From 9d8ab723402532ef0a1224fb0aa402444cbcdfdb Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 11:53:07 +0100
Subject: [PATCH 01/40] remove submodule

---
 .gitmodules                                | 6 ------
 anvio/data/interactive/lib/bootstrap-icons | 1 -
 anvio/data/interactive/lib/roboto          | 1 -
 3 files changed, 8 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/bootstrap-icons
 delete mode 160000 anvio/data/interactive/lib/roboto

diff --git a/.gitmodules b/.gitmodules
index e46512375a..05f46a77aa 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -37,9 +37,3 @@
 [submodule "anvio/data/interactive/lib/JavaScript-MD5"]
 	path = anvio/data/interactive/lib/JavaScript-MD5
 	url = https://github.com/blueimp/JavaScript-MD5.git
-[submodule "anvio/data/interactive/lib/bootstrap-icons"]
-	path = anvio/data/interactive/lib/bootstrap-icons
-	url = https://github.com/twbs/icons.git
-[submodule "anvio/data/interactive/lib/roboto"]
-	path = anvio/data/interactive/lib/roboto
-	url = https://github.com/googlefonts/roboto.git
diff --git a/anvio/data/interactive/lib/bootstrap-icons b/anvio/data/interactive/lib/bootstrap-icons
deleted file mode 160000
index 9727a0d634..0000000000
--- a/anvio/data/interactive/lib/bootstrap-icons
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 9727a0d6343ab9595ab98c7c9c57ccc5de305c95
diff --git a/anvio/data/interactive/lib/roboto b/anvio/data/interactive/lib/roboto
deleted file mode 160000
index cb3cde1a30..0000000000
--- a/anvio/data/interactive/lib/roboto
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit cb3cde1a3069f28b9a66f3d104f51fd6c0734be1

From 7a652d0a636a4dad532d9dab23b9128ece03d1a8 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 13:50:49 +0100
Subject: [PATCH 02/40] Bootstrap remove

---
 .gitmodules                          | 3 ---
 anvio/data/interactive/lib/bootstrap | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/bootstrap

diff --git a/.gitmodules b/.gitmodules
index 05f46a77aa..96785e2d16 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -13,9 +13,6 @@
 [submodule "anvio/data/interactive/lib/jquery"]
 	path = anvio/data/interactive/lib/jquery
 	url = https://github.com/jquery/jquery
-[submodule "anvio/data/interactive/lib/bootstrap"]
-	path = anvio/data/interactive/lib/bootstrap
-	url = https://github.com/twbs/bootstrap
 [submodule "anvio/data/interactive/lib/jquery-ui"]
 	path = anvio/data/interactive/lib/jquery-ui
 	url = https://github.com/jquery/jquery-ui
diff --git a/anvio/data/interactive/lib/bootstrap b/anvio/data/interactive/lib/bootstrap
deleted file mode 160000
index 6ffb0b48e4..0000000000
--- a/anvio/data/interactive/lib/bootstrap
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 6ffb0b48e455430f8a5359ed689ad64c1143fac2

From fc4df03592772bfb5930c0819194e0551b087e2e Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 13:54:14 +0100
Subject: [PATCH 03/40] bootstrap-waitingfor remove

---
 .gitmodules                                     | 3 ---
 anvio/data/interactive/lib/bootstrap-waitingfor | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/bootstrap-waitingfor

diff --git a/.gitmodules b/.gitmodules
index 96785e2d16..9b6dbc5c4a 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -19,9 +19,6 @@
 [submodule "anvio/data/interactive/lib/randomColor"]
 	path = anvio/data/interactive/lib/randomColor
 	url = https://github.com/davidmerfield/randomColor
-[submodule "anvio/data/interactive/lib/bootstrap-waitingfor"]
-	path = anvio/data/interactive/lib/bootstrap-waitingfor
-	url = https://github.com/ehpc/bootstrap-waitingfor.git
 [submodule "anvio/data/interactive/lib/toastr"]
 	path = anvio/data/interactive/lib/toastr
 	url = https://github.com/CodeSeven/toastr.git
diff --git a/anvio/data/interactive/lib/bootstrap-waitingfor b/anvio/data/interactive/lib/bootstrap-waitingfor
deleted file mode 160000
index 6ea6352324..0000000000
--- a/anvio/data/interactive/lib/bootstrap-waitingfor
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 6ea63523247fe772bca0e633dc51a62e9dfbc9ce

From 7184502c1e0f49ceca818d7bf3d484ac9e458398 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 13:59:59 +0100
Subject: [PATCH 04/40] bootstrap-markdown remove

---
 .gitmodules                                   | 3 ---
 anvio/data/interactive/lib/bootstrap-markdown | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/bootstrap-markdown

diff --git a/.gitmodules b/.gitmodules
index 9b6dbc5c4a..53fc781767 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -22,9 +22,6 @@
 [submodule "anvio/data/interactive/lib/toastr"]
 	path = anvio/data/interactive/lib/toastr
 	url = https://github.com/CodeSeven/toastr.git
-[submodule "anvio/data/interactive/lib/bootstrap-markdown"]
-	path = anvio/data/interactive/lib/bootstrap-markdown
-	url = https://github.com/toopay/bootstrap-markdown.git
 [submodule "anvio/data/interactive/lib/marked"]
 	path = anvio/data/interactive/lib/marked
 	url = https://github.com/chjj/marked.git
diff --git a/anvio/data/interactive/lib/bootstrap-markdown b/anvio/data/interactive/lib/bootstrap-markdown
deleted file mode 160000
index 0320bec0bd..0000000000
--- a/anvio/data/interactive/lib/bootstrap-markdown
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 0320bec0bdb3fa49754d8fc26bfe2159c5fbe4d2

From 032ac4d2e3df37a1ca59bcd67869feda0fde9da6 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 14:22:24 +0100
Subject: [PATCH 05/40] jquery remove

---
 .gitmodules                       | 3 ---
 anvio/data/interactive/lib/jquery | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/jquery

diff --git a/.gitmodules b/.gitmodules
index 53fc781767..c9af6c6c8d 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -10,9 +10,6 @@
 [submodule "anvio/data/interactive/lib/d3.js"]
 	path = anvio/data/interactive/lib/d3.js
 	url = https://github.com/mbostock/d3
-[submodule "anvio/data/interactive/lib/jquery"]
-	path = anvio/data/interactive/lib/jquery
-	url = https://github.com/jquery/jquery
 [submodule "anvio/data/interactive/lib/jquery-ui"]
 	path = anvio/data/interactive/lib/jquery-ui
 	url = https://github.com/jquery/jquery-ui
diff --git a/anvio/data/interactive/lib/jquery b/anvio/data/interactive/lib/jquery
deleted file mode 160000
index 1472290917..0000000000
--- a/anvio/data/interactive/lib/jquery
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 1472290917f17af05e98007136096784f9051fab

From 5304cb1eb49dbe0ba645837ba67e7dd31e5ec896 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 14:25:16 +0100
Subject: [PATCH 06/40] jquery-ui remove

---
 .gitmodules                          | 3 ---
 anvio/data/interactive/lib/jquery-ui | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/jquery-ui

diff --git a/.gitmodules b/.gitmodules
index c9af6c6c8d..6dcafcb459 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -10,9 +10,6 @@
 [submodule "anvio/data/interactive/lib/d3.js"]
 	path = anvio/data/interactive/lib/d3.js
 	url = https://github.com/mbostock/d3
-[submodule "anvio/data/interactive/lib/jquery-ui"]
-	path = anvio/data/interactive/lib/jquery-ui
-	url = https://github.com/jquery/jquery-ui
 [submodule "anvio/data/interactive/lib/randomColor"]
 	path = anvio/data/interactive/lib/randomColor
 	url = https://github.com/davidmerfield/randomColor
diff --git a/anvio/data/interactive/lib/jquery-ui b/anvio/data/interactive/lib/jquery-ui
deleted file mode 160000
index d6713024e1..0000000000
--- a/anvio/data/interactive/lib/jquery-ui
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit d6713024e16de90ea71dc0544ba34e1df01b4d8a

From de367beb203fa52a2b112dfd575c0a899f6d4495 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 17:09:50 +0100
Subject: [PATCH 07/40] marked removed

---
 .gitmodules                       | 3 ---
 anvio/data/interactive/lib/marked | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/marked

diff --git a/.gitmodules b/.gitmodules
index 6dcafcb459..3319ad1256 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -16,9 +16,6 @@
 [submodule "anvio/data/interactive/lib/toastr"]
 	path = anvio/data/interactive/lib/toastr
 	url = https://github.com/CodeSeven/toastr.git
-[submodule "anvio/data/interactive/lib/marked"]
-	path = anvio/data/interactive/lib/marked
-	url = https://github.com/chjj/marked.git
 [submodule "anvio/data/interactive/lib/JavaScript-MD5"]
 	path = anvio/data/interactive/lib/JavaScript-MD5
 	url = https://github.com/blueimp/JavaScript-MD5.git
diff --git a/anvio/data/interactive/lib/marked b/anvio/data/interactive/lib/marked
deleted file mode 160000
index 8f9d0b72f5..0000000000
--- a/anvio/data/interactive/lib/marked
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 8f9d0b72f5606ed32057049f387161dd41c36ade

From 1a7d2ec483a418400ecf7d0cf980d08d768aac2e Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 17:30:13 +0100
Subject: [PATCH 08/40] randomColor remove

---
 .gitmodules                            | 3 ---
 anvio/data/interactive/lib/randomColor | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/randomColor

diff --git a/.gitmodules b/.gitmodules
index 3319ad1256..1c62aec932 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -10,9 +10,6 @@
 [submodule "anvio/data/interactive/lib/d3.js"]
 	path = anvio/data/interactive/lib/d3.js
 	url = https://github.com/mbostock/d3
-[submodule "anvio/data/interactive/lib/randomColor"]
-	path = anvio/data/interactive/lib/randomColor
-	url = https://github.com/davidmerfield/randomColor
 [submodule "anvio/data/interactive/lib/toastr"]
 	path = anvio/data/interactive/lib/toastr
 	url = https://github.com/CodeSeven/toastr.git
diff --git a/anvio/data/interactive/lib/randomColor b/anvio/data/interactive/lib/randomColor
deleted file mode 160000
index 455f347ecd..0000000000
--- a/anvio/data/interactive/lib/randomColor
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 455f347ecde2f61f9d32d9d1dbe4f6f28e54fc9e

From 242a4d42b88d7868a21af27495210ae9ca048a76 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 17:30:49 +0100
Subject: [PATCH 09/40] toastr remove

