Merge commit 'b3c692172e5b5241b028a98e1977f9fb12eeaf42'

9 files changed, 167 insertions, 30 deletions

diff --git a/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix
index 0d23489696f1..d2615b391ffc 100644
--- a/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, gtest, fetchFromGitHub, cmake, boost, eigen, python, vtk, zlib, tbb }:
+{ lib, stdenv, gtest, fetchFromGitHub, cmake, boost, eigen, python3, vtk, zlib, tbb }:
 
 stdenv.mkDerivation rec {
   version = "2.0.0";
@@ -32,7 +32,7 @@ stdenv.mkDerivation rec {
   '';
 
   nativeBuildInputs = [ cmake gtest ];
-  buildInputs = [ boost eigen python vtk zlib tbb ];
+  buildInputs = [ boost eigen python3 vtk zlib tbb ];
 
   meta = with lib; {
     homepage = "https://github.com/BioMedIA/MIRTK";
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix
new file mode 100644
index 000000000000..1130f5c44e70
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix
@@ -0,0 +1,68 @@
+{ lib, stdenv, fetchFromGitHub, cmake, zlib, eigen, libGL, doxygen, spglib
+, mmtf-cpp, glew, python3, libarchive, libmsym, msgpack, qttools, wrapQtAppsHook
+}:
+
+let
+  pythonWP = python3.withPackages (p: with p; [ openbabel-bindings numpy ]);
+
+  # Pure data repositories
+  moleculesRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "molecules";
+    rev = "1.0.0";
+    sha256 = "guY6osnpv7Oqt+HE1BpIqL10POp+x8GAci2kY0bLmqg=";
+  };
+  crystalsRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "crystals";
+    rev = "1.0.1";
+    sha256 = "sH/WuvLaYu6akOc3ssAKhnxD8KNoDxuafDSozHqJZC4=";
+  };
+
+in stdenv.mkDerivation rec {
+  pname = "avogadrolibs";
+  version = "1.94.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = pname;
+    rev = version;
+    sha256 = "6bChJhqrjOxeEWZBNToq3JExHPu7DUMsEHWBDe75zAo=";
+  };
+
+  postUnpack = ''
+    cp -r ${moleculesRepo} molecules
+    cp -r ${crystalsRepo} crystals
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    eigen
+    zlib
+    libGL
+    spglib
+    mmtf-cpp
+    glew
+    libarchive
+    libmsym
+    msgpack
+    qttools
+  ];
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/${pname}/AvogadroLibsConfig.cmake \
+      --replace "''${AvogadroLibs_INSTALL_PREFIX}/$out" "''${AvogadroLibs_INSTALL_PREFIX}"
+  '';
+
+  meta = with lib; {
+    description = "Molecule editor and visualizer";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/avogadrolibs";
+    platforms = platforms.linux;
+    license = licenses.gpl2Only;
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/libmsym/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/libmsym/default.nix
new file mode 100644
index 000000000000..8c605f3e07d4
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/libmsym/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, lib, fetchFromGitHub, cmake } :
+
+stdenv.mkDerivation rec {
+  pname = "libmsym";
+  version = "0.2.3";
+
+  src = fetchFromGitHub  {
+    owner = "mcodev31";
+    repo = pname;
+    rev = "v${version}";
+    sha256= "k+OEwrA/saupP/wX6Ii5My0vffiJ0X9xMCTrliMSMik=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with lib; {
+    description = " molecular point group symmetry lib";
+    homepage = "https://github.com/rcsb/mmtf-cpp";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix
new file mode 100644
index 000000000000..ec1fed68ff93
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, lib, fetchFromGitHub, cmake, msgpack } :
+
+stdenv.mkDerivation rec {
+  pname = "mmtf-cpp";
+  version = "1.0.0";
+
+  src = fetchFromGitHub  {
+    owner = "rcsb";
+    repo = pname;
+    rev = "v${version}";
+    sha256= "17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ msgpack ];
+
+  meta = with lib; {
+    description = "A library of exchange-correlation functionals with arbitrary-order derivatives";
+    homepage = "https://github.com/rcsb/mmtf-cpp";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/molequeue/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/molequeue/default.nix
new file mode 100644
index 000000000000..1e8ca2d961d3
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/molequeue/default.nix
@@ -0,0 +1,33 @@
+{ lib, stdenv, fetchFromGitHub, cmake, qttools, wrapQtAppsHook }:
+
+stdenv.mkDerivation rec {
+  pname = "molequeue";
+  version = "0.9.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = pname;
+    rev = version;
+    sha256 = "+NoY8YVseFyBbxc3ttFWiQuHQyy1GN8zvV1jGFjmvLg=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [ qttools ];
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/molequeue/MoleQueueConfig.cmake \
+      --replace "''${MoleQueue_INSTALL_PREFIX}/$out" "''${MoleQueue_INSTALL_PREFIX}"
+  '';
+
+  meta = with lib; {
+    description = "Desktop integration of high performance computing resources";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/molequeue";
+    platforms = platforms.linux;
+    license = licenses.bsd3;
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
index 79e494a053b8..f81a02303a60 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
@@ -1,23 +1,20 @@
-{
-  lib, stdenv,
-  fetchFromGitHub,
-  gfortran,
-  cmake,
-  shared ? true
+{ lib
+, stdenv
+, fetchFromGitHub
+, gfortran
+, cmake
+, shared ? true
 }:
-let
-  inherit (lib) optional;
-in
 
