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Lib to npm #2349

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merged 40 commits into from
Oct 4, 2024
Merged

Lib to npm #2349

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9d8ab72
remove submodule
metehaansever Jan 22, 2024
7a652d0
Bootstrap remove
metehaansever Jan 22, 2024
fc4df03
bootstrap-waitingfor remove
metehaansever Jan 22, 2024
7184502
bootstrap-markdown remove
metehaansever Jan 22, 2024
032ac4d
jquery remove
metehaansever Jan 22, 2024
5304cb1
jquery-ui remove
metehaansever Jan 22, 2024
de367be
marked removed
metehaansever Jan 22, 2024
1a7d2ec
randomColor remove
metehaansever Jan 22, 2024
242a4d4
toastr remove
metehaansever Jan 22, 2024
a883b47
Javascript-MD5 remove
metehaansever Jan 22, 2024
b437f54
d3.js remove
metehaansever Jan 22, 2024
620aaa1
Fix lib > node_modules
metehaansever Jan 29, 2024
9743413
Fix sortable package update
metehaansever Jan 29, 2024
6943502
remove accordion functionality
metehaansever Feb 1, 2024
029c879
Add html5sortable package
metehaansever Feb 1, 2024
668d6e3
Remove func call
metehaansever Feb 1, 2024
ec4ce63
Fix jquery-ui order
metehaansever Feb 5, 2024
5665633
Update package.json += svg-pan-zoom
metehaansever Feb 5, 2024
4132e7f
Update symlink lib -> node_modules
metehaansever Feb 6, 2024
9f91ef4
Remove merge string
metehaansever Feb 6, 2024
d522032
Add disable class
metehaansever Feb 12, 2024
37ba1f2
Fix Settings btn z-index
metehaansever Feb 14, 2024
e08a379
Update browser control
metehaansever Feb 26, 2024
9c9a374
Fix table-sortable package
metehaansever Feb 26, 2024
645e305
Fix table-sortable +=
metehaansever Feb 26, 2024
c210a45
Remove gitmodule
metehaansever Feb 27, 2024
305c080
Remove unused func
metehaansever Feb 27, 2024
1253a45
Remove sortable codes
metehaansever Feb 29, 2024
0b949b1
Update package link
metehaansever Mar 4, 2024
707f73d
Delete chartjs package
metehaansever Sep 25, 2024
87a809e
Fix npm installation check
metehaansever Sep 25, 2024
c5506e3
Remove missing dependency
metehaansever Sep 25, 2024
6fb03a3
Update error message
metehaansever Sep 25, 2024
4a42ef7
Remove bootstrapSortable call
metehaansever Sep 25, 2024
85df59b
Remove popover.css
metehaansever Sep 30, 2024
3a1ed6e
Fix all bin deleting issue for pan-mode
metehaansever Sep 30, 2024
3d7bb9a
Add table responsive
metehaansever Sep 30, 2024
337fc8c
Remove treelib-js
metehaansever Sep 30, 2024
f20d423
Update package versions
metehaansever Sep 30, 2024
9a99979
Add nodejs package control
metehaansever Sep 30, 2024
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -8,6 +8,8 @@
/build/
/dist/
test-output/
node_modules/
package-lock.json
/*.egg-info/
anvio/__pycache__/
anvio/extensions/concoct/vbgmm.c
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45 changes: 0 additions & 45 deletions .gitmodules
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17 changes: 8 additions & 9 deletions anvio/data/interactive/charts.html
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Expand Up @@ -10,27 +10,26 @@
<meta http-equiv="pragma" content="no-cache" />
<meta name="google" value="notranslate">
<link rel="stylesheet" type="text/css" href="css/loading.css" />
<link rel="stylesheet" href="lib/bootstrap/dist/css/bootstrap.css" />
<link rel="stylesheet" href="./node_modules/bootstrap/dist/css/bootstrap.css" />
<link rel="stylesheet" type="text/css" href="css/charts.css" />
<link rel="stylesheet" href="lib/toastr/build/toastr.min.css" type="text/css" />
