Merge commit 'b09661d41fb93562fd53f31574dbf781b130ac44'

7 files changed, 147 insertions, 24 deletions

diff --git a/nixpkgs/pkgs/applications/science/misc/golly/beta.nix b/nixpkgs/pkgs/applications/science/misc/golly/beta.nix
index 7741f7ba65bb..9846be8a43a8 100644
--- a/nixpkgs/pkgs/applications/science/misc/golly/beta.nix
+++ b/nixpkgs/pkgs/applications/science/misc/golly/beta.nix
@@ -41,7 +41,6 @@ stdenv.mkDerivation rec {
   '';
 
   meta = {
-    inherit version;
     description = "Cellular automata simulation program";
     license = lib.licenses.gpl2;
     maintainers = [lib.maintainers.raskin];
diff --git a/nixpkgs/pkgs/applications/science/misc/golly/default.nix b/nixpkgs/pkgs/applications/science/misc/golly/default.nix
index be61ec86b324..724a1008c1fb 100644
--- a/nixpkgs/pkgs/applications/science/misc/golly/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/golly/default.nix
@@ -29,7 +29,6 @@ stdenv.mkDerivation rec {
   '';
 
   meta = {
-    inherit version;
     description = "Cellular automata simulation program";
     license = lib.licenses.gpl2;
     maintainers = [lib.maintainers.raskin];
diff --git a/nixpkgs/pkgs/applications/science/misc/root/5.nix b/nixpkgs/pkgs/applications/science/misc/root/5.nix
index 75607fdda348..0da3014507a5 100644
--- a/nixpkgs/pkgs/applications/science/misc/root/5.nix
+++ b/nixpkgs/pkgs/applications/science/misc/root/5.nix
@@ -1,6 +1,27 @@
-{ lib, stdenv, fetchurl, fetchpatch, cmake, pcre, pkg-config, python2
-, libX11, libXpm, libXft, libXext, libGLU, libGL, zlib, libxml2, lz4, xz, gsl_1, xxHash
-, Cocoa, OpenGL, noSplash ? false }:
+{ lib
+, stdenv
+, fetchurl
+, fetchpatch
+, cmake
+, pcre
+, pkg-config
+, python2
+, libX11
+, libXpm
+, libXft
+, libXext
+, libGLU
+, libGL
+, zlib
+, libxml2
+, lz4
+, xz
+, gsl_1
+, xxHash
+, Cocoa
+, OpenGL
+, noSplash ? false
+}:
 
 stdenv.mkDerivation rec {
   pname = "root";
@@ -15,7 +36,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ pcre python2 zlib libxml2 lz4 xz gsl_1 xxHash ]
     ++ lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
     ++ lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
-    ;
+  ;
 
   patches = [
     ./sw_vers_root5.patch
diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix
index a97be6ec76fd..8aa9006d5232 100644
--- a/nixpkgs/pkgs/applications/science/misc/root/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix
@@ -1,23 +1,73 @@
-{ stdenv, lib, fetchurl, makeWrapper, cmake, git, ftgl, gl2ps, glew, gsl
-, libX11, libXpm, libXft, libXext, libGLU, libGL, libxml2, lz4, xz, pcre, nlohmann_json
-, pkg-config, python, xxHash, zlib, zstd
-, libAfterImage, giflib, libjpeg, libtiff, libpng
-, Cocoa, CoreSymbolication, OpenGL, noSplash ? false }:
+{ stdenv
+, lib
+, fetchurl
+, makeWrapper
+, cmake
+, git
+, ftgl
+, gl2ps
+, glew
+, gsl
+, libX11
+, libXpm
+, libXft
+, libXext
+, libGLU
+, libGL
+, libxml2
+, lz4
+, xz
+, pcre
+, nlohmann_json
+, pkg-config
+, python
+, xxHash
+, zlib
+, zstd
+, libAfterImage
+, giflib
+, libjpeg
+, libtiff
+, libpng
+, Cocoa
+, CoreSymbolication
+, OpenGL
+, noSplash ? false
+}:
 
 stdenv.mkDerivation rec {
   pname = "root";
-  version = "6.24.00";
+  version = "6.24.02";
 
   src = fetchurl {
     url = "https://root.cern.ch/download/root_v${version}.source.tar.gz";
-    sha256 = "12crjzd7pzx5qpk2pb3z0rhmxlw5gsqaqzfl48qiq8c9l940b8wx";
+    sha256 = "sha256-BQfhCV4nnMxyQPZR0llmAkMlF5+oWhJZtpS1ZyOtfBw=";
   };
 
   nativeBuildInputs = [ makeWrapper cmake pkg-config git ];
-  buildInputs = [ ftgl gl2ps glew pcre zlib zstd libxml2 lz4 xz gsl xxHash libAfterImage giflib libjpeg libtiff libpng nlohmann_json python.pkgs.numpy ]
-    ++ lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
-    ++ lib.optionals (stdenv.isDarwin) [ Cocoa CoreSymbolication OpenGL ]
-    ;
+  buildInputs = [
+    ftgl
+    gl2ps
+    glew
+    pcre
+    zlib
+    zstd
+    libxml2
+    lz4
+    xz
+    gsl
+    xxHash
+    libAfterImage
+    giflib
+    libjpeg
+    libtiff
+    libpng
+    nlohmann_json
+    python.pkgs.numpy
+  ]
+  ++ lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
+  ++ lib.optionals (stdenv.isDarwin) [ Cocoa CoreSymbolication OpenGL ]
+  ;
 
