Merge staging-next into staging

pkgs/applications/science/logic/cbmc/0001-Do-not-download-sources-in-cmake.patch

@@ -0,0 +1,49 @@
+From fbc1488e8da0175e9c9bdf5892f8a65c71f2a266 Mon Sep 17 00:00:00 2001
+From: Jiajie Chen <c@jia.je>
+Date: Fri, 15 Jul 2022 18:33:15 +0800
+Subject: [PATCH] Do not download sources in cmake
+
+---
+ src/solvers/CMakeLists.txt | 20 +-------------------
+ 1 file changed, 1 insertion(+), 19 deletions(-)
+
+diff --git a/src/solvers/CMakeLists.txt b/src/solvers/CMakeLists.txt
+index 744def486..5b719a78a 100644
+--- a/src/solvers/CMakeLists.txt
++++ b/src/solvers/CMakeLists.txt
+@@ -106,31 +106,13 @@ elseif("${sat_impl}" STREQUAL "glucose")
+ elseif("${sat_impl}" STREQUAL "cadical")
+     message(STATUS "Building solvers with cadical")
+ 
+-    download_project(PROJ cadical
+-        URL https://github.com/arminbiere/cadical/archive/rel-1.4.1.tar.gz
+-        PATCH_COMMAND true
+-        COMMAND CXX=${CMAKE_CXX_COMPILER} ./configure -O3 -s CXXFLAGS=-std=c++14
+-        URL_MD5 b44874501a175106424f4bd5de29aa59
+-    )
+-
+     message(STATUS "Building CaDiCaL")
+-    execute_process(COMMAND make -j WORKING_DIRECTORY ${cadical_SOURCE_DIR})
+ 
+     target_compile_definitions(solvers PUBLIC
+         SATCHECK_CADICAL HAVE_CADICAL
+     )
+ 
+-    add_library(cadical STATIC IMPORTED)
+-
+-    set_target_properties(
+-        cadical
+-        PROPERTIES IMPORTED_LOCATION ${cadical_SOURCE_DIR}/build/libcadical.a
+-    )
+-
+-    target_include_directories(solvers
+-      PUBLIC
+-      ${cadical_SOURCE_DIR}/src
+-    )
++    target_include_directories(solvers PUBLIC ${cadical_INCLUDE_DIR})
+ 
+     target_link_libraries(solvers cadical)
+ elseif("${sat_impl}" STREQUAL "ipasir-cadical")
+-- 
+2.35.1
+

pkgs/applications/science/logic/cbmc/default.nix

@@ -0,0 +1,82 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, testers
+, bison
+, cadical
+, cbmc
+, cmake
+, flex
+, makeWrapper
+, perl
+}:
+
+stdenv.mkDerivation rec {
+  pname = "cbmc";
+  version = "5.63.0";
+
+  src = fetchFromGitHub {
+    owner = "diffblue";
+    repo = pname;
+    rev = "${pname}-${version}";
+    sha256 = "sha256-4tn3wsmaYdo5/QaZc3MLxVGF0x8dmRKeygF/8A+Ww1o=";
+  };
+
+  nativeBuildInputs = [
+    bison
+    cmake
+    flex
+    perl
+    makeWrapper
+  ];
+
+  buildInputs = [ cadical ];
+
+  # do not download sources
+  # link existing cadical instead
+  patches = [
+    ./0001-Do-not-download-sources-in-cmake.patch
+  ];
+
+  postPatch = ''
+    # do not hardcode gcc
+    substituteInPlace "scripts/bash-autocomplete/extract_switches.sh" \
+      --replace "gcc" "$CC" \
+      --replace "g++" "$CXX"
+    # fix library_check.sh interpreter error
+    patchShebangs .
+  '' + lib.optionalString (!stdenv.cc.isGNU) ''
+    # goto-gcc rely on gcc
+    substituteInPlace "regression/CMakeLists.txt" \
+      --replace "add_subdirectory(goto-gcc)" ""
+  '';
+
+  postInstall = ''
+    # goto-cc expects ls_parse.py in PATH
+    mkdir -p $out/share/cbmc
+    mv $out/bin/ls_parse.py $out/share/cbmc/ls_parse.py
+    chmod +x $out/share/cbmc/ls_parse.py
+    wrapProgram $out/bin/goto-cc \
+      --prefix PATH : "$out/share/cbmc" \
+  '';
+
+  # fix "argument unused during compilation"
+  NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang
+    "-Wno-unused-command-line-argument";
+
+  # TODO: add jbmc support
+  cmakeFlags = [ "-DWITH_JBMC=OFF" "-Dsat_impl=cadical" "-Dcadical_INCLUDE_DIR=${cadical.dev}/include" ];
+
+  passthru.tests.version = testers.testVersion {
+    package = cbmc;
+    command = "cbmc --version";
+  };
+
+  meta = with lib; {
+    description = "CBMC is a Bounded Model Checker for C and C++ programs";
+    homepage = "http://www.cprover.org/cbmc/";
+    license = licenses.bsdOriginal;
+    maintainers = with maintainers; [ jiegec ];
+    platforms = platforms.unix;
+  };
+}

