Merge staging-next into staging

lib/sources.nix

@@ -53,12 +53,16 @@ rec {
   # Filter sources by a list of regular expressions.
   #
   # E.g. `src = sourceByRegex ./my-subproject [".*\.py$" "^database.sql$"]`
-  sourceByRegex = src: regexes: cleanSourceWith {
-    filter = (path: type:
-      let relPath = lib.removePrefix (toString src + "/") (toString path);
-      in lib.any (re: builtins.match re relPath != null) regexes);
-    inherit src;
-  };
+  sourceByRegex = src: regexes:
+    let
+      isFiltered = src ? _isLibCleanSourceWith;
+      origSrc = if isFiltered then src.origSrc else src;
+    in lib.cleanSourceWith {
+      filter = (path: type:
+        let relPath = lib.removePrefix (toString origSrc + "/") (toString path);
+        in lib.any (re: builtins.match re relPath != null) regexes);
+      inherit src;
+    };
 
   # Get all files ending with the specified suffices from the given
   # directory or its descendants.  E.g. `sourceFilesBySuffices ./dir

nixos/doc/manual/configuration/matrix.xml

@@ -95,7 +95,7 @@ in {
 
         # forward all Matrix API calls to the synapse Matrix homeserver
         locations."/_matrix" = {
-          proxyPass = "http://[::1]:8008/_matrix";
+          proxyPass = "http://[::1]:8008"; # without a trailing /
         };
       };
     };

pkgs/applications/misc/kitty/default.nix

@@ -1,6 +1,6 @@
 { stdenv, substituteAll, fetchFromGitHub, python3Packages, glfw, libunistring,
   harfbuzz, fontconfig, pkgconfig, ncurses, imagemagick, xsel,
-  libstartup_notification, libX11, libXrandr, libXinerama, libXcursor,
+  libstartup_notification, libGL, libX11, libXrandr, libXinerama, libXcursor,
   libxkbcommon, libXi, libXext, wayland-protocols, wayland,
   which, dbus,
   Cocoa,
@@ -57,6 +57,8 @@ buildPythonApplication rec {
     optipng
   ];
 
+  propagatedBuildInputs = stdenv.lib.optional stdenv.isLinux libGL;
+
   outputs = [ "out" "terminfo" ];
 
   patches = [
@@ -70,6 +72,10 @@ buildPythonApplication rec {
     ./png2icns.patch
   ];
 
+  preConfigure  = stdenv.lib.optional (!stdenv.isDarwin) ''
+    substituteInPlace glfw/egl_context.c --replace "libEGL.so.1" "${stdenv.lib.getLib libGL}/lib/libEGL.so.1"
+  '';
+
   buildPhase = if stdenv.isDarwin then ''
     make app
   '' else ''

pkgs/build-support/build-bazel-package/default.nix

@@ -1,4 +1,8 @@
-{ stdenv, bazel, cacert }:
+{ stdenv
+, bazel
+, cacert
+, lib
+}:
 
 args@{ name, bazelFlags ? [], bazelTarget, buildAttrs, fetchAttrs, ... }:
 
@@ -109,6 +113,31 @@ in stdenv.mkDerivation (fBuildAttrs // {
   buildPhase = fBuildAttrs.buildPhase or ''
     runHook preBuild
 
+    '' + lib.optionalString stdenv.isDarwin ''
+    # Bazel sandboxes the execution of the tools it invokes, so even though we are
+    # calling the correct nix wrappers, the values of the environment variables
+    # the wrappers are expecting will not be set. So instead of relying on the
+    # wrappers picking them up, pass them in explicitly via `--copt`, `--linkopt`
+    # and related flags.
+    #
+    copts=()
+    host_copts=()
+    for flag in $NIX_CFLAGS_COMPILE; do
+      copts+=( "--copt=$flag" )
+      host_copts+=( "--host_copt=$flag" )
+    done
+    for flag in $NIX_CXXSTDLIB_COMPILE; do
+      copts+=( "--copt=$flag" )
+      host_copts+=( "--host_copt=$flag" )
+    done
+    linkopts=()
+    host_linkopts=()
+    for flag in $NIX_LD_FLAGS; do
+      linkopts+=( "--linkopt=$flag" )
+      host_linkopts+=( "--host_linkopt=$flag" )
+    done
+    '' + ''
+
     BAZEL_USE_CPP_ONLY_TOOLCHAIN=1 \
     USER=homeless-shelter \
     bazel \
@@ -116,6 +145,12 @@ in stdenv.mkDerivation (fBuildAttrs // {
       --output_user_root="$bazelUserRoot" \
       build \
       -j $NIX_BUILD_CORES \
+      '' + lib.optionalString stdenv.isDarwin ''
+      "''${copts[@]}" \
+      "''${host_copts[@]}" \
+      "''${linkopts[@]}" \
+      "''${host_linkopts[@]}" \
+      '' + ''
       $bazelFlags \
       $bazelTarget
 

pkgs/development/libraries/gstreamer/bad/default.nix

@@ -2,6 +2,7 @@
 , config
 , pkgconfig, python3, gst-plugins-base, orc
 , gobject-introspection
+, enableZbar ? true
 , faacSupport ? false, faac ? null
 , faad2, libass, libkate, libmms, librdf, ladspaH
 , libnice, webrtc-audio-processing, lilv, lv2, serd, sord, sratom
@@ -136,13 +137,13 @@ stdenv.mkDerivation rec {
     soundtouch
     spandsp
     srtp
-    zbar
     fluidsynth libvdpau
     libwebp xvidcore gnutls libGLU_combined
     libgme openssl x265 libxml2
     libintl
     srt
   ]
+    ++ optional enableZbar zbar
     ++ optional faacSupport faac
     ++ optional stdenv.isLinux wayland
     # wildmidi requires apple's OpenAL
@@ -158,6 +159,7 @@ stdenv.mkDerivation rec {
     "-Dexamples=disabled" # requires many dependencies and probably not useful for our users
 
