Merge pull request #8 from ModECI/development

Attrs to main..

Author: pgleeson

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 2.7, 3.7 , 3.9 ]
+        python-version: [ 3.7 , 3.9 ]
 
     steps:
     - uses: actions/checkout@v2
@@ -25,8 +25,7 @@ jobs:
     - name: Install package
       run: |
         python -m pip install --upgrade pip
-        pip install flake8
-        pip install .
+        pip install .[dev]
 
     - name: Lint with flake8
       run: |
@@ -43,15 +42,12 @@ jobs:
 
     - name: Run pytest
       run: |
-        pip install pytest
-        cd modelspec/test/
-        pytest -v
+        pytest tests
 
     - name: Install & test NeuroMLlite
       run: |
-          git clone https://github.com/NeuroML/NeuroMLlite.git
+          git clone --branch experimental https://github.com/NeuroML/NeuroMLlite.git
           cd NeuroMLlite
-          git checkout modelspec # specific branch...
           pip install .
           pip install pyneuroml>=0.5.18
           cd examples
@@ -66,13 +62,12 @@ jobs:
     - name: Install MDF
       if: ${{ matrix.python-version != '2.7' }}
       run: |
-      
-          # Install psyneulink - mdf branch
-          python -m pip install git+https://github.com/PrincetonUniversity/PsyNeuLink.git@mdf
 
-          git clone https://github.com/ModECI/MDF.git
+          # Install psyneulink
+          python -m pip install git+https://github.com/PrincetonUniversity/PsyNeuLink.git
+
+          git clone --branch attrs_test https://github.com/ModECI/MDF.git
           cd MDF
-          git checkout modelspec  # specific branch...
           pip install .
           cd examples/MDF
           python arrays.py -run   # test one example

.gitignore

@@ -7,3 +7,156 @@
 /modelspec/test/temp/Sim0.json
 /modelspec/test/temp/net0.json
 *acken.sh
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,51 @@
+repos:
+
+#- repo: https://github.com/psf/black
+#  rev: 20.8b1
+#  hooks:
+#  - id: black
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v3.4.0
+  hooks:
+  - id: check-added-large-files
+    args: ['--maxkb=800']
+  - id: check-case-conflict
+  - id: check-merge-conflict
+  - id: check-symlinks
+  - id: check-yaml
+  - id: check-json
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+  - id: requirements-txt-fixer
+  - id: trailing-whitespace
+
+#- repo: https://github.com/PyCQA/isort
+#  rev: 5.7.0
+#  hooks:
+#  - id: isort
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v2.7.4
+  hooks:
+  - id: pyupgrade
+    args: ["--py36-plus"]
+
+#- repo: https://github.com/pycqa/flake8
+#  rev: 3.8.4
+#  hooks:
+#  - id: flake8
+#    exclude: docs/conf.py
+#    additional_dependencies: [flake8-bugbear, flake8-print]
+#
+#- repo: https://github.com/pre-commit/mirrors-mypy
+#  rev: v0.800
+#  hooks:
+#  - id: mypy
+#    files: src
+
+- repo: https://github.com/psf/black
+  rev: 20.8b1
+  hooks:
+  - id: black

examples/document.json

@@ -3,11 +3,22 @@
         "title": "My life in Python",
         "sections": {
             "Abstract": {
-                "paragraphs": {
-                    "contents": "Blah blah blah"
-                }
+                "paragraphs": [
+                    {
+                        "contents": "Blah blah blah"
+                    },
+                    {
+                        "contents": "Blah2"
+                    }
+                ]
             },
-            "Chapter 1": {}
+            "Chapter 1": {
+                "paragraphs": [
+                    {
+                        "contents": "More..."
+                    }
+                ]
+            }
         }
     }
-}
+}

examples/document.md

@@ -1,88 +1,42 @@
 ## Document
-
 A model for documents
 
-### Allowed parameters
-<table>
-  <tr>
-    <td><b>title</b></td>
-    <td>str</td>
-    <td><i>Document title</i></td>
-  </tr>
-
-  <tr>
-    <td><b>ISBN</b></td>
-    <td>int</td>
-    <td><i>International Standard Book Number</i></td>
-  </tr>
-
-  <tr>
-    <td><b>id</b></td>
-    <td>str</td>
-    <td><i>Unique ID of element</i></td>
-  </tr>
-
-  <tr>
-    <td><b>notes</b></td>
-    <td>str</td>
-    <td><i>Human readable notes</i></td>
-  </tr>
+#### Allowed parameters
+<table><tr><td><b>id</b></td><td>str</td><td><i>The unique id of the document</i></td></tr>
+
+<tr><td><b>title</b></td><td>str</td><td><i>Document title</i></td></tr>
+
+<tr><td><b>ISBN</b></td><td>int</td><td><i>International Standard Book Number</i></td></tr>
+
 
 </table>
 
 #### Allowed children
+<table><tr><td><b>sections</b></td><td><a href="#section">Section</a></td><td><i>The sections of the document</i></td></tr>
 
-<table>
-  <tr>
-    <td><b>sections</b></td>
-    <td><a href="#section">Section</a></td>
-    <td><i>The sections of the document</i></td>
-  </tr>
 
 </table>
 
 ## Section
-
 A model of a section of the document. Will contain a <a href="#paragraph">Paragraph</a> or two
 
-### Allowed parameters
-<table>
-  <tr>
-    <td><b>id</b></td>
-    <td>str</td>
-    <td><i>Unique ID of element</i></td>
-  </tr>
+#### Allowed parameters
+<table><tr><td><b>id</b></td><td>str</td><td><i>The id of the section</i></td></tr>
 
-  <tr>
-    <td><b>notes</b></td>
-    <td>str</td>
-    <td><i>Human readable notes</i></td>
-  </tr>
 
 </table>
 
 #### Allowed children
+<table><tr><td><b>paragraphs</b></td><td><a href="#paragraph">Paragraph</a></td><td><i>The paragraphs</i></td></tr>
 
-<table>
-  <tr>
-    <td><b>paragraphs</b></td>
-    <td><a href="#paragraph">Paragraph</a></td>
-    <td><i>The paragraphs</i></td>
-  </tr>
 
 </table>
 
 ## Paragraph
-
 A model of a paragraph
 
-### Allowed parameters
-<table>
-  <tr>
-    <td><b>contents</b></td>
-    <td>str</td>
-    <td><i>Paragraph contents, which make up the <a href="#section">Section</a>s.</i></td>
-  </tr>
+#### Allowed parameters
+<table><tr><td><b>contents</b></td><td>str</td><td><i>Paragraph contents, which make up the <a href="#section">Section</a>s.</i></td></tr>
 
-</table>
 
+</table>