Merge staging-next into staging

pkgs/applications/editors/poke/default.nix

@@ -22,11 +22,11 @@ let
   isCross = stdenv.hostPlatform != stdenv.buildPlatform;
 in stdenv.mkDerivation rec {
   pname = "poke";
-  version = "2.2";
+  version = "2.3";
 
   src = fetchurl {
     url = "mirror://gnu/${pname}/${pname}-${version}.tar.gz";
-    sha256 = "sha256-xF6k5xpRohhTZzhcAc65dZbsW3EDOGm+xKYLHLciWQM=";
+    sha256 = "sha256-NpDPERbafLOp7GtPcAPiU+JotRAhKiiP04qv7Q68x2Y=";
   };
 
   outputs = [ "out" "dev" "info" "lib" "man" ];

pkgs/applications/networking/cluster/arkade/default.nix

@@ -6,13 +6,13 @@
 
 buildGoModule rec {
   pname = "arkade";
-  version = "0.8.18";
+  version = "0.8.19";
 
   src = fetchFromGitHub {
     owner = "alexellis";
     repo = "arkade";
     rev = version;
-    sha256 = "sha256-VQI2eAxOkOkwYkTM/UyyK6lnXFoLFHWE/ekm5qLN9OE=";
+    sha256 = "sha256-GbuDL0JSG0r2LVcdJgQFBMNDpAl2WbhjIX0Ls9yCDYg=";
   };
 
   CGO_ENABLED = 0;

pkgs/development/interpreters/janet/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "janet";
-  version = "1.21.1";
+  version = "1.21.2";
 
   src = fetchFromGitHub {
     owner = "janet-lang";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-wJwlGliXoj0XmC9qb6SCo8mUy4aqHvJtFiigUB7PFLE=";
+    sha256 = "sha256-6E726+DLs1hCUbr2/rqIdSn8u94LLFdKBBHkbB4rgm0=";
   };
 
   # This release fails the test suite on darwin, remove when debugged.

pkgs/development/libraries/igraph/default.nix

@@ -12,7 +12,9 @@
 , lapack
 , libxml2
 , libxslt
+, llvmPackages
 , pkg-config
+, plfit
 , python3
 , sourceHighlight
 , suitesparse
@@ -30,10 +32,6 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-SL9PcT18vFvykCv4VRXxXtlcDAcybmwEImnnKXMciFQ=";
   };
 
-  # Normally, igraph wants us to call bootstrap.sh, which will call
-  # tools/getversion.sh. Instead, we're going to put the version directly
-  # where igraph wants, and then let autoreconfHook do the rest of the
-  # bootstrap. ~ C.
   postPatch = ''
     echo "${version}" > IGRAPH_VERSION
   '' + lib.optionalString stdenv.isAarch64 ''
@@ -65,7 +63,10 @@ stdenv.mkDerivation rec {
     gmp
     lapack
     libxml2
+    plfit
     suitesparse
+  ] ++ lib.optionals stdenv.cc.isClang [
+    llvmPackages.openmp
   ];
 
   cmakeFlags = [
@@ -75,8 +76,10 @@ stdenv.mkDerivation rec {
     "-DIGRAPH_USE_INTERNAL_GLPK=OFF"
     "-DIGRAPH_USE_INTERNAL_CXSPARSE=OFF"
     "-DIGRAPH_USE_INTERNAL_GMP=OFF"
+    "-DIGRAPH_USE_INTERNAL_PLFIT=OFF"
     "-DIGRAPH_GLPK_SUPPORT=ON"
     "-DIGRAPH_GRAPHML_SUPPORT=ON"
+    "-DIGRAPH_OPENMP_SUPPORT=ON"
     "-DIGRAPH_ENABLE_LTO=AUTO"
     "-DIGRAPH_ENABLE_TLS=ON"
     "-DBUILD_SHARED_LIBS=ON"

pkgs/development/libraries/nlopt/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, cmake, octave ? null }:
+{ lib, stdenv, fetchFromGitHub, cmake, octave ? null, libiconv }:
 
 stdenv.mkDerivation rec {
   pname = "nlopt";
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-TgieCX7yUdTAEblzXY/gCN0r6F9TVDh4RdNDjQdXZ1o=";
   };
 