     "-Ddts=disabled" # required `libdca` library not packaged in nixpkgs as of writing, and marked as "BIG FAT WARNING: libdca is still in early development"
+    "-Dzbar=${if enableZbar then "enabled" else "disabled"}"
     "-Dfaac=${if faacSupport then "enabled" else "disabled"}"
     "-Diqa=disabled" # required `dssim` library not packaging in nixpkgs as of writing
     "-Dmsdk=disabled" # not packaged in nixpkgs as of writing / no Windows support

pkgs/development/libraries/gtk+/3.x.nix

@@ -154,17 +154,13 @@ stdenv.mkDerivation rec {
     done
   '';
 
-  # Make all demo related things in dev
-  postFixup =  ''
-    moveToOutput share/icons/hicolor "$dev"
-    moveToOutput share/applications "$dev"
-    moveToOutput share/gsettings-schemas "$dev"
-
+  # Wrap demos
+  postFixup =  optionalString (!stdenv.isDarwin) ''
     demos=(gtk3-demo gtk3-demo-application gtk3-icon-browser gtk3-widget-factory)
 
     for program in ''${demos[@]}; do
       wrapProgram $dev/bin/$program \
-        --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH:$dev/share/gsettings-schemas/${pname}-${version}"
+        --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH:$out/share/gsettings-schemas/${pname}-${version}"
     done
   '';
 

pkgs/development/libraries/rocksdb/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, lib, bzip2, cmake, gflags, lz4, snappy, zlib, zstd, enableLite ? false }:
+{ stdenv, fetchFromGitHub, lib, bzip2, cmake, lz4, snappy, zlib, zstd, enableLite ? false }:
 
 stdenv.mkDerivation rec {
   pname = "rocksdb";
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ cmake ];
-  buildInputs = [ bzip2 gflags lz4 snappy zlib zstd ];
+  buildInputs = [ bzip2 lz4 snappy zlib zstd ];
 
   patches = [ ./0001-findzlib.patch ];
 
@@ -27,6 +27,7 @@ stdenv.mkDerivation rec {
     "-DWITH_SNAPPY=1"
     "-DWITH_ZLIB=1"
     "-DWITH_ZSTD=1"
+    "-DWITH_GFLAGS=0"
     (lib.optional
         (stdenv.hostPlatform.system == "i686-linux"
          || stdenv.hostPlatform.system == "x86_64-linux")

pkgs/development/libraries/zeromq/4.x.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake, asciidoc }:
+{ stdenv, fetchFromGitHub, cmake, asciidoc, enableDrafts ? false }:
 
 stdenv.mkDerivation rec {
   name = "zeromq-${version}";
@@ -17,6 +17,8 @@ stdenv.mkDerivation rec {
 
   doCheck = false; # fails all the tests (ctest)
 
+  cmakeFlags = if enableDrafts then [ "-DENABLE_DRAFTS=ON" ] else null;
+
   meta = with stdenv.lib; {
     branch = "4";
     homepage = http://www.zeromq.org;

pkgs/development/lisp-modules/clwrapper/cl-wrapper.sh

@@ -8,7 +8,12 @@ eval "$NIX_LISP_PREHOOK"
 NIX_LISP_COMMAND="$1"
 shift
 
-[ -z "$NIX_LISP" ] && NIX_LISP="${NIX_LISP_COMMAND##*/}"
+if [ -z "$NIX_LISP" ]; then
+    while [ -h "${NIX_LISP_COMMAND}" ]; do
+        NIX_LISP_COMMAND="$(readlink -n "${NIX_LISP_COMMAND}")"
+    done
+    NIX_LISP="${NIX_LISP_COMMAND##*/}"
+fi
 
 export NIX_LISP NIX_LISP_LOAD_FILE NIX_LISP_EXEC_CODE NIX_LISP_COMMAND NIX_LISP_FINAL_PARAMETERS
 
@@ -116,8 +121,10 @@ nix_lisp_build_system(){
 
 eval "$NIX_LISP_PRELAUNCH_HOOK"
 
-[ -z "$NIX_LISP_SKIP_CODE" ] && "$NIX_LISP_COMMAND" $NIX_LISP_EARLY_OPTIONS \
-	$NIX_LISP_EXEC_CODE "${NIX_LISP_ASDF_LOAD:-"(load \"$NIX_LISP_ASDF/lib/common-lisp/asdf/build/asdf.$NIX_LISP_FASL_TYPE\")"}" \
-	$NIX_LISP_EXEC_CODE "$NIX_LISP_ASDF_REGISTRY_CODE" \
-	${NIX_LISP_FINAL_PARAMETERS[*]:+"${NIX_LISP_FINAL_PARAMETERS[@]}"} \
-	"$@"
+if [ -z "$NIX_LISP_SKIP_CODE" ]; then
+    "$NIX_LISP_COMMAND" $NIX_LISP_EARLY_OPTIONS \
+	                $NIX_LISP_EXEC_CODE "${NIX_LISP_ASDF_LOAD:-"(load \"$NIX_LISP_ASDF/lib/common-lisp/asdf/build/asdf.$NIX_LISP_FASL_TYPE\")"}" \
+	                $NIX_LISP_EXEC_CODE "$NIX_LISP_ASDF_REGISTRY_CODE" \
+	                ${NIX_LISP_FINAL_PARAMETERS[*]:+"${NIX_LISP_FINAL_PARAMETERS[@]}"} \
+	                "$@"
+fi

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

@@ -0,0 +1,27 @@
+{ lib, buildPythonPackage, fetchFromGitHub, humanfriendly, pytest, pytestcov }:
+
+buildPythonPackage rec {
+  pname = "capturer";
+  version = "2.4";
+
+  src = fetchFromGitHub {
+    owner = "xolox";
+    repo = "python-capturer";
+    rev = version;
+    sha256 = "07zy264xd0g7pz9sxjqcpwmrck334xcbb7wfss26lmvgdr5nhcb9";
+  };
+
+  propagatedBuildInputs = [ humanfriendly ];
+
+  checkPhase = ''
+    PATH=$PATH:$out/bin pytest .
+  '';
+  checkInputs = [ pytest ];
+
+  meta = with lib; {
+    description = "Easily capture stdout/stderr of the current process and subprocesses";
+    homepage = https://github.com/xolox/python-capturer;
+    license = licenses.mit;
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}

