From 4d603cfc57a37c635df98fc523f380d864ca1495 Mon Sep 17 00:00:00 2001
From: Christopher Andrew Mancuso <chrismancuso1984@gmail.com>
Date: Wed, 18 Dec 2024 09:24:38 -0500
Subject: [PATCH] Updates for new PyGenePlexus release (#56)

- update GCP functions to use geneplexus v2.0.1
- update frontend links to readthedocs to look for v2.0.1
---
 frontend/src/components/Footer.tsx                        | 2 +-
 frontend/src/pages/About.tsx                              | 4 ++--
 frontend/src/pages/Analysis.tsx                           | 2 +-
 frontend/src/pages/Home.tsx                               | 2 +-
 frontend/src/pages/NewAnalysis.tsx                        | 4 ++--
 functions/convert_ids/convert_ids_deploy/requirements.txt | 2 +-
 functions/ml/ml_deploy/requirements.txt                   | 2 +-
 7 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/frontend/src/components/Footer.tsx b/frontend/src/components/Footer.tsx
index c41812c..eab5dc2 100644
--- a/frontend/src/components/Footer.tsx
+++ b/frontend/src/components/Footer.tsx
@@ -23,7 +23,7 @@ const Footer = () => (
       </Link>
       <Link to="/about#terms-of-use">Terms of Use</Link>
       <Link
-        to="https://pygeneplexus.readthedocs.io/en/latest/appendix/license.html"
+        to="https://pygeneplexus.readthedocs.io/en/v2.0.2/appendix/license.html"
         showArrow={false}
       >
         License
diff --git a/frontend/src/pages/About.tsx b/frontend/src/pages/About.tsx
index e525eeb..5e3a904 100644
--- a/frontend/src/pages/About.tsx
+++ b/frontend/src/pages/About.tsx
@@ -67,7 +67,7 @@ const AboutPage = () => {
               flip
             />
             <Button
-              to="https://pygeneplexus.readthedocs.io/en/latest/"
+              to="https://pygeneplexus.readthedocs.io/en/v2.0.2/"
               text="Docs"
               icon={<FaBook />}
               tooltip="Detailed information on how to use the package and how to interpret results"
@@ -88,7 +88,7 @@ const AboutPage = () => {
               flip
             />
             <Button
-              to="https://pygeneplexus.readthedocs.io/en/latest/notes/faqs.html"
+              to="https://pygeneplexus.readthedocs.io/en/v2.0.2/notes/faqs.html"
               text="FAQs"
               icon={<FaQuestion />}
               tooltip="Detailed help on some frequently asked questions"
diff --git a/frontend/src/pages/Analysis.tsx b/frontend/src/pages/Analysis.tsx
index 4bbcd76..1d9f65b 100644
--- a/frontend/src/pages/Analysis.tsx
+++ b/frontend/src/pages/Analysis.tsx
@@ -136,7 +136,7 @@ const AnalysisPage = () => {
             <>
               <Summary results={results} />
 
-              <Link to="https://pygeneplexus.readthedocs.io/en/latest/">
+              <Link to="https://pygeneplexus.readthedocs.io/en/v2.0.2/">
                 Learn more
               </Link>
 
diff --git a/frontend/src/pages/Home.tsx b/frontend/src/pages/Home.tsx
index d663a5b..239168f 100644
--- a/frontend/src/pages/Home.tsx
+++ b/frontend/src/pages/Home.tsx
@@ -34,7 +34,7 @@ const HomePage = () => {
         </Flex>
 
         <p className="center">
-          <Link to="https://pygeneplexus.readthedocs.io/en/latest/notes/faqs.html">
+          <Link to="https://pygeneplexus.readthedocs.io/en/v2.0.2/notes/faqs.html">
             Looking for the old GenePlexus?
           </Link>
         </p>
diff --git a/frontend/src/pages/NewAnalysis.tsx b/frontend/src/pages/NewAnalysis.tsx
index ef534f9..f7ab7c1 100644
--- a/frontend/src/pages/NewAnalysis.tsx
+++ b/frontend/src/pages/NewAnalysis.tsx
@@ -263,7 +263,7 @@ const NewAnalysisPage = () => {
   };
 
   /** limit options based on species */
-  /** https://pygeneplexus.readthedocs.io/en/latest/notes/data.html#preprocessed-data */
+  /** https://pygeneplexus.readthedocs.io/en/v2.0.2/notes/data.html#preprocessed-data */
   const filteredNetworkOptions = networkOptions.filter((option) => {
     if (
       option.id === "BioGRID" &&
@@ -302,7 +302,7 @@ const NewAnalysisPage = () => {
     toast(
       <>
         Selected options changed to be compatible with selected species.{" "}
-        <Link to="https://pygeneplexus.readthedocs.io/en/latest/notes/data.html">
+        <Link to="https://pygeneplexus.readthedocs.io/en/v2.0.2/notes/data.html">
           Learn more
         </Link>
         .
diff --git a/functions/convert_ids/convert_ids_deploy/requirements.txt b/functions/convert_ids/convert_ids_deploy/requirements.txt
index 52ec7f0..46c3b80 100644
--- a/functions/convert_ids/convert_ids_deploy/requirements.txt
+++ b/functions/convert_ids/convert_ids_deploy/requirements.txt
@@ -1,4 +1,4 @@
 # An example requirements file. If your function has other dependencies,
 # add them below
 functions-framework==3.*
-geneplexus @ git+https://github.com/krishnanlab/PyGenePlexus@610ad9a
\ No newline at end of file
+geneplexus==2.0.2
\ No newline at end of file
diff --git a/functions/ml/ml_deploy/requirements.txt b/functions/ml/ml_deploy/requirements.txt
index 15e4b33..ee14200 100644
--- a/functions/ml/ml_deploy/requirements.txt
+++ b/functions/ml/ml_deploy/requirements.txt
@@ -1,5 +1,5 @@
 # An example requirements file. If your function has other dependencies,
 # add them below
 functions-framework==3.*
-geneplexus @ git+https://github.com/krishnanlab/PyGenePlexus@610ad9a
+geneplexus==2.0.2
 flask-compress==1.*
\ No newline at end of file