pkgs/applications/science/logic/fast-downward/default.nix

@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "fast-downward";
-  version = "21.12.0";
+  version = "22.06.0";
 
   src = fetchFromGitHub {
     owner = "aibasel";
     repo = "downward";
     rev = "release-${version}";
-    sha256 = "sha256-qc+SaUpIYm7bnOZlHH2mdvUaMBB+VRyOCQM/BOoOaPE=";
+    sha256 = "sha256-WzxLUuwZy+oNqmgj0n4Pe1QBYXXAaJqYhT+JSLbmyiM=";
   };
 
   nativeBuildInputs = [ cmake python3.pkgs.wrapPython ];

pkgs/development/interpreters/janet/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "janet";
-  version = "1.23.0";
+  version = "1.24.0";
 
   src = fetchFromGitHub {
     owner = "janet-lang";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-FQZ9I9ROC1gWGfMCxsNMN3g/arenRtC6LHsOIAKGyuE=";
+    sha256 = "sha256-scc29tS3jiGacHp90tGmn/qnbLscJ4sAOCm8IteXfh4=";
   };
 
   # This release fails the test suite on darwin, remove when debugged.

pkgs/development/libraries/babl/default.nix

@@ -1,5 +1,6 @@
 { stdenv
 , lib
+, fetchpatch
 , fetchurl
 , meson
 , ninja
@@ -20,6 +21,13 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-9mdzUCiUS2N1rRjxYKZM65P1x9zKqdh1HeNZd3SIosE=";
   };
 
+  patches = [
+    (fetchpatch {
+      url = "https://gitlab.gnome.org/GNOME/babl/-/commit/b05b2826365a7dbc6ca1bf0977b848055cd0cbb6.patch";
+      hash = "sha256-zyDOc6FcVyZeMij1XjJ46XXWLO5MMz9ZqLKjjT6VSCI=";
+    })
+  ];
+
   nativeBuildInputs = [
     meson
     ninja

pkgs/development/libraries/entt/default.nix

@@ -1,13 +1,13 @@
 { lib, stdenv, fetchFromGitHub, cmake }:
 stdenv.mkDerivation rec {
   pname = "entt";
-  version = "3.10.0";
+  version = "3.10.3";
 
   src = fetchFromGitHub {
     owner = "skypjack";
     repo = "entt";
     rev = "v${version}";
-    sha256 = "sha256-/4lc+/YiLPxrn+7Z67sEapYY0ocLWHPC8yeYD2VI+64=";
+    sha256 = "sha256-pewAwvNRCBS6rm3AmHthiayGfP71lqkAO+x6rT957Xg=";
   };
 
   nativeBuildInputs = [ cmake ];

pkgs/development/libraries/glibc/default.nix

@@ -64,8 +64,12 @@ callPackage ./common.nix { inherit stdenv; } {
     # store path than that determined when built (as a source for the
     # bootstrap-tools tarball)
     # Building from a proper gcc staying in the path where it was installed,
-    # libgcc_s will not be at {gcc}/lib, and gcc's libgcc will be found without
+    # libgcc_s will now be at {gcc}/lib, and gcc's libgcc will be found without
     # any special hack.
+    # TODO: remove this hack. Things that rely on this hack today:
+    # - dejagnu: during linux bootstrap tcl SIGSEGVs
+    # - clang-wrapper in cross-compilation
+    # Last attempt: https://github.com/NixOS/nixpkgs/pull/36948
     preInstall = ''
       if [ -f ${stdenv.cc.cc}/lib/libgcc_s.so.1 ]; then
           mkdir -p $out/lib

