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70ab9ad0cf803b48d2c37473fba3cf5ac8bfc860789f0525779f63cee0571512 | JavaScript | 66,303 | 1,525 | /* Copyright 2024 Satria Kautsar, Arjan Draisma, Nico Louwen, Catarina Loureiro */
var BigscapeFunc = {
ver: "2.0",
requires: [
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e16d5c26379abd4f6dedb8fbe42db785b3170613f31d709352d8aa54b743ca9f | JavaScript | 78,746 | 157 | /*! DataTables 1.10.4
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82f64f62bb03c1bc1824b0f9c9e05f70dba33e146818e63cdf5c306c8cf3dedd | JavaScript | 80,663 | 7 | /*!
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c3cc6fedbf7da8c79d1655be228fbf86ced95053cc463cbedccd0a0c89ab9df6 | JavaScript | 88,441 | 2,484 | /**
* @author zhixin wen <wenzhixin2010@gmail.com>
* version: 1.8.1
* https://github.com/wenzhixin/bootstrap-table/
*/
! function ($) {
'use strict';
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695143e42ec5ff94c3304aff6c4d667d6704ea45a75be2325144d19ef79de97c | JavaScript | 88,904 | 9 | /*!
* reveal.js 4.3.1
* https://revealjs.com
* MIT licensed
*
* Copyright (C) 2011-2022 Hakim El Hattab, https://hakim.se
*/
const e=(e,t)=>{for(let i in t)e[i]=t[i];return e},t=(e,t)=>Array.from(e.querySelectorAll(t)),i=(e,t,i)=>{i?e.classList.add(t):e.classList.remove(t)},s=e=>{if("string"==typeof e){if("null"===e)re... |
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5b023d6665ef91cb2a1e80c91af092014495ce8f1d11892566eadbc8c20a6d86 | JavaScript | 91,331 | 1 | !function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):(e="undefined"!=typeof globalThis?globalThis:e||self).RevealMarkdown=t()}(this,(function(){"use strict";function e(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Objec... |
c12f6098e641aaca96c60215800f18f5671039aecf812217fab3c0d152f6adb4 | JavaScript | 92,629 | 5 | /*! jQuery v1.9.1 | (c) 2005, 2012 jQuery Foundation, Inc. | jquery.org/license
//@ sourceMappingURL=jquery.min.map
*/(function(e,t){var n,r,i=typeof t,o=e.document,a=e.location,s=e.jQuery,u=e.$,l={},c=[],p="1.9.1",f=c.concat,d=c.push,h=c.slice,g=c.indexOf,m=l.toString,y=l.hasOwnProperty,v=p.trim,b=function(e,t){return... |
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2ecd295d295bec062cedebe177e54b9d6b19fc0a841dc5c178c654c9ccff09c0 | JavaScript | 95,931 | 4 | /*! jQuery v1.11.2 | (c) 2005, 2014 jQuery Foundation, Inc. | jquery.org/license */
!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof wind... |
668b046d12db350ccba6728890476b3efee53b2f42dbb84743e5e9f1ae0cc404 | JavaScript | 97,163 | 5 | /*! jQuery v1.12.4 | (c) jQuery Foundation | jquery.org/license */
!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,fu... |
1dc32019ad94d03e8085d4eb368d2c5b059c93133c835be2707136bc1b10ad1c | JavaScript | 102,503 | 2,257 | // ============================================================================
// py2Dmol/resources/viewer-seq.js
// -------------------------------
// AI Context: SEQUENCE VIEWER
// - Renders the protein/nucleotide sequence.
// - Handles sequence-structure interaction (hover, click).
// - Supports virtual scrolling f... |
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var Kinetic={};!function(a){var b=Math.PI/180;Kinetic={version:"5.1.0",stages:[],idCounter:0,ids:{},names:{},shapes:{},listenClickTap:!1,inDblClickWindow:!1,enableTr... |
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8b2355a0557228891c0ccb23bdcd94b9f98cd7caf6688f2db519040cc45f853c | JavaScript | 139,565 | 41 | /*
* This combined file was created by the DataTables downloader builder:
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*
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*
* Included libraries:
* D... |
1332832442c7016bb0265eacee7e43d382d10747499f0c40bf6ebf53ead407a2 | JavaScript | 141,324 | 5,541 | /*!
* svg.js - A lightweight library for manipulating and animating SVG.
