Merge commit '3239fd2b8f728106491154b44625662e10259af2'

Conflicts:
	nixpkgs/pkgs/applications/window-managers/sway/default.nix

46 files changed, 352 insertions, 91 deletions

diff --git a/nixpkgs/pkgs/applications/science/astronomy/gprojector/default.nix b/nixpkgs/pkgs/applications/science/astronomy/gprojector/default.nix
index 3864058828f4..26e8fe11a32b 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/gprojector/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/gprojector/default.nix
@@ -22,8 +22,8 @@ stdenvNoCC.mkDerivation rec {
     exec = "gprojector";
     desktopName = "G.Projector";
     comment = meta.description;
-    categories = "Science;";
-    extraEntries = "StartupWMClass = gov-nasa-giss-projector-GProjector";
+    categories = [ "Science" ];
+    startupWMClass = "gov-nasa-giss-projector-GProjector";
   }) ];
 
   buildInputs = [ jre ];
diff --git a/nixpkgs/pkgs/applications/science/biology/angsd/default.nix b/nixpkgs/pkgs/applications/science/biology/angsd/default.nix
new file mode 100644
index 000000000000..02e00cd19ad6
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/angsd/default.nix
@@ -0,0 +1,25 @@
+{ lib, stdenv, fetchFromGitHub, htslib, zlib, bzip2, xz, curl, openssl }:
+
+stdenv.mkDerivation rec {
+  pname = "angsd";
+  version = "0.937";
+
+  src = fetchFromGitHub {
+    owner = "ANGSD";
+    repo = "angsd";
+    sha256 = "1020gh066dprqhfi90ywqzqqnq7awn49wrkkjnizmmab52v00kxs";
+    rev = "${version}";
+  };
+
+  buildInputs = [ htslib zlib bzip2 xz curl openssl ];
+
+  makeFlags = [ "HTSSRC=systemwide" "prefix=$(out)" ];
+
+  meta = with lib; {
+    description = "Program for analysing NGS data";
+    homepage = "http://www.popgen.dk/angsd";
+    maintainers = [ maintainers.bzizou ];
+    license = licenses.gpl2;
+  };
+}
+
diff --git a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix
index f6aa5e8892ac..c04d6af080e3 100644
--- a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "bcftools";
-  version = "1.14";
+  version = "1.15";
 
   src = fetchurl {
     url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2";
-    sha256 = "sha256-t++Iron8tVZYxb6i6MuOdWsFXhOGADbWvhN1Z4KqGcs=";
+    sha256 = "sha256-GIXMtFCobpegCqkF1zgcqeB72JZ8BXBaYdAAfS4iKW4=";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix
index 68cdd9f120bf..bbe661b4f0a0 100644
--- a/nixpkgs/pkgs/applications/science/biology/last/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "last";
-  version = "1260";
+  version = "1268";
 
   src = fetchFromGitLab {
     owner = "mcfrith";
     repo = "last";
     rev = version;
-    sha256 = "sha256-bJNvoHr2sQYtiC3tr1GA0T0kRhDyx6hU3OOSTvKUSCs=";
+    sha256 = "sha256-9yzeLg3xporl32sZ1Ks8s63jXJNGUiI64XyQmhbQF4M=";
   };
 
   nativeBuildInputs = [ unzip ];
@@ -24,8 +24,8 @@ stdenv.mkDerivation rec {
 
   meta = with lib; {
     description = "Genomic sequence aligner";
-    homepage = "http://last.cbrc.jp/";
-    license = licenses.gpl3;
+    homepage = "https://gitlab.com/mcfrith/last";
+    license = licenses.gpl3Plus;
     maintainers = with maintainers; [ jbedo ];
     platforms = platforms.x86_64;
   };
diff --git a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix
index bba8a02b76e3..7e162e2d27c6 100644
--- a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix
@@ -13,6 +13,8 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ zlib ];
 
+  makeFlags = lib.optionals stdenv.isAarch64 [ "arm_neon=1" "aarch64=1" ];
+
   installPhase = ''
     mkdir -p $out/bin
     cp minimap2 $out/bin
@@ -25,7 +27,6 @@ stdenv.mkDerivation rec {
     homepage = "https://lh3.github.io/minimap2";
     license = licenses.mit;
     platforms = platforms.all;
-    badPlatforms = platforms.aarch64;
     maintainers = [ maintainers.arcadio ];
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix
index 804407968e1c..4dc850f50627 100644
--- a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix
@@ -14,7 +14,7 @@
 }:
 
 stdenv.mkDerivation rec {
-  pname = "neuron";
+  pname = "neuron${lib.optionalString useMpi "-mpi"}";
   version = "7.5";
 
   nativeBuildInputs = [ which pkg-config automake autoconf libtool ];
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index 33d581ffd018..526a5b3ed33b 100644
--- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "picard-tools";
-  version = "2.26.10";
+  version = "2.26.11";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "sha256-hKBWRmzyMVXiEmsz/eYbVIUhezZdSJnBvcgv6ShPI5U=";
+    sha256 = "sha256-0swggo1a5gExpj3VgaWKT/TYd7rfSFBcqRrAURnTPjM=";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/biology/raxml/default.nix b/nixpkgs/pkgs/applications/science/biology/raxml/default.nix
index 6e747e318f57..d02d47266297 100644
--- a/nixpkgs/pkgs/applications/science/biology/raxml/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/raxml/default.nix
@@ -5,12 +5,12 @@
 }:
 
 stdenv.mkDerivation rec {
-  pname = "RAxML";
+  pname = "RAxML${lib.optionalString useMpi "-mpi"}";
   version = "8.2.12";
 