<link rel="stylesheet" href="./node_modules/toastr/build/toastr.min.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="css/popover.css" />
<link rel="stylesheet" href="lib/colpick/colpick.css" type="text/css" />
<link rel="shortcut icon" href="#" />
<link href='https://fonts.googleapis.com/css?family=Lato:300,700' rel='stylesheet' type='text/css' />
<link rel="stylesheet" type="text/css" href="css/inspection.css" />
<!--[if lte IE 8]><style>.main{display:none;} .support-note .note-ie{display:block;}</style><![endif]-->
<script type="text/javascript" src="js/utils.js"></script>
<script type="text/javascript" src="lib/jquery/dist/jquery.min.js"></script>
<script type="text/javascript" src="lib/d3.js/d3.min.js"></script>
<script type="text/javascript" src="lib/popperjs/popper.min.js"></script>
<script type="text/javascript" src="lib/bootstrap/dist/js/bootstrap.bundle.min.js"></script>
<script type="text/javascript" src="./node_modules/jquery/dist/jquery.min.js"></script>
<script type="text/javascript" src="./node_modules/d3/d3.min.js"></script>
<script type="text/javascript" src="./node_modules/bootstrap/dist/js/bootstrap.bundle.min.js"></script>
<script type="text/javascript" src="lib/colpick/colpick.js"></script>
<script type="text/javascript" src="js/charts.js"></script>
<script type="text/javascript" src="js/inspectionutils.js"></script>
<script type="text/javascript" src="lib/toastr/build/toastr.min.js"></script>
<script type="text/javascript" src="lib/bootstrap-waitingfor/build/bootstrap-waitingfor.js"></script>
<script type="text/javascript" src="./node_modules/toastr/build/toastr.min.js"></script>
<script type="text/javascript" src="./node_modules/bootstrap-waitingfor/build/bootstrap-waitingfor.js"></script>
<script type="text/javascript" src="js/constants.js"></script>
<link rel="stylesheet" href="lib/bootstrap-icons/font/bootstrap-icons.min.css" type="text/css">
<link rel="stylesheet" href="./node_modules/bootstrap-icons/font/bootstrap-icons.min.css" type="text/css">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css">
</head>
<body onload="loadAll();">
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8 changes: 4 additions & 4 deletions anvio/data/interactive/contigs.html
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Expand Up @@ -3,12 +3,12 @@
<head>
<title>Contigs DB Stats</title>
<meta name="google" value="notranslate">
<script type="text/javascript" src="lib/jquery/dist/jquery.min.js"></script>
<script type="text/javascript" src="./node_modules/jquery/dist/jquery.min.js"></script>
<script type='text/javascript' src='js/utils.js'></script>
<script type='text/javascript' src='lib/d3.js/d3.min.js'></script>
<script type='text/javascript' src='./node_modules/d3/d3.min.js'></script>
<script type='text/javascript' src='js/contigs-plot.js'></script>
<link rel="stylesheet" href="lib/bootstrap/dist/css/bootstrap.css" />
<script type="text/javascript" src="lib/bootstrap/dist/js/bootstrap.bundle.js"></script>
<link rel="stylesheet" href="./node_modules/bootstrap/dist/css/bootstrap.css" />
<script type="text/javascript" src="./node_modules/bootstrap/dist/js/bootstrap.bundle.min.js"></script>
<link rel="stylesheet" type="text/css" href="css/contigs-plot.css" />
<script type="text/javascript">
var contigs_stats;
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6 changes: 6 additions & 0 deletions anvio/data/interactive/css/main.css
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Expand Up @@ -293,6 +293,7 @@ html, body, #wrapper {