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

@@ -0,0 +1,34 @@
+{ lib, buildPythonPackage, fetchFromGitHub, stdenv, isPy3k, fetchpatch, humanfriendly, verboselogs, capturer, pytest, mock, utillinux }:
+
+buildPythonPackage rec {
+  pname = "coloredlogs";
+  version = "10.0";
+
+  src = fetchFromGitHub {
+    owner = "xolox";
+    repo = "python-coloredlogs";
+    rev = version;
+    sha256 = "0rdvp4dfvzhx7z7s2jdl3fv7x1hazgpy5gc7bcf05bnbv2iia54a";
+  };
+
+  # patch by risicle
+  patches = lib.optional (stdenv.isDarwin && isPy3k) (fetchpatch {
+    name = "darwin-py3-capture-fix.patch";
+    url = "https://github.com/xolox/python-coloredlogs/pull/74.patch";
+    sha256 = "0pk7k94iz0gdripw623vzdl4hd83vwhsfzshl8pbvh1n6swi0xx9";
+  });
+
+  checkPhase = ''
+    PATH=$PATH:$out/bin pytest . -k "not test_plain_text_output_format"
+  '';
+  checkInputs = [ pytest mock utillinux ];
+
+  propagatedBuildInputs = [ humanfriendly verboselogs capturer ];
+
+  meta = with lib; {
+    description = "Colored stream handler for Python's logging module";
+    homepage = https://github.com/xolox/python-coloredlogs;
+    license = licenses.mit;
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}

pkgs/development/python-modules/dm-sonnet/default.nix

@@ -36,7 +36,7 @@ let
     bazelTarget = ":install";
 
     fetchAttrs = {
-      sha256 = "0f2rlzrlazmgjrsin8vq3jfv431cc8sx8lxsr6x4wgd4jx5d1zzy";
+      sha256 = "141k2caj5hlk31gnqryp6w2mzyz4i5s1rf8f3qr18isxy235k3w6";
     };
 
     bazelFlags = [

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

@@ -0,0 +1,31 @@
+{ lib, buildPythonPackage, fetchFromGitHub, coloredlogs, property-manager, fasteners, pytest, mock, virtualenv }:
+
+buildPythonPackage rec {
+  pname = "executor";
+  version = "21.3";
+
+  src = fetchFromGitHub {
+    owner = "xolox";
+    repo = "python-executor";
+    rev = version;
+    sha256 = "0rc14vjx3d6irfaw0pczzw1pn0xjl7xikv32hc1fvxv2ibnldv5d";
+  };
+
+  propagatedBuildInputs = [ coloredlogs property-manager fasteners ];
+
+  checkInputs = [ pytest mock virtualenv ];
+
+  # ignore impure tests
+  checkPhase = ''
+    pytest . -k "not option and not retry \
+                 and not remote and not ssh \
+                 and not foreach and not local_context"
+  '';
+
+  meta = with lib; {
+    description = "Programmer friendly subprocess wrapper";
+    homepage = https://github.com/xolox/python-executor;
+    license = licenses.mit;
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}

pkgs/development/python-modules/google-api-python-client/default.nix

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "google-api-python-client";
-  version = "1.7.9";
+  version = "1.7.10";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1v551xaavqff085gplinnnrz2sk6sikmm7j47gi0wf34hpba1384";
+    sha256 = "1mlx5dvkh6rjkvkd91flyhrmji2kw9rlr05n8n4wccv2np3sam9f";
   };
 
   # No tests included in archive

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

@@ -5,13 +5,17 @@
 
 buildPythonPackage rec {
   pname = "jsondiff";
-  version = "1.1.2";
+  version = "1.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7e18138aecaa4a8f3b7ac7525b8466234e6378dd6cae702b982c9ed851d2ae21";
+    sha256 = "00v3689175aqzdscrxpffm712ylp8jvcpqdg51ca22ni6721p51l";
   };
 
+  postPatch = ''
+    sed -e "/'jsondiff=jsondiff.cli:main_deprecated',/d" -i setup.py
+  '';
+
   # No tests
   doCheck = false;
 
@@ -20,5 +24,4 @@ buildPythonPackage rec {
     homepage = https://github.com/ZoomerAnalytics/jsondiff;
     license = lib.licenses.mit;
   };
-
-}
+}

pkgs/development/python-modules/mkl-service/default.nix

@@ -0,0 +1,26 @@
+{ lib, buildPythonPackage, fetchFromGitHub, cython, mkl, nose, six }:
+
+buildPythonPackage rec {
+  pname = "mkl-service";
+  version = "2.1.0";
+
+  src = fetchFromGitHub {
+    owner = "IntelPython";
+    repo = "mkl-service";
+    rev = "v${version}";
+    sha256 = "1bnpgx629rxqf0yhn0jn68ypj3dqv6njc3981j1g8j8rsm5lycrn";
+  };
+
+  MKLROOT = mkl;
+
+  checkInputs = [ nose ];
+  nativeBuildInputs = [ cython ];
+  propagatedBuildInputs = [ mkl six ];
+
+  meta = with lib; {
+    description = "Python hooks for Intel(R) Math Kernel Library runtime control settings";
+    homepage = "https://github.com/IntelPython/mkl-service";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ bhipple ];
+  };
+}