* @version 2.6.1
* https://svgdotjs.github.io/
*
* @copyright Wout Fierens <wout@mick-wout.com>
* @license MIT
*
* BUILT: Sun May 14 2017 13:10:43 GMT-0400 (EDT)
*/;
(function(root, factory) {
/* istanbul ignore next */
if (typeof define === '... |
9cf11a8b0b63d1803026efe4154c2881f9fb9f2f34555ba1a19ff97b460f5800 | JavaScript | 142,021 | 3,740 | /**
* InCHlib is an interactive JavaScript library which facilitates data
* visualization and exploration by means of a cluster heatmap. InCHlib
* is a versatile tool, and its use is not limited only to chemical or
* biological data. Source code, tutorial, documentation, and example
* data are freely available from InC... |
e164ef15edae1f1a0a1d1e3636abd098ca83929c92985d1344d1b78a2de54c9a | JavaScript | 144,745 | 5 | d3=function(){function n(n){return null!=n&&!isNaN(n)}function t(n){return n.length}function e(n){for(var t=1;n*t%1;)t*=10;return t}function r(n,t){try{for(var e in t)Object.defineProperty(n.prototype,e,{value:t[e],enumerable:!1})}catch(r){n.prototype=t}}function u(){}function i(){}function o(n,t,e){return function(){v... |
58ec1cd7185e1f59c0451a3b4d2c8676e9f8113e9ade18bca519d77ac93a1e4f | JavaScript | 144,746 | 5 | d3=function(){function n(n){return null!=n&&!isNaN(n)}function t(n){return n.length}function e(n){for(var t=1;n*t%1;)t*=10;return t}function r(n,t){try{for(var e in t)Object.defineProperty(n.prototype,e,{value:t[e],enumerable:!1})}catch(r){n.prototype=t}}function u(){}function i(){}function o(n,t,e){return function(){v... |
029bb98f9a51ce9376cf32c317db915744b7126560de3b596d41c6e70ede38c8 | JavaScript | 145,280 | 9 | /*!
* reveal.js 4.3.1
* https://revealjs.com
* MIT licensed
*
* Copyright (C) 2011-2022 Hakim El Hattab, https://hakim.se
*/
!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):(e="undefined"!=typeof globalThis?globalThis:e||self).Reveal... |
76c39718d1c0a3fb321676b3b7e29306c0907919a5716d5728bd1b08ae0169e7 | JavaScript | 151,725 | 5 | !function(){function n(n){return n&&(n.ownerDocument||n.document||n).documentElement}function t(n){return n&&(n.ownerDocument&&n.ownerDocument.defaultView||n.document&&n||n.defaultView)}function e(n,t){return t>n?-1:n>t?1:n>=t?0:NaN}function r(n){return null===n?NaN:+n}function i(n){return!isNaN(n)}function u(n){return... |
b81e673dc58af2faf97bcdec9eab4c5182769ffe536773d5f42091935a73a1be | JavaScript | 151,732 | 5 | !function(){function n(n){return n&&(n.ownerDocument||n.document||n).documentElement}function t(n){return n&&(n.ownerDocument&&n.ownerDocument.defaultView||n.document&&n||n.defaultView)}function e(n,t){return t>n?-1:n>t?1:n>=t?0:NaN}function r(n){return null===n?NaN:+n}function u(n){return!isNaN(n)}function i(n){return... |
9705475e38eb67e73a6304f1750866da80fc511655d826f16da8393d7a4d98f6 | JavaScript | 188,709 | 1 | (globalThis.TURBOPACK||(globalThis.TURBOPACK=[])).push(["object"==typeof document?document.currentScript:void 0,22737,(e,t,n)=>{"use strict";Object.defineProperty(n,"__esModule",{value:!0}),Object.defineProperty(n,"setAttributesFromProps",{enumerable:!0,get:function(){return o}});let r={acceptCharset:"accept-charset",c... |
560d59534b9e683e9ff5b66682b2088a3cf37f9f06242c23c05bd2737d592aec | JavaScript | 195,796 | 6,847 | !function(e){if("object"==typeof exports&&"undefined"!=typeof module)module.exports=e();else if("function"==typeof define&&define.amd)define([],e);else{var f;"undefined"!=typeof window?f=window:"undefined"!=typeof global?f=global:"undefined"!=typeof self&&(f=self),f.Viva=e()}}(function(){var define,module,exports;retur... |
14cd2ff05a61aed3ddb1e0395caf676f77f568ff2d5ed82a4674166588669602 | JavaScript | 200,000 | 6,091 | /******/ (function(modules) { // webpackBootstrap
/******/ // The module cache
/******/ var installedModules = {};
/******/
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/******/ function __webpack_require__(moduleId) {
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/******/ if(installedModules[moduleId]) {
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1c14097e81f91c7d79580cf89b957a9457b8203cf0393d1f299dc17757a6191f | JavaScript | 200,000 | 13 | /*!