.toggle-panel-left-pos {
left: 560px;
z-index: 1;
}

#toggle-panel-left:hover {
Expand Down Expand Up @@ -1183,6 +1184,11 @@ position: relative;
@include btn-border-drawing(#58afd1, #ffe593, 4px, bottom, right);
}

.disabled{
pointer-events:none;
opacity:0.6;
}

@media only screen and (min-width:1440px){
/* styles for browsers larger than 1460px; */
*:not(text) {
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14 changes: 6 additions & 8 deletions anvio/data/interactive/geneclusters.html
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Expand Up @@ -9,21 +9,19 @@
<meta http-equiv="pragma" content="no-cache" />
<meta name="google" value="notranslate">
<link rel="stylesheet" type="text/css" href="css/loading.css" />
<link rel="stylesheet" href="lib/bootstrap/dist/css/bootstrap.css" />
<link rel="stylesheet" href="./node_modules/bootstrap/dist/css/bootstrap.css" />
<link rel="stylesheet" type="text/css" href="css/geneclusters.css" />
<link rel="stylesheet" href="lib/toastr/build/toastr.min.css" type="text/css" />
<link rel="stylesheet" href="lib/bootstrap-icons/font/bootstrap-icons.min.css" type="text/css">
<link rel="stylesheet" href="./node_modules/toastr/build/toastr.min.css" type="text/css" />
<link href='https://fonts.googleapis.com/css?family=Lato:300,700' rel='stylesheet' type='text/css' />
<!--[if lte IE 8]><style>.main{display:none;} .support-note .note-ie{display:block;}</style><![endif]-->
<script type="text/javascript" src="js/utils.js"></script>
<script type="text/javascript" src="lib/jquery/dist/jquery.min.js"></script>
<script type="text/javascript" src="lib/d3.js/d3.min.js"></script>
<script type="text/javascript" src="lib/popperjs/popper.min.js"></script>
<script type="text/javascript" src="lib/bootstrap/dist/js/bootstrap.bundle.js"></script>
<script type="text/javascript" src="./node_modules/jquery/dist/jquery.min.js"></script>
<script type="text/javascript" src="./node_modules/d3/d3.min.js"></script>
<script type="text/javascript" src="./node_modules/bootstrap/dist/js/bootstrap.bundle.js"></script>
<script type="text/javascript" src="js/color-coding.js"></script>
<script type="text/javascript" src="js/geneclusters.js"></script>
<script type="text/javascript" src="js/inspectionutils.js"></script>
<script type="text/javascript" src="lib/toastr/build/toastr.min.js"></script>
<script type="text/javascript" src="./node_modules/toastr/build/toastr.min.js"></script>
<script type="text/javascript" src="js/constants.js"></script>
</head>
<body onload="loadAll();">
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55 changes: 28 additions & 27 deletions anvio/data/interactive/index.html
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Expand Up @@ -11,37 +11,38 @@
<meta http-equiv="pragma" content="no-cache" />
<meta name="google" value="notranslate">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" href="lib/bootstrap/dist/css/bootstrap.css" />
<link rel="stylesheet" href="./node_modules/bootstrap/dist/css/bootstrap.css" />
<link rel="stylesheet" href="lib/colpick/colpick.css" type="text/css" />
<link rel="stylesheet" href="lib/bootstrap-icons/font/bootstrap-icons.min.css" type="text/css">
<link rel="stylesheet" href="lib/toastr/build/toastr.min.css" type="text/css" />

<!-- Import packages from node_modules -->
<link rel="stylesheet" href="./node_modules/bootstrap-icons/font/bootstrap-icons.min.css" />
<link rel="stylesheet" href="./node_modules/toastr/build/toastr.min.css" type="text/css" />
<link rel="icon" type="image/png" href="images/logo-simple.png">
<script type="text/javascript" src="js/error.js"></script>

<script type="text/javascript" src="lib/jquery/dist/jquery.min.js" onerror='alertDependencyError("jquery-core")'></script>
<link href="lib/jquery-ui/themes/base/all.css" rel="stylesheet">
<script type="text/javascript" src="lib/popperjs/popper.min.js"></script>
<script type="text/javascript" src="lib/bootstrap/dist/js/bootstrap.bundle.js" onerror='alertDependencyError("bootstrap-core")'></script>
<script type="text/javascript" src="./node_modules/jquery/dist/jquery.min.js" onerror='alertDependencyError("jquery-core")'></script>
<script type="text/javascript" src="./node_modules/bootstrap/dist/js/bootstrap.bundle.js" onerror='alertDependencyError("bootstrap-core")'></script>
<link rel="stylesheet" href="css/main.css" type="text/css" />
<link rel="preconnect" href="https://fonts.googleapis.com">
<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>