pkgs/development/libraries/libzip/default.nix

@@ -16,11 +16,11 @@
 
 stdenv.mkDerivation rec {
   pname = "libzip";
-  version = "1.8.0";
+  version = "1.9.2";
 
   src = fetchurl {
     url = "https://libzip.org/download/${pname}-${version}.tar.gz";
-    sha256 = "17l3ygrnbszm3b99dxmw94wcaqpbljzg54h4c0y8ss8aij35bvih";
+    sha256 = "sha256-/Wp/dF3j1pz1YD7cnLM9KJDwGY5BUlXQmHoM8Q2CTG8=";
   };
 
   outputs = [ "out" "dev" "man" ];

pkgs/development/php-packages/composer/default.nix

@@ -1,14 +1,14 @@
 { mkDerivation, fetchurl, makeWrapper, unzip, lib, php }:
 let
   pname = "composer";
-  version = "2.3.10";
+  version = "2.4.0";
 in
 mkDerivation {
   inherit pname version;
 
   src = fetchurl {
     url = "https://getcomposer.org/download/${version}/composer.phar";
-    sha256 = "2AgnLyhPqOD4tHBwPhQ4rI82IDC7ydEuKVMCd9dnr/A=";
+    sha256 = "HNx090llkI0OmNAP7so3wjuG2lEXCjoRoVONif9E1N0=";
   };
 
   dontUnpack = true;

pkgs/development/python-modules/jaxlib/default.nix

@@ -8,9 +8,11 @@
 , binutils
 , buildBazelPackage
 , buildPythonPackage
+, cctools
 , cython
 , fetchFromGitHub
 , git
+, IOKit
 , jsoncpp
 , pybind11
 , setuptools
@@ -55,8 +57,11 @@ let
     homepage = "https://github.com/google/jax";
     license = licenses.asl20;
     maintainers = with maintainers; [ ndl ];
-    platforms = [ "x86_64-linux" "aarch64-darwin" "x86_64-darwin"];
+    platforms = platforms.unix;
-    hydraPlatforms = ["x86_64-linux" ]; # Don't think anybody is checking the darwin builds
+    # aarch64-darwin is broken because of https://github.com/bazelbuild/rules_cc/pull/136
+    # however even with that fix applied, it doesn't work for everyone:
+    # https://github.com/NixOS/nixpkgs/pull/184395#issuecomment-1207287129
+    broken = stdenv.isAarch64;
   };
 
   cudatoolkit_joined = symlinkJoin {
@@ -117,6 +122,8 @@ let
     ] ++ lib.optionals cudaSupport [
       cudatoolkit
       cudnn
+    ] ++ lib.optionals stdenv.isDarwin [
+      IOKit
     ];
 
     postPatch = ''
@@ -201,9 +208,7 @@ let
 
     # Make sure Bazel knows about our configuration flags during fetching so that the
     # relevant dependencies can be downloaded.
-    bazelFetchFlags = bazel-build.bazelBuildFlags;
+    bazelFlags = [
-
-    bazelBuildFlags = [
       "-c opt"
     ] ++ lib.optional (stdenv.targetPlatform.isx86_64 && stdenv.targetPlatform.isUnix) [
       "--config=avx_posix"
@@ -211,6 +216,11 @@ let
       "--config=cuda"
     ] ++ lib.optional mklSupport [
       "--config=mkl_open_source_only"
+    ] ++ lib.optionals stdenv.cc.isClang [
+      # bazel depends on the compiler frontend automatically selecting these flags based on file
+      # extension but our clang doesn't.
+      # https://github.com/NixOS/nixpkgs/issues/150655
+      "--cxxopt=-x" "--cxxopt=c++" "--host_cxxopt=-x" "--host_cxxopt=c++"
     ];
 