* Chart.js v4.4.1
* https://www.chartjs.org
* (c) 2023 Chart.js Contributors
* Released under the MIT License
*/
!function(t,e){"object"==typeof exports&&"undefined"!=typeof module?module.exports=e():"function"==typeof define&&define.amd?define(e):(t="undefined"!=typeof globalThis?globalThis:t||self).Chart=e()... |
1d47b63435d5f33405e4d4160dec4b005fd99bfa0b1cbc0efb7184ff4f4d262f | JavaScript | 200,000 | 4,784 | /*!
* Yet Another DataTables Column Filter - (yadcf)
*
* File: jquery.dataTables.yadcf.js
* Version: 0.9.4.beta.46
*
* Author: Daniel Reznick
* Info: https://github.com/vedmack/yadcf
* Contact: vedmack@gmail.com
* Twitter: @danielreznick
* Q&A http://stackoverflow.com/questions/t... |
21c047e4fd4b8090b0d3f867edf5be3174fa6caaa00cee1b1ed3f693689b163a | JavaScript | 200,000 | 4,712 | (function (window) {
'use strict';
/*global define, module, exports, require */
var c3 = { version: "0.4.10" };
var c3_chart_fn,
c3_chart_internal_fn,
c3_chart_internal_axis_fn;
function API(owner) {
this.owner = owner;
}
function inherit(base, derived) {
... |
223eb9373a91c27d953dc0d0e4635a4a5e56ab1b1eeffb1675290bee3f6e169a | JavaScript | 200,000 | 7,447 | /*!
* jQuery JavaScript Library v3.4.1
* https://jquery.com/
*
* Includes Sizzle.js
* https://sizzlejs.com/
*
* Copyright JS Foundation and other contributors
* Released under the MIT license
* https://jquery.org/license
*
* Date: 2019-05-01T21:04Z
*/
( function( global, factory ) {
"use strict";
if ( t... |
9a99f811996f790a0f1983319ed13a334421000ffc24e920eaef7692794aea2f | JavaScript | 200,000 | 8,174 | var pfams={
"PF00001":{
"col":"255,255,255",
"desc":"7 transmembrane receptor (rhodopsin family)"
},
"PF00002":{
"col":"255,255,255",
"desc":"7 transmembrane receptor (Secretin family)"
},
"PF00003":{
"col":"255,255,255",
"desc":"7 transmembrane sweet-... |
b9fbd13627e7e474cf83403420a0f2baa9eeba7750a28bf8fe3da11fc1cf84cf | JavaScript | 200,000 | 7 | var Clustergrammer=function(t){function e(n){if(r[n])return r[n].exports;var o=r[n]={exports:{},id:n,loaded:!1};return t[n].call(o.exports,o,o.exports,e),o.loaded=!0,o.exports}var r={};return e.m=t,e.c=r,e.p="",e(0)}([function(t,e,r){"use strict";function n(t){function e(){d3.select(S.params.viz.viz_svg).style("opacity... |
c317e632071f0e885082b4338c4fd108eeda3f81cdaf975b32a06405a0f997fe | JavaScript | 200,000 | 45 | /**
* math.js
* https://github.com/josdejong/mathjs
*
* Math.js is an extensive math library for JavaScript and Node.js,
* It features real and complex numbers, units, matrices, a large set of
* mathematical functions, and a flexible expression parser.
