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-rw-r--r--pkgs/development/libraries/jemalloc/common.nix7
-rw-r--r--pkgs/development/libraries/sundials/3.x.nix52
-rw-r--r--pkgs/development/libraries/sundials/default.nix48
-rw-r--r--pkgs/development/libraries/sundials/tests-parallel.patch45
-rw-r--r--pkgs/development/python-modules/django/2_2.nix4
-rw-r--r--pkgs/development/python-modules/scikits-odes/default.nix55
-rw-r--r--pkgs/development/tools/asn2quickder/default.nix6
-rw-r--r--pkgs/development/tools/build-managers/mill/default.nix4
-rw-r--r--pkgs/development/tools/misc/luarocks/darwin-3.0.x.patch27
-rw-r--r--pkgs/development/tools/misc/luarocks/luarocks-nix.nix9
-rw-r--r--pkgs/development/tools/nemiver/default.nix88
11 files changed, 299 insertions, 46 deletions
diff --git a/pkgs/development/libraries/jemalloc/common.nix b/pkgs/development/libraries/jemalloc/common.nix
index c41455a65441..128910e00f21 100644
--- a/pkgs/development/libraries/jemalloc/common.nix
+++ b/pkgs/development/libraries/jemalloc/common.nix
@@ -24,6 +24,13 @@ stdenv.mkDerivation rec {
   configureFlags = []
     ++ optional stripPrefix "--with-jemalloc-prefix="
     ++ optional disableInitExecTls "--disable-initial-exec-tls"
+    # jemalloc is unable to correctly detect transparent hugepage support on
+    # ARM (https://github.com/jemalloc/jemalloc/issues/526), and the default
+    # kernel ARMv6/7 kernel does not enable it, so we explicitly disable support
+    ++ optionals (stdenv.isAarch32 && versionOlder version "5") [
+      "--disable-thp"
+      "je_cv_thp=no"
+    ]
   ;
 
   doCheck = true;
diff --git a/pkgs/development/libraries/sundials/3.x.nix b/pkgs/development/libraries/sundials/3.x.nix
new file mode 100644
index 000000000000..879f13e8bf53
--- /dev/null
+++ b/pkgs/development/libraries/sundials/3.x.nix
@@ -0,0 +1,52 @@
+{ stdenv
+, cmake
+, fetchurl
+, python
+, liblapack
+, gfortran
+, lapackSupport ? true }:
+
+let liblapackShared = liblapack.override {
+  shared = true;
+};
+
+in stdenv.mkDerivation rec {
+  pname = "sundials";
+  version = "3.2.1";
+
+  buildInputs = [ python ] ++ stdenv.lib.optionals (lapackSupport) [ gfortran ];
+  nativeBuildInputs = [ cmake ];
+
+  src = fetchurl {
+    url = "https://computation.llnl.gov/projects/${pname}/download/${pname}-${version}.tar.gz";
+    sha256 = "0238r1qnwqz13wcjzfsbcfi8rfnlxcjjmxq2vpf2qf5jgablvna7";
+  };
+
+  patches = [
+    (fetchurl {
+      # https://github.com/LLNL/sundials/pull/19
+      url = "https://github.com/LLNL/sundials/commit/1350421eab6c5ab479de5eccf6af2dcad1eddf30.patch";
+      sha256 = "0g67lixp9m85fqpb9rzz1hl1z8ibdg0ldwq5z6flj5zl8a7cw52l";
+    })
+  ];
+
+  cmakeFlags = [
+    "-DEXAMPLES_INSTALL_PATH=${placeholder "out"}/share/examples"
+  ] ++ stdenv.lib.optionals (lapackSupport) [
+    "-DSUNDIALS_INDEX_TYPE=int32_t"
+    "-DLAPACK_ENABLE=ON"
+    "-DLAPACK_LIBRARIES=${liblapackShared}/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary};${liblapackShared}/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}"
+  ];
+
+  # flaky tests, and patch in https://github.com/LLNL/sundials/pull/21 doesn't apply cleanly for sundials_3
+  doCheck = false;
+  checkPhase = "make test";
+
+  meta = with stdenv.lib; {
+    description = "Suite of nonlinear differential/algebraic equation solvers";
+    homepage    = https://computation.llnl.gov/projects/sundials;
+    platforms   = platforms.all;
+    maintainers = with maintainers; [ flokli idontgetoutmuch ];
+    license     = licenses.bsd3;
+  };
+}
diff --git a/pkgs/development/libraries/sundials/default.nix b/pkgs/development/libraries/sundials/default.nix
index abe444c63c32..4bc066df32e2 100644
--- a/pkgs/development/libraries/sundials/default.nix
+++ b/pkgs/development/libraries/sundials/default.nix
@@ -1,28 +1,58 @@
-{ cmake, fetchurl, python, stdenv }:
+{ stdenv
+, cmake
+, fetchurl
+, python
+, liblapack
+, gfortran
+, lapackSupport ? true }:
 
