Merge commit 'a2e06fc3423c4be53181b15c28dfbe0bcf67dd73'

5 files changed, 48 insertions, 31 deletions

diff --git a/nixpkgs/pkgs/development/libraries/physics/geant4/datasets.nix b/nixpkgs/pkgs/development/libraries/physics/geant4/datasets.nix
index 22fda0cf9800..df44fa275f5d 100644
--- a/nixpkgs/pkgs/development/libraries/physics/geant4/datasets.nix
+++ b/nixpkgs/pkgs/development/libraries/physics/geant4/datasets.nix
@@ -35,78 +35,78 @@ in
   builtins.listToAttrs (map (a: { inherit (a) name; value = mkDataset a; }) [
     {
       name = "G4NDL";
-      version = "4.5";
-      sha256 = "cba928a520a788f2bc8229c7ef57f83d0934bb0c6a18c31ef05ef4865edcdf8e";
+      version = "4.6";
+      sha256 = "022l2jjhi57frfdv9nk6s6q23gmr9zkix06fmni8gf0gmvr7qa4x";
       envvar = "NEUTRONHP";
     }
 
     {
       name = "G4EMLOW";
-      version = "7.7";
-      sha256 = "16dec6adda6477a97424d749688d73e9bd7d0b84d0137a67cf341f1960984663";
+      version = "7.9.1";
+      sha256 = "1jrw0izw732bywq1k1srs3x2z0m3y2h377kcvwbwcr0wa1p10342";
       envvar = "LE";
     }
 
     {
       name = "G4PhotonEvaporation";
-      version = "5.3";
-      sha256 = "d47ababc8cbe548065ef644e9bd88266869e75e2f9e577ebc36bc55bf7a92ec8";
+      version = "5.5";
+      sha256 = "1mvnbs7yvkii41blks6bkqr8qhxgnj3xxvv1i3vdg2y14shxv5ar";
       envvar = "LEVELGAMMA";
     }
 
     {
       name = "G4RadioactiveDecay";
-      version = "5.3";
-      sha256 = "5c8992ac57ae56e66b064d3f5cdfe7c2fee76567520ad34a625bfb187119f8c1";
+      version = "5.4";
+      sha256 = "0qaark6mqzxr3lqawv6ai8z5211qihlp5x2hn86vzx8kgpd7j1r4";
       envvar = "RADIOACTIVE";
     }
 
     {
       name = "G4SAIDDATA";
       version = "2.0";
-      sha256 = "1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91";
+      sha256 = "149fqy801n1pj2g6lcai2ziyvdz8cxdgbfarax6y8wdakgksh9hx";
       envvar = "SAIDXS";
     }
 
     {
       name = "G4PARTICLEXS";
-      version = "1.1";
-      sha256 = "100a11c9ed961152acfadcc9b583a9f649dda4e48ab314fcd4f333412ade9d62";
+      version = "2.1";
+      sha256 = "0h8ba8jk197npbd9lzq2qlfiklbjgqwk45m1cc6piy5vf8ri0k89";
       envvar = "PARTICLEXS";
     }
 
     {
       name = "G4ABLA";
       version = "3.1";
-      sha256 = "7698b052b58bf1b9886beacdbd6af607adc1e099fc730ab6b21cf7f090c027ed";
+      sha256 = "1v97q28g1xqwnav0lwzwk7hc3b87yrmbvkgadf4bkwcbnm9b163n";
       envvar = "ABLA";
     }
 
     {
       name = "G4INCL";
       version = "1.0";
-      sha256 = "716161821ae9f3d0565fbf3c2cf34f4e02e3e519eb419a82236eef22c2c4367d";
+      sha256 = "0z9nqk125vvf4f19lhgb37jy60jf9zrjqg5zbxbd1wz93a162qbi";
       envvar = "INCL";
     }
 
     {
       name = "G4PII";
       version = "1.3";
-      sha256 = "6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926";
+      sha256 = "09p92rk1sj837m6n6yd9k9a8gkh6bby2bfn6k0f3ix3m4s8as9b2";
       envvar = "PII";
     }
 
     {
       name = "G4ENSDFSTATE";
       version = "2.2";
-      sha256 = "dd7e27ef62070734a4a709601f5b3bada6641b111eb7069344e4f99a01d6e0a6";
+      sha256 = "19p0sq0rmyg48j9hddqy24dn99md7ddiyq09lyj381q7cbpjfznx";
       envvar = "ENSDFSTATE";
     }
 
     {
       name = "G4RealSurface";
-      version = "2.1";
-      sha256 = "2a287adbda1c0292571edeae2082a65b7f7bd6cf2bf088432d1d6f889426dcf3";
+      version = "2.1.1";
+      sha256 = "0l3gs0nlp10cjlwiln3f72zfch0av2g1r8m2ny9afgvwgbwiyj4h";
       envvar = "REALSURFACE";
     }
   ])
diff --git a/nixpkgs/pkgs/development/libraries/physics/geant4/default.nix b/nixpkgs/pkgs/development/libraries/physics/geant4/default.nix
index 007e4ad0c32f..1897071b1259 100644
--- a/nixpkgs/pkgs/development/libraries/physics/geant4/default.nix
+++ b/nixpkgs/pkgs/development/libraries/physics/geant4/default.nix
@@ -8,7 +8,7 @@
 , enableRaytracerX11   ? false
 