   src = fetchFromGitHub {
     owner = "stamatak";
-    repo = "standard-${pname}";
+    repo = "standard-RAxML";
     rev = "v${version}";
     sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh";
   };
diff --git a/nixpkgs/pkgs/applications/science/chemistry/d-seams/default.nix b/nixpkgs/pkgs/applications/science/chemistry/d-seams/default.nix
index f5e21db4b55a..74260bacabcc 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/d-seams/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/d-seams/default.nix
@@ -2,13 +2,13 @@
 , eigen, lua, luaPackages, liblapack, blas, lib, boost, gsl }:
 
 clangStdenv.mkDerivation rec {
-  version = "v1.0.1";
+  version = "1.0.1";
   pname = "d-SEAMS";
 
   src = fetchFromGitHub {
     owner = "d-SEAMS";
     repo = "seams-core";
-    rev = "v1.0.1";
+    rev = "v${version}";
     sha256 = "03zhhl9vhi3rhc3qz1g3zb89jksgpdlrk15fcr8xcz8pkj6r5b1i";
   };
 
diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
index d1d6b436992c..3f837edb4c8b 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
@@ -12,19 +12,27 @@ let
     exec = "jmol";
     desktopName = "JMol";
     genericName = "Molecular Modeler";
-    mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
-    categories = "Graphics;Education;Science;Chemistry;";
+    mimeTypes = [
+      "chemical/x-pdb"
+      "chemical/x-mdl-molfile"
+      "chemical/x-mol2"
+      "chemical/seq-aa-fasta"
+      "chemical/seq-na-fasta"
+      "chemical/x-xyz"
+      "chemical/x-mdl-sdf"
+    ];
+    categories = [ "Graphics" "Education" "Science" "Chemistry" ];
   };
 in
 stdenv.mkDerivation rec {
-  version = "14.32.21";
+  version = "14.32.30";
   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";
-    sha256 = "sha256-jJw/y6lQ0bvzOmwOhedufxK0Tuq9Pq6lIPZ97o03Zec=";
+    sha256 = "sha256-VpOoduUA0iD+nI83GSQYQDHoK2Snog0NHkHWHfpLqFM=";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
index 3c2b11c0e292..698095715cc5 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
@@ -4,12 +4,12 @@ with lib;
 
 stdenv.mkDerivation rec {
   pname = "marvin";
-  version = "22.3.0";
+  version = "22.7.0";
 
   src = fetchurl {
     name = "marvin-${version}.deb";
     url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb";
-    sha256 = "sha256-ASnweoVBYSnO/FjE9tpLgaOAgiPQeUnw7CzwkKRXnAg=";
+    sha256 = "sha256-xK4C+0/Qpc2vXPmsI8KuHuDJLmJ5LXdAfRIREE+gkWA=";
   };
 
   nativeBuildInputs = [ dpkg makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix
index 39bbae77a66e..5f7c0c1f6be7 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix
@@ -24,8 +24,16 @@ let
     genericName = "Molecular Modeler";
     comment = description;
     icon = pname;
-    mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
-    categories = "Graphics;Education;Science;Chemistry;";
+    mimeTypes = [
+      "chemical/x-pdb"
+      "chemical/x-mdl-molfile"
+      "chemical/x-mol2"
+      "chemical/seq-aa-fasta"
+      "chemical/seq-na-fasta"
+      "chemical/x-xyz"
+      "chemical/x-mdl-sdf"
+    ];
+    categories = [ "Graphics" "Education" "Science" "Chemistry" ];
   };
 in
 python3Packages.buildPythonApplication rec {
diff --git a/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix b/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix
new file mode 100644
index 000000000000..24d9f642ec56
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix
@@ -0,0 +1,30 @@
+{ lib, stdenv, fetchFromGitHub, cmake, wrapQtAppsHook, qtbase }:
+
+stdenv.mkDerivation rec {
+  pname = "QtRVSim";
+  version = "0.9.1";
+
+  src = fetchFromGitHub {
+    owner = "cvut";
+    repo = "qtrvsim";
+    rev = "refs/tags/v${version}";
+    sha256 = "AOksVS0drIBnK4RCxZw40yVxf4E8GjG9kU0rIZsY9gA=";
+  };
+
+  nativeBuildInputs = [ cmake wrapQtAppsHook ];
+
+  buildInputs = [ qtbase ];
+
+  meta = with lib; {
+    description = "RISC-V CPU simulator for education purposes";
+    longDescription = ''
+      RISC-V CPU simulator for education purposes with pipeline and cache visualization.
+      Developed at FEE CTU for computer architecture classes.
+    '';
+    homepage = "https://github.com/cvut/qtrvsim";
+    license = licenses.gpl3Plus;
+    platforms = platforms.linux ++ platforms.darwin;
+    maintainers = with maintainers; [ jdupak ];
+    mainProgram = "qtrvsim_gui";
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/electronics/diylc/default.nix b/nixpkgs/pkgs/applications/science/electronics/diylc/default.nix
index 987f6156b4b9..ff4e3809fc2b 100644
--- a/nixpkgs/pkgs/applications/science/electronics/diylc/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/diylc/default.nix
@@ -27,7 +27,7 @@ let
     comment = "Multi platform circuit layout and schematic drawing tool";
     exec = "diylc";
     icon = "diylc_icon";
-    categories = "Development;Electronics;";
+    categories = [ "Development" "Electronics" ];
   };
 in
 stdenv.mkDerivation rec {
diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
index 2fb3b8c8b18c..5b4c8eb790fe 100644
--- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
@@ -27,7 +27,7 @@ let
       comment = "Schematic capture and PCB layout";
       desktopName = "Eagle";
       genericName = "Schematic editor";
-      categories = "Development;";
+      categories = [ "Development" ];
     };
 