     fetchAttrs = {
@@ -218,7 +228,7 @@ let
         if cudaSupport then
           "sha256-Ald+vplRx/DDG/7TfHAqD4Gktb1BGnf7FSCCJzSI0eo="
         else
-          "sha256-6acSbBNcUBw177HMVOmpV7pUfP1aFSe5cP6/zWFdGFo=";
+          "sha256-eK5IjTAncDarkWYKnXrEo7kw7J7iOH7in2L2GabnFYo=";
     };
 
     buildAttrs = {
@@ -226,8 +236,8 @@ let
 
       # Note: we cannot do most of this patching at `patch` phase as the deps are not available yet.
       # 1) Fix pybind11 include paths.
-      # 2) Force static protobuf linkage to prevent crashes on loading multiple extensions
+      # 2) Link protobuf from nixpkgs (through TF_SYSTEM_LIBS when using gcc) to prevent crashes on
-      #    in the same python program due to duplicate protobuf DBs.
+      #    loading multiple extensions in the same python program due to duplicate protobuf DBs.
       # 3) Patch python path in the compiler driver.
       # 4) Patch tensorflow sources to work with later versions of protobuf. See
       #    https://github.com/google/jax/issues/9534. Note that this should be
@@ -236,13 +246,25 @@ let
         for src in ./jaxlib/*.{cc,h}; do
           sed -i 's@include/pybind11@pybind11@g' $src
         done
-        sed -i 's@-lprotobuf@-l:libprotobuf.a@' ../output/external/org_tensorflow/third_party/systemlibs/protobuf.BUILD
-        sed -i 's@-lprotoc@-l:libprotoc.a@' ../output/external/org_tensorflow/third_party/systemlibs/protobuf.BUILD
         substituteInPlace ../output/external/org_tensorflow/tensorflow/compiler/xla/python/pprof_profile_builder.cc \
           --replace "status.message()" "std::string{status.message()}"
+        substituteInPlace ../output/external/rules_cc/cc/private/toolchain/osx_cc_wrapper.sh.tpl \
+          --replace "/usr/bin/install_name_tool" "${cctools}/bin/install_name_tool"
+        substituteInPlace ../output/external/rules_cc/cc/private/toolchain/unix_cc_configure.bzl \
+          --replace "/usr/bin/libtool" "${cctools}/bin/libtool"
       '' + lib.optionalString cudaSupport ''
         patchShebangs ../output/external/org_tensorflow/third_party/gpus/crosstool/clang/bin/crosstool_wrapper_driver_is_not_gcc.tpl
-      '';
+      '' + lib.optionalString stdenv.isDarwin ''
+        # Framework search paths aren't added by bintools hook
+        # https://github.com/NixOS/nixpkgs/pull/41914
+        export NIX_LDFLAGS+=" -F${IOKit}/Library/Frameworks"
+      '' + (if stdenv.cc.isGNU then ''
+        sed -i 's@-lprotobuf@-l:libprotobuf.a@' ../output/external/org_tensorflow/third_party/systemlibs/protobuf.BUILD
+        sed -i 's@-lprotoc@-l:libprotoc.a@' ../output/external/org_tensorflow/third_party/systemlibs/protobuf.BUILD
+      '' else if stdenv.cc.isClang then ''
+        sed -i 's@-lprotobuf@${pkgs.protobuf}/lib/libprotobuf.a@' ../output/external/org_tensorflow/third_party/systemlibs/protobuf.BUILD
+        sed -i 's@-lprotoc@${pkgs.protobuf}/lib/libprotoc.a@' ../output/external/org_tensorflow/third_party/systemlibs/protobuf.BUILD
+      '' else throw "Unsupported stdenv.cc: ${stdenv.cc}");
 
       installPhase = ''
         ./bazel-bin/build/build_wheel --output_path=$out --cpu=${stdenv.targetPlatform.linuxArch}
@@ -251,13 +273,21 @@ let
 
     inherit meta;
   };
+  platformTag =
+    if stdenv.targetPlatform.isLinux then
+      "manylinux2010_${stdenv.targetPlatform.linuxArch}"
+    else if stdenv.system == "x86_64-darwin" then
+      "macosx_10_9_${stdenv.targetPlatform.linuxArch}"
+    else if stdenv.system == "aarch64-darwin" then
+      "macosx_11_0_${stdenv.targetPlatform.linuxArch}"
+    else throw "Unsupported target platform: ${stdenv.targetPlatform}";
 
 in
 buildPythonPackage {
   inherit meta pname version;
   format = "wheel";
 