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake ] ++ lib.optionals stdenv.isDarwin [ libiconv ];
   buildInputs = [ octave ];
 
   configureFlags = [

pkgs/development/python-modules/adafruit-platformdetect/default.nix

@@ -6,13 +6,13 @@
 
 buildPythonPackage rec {
   pname = "adafruit-platformdetect";
-  version = "3.22.0";
+  version = "3.22.1";
   format = "setuptools";
 
   src = fetchPypi {
     pname = "Adafruit-PlatformDetect";
     inherit version;
-    sha256 = "sha256-XnB6aSTKRV72WjcXx9jPZ+FGmCNh6dvwiau7WDlyE5M=";
+    sha256 = "sha256-fOBs0aPekIvpwbrYxzh1wz7EKGko0Je1f/N5H0DIguw=";
   };
 
   nativeBuildInputs = [

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

@@ -1,4 +1,5 @@
 { lib
+, stdenv
 , buildPythonPackage
 , pythonOlder
 , fetchFromGitHub
@@ -58,6 +59,9 @@ buildPythonPackage rec {
     runHook postCheck
   '';
 
+  # Too many failures due to attempting to connect to com.apple.fonts daemon
+  doCheck = !stdenv.isDarwin;
+
   meta = with lib; {
     description = "Simple Python interface for Graphviz";
     homepage = "https://github.com/xflr6/graphviz";

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, setuptools }:
+{ lib, buildPythonPackage, fetchPypi, setuptools, python, which }:
 
 buildPythonPackage rec {
   pname = "nodeenv";
@@ -16,6 +16,13 @@ buildPythonPackage rec {
   # Tests not included in PyPI tarball
   doCheck = false;
 
+  preFixup = ''
+    substituteInPlace $out/${python.sitePackages}/nodeenv.py \
+      --replace '["which", candidate]' '["${lib.getBin which}/bin/which", candidate]'
+  '';
+
+  pythonImportsCheck = [ "nodeenv" ];
+
   meta = with lib; {
     description = "Node.js virtual environment builder";
     homepage = "https://github.com/ekalinin/nodeenv";

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

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "pypandoc";
-  version = "1.7.4";
+  version = "1.7.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-KN4j9kbZ6ARAPGth180yptdso1arx563IXvb/2dI+G4=";
+    sha256 = "sha256-gCwmquF7ZBNsbQBpSdjOGDp9TZ+9Ty0FHmb0+59FylA=";
   };
 
   patches = [

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

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "grcov";
-  version = "0.8.8";
+  version = "0.8.9";
 
   src = fetchFromGitHub {
     owner = "mozilla";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-OITtZdI9d5zQVI02s5gJF9lWCjZZgE7YZRfFROU040o=";
+    sha256 = "sha256-VSjKZoK/o05kYX5mRCnaS6r/+4dZep9Bp9Im1Zw7piM=";
   };
 
-  cargoSha256 = "sha256-AZVkS/huEsA1wdVB/xUGCCjY5AWJxaU1DD/OlEURw/c=";
+  cargoSha256 = "sha256-7I0BizeDbikpog0YG/X8vwoO4PGE1qYzRTWTr0RUQws=";
 
   # tests do not find grcov path correctly
   checkFlags = let

pkgs/development/tools/rust/cargo-flash/default.nix

@@ -10,16 +10,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-flash";
-  version = "0.12.0";
+  version = "0.12.1";
 
   src = fetchFromGitHub {
     owner = "probe-rs";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0s49q8x0iscy9rgn9zgymyg39cqm251a99m341znjn55lap3pdl8";
+    sha256 = "sha256-bd0TY8bdpLHLCdDQgJeJvqjAcSF67+LGSNx8yafYbys=";
   };
 