---
 .gitmodules                       | 3 ---
 anvio/data/interactive/lib/toastr | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/toastr

diff --git a/.gitmodules b/.gitmodules
index 1c62aec932..77fcf45c4c 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -10,9 +10,6 @@
 [submodule "anvio/data/interactive/lib/d3.js"]
 	path = anvio/data/interactive/lib/d3.js
 	url = https://github.com/mbostock/d3
-[submodule "anvio/data/interactive/lib/toastr"]
-	path = anvio/data/interactive/lib/toastr
-	url = https://github.com/CodeSeven/toastr.git
 [submodule "anvio/data/interactive/lib/JavaScript-MD5"]
 	path = anvio/data/interactive/lib/JavaScript-MD5
 	url = https://github.com/blueimp/JavaScript-MD5.git
diff --git a/anvio/data/interactive/lib/toastr b/anvio/data/interactive/lib/toastr
deleted file mode 160000
index b957ae9f38..0000000000
--- a/anvio/data/interactive/lib/toastr
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit b957ae9f38e6856346a0200e83281b08ca717a7d

From a883b47ceb50910856423d728b7ca24b947397fb Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 17:32:56 +0100
Subject: [PATCH 10/40] Javascript-MD5 remove

---
 .gitmodules                               | 3 ---
 anvio/data/interactive/lib/JavaScript-MD5 | 1 -
 2 files changed, 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/JavaScript-MD5

diff --git a/.gitmodules b/.gitmodules
index 77fcf45c4c..a2b5323e85 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -10,6 +10,3 @@
 [submodule "anvio/data/interactive/lib/d3.js"]
 	path = anvio/data/interactive/lib/d3.js
 	url = https://github.com/mbostock/d3
-[submodule "anvio/data/interactive/lib/JavaScript-MD5"]
-	path = anvio/data/interactive/lib/JavaScript-MD5
-	url = https://github.com/blueimp/JavaScript-MD5.git
diff --git a/anvio/data/interactive/lib/JavaScript-MD5 b/anvio/data/interactive/lib/JavaScript-MD5
deleted file mode 160000
index 9756d82db7..0000000000
--- a/anvio/data/interactive/lib/JavaScript-MD5
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 9756d82db70b0f678bc6cd055e7aa08f5c1a0390

From b437f5475a928f3c44b6fcd22db5a91bdd4166de Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 22 Jan 2024 17:36:47 +0100
Subject: [PATCH 11/40] d3.js remove

---
 .gitmodules                      | 4 +---
 anvio/data/interactive/lib/d3.js | 1 -
 2 files changed, 1 insertion(+), 4 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/d3.js

diff --git a/.gitmodules b/.gitmodules
index a2b5323e85..baa5bf182e 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -7,6 +7,4 @@
 [submodule "anvio/data/interactive/lib/bootstrap-sortable"]
 	path = anvio/data/interactive/lib/bootstrap-sortable
 	url = https://github.com/drvic10k/bootstrap-sortable
-[submodule "anvio/data/interactive/lib/d3.js"]
-	path = anvio/data/interactive/lib/d3.js
-	url = https://github.com/mbostock/d3
+
diff --git a/anvio/data/interactive/lib/d3.js b/anvio/data/interactive/lib/d3.js
deleted file mode 160000
index b48420930f..0000000000
--- a/anvio/data/interactive/lib/d3.js
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit b48420930f3848b1498c034387fac2588903d7cf

From 620aaa1086a638e74373e5951a5d0a06ebad977a Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 29 Jan 2024 14:15:44 +0100
Subject: [PATCH 12/40] Fix lib > node_modules

---
 .gitignore                               |  2 ++
 anvio/data/interactive/charts.html       | 17 +++++----
 anvio/data/interactive/contigs.html      |  8 ++---
 anvio/data/interactive/geneclusters.html | 15 ++++----
 anvio/data/interactive/index.html        | 45 ++++++++++++------------
 anvio/data/interactive/login.html        | 10 +++---
 anvio/data/interactive/metabolism.html   |  8 ++---
 anvio/data/interactive/package.json      | 37 +++++++++++++++++++
 8 files changed, 89 insertions(+), 53 deletions(-)
 create mode 100644 anvio/data/interactive/package.json

diff --git a/.gitignore b/.gitignore
index 223e6f2abd..4ecb3b22ce 100755
--- a/.gitignore
+++ b/.gitignore
@@ -8,6 +8,8 @@
 /build/
 /dist/
 test-output/
+node_modules/
+package-lock.json
 /*.egg-info/
 anvio/__pycache__/
 anvio/extensions/concoct/vbgmm.c
diff --git a/anvio/data/interactive/charts.html b/anvio/data/interactive/charts.html
index ac275cb34d..58b6a56b7c 100644
--- a/anvio/data/interactive/charts.html
+++ b/anvio/data/interactive/charts.html
@@ -10,9 +10,9 @@
         <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="#" />
@@ -20,17 +20,16 @@
         <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();">
diff --git a/anvio/data/interactive/contigs.html b/anvio/data/interactive/contigs.html
index 0ba90ec4d2..5b53a0e51d 100644
--- a/anvio/data/interactive/contigs.html
+++ b/anvio/data/interactive/contigs.html
@@ -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;
diff --git a/anvio/data/interactive/geneclusters.html b/anvio/data/interactive/geneclusters.html
index 6573df0545..7edcec502c 100644
--- a/anvio/data/interactive/geneclusters.html
+++ b/anvio/data/interactive/geneclusters.html
@@ -9,21 +9,20 @@
         <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" type="text/css" href="css/popover.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();">
diff --git a/anvio/data/interactive/index.html b/anvio/data/interactive/index.html
index d5c3dca319..d28815edd7 100644
--- a/anvio/data/interactive/index.html
+++ b/anvio/data/interactive/index.html
@@ -11,37 +11,36 @@
     <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>
+    <link href="./node_modules/jquery-ui/themes/base/all.css" rel="stylesheet">
+    <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 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>$.uiBackCompat = false;</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/widgets/button.js" onerror='alertDependencyError("jquery-button")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/position.js" onerror='alertDependencyError("jquery-position")'></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/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>
@@ -71,9 +70,9 @@
     <link href="lib/bootstrap-sortable/Contents/bootstrap-sortable.css" rel="stylesheet">
     <!-- /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" />
diff --git a/anvio/data/interactive/login.html b/anvio/data/interactive/login.html
index 04192a4c3b..d38eaefa7e 100644
--- a/anvio/data/interactive/login.html
+++ b/anvio/data/interactive/login.html
@@ -1,10 +1,10 @@
 <html>
     <head>
-        <script type="text/javascript" src="lib/jquery/dist/jquery.min.js"></script>
-        <link href="lib/jquery-ui/themes/base/all.css" rel="stylesheet">
-        <link rel="stylesheet" href="lib/bootstrap/dist/css/bootstrap.css" />
-        <script type="text/javascript" src="lib/bootstrap/dist/js/bootstrap.bundle.js" onerror='alertDependencyError("bootstrap-core")'></script>
-        <script type="text/javascript" src="lib/JavaScript-MD5/js/md5.js"></script>
+        <script type="text/javascript" src="./node_modules/jquery/dist/jquery.min.js"></script>
+        <link href="./node_modules/jquery-ui/themes/base/all.css" rel="stylesheet">
+        <link rel="stylesheet" href="./node_modules/bootstrap/dist/css/bootstrap.css" />
+        <script type="text/javascript" src="./node_modules/bootstrap/dist/js/bootstrap.bundle.js" onerror='alertDependencyError("bootstrap-core")'></script>
+        <script type="text/javascript" src="./node_modules/blueimp-md5/js/md5.js"></script>
         <script type="text/javascript" src="js/utils.js"></script>
         <style type="text/css">
             .account-panel
diff --git a/anvio/data/interactive/metabolism.html b/anvio/data/interactive/metabolism.html
index 278e69c326..4e81d6a83e 100644
--- a/anvio/data/interactive/metabolism.html
+++ b/anvio/data/interactive/metabolism.html
@@ -2,11 +2,11 @@
 
 <head>
     <title>Metabolism Display</title>
-    <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>
-    <link rel="stylesheet" href="lib/bootstrap/dist/css/bootstrap.css" />
-    <script type="text/javascript" src="lib/bootstrap/dist/js/bootstrap.bundle.js" onerror='alertDependencyError("bootstrap-core")'></script>
+    <script type='text/javascript' src='./node_modules/d3/d3.min.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" onerror='alertDependencyError("bootstrap-core")'></script>
     <!-- Load D3 and color palettes for the heatmap example -->
     <script src="https://d3js.org/d3.v4.js"></script>
     <script src="https://d3js.org/d3-scale-chromatic.v1.min.js"></script>
diff --git a/anvio/data/interactive/package.json b/anvio/data/interactive/package.json
new file mode 100644
index 0000000000..febf7bf818
--- /dev/null
+++ b/anvio/data/interactive/package.json
@@ -0,0 +1,37 @@
+{
+  "name": "interactive",
+  "version": "1.0.0",
+  "description": "",
+  "main": "js/main.js",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/merenlab/anvio.git"
+  },
+  "homepage": "https://anvio.org/",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "engines": {
+    "node": ">=18.0.0",
+    "npm": ">=9.0.0"
+  },
+  "dependencies": {
+    "@popperjs/core": "^2.11.8",
+    "blueimp-md5": "2.7.0",
+    "bootstrap": "4.6.0",
+    "bootstrap-icons": "1.11.3",
+    "bootstrap-markdown": "2.10.0",
+    "bootstrap-waitingfor": "1.2.7",
+    "d3": "3.5.6",
+    "html5sortable": "^0.13.3",
+    "jquery": "1.12.4",
+    "jquery-ui": "1.12.1",
+    "marked": "0.3.6",
+    "randomcolor": "0.6.2",
+    "roboto": "0.8.2",
+    "toastr": "2.1.2"
+  }
+}

From 97434136f70a29f63f7f42f74f3e816901a8fe1b Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 29 Jan 2024 14:24:51 +0100
Subject: [PATCH 13/40] Fix sortable package update

Sortable package changed with alternative and lightweight version
---
 anvio/data/interactive/index.html |  1 +
 anvio/data/interactive/js/main.js | 18 +++++++++++++++---
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/anvio/data/interactive/index.html b/anvio/data/interactive/index.html
index d28815edd7..52b1e5e1f7 100644
--- a/anvio/data/interactive/index.html
+++ b/anvio/data/interactive/index.html
@@ -34,6 +34,7 @@
     <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/button.js" onerror='alertDependencyError("jquery-button")'></script>
     <script type="text/javascript" src="./node_modules/jquery-ui/ui/position.js" onerror='alertDependencyError("jquery-position")'></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/html5sortable/dist/html5sortable.min.js" onerror='alertDependencyError("jquery-position")'></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>
diff --git a/anvio/data/interactive/js/main.js b/anvio/data/interactive/js/main.js
index e499aa1ffb..2e8125b2de 100644
--- a/anvio/data/interactive/js/main.js
+++ b/anvio/data/interactive/js/main.js
@@ -282,8 +282,20 @@ function initData() {
             var available_views = response.views[2];
             $('#views_container').append(getComboBoxContent(default_view, available_views));
 