     buildInputs =
diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle7.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle7.nix
index 94457c81ce93..f48d08d40799 100644
--- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle7.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle7.nix
@@ -37,7 +37,7 @@ stdenv.mkDerivation rec {
     comment = "Schematic capture and PCB layout";
     desktopName = "Eagle";
     genericName = "Schematic editor";
-    categories = "Development;";
+    categories = [ "Development" ];
   };
 
   buildInputs =
diff --git a/nixpkgs/pkgs/applications/science/electronics/gaw/default.nix b/nixpkgs/pkgs/applications/science/electronics/gaw/default.nix
new file mode 100644
index 000000000000..928613737b47
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/electronics/gaw/default.nix
@@ -0,0 +1,34 @@
+{ stdenv
+, fetchurl
+, lib
+, gtk3
+, pkg-config
+}:
+
+stdenv.mkDerivation rec {
+  pname = "gaw";
+  version = "20200922";
+
+  src = fetchurl {
+    url = "https://download.tuxfamily.org/gaw/download/gaw3-${version}.tar.gz";
+    sha256 = "0qmap11v470a1yj4ypfvdq6wkfni77ijqpknka8b4fndi62sl4wa";
+  };
+
+  nativeBuildInputs = [ pkg-config ];
+
+  buildInputs = [ gtk3 ];
+
+  meta = with lib; {
+    description = "Gtk Analog Wave viewer";
+    longDescription = ''
+      Gaw is a software tool for displaying analog waveforms from
+      sampled datas, for example from the output of simulators or
+      input from sound cards. Data can be imported to gaw using files,
+      direct tcp/ip connection or directly from the sound card.
+    '';
+    homepage = "http://gaw.tuxfamily.org";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ fbeffa ];
+    platforms = platforms.all;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/electronics/xschem/default.nix b/nixpkgs/pkgs/applications/science/electronics/xschem/default.nix
new file mode 100644
index 000000000000..25fa0aca4677
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/electronics/xschem/default.nix
@@ -0,0 +1,46 @@
+{ stdenv
+, fetchFromGitHub
+, lib
+, bison
+, cairo
+, flex
+, libX11
+, libXpm
+, pkg-config
+, tcl
+, tk
+}:
+
+stdenv.mkDerivation rec {
+  pname = "xschem";
+  version = "3.0.0";
+
+  src = fetchFromGitHub {
+    owner = "StefanSchippers";
+    repo = "xschem";
+    rev = version;
+    sha256 = "sha256-C57jo8tAbiqQAgf4Xp2lpFGOr6F1knPpFcYxPiqSM4k=";
+  };
+
+  nativeBuildInputs = [ bison flex pkg-config ];
+
+  buildInputs = [ cairo libX11 libXpm tcl tk ];
+
+  hardeningDisable = [ "format" ];
+
+  meta = with lib; {
+    description = "Schematic capture and netlisting EDA tool";
+    longDescription = ''
+      Xschem is a schematic capture program, it allows creation of
+      hierarchical representation of circuits with a top down approach.
+      By focusing on interfaces, hierarchy and instance properties a
+      complex system can be described in terms of simpler building
+      blocks. A VHDL or Verilog or Spice netlist can be generated from
+      the drawn schematic, allowing the simulation of the circuit.
+    '';
+    homepage = "https://xschem.sourceforge.io/stefan/";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ fbeffa ];
+    platforms = platforms.all;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/logic/abc/default.nix b/nixpkgs/pkgs/applications/science/logic/abc/default.nix
index fe73f4f4d6e2..60454ca9ce99 100644
--- a/nixpkgs/pkgs/applications/science/logic/abc/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/abc/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname   = "abc-verifier";
-  version = "2021.11.12";
+  version = "2022.03.04";
 
   src = fetchFromGitHub {
     owner = "yosyshq";
     repo  = "abc";
-    rev   = "f6fa2ddcfc89099726d60386befba874c7ac1e0d";
-    hash  = "sha256-0rvMPZ+kL0m/GjlCLx3eXYQ0osQ2wQiS3+csqPl3U9s=";
+    rev   = "d7ecb23eeee9c9b4924182ce570c2e33eb18abff";
+    hash  = "sha256-aufWRTggJNOaUFsjh5+HFDqEur+nuM0hZSsTfGptbks=";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix
index 837f25e320f7..096a648b4ddf 100644
--- a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix
@@ -12,36 +12,33 @@ let
   };
 
   useDune2 = true;
-
-  nativeBuildInputs = [ which ];
-
 in
 
 let alt-ergo-lib = ocamlPackages.buildDunePackage rec {
   pname = "alt-ergo-lib";
-  inherit version src useDune2 nativeBuildInputs;
+  inherit version src useDune2;
   configureFlags = pname;
+  nativeBuildInputs = [ which ];
   buildInputs = with ocamlPackages; [ dune-configurator ];
   propagatedBuildInputs = with ocamlPackages; [ num ocplib-simplex stdlib-shims zarith ];
 }; in
 
 let alt-ergo-parsers = ocamlPackages.buildDunePackage rec {
   pname = "alt-ergo-parsers";
-  inherit version src useDune2 nativeBuildInputs;
+  inherit version src useDune2;
   configureFlags = pname;
-  buildInputs = with ocamlPackages; [ menhir ];
+  nativeBuildInputs = [ which ocamlPackages.menhir ];
   propagatedBuildInputs = [ alt-ergo-lib ] ++ (with ocamlPackages; [ camlzip psmt2-frontend ]);
 }; in
 
 ocamlPackages.buildDunePackage {
 
-  inherit pname version src useDune2 nativeBuildInputs;
+  inherit pname version src useDune2;
 
   configureFlags = pname;
 
