import os
import time
+import warnings
from typing import *
from functools import wraps
+import requests
+
from bio_compose.processing_tools import get_job_signature
from bio_compose.runner import SimulationRunner, SimulationResult
from bio_compose.verifier import Verifier, VerificationResult
@@ -297,6 +298,45 @@ Source code for bio_compose.api
+
+[docs]
+def get_biomodel_archive(model_id: str, dest_dir: Optional[str] = None) -> str:
+ """
+ Download an OMEX archive from the Biomodels REST API, optionally specifying a download destination.
+
+ :param model_id: (`str`) A single biomodel id.
+ :param dest_dir: (`str`) destination directory at which to save downloaded file. If `None` is passed, downloads to cwd. Defaults to `None`.
+
+ :return: Filepath of the downloaded biomodel file
+ :rtype: `str`
+ """
+ url = "https://www.ebi.ac.uk/biomodels/search/download"
+ params = {"models": model_id}
+
+ try:
+ response = requests.get(url, params=params, stream=True)
+
+ # download the file if success, otherwise notify.
+ if response.status_code == 200:
+ file_name = f"{model_id}.omex"
+ dest = dest_dir or os.getcwd()
+ fp = os.path.join(dest, file_name)
+ with open(fp, "wb") as file:
+ for chunk in response.iter_content(chunk_size=8192):
+ file.write(chunk)
+ print(f"File downloaded successfully and saved as {fp}")
+ return fp
+ elif response.status_code == 400:
+ warnings.warn("Error 400: File Not Found")
+ elif response.status_code == 404:
+ warnings.warn("Error 404: Invalid Model ID Supplied")
+ else:
+ warnings.warn(f"Unexpected error: {response.status_code} - {response.text}")
+ except requests.RequestException as e:
+ return f"An error occurred: {e}"
+
+
+
rmse_data.append(score_vals)
if color_mapping is None:
- color_mapping = ['#1E3A8A', '#D97706']
+ color_mapping = "Blues"
# set up figure
- dimensions = fig_dimensions or (8, 6)
+ dimensions = fig_dimensions or (4, 3)
fig = plt.figure(figsize=dimensions)
sns.heatmap(
data=rmse_data,
@@ -472,6 +470,8 @@ Source code for bio_compose.verifier
xticklabels=simulators,
yticklabels=simulators,
cmap=color_mapping,
+ vmin=-0,
+ vmax=1,
linewidths=1
)
# set up plot annotations
diff --git a/documentation/build/html/_modules/index.html b/documentation/build/html/_modules/index.html
index 8451711..091ddcc 100644
--- a/documentation/build/html/_modules/index.html
+++ b/documentation/build/html/_modules/index.html
@@ -1,3 +1,5 @@
+
+
@@ -5,18 +7,14 @@
Overview: module code — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
diff --git a/documentation/build/html/_static/basic.css b/documentation/build/html/_static/basic.css
index f316efc..7ebbd6d 100644
--- a/documentation/build/html/_static/basic.css
+++ b/documentation/build/html/_static/basic.css
@@ -1,12 +1,5 @@
/*
- * basic.css
- * ~~~~~~~~~
- *
* Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
*/
/* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
/* -- search page ----------------------------------------------------------- */
ul.search {
- margin: 10px 0 0 20px;
- padding: 0;
+ margin-top: 10px;
}
ul.search li {
- padding: 5px 0 5px 20px;
- background-image: url(file.png);
- background-repeat: no-repeat;
- background-position: 0 7px;
+ padding: 5px 0;
}
ul.search li a {
diff --git a/documentation/build/html/_static/css/badge_only.css b/documentation/build/html/_static/css/badge_only.css
index c718cee..88ba55b 100644
--- a/documentation/build/html/_static/css/badge_only.css
+++ b/documentation/build/html/_static/css/badge_only.css
@@ -1 +1 @@
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diff --git a/documentation/build/html/_static/css/theme.css b/documentation/build/html/_static/css/theme.css
index 19a446a..0f14f10 100644
--- a/documentation/build/html/_static/css/theme.css
+++ b/documentation/build/html/_static/css/theme.css
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index 4d67807..0398ebb 100644
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- * ~~~~~~~~~~~
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* Base JavaScript utilities for all Sphinx HTML documentation.