-            $("#tbody_layers").sortable({helper: fixHelperModified, handle: '.drag-icon', items: "> tr"}).disableSelection();
-            $("#tbody_samples").sortable({helper: fixHelperModified, handle: '.drag-icon', items: "> tr"}).disableSelection();
+            //$("#tbody_layers").sortable({helper: fixHelperModified, handle: '.drag-icon', items: "> tr"}).disableSelection();
+            //$("#tbody_samples").sortable({helper: fixHelperModified, handle: '.drag-icon', items: "> tr"}).disableSelection();
+
+            sortable('#tbody_layers', {
+                forcePlaceholderSize: true,
+                handle: '.drag-icon',
+                items: 'tr'
+            });
+
+            sortable('#tbody_samples', {
+                forcePlaceholderSize: true,
+                handle: '.drag-icon',
+                items: 'tr'
+            });
 
             let merged = samplesMergeStackbarLayers(response.layers_information, response.layers_information_default_order);
 
@@ -1360,7 +1372,7 @@ function buildLayersTable(order, settings)
                 var norm = (mode == 'full') ? 'log' : 'none';
             }
 
-            var template = '<tr>' +
+            var template = '<tr class="sortable">' +
                 '<td><img class="drag-icon" src="images/drag.gif" /></td>' +
                 '<td title="{name}" class="titles" id="title{id}">{short-name}</td>' +
                 '<td>n/a</td>' +

From 69435028e8a16eae296d9897fb836169d4faeb3f Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Thu, 1 Feb 2024 09:35:12 +0100
Subject: [PATCH 14/40] remove accordion functionality

---
 anvio/data/interactive/js/main.js | 36 -------------------------------
 1 file changed, 36 deletions(-)

diff --git a/anvio/data/interactive/js/main.js b/anvio/data/interactive/js/main.js
index 2e8125b2de..ae722a7163 100644
--- a/anvio/data/interactive/js/main.js
+++ b/anvio/data/interactive/js/main.js
@@ -810,40 +810,6 @@ function populateColorDicts() {
 }
 
 function buildLegendTables() {
-    if(typeof $('#legend_settings').data("ui-accordion") != "undefined"){
-        $('#legend_settings').accordion("destroy");
-        $('#legend_settings').empty();
-    }
-
-    $('#legend_settings').accordion({
-        collapsible:true,
-    
-        beforeActivate: function(event, ui) {
-             // The accordion believes a panel is being opened
-            if (ui.newHeader[0]) {
-                var currHeader  = ui.newHeader;
-                var currContent = currHeader.next('.ui-accordion-content');
-             // The accordion believes a panel is being closed
-            } else {
-                var currHeader  = ui.oldHeader;
-                var currContent = currHeader.next('.ui-accordion-content');
-            }
-             // Since we've changed the default behavior, this detects the actual status
-            var isPanelSelected = currHeader.attr('aria-selected') == 'true';
-    
-             // Toggle the panel's header
-            currHeader.toggleClass('ui-corner-all',isPanelSelected).toggleClass('accordion-header-active ui-state-active ui-corner-top',!isPanelSelected).attr('aria-selected',((!isPanelSelected).toString()));
-    
-            // Toggle the panel's icon
-            currHeader.children('.ui-icon').toggleClass('ui-icon-triangle-1-e',isPanelSelected).toggleClass('ui-icon-triangle-1-s',!isPanelSelected);
-    
-             // Toggle the panel's content
-            currContent.toggleClass('accordion-content-active',!isPanelSelected)    
-            if (isPanelSelected) { currContent.slideUp(); }  else { currContent.slideDown(); }
-    
-            return false; // Cancels the default action
-        }
-    });
 
     legends = [];
     let toastr_warn_flag = false
@@ -1017,8 +983,6 @@ function buildLegendTables() {
         $('#legend_settings').append('<div class="alert alert-danger" role="alert">There are no legends to edit in this display.</div>');
     }
 
-    $('#legend_settings').accordion({heightStyle: "content", collapsible: true});
-
     $('.colorpicker').colpick({
         layout: 'hex',
         submit: 0,

From 029c879cae4cfc7461ace692494ccd4c3308aedc Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Thu, 1 Feb 2024 09:35:41 +0100
Subject: [PATCH 15/40] Add html5sortable package

---
 anvio/data/interactive/index.html | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/anvio/data/interactive/index.html b/anvio/data/interactive/index.html
index 52b1e5e1f7..68e8238746 100644
--- a/anvio/data/interactive/index.html
+++ b/anvio/data/interactive/index.html
@@ -21,7 +21,6 @@
     <script type="text/javascript" src="js/error.js"></script>
 
     <script type="text/javascript" src="./node_modules/jquery/dist/jquery.min.js" onerror='alertDependencyError("jquery-core")'></script>
-    <link href="./node_modules/jquery-ui/themes/base/all.css" rel="stylesheet">
     <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">
@@ -29,12 +28,8 @@
 
     <script type="text/javascript" src="lib/jquery-svgpan/jquery-svgpan.js" onerror='alertDependencyError("jquery-svg")'></script>
     <script>$.uiBackCompat = false;</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/widgets/button.js" onerror='alertDependencyError("jquery-button")'></script>
-    <script type="text/javascript" src="./node_modules/jquery-ui/ui/position.js" onerror='alertDependencyError("jquery-position")'></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/html5sortable/dist/html5sortable.min.js" onerror='alertDependencyError("jquery-position")'></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>

From 668d6e3a5bc67d9b6be78aad3ce00e2f38377a91 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Thu, 1 Feb 2024 14:26:06 +0100
Subject: [PATCH 16/40] Remove func call

---
 anvio/data/interactive/js/main.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/anvio/data/interactive/js/main.js b/anvio/data/interactive/js/main.js
index ae722a7163..41173e83a7 100644
--- a/anvio/data/interactive/js/main.js
+++ b/anvio/data/interactive/js/main.js
@@ -3024,7 +3024,6 @@ function processState(state_name, state) {
     }
 
     populateColorDicts();
-    buildLegendTables();
 
     current_state_name = state_name;
     toastr.success("State '" + current_state_name + "' successfully loaded.");

From ec4ce637b50e6b0acb71c570d14dbc8d2637d7e7 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 5 Feb 2024 17:24:19 +0100
Subject: [PATCH 17/40] Fix jquery-ui order

---
 anvio/data/interactive/index.html | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/anvio/data/interactive/index.html b/anvio/data/interactive/index.html
index 68e8238746..909ed69d7d 100644
--- a/anvio/data/interactive/index.html
+++ b/anvio/data/interactive/index.html
@@ -26,11 +26,18 @@
     <link rel="preconnect" href="https://fonts.googleapis.com">
     <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
 
+    <script>$.uiBackCompat = false; //Do not change the order of jquery-ui files</script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/jquery-patch.js" onerror='alertDependencyError("jquery-patch")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widget.js" onerror='alertDependencyError("jquery-widget")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/mouse.js" onerror='alertDependencyError("jquery-mouse")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/plugin.js" onerror='alertDependencyError("jquery-plugin")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/draggable.js" onerror='alertDependencyError("jquery-draggable")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/resizable.js" onerror='alertDependencyError("jquery-core")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/sortable.js" onerror='alertDependencyError("jquery-sortable")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/position.js" onerror='alertDependencyError("jquery-position")'></script>
+    
     <script type="text/javascript" src="lib/jquery-svgpan/jquery-svgpan.js" onerror='alertDependencyError("jquery-svg")'></script>
-    <script>$.uiBackCompat = false;</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/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="./node_modules/bootstrap-waitingfor/build/bootstrap-waitingfor.js" onerror='alertDependencyError("bootstrap-waitingfor")'></script>

From 5665633efdeb7d4c550d79ad7dbdaaab087b8cbe Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 5 Feb 2024 17:24:45 +0100
Subject: [PATCH 18/40] Update package.json += svg-pan-zoom

---
 anvio/data/interactive/package.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/anvio/data/interactive/package.json b/anvio/data/interactive/package.json
index febf7bf818..25a6dd389c 100644
--- a/anvio/data/interactive/package.json
+++ b/anvio/data/interactive/package.json
@@ -19,6 +19,7 @@
     "npm": ">=9.0.0"
   },
   "dependencies": {
+    "@fontsource/roboto": "^5.0.8",
     "@popperjs/core": "^2.11.8",
     "blueimp-md5": "2.7.0",
     "bootstrap": "4.6.0",
@@ -31,7 +32,7 @@
     "jquery-ui": "1.12.1",
     "marked": "0.3.6",
     "randomcolor": "0.6.2",
-    "roboto": "0.8.2",
+    "svg-pan-zoom": "^3.6.1",
     "toastr": "2.1.2"
   }
 }

From 4132e7f3e7b2d03c033a24d745fabaf0e941fbbc Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Tue, 6 Feb 2024 11:04:21 +0100
Subject: [PATCH 19/40] Update symlink lib -> node_modules