-  buildInputs = [ alt-ergo-parsers ] ++ (with ocamlPackages; [
-    cmdliner menhir ])
-  ;
+  nativeBuildInputs = [ which ocamlPackages.menhir ];
+  buildInputs = [ alt-ergo-parsers ocamlPackages.cmdliner ];
 
   meta = {
     description = "High-performance theorem prover and SMT solver";
diff --git a/nixpkgs/pkgs/applications/science/logic/anders/default.nix b/nixpkgs/pkgs/applications/science/logic/anders/default.nix
index 72e412fc3bdc..bb60b2b8321a 100644
--- a/nixpkgs/pkgs/applications/science/logic/anders/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/anders/default.nix
@@ -13,7 +13,10 @@ ocamlPackages.buildDunePackage rec {
     sha256 = "sha256-JUiZoo2rNLfgs94TlJqUNzul/7ODisCjSFAzhgSp1z4=";
   };
 
-  buildInputs = with ocamlPackages; [ zarith menhir ];
+  strictDeps = true;
+
+  nativeBuildInputs = [ ocamlPackages.menhir ];
+  buildInputs = [ ocamlPackages.zarith ];
 
   meta = with lib; {
     description = "Modal Homotopy Type System";
diff --git a/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/nixpkgs/pkgs/applications/science/logic/coq/default.nix
index bdd2796addcd..29959be2fa97 100644
--- a/nixpkgs/pkgs/applications/science/logic/coq/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/coq/default.nix
@@ -69,7 +69,9 @@ let
       { case = range "8.7" "8.10";  out = ocamlPackages_4_09; }
       { case = range "8.5" "8.6";   out = ocamlPackages_4_05; }
     ] ocamlPackages_4_12;
-  ocamlBuildInputs = [ ocamlPackages.ocaml ocamlPackages.findlib ]
+  ocamlNativeBuildInputs = [ ocamlPackages.ocaml ocamlPackages.findlib ]
+    ++ optional (versionAtLeast "8.14") ocamlPackages.dune_2;
+  ocamlBuildInputs = []
     ++ optional (!versionAtLeast "8.10") ocamlPackages.camlp5
     ++ optional (!versionAtLeast "8.13") ocamlPackages.num
     ++ optional (versionAtLeast "8.13") ocamlPackages.zarith;
@@ -79,7 +81,7 @@ self = stdenv.mkDerivation {
 
   passthru = {
     inherit coq-version;
-    inherit ocamlPackages ocamlBuildInputs;
+    inherit ocamlPackages ocamlBuildInputs ocamlNativeBuildInputs;
     # For compatibility
     inherit (ocamlPackages) ocaml camlp5 findlib num ;
     emacsBufferSetup = pkgs: ''
@@ -129,6 +131,7 @@ self = stdenv.mkDerivation {
   };
 
   nativeBuildInputs = [ pkg-config ]
+    ++ ocamlNativeBuildInputs
     ++ optional buildIde copyDesktopItems
     ++ optional (buildIde && versionAtLeast "8.10") wrapGAppsHook
     ++ optional (!versionAtLeast "8.6") gnumake42;
@@ -137,7 +140,6 @@ self = stdenv.mkDerivation {
       (if versionAtLeast "8.10"
        then [ ocamlPackages.lablgtk3-sourceview3 glib gnome.adwaita-icon-theme ]
        else [ ocamlPackages.lablgtk ])
-    ++ optional (versionAtLeast "8.14") ocamlPackages.dune_2
   ;
 
   postPatch = ''
@@ -168,7 +170,7 @@ self = stdenv.mkDerivation {
 
   prefixKey = "-prefix ";
 
-  buildFlags = [ "revision" "coq" "coqide" ] ++ optional (!versionAtLeast "8.14") "bin/votour";
+  buildFlags = [ "revision" "coq" ] ++ optional buildIde "coqide" ++ optional (!versionAtLeast "8.14") "bin/votour";
   enableParallelBuilding = true;
 
   createFindlibDestdir = true;
@@ -179,7 +181,7 @@ self = stdenv.mkDerivation {
     icon = "coq";
     desktopName = "CoqIDE";
     comment = "Graphical interface for the Coq proof assistant";
-    categories = "Development;Science;Math;IDE;GTK";
+    categories = [ "Development" "Science" "Math" "IDE" "GTK" ];
   });
 
   postInstall = let suffix = if versionAtLeast "8.14" then "-core" else ""; in ''
diff --git a/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix b/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix
index 0f0410024251..aaac288b615d 100644
--- a/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, coreutils, nettools, java, polyml, z3, veriT, vampire, eprover-ho, rlwrap, makeDesktopItem }:
+{ lib, stdenv, fetchurl, coreutils, nettools, java, scala, polyml, z3, veriT, vampire, eprover-ho, rlwrap, perl, makeDesktopItem }:
 # nettools needed for hostname
 
 stdenv.mkDerivation rec {
@@ -77,6 +77,10 @@ stdenv.mkDerivation rec {
     substituteInPlace lib/Tools/env \
       --replace /usr/bin/env ${coreutils}/bin/env
 