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

@@ -0,0 +1,20 @@
+{ lib, buildPythonPackage, fetchFromGitHub }:
+
+buildPythonPackage rec {
+  pname = "naturalsort";
+  version = "1.5.1";
+
+  src = fetchFromGitHub {
+    owner = "xolox";
+    repo = "python-naturalsort";
+    rev = version;
+    sha256 = "0w43vlddzh97hffnvxp2zkrns9qyirx5g8ijxnxkbx1c4b4gq5ih";
+  };
+
+  meta = with lib; {
+    description = "Simple natural order sorting API for Python that just works";
+    homepage = https://github.com/xolox/python-naturalsort;
+    license = licenses.mit;
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}

pkgs/development/python-modules/property-manager/default.nix

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchFromGitHub, humanfriendly, verboselogs, coloredlogs, pytest, pytestcov }:
+
+buildPythonPackage rec {
+  pname = "property-manager";
+  version = "2.3.1";
+
+  src = fetchFromGitHub {
+    owner = "xolox";
+    repo = "python-property-manager";
+    rev = version;
+    sha256 = "0s4nwipxd8c2vp4rd8mxrj8wbycniz5ki5n177d0dbrnll5amcz0";
+  };
+
+  propagatedBuildInputs = [ coloredlogs humanfriendly verboselogs ];
+  checkInputs = [ pytest pytestcov ];
+
+  meta = with lib; {
+    description = "Useful property variants for Python programming";
+    homepage = https://github.com/xolox/python-property-manager;
+    license = licenses.mit;
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}

pkgs/development/python-modules/update-dotdee/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchFromGitHub, executor, naturalsort }:
+
+buildPythonPackage rec {
+  pname = "update-dotdee";
+  version = "5.0";
+
+  src = fetchFromGitHub {
+    owner = "xolox";
+    repo = "python-update-dotdee";
+    rev = version;
+    sha256 = "1h3m593nwzx6vwa24k0wizb7la49yhqxwn73ipclxgxxi4dfdj01";
+  };
+
+  propagatedBuildInputs = [ executor naturalsort ];
+
+  meta = with lib; {
+    description = "Generic modularized configuration file manager";
+    homepage = https://github.com/xolox/python-update-dotdee;
+    license = licenses.mit;
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}

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

@@ -0,0 +1,26 @@
+{ lib, buildPythonPackage, fetchFromGitHub, pytest, mock }:
+
+buildPythonPackage rec {
+  pname = "verboselogs";
+  version = "1.7";
+
+  src = fetchFromGitHub {
+    owner = "xolox";
+    repo = "python-verboselogs";
+    rev = version;
+    sha256 = "10jzm8pkl49as4y2zyiidmfqqj5zmqg3p73jvx4lfxi0gmp1vhl5";
+  };
+
+  # do not run pylint plugin test, as astroid is a old unsupported version
+  checkPhase = ''
+    PATH=$PATH:$out/bin pytest . -k "not test_pylint_plugin"
+  '';
+  checkInputs = [ pytest mock ];
+
+  meta = with lib; {
+    description = "Verbose logging for Python's logging module";
+    homepage = https://github.com/xolox/python-verboselogs;
+    license = licenses.mit;
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}

pkgs/development/tools/build-managers/bazel/bazel-deps/default.nix

@@ -2,7 +2,7 @@
 
 buildBazelPackage rec {
   name = "bazel-deps-${version}";
-  version = "2019-02-01";
+  version = "2019-07-11";
 
   meta = with stdenv.lib; {
     homepage = "https://github.com/johnynek/bazel-deps";
@@ -10,13 +10,14 @@ buildBazelPackage rec {
     license = licenses.mit;
     maintainers = [ maintainers.uri-canva ];
     platforms = platforms.all;
+    broken = true; # global variable '_common_attrs_for_plugin_bootstrapping' is referenced before assignment.
   };
 
   src = fetchFromGitHub {
     owner = "johnynek";
     repo = "bazel-deps";
-    rev = "6585033409e09028852403ec15ec0c77851234be";
-    sha256 = "0hypf7mcbpx2djqm92k82vn1k6pbnv564xbnazx8nw60f6ns0x87";
+    rev = "48fdf7f8bcf3aadfa07f9f7e6f0c9f4247cb0f58";
+    sha256 = "0wpn5anfgq5wfljfhpn8gbgdmgcp0claffjgqcnv5dh70ch7i0gi";
   };
 
   bazelTarget = "//src/scala/com/github/johnynek/bazel_deps:parseproject_deploy.jar";
@@ -24,49 +25,7 @@ buildBazelPackage rec {
   buildInputs = [ git makeWrapper ];
 
   fetchAttrs = {
-    preInstall = ''
-      # Remove all built in external workspaces, Bazel will recreate them when building
-      rm -rf $bazelOut/external/{bazel_tools,\@bazel_tools.marker,embedded_jdk,\@embedded_jdk.marker,local_*,\@local_*}
-      # For each external workspace, remove all files that aren't referenced by Bazel
-      # Many of these files are non-hermetic (for example .git/refs/remotes/origin/HEAD)
-      files_to_delete=()
-      for workspace in $(find $bazelOut/external -maxdepth 2 -name "WORKSPACE" -print0 | xargs -0L1 dirname); do
-        workspaceOut="$NIX_BUILD_TOP/workspaces/$(basename workspace)/output"
-        workspaceUserRoot="$NIX_BUILD_TOP/workspaces/$(basename workspace)/tmp"
-        rm -rf $workspace/.git
-        if ! targets_and_files=$(cd "$workspace" && bazel --output_base="$workspaceOut" --output_user_root="$workspaceUserRoot" query '//...:*' 2> /dev/null | sort -u); then
-          continue
-        fi
-        if ! targets=$(cd "$workspace" && bazel --output_base="$workspaceOut" --output_user_root="$workspaceUserRoot" query '//...:all' 2> /dev/null | sort -u); then
-          continue
-        fi
-        mapfile -t referenced_files < <(comm -23 <(printf '%s' "$targets_and_files") <(printf '%s' "$targets") | sed -e 's,^//:,,g' | sed -e 's,^//,,g' | sed -e 's,:,/,g')
-        referenced_files+=( "WORKSPACE" )
-        for referenced_file in "''${referenced_files[@]}"; do
-          # Some of the referenced files are symlinks to non-referenced files.
-          # The symlink targets have deterministic contents, but non-deterministic
-          # paths. Copy them to the referenced path, which is deterministic.
-          if target=$(readlink "$workspace/$referenced_file"); then
-            rm "$workspace/$referenced_file"
-            cp -a "$target" "$workspace/$referenced_file"
-          fi
-        done
-        mapfile -t workspace_files_to_delete < <(find "$workspace" -type f -or -type l | sort -u | comm -23 - <(printf "$workspace/%s\n" "''${referenced_files[@]}" | sort -u))
-        for workspace_file_to_delete in "''${workspace_files_to_delete[@]}"; do
-          files_to_delete+=("$workspace_file_to_delete")
-        done
-        # We're running bazel in many different workspaces in a loop. Letting the
-        # daemon shut down on its own would leave several daemons alive at the
-        # same time, using up a lot of memory. Shut them down explicitly instead.
-        bazel --output_base="$workspaceOut" --output_user_root="$workspaceUserRoot" shutdown 2> /dev/null
-      done
-      for file_to_delete in "''${files_to_delete[@]}"; do
-        rm "$file_to_delete"
-      done
-      find . -type d -empty -delete
-    '';
-
-    sha256 = "1yirrzhhrsmbgd27fg709plhrhyi8pzwqv84yg72sd3799kswh9m";
+    sha256 = "1r5qxsbw2cgww7vcg5psh7404l3jcxpvc0ndgl3k8vj1x8y93nkf";
   };
 
