Merge branch 'nixos-unstable' of https://github.com/NixOS/nixpkgs

Conflicts:
	nixpkgs/pkgs/build-support/go/module.nix
	nixpkgs/pkgs/development/python-modules/django-mailman3/default.nix

31 files changed, 559 insertions, 112 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/bamtools/default.nix b/nixpkgs/pkgs/applications/science/biology/bamtools/default.nix
new file mode 100644
index 000000000000..05373dafd381
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/bamtools/default.nix
@@ -0,0 +1,41 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, jsoncpp
+, pkg-config
+, zlib
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "bamtools";
+  version = "2.5.2";
+
+  src = fetchFromGitHub {
+    owner = "pezmaster31";
+    repo = "bamtools";
+    rev = "refs/tags/v${finalAttrs.version}";
+    hash = "sha256-l2DmA4P1kPneTCL9YVACE6LcQHT0F+mufPyM69VkksE=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+  ];
+
+  buildInputs = [
+    jsoncpp
+    zlib
+  ];
+
+  doCheck = true;
+
+  meta = with lib; {
+    description = "C++ API & command-line toolkit for working with BAM data";
+    homepage = "https://github.com/pezmaster31/bamtools";
+    changelog = "https://github.com/pezmaster31/bamtools/releases/tag/${finalAttrs.src.rev}";
+    license = licenses.mit;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+})
diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix
index 95f8a75e662c..8ec08f22b7d1 100644
--- a/nixpkgs/pkgs/applications/science/biology/last/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix
@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "last";
-  version = "1460";
+  version = "1471";
 
   src = fetchFromGitLab {
     owner = "mcfrith";
     repo = "last";
     rev = "refs/tags/${version}";
-    hash = "sha256-9Er15zsq9Xrw66M8QOmARC1S/O5NvmpdUvOZUGc92P0=";
+    hash = "sha256-HQ2C7SFfJS6TOJZUm6szhu+hMm41BnH8A7DZE5yh9fM=";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/biology/macs2/default.nix b/nixpkgs/pkgs/applications/science/biology/macs2/default.nix
index 934da2e8ab61..8884d41d9064 100644
--- a/nixpkgs/pkgs/applications/science/biology/macs2/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/macs2/default.nix
@@ -1,31 +1,40 @@
-{ lib, python3, fetchPypi }:
+{ lib, python3, fetchpatch, fetchPypi }:
 
 python3.pkgs.buildPythonPackage rec {
   pname = "macs2";
-  version = "2.2.8";
+  version = "2.2.9.1";
   format = "pyproject";
 
   src = fetchPypi {
     pname = lib.toUpper pname;
     inherit version;
-    hash = "sha256-KgpDasidj4yUoeQQaQA3dg5eN5Ka1xnFRpbnTvhKmOA=";
+    hash = "sha256-jVa8N/uCP8Y4fXgTjOloQFxUoKjNl3ZoJwX9CYMlLRY=";
   };
 
-  postPatch = ''
-    # prevent setup.py from installing numpy
-    substituteInPlace setup.py \
-      --replace "subprocess.call([sys.executable, \"-m\", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd)" "0"
-  '';
+  patches = [
+    # https://github.com/macs3-project/MACS/pull/590
+    (fetchpatch {
+      name = "remove-pip-build-dependency.patch";
+      url = "https://github.com/macs3-project/MACS/commit/cf95a930daccf9f16e5b9a9224c5a2670cf67939.patch";
+      hash = "sha256-WB3Ubqk5fKtZt97QYo/sZDU/yya9MUo1NL4VsKXR+Yo=";
+    })
+  ];
 
   nativeBuildInputs = with python3.pkgs; [
     cython
+    numpy
     setuptools
+    wheel
+  ];
+
+  propagatedBuildInputs = with python3.pkgs; [
+    numpy
   ];
 
-  propagatedBuildInputs = with python3.pkgs; [ numpy ];
+  __darwinAllowLocalNetworking = true;
 
-  nativeCheckInputs = [
-    python3.pkgs.unittestCheckHook
+  nativeCheckInputs = with python3.pkgs; [
+    unittestCheckHook
   ];
 
   unittestFlagsArray = [
diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
index 13094e7484e6..b36104bcf769 100644
--- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
@@ -1,4 +1,4 @@
-{lib, nimPackages, fetchFromGitHub, pcre}:
+{ lib, nimPackages, fetchFromGitHub, docopt, hts, pcre }:
 
 nimPackages.buildNimPackage rec {
   pname = "mosdepth";
@@ -12,7 +12,8 @@ nimPackages.buildNimPackage rec {
     sha256 = "sha256-7uteYTCbAaXedPqk0WtHpqTfUWH/+rRW8aSlFixkEko=";
   };
 
-  buildInputs = with nimPackages; [ docopt hts-nim pcre ];
+  buildInputs = [ docopt hts pcre ];
+  nimFlags = hts.nimFlags ++ [ "--threads:off" ];
 
   meta = with lib; {
     description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing";
diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix
index 5e18d5ead58a..b5743df9a7ca 100644
--- a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "samtools";
-  version = "1.17";
+  version = "1.18";
 
   src = fetchurl {
     url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
-    sha256 = "sha256-Ot85C2KCGf1kCPFGAqTEqpDmPhizldrXIqtRlDiipyk";
+    sha256 = "sha256-1ob/piECO6YYIqKlC3DoXQsY55Nx3lrbB4KFGdP8BuE=";
   };
 