   patches = [
     ./sw_vers.patch
diff --git a/nixpkgs/pkgs/applications/science/misc/simgrid/default.nix b/nixpkgs/pkgs/applications/science/misc/simgrid/default.nix
index 76937d19651b..23815442da7e 100644
--- a/nixpkgs/pkgs/applications/science/misc/simgrid/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/simgrid/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitLab, cmake, perl, python3, boost, valgrind
+{ lib, stdenv, fetchFromGitLab, fetchpatch, cmake, perl, python3, boost, valgrind
 # Optional requirements
 # Lua 5.3 needed and not available now
 #, luaSupport ? false, lua5
@@ -18,17 +18,26 @@ in
 
 stdenv.mkDerivation rec {
   pname = "simgrid";
-  version = "3.27";
+  version = "3.28";
 
   src = fetchFromGitLab {
     domain = "framagit.org";
     owner = pname;
     repo = pname;
     rev = "v${version}";
-    sha256 = "13nwsyk030fhl3srhpc28j5s6594z0m38606f4ygc4qhv9wxw011";
+    sha256 = "0vylwgd4i89bvhbgfay0wq953324dwfmmr8jp9b4vvlc9m0017r9";
   };
 
-  nativeBuildInputs = [ cmake perl python3 boost valgrind ]
+  patches = [
+    (fetchpatch {
+      name = "fix-smpi-dirs-absolute.patch";
+      url = "https://framagit.org/simgrid/simgrid/-/commit/71f01e667577be1076646eb841e0a57bd5388545.patch";
+      sha256 = "0x3y324b6269687zfy43ilc48bwrs4nb7svh2mpg88lrz53rky15";
+    })
+  ];
+
+  propagatedBuildInputs = [ boost ];
+  nativeBuildInputs = [ cmake perl python3 valgrind ]
       ++ optionals fortranSupport [ gfortran ]
       ++ optionals buildJavaBindings [ openjdk ]
       ++ optionals buildDocumentation [ transfig ghostscript doxygen ]
@@ -90,6 +99,9 @@ stdenv.mkDerivation rec {
     cat <<EOW >CTestCustom.cmake
     SET(CTEST_CUSTOM_TESTS_IGNORE smpi-replay-multiple)
     EOW
+
+    # make sure tests are built in parallel (this can be long otherwise)
+    make tests -j $NIX_BUILD_CORES
   '';
 
   meta = {
diff --git a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
index 8919f85e44d9..419323cfa31f 100644
--- a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
@@ -2,20 +2,23 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "snakemake";
-  version = "6.5.0";
+  version = "6.6.1";
 
   propagatedBuildInputs = with python3Packages; [
     appdirs
-    ConfigArgParse
+    configargparse
     connection-pool
     datrie
     docutils
     filelock
     GitPython
+    jinja2
     jsonschema
     nbformat
+    networkx
     psutil
     pulp
+    pygraphviz
     pyyaml
     ratelimiter
     requests
@@ -28,7 +31,7 @@ python3Packages.buildPythonApplication rec {
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "b166ec74537e02553fcaf0ddcffc32dfdb9dcaa1260af297a56eded6a179b2ee";
+    sha256 = "91637a801342f3bc349c033b284fef7c0201b4e5e29d5650cb6c7f69096d4184";
   };
 
   doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json
diff --git a/nixpkgs/pkgs/applications/science/misc/toil/default.nix b/nixpkgs/pkgs/applications/science/misc/toil/default.nix
new file mode 100644
index 000000000000..a25fbe7565ce
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/misc/toil/default.nix
@@ -0,0 +1,39 @@
+{ lib, fetchFromGitHub, python3Packages }:
+
+python3Packages.buildPythonApplication rec {
+  pname = "toil";
+  version = "5.4.0";
+
+  src = python3Packages.fetchPypi {
+    inherit pname version;
+    sha256 = "73c0648828bd3610c07b7648dd06d6ec27efefdb09473bf01d05d91eb899c9fd";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "docker = " "docker = 'docker' #" \
+      --replace "addict = " "addict = 'addict' #"
+  '';
+
+  propagatedBuildInputs = with python3Packages; [
+    addict
+    docker
+    pytz
+    pyyaml
+    enlighten
+    psutil
+    python-dateutil
+    dill
+  ];
+  checkInputs = with python3Packages; [ pytestCheckHook ];
+
+  pytestFlagsArray = [ "src/toil/test" ];
+  pythonImportsCheck = [ "toil" ];
+
+  meta = with lib; {
+    homepage = "https://toil.ucsc-cgl.org/";
+    license = with licenses; [ asl20 ];
+    description = "Workflow engine written in pure Python";
+    maintainers = with maintainers; [ veprbl ];
+  };
+}