-stdenv.mkDerivation rec {
+let liblapackShared = liblapack.override {
+  shared = true;
+};
 
+in stdenv.mkDerivation rec {
   pname = "sundials";
   version = "4.1.0";
 
+  buildInputs = [ python ] ++ stdenv.lib.optionals (lapackSupport) [ gfortran ];
+  nativeBuildInputs = [ cmake ];
+
   src = fetchurl {
     url = "https://computation.llnl.gov/projects/${pname}/download/${pname}-${version}.tar.gz";
     sha256 = "19ca4nmlf6i9ijqcibyvpprxzsdfnackgjs6dw51fq13gg1f2398";
   };
 
-  preConfigure = ''
-    export cmakeFlags="-DCMAKE_INSTALL_PREFIX=$out -DEXAMPLES_INSTALL_PATH=$out/share/examples $cmakeFlags"
-  '';
+  patches = [
+    (fetchurl {
+      # https://github.com/LLNL/sundials/pull/19
+      url = "https://github.com/LLNL/sundials/commit/1350421eab6c5ab479de5eccf6af2dcad1eddf30.patch";
+      sha256 = "0g67lixp9m85fqpb9rzz1hl1z8ibdg0ldwq5z6flj5zl8a7cw52l";
+    })
+    (fetchurl {
+      # https://github.com/LLNL/sundials/pull/20
+      url = "https://github.com/LLNL/sundials/pull/20/commits/2d951bbe1ff7842fcd0dafa28c61b0aa94015f66.patch";
+      sha256 = "0lcr6m4lk14yqrxah4rdscpczny5l7m1zpfsjh8bgspadfsgk512";
+    })
+    # https://github.com/LLNL/sundials/pull/21
+    ./tests-parallel.patch
+  ];
 
-  nativeBuildInputs = [ cmake ];
-  buildInputs = [ python ];
+  cmakeFlags = [
+    "-DEXAMPLES_INSTALL_PATH=${placeholder "out"}/share/examples"
+  ] ++ stdenv.lib.optionals (lapackSupport) [
+    "-DSUNDIALS_INDEX_TYPE=int32_t"
+    "-DLAPACK_ENABLE=ON"
+    "-DLAPACK_LIBRARIES=${liblapackShared}/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary};${liblapackShared}/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}"
+  ];
+
+  doCheck = true;
+  checkPhase = "make test";
 
