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-rw-r--r--nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix15
-rw-r--r--nixpkgs/pkgs/applications/science/biology/bwa-mem2/default.nix55
-rw-r--r--nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix4
-rw-r--r--nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix4
-rw-r--r--nixpkgs/pkgs/applications/science/logic/cbmc/default.nix4
-rw-r--r--nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix4
-rw-r--r--nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix10
-rw-r--r--nixpkgs/pkgs/applications/science/math/sage/sage-src.nix7
8 files changed, 83 insertions, 20 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix b/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix
index 64e3f8713b2f..b5b92bd8fe4f 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix
@@ -7,8 +7,8 @@ let
 in
 
 stdenv.mkDerivation rec {
-  srcVersion = "feb23a";
-  version = "20230201_a";
+  srcVersion = "aug23a";
+  version = "20230801_a";
   pname = "gildas";
 
   src = fetchurl {
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
     # source code of the previous release to a different directory
     urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.xz"
       "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.xz" ];
-    sha256 = "sha256-A6jtcC8QMtJ7YcNaPiOjwNPDGPAjmRA3jZLEt5iBONE=";
+    sha256 = "sha256-jlyv2K1V+510C4uLek4oofm13d40nGJ46wqjW+tjfq4=";
   };
 
   nativeBuildInputs = [ pkg-config groff perl getopt gfortran which ];
@@ -38,14 +38,15 @@ stdenv.mkDerivation rec {
     echo "gag_doc:        $out/share/doc/" >> kernel/etc/gag.dico.lcl
   '';
 
+  userExec = "astro class greg imager mapping sic";
+
   postInstall=''
     mkdir -p $out/bin
     cp -a ../gildas-exe-${srcVersion}/* $out
     mv $out/$GAG_EXEC_SYSTEM $out/libexec
-    cp admin/wrapper.sh $out/bin/gildas-wrapper.sh
-    chmod 755 $out/bin/gildas-wrapper.sh
-    for i in $out/libexec/bin/* ; do
-      ln -s $out/bin/gildas-wrapper.sh $out/bin/$(basename "$i")
+    for i in ${userExec} ; do
+      cp admin/wrapper.sh $out/bin/$i
+      chmod 755 $out/bin/$i
     done
   '';
 
diff --git a/nixpkgs/pkgs/applications/science/biology/bwa-mem2/default.nix b/nixpkgs/pkgs/applications/science/biology/bwa-mem2/default.nix
new file mode 100644
index 000000000000..b34b6dc8c90f
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/bwa-mem2/default.nix
@@ -0,0 +1,55 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, zlib
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "bwa-mem2";
+  version = "unstable-2023-03-18";
+
+  src = fetchFromGitHub {
+    owner = "bwa-mem2";
+    repo = "bwa-mem2";
+    rev = "cf4306a47dac35e7e79a9e75398a35f33900cfd0";
+    fetchSubmodules = true;
+    hash = "sha256-1AYSn7nBrDwbX7oSrdEoa1d3t6xzwKnA0S87Y/XeXJg=";
+  };
+
+  buildInputs = [ zlib ];
+
+  # see https://github.com/bwa-mem2/bwa-mem2/issues/93
+  postPatch = lib.optionalString stdenv.isDarwin ''
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/include/safe_mem_lib.h
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset16_s.c
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset32_s.c
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset_s.c
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/wmemset_s.c
+  '';
+
+  buildFlags = [
+    (if stdenv.hostPlatform.sse4_2Support then "arch=sse42"
+    else if stdenv.hostPlatform.avxSupport then "arch=avx"
+    else if stdenv.hostPlatform.avx2Support then "arch=avx2"
+    else if stdenv.hostPlatform.avx512Support then "arch=avx512"
+    else "arch=sse41")
+  ];
+  enableParallelBuilding = true;
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin
+    cp bwa-mem2* $out/bin/
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequences against a large reference genome";
+    license = licenses.mit;
+    homepage = "https://github.com/bwa-mem2/bwa-mem2/";
+    changelog = "https://github.com/bwa-mem2/bwa-mem2/blob/${finalAttrs.src.rev}/NEWS.md";
+    platforms = platforms.x86_64;
+    maintainers = with maintainers; [ alxsimon ];
+  };
+})
diff --git a/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix
index a2ea5b901535..5343f102b249 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "ergoscf";
-  version = "3.8";
+  version = "3.8.2";
 
   src = fetchurl {
     url = "http://www.ergoscf.org/source/tarfiles/ergo-${version}.tar.gz";
-    sha256 = "1s50k2gfs3y6r5kddifn4p0wmj0yk85wm5vf9v3swm1c0h43riix";
+    sha256 = "sha256-U0NVREEZ8HI0Q0ZcbwvZsYA76PWMh7bqgDG1uaUc01c=";
   };
 