---
 .../content/css/bootstrap-icons/font/bootstrap-icons.min.css    | 2 +-
 .../content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff | 2 +-
 .../css/bootstrap-icons/font/fonts/bootstrap-icons.woff2        | 2 +-
 anvio/data/static/content/css/bootstrap.css                     | 2 +-
 anvio/data/static/content/fonts/roboto/README                   | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-Black.ttf         | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-BlackItalic.ttf   | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-Bold.ttf          | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-BoldItalic.ttf    | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-Italic.ttf        | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-Light.ttf         | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-LightItalic.ttf   | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-Medium.ttf        | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-MediumItalic.ttf  | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-Regular.ttf       | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-Thin.ttf          | 1 -
 anvio/data/static/content/fonts/roboto/Roboto-ThinItalic.ttf    | 1 -
 anvio/data/static/content/fonts/roboto/RobotoCondensed-Bold.ttf | 1 -
 .../static/content/fonts/roboto/RobotoCondensed-BoldItalic.ttf  | 1 -
 .../data/static/content/fonts/roboto/RobotoCondensed-Italic.ttf | 1 -
 .../data/static/content/fonts/roboto/RobotoCondensed-Light.ttf  | 1 -
 .../static/content/fonts/roboto/RobotoCondensed-LightItalic.ttf | 1 -
 .../static/content/fonts/roboto/RobotoCondensed-Regular.ttf     | 1 -
 .../static/content/fonts/roboto/roboto-latin-100-italic.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-100-italic.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-100-normal.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-100-normal.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-300-italic.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-300-italic.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-300-normal.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-300-normal.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-400-italic.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-400-italic.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-400-normal.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-400-normal.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-500-italic.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-500-italic.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-500-normal.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-500-normal.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-700-italic.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-700-italic.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-700-normal.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-700-normal.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-900-italic.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-900-italic.woff2   | 1 +
 .../static/content/fonts/roboto/roboto-latin-900-normal.woff    | 1 +
 .../static/content/fonts/roboto/roboto-latin-900-normal.woff2   | 1 +
 .../content/fonts/roboto/roboto-latin-ext-100-italic.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-100-italic.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-100-normal.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-100-normal.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-300-italic.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-300-italic.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-300-normal.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-300-normal.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-400-italic.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-400-italic.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-400-normal.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-400-normal.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-500-italic.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-500-italic.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-500-normal.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-500-normal.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-700-italic.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-700-italic.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-700-normal.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-700-normal.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-900-italic.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-900-italic.woff2      | 1 +
 .../content/fonts/roboto/roboto-latin-ext-900-normal.woff       | 1 +
 .../content/fonts/roboto/roboto-latin-ext-900-normal.woff2      | 1 +
 anvio/data/static/content/js/bootstrap.min.js                   | 2 +-
 anvio/data/static/content/js/jquery.min.js                      | 2 +-
 anvio/data/static/content/js/popper.min.js                      | 2 +-
 74 files changed, 55 insertions(+), 26 deletions(-)
 delete mode 120000 anvio/data/static/content/fonts/roboto/README
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-Black.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-BlackItalic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-Bold.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-BoldItalic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-Italic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-Light.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-LightItalic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-Medium.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-MediumItalic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-Regular.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-Thin.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/Roboto-ThinItalic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/RobotoCondensed-Bold.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/RobotoCondensed-BoldItalic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/RobotoCondensed-Italic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/RobotoCondensed-Light.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/RobotoCondensed-LightItalic.ttf
 delete mode 120000 anvio/data/static/content/fonts/roboto/RobotoCondensed-Regular.ttf
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-100-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-100-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-100-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-100-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-300-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-300-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-300-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-300-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-400-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-400-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-400-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-400-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-500-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-500-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-500-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-500-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-700-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-700-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-700-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-700-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-900-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-900-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-900-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-900-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-normal.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-italic.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-italic.woff2
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-normal.woff
 create mode 120000 anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-normal.woff2

diff --git a/anvio/data/static/content/css/bootstrap-icons/font/bootstrap-icons.min.css b/anvio/data/static/content/css/bootstrap-icons/font/bootstrap-icons.min.css
index 45ffe7cae7..f3928b36b7 120000
--- a/anvio/data/static/content/css/bootstrap-icons/font/bootstrap-icons.min.css
+++ b/anvio/data/static/content/css/bootstrap-icons/font/bootstrap-icons.min.css
@@ -1 +1 @@
-../../../../../interactive/lib/bootstrap-icons/font/bootstrap-icons.min.css
\ No newline at end of file
+../../../../../interactive/node_modules/bootstrap-icons/font/bootstrap-icons.min.css
\ No newline at end of file
diff --git a/anvio/data/static/content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff b/anvio/data/static/content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff
index 22f10c943f..ce876c26a3 120000
--- a/anvio/data/static/content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff
+++ b/anvio/data/static/content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff
@@ -1 +1 @@
-../../../../../../interactive/lib/bootstrap-icons/font/fonts/bootstrap-icons.woff
\ No newline at end of file
+../../../../../../interactive/node_modules/bootstrap-icons/font/fonts/bootstrap-icons.woff
\ No newline at end of file
diff --git a/anvio/data/static/content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff2 b/anvio/data/static/content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff2
index 4c69f67bd4..edcf567748 120000
--- a/anvio/data/static/content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff2
+++ b/anvio/data/static/content/css/bootstrap-icons/font/fonts/bootstrap-icons.woff2
@@ -1 +1 @@
-../../../../../../interactive/lib/bootstrap-icons/font/fonts/bootstrap-icons.woff2
\ No newline at end of file
+../../../../../../interactive/node_modules/bootstrap-icons/font/fonts/bootstrap-icons.woff2
\ No newline at end of file
diff --git a/anvio/data/static/content/css/bootstrap.css b/anvio/data/static/content/css/bootstrap.css
index cddb7eb337..1166f36a1d 120000
--- a/anvio/data/static/content/css/bootstrap.css
+++ b/anvio/data/static/content/css/bootstrap.css
@@ -1 +1 @@
-../../../../data/interactive/lib/bootstrap/dist/css/bootstrap.css
\ No newline at end of file
+../../../interactive/node_modules/bootstrap/dist/css/bootstrap.min.css
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/README b/anvio/data/static/content/fonts/roboto/README
deleted file mode 120000
index 7ef2504177..0000000000
--- a/anvio/data/static/content/fonts/roboto/README
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/README
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-Black.ttf b/anvio/data/static/content/fonts/roboto/Roboto-Black.ttf
deleted file mode 120000
index 2a82996063..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-Black.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-Black.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-BlackItalic.ttf b/anvio/data/static/content/fonts/roboto/Roboto-BlackItalic.ttf
deleted file mode 120000
index 2fa195097a..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-BlackItalic.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-BlackItalic.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-Bold.ttf b/anvio/data/static/content/fonts/roboto/Roboto-Bold.ttf
deleted file mode 120000
index d6d0638a92..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-Bold.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-Bold.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-BoldItalic.ttf b/anvio/data/static/content/fonts/roboto/Roboto-BoldItalic.ttf
deleted file mode 120000
index 3451d31752..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-BoldItalic.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-BoldItalic.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-Italic.ttf b/anvio/data/static/content/fonts/roboto/Roboto-Italic.ttf
deleted file mode 120000
index e70653abb6..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-Italic.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-Italic.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-Light.ttf b/anvio/data/static/content/fonts/roboto/Roboto-Light.ttf
deleted file mode 120000
index e639ec4263..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-Light.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-Light.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-LightItalic.ttf b/anvio/data/static/content/fonts/roboto/Roboto-LightItalic.ttf
deleted file mode 120000
index 2b8d395583..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-LightItalic.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-LightItalic.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-Medium.ttf b/anvio/data/static/content/fonts/roboto/Roboto-Medium.ttf
deleted file mode 120000
index 37c318212b..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-Medium.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-Medium.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-MediumItalic.ttf b/anvio/data/static/content/fonts/roboto/Roboto-MediumItalic.ttf
deleted file mode 120000
index 42f1963977..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-MediumItalic.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-MediumItalic.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-Regular.ttf b/anvio/data/static/content/fonts/roboto/Roboto-Regular.ttf
deleted file mode 120000
index 5cbe1bd4b3..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-Regular.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-Regular.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-Thin.ttf b/anvio/data/static/content/fonts/roboto/Roboto-Thin.ttf
deleted file mode 120000
index ca310914d7..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-Thin.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-Thin.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/Roboto-ThinItalic.ttf b/anvio/data/static/content/fonts/roboto/Roboto-ThinItalic.ttf
deleted file mode 120000
index 6fadc1dc6d..0000000000
--- a/anvio/data/static/content/fonts/roboto/Roboto-ThinItalic.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/Roboto-ThinItalic.ttf
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/RobotoCondensed-Bold.ttf b/anvio/data/static/content/fonts/roboto/RobotoCondensed-Bold.ttf
deleted file mode 120000
index 1497c5ad94..0000000000
--- a/anvio/data/static/content/fonts/roboto/RobotoCondensed-Bold.ttf
+++ /dev/null
@@ -1 +0,0 @@
-../../../../interactive/lib/roboto/src/hinted/RobotoCondensed-Bold.ttf
\ No newline at end of file
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deleted file mode 120000
index 743f6c306b..0000000000
--- a/anvio/data/static/content/fonts/roboto/RobotoCondensed-BoldItalic.ttf
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/RobotoCondensed-Italic.ttf b/anvio/data/static/content/fonts/roboto/RobotoCondensed-Italic.ttf
deleted file mode 120000
index e1aa93aaa3..0000000000
--- a/anvio/data/static/content/fonts/roboto/RobotoCondensed-Italic.ttf
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/RobotoCondensed-Light.ttf b/anvio/data/static/content/fonts/roboto/RobotoCondensed-Light.ttf
deleted file mode 120000
index 84769aefe5..0000000000
--- a/anvio/data/static/content/fonts/roboto/RobotoCondensed-Light.ttf
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@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/RobotoCondensed-LightItalic.ttf b/anvio/data/static/content/fonts/roboto/RobotoCondensed-LightItalic.ttf
deleted file mode 120000
index 237b5eca91..0000000000
--- a/anvio/data/static/content/fonts/roboto/RobotoCondensed-LightItalic.ttf
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@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/RobotoCondensed-Regular.ttf b/anvio/data/static/content/fonts/roboto/RobotoCondensed-Regular.ttf
deleted file mode 120000
index e45db29d6f..0000000000
--- a/anvio/data/static/content/fonts/roboto/RobotoCondensed-Regular.ttf
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@@ -1 +0,0 @@
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\ No newline at end of file
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new file mode 120000
index 0000000000..05ce143487
--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-100-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-100-italic.woff2
new file mode 120000
index 0000000000..d12a6cc4e9
--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-100-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-100-normal.woff
new file mode 120000
index 0000000000..b2b178848d
--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-100-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-100-normal.woff2
new file mode 120000
index 0000000000..f9e6f7a5e2
--- /dev/null
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\ No newline at end of file
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new file mode 120000
index 0000000000..0493260e4a
--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-300-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-300-italic.woff2
new file mode 120000
index 0000000000..9ab1b60c5c
--- /dev/null
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-300-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-300-normal.woff
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-300-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-300-normal.woff2
new file mode 120000
index 0000000000..53b720a956
--- /dev/null
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new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-400-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-400-italic.woff2
new file mode 120000
index 0000000000..9f018df9fc
--- /dev/null
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-400-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-400-normal.woff
new file mode 120000
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--- /dev/null
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-400-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-400-normal.woff2
new file mode 120000
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--- /dev/null
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new file mode 120000
index 0000000000..2c4546e245
--- /dev/null
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-500-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-500-italic.woff2
new file mode 120000
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--- /dev/null
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-500-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-500-normal.woff
new file mode 120000
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--- /dev/null
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-500-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-500-normal.woff2
new file mode 120000
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--- /dev/null
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new file mode 120000
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-700-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-700-italic.woff2
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-700-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-700-normal.woff
new file mode 120000
index 0000000000..40b3aa8995
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-700-normal.woff
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-700-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-700-normal.woff2
new file mode 120000
index 0000000000..be87704a32
--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-900-italic.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-900-italic.woff
new file mode 120000
index 0000000000..1f9b5053e0
--- /dev/null
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-900-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-900-italic.woff2
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-900-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-900-normal.woff
new file mode 120000
index 0000000000..5c9240966a
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-900-normal.woff
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-900-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-900-normal.woff2
new file mode 120000
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--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-900-normal.woff2
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-italic.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-italic.woff
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-italic.woff2
new file mode 120000
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--- /dev/null
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diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-normal.woff
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-100-normal.woff2
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-italic.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-italic.woff
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-italic.woff2
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-normal.woff
new file mode 120000
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--- /dev/null
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-300-normal.woff2
new file mode 120000
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--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-italic.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-italic.woff
new file mode 120000
index 0000000000..0686285083
--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-italic.woff2
new file mode 120000
index 0000000000..40a3cebe1f
--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-normal.woff
new file mode 120000
index 0000000000..786c54747e
--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-400-normal.woff2
new file mode 120000
index 0000000000..c56fc797c2
--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-italic.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-italic.woff
new file mode 120000
index 0000000000..5016537c5e
--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-italic.woff2
new file mode 120000
index 0000000000..75ab3638bc
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-italic.woff2
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-normal.woff
new file mode 120000
index 0000000000..a022dc7817
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-normal.woff
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-normal.woff2
new file mode 120000
index 0000000000..e780e0fd32
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-500-normal.woff2
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-500-normal.woff2
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-italic.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-italic.woff
new file mode 120000
index 0000000000..c617076863
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-italic.woff
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-700-italic.woff
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-italic.woff2
new file mode 120000
index 0000000000..84e77ed02a
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-italic.woff2
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-700-italic.woff2
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-normal.woff
new file mode 120000
index 0000000000..9333af1df5
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-normal.woff
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-700-normal.woff
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-normal.woff2
new file mode 120000
index 0000000000..3d8e8c50c6
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-700-normal.woff2
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-700-normal.woff2
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-italic.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-italic.woff
new file mode 120000
index 0000000000..f6c8fe542d
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-italic.woff
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-900-italic.woff
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-italic.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-italic.woff2
new file mode 120000
index 0000000000..180dcf20ca
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-italic.woff2
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-900-italic.woff2
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-normal.woff b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-normal.woff
new file mode 120000
index 0000000000..81f4d587dd
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-normal.woff
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-900-normal.woff
\ No newline at end of file
diff --git a/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-normal.woff2 b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-normal.woff2
new file mode 120000
index 0000000000..6ef2f48f6a
--- /dev/null
+++ b/anvio/data/static/content/fonts/roboto/roboto-latin-ext-900-normal.woff2
@@ -0,0 +1 @@
+../../../../interactive/node_modules/@fontsource/roboto/files/roboto-latin-ext-900-normal.woff2
\ No newline at end of file
diff --git a/anvio/data/static/content/js/bootstrap.min.js b/anvio/data/static/content/js/bootstrap.min.js
index 1fc6db434b..e3aa0ba450 120000
--- a/anvio/data/static/content/js/bootstrap.min.js
+++ b/anvio/data/static/content/js/bootstrap.min.js
@@ -1 +1 @@
-../../../interactive/lib/bootstrap/dist/js/bootstrap.min.js
\ No newline at end of file
+../../../interactive/node_modules/bootstrap/dist/js/bootstrap.bundle.min.js
\ No newline at end of file
diff --git a/anvio/data/static/content/js/jquery.min.js b/anvio/data/static/content/js/jquery.min.js
index caf40c24f4..23adb6d62b 120000
--- a/anvio/data/static/content/js/jquery.min.js
+++ b/anvio/data/static/content/js/jquery.min.js
@@ -1 +1 @@
-../../../interactive/lib/jquery/dist/jquery.min.js
\ No newline at end of file
+../../../interactive/node_modules/jquery/dist/jquery.min.js
\ No newline at end of file
diff --git a/anvio/data/static/content/js/popper.min.js b/anvio/data/static/content/js/popper.min.js
index 7d7033c43c..bd9a811737 120000
--- a/anvio/data/static/content/js/popper.min.js
+++ b/anvio/data/static/content/js/popper.min.js
@@ -1 +1 @@
-../../../interactive/lib/popperjs/popper.min.js
\ No newline at end of file
+../../../interactive/node_modules/popper.js/dist/popper.min.js
\ No newline at end of file