-  cargoSha256 = "0rb4s5bwjs7hri636r2viva96a6z9qjv9if6i220j9yglrvi7c8i";
+  cargoSha256 = "sha256-bx2N8zP7BmqU6oM/7Nf2i9S1uNWItReQMD59vtG1RKE=";
 
   nativeBuildInputs = [ pkg-config rustfmt ];
   buildInputs = [ libusb1 ] ++ lib.optionals stdenv.isDarwin [ AppKit ];

pkgs/development/tools/sentry-cli/default.nix

@@ -9,13 +9,13 @@
 }:
 rustPlatform.buildRustPackage rec {
   pname = "sentry-cli";
-  version = "1.74.2";
+  version = "1.74.3";
 
   src = fetchFromGitHub {
     owner = "getsentry";
     repo = "sentry-cli";
     rev = version;
-    sha256 = "sha256-1A/c5HiXtT6xUTxVInv9DbbCsqpu8iCJ7I0A9wFeaQ0=";
+    sha256 = "sha256-savbS/1j6PJqmkk6c+XMOUEkrLZNU2p0YbN8rHfz2po=";
   };
   doCheck = false;
 
@@ -25,7 +25,7 @@ rustPlatform.buildRustPackage rec {
   buildInputs = [ openssl ] ++ lib.optionals stdenv.isDarwin [ Security SystemConfiguration ];
   nativeBuildInputs = [ pkg-config ];
 
-  cargoSha256 = "sha256-z++t+Zt40az11z/xhobvvbbSNUBpnMzqlRzoOuYgY2U=";
+  cargoSha256 = "sha256-7B8cmrDYufhlIMv2r6TSD+C8NLE2Juewgy4XYYr+QKs=";
 
   meta = with lib; {
     homepage = "https://docs.sentry.io/cli/";

pkgs/tools/misc/plfit/default.nix

@@ -0,0 +1,54 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, fetchpatch
+, cmake
+, python ? null
+, swig
+, llvmPackages
+}:
+
+stdenv.mkDerivation rec {
+  pname = "plfit";
+  version = "0.9.3";
+
+  src = fetchFromGitHub {
+    owner = "ntamas";
+    repo = "plfit";
+    rev = version;
+    hash = "sha256-y4n6AlGtuuUuA+33oF7lGOYuKSqea4GMSJlv9PaSpQ8=";
+  };
+
+  patches = [
+    # https://github.com/ntamas/plfit/pull/41
+    (fetchpatch {
+      name = "use-cmake-install-full-dir.patch";
+      url = "https://github.com/ntamas/plfit/commit/d0e77c80e6e899298240e6be465cf580603f6ee2.patch";
+      hash = "sha256-wi3qCp6ZQtrKuM7XDA6xCXunCiqsyhnkxmg2eSmxjYM=";
+    })
+  ];
+
+  nativeBuildInputs = [
+    cmake
+  ] ++ lib.optionals (!isNull python) [
+    python
+    swig
+  ];
+
+  cmakeFlags = [
+    "-DPLFIT_USE_OPENMP=ON"
+  ] ++ lib.optionals (!isNull python) [
+    "-DPLFIT_COMPILE_PYTHON_MODULE=ON"
+  ];
+
+  buildInputs = lib.optionals stdenv.cc.isClang [
+    llvmPackages.openmp
+  ];
+
+  meta = with lib; {
+    description = "Fitting power-law distributions to empirical data";
+    homepage = "https://github.com/ntamas/plfit";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ dotlambda ];
+  };
+}

pkgs/tools/misc/pre-commit/default.nix

@@ -1,17 +1,27 @@
-{ lib, python3Packages }:
+{ lib
+, python3Packages
+, fetchFromGitHub
+  # tests
+, cargo
+, dotnet-sdk
+, git
+, go
+, nodejs
+}:
 
 with python3Packages;
 buildPythonPackage rec {
   pname = "pre-commit";
-  version = "2.17.0";
+  version = "2.18.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
-  src = fetchPypi {
-    inherit version;
-    pname = "pre_commit";
-    sha256 = "c1a8040ff15ad3d648c70cc3e55b93e4d2d5b687320955505587fd79bbaed06a";
+  src = fetchFromGitHub {
+    owner = "pre-commit";
+    repo = "pre-commit";
+    rev = "v${version}";
+    sha256 = "sha256-d/ukUTjNgpqr6IeDJHDaOXQm0EdsX+vq0sVX7HG3gSE=";
   };
 
   patches = [
@@ -32,18 +42,103 @@ buildPythonPackage rec {
     importlib-resources
   ];
 