 stdenv.mkDerivation rec {
   pname = "liblapack";
-  version = "3.9.1";
+  version = "3.10.0";
 
   src = fetchFromGitHub {
     owner = "Reference-LAPACK";
     repo = "lapack";
     rev = "v${version}";
-    sha256 = "sha256-B7eRaEY9vaLvuKkJ7d2KWanGE7OXh43O0UbXFheUWK8=";
+    sha256 = "sha256-ewYUM+M7jDO5LLnB4joiKkqgXjEDmWbFZbgad8x98gc=";
   };
 
   nativeBuildInputs = [ gfortran cmake ];
@@ -30,8 +27,7 @@ stdenv.mkDerivation rec {
     "-DLAPACKE=ON"
     "-DCBLAS=ON"
     "-DBUILD_TESTING=ON"
-  ]
-  ++ optional shared "-DBUILD_SHARED_LIBS=ON";
+  ] ++ lib.optional shared "-DBUILD_SHARED_LIBS=ON";
 
   doCheck = true;
 
@@ -58,6 +54,7 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     description = "Linear Algebra PACKage";
     homepage = "http://www.netlib.org/lapack/";
+    maintainers = with maintainers; [ ];
     license = licenses.bsd3;
     platforms = platforms.all;
   };
diff --git a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix
index cb72fbd2ca48..4422a908838f 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix
@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   pname = "openspecfun";
-  version = "0.5.3";
+  version = "0.5.5";
   src = fetchFromGitHub {
     owner = "JuliaLang";
     repo = "openspecfun";
     rev = "v${version}";
-    sha256 = "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh";
+    sha256 = "sha256-fX2wc8LHUcF5nN/hiA60ZZ7emRTs0SznOm/0q6lD+Ko=";
   };
 
   makeFlags = [ "prefix=$(out)" ];
diff --git a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
index ee495deedc1e..cbd5fa879ee7 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
@@ -18,11 +18,11 @@ assert petsc-withp4est -> p4est.mpiSupport;
 
 stdenv.mkDerivation rec {
   pname = "petsc";
-  version = "3.14.2";
+  version = "3.14.3";
 
   src = fetchurl {
     url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz";
-    sha256 = "04vy3qyakikslc58qyv8c9qrwlivix3w6znc993i37cvfg99dch9";
+    sha256 = "sha256-1rdyLNSH8jMkmIg88uHMN3ZXqTHAtzU1adybJEZzJ9M=";
   };
 
   mpiSupport = !withp4est || p4est.mpiSupport;
diff --git a/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix b/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix
index 4a90f082dc08..1419a154d90e 100644
--- a/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix
@@ -1,6 +1,5 @@
 { stdenv
 , fetchFromGitLab
-, fetchpatch
 , python
 , wafHook
 
@@ -39,13 +38,13 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "ns-3";
-  version = "33";
+  version = "34";
 
   src = fetchFromGitLab {
     owner = "nsnam";
     repo   = "ns-3-dev";
     rev    = "ns-3.${version}";
-    sha256 = "0ds8h0f2qcb0gc2a8bk38cbhdb122i4sbg589bjn59rblzw0hkq4";
+    sha256 = "sha256-udP7U+pHnNUdo35d9sN1o+aR9ctw9fgU3UunCjisGUI=";
   };
 
   nativeBuildInputs = [ wafHook python ];
@@ -98,14 +97,6 @@ stdenv.mkDerivation rec {
     ${pythonEnv.interpreter} ./test.py --nowaf
   '';
 
-  patches = [
-    (fetchpatch {
-      name = "upstream-issue-336.patch";
-      url = "https://gitlab.com/nsnam/ns-3-dev/-/commit/673004edae1112e6cb249b698aad856d728530fb.patch";
-      sha256 = "0q96ividinbh9xlws014b2ir6gaavygnln5ca9m1db06m4vfwhng";
-    })
-  ];
-
   # strictoverflow prevents clang from discovering pyembed when bindings
   hardeningDisable = [ "fortify" "strictoverflow"];