   buildAttrs = {

pkgs/development/tools/build-managers/bazel/bazel-remote/default.nix

@@ -76,5 +76,6 @@ buildBazelPackage rec {
     license = licenses.asl20;
     maintainers = [ maintainers.uri-canva ];
     platforms = platforms.darwin;
+    broken = true; # global variable '_layer' is referenced before assignment.
   };
 }

pkgs/development/tools/build-managers/bazel/default.nix

@@ -1,4 +1,5 @@
-{ stdenv, callPackage, lib, fetchurl, fetchFromGitHub, runCommand, runCommandCC, makeWrapper
+{ stdenv, callPackage, lib, fetchurl, fetchFromGitHub
+, runCommand, runCommandCC, makeWrapper, recurseIntoAttrs
 # this package (through the fixpoint glass)
 , bazel
 , lr, xe, zip, unzip, bash, writeCBin, coreutils
@@ -11,6 +12,8 @@
 , buildJdk, runJdk
 , buildJdkName
 , runtimeShell
+# Downstream packages for tests
+, bazel-watcher
 # Always assume all markers valid (don't redownload dependencies).
 # Also, don't clean up environment variables.
 , enableNixHacks ? false
@@ -221,10 +224,22 @@ stdenv.mkDerivation rec {
       pythonBinPath = callPackage ./python-bin-path-test.nix { inherit runLocal bazelTest; };
 
       bashToolsWithNixHacks = callPackage ./bash-tools-test.nix { inherit runLocal bazelTest; bazel = bazelWithNixHacks; };
+
       cppWithNixHacks = callPackage ./cpp-test.nix { inherit runLocal bazelTest bazel-examples; bazel = bazelWithNixHacks; };
       javaWithNixHacks = callPackage ./java-test.nix { inherit runLocal bazelTest bazel-examples; bazel = bazelWithNixHacks; };
       protobufWithNixHacks = callPackage ./protobuf-test.nix { inherit runLocal bazelTest; bazel = bazelWithNixHacks; };
       pythonBinPathWithNixHacks = callPackage ./python-bin-path-test.nix { inherit runLocal bazelTest; bazel = bazelWithNixHacks; };
+
+      # downstream packages using buildBazelPackage
+      # fixed-output hashes of the fetch phase need to be spot-checked manually
+      downstream = recurseIntoAttrs ({
+        inherit bazel-watcher;
+      }
+          # dm-sonnet is only packaged for linux
+      // (lib.optionalAttrs stdenv.isLinux {
+          # TODO(timokau) dm-sonnet is broken currently
+          # dm-sonnet-linux = python3.pkgs.dm-sonnet;
+      }));
     };
 
   # update the list of workspace dependencies

pkgs/development/tools/build-managers/conan/default.nix

@@ -37,13 +37,7 @@ let newPython = python3.override {
         sha256 = "c0abe3218b86533cca287e7057a37481883c07acef7814b70583406938214cc8";
       };
     });
-    pyyaml = super.pyyaml.overridePythonAttrs (oldAttrs: rec {
-      version = "3.13";
-      src = oldAttrs.src.override {
-        inherit version;
-        sha256 = "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf";
-      };
-    });
+    pyyaml = super.pyyaml_3;
   };
 };
 

pkgs/misc/emulators/wine/base.nix

@@ -46,7 +46,9 @@ stdenv.mkDerivation ((lib.optionalAttrs (buildScript != null) {
   ++ lib.optional udevSupport            pkgs.udev
   ++ lib.optional vulkanSupport          pkgs.vulkan-loader
   ++ lib.optional sdlSupport             pkgs.SDL2
-  ++ lib.optionals gstreamerSupport      (with pkgs.gst_all_1; [ gstreamer gst-plugins-base gst-plugins-good gst-plugins-bad gst-plugins-ugly gst-libav ])
+  ++ lib.optionals gstreamerSupport      (with pkgs.gst_all_1;
+    [ gstreamer gst-plugins-base gst-plugins-good gst-plugins-ugly gst-libav 
+    (gst-plugins-bad.override { enableZbar = false; }) ])
   ++ lib.optionals gtkSupport    [ pkgs.gtk3 pkgs.glib ]
   ++ lib.optionals openclSupport [ pkgs.opencl-headers pkgs.ocl-icd ]
   ++ lib.optionals xmlSupport    [ pkgs.libxml2 pkgs.libxslt ]

pkgs/misc/tmux-plugins/default.nix

@@ -1,4 +1,5 @@
 { fetchgit
+, fetchFromGitHub
 , lib
 , pkgs
 , reattach-to-user-namespace
@@ -90,6 +91,15 @@ in rec {
     };
   };
 