-  src = "${bazel-build}/jaxlib-${version}-cp${builtins.replaceStrings ["."] [""] python.pythonVersion}-none-manylinux2010_${stdenv.targetPlatform.linuxArch}.whl";
+  src = "${bazel-build}/jaxlib-${version}-cp${builtins.replaceStrings ["."] [""] python.pythonVersion}-none-${platformTag}.whl";
 
   # Note that cudatoolkit is necessary since jaxlib looks for "ptxas" in $PATH.
   # See https://github.com/NixOS/nixpkgs/pull/164176#discussion_r828801621 for

pkgs/development/python-modules/peaqevcore/default.nix

@@ -6,14 +6,14 @@
 
 buildPythonPackage rec {
   pname = "peaqevcore";
-  version = "5.2.0";
+  version = "5.4.3";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-8zllJh34tAymjW3OaFNiDuChdk/og09l51OFlt0jNqs=";
+    hash = "sha256-WeAYa1Iggog5VX1oiANZCeVpuEF5JdabdUjQ+fkAwxE=";
   };
 
   postPatch = ''

pkgs/development/python-modules/pymavlink/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pymavlink";
-  version = "2.4.31";
+  version = "2.4.34";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-p7cvwMpW1fS9Ml72vsD9L35wqPjtsQHW5lclw5SJ4P0=";
+    sha256 = "sha256-2JPBjEXiJWDJJPwS7SjNr3L4Ct+U44QaJiiv8MtSnEk=";
   };
 
   propagatedBuildInputs = [ future lxml ];

pkgs/development/python-modules/pypoolstation/default.nix

@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "pypoolstation";
-  version = "0.4.8";
+  version = "0.4.9";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "PyPoolstation";
     inherit version;
-    sha256 = "sha256-6Fdam/LS3Nicrhe5jHHvaKCpE0HigfOVszjb5c1VM3Y=";
+    sha256 = "sha256-2smgsR5f2fzmutr4EjhyrFWrO9odTba0ux+0B6k3+9Y=";
   };
 
   nativeBuildInputs = [

pkgs/development/python-modules/pysma/default.nix

@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "pysma";
-  version = "0.6.11";
+  version = "0.6.12";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-x0sFJAdueSny0XoaOYbYLN8ZRS5B/iEVT62mqd4Voe4=";
+    sha256 = "sha256-uxMxqx5qbahMvTm3akiOTODhKLNVhHzBAUsOcZo/35I=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/qcengine/default.nix

@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "qcengine";
-  version = "0.24.0";
+  version = "0.24.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-T6/gC3HHCnI3O1Gkj/MdistL93bwymtEfNF6PmA7TN0=";
+    hash = "sha256-KUOGbGQd1ffXNkQiW8yeUxValCOAfd8nBv9nnk9giVU=";
   };
 
   propagatedBuildInputs = [

pkgs/development/tools/misc/cvise/default.nix

@@ -1,6 +1,6 @@
 { lib, buildPythonApplication, fetchFromGitHub, bash, cmake, flex
 , libclang, llvm, unifdef
-, chardet, pebble, psutil, pytestCheckHook, pytest-flake8
+, chardet, pebble, psutil
 }:
 
 buildPythonApplication rec {
@@ -22,7 +22,6 @@ buildPythonApplication rec {
   nativeBuildInputs = [ cmake flex llvm.dev ];
   buildInputs = [ bash libclang llvm llvm.dev unifdef ];
   propagatedBuildInputs = [ chardet pebble psutil ];
-  checkInputs = [ pytestCheckHook pytest-flake8 unifdef ];
 
   # 'cvise --command=...' generates a script with hardcoded shebang.
   postPatch = ''
@@ -30,14 +29,8 @@ buildPythonApplication rec {
       --replace "#!/bin/bash" "#!${bash}/bin/bash"
   '';
 
