Skip to content

Commit

Permalink
Regnet Bug Fixes (#852)
Browse files Browse the repository at this point in the history
## Summary of Changes
This addresses some bug that TA4 pointed out in our Regnet generation.
Being generation of correct initial condition id's and fixing the json
schema for edges, being the `source` and `target` fields are scalars and
not arrays.

### Related issues

Resolves #851

---------

Co-authored-by: Justin <lieffers@arizona.edu> b29cbcf
  • Loading branch information
github-actions[bot] committed Mar 14, 2024
1 parent ca046e6 commit c4f0176
Show file tree
Hide file tree
Showing 1,342 changed files with 221,403 additions and 221,357 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -365,7 +365,7 @@ <h3>Instance variables</h3>
<h3>Methods</h3>
<dl>
<dt id="skema.img2mml.models.decoders.xfmer_decoder.Transformer_Decoder.create_pad_mask"><code class="name flex">
<span>def <span class="ident">create_pad_mask</span></span>(<span>self, matrix: <built-in method tensor of type object at 0x7f26c4b5b500>, pad_token: int) ‑> <built-in method tensor of type object at 0x7f26c4b5b500></span>
<span>def <span class="ident">create_pad_mask</span></span>(<span>self, matrix: <built-in method tensor of type object at 0x7b3a0815b500>, pad_token: int) ‑> <built-in method tensor of type object at 0x7b3a0815b500></span>
</code></dt>
<dd>
<div class="desc"></div>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@ <h3>Class variables</h3>
<h3>Methods</h3>
<dl>
<dt id="skema.img2mml.models.encoding.positional_encoding_for_xfmer.PositionalEncoding.forward"><code class="name flex">
<span>def <span class="ident">forward</span></span>(<span>self, x: <built-in method tensor of type object at 0x7f26c4b5b500>) ‑> <built-in method tensor of type object at 0x7f26c4b5b500></span>
<span>def <span class="ident">forward</span></span>(<span>self, x: <built-in method tensor of type object at 0x7b3a0815b500>) ‑> <built-in method tensor of type object at 0x7b3a0815b500></span>
</code></dt>
<dd>
<div class="desc"><p>Defines the computation performed at every call.</p>
Expand Down
4 changes: 2 additions & 2 deletions api/rust/help.html
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="generator" content="rustdoc"><meta name="description" content="Documentation for Rustdoc"><title>Help</title><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/SourceSerif4-Regular-46f98efaafac5295.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/FiraSans-Regular-018c141bf0843ffd.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/FiraSans-Medium-8f9a781e4970d388.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2"><link rel="stylesheet" href="./static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="./static.files/rustdoc-ac92e1bbe349e143.css"><meta name="rustdoc-vars" data-root-path="./" data-static-root-path="./static.files/" data-current-crate="gromet2graphdb" data-themes="" data-resource-suffix="" data-rustdoc-version="1.76.0 (07dca489a 2024-02-04)" data-channel="1.76.0" data-search-js="search-2b6ce74ff89ae146.js" data-settings-js="settings-4313503d2e1961c2.js" ><script src="./static.files/storage-f2adc0d6ca4d09fb.js"></script><script defer src="./static.files/main-305769736d49e732.js"></script><noscript><link rel="stylesheet" href="./static.files/noscript-feafe1bb7466e4bd.css"></noscript><link rel="alternate icon" type="image/png" href="./static.files/favicon-16x16-8b506e7a72182f1c.png"><link rel="alternate icon" type="image/png" href="./static.files/favicon-32x32-422f7d1d52889060.png"><link rel="icon" type="image/svg+xml" href="./static.files/favicon-2c020d218678b618.svg"></head><body class="rustdoc mod sys"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="mobile-topbar"><button class="sidebar-menu-toggle">&#9776;</button><a class="logo-container" href="./index.html"><img class="rust-logo" src="./static.files/rust-logo-151179464ae7ed46.svg" alt=""></a></nav><nav class="sidebar"><div class="sidebar-crate"><a class="logo-container" href="./index.html"><img class="rust-logo" src="./static.files/rust-logo-151179464ae7ed46.svg" alt="logo"></a><h2><a href="./index.html">Rustdoc</a><span class="version">1.76.0</span></h2></div><div class="version">(07dca489a 2024-02-04)</div><h2 class="location">Help</h2><div class="sidebar-elems"></div></nav><div class="sidebar-resizer"></div>
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="./gromet2graphdb/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="./help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="./settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="./static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Rustdoc help</h1><span class="out-of-band"><a id="back" href="javascript:void(0)" onclick="history.back();">Back</a></span></div><noscript><section><p>You need to enable JavaScript to use keyboard commands or search.</p><p>For more information, browse the <a href="https://doc.rust-lang.org/rustdoc/">rustdoc handbook</a>.</p></section></noscript></section></div></main></body></html>