+  ctrlw = mkDerivation {
+    pluginName = "ctrlw";
+    src = fetchgit {
+      url = "https://github.com/eraserhd/tmux-ctrlw";
+      rev = "2354b5d56828813d0f7a4b228ca74b6134c2695f";
+      sha256 = "00hy1axmki8h2285mivsj923z327xkq89wfl2x4dxc71xjhdl216";
+    };
+  };
+
   fpp = mkDerivation {
     pluginName = "fpp";
     src = fetchgit {
@@ -215,6 +225,16 @@ in rec {
     };
   };
 
+  tmux-colors-solarized = mkDerivation {
+    pluginName = "tmuxcolors";
+    src = fetchFromGitHub {
+      owner = "seebi";
+      repo = "tmux-colors-solarized";
+      rev = "e5e7b4f1af37f8f3fc81ca17eadee5ae5d82cd09";
+      sha256 = "1l3i82abzi4b395cgdsjg7lcfaq15kyyhijwvrgchzxi95z3hl4x";
+    };
+  };
+
   urlview = mkDerivation {
     pluginName = "urlview";
     src = fetchgit {

pkgs/os-specific/linux/checksec/0001-attempt-to-modprobe-config-before-checking-kernel.patch

@@ -8,20 +8,21 @@ Signed-off-by: Austin Seipp <aseipp@pobox.com>
  checksec.sh | 3 ++-
  1 file changed, 2 insertions(+), 1 deletion(-)
 
-diff --git a/checksec.sh b/checksec.sh
+diff --git a/checksec b/checksec
 index dd1f72e..63acc29 100644
---- a/checksec.sh
-+++ b/checksec.sh
-@@ -337,7 +337,8 @@ kernelcheck() {
-   printf "  userspace processes, this option lists the status of kernel configuration\n"
-   printf "  options that harden the kernel itself against attack.\n\n"
-   printf "  Kernel config: "
-- 
+--- a/checksec
++++ b/checksec
+@@ -676,7 +676,8 @@ kernelcheck() {
+   echo_message "  userspace processes, this option lists the status of kernel configuration\n" '' '' ''
+   echo_message "  options that harden the kernel itself against attack.\n\n" '' '' ''
+   echo_message "  Kernel config:\n" '' '' '{ "kernel": '
+-
 +
 +  modprobe configs 2> /dev/null
-   if [ -f /proc/config.gz ] ; then
-     kconfig="zcat /proc/config.gz"
-     printf "\033[32m/proc/config.gz\033[m\n\n"
+   if [[ ! "${1}" == "" ]] ; then
+     kconfig="cat ${1}"
+     echo_message "  Warning: The config ${1} on disk may not represent running kernel config!\n\n" "${1}" "<kernel config=\"${1}\"" "{ \"KernelConfig\":\"${1}\","
+     # update the architecture based on the config rather than the system
 -- 
 1.8.3.2
 

pkgs/os-specific/linux/checksec/default.nix

@@ -1,43 +1,39 @@
-{ stdenv, fetchurl, file, findutils, binutils-unwrapped, glibc, coreutils, sysctl }:
+{ stdenv, fetchFromGitHub, makeWrapper, file, findutils
+, binutils-unwrapped, glibc, coreutils, sysctl, openssl
+}:
 
 stdenv.mkDerivation rec {
-  name = "checksec-${version}";
-  version = "1.5";
+  pname = "checksec";
+  version = "2.0.1";
 
-  src = fetchurl {
-    url    = "https://www.trapkit.de/tools/checksec.sh";
-    sha256 = "0iq9v568mk7g7ksa1939g5f5sx7ffq8s8n2ncvphvlckjgysgf3p";
+  src = fetchFromGitHub {
+    owner = "slimm609";
+    repo = "checksec.sh";
+    rev = version;
+    sha256 = "04lzwm24d576h425rgvgjj2wim29i3961jrj35r43wrswmrsc3r2";
   };
 
   patches = [ ./0001-attempt-to-modprobe-config-before-checking-kernel.patch ];
+  nativeBuildInputs = [ makeWrapper ];
 
-  unpackPhase = ''
-    mkdir ${name}
-    cp $src ${name}/checksec.sh
-    cd ${name}
-  '';
-
-  installPhase = ''
+  installPhase = let
+    path = stdenv.lib.makeBinPath [
+      findutils file binutils-unwrapped sysctl openssl
+    ];
+  in ''
     mkdir -p $out/bin
-    cp checksec.sh $out/bin/checksec
-    chmod +x $out/bin/checksec
-    substituteInPlace $out/bin/checksec --replace /bin/bash ${stdenv.shell}
+    install checksec $out/bin
     substituteInPlace $out/bin/checksec --replace /lib/libc.so.6 ${glibc.out}/lib/libc.so.6
-    substituteInPlace $out/bin/checksec --replace find ${findutils}/bin/find
-    substituteInPlace $out/bin/checksec --replace "file $" "${file}/bin/file $"
-    substituteInPlace $out/bin/checksec --replace "xargs file" "xargs ${file}/bin/file"
-    substituteInPlace $out/bin/checksec --replace " readelf -" " ${binutils-unwrapped}/bin/readelf -"
-    substituteInPlace $out/bin/checksec --replace "(readelf -" "(${binutils-unwrapped}/bin/readelf -"
-    substituteInPlace $out/bin/checksec --replace "command_exists readelf" "command_exists ${binutils-unwrapped}/bin/readelf"
-    substituteInPlace $out/bin/checksec --replace "/sbin/sysctl -" "${sysctl}/bin/sysctl -"
     substituteInPlace $out/bin/checksec --replace "/usr/bin/id -" "${coreutils}/bin/id -"
+    wrapProgram $out/bin/checksec \
+      --prefix PATH : ${path}
   '';
 