*
* @version 3.2.1
* @date 2016-04-26
*
* @license
*... |
dad68b335c4f38f3453820c026fa2212f448a955a4a0070d4cb9a74cc1947a6c | JavaScript | 200,000 | 5 | // Embedded proteome data for offline use
// Only includes proteins with AF2BIND predictions (no server required)
// Format: Array of [uniprot_id, swissprot_id, md5_hash]
window.EMBEDDED_PROTEOME_DATA = [["A0A087X1C5","CP2D7_HUMAN","a3e7cd422fcc857d4942019ec793d60a"],["A0A0B4J2F0","PIOS1_HUMAN","38e39e0b28141ce0a15838... |
ff4f9e85d9088a557bd65920e3722cd9349bde89843ec240b800fb110831ce46 | JavaScript | 200,000 | 101 |
// We are modularizing this manually because the current modularize setting in Emscripten has some issues:
// https://github.com/kripken/emscripten/issues/5820
// In addition, When you use emcc's modularization, it still expects to export a global object called `Module`,
// which is able to be used/called before the W... |
5aed0bf1abee3a9b1924e5e51a611c4821a49e46bc396193b598ac3f3a29a70f | JavaScript | 200,002 | 6 | /*! jQuery UI - v1.13.2 - 2022-07-14
* http://jqueryui.com
* Includes: widget.js, position.js, data.js, disable-selection.js, effect.js, effects/effect-blind.js, effects/effect-bounce.js, effects/effect-clip.js, effects/effect-drop.js, effects/effect-explode.js, effects/effect-fade.js, effects/effect-fold.js, effects/e... |
cf24f7da0cb7d5289511369b9e51f8b02ce83372f3d29fa260df4044e5a86bcd | JavaScript | 200,002 | 2 | /*! antismash-js, version: 0.4.4 */
var viewer=function(t){var e={};function n(r){if(e[r])return e[r].exports;var i=e[r]={i:r,l:!1,exports:{}};return t[r].call(i.exports,i,i.exports,n),i.l=!0,i.exports}return n.m=t,n.c=e,n.d=function(t,e,r){n.o(t,e)||Object.defineProperty(t,e,{enumerable:!0,get:r})},n.r=function(t){"un... |
24d4f2b8763df37f2c484bac8b9d21e34a3257ffcc8ad8eed405a70bcabe6d84 | JavaScript | 200,004 | 1 | (globalThis.TURBOPACK||(globalThis.TURBOPACK=[])).push(["object"==typeof document?document.currentScript:void 0,67398,(e,t,n)=>{"use strict";t.exports={}},10560,(e,t,n)=>{"trimStart"in String.prototype||(String.prototype.trimStart=String.prototype.trimLeft),"trimEnd"in String.prototype||(String.prototype.trimEnd=String... |
fed0018c9f57866cbc49a04cfed77b56b9f2492adab23cd2c6da7d80731d7eec | JavaScript | 200,004 | 1 | (globalThis.TURBOPACK||(globalThis.TURBOPACK=[])).push(["object"==typeof document?document.currentScript:void 0,67398,(e,t,n)=>{"use strict";t.exports={}},10560,(e,t,n)=>{"trimStart"in String.prototype||(String.prototype.trimStart=String.prototype.trimLeft),"trimEnd"in String.prototype||(String.prototype.trimEnd=String... |
8d838d989f44a2f84e4fd47f7dc2bfcd9709d050a50ec6ddfcb41dafed012389 | JavaScript | 200,018 | 4,291 | // ============================================================================
// py2Dmol/resources/viewer-mol.js
// -------------------------------
// AI Context: CORE RENDERER (Pseudo3DRenderer)
// - This is the heart of the visualization.
// - Implements `Pseudo3DRenderer` class.
// - Handles 3D projection, depth s... |
4e9472f143a249312ec248a363201d2366838fd54a1f36c2f57f39edb70942a8 | JavaScript | 201,094 | 5,678 | !function() {
var d3 = {
version: "3.5.16"
};
var d3_arraySlice = [].slice, d3_array = function(list) {
return d3_arraySlice.call(list);
};
var d3_document = this.document;
function d3_documentElement(node) {
return node && (node.ownerDocument || node.document || node).documentElement;
}
fun... |
2928c291f4660a11f847d1ada099ff70bdc8a695c16ae9aa7c7d188d1ac31bb3 | JavaScript | 226,208 | 1 | function e(t){return(e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e})(t)}function t(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function... |
b1ee8fc78b8706fc5736e1c6d836a565120d8eb15f4e71be89826eac472e1797 | JavaScript | 226,208 | 1 | !function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):(e="undefined"!=typeof globalThis?globalThis:e||self).RevealHighlight=t()}(this,(function(){"use strict";function e(t){return(e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterat... |
