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pgleesonpgleeson
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Merge pull request #57 from ModECI/development
Mainly contribs from Outreachy May-Aug 2023
2 parents 40185ef + d3aa38b commit 67382cb

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‎.github/workflows/ci.yml

+26-3
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@@ -19,12 +19,13 @@ jobs:
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extra_args: --hook-stage manual --all-files
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build:
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runs-on: ubuntu-latest
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name: Build for Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
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runs-on: ${{ matrix.runs-on }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.7", "3.8", "3.9", "3.10"]
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python-version: [ "3.7", "3.8", "3.9", "3.10"]
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runs-on: [ubuntu-latest, macos-latest, windows-latest]
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steps:
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- uses: actions/checkout@v2
@@ -54,6 +55,17 @@ jobs:
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cd test
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python test.py
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## Test NeuroML example
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cd ../neuroml2
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python neuroml2_spec.py
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pip install pyneuroml
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# Requires: pip install pyneuroml
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pynml -validate hello_world_neuroml.net.nml
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pynml -validate TestNeuroML.xml
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- name: Run pytest
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run: |
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pytest tests
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cd examples/MDF
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python arrays.py -run # test one example
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- name: Build Documentation
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run: |
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pip install .[docs]
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cd docs
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python generate.py
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python contributors.py
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cd sphinx
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make clean
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make html
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- name: Final version info
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run: |
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pip list

‎.gitignore

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

‎docs/contributors.py

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import requests
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import pandas as pd
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import json
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import textwrap
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from datetime import date
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url = "https://api.github.com/repos/modeci/modelspec/contributors"
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response = requests.get(url=url, auth=("<github_username>", "<github_token>"))
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json_data = response.json()
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df = pd.DataFrame(json_data)
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per_info = list(df["url"].unique())
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len_per_info = len(per_info)
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empty_list = []
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for i in range(len_per_info):
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url = per_info[i]
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print(url)
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data = requests.get(url=url)
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requests_status = "unknown"
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while (requests_status == "unknown") or (requests_status == "unsuccessful"):
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if data.status_code == 200:
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requests_status = "successful"
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empty_list.append(data.json())
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else:
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# handle failure on requests to the url for mac os
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requests_status = "unsuccessful"
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print(f"Failed to get data from: {url}")
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# make request again to get data from the url
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data = requests.get(url=url)
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df1 = pd.DataFrame(empty_list)
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df1["name"] = df1["name"].fillna("")
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name = df1["name"]
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login = df1["login"]
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url_html = df1["html_url"]
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url_id = df1["id"]
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login_html = list(zip(name, login, url_html))
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zip_dict = dict(zip(url_id, login_html))
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file = "sphinx/source/api/Contributors.md"
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with open(file, "w") as f:
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print(
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textwrap.dedent(
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"""\
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(Modelspec:contributors)=
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# Modelspec contributors
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This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
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This page is generated periodically, most recently on {}.""".format(
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date.today()
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)
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),
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file=f,
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)
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print("", file=f)
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for key, val in zip_dict.items():
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print("- {} ([@{}]({}))".format(val[0], val[1], val[2]), file=f)

‎docs/generate.py

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

‎docs/sphinx/Makefile

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

‎docs/sphinx/make.bat

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

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

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

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

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

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

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

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

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

‎docs/sphinx/source/api/Contributors.md

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(Modelspec:contributors)=
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# Modelspec contributors
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This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
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This page is generated periodically, most recently on 2023-07-05.
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- Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
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- David Turner ([@davidt0x](https://github.com/davidt0x))
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- Parikshit Singh Rathore ([@parikshit14](https://github.com/parikshit14))
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- Katherine Mantel ([@kmantel](https://github.com/kmantel))

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