+    substituteInPlace src/Tools/Setup/src/Environment.java \
+      --replace 'cmd.add("/usr/bin/env");' "" \
+      --replace 'cmd.add("bash");' "cmd.add(\"$SHELL\");"
+
     rm -r heaps
   '' + (if ! stdenv.isLinux then "" else ''
     arch=${if stdenv.hostPlatform.system == "x86_64-linux" then "x86_64-linux" else "x86-linux"}
@@ -90,6 +94,24 @@ stdenv.mkDerivation rec {
 
   buildPhase = ''
     export HOME=$TMP # The build fails if home is not set
+    setup_name=$(basename contrib/isabelle_setup*)
+
+    #The following is adapted from https://isabelle.sketis.net/repos/isabelle/file/Isabelle2021-1/Admin/lib/Tools/build_setup
+    TARGET_DIR="contrib/$setup_name/lib"
+    rm -rf "$TARGET_DIR"
+    mkdir -p "$TARGET_DIR/isabelle/setup"
+    declare -a ARGS=("-Xlint:unchecked")
+
+    SOURCES="$(${perl}/bin/perl -e 'while (<>) { if (m/(\S+\.java)/)  { print "$1 "; } }' "src/Tools/Setup/etc/build.props")"
+    for SRC in $SOURCES
+    do
+      ARGS["''${#ARGS[@]}"]="src/Tools/Setup/$SRC"
+    done
+    ${java}/bin/javac -d "$TARGET_DIR" -classpath ${scala}/lib/scala-compiler.jar "''${ARGS[@]}"
+    ${java}/bin/jar -c -f "$TARGET_DIR/isabelle_setup.jar" -e "isabelle.setup.Setup" -C "$TARGET_DIR" isabelle
+    rm -rf "$TARGET_DIR/isabelle"
+
+    # Prebuild HOL Session
     bin/isabelle build -v -o system_heaps -b HOL
   '';
 
@@ -114,7 +136,7 @@ stdenv.mkDerivation rec {
     icon = "isabelle";
     desktopName = "Isabelle";
     comment = meta.description;
-    categories = "Education;Science;Math;";
+    categories = [ "Education" "Science" "Math" ];
   };
 
   meta = with lib; {
diff --git a/nixpkgs/pkgs/applications/science/logic/key/default.nix b/nixpkgs/pkgs/applications/science/logic/key/default.nix
index 762acbe4ec44..85a7ecb08c39 100644
--- a/nixpkgs/pkgs/applications/science/logic/key/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/key/default.nix
@@ -61,7 +61,7 @@ in stdenv.mkDerivation rec {
       comment = meta.description;
       desktopName = "KeY";
       genericName = "KeY";
-      categories = "Science;";
+      categories = [ "Science" ];
     })
   ];
 
diff --git a/nixpkgs/pkgs/applications/science/logic/lean/default.nix b/nixpkgs/pkgs/applications/science/logic/lean/default.nix
index 22e755bd852e..1eea97a0fd23 100644
--- a/nixpkgs/pkgs/applications/science/logic/lean/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/lean/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   pname = "lean";
-  version = "3.39.2";
+  version = "3.41.0";
 
   src = fetchFromGitHub {
     owner  = "leanprover-community";
@@ -11,8 +11,8 @@ stdenv.mkDerivation rec {
     # from. this is then used to check whether an olean file should be
     # rebuilt. don't use a tag as rev because this will get replaced into
     # src/githash.h.in in preConfigure.
-    rev    = "402f41cdedbd46a368fb7807bebe83550d887631";
-    sha256 = "0jddakr07ixspw19xblpj1882vxxaljg3fflhn4myvigwzkav334";
+    rev    = "154ac72f4ff674bc4486ac611f926a3d6b999f9f";
+    sha256 = "0mpxlfjq460x1vi3v6qzgjv74asg0qlhykd51pj347795x5b1hf1";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/logic/logisim-evolution/default.nix b/nixpkgs/pkgs/applications/science/logic/logisim-evolution/default.nix
index 688c8c319bd8..67e699bc63fa 100644
--- a/nixpkgs/pkgs/applications/science/logic/logisim-evolution/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/logisim-evolution/default.nix
@@ -20,7 +20,7 @@ stdenv.mkDerivation rec {
       exec = "logisim-evolution";
       icon = "logisim-evolution";
       comment = meta.description;
-      categories = "Education;";
+      categories = [ "Education" ];
     })
   ];
 
diff --git a/nixpkgs/pkgs/applications/science/logic/logisim/default.nix b/nixpkgs/pkgs/applications/science/logic/logisim/default.nix
index b4741aaed86e..06dc024e6d23 100644
--- a/nixpkgs/pkgs/applications/science/logic/logisim/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/logisim/default.nix
@@ -20,7 +20,7 @@ stdenv.mkDerivation rec {
       exec = "logisim";
       icon = "logisim";
       comment = meta.description;
-      categories = "Education;";
+      categories = [ "Education" ];
     })
   ];
 
diff --git a/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix b/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix
index e701fb2711f0..ef6f9b157d2f 100644
--- a/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix
@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   pname = "opensmt";
-  version = "2.2.0";
+  version = "2.3.0";
 
   src = fetchFromGitHub {
     owner = "usi-verification-and-security";
     repo = "opensmt";
     rev = "v${version}";
-    sha256 = "sha256-6VkBGDzqG3mplpvFh5DIR0I1I2/J0Pi7xYk/yVn04Kg=";
+    sha256 = "sha256-5Gw9+J+3LHNUNbcHxsQR/ivWndL2P7yBt/Q35fBMg58=";
   };
 
   nativeBuildInputs = [ cmake bison flex ];
diff --git a/nixpkgs/pkgs/applications/science/logic/tlaplus/tlaps.nix b/nixpkgs/pkgs/applications/science/logic/tlaplus/tlaps.nix
index 90a4aeb4f8ab..14b3055ab36b 100644
--- a/nixpkgs/pkgs/applications/science/logic/tlaplus/tlaps.nix
+++ b/nixpkgs/pkgs/applications/science/logic/tlaplus/tlaps.nix
@@ -11,10 +11,10 @@
 