-  # slow and impure
-  doCheck = false;
+  checkInputs = [
+    cargo
+    dotnet-sdk
+    git
+    go
+    nodejs
+    pytest-env
+    pytest-xdist
+    pytestCheckHook
+    re-assert
+  ];
 
-  preFixup = ''
-    substituteInPlace $out/${python.sitePackages}/pre_commit/resources/hook-tmpl \
+  doCheck = true;
+
+  postPatch = ''
+    substituteInPlace pre_commit/resources/hook-tmpl \
       --subst-var-by pre-commit $out
-    substituteInPlace $out/${python.sitePackages}/pre_commit/languages/python.py \
+    substituteInPlace pre_commit/languages/python.py \
       --subst-var-by virtualenv ${virtualenv}
-    substituteInPlace $out/${python.sitePackages}/pre_commit/languages/node.py \
+    substituteInPlace pre_commit/languages/node.py \
       --subst-var-by nodeenv ${nodeenv}
+
+    patchShebangs pre_commit/resources/hook-tmpl
   '';
 
+  pytestFlagsArray = [
+    "--numprocesses $NIX_BUILD_CORES"
+    "--forked"
+  ];
+
+  preCheck = ''
+    export GIT_AUTHOR_NAME=test GIT_COMMITTER_NAME=test \
+           GIT_AUTHOR_EMAIL=test@example.com GIT_COMMITTER_EMAIL=test@example.com \
+           VIRTUALENV_NO_DOWNLOAD=1 PRE_COMMIT_NO_CONCURRENCY=1 LANG=en_US.UTF-8
+
+    git init -b master
+
+    export HOME=$(mktemp -d)
+
+    python -m venv --system-site-packages venv
+    source "$PWD/venv/bin/activate"
+    #$out/bin/pre-commit install
+    python setup.py develop
+  '';
+
+  postCheck = ''
+    deactivate
+  '';
+
+  disabledTests = [
+    # ERROR: The install method you used for conda--probably either `pip install conda`
+    # or `easy_install conda`--is not compatible with using conda as an application.
+    "test_conda_"
+    "test_local_conda_"
+
+    # /build/pytest-of-nixbld/pytest-0/test_install_ruby_with_version0/rbenv-2.7.2/libexec/rbenv-init:
+    # /usr/bin/env: bad interpreter: No such file or directory
+    "ruby"
+
+    # network
+    "test_additional_dependencies_roll_forward"
+    "test_additional_golang_dependencies_installed"
+    "test_additional_node_dependencies_installed"
+    "test_additional_rust_cli_dependencies_installed"
+    "test_additional_rust_lib_dependencies_installed"
+    "test_dart_hook"
+    "test_dotnet_hook"
+    "test_golang_hook"
+    "test_golang_hook_still_works_when_gobin_is_set"
+    "test_installs_without_links_outside_env"
+    "test_local_dart_additional_dependencies"
+    "test_local_golang_additional_dependencies"
+    "test_local_lua_additional_dependencies"
+    "test_local_perl_additional_dependencies"
+    "test_local_rust_additional_dependencies"
+    "test_lua_hook"
+    "test_perl_hook"
+    "test_r_hook"
+    "test_r_inline_hook"
+    "test_r_local_with_additional_dependencies_hook"
+    "test_r_with_additional_dependencies_hook"
+    "test_run_a_node_hook_default_version"
+    "test_run_versioned_node_hook"
+
+    # python2, no explanation needed
+    "python2"
+    "test_switch_language_versions_doesnt_clobber"
+
+    # docker
+    "test_run_a_docker_hook"
+
+    # i don't know why these fail
+    "test_install_existing_hooks_no_overwrite"
+    "test_installed_from_venv"
+    "test_uninstall_restores_legacy_hooks"
+  ];
+
   pythonImportsCheck = [
     "pre_commit"
   ];