<script>$.uiBackCompat = false; //Do not change the order of jquery-ui files</script>
<script type="text/javascript" src="./node_modules/jquery-ui/ui/widget.js" onerror='alertDependencyError("jquery-widget")'></script>
<script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/mouse.js" onerror='alertDependencyError("jquery-mouse")'></script>
<script type="text/javascript" src="./node_modules/jquery-ui/ui/plugin.js" onerror='alertDependencyError("jquery-plugin")'></script>
<script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/draggable.js" onerror='alertDependencyError("jquery-draggable")'></script>
<script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/resizable.js" onerror='alertDependencyError("jquery-core")'></script>
<script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/sortable.js" onerror='alertDependencyError("jquery-sortable")'></script>
<script type="text/javascript" src="./node_modules/jquery-ui/ui/position.js" onerror='alertDependencyError("jquery-position")'></script>

<script type="text/javascript" src="lib/jquery-svgpan/jquery-svgpan.js" onerror='alertDependencyError("jquery-svg")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/core.js" onerror='alertDependencyError("jquery-core")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/widget.js" onerror='alertDependencyError("jquery-widget")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/mouse.js" onerror='alertDependencyError("jquery-mouse")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/sortable.js" onerror='alertDependencyError("jquery-sortable")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/draggable.js" onerror='alertDependencyError("jquery-draggable")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/accordion.js" onerror='alertDependencyError("jquery-accordian")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/resizable.js" onerror='alertDependencyError("jquery-resizable")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/button.js" onerror='alertDependencyError("jquery-button")'></script>
<script type="text/javascript" src="lib/jquery-ui/ui/position.js" onerror='alertDependencyError("jquery-position")'></script>
<script type="text/javascript" src="lib/randomColor/randomColor.js" onerror='alertDependencyError("random-color")'></script>
<script type="text/javascript" src="./node_modules/html5sortable/dist/html5sortable.min.js" onerror='alertDependencyError("html5sortable")'></script>
<script type="text/javascript" src="./node_modules/randomcolor/randomColor.js" onerror='alertDependencyError("random-color")'></script>
<script type="text/javascript" src="lib/svg-crowbar/svg-crowbar.js"onerror='alertDependencyError("svg-crowbar")'></script>
<script type="text/javascript" src="lib/bootstrap-waitingfor/build/bootstrap-waitingfor.js" onerror='alertDependencyError("bootstrap-waitingfor")'></script>
<script type="text/javascript" src="lib/JavaScript-MD5/js/md5.js" onerror='alertDependencyError("md5")'></script>
<script type="text/javascript" src="./node_modules/bootstrap-waitingfor/build/bootstrap-waitingfor.js" onerror='alertDependencyError("bootstrap-waitingfor")'></script>
<script type="text/javascript" src="./node_modules/blueimp-md5/js/md5.js" onerror='alertDependencyError("md5")'></script>
<script type="text/javascript" src="lib/colpick/colpick.js" onerror='alertDependencyError("col-picker")'></script>
<script type="text/javascript" src="lib/toastr/build/toastr.min.js" onerror='alertDependencyError("toastr")'></script>
<script type="text/javascript" src="./node_modules/toastr/build/toastr.min.js" onerror='alertDependencyError("toastr")'></script>

<script type="text/javascript" src="js/utils.js"></script>
<script type="text/javascript" src="js/main.js"></script>
Expand All @@ -66,14 +67,14 @@
<script type="text/javascript" src="js/migrations.js"></script>
<script type="text/javascript" src="js/inspectionutils.js"></script>