   # tests require `bgzip` from the htslib package
diff --git a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix
index e785d6c25f3f..32f46e485098 100644
--- a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix
@@ -5,13 +5,13 @@
 
 buildGoModule rec {
   pname = "seqkit";
-  version = "2.5.0";
+  version = "2.5.1";
 
   src = fetchFromGitHub {
     owner = "shenwei356";
     repo = "seqkit";
     rev = "v${version}";
-    sha256 = "sha256-pk4HNtG2x3zZ+GEH5MNn/XPNSmx8zGWbVYPGCYIZucs=";
+    sha256 = "sha256-aS8aTh8Lszob9It89shhKyqxCDjFs7zxE3VhMCHYaGM=";
   };
 
   vendorHash = "sha256-54kb9Na76+CgW61SnXu7EfO0InH/rjliNRcH2M/gxII=";
diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
index 097addca18f3..e4ffb94eeba7 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
@@ -25,14 +25,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "16.1.13";
+  version = "16.1.33";
   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-BiCv1meuefFgzuhm/u5XmQNzM94xBOQsGtJceEBnu6s=";
+    hash = "sha256-vOFGmLsCQNYRBMuDRVrdjWE6/MxY7IucB1OpV4cdZrs=";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix b/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
index f016b53d553c..9d643c6eda3c 100644
--- a/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
@@ -1,18 +1,18 @@
-{ lib, mkDerivation, fetchFromGitHub, pkg-config, cmake
-, libzip, boost, fftw, qtbase, libusb1
+{ stdenv, lib, fetchFromGitHub, pkg-config, cmake, wrapQtAppsHook
+, libzip, boost, fftw, qtbase, qtwayland, qtsvg, libusb1
 , python3, fetchpatch
 }:
 
-mkDerivation rec {
+stdenv.mkDerivation rec {
   pname = "dsview";
 
-  version = "1.2.2";
+  version = "1.3.0";
 
   src = fetchFromGitHub {
       owner = "DreamSourceLab";
       repo = "DSView";
       rev = "v${version}";
-      sha256 = "sha256-QaCVu/n9PDbAiJgPDVN6SJMILeUO/KRkKcHYAstm86Q=";
+      sha256 = "sha256-wnBVhZ3Ky9PXs48OVvSbD1aAUSEqAwaNLg7Ntim7yFM=";
   };
 
   patches = [
@@ -20,10 +20,10 @@ mkDerivation rec {
     ./install.patch
   ];
 
-  nativeBuildInputs = [ cmake pkg-config ];
+  nativeBuildInputs = [ cmake pkg-config wrapQtAppsHook ];
 
   buildInputs = [
-    boost fftw qtbase libusb1 libzip
+    boost fftw qtbase qtwayland qtsvg libusb1 libzip
     python3
   ];
 
diff --git a/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix b/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
index 276c59aee7d5..3259f0f4ca95 100644
--- a/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
@@ -16,11 +16,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gtkwave";
-  version = "3.3.115";
+  version = "3.3.117";
 
   src = fetchurl {
     url = "mirror://sourceforge/gtkwave/${pname}-gtk3-${version}.tar.gz";
-    sha256 = "sha256-rbenwCsYygg1oGS2cvbNxR+HXEVLAYmnQ/LOi5HmSqU=";
+    sha256 = "sha256-PPFTdYapEcuwYBr4+hjPbacIyKFKcfac48uRGOhXHbk=";
   };
 