 stdenv.mkDerivation rec {
   pname = "tlaps";
-  version = "1.4.3";
+  version = "1.4.5";
   src = fetchurl {
-    url = "https://tla.msr-inria.inria.fr/tlaps/dist/current/tlaps-${version}.tar.gz";
-    sha256 = "1w5z3ns5xxmhmp8r4x2kjmy3clqam935gmvx82imyxrr1bamx6gf";
+    url = "https://tla.msr-inria.inria.fr/tlaps/dist/${version}/tlaps-${version}.tar.gz";
+    sha256 = "c296998acd14d5b93a8d5be7ee178007ef179957465966576bda26944b1b7fca";
   };
 
   buildInputs = [ ocaml isabelle cvc3 perl wget which ];
@@ -52,7 +52,7 @@ stdenv.mkDerivation rec {
     homepage = "https://tla.msr-inria.inria.fr/tlaps/content/Home.html";
     license = lib.licenses.bsd2;
     platforms = lib.platforms.unix;
-    maintainers = [ ];
+    maintainers = with lib.maintainers; [ florentc ];
   };
 
 }
diff --git a/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix b/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
index 21c60d03ac1e..7b1ee4384c9e 100644
--- a/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
+++ b/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
@@ -18,10 +18,8 @@ let
     comment = "IDE for TLA+";
     desktopName = name;
     genericName = comment;
-    categories = "Development";
-    extraEntries = ''
-      StartupWMClass=TLA+ Toolbox
-    '';
+    categories = [ "Development" ];
+    startupWMClass = "TLA+ Toolbox";
   };
 
 
diff --git a/nixpkgs/pkgs/applications/science/logic/why3/default.nix b/nixpkgs/pkgs/applications/science/logic/why3/default.nix
index 78631486554a..0f3dab8038ee 100644
--- a/nixpkgs/pkgs/applications/science/logic/why3/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/why3/default.nix
@@ -3,15 +3,15 @@
 
 stdenv.mkDerivation rec {
   pname = "why3";
-  version = "1.4.0";
+  version = "1.4.1";
 
   src = fetchurl {
-    url = "https://gforge.inria.fr/frs/download.php/file/38425/why3-${version}.tar.gz";
-    sha256 = "0lw0cpx347zz9vvwqibmbxgs80fsd16scgk3isscvwxnajpc3rv8";
+    url = "https://why3.gitlabpages.inria.fr/releases/${pname}-${version}.tar.gz";
+    sha256 = "sha256:1rqyypzlvagrn43ykl0c5wxyvnry5fl1ykn3xcvlzgghk96yq3jq";
   };
 
   buildInputs = with ocamlPackages; [
-    ocaml findlib ocamlgraph zarith menhir menhirLib
+    ocaml findlib ocamlgraph zarith menhir
     # Emacs compilation of why3.el
     emacs
     # Documentation
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
     coqPackages.coq coqPackages.flocq
   ];
 
-  propagatedBuildInputs = with ocamlPackages; [ camlzip num re sexplib ];
+  propagatedBuildInputs = with ocamlPackages; [ camlzip menhirLib num re sexplib ];
 
   enableParallelBuilding = true;
 
diff --git a/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix b/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix
index 2829cb59340b..0c20faceb54e 100644
--- a/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "workcraft";
-  version = "3.3.5";
+  version = "3.3.6";
 
   src = fetchurl {
     url = "https://github.com/workcraft/workcraft/releases/download/v${version}/workcraft-v${version}-linux.tar.gz";
-    sha256 = "sha256-KErKYK3mmjp5uNdGQnjzUUIEwXT5fqbAPUunH72Mtig=";
+    sha256 = "sha256-5J4HOTz92ALUcZZr15jJ6vplc3KDwbFCXqjEhlOV4kE=";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/math/geogebra/default.nix b/nixpkgs/pkgs/applications/science/math/geogebra/default.nix
index 7ebfe2030d4a..8ab498c61d93 100644
--- a/nixpkgs/pkgs/applications/science/math/geogebra/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/geogebra/default.nix
@@ -15,8 +15,8 @@ let
     desktopName = "Geogebra";
     genericName = "Geogebra";
     comment = meta.description;
-    categories = "Education;Science;Math;";
-    mimeType = "application/vnd.geogebra.file;application/vnd.geogebra.tool;";
+    categories = [ "Education" "Science" "Math" ];
+    mimeTypes = [ "application/vnd.geogebra.file" "application/vnd.geogebra.tool" ];
   };
 
   meta = with lib; {
diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
index 76fc20c4b048..4306ae091515 100644
--- a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
@@ -5,11 +5,11 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "gmsh";
-  version = "4.9.4";
+  version = "4.9.5";
 
   src = fetchurl {
     url = "https://gmsh.info/src/gmsh-${version}-source.tgz";
-    sha256 = "sha256-rP8zQtGQfEKaS+PkWW7UT2zUP9WpSrdWZ/SGPNzy92k=";
+    sha256 = "sha256-/9ZJAIRCCHGciNkaZsKBiJAjEyt6nigsUVSMufbzrUQ=";
   };
 
   buildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix
index 91ee7c1c65e0..dc947a94001b 100644
--- a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gurobi";
-  version = "9.1.2";
+  version = "9.5.0";
 
   src = fetchurl {
     url = "https://packages.gurobi.com/${lib.versions.majorMinor version}/gurobi${version}_linux64.tar.gz";
-    sha256 = "7f60bd675f79476bb2b32cd632aa1d470f8246f2b033b7652d8de86f6e7e429b";
+    sha256 = "sha256-u1QuWl0WhfbjZOrwXqbFVySF/8N6IkUWnPPLQCiLwp4=";
   };
 
   sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64";
diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
index 03f4b223803c..7ba5838faba1 100644
--- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "qalculate-gtk";
-  version = "3.22.0";
+  version = "4.0.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "sha256-BarbO25c103YImOOnjVgwgqpa3mUVvndgJeUHRf2I60=";
+    sha256 = "sha256-l9lR5MVHWiRz5RG/I/nXRY4GQSSaXXP7PlRNoAu9+yo=";
   };
 
   hardeningDisable = [ "format" ];
diff --git a/nixpkgs/pkgs/applications/science/math/sage/default.nix b/nixpkgs/pkgs/applications/science/math/sage/default.nix
index 2066087692a0..70e24e2608d0 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/default.nix
@@ -1,5 +1,7 @@
 { pkgs
 , withDoc ? false
+, requireSageTests ? true
+, extraPythonPackages ? ps: []
 }:
 