   meta = with stdenv.lib; {
     description = "Suite of nonlinear differential/algebraic equation solvers";
     homepage    = https://computation.llnl.gov/projects/sundials;
     platforms   = platforms.all;
-    maintainers = [ maintainers.idontgetoutmuch ];
+    maintainers = with maintainers; [ flokli idontgetoutmuch ];
     license     = licenses.bsd3;
   };
-
 }
diff --git a/pkgs/development/libraries/sundials/tests-parallel.patch b/pkgs/development/libraries/sundials/tests-parallel.patch
new file mode 100644
index 000000000000..a785a1dade9b
--- /dev/null
+++ b/pkgs/development/libraries/sundials/tests-parallel.patch
@@ -0,0 +1,45 @@
+diff --git a/config/SundialsAddTest.cmake b/config/SundialsAddTest.cmake
+index e965fed..a7fb1d2 100644
+--- a/config/SundialsAddTest.cmake
++++ b/config/SundialsAddTest.cmake
+@@ -70,7 +70,7 @@ MACRO(SUNDIALS_ADD_TEST NAME EXECUTABLE)
+         "--verbose"
+         "--testname=${NAME}"
+         "--executablename=$<TARGET_FILE:${EXECUTABLE}>"
+-        "--outputdir=${CMAKE_BINARY_DIR}/Testing/output"
++        "--outputdir=${TEST_OUTPUT_DIR}"
+         )
+ 
+       # do not diff the output and answer files
+diff --git a/config/SundialsTesting.cmake b/config/SundialsTesting.cmake
+index 815576a..d91801a 100644
+--- a/config/SundialsTesting.cmake
++++ b/config/SundialsTesting.cmake
+@@ -29,6 +29,13 @@ IF(SUNDIALS_DEVTESTS)
+     ENDIF()
+   ENDIF()
+ 
++  # Directory for test output
++  SET(TEST_OUTPUT_DIR ${PROJECT_BINARY_DIR}/Testing/output)
++
++  IF(NOT EXISTS ${TEST_OUTPUT_DIR})
++    FILE(MAKE_DIRECTORY ${TEST_OUTPUT_DIR})
++  ENDIF()
++
+   # look for the testRunner script in the test directory
+   FIND_PROGRAM(TESTRUNNER testRunner PATHS test)
+   HIDE_VARIABLE(TESTRUNNER)
+diff --git a/test/testRunner b/test/testRunner
+index f450ec2..f1c8deb 100755
+--- a/test/testRunner
++++ b/test/testRunner
+@@ -106,7 +106,8 @@ def main():
+ 
+     # create output directory if necessary
+     if not os.path.exists(outDir):
+-        os.makedirs(outDir)
++        error("Output directory does not exist, it must be created.", outDir)
++        sys.exit(1)
+     elif not os.path.isdir(outDir):
+         error("Output directory exists but is not a directory, it must be deleted.", outDir)
+         sys.exit(1)
diff --git a/pkgs/development/python-modules/django/2_2.nix b/pkgs/development/python-modules/django/2_2.nix
index efc13e455e57..95fd8a769289 100644
--- a/pkgs/development/python-modules/django/2_2.nix
+++ b/pkgs/development/python-modules/django/2_2.nix
@@ -6,13 +6,13 @@
 
 buildPythonPackage rec {
   pname = "Django";
-  version = "2.2.4";
+  version = "2.2.5";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1s5ad5zlmwdn4h5lwn4s4m8mqy0gz4w9nfzyknn815sr252db98n";
+    sha256 = "0mpxmckd1mah0yrp6n8vjk6mq7hxf6d5xcbk6rcmi6z572h0mdyy";
   };
 
   patches = stdenv.lib.optional withGdal
diff --git a/pkgs/development/python-modules/scikits-odes/default.nix b/pkgs/development/python-modules/scikits-odes/default.nix
new file mode 100644
index 000000000000..89ffe334e7ff
--- /dev/null
+++ b/pkgs/development/python-modules/scikits-odes/default.nix
@@ -0,0 +1,55 @@
+{ stdenv
+, lib
+, buildPythonPackage
+, fetchFromGitHub
+, fetchurl
+, cython
+, enum34
+, gfortran
+, isPy3k
+, numpy
+, pytest
+, python
+, scipy
+, sundials_3
+}:
+
+buildPythonPackage rec {
+  pname = "scikits.odes";
+  version = "2.4.0-9-g93075ae";
+
+  # we fetch github instead of Pypi, as we want #104 and #105, which don't apply cleanly on 2.4.0
+  src = fetchFromGitHub {
+    owner = "bmcage";
+    repo = "odes";
+    rev = "93075ae25c409f572f13ca7207fada5706f73c73";
+    sha256 = "161rab7hy6r1a9xw1zby9xhnnmxi0zwdpzxfpjkw9651xn2k5xyw";
+  };
+
+  nativeBuildInputs = [
+    gfortran
+    cython
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    sundials_3
+    scipy
+  ] ++ lib.optionals (!isPy3k) [ enum34 ];
+
+  doCheck = true;
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    cd $out/${python.sitePackages}/scikits/odes/tests
+    pytest
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A scikit offering extra ode/dae solvers, as an extension to what is available in scipy";
+    homepage = https://github.com/bmcage/odes;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ flokli idontgetoutmuch ];
+    platforms = [ "aarch64-linux" "x86_64-linux" "x86_64-darwin" ];
+  };
+}
diff --git a/pkgs/development/tools/asn2quickder/default.nix b/pkgs/development/tools/asn2quickder/default.nix
index e0b9aec9ee15..335a2238b91e 100644
--- a/pkgs/development/tools/asn2quickder/default.nix
+++ b/pkgs/development/tools/asn2quickder/default.nix
@@ -12,11 +12,13 @@ buildPythonApplication rec {
     repo = "quick-der";
   };
 