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+ - Languages
+ ${languages
+ .map(
+ (translation) => `
+ -
+ ${translation.language.code}
+
+ `,
+ )
+ .join("\n")}
+
+ `;
+ return languagesHTML;
+ }
+
+ function renderVersions(config) {
+ if (!config.versions.active.length) {
+ return "";
+ }
+ const versionsHTML = `
+
+ - Versions
+ ${config.versions.active
+ .map(
+ (version) => `
+ -
+ ${version.slug}
+
+ `,
+ )
+ .join("\n")}
+
+ `;
+ return versionsHTML;
+ }
+
+ function renderDownloads(config) {
+ if (!Object.keys(config.versions.current.downloads).length) {
+ return "";
+ }
+ const downloadsNameDisplay = {
+ pdf: "PDF",
+ epub: "Epub",
+ htmlzip: "HTML",
+ };
+
+ const downloadsHTML = `
+
+ - Downloads
+ ${Object.entries(config.versions.current.downloads)
+ .map(
+ ([name, url]) => `
+ -
+ ${downloadsNameDisplay[name]}
+
+ `,
+ )
+ .join("\n")}
+
+ `;
+ return downloadsHTML;
+ }
+
+ document.addEventListener("readthedocs-addons-data-ready", function (event) {
+ const config = event.detail.data();
+
+ const flyout = `
+
+
+ Read the Docs
+ v: ${config.versions.current.slug}
+
+
+
+
+ ${renderLanguages(config)}
+ ${renderVersions(config)}
+ ${renderDownloads(config)}
+
+ - On Read the Docs
+ -
+ Project Home
+
+ -
+ Builds
+
+ -
+ Downloads
+
+
+
+ - Search
+ -
+
+
+
+
+
+ Hosted by Read the Docs
+
+
+
+ `;
+
+ // Inject the generated flyout into the body HTML element.
+ document.body.insertAdjacentHTML("beforeend", flyout);
+
+ // Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout.
+ document
+ .querySelector("#flyout-search-form")
+ .addEventListener("focusin", () => {
+ const event = new CustomEvent("readthedocs-search-show");
+ document.dispatchEvent(event);
+ });
+ })
+}
+
+if (themeLanguageSelector || themeVersionSelector) {
+ function onSelectorSwitch(event) {
+ const option = event.target.selectedIndex;
+ const item = event.target.options[option];
+ window.location.href = item.dataset.url;
+ }
+
+ document.addEventListener("readthedocs-addons-data-ready", function (event) {
+ const config = event.detail.data();
+
+ const versionSwitch = document.querySelector(
+ "div.switch-menus > div.version-switch",
+ );
+ if (themeVersionSelector) {
+ let versions = config.versions.active;
+ if (config.versions.current.hidden || config.versions.current.type === "external") {
+ versions.unshift(config.versions.current);
+ }
+ const versionSelect = `
+
+ `;
+
+ versionSwitch.innerHTML = versionSelect;
+ versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch);
+ }
+
+ const languageSwitch = document.querySelector(
+ "div.switch-menus > div.language-switch",
+ );
+
+ if (themeLanguageSelector) {
+ if (config.projects.translations.length) {
+ // Add the current language to the options on the selector
+ let languages = config.projects.translations.concat(
+ config.projects.current,
+ );
+ languages = languages.sort((a, b) =>
+ a.language.name.localeCompare(b.language.name),
+ );
+
+ const languageSelect = `
+
+ `;
+
+ languageSwitch.innerHTML = languageSelect;
+ languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch);
+ }
+ else {
+ languageSwitch.remove();
+ }
+ }
+ });
+}
+
+document.addEventListener("readthedocs-addons-data-ready", function (event) {
+ // Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav.
+ document
+ .querySelector("[role='search'] input")
+ .addEventListener("focusin", () => {
+ const event = new CustomEvent("readthedocs-search-show");
+ document.dispatchEvent(event);
+ });
+});
\ No newline at end of file
diff --git a/documentation/build/html/_static/language_data.js b/documentation/build/html/_static/language_data.js
index 367b8ed..c7fe6c6 100644
--- a/documentation/build/html/_static/language_data.js
+++ b/documentation/build/html/_static/language_data.js
@@ -1,13 +1,6 @@
/*
- * language_data.js
- * ~~~~~~~~~~~~~~~~
- *
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
*/
var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
diff --git a/documentation/build/html/_static/searchtools.js b/documentation/build/html/_static/searchtools.js
index b08d58c..2c774d1 100644
--- a/documentation/build/html/_static/searchtools.js
+++ b/documentation/build/html/_static/searchtools.js
@@ -1,12 +1,5 @@
/*
- * searchtools.js
- * ~~~~~~~~~~~~~~~~
- *
* Sphinx JavaScript utilities for the full-text search.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
*/
"use strict";
@@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") {
// and returns the new score.
