2d_test_cell_nml_xz.png
+/tests/plot/test_schematic_plot_2d_test_cell_nml_yz.png
+/tests/analysis/*png

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    -   id: black

.readthedocs.yaml

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