   nativeBuildInputs = [ pkg-config wrapGAppsHook ];
@@ -46,7 +46,7 @@ stdenv.mkDerivation rec {
     description = "VCD/Waveform viewer for Unix and Win32";
     homepage = "https://gtkwave.sourceforge.net";
     license = lib.licenses.gpl2Plus;
-    maintainers = with lib.maintainers; [ thoughtpolice jiegec ];
+    maintainers = with lib.maintainers; [ thoughtpolice jiegec jleightcap ];
     platforms = lib.platforms.linux ++ lib.platforms.darwin;
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
index 8bfd4681f785..9c98d7302f2b 100644
--- a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
@@ -3,45 +3,45 @@
 {
   "kicad" = {
     kicadVersion = {
-      version =			"7.0.6";
+      version =			"7.0.7";
       src = {
-        rev =			"c1a1259ded090202d87d49f4eb4e42f367764622";
-        sha256 =		"1bifg73id0grn37a4n5wpq440z9xz14q0fvkva5vajx0xfd34llv";
+        rev =			"dc7665e950aa0d42de36e928af48be3b060ba5d1";
+        sha256 =		"1xbzf29rhqh6kl0vggdn2dblgp927096fc1lr3y4yw63b8n0qq50";
       };
     };
     libVersion = {
-      version =			"7.0.6";
+      version =			"7.0.7";
       libSources = {
-        symbols.rev =		"b591556d93f52d3394b45f3f4c7d1b89f0caacc7";
-        symbols.sha256 =	"0p60dvig7xx8svzsgp871r0aix2m95bmzg3snz372nmgnza2nnvf";
-        templates.rev =		"39d8fccb7400713f3f917799d8b770ad3e786963";
+        symbols.rev =		"c7df225d1c79b3ea842c77d928ce1f9bc1a63c5b";
+        symbols.sha256 =	"1wr754m4ykidds3i14gqhvyrj3mbkchp2hkfnr0rjsdaqf4zmqdf";
+        templates.rev =		"1561dd81d116a661a17147c3b941a3e96335eecc";
         templates.sha256 =	"1qi20mrsfn4fxmr1fyphmil2i9p2nzmwk5rlfchc5aq2194nj3lq";
-        footprints.rev =	"5fca0686ef0d6c4a9eafb307e346c7b9444e8045";
-        footprints.sha256 =	"0fqnviaxsai0xwyq8xq5ks26j4vd390ns6h6lr0fx2ikv1ghaml5";
-        packages3d.rev =	"6acf40ee68422ea952c3ba8078bbe4cc05d64bff";
-        packages3d.sha256 =	"0dmssyhqd94d9wj8w7g7xjan560b2rwcs540sgl0rc77cw2jify8";
+        footprints.rev =	"ecb85886616b7a6bb957699037f6fb680ce01d30";
+        footprints.sha256 =	"0xnnivlqgcyaz9qay73p43jnvmvshp2b3fbh3569j7rmgi5pn8x0";
+        packages3d.rev =	"4fb0672db1d405b661d0cde8edb5d54ac0a95fc7";
+        packages3d.sha256 =	"141r5wd8s1bgyf77kvb9q14cpsiwwv4zmfzwbgcd42rflsk2lcbc";
       };
     };
   };
   "kicad-unstable" = {
     kicadVersion = {
-      version =			"2023-06-24";
+      version =			"2023-08-15";
       src = {
-        rev =			"1c1849ec1a6614247abe4c623c086def2b3192e0";
-        sha256 =		"0faf4fw7nrfwdrl4pjqdyfzqbvb9jd4nk4aq83v1w358yqyk7zg9";
+        rev =			"e0d4cf2d5b023a7e5b70d854452376aa3510acd8";
+        sha256 =		"0666j4q3vz24smcjw9m4ib3ca2dqiqgx2amhv7ys4rzqb6v2pvn2";
       };
     };
     libVersion = {
-      version =			"2023-06-24";
+      version =			"2023-08-15";
       libSources = {
-        symbols.rev =		"43456780d309682f6da4a6f14710355b06fc4c5d";
-        symbols.sha256 =	"1ql2w3q3dv13ascw8s0hzwda486763qma7i2m877jw3p78gjhldr";
+        symbols.rev =		"06d20a4b9f7e5375329194d141b096dcdcb7518a";
+        symbols.sha256 =	"1wr754m4ykidds3i14gqhvyrj3mbkchp2hkfnr0rjsdaqf4zmqdf";
         templates.rev =		"867eef383a0f61015cb69677d5c632d78a2ea01a";
         templates.sha256 =	"1qi20mrsfn4fxmr1fyphmil2i9p2nzmwk5rlfchc5aq2194nj3lq";
-        footprints.rev =	"6a59a2d3940dbab7b3e8254a5b9bf06cc5330301";
-        footprints.sha256 =	"0jlz0ln9vzj1av1fmw8ma8kfqlb8w0r9vrfng19bkc3cgh9lvh9x";
-        packages3d.rev =	"8a2c5c4c85457832f3320902456d066d29561806";
-        packages3d.sha256 =	"0dmssyhqd94d9wj8w7g7xjan560b2rwcs540sgl0rc77cw2jify8";
+        footprints.rev =	"5d2ac73ae72bfe8b8ee9eeb081a7851b2ca84c24";
+        footprints.sha256 =	"1qg016ysf0ddm3bd5bkjawlrc0z4r3zhmdjkqkwaaaydnpwp23qz";
+        packages3d.rev =	"f1dae9f95e59216f3b974f585e5b420db853da9e";
+        packages3d.sha256 =	"0ciri6lhnh0w9i00z167snj5acnjndi1rgmyls08p45zj4rma8y2";
       };
     };
   };
diff --git a/nixpkgs/pkgs/applications/science/electronics/linux-gpib/common.nix b/nixpkgs/pkgs/applications/science/electronics/linux-gpib/common.nix
new file mode 100644
index 000000000000..e87751a18860
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/electronics/linux-gpib/common.nix
@@ -0,0 +1,24 @@
+{ pname, fetchurl, lib }: rec {
+  version = "4.3.6";
+  inherit pname;
+
+  src = fetchurl {
+    url = "mirror://sourceforge/project/linux-gpib/linux-gpib%20for%203.x.x%20and%202.6.x%20kernels/${version}/linux-gpib-${version}.tar.gz";
+    hash = "sha256-Gze4xrvkhEgn+J5Jhrycezjp2uhlD1v6aX0WGv4J2Jg=";
+  };
+
+  unpackPhase = ''
+    tar xf $src
+    tar xf linux-gpib-${version}/${pname}-${version}.tar.gz
+  '';
+
+  sourceRoot = "${pname}-${version}";
+
+  meta = with lib; {
+    description = "Support package for GPIB (IEEE 488) hardware";
+    homepage = "https://linux-gpib.sourceforge.io/";
+    license = licenses.gpl2Only;
+    maintainers = with maintainers; [ fsagbuya ];
+    platforms = platforms.linux;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/electronics/linux-gpib/kernel.nix b/nixpkgs/pkgs/applications/science/electronics/linux-gpib/kernel.nix
new file mode 100644
index 000000000000..d64e2fc81fbd
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/electronics/linux-gpib/kernel.nix
@@ -0,0 +1,23 @@
+{ lib
+, stdenv
+, fetchurl
+, kernel
+, pahole
+}:
+
+stdenv.mkDerivation (import ./common.nix { inherit fetchurl lib; pname = "linux-gpib-kernel"; } // {
+
+  postPatch = ''
+    sed -i 's@/sbin/depmod -A@@g' Makefile
+  '';
+
+  buildInputs = [ pahole ] ++ kernel.moduleBuildDependencies;
+
+  makeFlags = [
+    "LINUX_SRCDIR=${kernel.dev}/lib/modules/${kernel.modDirVersion}/build"
+  ];
+
+  installFlags = [
+    "INSTALL_MOD_PATH=$(out)"
+  ];
+})
diff --git a/nixpkgs/pkgs/applications/science/electronics/linux-gpib/user.nix b/nixpkgs/pkgs/applications/science/electronics/linux-gpib/user.nix
new file mode 100644
index 000000000000..f9c9a2e1e6cb
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/electronics/linux-gpib/user.nix
@@ -0,0 +1,25 @@
+{ lib
+, stdenv
+, fetchurl
+, autoconf
+, libtool
+, bison
+, flex
+, automake
+}:
+
+stdenv.mkDerivation (import ./common.nix { inherit fetchurl lib; pname = "linux-gpib-user"; } // {
+
+  nativeBuildInputs = [
+    autoconf
+    libtool
+    bison
+    flex
+    automake
+  ];
+
+  configureFlags = [
+    "--sysconfdir=$(out)/etc"
+    "--prefix=$(out)"
+  ];
+})
diff --git a/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix b/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix
index f5ecbac9e852..b6e5d89a3e97 100644
--- a/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix
@@ -2,13 +2,13 @@
 
 mkDerivation rec {
   pname = "openhantek6022";
-  version = "3.3.2.2";
+  version = "3.3.3";
 
   src = fetchFromGitHub {
     owner = "OpenHantek";
     repo = "OpenHantek6022";
     rev = version;
-    sha256 = "sha256-0k9Q60+T28m1hPYf5viSdpt0s4d828lfjVo3GjLDm7c=";
+    sha256 = "sha256-y2pNLAa0P/r0YEdKjQ3iP66cqtTWERG8lTOZDR64WTk=";
   };
 
   nativeBuildInputs = [ cmake makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix b/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix
index 06872eae740f..4709065e45bd 100644
--- a/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix
@@ -31,27 +31,32 @@
 
 assert withMPI -> trilinos.withMPI;
 