8ace39cda1b76db070067c147021c8df8ae048836a524794cfad48a9eb50f3e6 | Julia | 33 | 3 | module Chimera_EGT_Kuramoto
end
|
71d7cdee3ac8b72af4d03526f6bb0f6c875938d3374b5f41cee474ef03adc40a | Julia | 535 | 26 | # SPDX-License-Identifier: GPL-3.0-or-later
using DrWatson, Test
quickactivate("..", "Chimera_EGT_Kuramoto")
# Run test suite
println("Starting tests")
ti = time()
@testset "Chimera_EGT_Kuramoto tests" begin
@testset "Utils tests" begin
include("utils_tests.jl")
end
@testset "Moran tests" begin
includ... |
51e9cf68dfb197470dc08fab98599c6cb8d536b4a47567165a3e806e696cd17e | Julia | 624 | 16 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
3eafc538485327870369a8dba2c135b609908ba5826a6e9a3efb038b43eccba6 | Julia | 643 | 17 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
b5eb7eae40f300a54907b621c876f0ab7c634b94f365892a595a6316b7631bc2 | Julia | 672 | 18 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
6e9ff1a16116cf79c2d1cdc8357734e6a6dfd94746c481c52ce4449e3b41eab7 | Julia | 874 | 23 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
645a11dec2b18113bfb2ef4311c12b07a94af80f88b4a27310714d1fafe02fad | Julia | 906 | 25 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
18f0fd0e765b40be415f089be4f01fd0c5e36606e044402d315ab3dd39dbc2cb | Julia | 995 | 25 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
4f673ffe8f61eda488ad1c0f42316114d0054ddef0c8e6174c0e890a8d2b66b0 | Julia | 1,032 | 28 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
a61e6642c83738079a6a90c0cbbfc3276f172927e8671db1805e58d709207733 | Julia | 1,049 | 44 | using Distributed
@everywhere using LinearAlgebra
# Function to construct reciprocal space Hamiltonian and overlap matrices
@everywhere function reciprocal_space_matrices(H_real, S_real, R, k)
N = size(H_real)[3]
dim = size(H_real)[1]
H_k = zeros(Complex{Float64}, dim, dim)
S_k = zeros(Complex{Floa... |
ba2b040ded09e1e076e817e79857c4cae31f073f7d72b5051f52e92ac410c354 | Julia | 1,172 | 33 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
49810b06b31a1a4b776febd2721dc635d82acbe5ad418b1dd55a8acd98add9e5 | Julia | 1,219 | 32 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
9e14cbad09677fa3f9d289a64b910122922715c0f19215ccd3dc81f65b0f5d34 | Julia | 1,234 | 27 | #####################################################################
using Lux, Random, Zygote
struct DenseWithMask <: Lux.AbstractLuxLayer
init_weight
init_bias
init_W_mask
init_b_mask
activation
end
function DenseWithMask(weight::AbstractArray, bias::AbstractArray, W_mask::AbstractArra... |
38f99a3b6e4d5ed2b9022cef06c9891275150f8584c95d56c87da21f6c247571 | Julia | 1,293 | 29 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
5965764aa01252c2511cd87cb8d6ef95fc367dc453fb1f263bcf89c9c769eb9e | Julia | 1,353 | 49 | using DataFrames, CSV
using Statistics, Distributions, Random
using Plots
using ExpectationMaximization, Lux
Random.seed!(100)
include("s00_simulator_functions.jl")
######### Simulate a training dataset
df_sim = simulate_full_dataset(30000, 115)
df1 = filter_data_state(df_sim, 1)
df2 = filter_data_stat... |
2afffc6a89f9b664cd564b18f5fb4f40e5597a82362e0f842efdd22ccd75f39a | Julia | 1,390 | 36 | #####################################################################
using Lux, Random, Zygote
struct DenseWithMask <: Lux.AbstractLuxLayer
init_weight
init_bias
init_W_mask
init_b_mask
activation
end
# struct DenseWithMask <: Lux.AbstractExplicitLayer
# init_weight
# init_bi... |
f785376f8e995259034bfa77f2e9d2aa2fcf417357acfe10670b42a79ea0c4b5 | Julia | 1,398 | 37 | using DataFrames, CSV
using Statistics, Distributions, Random
#########################################################################