 # Standard build environment with cmake.
-, stdenv, fetchurl, cmake
+, stdenv, fetchurl, fetchpatch, cmake
 
 # Optional system packages, otherwise internal GEANT4 packages are used.
 , clhep ? null # not packaged currently
@@ -36,12 +36,12 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "10.5.1";
+  version = "10.6.1";
   pname = "geant4";
 
   src = fetchurl{
-    url = "http://cern.ch/geant4-data/releases/geant4.10.05.p01.tar.gz";
-    sha256 = "f4a292220500fad17e0167ce3153e96e3410ecbe96284e572dc707f63523bdff";
+    url = "https://geant4-data.web.cern.ch/geant4-data/releases/geant4.10.06.p01.tar.gz";
+    sha256 = "0ssxg7dd7vxljb3fdyb0llg7gsxack21qjfsb3n23k107a19yibk";
   };
 
   cmakeFlags = [
@@ -64,11 +64,14 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
   nativeBuildInputs =  [ cmake ];
-  buildInputs = [ clhep expat zlib libGLU libGL xlibsWrapper libXmu ]
+
+  buildInputs = [ libGLU xlibsWrapper libXmu ]
+    ++ stdenv.lib.optionals enableInventor [ libXpm coin3d soxt motif ];
+
+  propagatedBuildInputs = [ clhep expat zlib libGL ]
     ++ stdenv.lib.optionals enableGDML [ xercesc ]
     ++ stdenv.lib.optionals enableXM [ motif ]
-    ++ stdenv.lib.optionals enableQT [ qtbase ]
-    ++ stdenv.lib.optionals enableInventor [ libXpm coin3d soxt motif ];
+    ++ stdenv.lib.optionals enableQT [ qtbase ];
 
   postFixup = ''
     # Don't try to export invalid environment variables.
diff --git a/nixpkgs/pkgs/development/libraries/physics/geant4/g4py/default.nix b/nixpkgs/pkgs/development/libraries/physics/geant4/g4py/default.nix
index dddd7078b86e..69fb5a99738a 100644
--- a/nixpkgs/pkgs/development/libraries/physics/geant4/g4py/default.nix
+++ b/nixpkgs/pkgs/development/libraries/physics/geant4/g4py/default.nix
@@ -18,13 +18,15 @@ stdenv.mkDerivation {
   inherit (geant4_nomt) version src;
   pname = "g4py";
 
-  sourceRoot = "geant4.10.05.p01/environments/g4py";
-
   nativeBuildInputs = [ cmake ];
   buildInputs = [ geant4_nomt xercesc boost_python python ];
 
   GEANT4_INSTALL = geant4_nomt;
 
+  postPatch = ''
+    cd environments/g4py
+  '';
+
   preConfigure = ''
     # Fix for boost 1.67+
     substituteInPlace CMakeLists.txt \
diff --git a/nixpkgs/pkgs/development/libraries/physics/lhapdf/pdf_sets.nix b/nixpkgs/pkgs/development/libraries/physics/lhapdf/pdf_sets.nix
index 8f693a32e35c..2309e6671f85 100644
--- a/nixpkgs/pkgs/development/libraries/physics/lhapdf/pdf_sets.nix
+++ b/nixpkgs/pkgs/development/libraries/physics/lhapdf/pdf_sets.nix
@@ -6,7 +6,7 @@ let
       inherit name;
 
       src = fetchurl {
-        url = "https://www.hepforge.org/archive/lhapdf/pdfsets/6.2/${name}.tar.gz";
+        url = "http://lhapdfsets.web.cern.ch/lhapdfsets/current/${name}.tar.gz";
         inherit sha256;
       };
 
diff --git a/nixpkgs/pkgs/development/libraries/physics/yoda/default.nix b/nixpkgs/pkgs/development/libraries/physics/yoda/default.nix
index c6c6f742d0bf..8ed0a2c4ae3a 100644
--- a/nixpkgs/pkgs/development/libraries/physics/yoda/default.nix
+++ b/nixpkgs/pkgs/development/libraries/physics/yoda/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, python2Packages, root, makeWrapper, zlib, withRootSupport ? false }:
+{ stdenv, fetchurl, fetchpatch, python, root, makeWrapper, zlib, withRootSupport ? false }:
 
 stdenv.mkDerivation rec {
   pname = "yoda";
@@ -9,14 +9,26 @@ stdenv.mkDerivation rec {
     sha256 = "1ki88rscnym0vjxpfgql8m1lrc7vm1jb9w4jhw9lvv3rk84lpdng";
   };
 
-  pythonPath = []; # python wrapper support
-
-  buildInputs = with python2Packages; [ python numpy matplotlib makeWrapper ]
+  patches = [
+    # fixes "TypeError: expected bytes, str found" in writeYODA()
+    (fetchpatch {
+      url = "https://gitlab.com/hepcedar/yoda/commit/d2bbbe92912457f8a29b440cbfa0b39daf28ec34.diff";
+      sha256 = "1x60piswpxwak61r2sdclsc8pzi1fshpkjnxlyflsa1iap77vkq8";
+    })
+  ];
+
+  nativeBuildInputs = with python.pkgs; [ cython makeWrapper ];
+  buildInputs = [ python ]
+    ++ (with python.pkgs; [ numpy matplotlib ])
     ++ stdenv.lib.optional withRootSupport root;
   propagatedBuildInputs = [ zlib ];
 
   enableParallelBuilding = true;
 
+  postPatch = ''
+    touch pyext/yoda/*.{pyx,pxd}
+  '';
+
   postInstall = ''
     for prog in "$out"/bin/*; do
       wrapProgram "$prog" --set PYTHONPATH $PYTHONPATH:$(toPythonPath "$out")