+let
+  version = "7.6.0";
+
+  # useing fetchurl or fetchFromGitHub doesn't include the manuals
+  # due to .gitattributes files
+  xyce_src = fetchgit {
+    url = "https://github.com/Xyce/Xyce.git";
+    rev = "Release-${version}";
+    sha256 = "sha256-HYIzmODMWXBuVRZhcC7LntTysuyXN5A9lb2DeCQQtVw=";
+  };
+
+  regression_src = fetchFromGitHub {
+    owner = "Xyce";
+    repo = "Xyce_Regression";
+    rev = "Release-${version}";
+    sha256 = "sha256-uEoiKpYyHmdK7LZ1UNm2d3Jk8+sCwBwB0TCoHilIh74=";
+  };
+in
+
 stdenv.mkDerivation rec {
   pname = "xyce";
-  version = "7.6.0";
+  inherit version;
 
-  srcs = [
-    # useing fetchurl or fetchFromGitHub doesn't include the manuals
-    # due to .gitattributes files
-    (fetchgit {
-      url = "https://github.com/Xyce/Xyce.git";
-      rev = "Release-${version}";
-      sha256 = "sha256-HYIzmODMWXBuVRZhcC7LntTysuyXN5A9lb2DeCQQtVw=";
-    })
-    (fetchFromGitHub {
-      owner = "Xyce";
-      repo = "Xyce_Regression";
-      rev = "Release-${version}";
-      sha256 = "sha256-uEoiKpYyHmdK7LZ1UNm2d3Jk8+sCwBwB0TCoHilIh74=";
-    })
-  ];
+  srcs = [ xyce_src regression_src ];
 
-  sourceRoot = "./Xyce";
+  sourceRoot = "./${xyce_src.name}";
 
   preConfigure = "./bootstrap";
 
@@ -101,7 +106,7 @@ stdenv.mkDerivation rec {
   doCheck = enableTests;
 
   postPatch = ''
-    pushd ../source
+    pushd ../${regression_src.name}
     find Netlists -type f -regex ".*\.sh\|.*\.pl" -exec chmod ugo+x {} \;
     # some tests generate new files, some overwrite netlists
     find . -type d -exec chmod u+w {} \;
@@ -124,7 +129,7 @@ stdenv.mkDerivation rec {
   checkPhase = ''
     XYCE_BINARY="$(pwd)/src/Xyce"
     EXECSTRING="${lib.optionalString withMPI "mpirun -np 2 "}$XYCE_BINARY"
-    TEST_ROOT="$(pwd)/../source"
+    TEST_ROOT="$(pwd)/../${regression_src.name}"
 
     # Honor the TMP variable
     sed -i -E 's|/tmp|\$TMP|' $TEST_ROOT/TestScripts/suggestXyceTagList.sh
diff --git a/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix b/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix
index c287a74010d5..228027d187bd 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 = "5.88.1";
+  version = "5.89.0";
 
   src = fetchFromGitHub {
     owner = "diffblue";
     repo = pname;
     rev = "${pname}-${version}";
-    sha256 = "sha256-bfrtYqTMU/Nib0wZjS/t0kg5sBsuQuq9GaHX4PxL7tU=";
+    sha256 = "sha256-pgZdR1X0aOCfCKAGo2h9bAIO2XTTiWL8ERgandOQj/M=";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/logic/cvc5/default.nix b/nixpkgs/pkgs/applications/science/logic/cvc5/default.nix
index 23310163f279..5357e1df5454 100644
--- a/nixpkgs/pkgs/applications/science/logic/cvc5/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/cvc5/default.nix
@@ -2,19 +2,19 @@
 
 stdenv.mkDerivation rec {
   pname = "cvc5";
-  version = "1.0.5";
+  version = "1.0.6";
 
   src = fetchFromGitHub {
     owner  = "cvc5";
     repo   = "cvc5";
     rev    = "cvc5-${version}";
-    hash  = "sha256-l+L59QLLrAEVkAZjhxICJpa+j+jr1k/7B61JlapXGRI=";
+    hash  = "sha256-pZiXAO92cwnYtaVMDFBEmk+NzDf4eKdc0eY0RltofPA=";
   };
 
   nativeBuildInputs = [ pkg-config cmake flex ];
   buildInputs = [
     cadical.dev symfpu gmp gtest libantlr3c antlr3_4 boost jdk
-    (python3.withPackages (ps: with ps; [ pyparsing toml ]))
+    (python3.withPackages (ps: with ps; [ pyparsing tomli ]))
   ];
 
   preConfigure = ''
diff --git a/nixpkgs/pkgs/applications/science/logic/egglog/Cargo.lock b/nixpkgs/pkgs/applications/science/logic/egglog/Cargo.lock
index b2d8ef8a904e..cb023f2e05c1 100644
--- a/nixpkgs/pkgs/applications/science/logic/egglog/Cargo.lock
+++ b/nixpkgs/pkgs/applications/science/logic/egglog/Cargo.lock
@@ -131,6 +131,15 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "630be753d4e58660abd17930c71b647fe46c27ea6b63cc59e1e3851406972e42"
 
 [[package]]
+name = "block-buffer"
+version = "0.10.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71"
+dependencies = [
+ "generic-array",
+]
+
+[[package]]
 name = "bumpalo"
 version = "3.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -186,7 +195,7 @@ dependencies = [
  "heck",
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.25",
 ]
 
 [[package]]
@@ -212,18 +221,47 @@ dependencies = [
 ]
 
 [[package]]
+name = "cpufeatures"
+version = "0.2.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a17b76ff3a4162b0b27f354a0c87015ddad39d35f9c0c36607a3bdd175dde1f1"
+dependencies = [
+ "libc",
+]
+
+[[package]]
 name = "crunchy"
 version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7"
 