####################################################################
include("s00_simulator_functions.jl")
## extract pseudo observations
df = CSV.read("Data/Full_dataset_val... |
8345f45cf33d28393a4d09bc1fae9affc41bc45baffff388c5b6ee786a209a60 | Julia | 1,710 | 52 | # SPDX-License-Identifier: GPL-3.0-or-later
using CairoMakie
using Graphs
using GraphMakie
using Colors
using NetworkLayout
include("utils.jl")
function plot_graph_evolution(data::Dict, interaction_graph::AbstractGraph)
# Decode data
time_steps = size(data["deltas"])[2]
data["all_populations"] = decode_delta... |
c271d0d92fad93bca560c1dba1a9e3bedc3358368f22cf1488160a6bbdc7686c | Julia | 1,846 | 44 | ####################
## Mixture model to estimate right censoring distribution
###################
using DataFrames, CSV
using Statistics, Distributions, Random
using Plots
using ExpectationMaximization
###########################################################################
include("s00_simulator_function... |
2b62082028cd0be69a901e4c5112fba21c3b304f674d77c449259426a8206ddf | Julia | 1,941 | 40 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
7d9e5c9da74463f6eb8184cc9f0549861058d57f7b2b90a6d54cff1ceb65b04a | Julia | 2,033 | 43 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
e9f0097bfa33cd23d3872295aae9abd64d4eb14726f2889d1b857478299ccd14 | Julia | 2,073 | 50 |
########################################################################################################
########################################################################################################
############ PRUNING ##############################################################################
#####... |
f97481c9b4fe9201dd829882a228e8557120ec18b79a9c1e539445a2d5fc0f1b | Julia | 2,081 | 59 | using DataFrames, CSV
using Statistics, Distributions, Random
using DifferentialEquations
include("s04_pseudo_obs_and_state_occupation.jl")
################## PREDICTIONS ################################################
df = CSV.read("Data/S1_val.csv", DataFrame)
df = select(df, Not(:Tl, :Tu, :time, :state, :... |
d81ed9737835af43f9c6b3ae53b32480bfee423c165477d7ff5465632ee0728e | Julia | 2,139 | 55 | using DataFrames, CSV
using Statistics, Distributions, Random
using Plots
using ExpectationMaximization
using Lux
include("s00_simulator_functions.jl")
include("s02_Mixture_model.jl")
###########################################################################
### Load datasets ########
##################... |
7bb974e760760693ff3128747cedabbe341e7e9e223619b141ccd0969a2f6e22 | Julia | 2,357 | 45 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
6a38c09b33e4ee424168028e347797fc0228cc8157a9faf331f72ccccb6f6ca2 | Julia | 2,407 | 52 | using Lux, Zygote, Distributions, Optimisers, Random, MLUtils
using ComponentArrays
using CSV, DataFrames
#using Plots
using JLD2
include("s00_functions.jl")
include("s00_maskdense_objects.jl")
rng = Random.default_rng()
Random.seed!(1)
########################################################################... |
04ab49ca0d8065ac50a02c7def674c3b17eb4667d637f0f7d4c828c478af5834 | Julia | 2,429 | 61 | # SPDX-License-Identifier: GPL-3.0-or-later
using Symbolics
function check_formulas(nb_phases::Integer, nb_players::Integer)
# Define symbols
@variables B_0 beta_0 phi delta c i j k q r d n
# Define constants
d = nb_phases
n = nb_players
# Define functions
B(phi) = B_0 * (1 + cos(phi)) /... |
1e3d781ae19eec7473755f8edb1c52299cd4742adbfd1f585159e9fb5b7f0be6 | Julia | 2,524 | 87 | import OMEinsum
import ArgParse
import JSON
using KaHyPar
function parse_commandline()
s = ArgParse.ArgParseSettings()
@ArgParse.add_arg_table s begin
"--einsum_json"
arg_type = String
default = "einsum.json"
"--result_json"
arg_type = String
def... |
7720654d41d5335e6c6c5eee01ab09f4b0b1a5c56dbd5f2c4b02e336a2c4b373 | Julia | 2,555 | 55 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