From 9f91ef4488755626c81e5a20e658e14e3e6d5db5 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Tue, 6 Feb 2024 11:15:49 +0100
Subject: [PATCH 20/40] Remove merge string

---
 anvio/utils.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/anvio/utils.py b/anvio/utils.py
index f1632d8f38..4dd7c858a8 100644
--- a/anvio/utils.py
+++ b/anvio/utils.py
@@ -822,6 +822,11 @@ def add_to_2D_numeric_array(x, y, a, count=1):
     return a
 
 
+def is_all_columns_present_in_TAB_delim_file(columns, file_path, including_first_column=False):
+    columns_in_file = get_columns_of_TAB_delim_file(file_path, include_first_column=including_first_column)
+    return False if len([False for c in columns if c not in columns_in_file]) else True
+
+
 def is_all_submodules_present():
     """A function to test whether all anvi'o submodules are present.
 

From d5220324436c829db90d1b6300043b61f9556220 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 12 Feb 2024 18:23:54 +0100
Subject: [PATCH 21/40] Add disable class

---
 anvio/data/interactive/css/main.css | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/anvio/data/interactive/css/main.css b/anvio/data/interactive/css/main.css
index c5571855c1..9e2b9723cc 100644
--- a/anvio/data/interactive/css/main.css
+++ b/anvio/data/interactive/css/main.css
@@ -1183,6 +1183,11 @@ 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) {

From 37ba1f2fb9001022e7db8b30cc605bf90f5419a6 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Wed, 14 Feb 2024 10:27:58 +0100
Subject: [PATCH 22/40] Fix Settings btn z-index

---
 anvio/data/interactive/css/main.css | 1 +
 1 file changed, 1 insertion(+)

diff --git a/anvio/data/interactive/css/main.css b/anvio/data/interactive/css/main.css
index 9e2b9723cc..88bf3fc8bc 100644
--- a/anvio/data/interactive/css/main.css
+++ b/anvio/data/interactive/css/main.css
@@ -293,6 +293,7 @@ html, body, #wrapper {
 
 .toggle-panel-left-pos {
     left: 560px;
+    z-index: 1;
 }
 
 #toggle-panel-left:hover {

From e08a379cabaf538697d215f9a315520076229bf6 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 26 Feb 2024 21:30:51 +0100
Subject: [PATCH 23/40] Update browser control

---
 anvio/data/interactive/js/main.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/anvio/data/interactive/js/main.js b/anvio/data/interactive/js/main.js
index 41173e83a7..d8f46d7856 100644
--- a/anvio/data/interactive/js/main.js
+++ b/anvio/data/interactive/js/main.js
@@ -195,8 +195,8 @@ $(document).ready(function() {
         }
     });
 
-    if (!$.browser.chrome)
-    {
+
+    if (!(/Chrome/.test(navigator.userAgent))) {
         toastr.warning("We tested anvi'o only on Google Chrome, and it seems you are using a different browser.\
                         For the best performance, and to avoid unexpected issues, please consider using anvi'o with\
                         the lastest version of Chrome.", "", { 'timeOut': '0', 'extendedTimeOut': '0' });

From 9c9a374f548337917bc1fd58ec49afa69892fc62 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 26 Feb 2024 23:32:03 +0100
Subject: [PATCH 24/40] Fix table-sortable package

---
 anvio/data/interactive/index.html                  | 6 +++---
 anvio/data/interactive/lib/bootstrap-sortable      | 1 -
 anvio/data/static/content/bootstrap-sortable       | 1 -
 anvio/data/static/content/css/sortable.min.css     | 1 +
 anvio/data/static/content/js/sortable.min.js       | 1 +
 anvio/data/static/template/inversions.tmpl         | 5 ++++-
 anvio/data/static/template/pan-index.tmpl          | 7 ++++---
 anvio/data/static/template/profile-index-mini.tmpl | 7 ++++---
 anvio/data/static/template/profile-index.tmpl      | 7 ++++---
 anvio/data/static/template/saavs-index.tmpl        | 7 ++++---
 10 files changed, 25 insertions(+), 18 deletions(-)
 delete mode 160000 anvio/data/interactive/lib/bootstrap-sortable
 delete mode 160000 anvio/data/static/content/bootstrap-sortable
 create mode 120000 anvio/data/static/content/css/sortable.min.css
 create mode 120000 anvio/data/static/content/js/sortable.min.js

diff --git a/anvio/data/interactive/index.html b/anvio/data/interactive/index.html
index 909ed69d7d..93a6e7fd6a 100644
--- a/anvio/data/interactive/index.html
+++ b/anvio/data/interactive/index.html
@@ -68,9 +68,9 @@
     <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="./node_modules/marked/marked.min.js" onerror='alertDependencyError("marked")'></script>
diff --git a/anvio/data/interactive/lib/bootstrap-sortable b/anvio/data/interactive/lib/bootstrap-sortable
deleted file mode 160000
index 159505ae6a..0000000000
--- a/anvio/data/interactive/lib/bootstrap-sortable
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 159505ae6ad99aefd727e8ffd9dc31cad58905b7
diff --git a/anvio/data/static/content/bootstrap-sortable b/anvio/data/static/content/bootstrap-sortable
deleted file mode 160000
index 64e1a43425..0000000000
--- a/anvio/data/static/content/bootstrap-sortable
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 64e1a43425d3b87605f2bf365d681056a14cd30a
diff --git a/anvio/data/static/content/css/sortable.min.css b/anvio/data/static/content/css/sortable.min.css
new file mode 120000
index 0000000000..3ce1d64d5f
--- /dev/null
+++ b/anvio/data/static/content/css/sortable.min.css
@@ -0,0 +1 @@
+../../../interactive/node_modules/sortable-tablesort/sortable.min.css
\ No newline at end of file
diff --git a/anvio/data/static/content/js/sortable.min.js b/anvio/data/static/content/js/sortable.min.js
new file mode 120000
index 0000000000..9838536a39
--- /dev/null
+++ b/anvio/data/static/content/js/sortable.min.js
@@ -0,0 +1 @@
+../../../interactive/node_modules/sortable-tablesort/sortable.min.js
\ No newline at end of file
diff --git a/anvio/data/static/template/inversions.tmpl b/anvio/data/static/template/inversions.tmpl
index 2d794af75e..304c71a2f9 100644
--- a/anvio/data/static/template/inversions.tmpl
+++ b/anvio/data/static/template/inversions.tmpl
@@ -22,7 +22,10 @@
 