 [[package]]
+name = "crypto-common"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3"
+dependencies = [
+ "generic-array",
+ "typenum",
+]
+
+[[package]]
 name = "diff"
 version = "0.1.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "56254986775e3233ffa9c4d7d3faaf6d36a2c09d30b20687e9f88bc8bafc16c8"
 
 [[package]]
+name = "digest"
+version = "0.10.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292"
+dependencies = [
+ "block-buffer",
+ "crypto-common",
+]
+
+[[package]]
 name = "dirs-next"
 version = "2.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -245,12 +283,28 @@ dependencies = [
 ]
 
 [[package]]
+name = "dot-generator"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0aaac7ada45f71873ebce336491d1c1bc4a7c8042c7cea978168ad59e805b871"
+dependencies = [
+ "dot-structures",
+]
+
+[[package]]
+name = "dot-structures"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "675e35c02a51bb4d4618cb4885b3839ce6d1787c97b664474d9208d074742e20"
+
+[[package]]
 name = "egglog"
 version = "0.1.0"
 dependencies = [
  "clap",
  "egraph-serialize",
  "env_logger",
+ "getrandom",
  "glob",
  "hashbrown 0.14.0",
  "indexmap 2.0.0",
@@ -276,8 +330,9 @@ dependencies = [
 [[package]]
 name = "egraph-serialize"
 version = "0.1.0"
-source = "git+https://github.com/egraphs-good/egraph-serialize?rev=54b1a4f1e2f2135846b084edcb495cd159839540#54b1a4f1e2f2135846b084edcb495cd159839540"
+source = "git+https://github.com/egraphs-good/egraph-serialize?rev=e406ffcec8c6e841089fd3e4f9b76c35ce448950#e406ffcec8c6e841089fd3e4f9b76c35ce448950"
 dependencies = [
+ "graphviz-rust",
  "indexmap 2.0.0",
  "once_cell",
  "ordered-float",
@@ -341,20 +396,38 @@ dependencies = [
 ]
 
 [[package]]
+name = "fastrand"
+version = "2.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6999dc1837253364c2ebb0704ba97994bd874e8f195d665c50b7548f6ea92764"
+
+[[package]]
 name = "fixedbitset"
 version = "0.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80"
 
 [[package]]
+name = "generic-array"
+version = "0.14.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a"
+dependencies = [
+ "typenum",
+ "version_check",
+]
+
+[[package]]
 name = "getrandom"
 version = "0.2.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "be4136b2a15dd319360be1c07d9933517ccf0be8f16bf62a3bee4f0d618df427"
 dependencies = [
  "cfg-if 1.0.0",
+ "js-sys",
  "libc",
  "wasi",
+ "wasm-bindgen",
 ]
 
 [[package]]
@@ -364,6 +437,22 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
 
 [[package]]
+name = "graphviz-rust"
+version = "0.6.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "27dafd1ac303e0dfb347a3861d9ac440859bab26ec2f534bbceb262ea492a1e0"
+dependencies = [
+ "dot-generator",
+ "dot-structures",
+ "into-attr",
+ "into-attr-derive",
+ "pest",
+ "pest_derive",
+ "rand",
+ "tempfile",
+]
+
+[[package]]
 name = "hashbrown"
 version = "0.12.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -434,6 +523,28 @@ dependencies = [
 ]
 
 [[package]]
+name = "into-attr"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "18b48c537e49a709e678caec3753a7dba6854661a1eaa27675024283b3f8b376"
+dependencies = [
+ "dot-structures",
+]
+
+[[package]]
+name = "into-attr-derive"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ecac7c1ae6cd2c6a3a64d1061a8bdc7f52ff62c26a831a2301e54c1b5d70d5b1"
+dependencies = [
+ "dot-generator",
+ "dot-structures",
+ "into-attr",
+ "quote",
+ "syn 1.0.109",
+]
+
+[[package]]
 name = "is-terminal"
 version = "0.4.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -656,6 +767,50 @@ dependencies = [
 ]
 
 [[package]]
+name = "pest"
+version = "2.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1acb4a4365a13f749a93f1a094a7805e5cfa0955373a9de860d962eaa3a5fe5a"
+dependencies = [
+ "thiserror",
+ "ucd-trie",
+]
+
+[[package]]
+name = "pest_derive"
+version = "2.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "666d00490d4ac815001da55838c500eafb0320019bbaa44444137c48b443a853"
+dependencies = [
+ "pest",
+ "pest_generator",
+]
+
+[[package]]
+name = "pest_generator"
+version = "2.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "68ca01446f50dbda87c1786af8770d535423fa8a53aec03b8f4e3d7eb10e0929"
+dependencies = [
+ "pest",
+ "pest_meta",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.25",
+]
+
+[[package]]
+name = "pest_meta"
+version = "2.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "56af0a30af74d0445c0bf6d9d051c979b516a1a5af790d251daee76005420a48"
+dependencies = [
+ "once_cell",
+ "pest",
+ "sha2",
+]
+
+[[package]]
 name = "petgraph"
 version = "0.6.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -681,6 +836,12 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5be167a7af36ee22fe3115051bc51f6e6c7054c9348e28deb4f49bd6f705a315"
 
 [[package]]
+name = "ppv-lite86"
+version = "0.2.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
+
+[[package]]
 name = "precomputed-hash"
 version = "0.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -710,16 +871,29 @@ version = "0.8.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404"
 dependencies = [
+ "libc",
+ "rand_chacha",
  "rand_core",
  "serde",
 ]
 
 [[package]]
+name = "rand_chacha"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88"
+dependencies = [
+ "ppv-lite86",
+ "rand_core",
+]
+
+[[package]]
 name = "rand_core"
 version = "0.6.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c"
 dependencies = [
+ "getrandom",
  "serde",
 ]
 
@@ -835,7 +1009,7 @@ checksum = "389894603bd18c46fa56231694f8d827779c0951a667087194cf9de94ed24682"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.25",
 ]
 