e0daa3eac51711fb4efc38b6a9473d59605dd7ed9c3eb9713b7f2ecc9a468e6f | Julia | 2,565 | 55 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
5a0fe2dd87b6fc38672002c656d333e4ae2e2005d66a14b2ebf7b4325460d669 | Julia | 2,787 | 72 | # SPDX-License-Identifier: GPL-3.0-or-later
# Load SparseArrays since all scripts either save or load
# a dataDict containing a SparseArray
using SparseArrays
using CSV
using DataFrames
using StatsBase
function parse_string(string::String)::Union{String,Int64,Float64}
value = tryparse(Float64,string)
if isnothing... |
caca780c9a9103c0485adec4f78853a3436692b084ccc9279cd32fc7cd7c4b8d | Julia | 2,913 | 76 | # SPDX-License-Identifier: GPL-3.0-or-later
using DrWatson
include("moran.jl")
include("utils.jl")
function calc_cumulative(;selection_strength::Real, symmetry_breaking::Real,
adj_matrix_source::String="well-mixed",
time_steps::Integer=2_000_000,
nb_phases::Integ... |
a88488e39cec88e66d18d90f61da8317c96cf07720c024cbb41a67989523b8d3 | Julia | 3,059 | 68 | using DataFrames, CSV
using Statistics, Distributions, Random
using Lux
include("s04_pseudo_obs_and_state_occupation.jl")
################## PREDICTIONS ################################################
λ12(icovs, AGE) = sigmoid( -7.349414447202377 + 3.3382179379095525*AGE^2 )
λ13(icovs, AGE) = sigmoid( -3.7704... |
32ef889c7c4ad44f68de91d7eceb6cd427700eccae9537c96f8486556e35ee75 | Julia | 3,298 | 65 | # SPDX-License-Identifier: GPL-3.0-or-later
using DrWatson, Test
using LinearAlgebra
using Graphs
quickactivate("..", "Chimera_EGT_Kuramoto")
include(srcdir("julia", "utils.jl"))
@testset "Extract number communicative" begin
@test extract_num_communicative([5,0]) == 5
@test extract_num_communicative([0,3]) =... |
47527b004eb272372dfb6a23ef47f39937c998c0410b0b6811f2917eb59c5620 | Julia | 3,326 | 90 | using HopTB
using DelimitedFiles
using StaticArrays
using HDF5
using LinearAlgebra
@everywhere function extract_chemical_potential_from_scfout(scfout_path)
# Open the SCFOUT file
openmx_file = open(scfout_path, "r")
# Read the file line by line
for line in eachline(openmx_file)
# Look for ... |
f2aa5dad0d1077f79c3b02c400d717c54606356e978045812275219596ca6618 | Julia | 3,962 | 73 | # SPDX-License-Identifier: GPL-3.0-or-later
@enum GameType chicken battle hero compromise deadlock dilemma staghunt assurance coordination peace harmony concord neutral allCommunicative allNoncommunicative disconnectedSynchronizedPopulations
@enum TieType lowTie midTie highTie doubleTie tripleTie basicTie zeroTie
co... |
b1e6c9c7bc4c49239b2978a05a0cf7b076c51c88797edefda7070d5d24d707c7 | Julia | 4,128 | 105 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
75e5aee45cfb8625b58d12490cb68c789b414ee7b0b22a3358f45143881a3eef | Julia | 4,181 | 131 | # SPDX-License-Identifier: GPL-3.0-or-later
using DrWatson, Test
using LinearAlgebra
using Random
using Graphs
using SimpleWeightedGraphs
quickactivate("..", "Chimera_EGT_Kuramoto")
include(srcdir("julia", "moran.jl"))
@testset "Deterministic, undirected, prisoner's dilemma, well-mixed graph" begin
payoff_matrix... |
8876c4f5b8588cdba928a1929defbd424fb80396fed0912c0130184fa7299f3f | Julia | 4,399 | 101 | using Symbolics
using Lux, Zygote, Distributions, Optimisers, Random, MLUtils
using ComponentArrays
using CSV, DataFrames
using JLD2
@variables x1 x2 x3 x4 x5 x6 x7 x8 x9 x10
include("s00_functions.jl")
include("s00_maskdense_objects.jl")
df4 = CSV.read("Data/S4.csv", DataFrame)
df4_test, df4 = train_test_... |
24e2c5084c70508de80e76ec7d0fb5dffe9e110d05cdc1c9feacddc963c68bd6 | Julia | 6,162 | 135 | # SPDX-License-Identifier: GPL-3.0-or-later
using DataToolkit
using LinearAlgebra
using BlockArrays
using Random
using Graphs
using SimpleWeightedGraphs
using XLSX
"Add together the elements from the first half of a list with an even number of elements."