-  meta = {
+  meta = with stdenv.lib; {
     description = "A tool for checking security bits on executables";
     homepage    = "http://www.trapkit.de/tools/checksec.html";
-    license     = stdenv.lib.licenses.bsd3;
-    platforms   = stdenv.lib.platforms.linux;
-    maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
+    license     = licenses.bsd3;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice globin ];
   };
 }

pkgs/servers/home-assistant/appdaemon.nix

@@ -38,15 +38,6 @@ let
           sha256 = "0f390693f46173d8ffb95669acbb0e2a3ec54ecce676703510ad47f1a6d9dc83";
         };
       });
-
-      pyyaml = super.pyyaml.overridePythonAttrs (oldAttrs: rec {
-        version = "5.1";
-        src = oldAttrs.src.override {
-          inherit version;
-          sha256 = "436bc774ecf7c103814098159fbb84c2715d25980175292c648f2da143909f95";
-        };
-      });
-
     };
   };
 

pkgs/servers/home-assistant/default.nix

@@ -36,8 +36,6 @@ let
       "03f38115dccb266dd96538f94067442a877932c2322661bdc5bf2502c76658af")
     (mkOverride "python-slugify" "3.0.2"
       "57163ffb345c7e26063435a27add1feae67fa821f1ef4b2f292c25847575d758")
-    (mkOverride "pyyaml" "3.13"
-      "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf")
     (mkOverride "requests" "2.21.0"
       "502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e")
     (mkOverride "ruamel_yaml" "0.15.94"
@@ -63,6 +61,10 @@ let
       };
     })
 
+    (self: super: {
+      pyyaml = super.pyyaml_3;
+    })
+
     # hass-frontend does not exist in python3.pkgs
     (self: super: {
       hass-frontend = self.callPackage ./frontend.nix { };
@@ -78,7 +80,7 @@ let
         };
       });
     };
-    
+
   py = python3.override {
     # Put packageOverrides at the start so they are applied after defaultOverrides
     packageOverrides = lib.foldr lib.composeExtensions (self: super: { }) ([ packageOverrides ] ++ defaultOverrides);

pkgs/servers/home-assistant/esphome.nix

@@ -3,13 +3,6 @@
 let
   python = python3.override {
     packageOverrides = self: super: {
-      pyyaml = super.pyyaml.overridePythonAttrs (oldAttrs: rec {
-        version = "5.1";
-        src = oldAttrs.src.override {
-          inherit version;
-          sha256 = "436bc774ecf7c103814098159fbb84c2715d25980175292c648f2da143909f95";
-        };
-      });
       tornado = super.tornado.overridePythonAttrs (oldAttrs: rec {
         version = "5.1.1";
         src = oldAttrs.src.override {

pkgs/tools/admin/awscli/default.nix

@@ -22,18 +22,7 @@ let
           sha256 = "48eb22f4f8461b1df5734a074b57042430fb06e1d61bd1e11b078c0fe6d7a1f1";
         };
       });
-      pyyaml = super.pyyaml.overridePythonAttrs (oldAttrs: rec {
-        version = "3.13";
-        src = oldAttrs.src.override {
-          inherit version;
-          sha256 = "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf";
-        };
-        # https://github.com/yaml/pyyaml/issues/298#issuecomment-511990948
-        patches = lib.singleton (fetchpatch {
-          url = "https://github.com/yaml/pyyaml/commit/c5b135fe39d41cffbdc006f28ccb2032df6005e0.patch";
-          sha256 = "0x1v45rkmj194c41d1nqi3ihj9z4rsy8zvpfcd8p960g1fia7fhn";
-        });
-      });
+      pyyaml = super.pyyaml_3;
     };
   };
 

pkgs/tools/archivers/unzip/default.nix

@@ -26,11 +26,6 @@ stdenv.mkDerivation {
     ./CVE-2016-9844.patch
     ./CVE-2018-18384.patch
     ./dont-hardcode-cc.patch
-    (fetchurl {
-      url = "https://github.com/madler/unzip/commit/47b3ceae397d21bf822bc2ac73052a4b1daf8e1c.patch";
-      name = "CVE-2019-13232.patch";
-      sha256 = "0iy2wcjyvzwrjk02iszwcpg85fkjxs1bvb9isvdiywszav4yjs32";
-    })
   ] ++ stdenv.lib.optional enableNLS
     (fetchurl {
       url = "http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/app-arch/unzip/files/unzip-6.0-natspec.patch?revision=1.1";

pkgs/tools/backup/rotate-backups/default.nix

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchFromGitHub, update-dotdee, simpleeval, dateutil }:
+
+buildPythonPackage rec {
+  pname = "rotate-backups";
+  version = "6.0";
+
+  src = fetchFromGitHub {
+    owner = "xolox";
+    repo = "python-rotate-backups";
+    rev = version;
+    sha256 = "0i59qfv1cfm0ss63ab2nrkn5wr4rxpqqmvfd7pf9c3pl9dbfq20c";
+  };
+
+  propagatedBuildInputs = [ update-dotdee simpleeval dateutil ];
+
+  meta = with lib; {
+    description = "Simple command line interface for backup rotation";
+    homepage = https://github.com/xolox/python-rotate-backups;
+    license = licenses.mit;
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}
+

pkgs/tools/networking/ngrok-2/default.nix

@@ -24,7 +24,7 @@ stdenv.mkDerivation {
 
   sourceRoot = ".";
 
-  nativeBuildInputs = [ patchelfUnstable ];
+  nativeBuildInputs = optionals stdenv.isLinux [ patchelfUnstable ];
 
   unpackPhase = "cp $src ngrok";
 
@@ -32,10 +32,10 @@ stdenv.mkDerivation {
 
   installPhase = ''
     install -D ngrok $out/bin/ngrok
-
+  '' + optionalString stdenv.isLinux ''
     patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
               $out/bin/ngrok
-    '';
+  '';
 
   passthru.updateScript = ./update.sh;
 

pkgs/top-level/all-packages.nix

@@ -1312,6 +1312,8 @@ in
 
   clprover = callPackage ../applications/science/logic/clprover/clprover.nix { };
 
+  coloredlogs = with python3Packages; toPythonApplication coloredlogs;
+
   colord-kde = libsForQt5.callPackage ../tools/misc/colord-kde {};
 
   colpack = callPackage ../applications/science/math/colpack { };
@@ -2871,6 +2873,8 @@ in
 
   execline = skawarePackages.execline;
 