/*
score: result => {
- const [docname, title, anchor, descr, score, filename] = result
+ const [docname, title, anchor, descr, score, filename, kind] = result
return score
},
*/
@@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") {
};
}
+// Global search result kind enum, used by themes to style search results.
+class SearchResultKind {
+ static get index() { return "index"; }
+ static get object() { return "object"; }
+ static get text() { return "text"; }
+ static get title() { return "title"; }
+}
+
const _removeChildren = (element) => {
while (element && element.lastChild) element.removeChild(element.lastChild);
};
@@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
const contentRoot = document.documentElement.dataset.content_root;
- const [docName, title, anchor, descr, score, _filename] = item;
+ const [docName, title, anchor, descr, score, _filename, kind] = item;
let listItem = document.createElement("li");
+ // Add a class representing the item's type:
+ // can be used by a theme's CSS selector for styling
+ // See SearchResultKind for the class names.
+ listItem.classList.add(`kind-${kind}`);
let requestUrl;
let linkUrl;
if (docBuilder === "dirhtml") {
@@ -115,8 +120,10 @@ const _finishSearch = (resultCount) => {
"Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
);
else
- Search.status.innerText = _(
- "Search finished, found ${resultCount} page(s) matching the search query."
+ Search.status.innerText = Documentation.ngettext(
+ "Search finished, found one page matching the search query.",
+ "Search finished, found ${resultCount} pages matching the search query.",
+ resultCount,
).replace('${resultCount}', resultCount);
};
const _displayNextItem = (
@@ -138,7 +145,7 @@ const _displayNextItem = (
else _finishSearch(resultCount);
};
// Helper function used by query() to order search results.
-// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Each input is an array of [docname, title, anchor, descr, score, filename, kind].
// Order the results by score (in opposite order of appearance, since the
// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
const _orderResultsByScoreThenName = (a, b) => {
@@ -248,6 +255,7 @@ const Search = {
searchSummary.classList.add("search-summary");
searchSummary.innerText = "";
const searchList = document.createElement("ul");
+ searchList.setAttribute("role", "list");
searchList.classList.add("search");
const out = document.getElementById("search-results");
@@ -318,7 +326,7 @@ const Search = {
const indexEntries = Search._index.indexentries;
// Collect multiple result groups to be sorted separately and then ordered.
- // Each is an array of [docname, title, anchor, descr, score, filename].
+ // Each is an array of [docname, title, anchor, descr, score, filename, kind].
const normalResults = [];
const nonMainIndexResults = [];
@@ -337,6 +345,7 @@ const Search = {
null,
score + boost,
filenames[file],
+ SearchResultKind.title,
]);
}
}
@@ -354,6 +363,7 @@ const Search = {
null,
score,
filenames[file],
+ SearchResultKind.index,
];
if (isMain) {
normalResults.push(result);
@@ -475,6 +485,7 @@ const Search = {
descr,
score,
filenames[match[0]],
+ SearchResultKind.object,
]);
};
Object.keys(objects).forEach((prefix) =>
@@ -585,6 +596,7 @@ const Search = {
null,
score,
filenames[file],
+ SearchResultKind.text,
]);
}
return results;
diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
index abcff3d..f2a7cc4 100644
--- a/documentation/build/html/bio_compose.html
+++ b/documentation/build/html/bio_compose.html
@@ -1,3 +1,5 @@
+
+
@@ -6,18 +8,14 @@
bio_compose — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
@@ -52,6 +50,7 @@
Command Line Interface
API Documentation
- bio_compose
+get_biomodel_archive()get_compatible_verification_simulators()get_output()run_simulation()
bio_compose
+
+-
+bio_compose.api.get_biomodel_archive(model_id: str, dest_dir: str | None = None) str[source]
+Download an OMEX archive from the Biomodels REST API, optionally specifying a download destination.
+
+- Parameters:
+
+model_id – (str) A single biomodel id.
dest_dir – (str) destination directory at which to save downloaded file. If None is passed, downloads to cwd. Defaults to None.