function extract_num_communicative(players_per_strategy::Abstra... |
7cb4f73ef4b1791d9b71db9076ff48cb186f746ac29635a22b2ae8323bdae9c6 | Julia | 7,067 | 153 | # SPDX-License-Identifier: GPL-3.0-or-later
using DrWatson, Test
using DimensionalData
quickactivate("..", "Chimera_EGT_Kuramoto")
include(srcdir("julia", "postprocess.jl"))
@testset "Order parameter" begin
# All players have the same strategy
@test extract_order_parameters([0,5,0,0],2) == 1
# All players have di... |
4306e456c8f62faa86732841ba91895c97e37b1f661ea4ffce3e57154c9377cc | Julia | 7,238 | 157 | # SPDX-License-Identifier: GPL-3.0-or-later
# Workaround to force snakemake to use Project.toml
# Source: https://github.com/snakemake/snakemake/issues/2215#issuecomment-1747136802
dirname(Base.active_project()) != pwd() && exit(run(`julia --project=@. $(@__FILE__)`).exitcode)
# Creates wildcards NamedTuple with snak... |
288cc565f8433a9bdc6a6ee28b59398324b01c06470873555d1962ec04c1a69c | Julia | 8,278 | 159 | #using Symbolics
using Lux, Zygote, Distributions, Optimisers, Random, MLUtils
using ComponentArrays
using CSV, DataFrames
#using Plots
using JLD2
include("s00_functions.jl")
include("s00_maskdense_objects.jl")
rng = Random.default_rng()
Random.seed!(3)
#@variables x1 x2 x3 x4 x5 x6 x7 x8 x9 x10
########... |
bda95064fd99afebc1706090abdc975952759584c468dedc6ab45eeabaa21b41 | Julia | 10,697 | 273 | using DelimitedFiles, LinearAlgebra, JSON
using HDF5
using ArgParse
using SparseArrays
using Arpack
using JLD
function parse_commandline()
s = ArgParseSettings()
@add_arg_table! s begin
"--input_dir", "-i"
help = "path of rlat.dat, orbital_types.dat, site_positions.dat, hamiltonians_pred.h... |
220ca4d8c752a314040ae8e802a27be9e6ebd2e02ec9bfc67133bc8bac38b68e | Julia | 10,754 | 258 | # SPDX-License-Identifier: GPL-3.0-or-later
using GameTheory
using Random
using StatsBase
using Graphs
using GNNGraphs
using DataFrames
using SparseArrays
struct Moran{N,T1<:Real,S<:Integer,S2<:Integer,T2<:Real,T3<:Real,
AT1<:AbstractMatrix{<:T1},AT2<:AbstractMatrix{<:T1},
... |
9df3343a6828b85f0587c770d644fca15ff116e666af617061e039df487e9925 | Julia | 11,944 | 307 | # Usage of Pardiso.jl: see https://github.com/JuliaSparse/Pardiso.jl
# Rremember to export OMP_NUM_THREADS and JULIA_NUM_THREADS variables before running this script.
using DelimitedFiles, LinearAlgebra, JSON
using HDF5
using ArgParse
using SparseArrays
using Pardiso, Arpack, LinearMaps
using JLD
function parse_comm... |
c82df92f88b38ef267c9bbf3ed27e78d1f9fd3ec9948feeed10af30ed6a784b7 | Julia | 18,205 | 472 | using StaticArrays
using LinearAlgebra
using HDF5
using JSON
using DelimitedFiles
using Statistics
using ArgParse
function parse_commandline()
s = ArgParseSettings()
@add_arg_table! s begin
"--input_dir", "-i"
help = ""
arg_type = String
default = "raw/openmx_test_in... |
f5ec3415aa09408e84a3a9fdcc9de8bf8a0f38cdecf1fb7a1e08a3bd90f48adb | Julia | 23,441 | 582 | # SPDX-License-Identifier: GPL-3.0-or-later
using DrWatson
using Graphs
using Random
using SimpleWeightedGraphs
using DataFramesMeta
using Memoize
using DimensionalData
using DimensionalData.Lookups
using NetworkLayout
using CSV
using Statistics
using PlotUtils
using SplitApplyCombine
using JLD2
using YAXArrays
using ... |
276a77a9c4e523b3540dbd1d214e88814ef29590d6484b57d11030b64f17a36c | Julia | 29,972 | 720 |
###########################################################
####### Functions ########################################
#########################################################
function train_test_data_split(df, frac)
state = df.state
unique_state = unique(state)
Number_of_groups = length(unique_state)
... |
d8a7f04530b5f99478ffd7dfe4483ddb0440cc58e35310aed3d3839ad50efca3 | Julia | 30,036 | 732 |
###########################################################
####### Functions ########################################
#########################################################
function train_test_data_split(df, frac)
state = df.state
unique_state = unique(state)
Number_of_groups = length(unique_state)
... |
67b0a95561c433ba50e10d094e36e8dd79af34f940d0c90b46be693375c5f7f9 | Julia | 30,058 | 766 |
###########################################################
####### Functions ########################################
#########################################################
function covariate_transformation_age_change(TIME, COVS, state)
upper = TIME[:,2]
time_vector = []
id_vec = []
state_vec = []
... |
2670cb65259cf12958cbf9fd47ea8b0962577be88702926c12b525228660f912 | Julia | 40,191 | 969 |
###########################################################
####### Functions ########################################
#########################################################
function train_test_data_split(df, frac)
state = df.state
unique_state = unique(state)
Number_of_groups = length(unique_state)
... |
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