 # Here sage and its dependencies are put together. Some dependencies may be pinned
@@ -109,7 +111,7 @@ let
     rpy2
     sphinx
     pillow
-  ];
+  ] ++ extraPythonPackages python3.pkgs;
 
   pythonEnv = python3.buildEnv.override {
     extraLibs = pythonRuntimeDeps;
@@ -166,5 +168,5 @@ in
 # A wrapper around sage that makes sure sage finds its docs (if they were build).
 callPackage ./sage.nix {
   inherit sage-tests sage-with-env sagedoc jupyter-kernel-definition;
-  inherit withDoc;
+  inherit withDoc requireSageTests;
 }
diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/tachyon-renamed-focallength.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/tachyon-renamed-focallength.patch
new file mode 100644
index 000000000000..5fea88309036
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/math/sage/patches/tachyon-renamed-focallength.patch
@@ -0,0 +1,81 @@
+diff --git a/src/sage/interfaces/tachyon.py b/src/sage/interfaces/tachyon.py
+index 3f1dcdb538..b6fa8d1fbd 100644
+--- a/src/sage/interfaces/tachyon.py
++++ b/src/sage/interfaces/tachyon.py
+@@ -261,13 +261,13 @@ written in the sequence they are listed in the examples in this section.
+   The {\bf PROJECTION} keyword must be followed by one of the supported
+ camera projection mode identifiers {\bf PERSPECTIVE}, {\bf PERSPECTIVE_DOF},
+ {\bf ORTHOGRAPHIC}, or {\bf FISHEYE}.  The {\bf FISHEYE} projection mode
+-requires two extra parameters {\bf FOCALLENGTH} and {\bf APERTURE}
++requires two extra parameters {\bf FOCALDIST} and {\bf APERTURE}
+ which precede the regular camera options.
+ 
+ \begin{verbatim}
+ Camera
+   projection perspective_dof
+-  focallength 0.75
++  focaldist 0.75
+   aperture 0.02
+   Zoom 0.666667
+   Aspectratio 1.000000
+diff --git a/src/sage/plot/plot3d/tachyon.py b/src/sage/plot/plot3d/tachyon.py
+index 08caf38d67..3e827411ce 100644
+--- a/src/sage/plot/plot3d/tachyon.py
++++ b/src/sage/plot/plot3d/tachyon.py
+@@ -92,7 +92,7 @@ angle, right angle)::
+ Finally there is the ``projection='perspective_dof'`` option. ::
+ 
+     sage: T = Tachyon(xres=800, antialiasing=4, raydepth=10,
+-    ....: projection='perspective_dof', focallength='1.0', aperture='.0025')
++    ....: projection='perspective_dof', focaldist='1.0', aperture='.0025')
+     sage: T.light((0,5,7), 1.0, (1,1,1))
+     sage: T.texture('t1', opacity=1, specular=.3)
+     sage: T.texture('t2', opacity=1, specular=.3, color=(0,0,1))
+@@ -186,7 +186,7 @@ class Tachyon(WithEqualityById, SageObject):
+       or ``'fisheye'``.
+     - ``frustum`` - (default ''), otherwise list of four numbers. Only
+       used with projection='fisheye'.
+-    - ``focallength`` - (default ''), otherwise a number. Only used
++    - ``focaldist`` - (default ''), otherwise a number. Only used
+       with projection='perspective_dof'.
+     - ``aperture`` - (default ''), otherwise a number.  Only used
+       with projection='perspective_dof'.
+@@ -331,7 +331,7 @@ class Tachyon(WithEqualityById, SageObject):
+     Use of the ``projection='perspective_dof'`` option.  This may not be
+     implemented correctly. ::
+ 
+-        sage: T = Tachyon(xres=800,antialiasing=4, raydepth=10, projection='perspective_dof', focallength='1.0', aperture='.0025')
++        sage: T = Tachyon(xres=800,antialiasing=4, raydepth=10, projection='perspective_dof', focaldist='1.0', aperture='.0025')
+         sage: T.light((0,5,7), 1.0, (1,1,1))
+         sage: T.texture('t1', opacity=1, specular=.3)
+         sage: T.texture('t2', opacity=1, specular=.3, color=(0,0,1))
+@@ -365,7 +365,7 @@ class Tachyon(WithEqualityById, SageObject):
+                  look_at=[0, 0, 0],
+                  viewdir=None,
+                  projection='PERSPECTIVE',
+-                 focallength='',
++                 focaldist='',
+                  aperture='',
+                  frustum=''):
+         r"""
+@@ -391,7 +391,7 @@ class Tachyon(WithEqualityById, SageObject):
+             self._camera_position = (-3, 0, 0) # default value
+         self._updir = updir
+         self._projection = projection
+-        self._focallength = focallength
++        self._focaldist = focaldist
+         self._aperture = aperture
+         self._frustum = frustum
+         self._objects = []
+@@ -624,9 +624,9 @@ class Tachyon(WithEqualityById, SageObject):
+         camera_out = r"""
+            camera
+               projection %s""" % (tostr(self._projection))
+-        if self._focallength != '':
++        if self._focaldist != '':
+             camera_out = camera_out + r"""
+-              focallength %s""" % (float(self._focallength))
++              focaldist %s""" % (float(self._focaldist))
+         if self._aperture != '':
+             camera_out = camera_out + r"""
+               aperture %s""" % (float(self._aperture))
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
index 73a5881d2142..bae33802d301 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
@@ -155,6 +155,9 @@ stdenv.mkDerivation rec {
       rev = "97d7958bed441cf2ccc714d88f83d3a8426bc085";
       sha256 = "sha256-y1STE0oxswnijGCsBw8eHWWqpmT1XMznIfA0vvX9pFA=";
     })
+
+    # adapted from https://trac.sagemath.org/ticket/23712#comment:22
+    ./patches/tachyon-renamed-focallength.patch
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage.nix b/nixpkgs/pkgs/applications/science/math/sage/sage.nix
index 5805a5c7b0c7..96122fba5ab4 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage.nix
@@ -6,6 +6,7 @@
 , jupyter-kernel
 , sagedoc
 , withDoc
+, requireSageTests
 }:
 