     <!-- Bootstrap Core CSS -->
     <link href=".html/css/bootstrap.css" rel="stylesheet">
-    <link href=".html/bootstrap-sortable/Contents/bootstrap-sortable.css" rel="stylesheet">
+
+    <!-- Table sorter -->
+    <link href=".html/css/sortable.min.css" rel="stylesheet">
+    <script src=".html/js/sortable.min.js"></script>
 
     <!-- Custom CSS -->
     <link href=".html/css/anvio.css" rel="stylesheet">
diff --git a/anvio/data/static/template/pan-index.tmpl b/anvio/data/static/template/pan-index.tmpl
index 2a84585b8d..90819a4484 100644
--- a/anvio/data/static/template/pan-index.tmpl
+++ b/anvio/data/static/template/pan-index.tmpl
@@ -13,7 +13,8 @@
 
     <!-- Bootstrap Core CSS -->
     <link href=".html/css/bootstrap.css" rel="stylesheet">
-    <link href=".html/bootstrap-sortable/Contents/bootstrap-sortable.css" rel="stylesheet">
+
+    <link href=".html/css/sortable.min.css" rel="stylesheet">
 
     <!-- Custom CSS -->
     <link href=".html/css/anvio.css" rel="stylesheet">
@@ -210,8 +211,8 @@
     <!-- Bootstrap Core JavaScript -->
     <script src=".html/js/bootstrap.min.js"></script>
 
-    <!-- Table sorter, source: https://github.com/drvic10k/bootstrap-sortable -->
-    <script src=".html/bootstrap-sortable/Scripts/bootstrap-sortable.js"></script>
+    <!-- Table sorter -->
+    <script src=".html/js/sortable.min.js"></script>
 
     <!-- Activate tooltips... -->
     <script type="text/javascript">
diff --git a/anvio/data/static/template/profile-index-mini.tmpl b/anvio/data/static/template/profile-index-mini.tmpl
index a862d4656a..f5e5db0fef 100644
--- a/anvio/data/static/template/profile-index-mini.tmpl
+++ b/anvio/data/static/template/profile-index-mini.tmpl
@@ -13,7 +13,8 @@
 
     <!-- Bootstrap Core CSS -->
     <link href=".html/css/bootstrap.css" rel="stylesheet">
-    <link href=".html/bootstrap-sortable/Contents/bootstrap-sortable.css" rel="stylesheet">
+    
+    <link href=".html/css/sortable.min.css" rel="stylesheet">
 
     <!-- Custom CSS -->
     <link href=".html/css/anvio.css" rel="stylesheet">
@@ -231,8 +232,8 @@
     <!-- Bootstrap Core JavaScript -->
     <script src=".html/js/bootstrap.min.js"></script>
 
-    <!-- Table sorter, source: https://github.com/drvic10k/bootstrap-sortable -->
-    <script src=".html/bootstrap-sortable/Scripts/bootstrap-sortable.js"></script>
+    <!-- Table sorter -->
+    <script src=".html/js/sortable.min.js"></script>
 
     <!-- Activate tooltips... -->
     <script type="text/javascript">
diff --git a/anvio/data/static/template/profile-index.tmpl b/anvio/data/static/template/profile-index.tmpl
index 43f7f84d4c..fc8d82f451 100644
--- a/anvio/data/static/template/profile-index.tmpl
+++ b/anvio/data/static/template/profile-index.tmpl
@@ -13,7 +13,8 @@
 
     <!-- Bootstrap Core CSS -->
     <link href=".html/css/bootstrap.css" rel="stylesheet">
-    <link href=".html/bootstrap-sortable/Contents/bootstrap-sortable.css" rel="stylesheet">
+
+    <link href=".html/css/sortable.min.css" rel="stylesheet">
 
     <!-- Custom CSS -->
     <link href=".html/css/anvio.css" rel="stylesheet">
@@ -735,8 +736,8 @@
     <!-- Bootstrap Core JavaScript -->
     <script src=".html/js/bootstrap.min.js"></script>
 
-    <!-- Table sorter, source: https://github.com/drvic10k/bootstrap-sortable -->
-    <script src=".html/bootstrap-sortable/Scripts/bootstrap-sortable.js"></script>
+    <!-- Table sorter -->
+    <script src=".html/js/sortable.min.js"></script>
 
     <!-- Activate tooltips... -->
     <script type="text/javascript">
diff --git a/anvio/data/static/template/saavs-index.tmpl b/anvio/data/static/template/saavs-index.tmpl
index cb6214bcf8..279cd6c711 100644
--- a/anvio/data/static/template/saavs-index.tmpl
+++ b/anvio/data/static/template/saavs-index.tmpl
@@ -13,7 +13,8 @@
 
     <!-- Bootstrap Core CSS -->
     <link href=".html/css/bootstrap.css" rel="stylesheet">
-    <link href=".html/bootstrap-sortable/Contents/bootstrap-sortable.css" rel="stylesheet">
+
+    <link href=".html/css/sortable.min.css" rel="stylesheet">
 
     <!-- Custom CSS -->
     <link href=".html/css/anvio.css" rel="stylesheet">
@@ -85,8 +86,8 @@
     <!-- Bootstrap Core JavaScript -->
     <script src=".html/js/bootstrap.min.js"></script>
 
-    <!-- Table sorter, source: https://github.com/drvic10k/bootstrap-sortable -->
-    <script src=".html/bootstrap-sortable/Scripts/bootstrap-sortable.js"></script>
+    <!-- Table sorter -->
+    <script src=".html/js/sortable.min.js"></script>
 
     <!-- Activate tooltips... -->
     <script type="text/javascript">

From 645e305421efead48b9aa895adfd03932774cd60 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 26 Feb 2024 23:32:25 +0100
Subject: [PATCH 25/40] Fix table-sortable +=

---
 anvio/data/interactive/package.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/anvio/data/interactive/package.json b/anvio/data/interactive/package.json
index 25a6dd389c..0cc729b1de 100644
--- a/anvio/data/interactive/package.json
+++ b/anvio/data/interactive/package.json
@@ -32,6 +32,7 @@
     "jquery-ui": "1.12.1",
     "marked": "0.3.6",
     "randomcolor": "0.6.2",
+    "sortable-tablesort": "^3.2.2",
     "svg-pan-zoom": "^3.6.1",
     "toastr": "2.1.2"
   }

From c210a4597675b0d676d5e0fde00445d42b4c8e9c Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Tue, 27 Feb 2024 11:46:06 +0100
Subject: [PATCH 26/40] Remove gitmodule

---
 .gitmodules | 10 ----------
 1 file changed, 10 deletions(-)
 delete mode 100644 .gitmodules

diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index baa5bf182e..0000000000
--- a/.gitmodules
+++ /dev/null
@@ -1,10 +0,0 @@
-[submodule "anvio/data/static/content/chartsjs"]
-	path = anvio/data/static/content/chartsjs
-	url = https://github.com/nnnick/Chart.js
-[submodule "anvio/data/static/content/bootstrap-sortable"]
-	path = anvio/data/static/content/bootstrap-sortable
-	url = https://github.com/drvic10k/bootstrap-sortable
-[submodule "anvio/data/interactive/lib/bootstrap-sortable"]
-	path = anvio/data/interactive/lib/bootstrap-sortable
-	url = https://github.com/drvic10k/bootstrap-sortable
-

From 305c0805d88bf8ddbeee4eea1955c2aacafb1c94 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Tue, 27 Feb 2024 11:46:40 +0100
Subject: [PATCH 27/40] Remove unused func

---
 anvio/data/interactive/js/main.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/anvio/data/interactive/js/main.js b/anvio/data/interactive/js/main.js
index d8f46d7856..23deecd9ef 100644
--- a/anvio/data/interactive/js/main.js
+++ b/anvio/data/interactive/js/main.js
@@ -282,8 +282,6 @@ function initData() {
             var available_views = response.views[2];
             $('#views_container').append(getComboBoxContent(default_view, available_views));
 
-            //$("#tbody_layers").sortable({helper: fixHelperModified, handle: '.drag-icon', items: "> tr"}).disableSelection();
-            //$("#tbody_samples").sortable({helper: fixHelperModified, handle: '.drag-icon', items: "> tr"}).disableSelection();
 
             sortable('#tbody_layers', {
                 forcePlaceholderSize: true,

From 1253a457eb4ece7fddea9f35d330a3de6ce218e7 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Thu, 29 Feb 2024 10:06:57 +0100
Subject: [PATCH 28/40] Remove sortable codes

---
 anvio/data/interactive/index.html  |  2 +-
 anvio/data/interactive/js/utils.js | 13 ++-----------
 2 files changed, 3 insertions(+), 12 deletions(-)

diff --git a/anvio/data/interactive/index.html b/anvio/data/interactive/index.html
index 93a6e7fd6a..ff5bafe62e 100644
--- a/anvio/data/interactive/index.html
+++ b/anvio/data/interactive/index.html
@@ -856,7 +856,7 @@ <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>
diff --git a/anvio/data/interactive/js/utils.js b/anvio/data/interactive/js/utils.js
index a827ecd047..a5909a02dc 100644
--- a/anvio/data/interactive/js/utils.js
+++ b/anvio/data/interactive/js/utils.js
@@ -349,9 +349,6 @@ function showTaxonomyTableDialog(title, content)
     $('#modal' + randomID).on('hidden.bs.modal', function () {
         $(this).remove();
     });
-
-    // trigger bootstrap-sortable in case newly generated page content may have sortable tables.
-    $.bootstrapSortable({ applyLast: true })
 }
 
 
@@ -386,10 +383,7 @@ function showGeneClusterFunctionsSummaryTableDialog(title, content)
     $('#modal' + randomID).modal({'show': true, 'backdrop': true, 'keyboard': false}).find('.modal-dialog').draggable({handle: '.modal-header'});
     $('#modal' + randomID).on('hidden.bs.modal', function () {
         $(this).remove();
-    });
-
-    // trigger bootstrap-sortable in case newly generated page content may have sortable tables.
-    $.bootstrapSortable({ applyLast: true })
+    });    
 }
 
 
@@ -428,10 +422,7 @@ function showDraggableDialog(title, content, updateOnly)
     $('#modal' + randomID).modal({'show': true, 'backdrop': false, 'keyboard': false}).find('.modal-dialog').draggable({handle: '.modal-header'});
     $('#modal' + randomID).on('hidden.bs.modal', function () {
         $(this).remove();
-    });
-
-    // trigger bootstrap-sortable in case newly generated page content may have sortable tables.
-    $.bootstrapSortable({ applyLast: true })
+    });    
 }
 