 [[package]]
@@ -851,6 +1025,17 @@ dependencies = [
 ]
 
 [[package]]
+name = "sha2"
+version = "0.10.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "479fb9d862239e610720565ca91403019f2f00410f1864c5aa7479b950a76ed8"
+dependencies = [
+ "cfg-if 1.0.0",
+ "cpufeatures",
+ "digest",
+]
+
+[[package]]
 name = "siphasher"
 version = "0.3.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -897,6 +1082,17 @@ source = "git+https://github.com/oflatt/symbolic-expressions?rev=4c0ea5ca008f972
 
 [[package]]
 name = "syn"
+version = "1.0.109"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "syn"
 version = "2.0.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "15e3fc8c0c74267e2df136e5e5fb656a464158aa57624053375eb9c8c6e25ae2"
@@ -907,6 +1103,19 @@ dependencies = [
 ]
 
 [[package]]
+name = "tempfile"
+version = "3.7.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dc02fddf48964c42031a0b3fe0428320ecf3a73c401040fc0096f97794310651"
+dependencies = [
+ "cfg-if 1.0.0",
+ "fastrand",
+ "redox_syscall 0.3.5",
+ "rustix",
+ "windows-sys",
+]
+
+[[package]]
 name = "term"
 version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -943,7 +1152,7 @@ checksum = "463fe12d7993d3b327787537ce8dd4dfa058de32fc2b195ef3cde03dc4771e8f"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.25",
 ]
 
 [[package]]
@@ -965,6 +1174,18 @@ dependencies = [
 ]
 
 [[package]]
+name = "typenum"
+version = "1.16.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "497961ef93d974e23eb6f433eb5fe1b7930b659f06d12dec6fc44a8f554c0bba"
+
+[[package]]
+name = "ucd-trie"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ed646292ffc8188ef8ea4d1e0e0150fb15a5c2e12ad9b8fc191ae7a8a7f3c4b9"
+
+[[package]]
 name = "unicode-ident"
 version = "1.0.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
@@ -1015,7 +1236,7 @@ dependencies = [
  "once_cell",
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.25",
  "wasm-bindgen-shared",
 ]
 
@@ -1037,7 +1258,7 @@ checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.25",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
diff --git a/nixpkgs/pkgs/applications/science/logic/egglog/default.nix b/nixpkgs/pkgs/applications/science/logic/egglog/default.nix
index 65dbcd5a1b43..c74594df28fd 100644
--- a/nixpkgs/pkgs/applications/science/logic/egglog/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/egglog/default.nix
@@ -5,19 +5,19 @@
 
 rustPlatform.buildRustPackage {
   pname = "egglog";
-  version = "unstable-2023-07-19";
+  version = "unstable-2023-08-19";
 
   src = fetchFromGitHub {
     owner = "egraphs-good";
     repo = "egglog";
-    rev = "9fe03ad35a2a975a2c9140a641ba91266b7a72ce";
-    hash = "sha256-9JeJJdZW8ecogReJzQrp3hFkK/pp/+pLxJMNREWuiyI=";
+    rev = "a4768b1751b72292b0e79e6e442d54ab270748fb";
+    hash = "sha256-WTdMhtdPvBtS6WAS3S4dui/8ospJ7nkeRhLce2zY8KE=";
   };
 
   cargoLock = {
     lockFile = ./Cargo.lock;
     outputHashes = {
-      "egraph-serialize-0.1.0" = "sha256-1lDaoR/1TNFW+uaf3UdfDZgXlxyAb37Ij7yky16xCG8=";
+      "egraph-serialize-0.1.0" = "sha256-sdkn7lmtmbLwAopabLWkrD6GjM3LIHseysuvwPz26G4=";
       "symbol_table-0.2.0" = "sha256-f9UclMOUig+N5L3ibBXou0pJ4S/CQqtaji7tnebVbis=";
       "symbolic_expressions-5.0.3" = "sha256-mSxnhveAItlTktQC4hM8o6TYjgtCUgkdZj7i6MR4Oeo=";
     };
diff --git a/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix b/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix
index 98db5682e7e7..a73d141f45b8 100644
--- a/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix
@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "fast-downward";
-  version = "22.12.0";
+  version = "23.06.0";
 
   src = fetchFromGitHub {
     owner = "aibasel";
     repo = "downward";
     rev = "release-${version}";
-    sha256 = "sha256-GwZ5BGzLRMgWNBaA7M2D2p9OxvdyWqm+sTwxGpcI/qY=";
+    sha256 = "sha256-yNaMyS47yxc/p5Rs/kHwD/pgjGXnHBdybYdo1GIEmA4=";
   };
 
   nativeBuildInputs = [ cmake python3.pkgs.wrapPython ];
diff --git a/nixpkgs/pkgs/applications/science/logic/poly/default.nix b/nixpkgs/pkgs/applications/science/logic/poly/default.nix
index 7eff519375f2..e54f822921ca 100644
--- a/nixpkgs/pkgs/applications/science/logic/poly/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/poly/default.nix
@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   pname = "libpoly";
-  version = "0.1.11";
+  version = "0.1.13";
 
   src = fetchFromGitHub {
     owner = "SRI-CSL";
     repo = "libpoly";
     # they've pushed to the release branch, use explicit tag
     rev = "refs/tags/v${version}";
-    sha256 = "sha256-vrYB6RQYShipZ0c0j1KcSTJR1h0rQKAAeJvODMar1GM=";
+    sha256 = "sha256-7aFz+6XJOVEA/Fmi0ywd6rZdTW8sHq8MoHqXR0Hc2o4=";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix
index 9ff9d693a885..d3ca419c48d3 100644
--- a/nixpkgs/pkgs/applications/science/math/R/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/R/default.nix
@@ -1,5 +1,5 @@
 { lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
-, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texLive, tk, xz, zlib
+, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texLive, tk, xz, zlib
 , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack
 , curl, Cocoa, Foundation, libobjc, libcxx, tzdata
 , withRecommendedPackages ? true
@@ -24,6 +24,8 @@ stdenv.mkDerivation (finalAttrs: {
     sha256 = "sha256-jdC/JPECPG9hjDsxc4PSkbSklPQNc7mDrCL/6pnkupk=";
   };
 