   buildInputs = [ blas lapack ];
diff --git a/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix b/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix
index 14cfac4c1e6e..652a96617cbc 100644
--- a/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix
@@ -13,13 +13,13 @@
 
 stdenv.mkDerivation rec {
   pname = "gerbv";
-  version = "2.9.8";
+  version = "2.10.0";
 
   src = fetchFromGitHub {
     owner = "gerbv";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-6r9C5qDOXsQoLsYMSCuIS01gI0ijH7WDoepcowo1yQw=";
+    hash = "sha256-sr48RGLYcMKuyH9p+5BhnR6QpKBvNOqqtRryw3+pbBk=";
   };
 
   postPatch = ''
diff --git a/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix b/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix
index 228027d187bd..9cc88ca7081d 100644
--- a/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix
@@ -13,13 +13,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cbmc";
-  version = "5.89.0";
+  version = "5.90.0";
 
   src = fetchFromGitHub {
     owner = "diffblue";
     repo = pname;
     rev = "${pname}-${version}";
-    sha256 = "sha256-pgZdR1X0aOCfCKAGo2h9bAIO2XTTiWL8ERgandOQj/M=";
+    sha256 = "sha256-c6Ms/IStmKug5nz37TzjeexkY3YfWaUqEKIC2viMK9g=";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix
index 1d402573146e..c5e263c319e6 100644
--- a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix
@@ -8,13 +8,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cryptominisat";
-  version = "5.11.11";
+  version = "5.11.12";
 
   src = fetchFromGitHub {
     owner = "msoos";
     repo = "cryptominisat";
     rev = version;
-    hash = "sha256-TYuOgOOs1EsdNz7ctZMsArTlw3QzHjiPZVozuniiPcI=";
+    hash = "sha256-1AJx8gPf+qDpAp0p4cfCObKZDWKDAKdGopllr2ajpHw=";
   };
 
   buildInputs = [ python3 boost ];
diff --git a/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix b/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix
index db066ea46317..38b668804ad1 100644
--- a/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix
+++ b/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix
@@ -1,7 +1,7 @@
 { lib, stdenv, unzip, fetchurl, electron, makeWrapper, geogebra }:
 let
   pname = "geogebra";
-  version = "6-0-785-0";
+  version = "6-0-794-0";
 
   srcIcon = geogebra.srcIcon;
   desktopItem = geogebra.desktopItem;
@@ -30,9 +30,9 @@ let
     src = fetchurl {
       urls = [
         "https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
-        "https://web.archive.org/web/20230627211859/https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
+        "https://web.archive.org/web/20230824011801/https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
       ];
-      hash = "sha256-Yv8pTCKkyM7XMUNV2Pcn/YxWo1MbOTNMQBFuJFhB/uE=";
+      hash = "sha256-sNCq1Xcx/Y5r+SIRiqQYcG9dVsfIC2Ef5KJf+tgfxC8=";
     };
 
     dontConfigure = true;
@@ -65,9 +65,9 @@ let
     src = fetchurl {
       urls = [
         "https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip"
-        "https://web.archive.org/web/20230627214413/https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip"
+        "https://web.archive.org/web/20230824012900/https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip"
       ];
-      hash = "sha256-HtIhhq8E1Q5B6xZ7q6Ok95Rt53VWLoGf8PbY+UEOSKg=";
+      hash = "sha256-CrSoKAjXiejfJHyv8wIpcRr2d8u/50HnatiDm1CdnGQ=";
     };
 
     dontUnpack = true;
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
index dee6e8eb0d4b..9fe07603fe7d 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
@@ -103,6 +103,13 @@ stdenv.mkDerivation rec {
       url = "https://github.com/sagemath/sage/commit/1a1b49f814cdf4c4c8d0ac8930610f3fef6af5b0.diff";
       sha256 = "sha256-GqMgoi0tsP7zcCcPumhdsbvhPB6fgw1ufx6gHlc6iSc=";
     })
+
+    # https://github.com/sagemath/sage/pull/36006, positively reviewed
+    (fetchpatch {
+      name = "gmp-6.3-upgrade.patch";
+      url = "https://github.com/sagemath/sage/commit/d88bc3815c0901bfdeaa3e4a31107c084199f614.diff";
+      sha256 = "sha256-dXaEwk2wXxmx02sCw4Vu9mF0ZrydhFD4LRwNAiQsPgM=";
+    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;