-  preCheck = ''
+  # pytest-flake8 is broken in nixpkgs: https://github.com/tholo/pytest-flake8/issues/87
-    patchShebangs cvise.py
+  doCheck = false;
-  '';
-  disabledTests = [
-    # Needs gcc, fails when run noninteractively (without tty).
-    "test_simple_reduction"
-  ];
-
   dontUsePipInstall = true;
   dontUseSetuptoolsBuild = true;
   dontUseSetuptoolsCheck = true;

pkgs/os-specific/linux/pax-utils/default.nix

@@ -1,6 +1,7 @@
 { stdenv
 , lib
 , fetchurl
+, buildPackages
 , docbook_xml_dtd_44
 , docbook_xsl
 , libcap
@@ -23,6 +24,7 @@ stdenv.mkDerivation rec {
 
   strictDeps = true;
 
+  depsBuildBuild = [ buildPackages.stdenv.cc ];
   nativeBuildInputs = [ docbook_xml_dtd_44 docbook_xsl meson ninja pkg-config xmlto ];
   buildInputs = [ libcap ];
 

pkgs/tools/admin/gam/default.nix

@@ -0,0 +1,73 @@
+{ lib
+, fetchFromGitHub
+, python3
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "gam";
+  version = "6.22";
+  format = "other";
+
+  src = fetchFromGitHub {
+    owner = "GAM-team";
+    repo = "gam";
+    rev = "v${version}";
+    sha256 = "sha256-G/S1Rrm+suiy1CTTFLcBGt/QhARL7puHgR65nCxodH0=";
+  };
+
+  sourceRoot = "source/src";
+
+  patches = [
+    # Also disables update check
+    ./signal_files_as_env_vars.patch
+  ];
+
+  propagatedBuildInputs = with python3.pkgs; [
+    distro
+    filelock
+    google-api-python-client
+    google-auth
+    google-auth-oauthlib
+    passlib
+    pathvalidate
+    python-dateutil
+    setuptools
+  ];
+
+  # Use XDG-ish dirs for configuration. These would otherwise be in the gam
+  # package.
+  #
+  # Using --run as `makeWapper` evaluates variables for --set and --set-default
+  # at build time and then single quotes the vars in the wrapper, thus they
+  # wouldn't get expanded. But using --run allows setting default vars that are
+  # evaluated on run and not during build time.
+   makeWrapperArgs = [
+    ''--run 'export GAMUSERCONFIGDIR="''${XDG_CONFIG_HOME:-$HOME/.config}/gam"' ''
+    ''--run 'export GAMSITECONFIGDIR="''${XDG_CONFIG_HOME:-$HOME/.config}/gam"' ''
+    ''--run 'export GAMCACHEDIR="''${XDG_CACHE_HOME:-$HOME/.cache}/gam"' ''
+    ''--run 'export GAMDRIVEDIR="$PWD"' ''
+  ];
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out/bin
+    cp gam.py $out/bin/gam
+    mkdir -p $out/lib/${python3.libPrefix}/site-packages
+    cp -r gam $out/lib/${python3.libPrefix}/site-packages
+    runHook postInstall
+  '';
+
+  checkPhase = ''
+    runHook preCheck
+    ${python3.interpreter} -m unittest discover --pattern "*_test.py" --buffer
+    runHook postCheck
+  '';
+
+  meta = with lib; {
+    description = "Command line management for Google Workspace";
+    homepage = "https://github.com/GAM-team/GAM/wiki";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ thanegill ];
+  };
+
+}