 //--------------------------------------------------------------------------------------------------

From 0b949b1ba7e06008d44f398ee9346cb43a94b411 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 4 Mar 2024 11:52:16 +0100
Subject: [PATCH 29/40] Update package link

---
 anvio/data/interactive/structure.html | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/anvio/data/interactive/structure.html b/anvio/data/interactive/structure.html
index 0e57877c67..2f9d92bdbd 100644
--- a/anvio/data/interactive/structure.html
+++ b/anvio/data/interactive/structure.html
@@ -6,19 +6,19 @@
     <script type='text/javascript' src='js/utils.js'></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-slider/10.0.0/bootstrap-slider.min.js"></script>
     <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-slider/10.0.0/css/bootstrap-slider.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" href="lib/colpick/colpick.css" type="text/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" href="css/structure.css" />
-    <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" />
     <script type="text/javascript" src="lib/bootstrap/dist/js/bootstrap.bundle.js"></script>
-    <script type="text/javascript" src="lib/randomColor/randomColor.js"></script>
+    <script type="text/javascript" src="./node_modules/randomcolor/randomColor.js" onerror='alertDependencyError("random-color")'></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/4.13.0/d3.min.js"></script>
     <script type="text/javascript" src="https://cdn.jsdelivr.net/gh/arose/ngl@v0.10.4/dist/ngl.js"></script>
     <script type="text/javascript" src="lib/colpick/colpick.js"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.5/jszip.min.js"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/FileSaver.js/1.3.8/FileSaver.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" onerror='alertDependencyError("toastr")'></script>
     <script type="text/javascript" src="js/constants.js"></script>
     <script type="text/javascript" src="js/structure.js"></script>
 </head>

From 707f73dec66aafc830038b28ada3fa9c0592da82 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Wed, 25 Sep 2024 15:01:02 +0200
Subject: [PATCH 30/40] Delete chartjs package

---
 anvio/data/static/content/chartsjs | 1 -
 1 file changed, 1 deletion(-)
 delete mode 160000 anvio/data/static/content/chartsjs

diff --git a/anvio/data/static/content/chartsjs b/anvio/data/static/content/chartsjs
deleted file mode 160000
index cc57b9e581..0000000000
--- a/anvio/data/static/content/chartsjs
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit cc57b9e58192e28e061eec93ec5e646ba9cfd99b

From 87a809ead995cabef93e915609eba2c4a8e6cf61 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Wed, 25 Sep 2024 15:57:34 +0200
Subject: [PATCH 31/40] Fix npm installation check

---
 anvio/utils.py                 | 50 +++++++++++-----------------------
 bin/anvi-display-contigs-stats |  2 +-
 bin/anvi-display-functions     |  2 +-
 bin/anvi-display-metabolism    |  2 +-
 bin/anvi-display-pan           |  2 +-
 bin/anvi-display-structure     |  2 +-
 bin/anvi-interactive           |  2 +-
 7 files changed, 22 insertions(+), 40 deletions(-)

diff --git a/anvio/utils.py b/anvio/utils.py
index 4dd7c858a8..5b4b9afabe 100644
--- a/anvio/utils.py
+++ b/anvio/utils.py
@@ -827,52 +827,34 @@ def is_all_columns_present_in_TAB_delim_file(columns, file_path, including_first
     return False if len([False for c in columns if c not in columns_in_file]) else True
 
 
-def is_all_submodules_present():
-    """A function to test whether all anvi'o submodules are present.
+def is_all_npm_packages_installed():
+    """A function to test whether all npm packages are installed in the interactive directory.
 
-    This check is particularly important for those who run anvi'o from a git clone
-    rather than using it via a regular installation.
+    This check is for ensuring that necessary npm packages are installed in the 
+    anvio/data/interactive directory.
     """
 
     # find the root directory of anvi'o module
     anvio_module_path = os.path.dirname(os.path.abspath(anvio.__file__))
+    interactive_dir_path = os.path.join(anvio_module_path, 'data', 'interactive')
 
-    gitmodules_path = os.path.join(anvio_module_path, '../.gitmodules')
+    if not os.path.exists(interactive_dir_path):
+        raise ConfigError("The interactive directory does not exist in the anvi'o module. "
+                          "Please ensure the directory is present.")
 
-    if not os.path.exists(gitmodules_path):
-        # if this file does not exist, we are likely looking at a case where anvi'o is
-        # installed on the user's computer, so we will let them go.
-        return True
-
-    gitmodules = configparser.ConfigParser()
+    # Check if node_modules exists and is not empty
+    node_modules_path = os.path.join(interactive_dir_path, 'node_modules')
 
-    try:
-        gitmodules.read(gitmodules_path)
-    except Exception:
-        raise ConfigError("The config file here does not look like a config file :/ Anvi'o "
-                          "needs an adult :(")
-
-    # figure out missing modules
-    missing_gitmodules = []
-    for gitmodule in gitmodules.sections():
-        for key, value in gitmodules.items(gitmodule):
-            if key == 'path':
-                gitmodule_path = os.path.join(anvio_module_path, '..', value)
-
-                if not os.path.exists(gitmodule_path) or not len(os.listdir(gitmodule_path)):
-                    missing_gitmodules.append(value)
-
-    if len(missing_gitmodules):
+    if not os.path.exists(node_modules_path) or not os.listdir(node_modules_path):
         run.warning("Please read the error below, and then run the commands shown below in your terminal, "
-                    "and you will be fine :)", header="⚠️  ANVI'O WANTS YOU TO DO SOMETHING ⚠️", overwrite_verbose=True,
+                    "and you will be fine :)", header="⚠️  ANVI'O NEEDS NPM PACKAGES ⚠️", overwrite_verbose=True,
                     lc='yellow')
-        run.info_single(f"1) cd {anvio_module_path}", level=0, overwrite_verbose=True)
-        run.info_single("2) git submodule update --init", level=0, overwrite_verbose=True)
+        run.info_single(f"1) cd {interactive_dir_path}", level=0, overwrite_verbose=True)
+        run.info_single("2) npm install", level=0, overwrite_verbose=True)
         run.info_single("3) cd -", level=0, overwrite_verbose=True)
 
-        raise ConfigError("Some of the git modules anvi'o depends upon seem to be missing in your anvi'o "
-                          "codebase. If you run the commands shown above, you should be golden to try "
-                          "again.")
+        raise ConfigError("Some npm packages seem to be missing in your interactive directory. "
+                          "Please run 'npm install' in the interactive directory and try again.")
     else:
         return True
 
diff --git a/bin/anvi-display-contigs-stats b/bin/anvi-display-contigs-stats
index 11480ae3a2..772f4b536d 100755
--- a/bin/anvi-display-contigs-stats
+++ b/bin/anvi-display-contigs-stats
@@ -66,7 +66,7 @@ if __name__ == '__main__':
     A = lambda x: args.__dict__[x] if x in args.__dict__ else None
 
     try:
-        utils.is_all_submodules_present()
+        utils.is_all_npm_packages_installed()
 
         if A('report_as_text'):
             if not A('output_file'):
diff --git a/bin/anvi-display-functions b/bin/anvi-display-functions
index c699578712..d7c4e38bff 100755
--- a/bin/anvi-display-functions
+++ b/bin/anvi-display-functions
@@ -89,7 +89,7 @@ if __name__ == '__main__':
     args = parser.get_args(parser)
 
     try:
-        utils.is_all_submodules_present()
+        utils.is_all_npm_packages_installed()
         args.mode = 'functional'
         d = interactive.Interactive(args)
 
diff --git a/bin/anvi-display-metabolism b/bin/anvi-display-metabolism
index 4485ce1064..af4044a6d8 100755
--- a/bin/anvi-display-metabolism
+++ b/bin/anvi-display-metabolism
@@ -59,7 +59,7 @@ if __name__ == '__main__':
     A = lambda x: args.__dict__[x] if x in args.__dict__ else None
 
     try:
-        utils.is_all_submodules_present()
+        utils.is_all_npm_packages_installed()
 
         args.mode = 'metabolism'
         d = interactive.MetabolismInteractive(args)
diff --git a/bin/anvi-display-pan b/bin/anvi-display-pan
index 804a0061a8..986c1fa30e 100755
--- a/bin/anvi-display-pan
+++ b/bin/anvi-display-pan
@@ -73,7 +73,7 @@ if __name__ == '__main__':
     args = parser.get_args(parser, auto_fill_anvio_dbs=True)
 
     try:
-        utils.is_all_submodules_present()
+        utils.is_all_npm_packages_installed()
 
         args.mode = 'pan'
         d = interactive.Interactive(args)
diff --git a/bin/anvi-display-structure b/bin/anvi-display-structure
index 65852f3dab..166657134f 100755
--- a/bin/anvi-display-structure
+++ b/bin/anvi-display-structure
@@ -85,7 +85,7 @@ if __name__ == '__main__':
     groupP.add_argument(*anvio.A('password-protected'), **anvio.K('password-protected'))
 
     try:
-        utils.is_all_submodules_present()
+        utils.is_all_npm_packages_installed()
 
         args = parser.get_args(parser)
         args.mode = 'structure'
diff --git a/bin/anvi-interactive b/bin/anvi-interactive
index e7fc06b45e..9043327021 100755
--- a/bin/anvi-interactive
+++ b/bin/anvi-interactive
@@ -118,7 +118,7 @@ if __name__ == '__main__':
     args = parser.get_args(parser, auto_fill_anvio_dbs=True)
 
     try:
-        utils.is_all_submodules_present()
+        utils.is_all_npm_packages_installed()
         d = interactive.Interactive(args)
         args.port_number = utils.get_port_num(args.port_number, args.ip_address, run=run)
     except ConfigError as e:

From c5506e391e17d031257933bdb34c5975ed773455 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Wed, 25 Sep 2024 17:05:11 +0200
Subject: [PATCH 32/40] Remove missing dependency

---
 anvio/data/interactive/index.html | 1 -
 1 file changed, 1 deletion(-)

diff --git a/anvio/data/interactive/index.html b/anvio/data/interactive/index.html
index ff5bafe62e..3ffacd8f96 100644
--- a/anvio/data/interactive/index.html
+++ b/anvio/data/interactive/index.html
@@ -27,7 +27,6 @@
     <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/jquery-patch.js" onerror='alertDependencyError("jquery-patch")'></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>

From 6fb03a3ced587c33cad6d271935b1f61de4ffccf Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Wed, 25 Sep 2024 17:05:42 +0200
Subject: [PATCH 33/40] Update error message

