Merge pull request #57 from ModECI/development

Mainly contribs from Outreachy May-Aug 2023

.github/workflows/ci.yml

@@ -19,12 +19,13 @@ jobs:
         extra_args: --hook-stage manual --all-files
 
   build:
-
-    runs-on: ubuntu-latest
+    name: Build for 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", "3.10"]
+        python-version: [ "3.7", "3.8", "3.9", "3.10"]
+        runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
     - uses: actions/checkout@v2
@@ -54,6 +55,17 @@ jobs:
         cd test
         python test.py
 
+        ## Test NeuroML example
+
+        cd ../neuroml2
+        python neuroml2_spec.py
+
+        pip install pyneuroml
+
+        # Requires: pip install pyneuroml
+        pynml -validate hello_world_neuroml.net.nml
+        pynml -validate TestNeuroML.xml
+
     - name: Run pytest
       run: |
         pytest tests
@@ -76,6 +88,17 @@ jobs:
           cd examples/MDF
           python arrays.py -run   # test one example
 
+    - name: Build Documentation
+      run: |
+
+        pip install .[docs]
+        cd docs
+        python generate.py
+        python contributors.py
+        cd sphinx
+        make clean
+        make html
+
     - name: Final version info
       run: |
           pip list

.gitignore

@@ -80,6 +80,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/sphinx/source/api/_autosummary
 
 # PyBuilder
 .pybuilder/
@@ -161,3 +162,4 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
 /examples/document.specification.bson
+/examples/neuroml2/hello_world.v.dat

docs/contributors.py

@@ -0,0 +1,66 @@
+import requests
+import pandas as pd
+import json
+import textwrap
+from datetime import date
+
+
+url = "https://api.github.com/repos/modeci/modelspec/contributors"
+
+response = requests.get(url=url, auth=("<github_username>", "<github_token>"))
+
+json_data = response.json()
+
+df = pd.DataFrame(json_data)
+
+per_info = list(df["url"].unique())
+len_per_info = len(per_info)
+
+empty_list = []
+for i in range(len_per_info):
+    url = per_info[i]
+    print(url)
+    data = requests.get(url=url)
+    requests_status = "unknown"
+    while (requests_status == "unknown") or (requests_status == "unsuccessful"):
+        if data.status_code == 200:
+            requests_status = "successful"
+            empty_list.append(data.json())
+        else:
+            # handle failure on requests to the url for mac os
+            requests_status = "unsuccessful"
+            print(f"Failed to get data from: {url}")
+            # make request again to get data from the url
+            data = requests.get(url=url)
+
+df1 = pd.DataFrame(empty_list)
+df1["name"] = df1["name"].fillna("")
+name = df1["name"]
+login = df1["login"]
+url_html = df1["html_url"]
+url_id = df1["id"]
+
+login_html = list(zip(name, login, url_html))
+zip_dict = dict(zip(url_id, login_html))
+
+file = "sphinx/source/api/Contributors.md"
+with open(file, "w") as f:
+    print(
+        textwrap.dedent(
+            """\
+        (Modelspec:contributors)=
+
+        # 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 {}.""".format(
+                date.today()
+            )
+        ),
+        file=f,
+    )
+
+    print("", file=f)
+
+    for key, val in zip_dict.items():
+        print("- {} ([@{}]({}))".format(val[0], val[1], val[2]), file=f)

docs/generate.py

@@ -0,0 +1,10 @@
+import shutil
+import os
+
+shutil.copy("../README.md", "sphinx/source/api/Introduction.md")
+
+for file_ in os.listdir("../examples"):
+    if ("document" in file_) or ("README" in file_):
+        shutil.copy(
+            "../examples/%s" % file_, os.path.join("sphinx/source/api/examples", file_)
+        )

docs/sphinx/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/sphinx/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/sphinx/source/_static/pydata-custom.css

@@ -0,0 +1,10 @@
+/*Tweaks to the Pydata default CSS */
+
+/*No yellow background highlight when targeted by summary tables */
+/*dt:target { background-color: #f8f8f8; border: 1px solid black, }*/
+dt:target { background: transparent;}
+/*More space between H1s and signatures in API reference*/
+h1 { margin-bottom: 40px; }
+
+/*No line underneath summary table headings (clashes with line above first member)*/
+p.rubric { border-bottom: 0px; }

docs/sphinx/source/_static/rtd-custom.css

@@ -0,0 +1,35 @@
+/* Override nav bar color */
+/*.wy-side-nav-search {
+    background-color: #fbfbb6;
+}
+.wy-side-nav-search > a {
+    color: #b2355c
+}*/
+
+/* Override text bar color */
+/*.caption-text {
+    color: #b2355c;
+}*/
+
+/* Override code signature colour */
+/*.rst-content dl:not(.docutils) dt {
+    background: #fbfbb6;
+    color: #b2355c;
+    border-top: solid 3px #b2355c;
+}*/
+
+/* Override hyperlink colour */
+/* a {
+    color: #b2355c;
+}*/
+
+/* Make content width wider*/
+.wy-nav-content {
+    max-width: 75% !important;
+}
+
+/* Word-wrap tables */
+.wy-table-responsive table td,
+.wy-table-responsive table th {
+  white-space: normal;
+}

docs/sphinx/source/_templates/custom-class-template.rst

@@ -0,0 +1,23 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :special-members: __call__, __add__, __mul__
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      {%- if not item.startswith('_') %}
+        {%- if item not in inherited_members %}
+            ~{{ name }}.{{ item }}
+        {%- endif -%}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/sphinx/source/_templates/custom-module-template.rst

@@ -0,0 +1,67 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {%- if not item.startswith('_') %}
+        {{ item }}
+      {% endif %}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/sphinx/source/api/Contributors.md

@@ -0,0 +1,11 @@
+(Modelspec:contributors)=
+
+# 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 2023-07-05.
+
+- Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
+- David Turner ([@davidt0x](https://github.com/davidt0x))
+- Parikshit Singh Rathore ([@parikshit14](https://github.com/parikshit14))
+- Katherine Mantel ([@kmantel](https://github.com/kmantel))