From 2f56302798ea1d5edb676937647dbc70d1fe5e7a Mon Sep 17 00:00:00 2001
From: Brian Drawert <brian@drawert.net>
Date: Mon, 26 Sep 2022 15:28:19 -0700
Subject: [PATCH 1/3] fixing broken example library links

---
 stochss/handlers/file_browser.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/file_browser.py b/stochss/handlers/file_browser.py
index e14996e495..db3b011afa 100644
--- a/stochss/handlers/file_browser.py
+++ b/stochss/handlers/file_browser.py
@@ -817,7 +817,12 @@ async def get(self):
         Attributes
         ----------
         '''
-        home = "/hub/spawn" if str(self.request.path).startswith("/user") else "stochss/home"
+        if str(self.request.path).startswith("/user"):
+            home = self.request.path
+            home = home.replace('api/example-library','home')
+        else:
+            home = "stochss/home"
+
         try:
             system = StochSSBase(path=".example-library.json")
             examples = system.load_example_library(home)

From 91fc18de7f27fbd7f724e1a0b65c0742db494c20 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 27 Sep 2022 10:59:45 -0400
Subject: [PATCH 2/3] Fixed the display for user logs.

---
 client/styles/styles.css  | 19 ++++---------------
 client/templates/body.pug |  2 +-
 client/views/main.js      |  2 ++
 3 files changed, 7 insertions(+), 16 deletions(-)

diff --git a/client/styles/styles.css b/client/styles/styles.css
index abb6cc5663..3f3e7906a3 100644
--- a/client/styles/styles.css
+++ b/client/styles/styles.css
@@ -38,7 +38,7 @@ img.quickstart {
 }
 
 .side-navbar {
-  z-index: 1;
+  z-index: 0;
 }
 
 .user-logs {
@@ -115,6 +115,9 @@ img.quickstart {
   .user-logs {
     width: 100%;
   }
+  .expand-logs {
+    width: 90%;
+  }
 }
 
 .inline{
@@ -622,20 +625,6 @@ span.checkbox {
   background-color: inherit;
 }
 
-.nav-drop {
-  color: #007bff;
-  text-align: match-parent;
-}
-
-.nav-drop-content {
-  overflow-y: scroll;
-  max-height: 375px;
-}
-
-.nav-drop-item {
-  padding: 0px 8px 0px 8px;
-}
-
 .dropdown {
   background-color: inherit;
 }
diff --git a/client/templates/body.pug b/client/templates/body.pug
index 5147772004..4d4844508b 100644
--- a/client/templates/body.pug
+++ b/client/templates/body.pug
@@ -32,7 +32,7 @@ body
 
   div.container-fluid
     div.row
-      div.col-sm-12.col-md-2.col-xxl-1(data-hook="side-navbar")
+      div.col-sm-12.col-md-2.col-xxl-1.side-navbar(data-hook="side-navbar")
         nav.sidebar.d-md-block
           div.sidebar-sticky
             ul.nav.nav-flex-column
diff --git a/client/views/main.js b/client/views/main.js
index 0f8fa273e1..bd8ae35a9e 100644
--- a/client/views/main.js
+++ b/client/views/main.js
@@ -142,11 +142,13 @@ module.exports = View.extend({
       logs.removeClass("show");
       $(this.queryByHook(e.target.dataset.hook)).html("+");
       $(".user-logs").removeClass("expand-logs");
+      $(".side-navbar").css("z-index", 0);
     }else{
       logs.addClass("show");
       $(this.queryByHook(e.target.dataset.hook)).html("-");
       if($(".sidebar-sticky").css("position") === "fixed") {
         $(".user-logs").addClass("expand-logs");
+        $(".side-navbar").css("z-index", 1);
       }
     }
     let element = document.querySelector("#user-logs");

From 71035d3ada145030f7c8e61bcb3899fb6d225779 Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Tue, 27 Sep 2022 11:05:28 -0400
Subject: [PATCH 3/3] Updated version to v2.4.13

---
 __version__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/__version__.py b/__version__.py
index c3d296bd19..c109dcfc97 100644
--- a/__version__.py
+++ b/__version__.py
@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.4.12'
+__version__ = '2.4.13'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'