---
 anvio/data/interactive/js/error.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/anvio/data/interactive/js/error.js b/anvio/data/interactive/js/error.js
index 4873d0a14d..8596275e8f 100644
--- a/anvio/data/interactive/js/error.js
+++ b/anvio/data/interactive/js/error.js
@@ -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',

From 4a42ef78c8dc4ffd94c30ffce6444ae6c06ae89b Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Wed, 25 Sep 2024 17:07:36 +0200
Subject: [PATCH 34/40] Remove bootstrapSortable call

I remove that until I find a better solution for that part.
---
 anvio/data/interactive/js/main.js | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/anvio/data/interactive/js/main.js b/anvio/data/interactive/js/main.js
index 23deecd9ef..18ba5ba56c 100644
--- a/anvio/data/interactive/js/main.js
+++ b/anvio/data/interactive/js/main.js
@@ -217,10 +217,6 @@ $(document).ready(function() {
                 return text === "Hide" ? "Show" : "Hide";
             });
         });
-
-        $('#bin_settings').on('click', function() {
-            $.bootstrapSortable();
-        });
 });
 
 function initData() {

From 85df59bd2d934dd195fa5971ee197ec340b98bc4 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 30 Sep 2024 10:24:03 +0200
Subject: [PATCH 35/40] Remove popover.css

---
 anvio/data/interactive/geneclusters.html | 1 -
 1 file changed, 1 deletion(-)

diff --git a/anvio/data/interactive/geneclusters.html b/anvio/data/interactive/geneclusters.html
index 7edcec502c..be55cd8855 100644
--- a/anvio/data/interactive/geneclusters.html
+++ b/anvio/data/interactive/geneclusters.html
@@ -11,7 +11,6 @@
         <link rel="stylesheet" type="text/css" href="css/loading.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" type="text/css" href="css/popover.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]-->	

From 3a1ed6ee02a401ee3ea9b1f96c9b1f893908917c Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 30 Sep 2024 10:35:09 +0200
Subject: [PATCH 36/40] Fix all bin deleting issue for pan-mode

---
 anvio/data/interactive/js/bin.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/anvio/data/interactive/js/bin.js b/anvio/data/interactive/js/bin.js
index 42a0acf569..097dc13aeb 100644
--- a/anvio/data/interactive/js/bin.js
+++ b/anvio/data/interactive/js/bin.js
@@ -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;">

From 3d7bb9a23227cb4b8e7f7caac55bc8145712f77b Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 30 Sep 2024 11:02:41 +0200
Subject: [PATCH 37/40] Add table responsive

---
 anvio/data/static/template/profile-index.tmpl | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/anvio/data/static/template/profile-index.tmpl b/anvio/data/static/template/profile-index.tmpl
index fc8d82f451..53f6503ee1 100644
--- a/anvio/data/static/template/profile-index.tmpl
+++ b/anvio/data/static/template/profile-index.tmpl
@@ -99,7 +99,7 @@
                                 Profile DB (<b>{{ meta|lookup:"profile"|lookup:"sample_id"|humanize }}</b> w/ {{ meta|lookup:"profile"|lookup:"samples"|length|pretty }} samples).
                             </div>
                             <div class="card-body">
-                                <table class="table table-striped">
+                                <table class="table table-striped table-responsive">
                                     <thead id="tblHead_basics_profile">
                                         <tr>
                                             <th>Key</th>
@@ -126,7 +126,7 @@
                                 Contigs DB (<b>{{ meta|lookup:"contigs"|lookup:"project_name"|humanize }}</b>)
                             </div>
                             <div class="card-body">
-                                <table class="table table-striped">
+                                <table class="table table-striped table-responsive">
                                     <thead id="tblHead_basics_contigs">
                                         <tr>
                                             <th>Key</th>
@@ -183,7 +183,7 @@
 
                         <div class="card col-12" id="summary-card">
                             <div class="card-body">
-                                <table class="table table-striped sortable" id="tblGrid_bin">
+                                <table class="table table-striped table-responsive sortable" id="tblGrid_bin">
                                     <thead id="tblHead_bin">
                                         <tr>
                                             <th data-defaultsort='disabled' class="text-center"></th>
@@ -254,7 +254,7 @@
             <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
           </div>
           <div class="modal-body">
-            <table class="table table-striped" id="tblGrid_tax_{{ bin }}">
+            <table class="table table-striped table-responsive" id="tblGrid_tax_{{ bin }}">
                 <thead id="tblHead_tax_{{ bin }}">
                   <tr>
                     <th>Taxon call</th>
@@ -289,7 +289,7 @@
             <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
           </div>
           <div class="modal-body">
-            <table class="table table-striped" id="tblGrid_files_{{ bin }}">
+            <table class="table table-striped table-responsive" id="tblGrid_files_{{ bin }}">
                 <thead id="tblHead_files_{{ bin }}">
                   <tr>
                     <th>File</th>
@@ -331,7 +331,7 @@
             <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
           </div>
           <div class="modal-body">
-            <table class="table table-striped" id="tblGrid_completeness_{{ bin }}">
+            <table class="table table-striped table-responsive" id="tblGrid_completeness_{{ bin }}">
                 <thead id="tblHead_completeness_{{ bin }}">
                   <tr>
                     <th>Source</th>
@@ -395,7 +395,7 @@
 
                             <div class="card">
                                 <div class="card-body">
-                                    <table class="table table-striped sortable">
+                                    <table class="table table-striped table-responsive sortable">
                                         <thead id="tblHead_bin">
                                            <tr>
                                                <th data-defaultsort='disabled' class="text-center"></th>
@@ -461,7 +461,7 @@
 
                         <div class="card ">
                             <div class="card-body">
-                                <table class="table table-striped sortable" id="tblGrid_bin">
+                                <table class="table table-striped table-responsive sortable" id="tblGrid_bin">
                                     <thead id="tblHead_bin">
                                         <tr>
                                             <th>Sample</th>
@@ -520,7 +520,7 @@
 
                     <div class="card ">
                         <div class="card-body">
-                            <table class="table table-striped sortable" id="tblGrid_bin">
+                            <table class="table table-striped table-responsive sortable" id="tblGrid_bin">
                                 <thead id="tblHead_bin">
                                     <tr>
                                         <th data-defaultsort='disabled' class="text-center"></th>
@@ -588,7 +588,7 @@
                         <!-- SINGLE TABLE FOR TOTAL NUMBER OF HMM HITS PER HMM PROFILE: -->
                         <div class="card" id="scg-hit-sum">
                             <div class="card-body">
-                                <table class="table table-striped sortable" id="tblGrid_bin">
+                                <table class="table table-striped table-responsive sortable" id="tblGrid_bin">
                                     <thead id="tblHead_bin">
                                        <tr>
                                            <th data-defaultsort='disabled' class="text-center"></th>
@@ -636,7 +636,7 @@
                                     <!-- INDIVIDUAL TABLES PER HMM ITEM and HMM PROFILE -->
                                     <div class="card">
                                         <div class="card-body">
-                                        <table class="table table-striped sortable">
+                                        <table class="table table-striped table-responsive sortable">
                                             <thead id="tblHead_bin">
                                                <tr>
                                                    <th data-defaultsort='disabled' class="text-center"></th>

From 337fc8cb8263aad99d76df5e44d1b27898032ec7 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 30 Sep 2024 13:53:05 +0200
Subject: [PATCH 38/40] Remove treelib-js

---
 anvio/data/interactive/lib/treelib-js/LICENSE | 21 -------------------
 1 file changed, 21 deletions(-)
 delete mode 100644 anvio/data/interactive/lib/treelib-js/LICENSE

diff --git a/anvio/data/interactive/lib/treelib-js/LICENSE b/anvio/data/interactive/lib/treelib-js/LICENSE
deleted file mode 100644
index 8b75036018..0000000000
--- a/anvio/data/interactive/lib/treelib-js/LICENSE
+++ /dev/null
@@ -1,21 +0,0 @@
-The MIT License (MIT)
-
-Copyright (c) 2013 Roderic D. M. Page
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
\ No newline at end of file

From f20d423a5c2764a92571f5de07b500cf27bfdbd3 Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 30 Sep 2024 15:47:30 +0200
Subject: [PATCH 39/40] Update package versions

---
 anvio/data/interactive/package.json | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/anvio/data/interactive/package.json b/anvio/data/interactive/package.json
index 0cc729b1de..55bba502fb 100644
--- a/anvio/data/interactive/package.json
+++ b/anvio/data/interactive/package.json
@@ -19,21 +19,21 @@
     "npm": ">=9.0.0"
   },
   "dependencies": {
-    "@fontsource/roboto": "^5.0.8",
-    "@popperjs/core": "^2.11.8",
+    "@fontsource/roboto": "5.0.8",
+    "@popperjs/core": "2.11.8",
     "blueimp-md5": "2.7.0",
     "bootstrap": "4.6.0",
     "bootstrap-icons": "1.11.3",
     "bootstrap-markdown": "2.10.0",
     "bootstrap-waitingfor": "1.2.7",
     "d3": "3.5.6",
-    "html5sortable": "^0.13.3",
+    "html5sortable": "0.13.3",
     "jquery": "1.12.4",
     "jquery-ui": "1.12.1",
     "marked": "0.3.6",
     "randomcolor": "0.6.2",
-    "sortable-tablesort": "^3.2.2",
-    "svg-pan-zoom": "^3.6.1",
+    "sortable-tablesort": "3.2.2",
+    "svg-pan-zoom": "3.6.1",
     "toastr": "2.1.2"
   }
 }

From 9a99979b77ee09f8cd8fa75c684cbf0a725b2c6e Mon Sep 17 00:00:00 2001
From: Metehan Sever <metehaansever@gmail.com>
Date: Mon, 30 Sep 2024 16:24:54 +0200
Subject: [PATCH 40/40] Add nodejs package control

---
 anvio/utils.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/anvio/utils.py b/anvio/utils.py
index 5b4b9afabe..c9a21db0f2 100644
--- a/anvio/utils.py
+++ b/anvio/utils.py
@@ -842,6 +842,12 @@ def is_all_npm_packages_installed():
         raise ConfigError("The interactive directory does not exist in the anvi'o module. "
                           "Please ensure the directory is present.")
 
+    # Check if Node.js is installed
+    if shutil.which("node") is None:
+        run.warning("Please install Node.js before proceeding.", header="⚠️  NODE.JS IS NOT INSTALLED ⚠️", overwrite_verbose=True, lc='yellow')
+        run.info_single("1) conda install -c conda-forge nodejs", level=0, overwrite_verbose=True)
+        raise ConfigError("Node.js is not installed. Please install it using conda and try again.")
+
     # Check if node_modules exists and is not empty
     node_modules_path = os.path.join(interactive_dir_path, 'node_modules')