+  outputs = [ "out" "tex" ];
+
   dontUseImakeConfigure = true;
 
   nativeBuildInputs = [ pkg-config ];
@@ -89,6 +91,13 @@ stdenv.mkDerivation (finalAttrs: {
 
   installTargets = [ "install" "install-info" "install-pdf" ];
 
+  # move tex files to $tex for use with texlive.combine
+  # add link in $out since ${R_SHARE_DIR}/texmf is hardcoded in several places
+  postInstall = ''
+    mv -T "$out/lib/R/share/texmf" "$tex"
+    ln -s "$tex" "$out/lib/R/share/texmf"
+  '';
+
   # The store path to "which" is baked into src/library/base/R/unix/system.unix.R,
   # but Nix cannot detect it as a run-time dependency because the installed file
   # is compiled and compressed, which hides the store path.
@@ -103,6 +112,12 @@ stdenv.mkDerivation (finalAttrs: {
 
   passthru.tests.pkg-config = testers.testMetaPkgConfig finalAttrs.finalPackage;
 
+  # make tex output available to texlive.combine
+  passthru.pkgs = [ finalAttrs.finalPackage.tex ];
+  passthru.tlType = "run";
+  # dependencies (based on \RequirePackage in jss.cls, Rd.sty, Sweave.sty)
+  passthru.tlDeps = with texlive; [ amsfonts amsmath fancyvrb graphics hyperref iftex jknapltx latex lm tools upquote url ];
+
   meta = with lib; {
     homepage = "http://www.r-project.org/";
     description = "Free software environment for statistical computing and graphics";
diff --git a/nixpkgs/pkgs/applications/science/math/calc/default.nix b/nixpkgs/pkgs/applications/science/math/calc/default.nix
index 2ece6295b48e..0c70a6e03b2c 100644
--- a/nixpkgs/pkgs/applications/science/math/calc/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/calc/default.nix
@@ -10,14 +10,14 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "calc";
-  version = "2.14.1.6";
+  version = "2.14.3.5";
 
   src = fetchurl {
     urls = [
       "https://github.com/lcn2/calc/releases/download/v${finalAttrs.version}/calc-${finalAttrs.version}.tar.bz2"
       "http://www.isthe.com/chongo/src/calc/calc-${finalAttrs.version}.tar.bz2"
     ];
-    hash = "sha256-zlmzCCltGB3ipgWBF9vu2szmAZguPDiR2K3xdTnWf0A=";
+    hash = "sha256-4eXs6NDfsJO5Vr9Mo2jC16hTRAyt++1s+Z/JrWDKwUk=";
   };
 
   postPatch = ''
diff --git a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix
index a408f105c8bf..8abcd96f08d2 100644
--- a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix
@@ -7,13 +7,13 @@
 
 stdenv.mkDerivation rec {
   pname = "eigenmath";
-  version = "unstable-2023-06-16";
+  version = "unstable-2023-08-03";
 
   src = fetchFromGitHub {
     owner = "georgeweigt";
     repo = pname;
-    rev = "800adc5c0bd654eb9ad28497e1b78c4061b3a4cb";
-    hash = "sha256-/ViU44E3myAc7B8amm/TaIh70g2Z7IC4KRRG3++nOKs=";
+    rev = "f202cf0c342e54e994c4d416daecc1b1dc8b9c98";
+    hash = "sha256-kp4zWTPYt2DiuPgTK+ib8NbKg2BJVxJDDCvIlWNuwgs=";
   };
 
   checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in ''
@@ -43,5 +43,6 @@ stdenv.mkDerivation rec {
     homepage = "https://georgeweigt.github.io";
     license = licenses.bsd2;
     maintainers = with maintainers; [ nickcao ];
+    platforms = platforms.unix;
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/math/polymake/default.nix b/nixpkgs/pkgs/applications/science/math/polymake/default.nix
index 18d6912a2b8a..2e79ca03635a 100644
--- a/nixpkgs/pkgs/applications/science/math/polymake/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/polymake/default.nix
@@ -1,7 +1,6 @@
 { lib
 , stdenv
 , fetchurl
-, perl
 , gmp
 , mpfr
 , flint
@@ -15,10 +14,14 @@
 , ninja
 , ant
 , openjdk
-, perlPackages
+, perl536Packages
 , makeWrapper
 }:
-
+let
+  # log says: polymake does not work with perl 5.37 or newer;
+  perlPackages = perl536Packages;
+  inherit (perlPackages) perl;
+in
 # polymake compiles its own version of sympol and atint because we
 # don't have those packages. other missing optional dependencies:
 # javaview, libnormaliz, scip, soplex, jreality.
diff --git a/nixpkgs/pkgs/applications/science/math/pspp/default.nix b/nixpkgs/pkgs/applications/science/math/pspp/default.nix
index dbc5c8a0f179..56f3fdcb1e40 100644
--- a/nixpkgs/pkgs/applications/science/math/pspp/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/pspp/default.nix
@@ -1,23 +1,28 @@
 { lib, stdenv, fetchurl, libxml2, readline, zlib, perl, cairo, gtk3, gsl
-, pkg-config, gtksourceview, pango, gettext, dconf
+, pkg-config, gtksourceview4, pango, gettext, dconf
 , makeWrapper, gsettings-desktop-schemas, hicolor-icon-theme
-, texinfo, ssw, python3
+, texinfo, ssw, python3, iconv
 }:
 
 stdenv.mkDerivation rec {
   pname = "pspp";
-  version = "1.4.1";
+  version = "1.6.2";
 
   src = fetchurl {
     url = "mirror://gnu/pspp/${pname}-${version}.tar.gz";
-    sha256 = "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan";
+    sha256 = "sha256-cylMovWy9/xBu/i3jFiIyAdfQ8YJf9SCq7BPhasIR7Y=";
   };
 