<!-- Table sorter, source: https://github.com/drvic10k/bootstrap-sortable -->
<script type="text/javascript" src="lib/bootstrap-sortable/Scripts/bootstrap-sortable.js" onerror='alertDependencyError("bootstrap-sortable")' defer></script>
<link href="lib/bootstrap-sortable/Contents/bootstrap-sortable.css" rel="stylesheet">
<!-- Table sorter -->
<link href="./node_modules/sortable-tablesort/sortable.min.css" rel="stylesheet">
<script type="text/javascript" src="./node_modules/sortable-tablesort/sortable.min.js" onerror='alertDependencyError("table-sorter")'></script>
<!-- /Table sorter -->

<script type="text/javascript" src="lib/marked/lib/marked.js" onerror='alertDependencyError("marked")'></script>
<link rel="stylesheet" href="lib/bootstrap-markdown/css/bootstrap-markdown.min.css" type="text/css" />
<script type="text/javascript" src="lib/bootstrap-markdown/js/bootstrap-markdown.js" onerror='alertDependencyError("bootstrap-markdown", true)' onload='alertDependencyError(null, true)'></script>
<script type="text/javascript" src="./node_modules/marked/marked.min.js" onerror='alertDependencyError("marked")'></script>
<link rel="stylesheet" href="./node_modules/bootstrap-markdown/css/bootstrap-markdown.min.css" type="text/css" />
<script type="text/javascript" src="./node_modules/bootstrap-markdown/js/bootstrap-markdown.js" onerror='alertDependencyError("bootstrap-markdown", true)' onload='alertDependencyError(null, true)'></script>
<link rel="stylesheet" href="css/markdown-local.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="css/loading.css" />
<link rel="stylesheet" type="text/css" href="css/glowing-button.css" />
Expand Down Expand Up @@ -854,7 +855,7 @@ <h5 class="modal-title" id="define-range-modal-label">Define multiple threshold
</p>
</div>

<table class="table sortable" id="bins-table">
<table class="table" id="bins-table">
<thead id="thead_bins">
<tr>
<th data-defaultsort='disabled'><span class="new-bin-icon bi bi-plus-circle-fill fa-lg" aria-hidden="true" alt="Add bins" title="Add bins" onClick="bins.NewBin();"></span></th>
Expand Down
2 changes: 1 addition & 1 deletion anvio/data/interactive/js/bin.js
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Expand Up @@ -93,7 +93,7 @@ Bins.prototype.NewBin = function(id, binState) {
`}
<td><center><span class="default-bin-icon bi bi-trash-fill fa-lg" aria-hidden="true" alt="Delete this bin" title="Delete this bin" onClick="bins.DeleteBin(${id});"></span></center></td>
</tr>
${ mode === 'full' || mode === 'refine' || mode === 'manual' ? `<tr style="${ $('#estimate_taxonomy').is(':checked') ? `` : `display: none;`}" data-parent="${id}">
${ mode === 'full' || mode === 'refine' || mode === 'manual' || mode === 'pan' ? `<tr style="${ $('#estimate_taxonomy').is(':checked') ? `` : `display: none;`}" data-parent="${id}">
<td style="border-top: 0px;">&nbsp;</td>
<td style="border-top: 0px;">&nbsp;</td>
<td colspan="6" style="border-top: 0px; padding-top: 0px;">
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4 changes: 2 additions & 2 deletions anvio/data/interactive/js/error.js
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Expand Up @@ -16,8 +16,8 @@ let ERROR_COUNT = 0
const issueCategories = [
{
'category' : 'Dependencies failed to load',
'content' : `This can occur when git submodules that Anvi'o relies on fail to load. If you are tracking the main development branch of Anvi'o,
try running <b> git submodule update --init </b>`
'content' : `This can occur when npm packages that Anvi'o relies on fail to load.
Try running <b> npm install </b> in the <b>anvio/data/interactive</b> directory.`
},
{
'category' : 'ReferenceError - ___ is not defined',
Expand Down
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