Merge branch 'master' into staging-next

20 files changed, 57 insertions, 41 deletions

diff --git a/pkgs/applications/science/astronomy/gprojector/default.nix b/pkgs/applications/science/astronomy/gprojector/default.nix
index 3864058828f..26e8fe11a32 100644
--- a/pkgs/applications/science/astronomy/gprojector/default.nix
+++ b/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/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
index f6aa5e8892a..c04d6af080e 100644
--- a/pkgs/applications/science/biology/bcftools/default.nix
+++ b/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/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index 33d581ffd01..526a5b3ed33 100644
--- a/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/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/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix
index d1d6b436992..cc983e24618 100644
--- a/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/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 = "14.32.24";
   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-YxYNb2fS7KiUkZDSRx4FN+ZeMMNpfTaElitRE4RtD0g=";
   };
 
   patchPhase = ''
diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix
index 39bbae77a66..5f7c0c1f6be 100644
--- a/pkgs/applications/science/chemistry/pymol/default.nix
+++ b/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/pkgs/applications/science/electronics/diylc/default.nix b/pkgs/applications/science/electronics/diylc/default.nix
index 987f6156b4b..ff4e3809fc2 100644
--- a/pkgs/applications/science/electronics/diylc/default.nix
+++ b/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/pkgs/applications/science/electronics/eagle/eagle.nix b/pkgs/applications/science/electronics/eagle/eagle.nix
index 2fb3b8c8b18..5b4c8eb790f 100644
--- a/pkgs/applications/science/electronics/eagle/eagle.nix
+++ b/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/pkgs/applications/science/electronics/eagle/eagle7.nix b/pkgs/applications/science/electronics/eagle/eagle7.nix
index 94457c81ce9..f48d08d4079 100644
--- a/pkgs/applications/science/electronics/eagle/eagle7.nix
+++ b/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/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix
index bdd2796addc..29959be2fa9 100644
--- a/pkgs/applications/science/logic/coq/default.nix
+++ b/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/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix
index 0f041002425..96e8da059a4 100644
--- a/pkgs/applications/science/logic/isabelle/default.nix
+++ b/pkgs/applications/science/logic/isabelle/default.nix
@@ -114,7 +114,7 @@ stdenv.mkDerivation rec {
     icon = "isabelle";
     desktopName = "Isabelle";
     comment = meta.description;
-    categories = "Education;Science;Math;";
+    categories = [ "Education" "Science" "Math" ];
   };
 
   meta = with lib; {
diff --git a/pkgs/applications/science/logic/key/default.nix b/pkgs/applications/science/logic/key/default.nix
index 762acbe4ec4..85a7ecb08c3 100644
--- a/pkgs/applications/science/logic/key/default.nix
+++ b/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/pkgs/applications/science/logic/logisim-evolution/default.nix b/pkgs/applications/science/logic/logisim-evolution/default.nix
index 688c8c319bd..67e699bc63f 100644
--- a/pkgs/applications/science/logic/logisim-evolution/default.nix
+++ b/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/pkgs/applications/science/logic/logisim/default.nix b/pkgs/applications/science/logic/logisim/default.nix
index b4741aaed86..06dc024e6d2 100644
--- a/pkgs/applications/science/logic/logisim/default.nix
+++ b/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/pkgs/applications/science/logic/tlaplus/toolbox.nix b/pkgs/applications/science/logic/tlaplus/toolbox.nix
index 21c60d03ac1..7b1ee4384c9 100644
--- a/pkgs/applications/science/logic/tlaplus/toolbox.nix
+++ b/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/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix
index 78631486554..0f3dab8038e 100644
--- a/pkgs/applications/science/logic/why3/default.nix
+++ b/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/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix
index 7ebfe2030d4..8ab498c61d9 100644
--- a/pkgs/applications/science/math/geogebra/default.nix
+++ b/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/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix
index 76fc20c4b04..4306ae09151 100644
--- a/pkgs/applications/science/math/gmsh/default.nix
+++ b/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/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix
index 390a421c1a9..b3647e0f1b6 100644
--- a/pkgs/applications/science/misc/cwltool/default.nix
+++ b/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/pkgs/applications/science/misc/netlogo/default.nix b/pkgs/applications/science/misc/netlogo/default.nix
index b22c6294fba..ed92dfb90da 100644
--- a/pkgs/applications/science/misc/netlogo/default.nix
+++ b/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/pkgs/applications/science/programming/groove/default.nix b/pkgs/applications/science/programming/groove/default.nix
index 86d77072ee8..f4c323defd6 100644
--- a/pkgs/applications/science/programming/groove/default.nix
+++ b/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 {