   nativeBuildInputs = [ pkg-config texinfo python3 makeWrapper ];
   buildInputs = [ libxml2 readline zlib perl cairo gtk3 gsl
-    gtksourceview pango gettext
-    gsettings-desktop-schemas hicolor-icon-theme ssw
-  ];
+                  gtksourceview4 pango gettext
+                  gsettings-desktop-schemas hicolor-icon-theme ssw iconv
+                ];
+
+  C_INCLUDE_PATH =
+    "${libxml2.dev}/include/libxml2/:" +
+    lib.makeSearchPathOutput "dev" "include" buildInputs;
+  LIBRARY_PATH = lib.makeLibraryPath buildInputs;
 
   doCheck = false;
 
diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch
new file mode 100644
index 000000000000..539afc4b3b77
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch
@@ -0,0 +1,18 @@
+diff --git a/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py b/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py
+index aa153fd4cd..eebbe87aff 100644
+--- a/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py
++++ b/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py
+@@ -134,11 +134,11 @@ Sage example in ./graphique.tex, line 1120::
+   sage: t = srange(0, 5, 0.1); p = Graphics()
+   sage: for k in srange(0, 10, 0.15):
+   ....:       y = integrate.odeint(f, k, t)
+-  ....:       p += line(zip(t, flatten(y)))
++  ....:       p += line(zip(t, y.flatten()))
+   sage: t = srange(0, -5, -0.1); q = Graphics()
+   sage: for k in srange(0, 10, 0.15):
+   ....:       y = integrate.odeint(f, k, t)
+-  ....:       q += line(zip(t, flatten(y)))
++  ....:       q += line(zip(t, y.flatten()))
+   sage: y = var('y')
+   sage: v = plot_vector_field((1, -cos(x*y)), (x,-5,5), (y,-2,11))
+   sage: g = p + q + v; g.show()
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
index d890a65230cb..dee6e8eb0d4b 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
@@ -80,6 +80,23 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-k8Oam+EiRcfXC7qCdLacCx+7vpUAw2K1wsjKcQbeGb4=";
     })
 
+    # https://github.com/sagemath/sage/pull/35826, landed in 10.1.beta5
+    (fetchpatch {
+      name = "numpy-1.25.0-upgrade.patch";
+      url = "https://github.com/sagemath/sage/commit/ecfe06b8f1fe729b07e885f0de55244467e5c137.diff";
+      sha256 = "sha256-G0xhl+LyNdDYPzRqSHK3fHaepcIzpuwmqRiussraDf0=";
+    })
+
+    # https://github.com/sagemath/sage/pull/35826#issuecomment-1658569891
+    ./patches/numpy-1.25-deprecation.patch
+
+    # https://github.com/sagemath/sage/pull/35842, landed in 10.1.beta5
+    (fetchpatch {
+      name = "scipy-1.11-upgrade.patch";
+      url = "https://github.com/sagemath/sage/commit/90ece168c3c61508baa36659b0027b7dd8b43add.diff";
+      sha256 = "sha256-Y5TmuJcUJR+veb2AuSVODGs+xkVV+pTM8fWTm4q+NDs=";
+    })
+
     # https://github.com/sagemath/sage/pull/35825, landed in 10.1.beta6
     (fetchpatch {
       name = "singular-4.3.2p2-upgrade.patch";
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix
index 7632b851773c..378f7e29dd99 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix
@@ -1,6 +1,5 @@
 { stdenv
 , lib
-, makeWrapper
 , sage-env
 , blas
 , lapack
@@ -72,7 +71,7 @@ let
       []
     );
 
-  allInputs = lib.remove null (nativeBuildInputs ++ buildInputs ++ pythonEnv.extraLibs ++ [ makeWrapper ]);
+  allInputs = lib.remove null (nativeBuildInputs ++ buildInputs ++ pythonEnv.extraLibs);
   transitiveDeps = lib.unique (builtins.concatLists (map transitiveClosure allInputs ));
   # fix differences between spkg and sage names
   # (could patch sage instead, but this is more lightweight and also works for packages depending on sage)
diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix
index 39591eceb40d..360fea56fedf 100644
--- a/nixpkgs/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix
@@ -46,8 +46,8 @@ mkOpenModelicaDerivation ({
 
   preFixup = ''
     for entry in $(find $out -name libipopt.so); do
-      patchelf --shrink-rpath --allowed-rpath-prefixes /nix/store $entry
-      patchelf --set-rpath '$ORIGIN':"$(patchelf --print-rpath $entry)" $entry
+      patchelf --shrink-rpath --allowed-rpath-prefixes "$NIX_STORE" "$entry"
+      patchelf --set-rpath '$ORIGIN':"$(patchelf --print-rpath $entry)" "$entry"
     done
   '';
 
diff --git a/nixpkgs/pkgs/applications/science/misc/reason-shell/default.nix b/nixpkgs/pkgs/applications/science/misc/reason-shell/default.nix
new file mode 100644
index 000000000000..aa1544669ed8
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/misc/reason-shell/default.nix
@@ -0,0 +1,40 @@
+{ lib
+, rustPlatform
+, fetchFromGitHub
+, pkg-config
+, openssl
+, stdenv
+, darwin
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "reason";
+  version = "0.3.10";
+
+  src = fetchFromGitHub {
+    owner = "jaywonchung";
+    repo = "reason";
+    rev = "v${version}";
+    hash = "sha256-oytRquZJgb1sfpZil1bSGwIIvm+5N4mkVmIMzWyzDco=";
+  };
+
+  cargoHash = "sha256-4AEuFSM2dY6UjjIFRU8ipkRMoEb2LjnOr3H6rZrLokE=";
+
+  nativeBuildInputs = [
+    pkg-config
+  ];
+
+  buildInputs = [
+    openssl
+  ] ++ lib.optionals stdenv.isDarwin [
+    darwin.apple_sdk.frameworks.CoreServices
+  ];
+
+  meta = with lib; {
+    description = "A shell for research papers";
+    homepage = "https://github.com/jaywonchung/reason";
+    changelog = "https://github.com/jaywonchung/reason/releases/tag/${src.rev}";
+    license = licenses.mit;
+    maintainers = with maintainers; [ figsoda ];
+  };
+}