-  patchPhase = ''
+  postPatch = ''
     patchShebangs ./python/scripts/*
   '';
 
-  buildInputs = [ makeWrapper cmake ];
+  dontUseCmakeConfigure = true;
+
+  nativeBuildInputs = [ makeWrapper cmake ];
   checkInputs = [ pytestrunner pytest ];
 
   propagatedBuildInputs = [ pyparsing asn1ate six ];
diff --git a/pkgs/development/tools/build-managers/mill/default.nix b/pkgs/development/tools/build-managers/mill/default.nix
index b7e6e08cb04a..a07fc2643f6c 100644
--- a/pkgs/development/tools/build-managers/mill/default.nix
+++ b/pkgs/development/tools/build-managers/mill/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "mill";
-  version = "0.5.0";
+  version = "0.5.1";
 
   src = fetchurl {
     url = "https://github.com/lihaoyi/mill/releases/download/${version}/${version}";
-    sha256 = "ecf83db96a32024f14b031ce458b1b3eed01e713265e16c42eb4a894a1a0d654";
+    sha256 = "1y5044m0qlwa1wlg7xkhg76agmfn7bgcf040wf56fvxhf0w78zjw";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/development/tools/misc/luarocks/darwin-3.0.x.patch b/pkgs/development/tools/misc/luarocks/darwin-3.0.x.patch
deleted file mode 100644
index 013ac5180afa..000000000000
--- a/pkgs/development/tools/misc/luarocks/darwin-3.0.x.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff --git a/src/luarocks/core/cfg.lua b/src/luarocks/core/cfg.lua
-index f93e67a..2eb2db9 100644
---- a/src/luarocks/core/cfg.lua
-+++ b/src/luarocks/core/cfg.lua
-@@ -425,9 +425,9 @@ local function make_defaults(lua_version, target_cpu, platforms, home)
-       defaults.external_lib_extension = "dylib"
-       defaults.arch = "macosx-"..target_cpu
-       defaults.variables.LIBFLAG = "-bundle -undefined dynamic_lookup -all_load"
--      defaults.variables.STAT = "/usr/bin/stat"
-+      defaults.variables.STAT = "stat"
-       defaults.variables.STATFLAG = "-f '%A'"
--      local version = util.popen_read("sw_vers -productVersion")
-+      local version = os.getenv("MACOSX_DEPLOYMENT_TARGET") or "10.12"
-       version = tonumber(version and version:match("^[^.]+%.([^.]+)")) or 3
-       if version >= 10 then
-          version = 8
-@@ -436,8 +436,8 @@ local function make_defaults(lua_version, target_cpu, platforms, home)
-       else
-          defaults.gcc_rpath = false
-       end
--      defaults.variables.CC = "env MACOSX_DEPLOYMENT_TARGET=10."..version.." gcc"
--      defaults.variables.LD = "env MACOSX_DEPLOYMENT_TARGET=10."..version.." gcc"
-+      defaults.variables.CC = "env MACOSX_DEPLOYMENT_TARGET=10."..version.." clang"
-+      defaults.variables.LD = "env MACOSX_DEPLOYMENT_TARGET=10."..version.." clang"
-       defaults.web_browser = "open"
-    end
- 
diff --git a/pkgs/development/tools/misc/luarocks/luarocks-nix.nix b/pkgs/development/tools/misc/luarocks/luarocks-nix.nix
index 8da224f0ef8c..21611f05579b 100644
--- a/pkgs/development/tools/misc/luarocks/luarocks-nix.nix