<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="generator" content="rustdoc"><meta name="description" content="Documentation for Rustdoc"><title>Help</title><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/SourceSerif4-Regular-46f98efaafac5295.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/FiraSans-Regular-018c141bf0843ffd.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/FiraSans-Medium-8f9a781e4970d388.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./static.files/SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2"><link rel="stylesheet" href="./static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="./static.files/rustdoc-ac92e1bbe349e143.css"><meta name="rustdoc-vars" data-root-path="./" data-static-root-path="./static.files/" data-current-crate="skema_service" data-themes="" data-resource-suffix="" data-rustdoc-version="1.76.0 (07dca489a 2024-02-04)" data-channel="1.76.0" data-search-js="search-2b6ce74ff89ae146.js" data-settings-js="settings-4313503d2e1961c2.js" ><script src="./static.files/storage-f2adc0d6ca4d09fb.js"></script><script defer src="./static.files/main-305769736d49e732.js"></script><noscript><link rel="stylesheet" href="./static.files/noscript-feafe1bb7466e4bd.css"></noscript><link rel="alternate icon" type="image/png" href="./static.files/favicon-16x16-8b506e7a72182f1c.png"><link rel="alternate icon" type="image/png" href="./static.files/favicon-32x32-422f7d1d52889060.png"><link rel="icon" type="image/svg+xml" href="./static.files/favicon-2c020d218678b618.svg"></head><body class="rustdoc mod sys"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="mobile-topbar"><button class="sidebar-menu-toggle">&#9776;</button><a class="logo-container" href="./index.html"><img class="rust-logo" src="./static.files/rust-logo-151179464ae7ed46.svg" alt=""></a></nav><nav class="sidebar"><div class="sidebar-crate"><a class="logo-container" href="./index.html"><img class="rust-logo" src="./static.files/rust-logo-151179464ae7ed46.svg" alt="logo"></a><h2><a href="./index.html">Rustdoc</a><span class="version">1.76.0</span></h2></div><div class="version">(07dca489a 2024-02-04)</div><h2 class="location">Help</h2><div class="sidebar-elems"></div></nav><div class="sidebar-resizer"></div>
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="./skema_service/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="./help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="./settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="./static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Rustdoc help</h1><span class="out-of-band"><a id="back" href="javascript:void(0)" onclick="history.back();">Back</a></span></div><noscript><section><p>You need to enable JavaScript to use keyboard commands or search.</p><p>For more information, browse the <a href="https://doc.rust-lang.org/rustdoc/">rustdoc handbook</a>.</p></section></noscript></section></div></main></body></html>
2 changes: 1 addition & 1 deletion api/rust/mathml/acset/index.html
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="generator" content="rustdoc"><meta name="description" content="Structs to represent elements of ACSets (Annotated C-Sets, a concept from category theory). JSON-serialized ACSets are the form of model exchange between TA1 and TA2."><title>mathml::acset - Rust</title><link rel="preload" as="font" type="font/woff2" crossorigin href="../../static.files/SourceSerif4-Regular-46f98efaafac5295.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../static.files/FiraSans-Regular-018c141bf0843ffd.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../static.files/FiraSans-Medium-8f9a781e4970d388.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../static.files/SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../static.files/SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2"><link rel="stylesheet" href="../../static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="../../static.files/rustdoc-ac92e1bbe349e143.css"><meta name="rustdoc-vars" data-root-path="../../" data-static-root-path="../../static.files/" data-current-crate="mathml" data-themes="" data-resource-suffix="" data-rustdoc-version="1.76.0 (07dca489a 2024-02-04)" data-channel="1.76.0" data-search-js="search-2b6ce74ff89ae146.js" data-settings-js="settings-4313503d2e1961c2.js" ><script src="../../static.files/storage-f2adc0d6ca4d09fb.js"></script><script defer src="../sidebar-items.js"></script><script defer src="../../static.files/main-305769736d49e732.js"></script><noscript><link rel="stylesheet" href="../../static.files/noscript-feafe1bb7466e4bd.css"></noscript><link rel="alternate icon" type="image/png" href="../../static.files/favicon-16x16-8b506e7a72182f1c.png"><link rel="alternate icon" type="image/png" href="../../static.files/favicon-32x32-422f7d1d52889060.png"><link rel="icon" type="image/svg+xml" href="../../static.files/favicon-2c020d218678b618.svg"></head><body class="rustdoc mod"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="mobile-topbar"><button class="sidebar-menu-toggle">&#9776;</button></nav><nav class="sidebar"><div class="sidebar-crate"><h2><a href="../../mathml/index.html">mathml</a><span class="version">0.1.0</span></h2></div><h2 class="location"><a href="#">Module acset</a></h2><div class="sidebar-elems"><section><ul class="block"><li><a href="#structs">Structs</a></li></ul></section><h2><a href="../index.html">In crate mathml</a></h2></div></nav><div class="sidebar-resizer"></div>
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="../../mathml/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="../../help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="../../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../../static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Module <a href="../index.html">mathml</a>::<wbr><a class="mod" href="#">acset</a><button id="copy-path" title="Copy item path to clipboard"><img src="../../static.files/clipboard-7571035ce49a181d.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="src" href="../../src/mathml/acset.rs.html#1-1058">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></span></div><details class="toggle top-doc" open><summary class="hideme"><span>Expand description</span></summary><div class="docblock"><p>Structs to represent elements of ACSets (Annotated C-Sets, a concept from category theory).
