From df4ed58e097d344751b8ac6da547135fdde8c1fb Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 18 Oct 2024 10:42:18 +0000
Subject: [PATCH 1/2] jmol: 16.2.21 -> 16.3.1

---
 pkgs/applications/science/chemistry/jmol/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix
index a48019febb1d..80704698c07b 100644
--- a/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/pkgs/applications/science/chemistry/jmol/default.nix
@@ -25,14 +25,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "16.2.21";
+  version = "16.3.1";
   pname = "jmol";
 
   src = let
     baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
   in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    hash = "sha256-9gIOrHoy0JyoPXaHOfBDHCL+ykmmHNam+Um12sHqZsE=";
+    hash = "sha256-mjID6o+2yhzKd1g3MO4as1dA11nhessjzCDHSUyUQBw=";
   };
 
   patchPhase = ''

From 14727d96ebe499b6295a11adb5a0a50382dfef9f Mon Sep 17 00:00:00 2001
From: Mauricio Collares <mauricio@collares.org>
Date: Tue, 22 Oct 2024 22:24:05 +0200
Subject: [PATCH 2/2] sage: use jre8

---
 pkgs/applications/science/math/sage/sage-env.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix
index 1503d3a89957..2dffa14c6614 100644
--- a/pkgs/applications/science/math/sage/sage-env.nix
+++ b/pkgs/applications/science/math/sage/sage-env.nix
@@ -49,7 +49,7 @@
 , zlib
 , gsl
 , ntl
-, jdk
+, jre8
 , less
 }:
 
@@ -96,7 +96,7 @@ let
     ecm
     lcalc
     rubiks
-    jdk # only needed for `jmol` which may be replaced in the future
+    jre8 # only needed for `jmol` (https://sourceforge.net/p/jmol/mailman/message/58818762/), which will be optional in sage 10.5
     less # needed to prevent transient test errors until https://github.com/ipython/ipython/pull/11864 is resolved
   ]
   ));