+- Returns:
+Filepath of the downloaded biomodel file
+- Return type:
+str
+
+
+
-
bio_compose.api.get_compatible_verification_simulators(entrypoint_file: str, return_versions: bool = False)[source]
diff --git a/documentation/build/html/cli.html b/documentation/build/html/cli.html
index bcdb4e4..2991f59 100644
--- a/documentation/build/html/cli.html
+++ b/documentation/build/html/cli.html
@@ -1,3 +1,5 @@
+
+
@@ -6,18 +8,14 @@
Command Line Interface — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
diff --git a/documentation/build/html/genindex.html b/documentation/build/html/genindex.html
index 611ce88..e5997f8 100644
--- a/documentation/build/html/genindex.html
+++ b/documentation/build/html/genindex.html
@@ -1,3 +1,5 @@
+
+
@@ -5,18 +7,14 @@
Index — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
@@ -217,15 +215,17 @@ G
- generate_port_spec() (bio_compose.bundles.BioBundle method)
- generate_simularium_file() (bio_compose.runner.SimulationRunner method)
+
+ - get_biomodel_archive() (in module bio_compose.api)
- get_comparison() (bio_compose.verifier.VerificationResult method)
- get_compatible() (bio_compose.verifier.Verifier method)
-
- - get_compatible_verification_simulators() (in module bio_compose.api)
+ - get_compatible_verification_simulators() (in module bio_compose.api)
+
- get_job_signature() (in module bio_compose.processing_tools)
- get_job_status() (bio_compose.data_model.Api method)
diff --git a/documentation/build/html/getting_started.html b/documentation/build/html/getting_started.html
index 9d6dcde..b028aec 100644
--- a/documentation/build/html/getting_started.html
+++ b/documentation/build/html/getting_started.html
@@ -1,3 +1,5 @@
+
+
@@ -6,18 +8,14 @@
Getting Started — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
diff --git a/documentation/build/html/index.html b/documentation/build/html/index.html
index 4fe2665..9a577b7 100644
--- a/documentation/build/html/index.html
+++ b/documentation/build/html/index.html
@@ -1,3 +1,5 @@
+
+
@@ -6,18 +8,14 @@
BioCompose documentation — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
diff --git a/documentation/build/html/installation.html b/documentation/build/html/installation.html
index 146bada..984ee1b 100644
--- a/documentation/build/html/installation.html
+++ b/documentation/build/html/installation.html
@@ -1,3 +1,5 @@
+
+
@@ -6,18 +8,14 @@
Installation — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
diff --git a/documentation/build/html/modules.html b/documentation/build/html/modules.html
index b013f32..e4a0ce2 100644
--- a/documentation/build/html/modules.html
+++ b/documentation/build/html/modules.html
@@ -1,3 +1,5 @@
+
+
@@ -6,18 +8,14 @@
API Documentation — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
@@ -86,6 +84,7 @@ API Documentation
- bio_compose
+get_biomodel_archive()get_compatible_verification_simulators()get_output()run_simulation()Python Module Index — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
diff --git a/documentation/build/html/search.html b/documentation/build/html/search.html
index ea289b7..c84f5ce 100644
--- a/documentation/build/html/search.html
+++ b/documentation/build/html/search.html
@@ -1,3 +1,5 @@
+
+
@@ -5,19 +7,15 @@
Search — BioCompose 0.5.5 documentation
-
+
-
-
-
-
-
-
-
+
+
+
+
+
diff --git a/documentation/build/html/searchindex.js b/documentation/build/html/searchindex.js
index df1163a..d9e05df 100644
--- a/documentation/build/html/searchindex.js
+++ b/documentation/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"API Documentation": [[5, null]], "BioCompose documentation": [[3, null]], "Command Line Interface": [[1, null]], "Contents": [[3, null]], "Getting Started": [[2, null]], "Installation": [[2, "installation"], [4, null]], "Simulation Runs": [[6, null]], "Verification": [[2, "verification"], [7, null]], "bio_compose": [[0, null]], "bio_compose.bundles": [[0, "module-bio_compose.bundles"]], "bio_compose.composer": [[0, "module-bio_compose.composer"]], "bio_compose.data_model": [[0, "module-bio_compose.data_model"]], "bio_compose.processing_tools": [[0, "module-bio_compose.processing_tools"]], "bio_compose.runner": [[0, "module-bio_compose.runner"]], "bio_compose.verifier": [[0, "module-bio_compose.verifier"]]}, "docnames": ["bio_compose", "cli", "getting_started", "index", "installation", "modules", "simulation_runs", "verification"], "envversion": {"sphinx": 63, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["bio_compose.rst", "cli.rst", "getting_started.rst", "index.rst", "installation.rst", "modules.rst", "simulation_runs.rst", "verification.rst"], "indexentries": {"add_emitter_node() (bio_compose.bundles.biobundle method)": [[0, "bio_compose.bundles.BioBundle.add_emitter_node", false]], "api (class in bio_compose.data_model)": [[0, "bio_compose.data_model.Api", false]], "bio_compose.api": [[0, "module-bio_compose.api", false]], "bio_compose.bundles": [[0, "module-bio_compose.bundles", false]], "bio_compose.composer": [[0, "module-bio_compose.composer", false]], "bio_compose.data_model": [[0, "module-bio_compose.data_model", false]], "bio_compose.processing_tools": [[0, "module-bio_compose.processing_tools", false]], "bio_compose.runner": [[0, 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diff --git a/documentation/build/html/simulation_runs.html b/documentation/build/html/simulation_runs.html
index 74e1cad..9246033 100644
--- a/documentation/build/html/simulation_runs.html
+++ b/documentation/build/html/simulation_runs.html
@@ -1,3 +1,5 @@
+
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@@ -6,18 +8,14 @@
Simulation Runs — BioCompose 0.5.5 documentation
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+
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-
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+
+
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+
+
diff --git a/documentation/build/html/verification.html b/documentation/build/html/verification.html
index 1786cbb..3379cc0 100644
--- a/documentation/build/html/verification.html
+++ b/documentation/build/html/verification.html
@@ -1,3 +1,5 @@
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@@ -6,18 +8,14 @@
Verification — BioCompose 0.5.5 documentation
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diff --git a/poetry.lock b/poetry.lock
index a76255a..07eeef3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -3122,6 +3122,25 @@ docs = ["furo (>=2024.8.6)"]
numpy = ["nptyping (>=2.5)"]
testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "defusedxml (>=0.7.1)", "diff-cover (>=9.1.1)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "sphobjinv (>=2.3.1.1)", "typing-extensions (>=4.12.2)"]
+[[package]]
+name = "sphinx-rtd-theme"
+version = "3.0.2"
+description = "Read the Docs theme for Sphinx"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "sphinx_rtd_theme-3.0.2-py2.py3-none-any.whl", hash = "sha256:422ccc750c3a3a311de4ae327e82affdaf59eb695ba4936538552f3b00f4ee13"},
+ {file = "sphinx_rtd_theme-3.0.2.tar.gz", hash = "sha256:b7457bc25dda723b20b086a670b9953c859eab60a2a03ee8eb2bb23e176e5f85"},
+]
+
+[package.dependencies]
+docutils = ">0.18,<0.22"
+sphinx = ">=6,<9"
+sphinxcontrib-jquery = ">=4,<5"
+
+[package.extras]
+dev = ["bump2version", "transifex-client", "twine", "wheel"]
+
[[package]]
name = "sphinxcontrib-applehelp"
version = "2.0.0"
@@ -3170,6 +3189,20 @@ lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
standalone = ["Sphinx (>=5)"]
test = ["html5lib", "pytest"]
+[[package]]
+name = "sphinxcontrib-jquery"
+version = "4.1"
+description = "Extension to include jQuery on newer Sphinx releases"
+optional = false
+python-versions = ">=2.7"
+files = [
+ {file = "sphinxcontrib-jquery-4.1.tar.gz", hash = "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a"},
+ {file = "sphinxcontrib_jquery-4.1-py2.py3-none-any.whl", hash = "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"},
+]
+
+[package.dependencies]
+Sphinx = ">=1.8"
+
[[package]]
name = "sphinxcontrib-jsmath"
version = "1.0.1"
@@ -3491,4 +3524,4 @@ test = ["websockets"]
[metadata]
lock-version = "2.0"
python-versions = "^3.10"
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diff --git a/pyproject.toml b/pyproject.toml
index 4b875e9..f294f5f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,6 +22,7 @@ antimony = "*"
toml = "^0.10.2"
process-bigraph = "^0.0.21"
requests = "^2.32.3"
+sphinx-rtd-theme = "^3.0.2"
[tool.poetry.group.docs.dependencies]