 # A wrapper that makes sure sage finds its docs (if they were build) and the
@@ -26,7 +27,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     makeWrapper
-
+  ] ++ lib.optionals requireSageTests [
     # This is a hack to make sure sage-tests is evaluated. It doesn't acutally
     # produce anything of value, it just decouples the tests from the build.
     sage-tests
diff --git a/nixpkgs/pkgs/applications/science/misc/cwltool/default.nix b/nixpkgs/pkgs/applications/science/misc/cwltool/default.nix
index 390a421c1a92..b3647e0f1b60 100644
--- a/nixpkgs/pkgs/applications/science/misc/cwltool/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/cwltool/default.nix
@@ -7,14 +7,14 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "cwltool";
-  version = "3.1.20220217222804";
+  version = "3.1.20220221074232";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "common-workflow-language";
     repo = pname;
     rev = version;
-    sha256 = "sha256-7zID/lChliEJxu6Dawz9DNP2YvSwtMo8G+ooXNh2Phc=";
+    sha256 = "sha256-hUdwtqYHcfyJ68LzwwCXAxr7YIkJm64brb+kA/WJqU8=";
   };
 
   postPatch = ''
diff --git a/nixpkgs/pkgs/applications/science/misc/netlogo/default.nix b/nixpkgs/pkgs/applications/science/misc/netlogo/default.nix
index b22c6294fba6..ed92dfb90dab 100644
--- a/nixpkgs/pkgs/applications/science/misc/netlogo/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/netlogo/default.nix
@@ -8,7 +8,7 @@ let
     icon = name;
     comment = "A multi-agent programmable modeling environment";
     desktopName = "NetLogo";
-    categories = "Science;";
+    categories = [ "Science" ];
   };
 
 in
diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix
index f8037c01e087..872438158d66 100644
--- a/nixpkgs/pkgs/applications/science/misc/root/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix
@@ -107,7 +107,7 @@ stdenv.mkDerivation rec {
 
     # Hardcode path to fix use with cmake
     sed -i cmake/scripts/ROOTConfig.cmake.in \
-      -e 'iset(nlohmann_json_DIR "${nlohmann_json}/lib/cmake/nlohmann_json/")'
+      -e '1iset(nlohmann_json_DIR "${nlohmann_json}/lib/cmake/nlohmann_json/")'
 
     patchShebangs build/unix/
   '' + lib.optionalString noSplash ''
diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
index dd4bb6ef1425..69810f95b846 100644
--- a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
@@ -19,11 +19,11 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "gromacs";
-  version = "2021.5";
+  version = "2022";
 
   src = fetchurl {
     url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz";
-    sha256 = "1dh9l2gcv61h1r6qsg8vr3k1xp8jgd27czzg24kzf4k823k3z9pb";
+    sha256 = "0s1bv8nvmdpiyk2yhcmzq8q936hm5jgnqb393101drh2dih0vmps";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/programming/groove/default.nix b/nixpkgs/pkgs/applications/science/programming/groove/default.nix
index 86d77072ee8c..f4c323defd6f 100644
--- a/nixpkgs/pkgs/applications/science/programming/groove/default.nix
+++ b/nixpkgs/pkgs/applications/science/programming/groove/default.nix
@@ -7,7 +7,7 @@ let
     icon = "groove";
     desktopName = "GROOVE Simulator";
     comment = "GRaphs for Object-Oriented VErification";
-    categories = "Science;ComputerScience;";
+    categories = [ "Science" "ComputerScience" ];
   };
 
 in stdenv.mkDerivation rec {
diff --git a/nixpkgs/pkgs/applications/science/robotics/mission-planner/default.nix b/nixpkgs/pkgs/applications/science/robotics/mission-planner/default.nix
index 3dbb1a4bf5af..3f0a6a6cde50 100644
--- a/nixpkgs/pkgs/applications/science/robotics/mission-planner/default.nix
+++ b/nixpkgs/pkgs/applications/science/robotics/mission-planner/default.nix
@@ -12,11 +12,11 @@ let
   };
 in stdenv.mkDerivation rec {
   inherit pname;
-  version = "1.3.74";
+  version = "1.3.76";
 
   src = fetchurl {
     url = "https://firmware.ardupilot.org/Tools/MissionPlanner/MissionPlanner-${version}.zip";
-    sha256 = "1cgpmsmmnbzw1lwsdafp8yklk1rwc61yf12vc1ahcc6bl7q2385x";
+    sha256 = "sha256-vdunUGwLjDKf1LDhtyTQAExddecyWc1TdZOyuu0qMlk=";
   };
 
   nativeBuildInputs = [ makeWrapper mono unzip ];