+++ b/pkgs/development/tools/misc/luarocks/luarocks-nix.nix
@@ -1,13 +1,14 @@
 { luarocks, fetchFromGitHub }:
 luarocks.overrideAttrs(old: {
   pname = "luarocks-nix";
+  version = "2019-09-07";
   src = fetchFromGitHub {
-    owner = "teto";
+    owner = "nix-community";
     repo = "luarocks";
-    rev = "38ed82ba3e5682d7d55ef9a870dfb464ca180df9";
-    sha256 = "0vlzywiv3sxkpjg1fzzxicmfr6kh04fxw5q9n8vsd2075xjxg6bs";
+    rev = "fa7c367bcdad36768db5f19fd4fcdd9681a14429";
+    sha256 = "0kziwfw5gqq5xsckl7qf9wasaiy8rp42h5qrcnjx07qp47a9ldx7";
   };
   patches = [
-    ./darwin-3.0.x.patch
+    ./darwin-3.1.3.patch
   ];
 })
diff --git a/pkgs/development/tools/nemiver/default.nix b/pkgs/development/tools/nemiver/default.nix
new file mode 100644
index 000000000000..1f3556fc9047
--- /dev/null
+++ b/pkgs/development/tools/nemiver/default.nix
@@ -0,0 +1,88 @@
+{ stdenv
+, fetchurl
+, fetchpatch
+, pkgconfig
+, gnome3
+, gtk3
+, libxml2
+, intltool
+, itstool
+, gdb
+, boost
+, sqlite
+, libgtop
+, glibmm
+, gtkmm3
+, vte
+, gtksourceview
+, gsettings-desktop-schemas
+, gtksourceviewmm
+, wrapGAppsHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "nemiver";
+  version = "0.9.6";
+
+  src = fetchurl {
+    url = "mirror://gnome/sources/nemiver/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
+    sha256 = "85ab8cf6c4f83262f441cb0952a6147d075c3c53d0687389a3555e946b694ef2";
+  };
+
+  nativeBuildInputs = [
+    libxml2
+    intltool
+    itstool
+    pkgconfig
+    wrapGAppsHook
+  ];
+
+  buildInputs = [
+    gtk3
+    gdb
+    boost
+    sqlite
+    libgtop
+    glibmm
+    gtkmm3
+    vte
+    gtksourceview
+    gtksourceviewmm
+    gsettings-desktop-schemas
+  ];
+
+  patches = [
+    # build fixes
+    (fetchpatch {
+      url = https://gitlab.gnome.org/GNOME/nemiver/commit/e0e42221ceb77d88be64fac1c09792dc5c9e2f43.patch;
+      sha256 = "1g0ixll6yqfj6ysf50p0c7nmh3lgmb6ds15703q7ibnw7dyidvj8";
+    })
+    (fetchpatch {
+      url = https://gitlab.gnome.org/GNOME/nemiver/commit/7005393a8c4d914eac9705e7f47818d0f4de3578.patch;
+      sha256 = "1mxb1sdqdj7dm204gja8cdygx8579bjriqqbb7cna9rj0m9c8pjg";
+    })
+    (fetchpatch {
+      url = https://gitlab.gnome.org/GNOME/nemiver/commit/262cf9657f9c2727a816972b348692adcc666008.patch;
+      sha256 = "03jv6z54b8nzvplplapk4aj206zl1gvnv6iz0mad19g6yvfbw7a7";
+    })
+  ];
+
+  configureFlags = [
+    "--enable-gsettings"
+  ];
+
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = "nemiver";
+      versionPolicy = "none";
+    };
+  };
+
+  meta = with stdenv.lib; {
+    homepage = https://wiki.gnome.org/Apps/Nemiver;
+    description = "Easy to use standalone C/C++ debugger";
+    license = licenses.gpl2;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.juliendehos ];
+  };
+}
generated by cgit-pink 1.4.1 (git 2.36.1) at 2024-07-06 18:10:31 +0000