pkgs/tools/admin/gam/signal_files_as_env_vars.patch

@@ -0,0 +1,38 @@
+diff --git a/gam/__init__.py b/gam/__init__.py
+index 1c187ce..b2de793 100755
+--- a/gam/__init__.py
++++ b/gam/__init__.py
+@@ -549,22 +549,16 @@ def SetGlobalVariables():
+     _getOldEnvVar(GC_TLS_MIN_VERSION, 'GAM_TLS_MIN_VERSION')
+     _getOldEnvVar(GC_TLS_MAX_VERSION, 'GAM_TLS_MAX_VERSION')
+     _getOldEnvVar(GC_CA_FILE, 'GAM_CA_FILE')
+-    _getOldSignalFile(GC_DEBUG_LEVEL,
+-                      'debug.gam',
+-                      filePresentValue=4,
+-                      fileAbsentValue=0)
+-    _getOldSignalFile(GC_NO_BROWSER, 'nobrowser.txt')
+-    _getOldSignalFile(GC_NO_TDEMAIL, 'notdemail.txt')
+-    _getOldSignalFile(GC_OAUTH_BROWSER, 'oauthbrowser.txt')
++    _getOldEnvVar(GC_DEBUG_LEVEL, 'GAM_DEBUG')
++    _getOldEnvVar(GC_NO_BROWSER, 'GAM_NO_BROWSER')
++    _getOldEnvVar(GC_NO_TDEMAIL, 'GAM_NO_TDEMAIL')
++    _getOldEnvVar(GC_OAUTH_BROWSER, 'GAM_OAUTH_BROWSER')
+     #  _getOldSignalFile(GC_NO_CACHE, u'nocache.txt')
+     #  _getOldSignalFile(GC_CACHE_DISCOVERY_ONLY, u'allcache.txt', filePresentValue=False, fileAbsentValue=True)
+-    _getOldSignalFile(GC_NO_CACHE,
+-                      'allcache.txt',
+-                      filePresentValue=False,
+-                      fileAbsentValue=True)
+-    _getOldSignalFile(GC_NO_SHORT_URLS, 'noshorturls.txt')
+-    _getOldSignalFile(GC_NO_UPDATE_CHECK, 'noupdatecheck.txt')
+-    _getOldSignalFile(GC_ENABLE_DASA, FN_ENABLEDASA_TXT)
++    _getOldEnvVar(GC_NO_CACHE, 'GAM_NO_CACHE')
++    _getOldEnvVar(GC_NO_SHORT_URLS, 'GAM_NO_SHORT_URLS')
++    GC_Defaults[GC_NO_UPDATE_CHECK] = True
++    _getOldEnvVar(GC_ENABLE_DASA, FN_ENABLEDASA_TXT)
+     # Assign directories first
+     for itemName in GC_VAR_INFO:
+         if GC_VAR_INFO[itemName][GC_VAR_TYPE] == GC_TYPE_DIRECTORY:
+--
+2.36.0
+

pkgs/top-level/all-packages.nix

@@ -1222,6 +1222,8 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) ApplicationServices Carbon Cocoa VideoToolbox;
   };
 
+  gam = callPackage ../tools/admin/gam { };
+
   gfshare = callPackage ../tools/security/gfshare { };
 
   gh-cal = callPackage ../tools/misc/gh-cal {
@@ -34345,6 +34347,8 @@ with pkgs;
 
   boogie = dotnetPackages.Boogie;
 
+  cbmc = callPackage ../applications/science/logic/cbmc { };
+
   cadical = callPackage ../applications/science/logic/cadical {};
 
   inherit (callPackage ./coq-packages.nix {

pkgs/top-level/python-packages.nix

@@ -4596,12 +4596,17 @@ in {
     cudaPackages = pkgs.cudaPackages_11_6;
   };
 
-  jaxlib-build = callPackage ../development/python-modules/jaxlib {
+  jaxlib-build = callPackage ../development/python-modules/jaxlib rec {
+    inherit (pkgs.darwin) cctools;
+    buildBazelPackage = pkgs.buildBazelPackage.override {
+      stdenv = if stdenv.isDarwin then pkgs.darwin.apple_sdk_11_0.stdenv else stdenv;
+    };
     # Some platforms don't have `cudaSupport` defined, hence the need for 'or false'.
     cudaSupport = pkgs.config.cudaSupport or false;
     # At the time of writing (2022-04-18), `cudaPackages.nccl` is broken, so we
     # pin to `cudaPackages_11_6` instead.
     cudaPackages = pkgs.cudaPackages_11_6;
+    IOKit = pkgs.darwin.apple_sdk_11_0.IOKit;
   };
 
   jaxlib = self.jaxlib-build;