+  executor = with python3Packages; toPythonApplication executor;
+
   exif = callPackage ../tools/graphics/exif { };
 
   exiftags = callPackage ../tools/graphics/exiftags { };
@@ -3741,6 +3745,8 @@ in
 
   hubicfuse = callPackage ../tools/filesystems/hubicfuse { };
 
+  humanfriendly = with python3Packages; toPythonApplication humanfriendly;
+
   hwinfo = callPackage ../tools/system/hwinfo { };
 
   hybridreverb2 = callPackage ../applications/audio/hybridreverb2 { };
@@ -5124,6 +5130,8 @@ in
 
   oppai-ng = callPackage ../tools/misc/oppai-ng { };
 
+  update-dotdee = with python3Packages; toPythonApplication update-dotdee;
+
   update-resolv-conf = callPackage ../tools/networking/openvpn/update-resolv-conf.nix { };
 
   opae = callPackage ../development/libraries/opae { };
@@ -13160,6 +13168,8 @@ in
 
   rocksdb_lite = rocksdb.override { enableLite = true; };
 
+  rotate-backups = with python3Packages; toPythonApplication rotate-backups;
+
   rote = callPackage ../development/libraries/rote { };
 
   ronn = callPackage ../development/tools/ronn { };

pkgs/top-level/emacs-packages.nix

@@ -434,7 +434,10 @@ let
     };
     stripDebugList = [ "share" ];
     packageRequires = [ emacs ];
-    nativeBuildInputs = [ external.autoconf external.automake external.pkgconfig external.libtool external.zeromq ];
+    nativeBuildInputs = [
+      external.autoconf external.automake external.pkgconfig external.libtool
+      (external.zeromq.override { enableDrafts = true; })
+    ];
     preBuild = ''
       make
     '';

pkgs/top-level/python-packages.nix

@@ -684,10 +684,12 @@ in {
 
   maxminddb = callPackage ../development/python-modules/maxminddb { };
 
-  monty = callPackage ../development/python-modules/monty { };
-
   mininet-python = (toPythonModule (pkgs.mininet.override{ inherit python; })).py;
 
+  mkl-service = callPackage ../development/python-modules/mkl-service { };
+
+  monty = callPackage ../development/python-modules/monty { };
+
   mpi4py = callPackage ../development/python-modules/mpi4py {
     mpi = pkgs.openmpi;
   };
@@ -1473,6 +1475,8 @@ in {
 
   capstone = callPackage ../development/python-modules/capstone { };
 
+  capturer = callPackage ../development/python-modules/capturer { };
+
   cement = callPackage ../development/python-modules/cement {};
 
   cgen = callPackage ../development/python-modules/cgen { };
@@ -1497,6 +1501,8 @@ in {
 
   colorcet = callPackage ../development/python-modules/colorcet { };
 
+  coloredlogs = callPackage ../development/python-modules/coloredlogs { };
+
   colorclass = callPackage ../development/python-modules/colorclass {};
 
   colorlog = callPackage ../development/python-modules/colorlog { };
@@ -2186,6 +2192,8 @@ in {
 
   execnet = callPackage ../development/python-modules/execnet { };
 
+  executor = callPackage ../development/python-modules/executor { };
+
   ezdxf = callPackage ../development/python-modules/ezdxf {};
 
   facebook-sdk = callPackage ../development/python-modules/facebook-sdk { };
@@ -2460,6 +2468,8 @@ in {
 
   natsort = callPackage ../development/python-modules/natsort { };
 
+  naturalsort = callPackage ../development/python-modules/naturalsort { };
+
   ncclient = callPackage ../development/python-modules/ncclient {};
 
   logfury = callPackage ../development/python-modules/logfury { };
@@ -2677,6 +2687,8 @@ in {
 
   roman = callPackage ../development/python-modules/roman { };
 
+  rotate-backups = callPackage ../tools/backup/rotate-backups { };
+
   librosa = callPackage ../development/python-modules/librosa { };
 
   samplerate = callPackage ../development/python-modules/samplerate { };
@@ -4109,6 +4121,8 @@ in {
 
   prettytable = callPackage ../development/python-modules/prettytable { };
 
+  property-manager = callPackage ../development/python-modules/property-manager { };
+
   prompt_toolkit = let
     filename = if isPy3k then ../development/python-modules/prompt_toolkit else ../development/python-modules/prompt_toolkit/1.nix;
   in callPackage filename { };
@@ -4440,6 +4454,21 @@ in {
 
   pyyaml = callPackage ../development/python-modules/pyyaml { };
 
+  pyyaml_3 = (callPackage ../development/python-modules/pyyaml { }).overridePythonAttrs (oldAttrs: rec {
+    version = "3.13";
+    src = oldAttrs.src.override {
+      inherit version;
+      sha256 = "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf";
+    };
+    # https://github.com/yaml/pyyaml/issues/298#issuecomment-511990948
+    patches = singleton (pkgs.fetchpatch {
+      url = "https://github.com/yaml/pyyaml/commit/c5b135fe39d41cffbdc006f28ccb2032df6005e0.patch";
+      sha256 = "0x1v45rkmj194c41d1nqi3ihj9z4rsy8zvpfcd8p960g1fia7fhn";
+    });
+    # https://github.com/yaml/pyyaml/issues/298#issuecomment-511990948
+    doCheck = false;
+  });
+
   rabbitpy = callPackage ../development/python-modules/rabbitpy { };
 
   rasterio = callPackage ../development/python-modules/rasterio {
@@ -4833,6 +4862,8 @@ in {
 
   update-copyright = callPackage ../development/python-modules/update-copyright {};
 
+  update-dotdee = callPackage ../development/python-modules/update-dotdee { };
+
   uritemplate = callPackage ../development/python-modules/uritemplate { };
 
   uproot = callPackage ../development/python-modules/uproot {};
@@ -4845,6 +4876,8 @@ in {
 
   user-agents = callPackage ../development/python-modules/user-agents { };
 
+  verboselogs = callPackage ../development/python-modules/verboselogs { };
+
   vega_datasets = callPackage ../development/python-modules/vega_datasets { };
 
   virtkey = callPackage ../development/python-modules/virtkey {