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="../../mathml/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="../../help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="../../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../../static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Module <a href="../index.html">mathml</a>::<wbr><a class="mod" href="#">acset</a><button id="copy-path" title="Copy item path to clipboard"><img src="../../static.files/clipboard-7571035ce49a181d.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="src" href="../../src/mathml/acset.rs.html#1-1075">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></span></div><details class="toggle top-doc" open><summary class="hideme"><span>Expand description</span></summary><div class="docblock"><p>Structs to represent elements of ACSets (Annotated C-Sets, a concept from category theory).
JSON-serialized ACSets are the form of model exchange between TA1 and TA2.</p>
</div></details><h2 id="structs" class="section-header"><a href="#structs">Structs</a></h2><ul class="item-table"><li><div class="item-name"><a class="struct" href="struct.ACSet.html" title="struct mathml::acset::ACSet">ACSet</a></div></li><li><div class="item-name"><a class="struct" href="struct.ACSetTransition.html" title="struct mathml::acset::ACSetTransition">ACSetTransition</a></div></li><li><div class="item-name"><a class="struct" href="struct.AMRmathml.html" title="struct mathml::acset::AMRmathml">AMRmathml</a></div></li><li><div class="item-name"><a class="struct" href="struct.Distribution.html" title="struct mathml::acset::Distribution">Distribution</a></div></li><li><div class="item-name"><a class="struct" href="struct.GeneralSemantics.html" title="struct mathml::acset::GeneralSemantics">GeneralSemantics</a></div></li><li><div class="item-name"><a class="struct" href="struct.GeneralizedAMR.html" title="struct mathml::acset::GeneralizedAMR">GeneralizedAMR</a></div></li><li><div class="item-name"><a class="struct" href="struct.Grounding.html" title="struct mathml::acset::Grounding">Grounding</a></div></li><li><div class="item-name"><a class="struct" href="struct.Header.html" title="struct mathml::acset::Header">Header</a></div></li><li><div class="item-name"><a class="struct" href="struct.Identifier.html" title="struct mathml::acset::Identifier">Identifier</a></div></li><li><div class="item-name"><a class="struct" href="struct.Initial.html" title="struct mathml::acset::Initial">Initial</a></div></li><li><div class="item-name"><a class="struct" href="struct.InputArc.html" title="struct mathml::acset::InputArc">InputArc</a></div></li><li><div class="item-name"><a class="struct" href="struct.Metadata.html" title="struct mathml::acset::Metadata">Metadata</a></div></li><li><div class="item-name"><a class="struct" href="struct.ModelPetriNet.html" title="struct mathml::acset::ModelPetriNet">ModelPetriNet</a></div></li><li><div class="item-name"><a class="struct" href="struct.ModelRegNet.html" title="struct mathml::acset::ModelRegNet">ModelRegNet</a></div></li><li><div class="item-name"><a class="struct" href="struct.Observable.html" title="struct mathml::acset::Observable">Observable</a></div></li><li><div class="item-name"><a class="struct" href="struct.Ode.html" title="struct mathml::acset::Ode">Ode</a></div></li><li><div class="item-name"><a class="struct" href="struct.OutputArc.html" title="struct mathml::acset::OutputArc">OutputArc</a></div></li><li><div class="item-name"><a class="struct" href="struct.Parameter.html" title="struct mathml::acset::Parameter">Parameter</a></div></li><li><div class="item-name"><a class="struct" href="struct.PetriNet.html" title="struct mathml::acset::PetriNet">PetriNet</a></div></li><li><div class="item-name"><a class="struct" href="struct.Properties.html" title="struct mathml::acset::Properties">Properties</a></div></li><li><div class="item-name"><a class="struct" href="struct.Rate.html" title="struct mathml::acset::Rate">Rate</a></div></li><li><div class="item-name"><a class="struct" href="struct.RegNet.html" title="struct mathml::acset::RegNet">RegNet</a></div></li><li><div class="item-name"><a class="struct" href="struct.RegState.html" title="struct mathml::acset::RegState">RegState</a></div></li><li><div class="item-name"><a class="struct" href="struct.RegTransition.html" title="struct mathml::acset::RegTransition">RegTransition</a></div></li><li><div class="item-name"><a class="struct" href="struct.Semantics.html" title="struct mathml::acset::Semantics">Semantics</a></div></li><li><div class="item-name"><a class="struct" href="struct.Specie.html" title="struct mathml::acset::Specie">Specie</a></div></li><li><div class="item-name"><a class="struct" href="struct.State.html" title="struct mathml::acset::State">State</a></div></li><li><div class="item-name"><a class="struct" href="struct.Time.html" title="struct mathml::acset::Time">Time</a></div></li><li><div class="item-name"><a class="struct" href="struct.Transition.html" title="struct mathml::acset::Transition">Transition</a></div></li><li><div class="item-name"><a class="struct" href="struct.Units.html" title="struct mathml::acset::Units">Units</a></div></li></ul></section></div></main></body></html>
Loading

0 comments on commit c4f0176

Please sign in to comment.