pkgs/tools/networking/mosh/default.nix

@@ -11,8 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "05hjhlp6lk8yjcy59zywpf0r6s0h0b9zxq0lw66dh9x8vxrhaq6s";
   };
 
-  nativeBuildInputs = [ autoreconfHook pkg-config makeWrapper protobuf ];
-  buildInputs = [ protobuf ncurses zlib openssl bash-completion perlPackages.perl ]
+  nativeBuildInputs = [ autoreconfHook pkg-config makeWrapper protobuf perlPackages.perl ];
+  buildInputs = [ protobuf ncurses zlib openssl bash-completion ]
     ++ lib.optional withUtempter libutempter;
 
   strictDeps = true;

pkgs/tools/networking/smartdns/default.nix

@@ -1,34 +1,32 @@
-{ lib, stdenv, fetchFromGitHub, openssl }:
+{ lib, stdenv, fetchFromGitHub, openssl, testVersion, smartdns }:
 
 stdenv.mkDerivation rec {
   pname = "smartdns";
-  version = "35";
+  version = "36";
 
   src = fetchFromGitHub {
     owner = "pymumu";
     repo = pname;
     rev = "Release${version}";
-    sha256 = "sha256-5822qe3mdn4wPO8fHW5AsgMA7xbJnMjZn9DbiMU3GX0=";
+    sha256 = "sha256-sjrRPmTJRCUnMrA08M/VdYhL7/OfQY30/t1loLPSrlQ=";
   };
 
   buildInputs = [ openssl ];
 
-  # Force the systemd service file to be regenerated from it's template.  This
-  # file is erroneously added in version 35 and it has already been deleted from
-  # upstream's git repository.  So this "postPatch" phase can be deleted in next
-  # release.
-  postPatch = ''
-    rm -f systemd/smartdns.service
-  '';
-
   makeFlags = [
     "PREFIX=${placeholder "out"}"
     "SYSTEMDSYSTEMUNITDIR=${placeholder "out"}/lib/systemd/system"
     "RUNSTATEDIR=/run"
+    # by default it is the build time... weird... https://github.com/pymumu/smartdns/search?q=ver
+    "VER=${version}"
   ];
 
   installFlags = [ "SYSCONFDIR=${placeholder "out"}/etc" ];
 
+  passthru.tests = {
+    version = testVersion { package = smartdns; };
+  };
+
   meta = with lib; {
     description =
       "A local DNS server to obtain the fastest website IP for the best Internet experience";

pkgs/top-level/all-packages.nix

@@ -9081,6 +9081,10 @@ with pkgs;
 
   pleroma = callPackage ../servers/pleroma { };
 
+  plfit = callPackage ../tools/misc/plfit {
+    python = null;
+  };
+
   ploticus = callPackage ../tools/graphics/ploticus {
     libpng = libpng12;
   };
@@ -23372,7 +23376,7 @@ with pkgs;
     withCryptsetup = true;
     withFido2 = true;
     withTpm2Tss = true;
-    inherit lvm2 libfido2 p11-kit;
+    inherit libfido2 p11-kit;
   };
   systemdStage1Network = systemdStage1.override {
     pname = "systemd-stage-1-network";

pkgs/top-level/python-packages.nix

@@ -6383,6 +6383,10 @@ in {
 
   plexwebsocket = callPackage ../development/python-modules/plexwebsocket { };
 
+  plfit = toPythonModule (pkgs.plfit.override {
+    inherit (self) python;
+  });
+
   plone-testing = callPackage ../development/python-modules/plone-testing { };
 
   plotly = callPackage ../development/python-modules/plotly { };