Merge staging-next into staging

pkgs/build-support/build-fhs-userenv-bubblewrap/env.nix

@@ -156,7 +156,7 @@ let
     done
     cd ..
 
-    for i in var etc; do
+    for i in var etc opt; do
       if [ -d "${staticUsrProfileTarget}/$i" ]; then
         cp -rsHf "${staticUsrProfileTarget}/$i" "$i"
       fi

pkgs/build-support/build-fhs-userenv/chrootenv/chrootenv.c

@@ -18,7 +18,7 @@
   if (expr)                                                                    \
     fail(#expr, errno);
 
-const gchar *bind_blacklist[] = {"bin", "etc", "host", "real-host", "usr", "lib", "lib64", "lib32", "sbin", NULL};
+const gchar *bind_blacklist[] = {"bin", "etc", "host", "real-host", "usr", "lib", "lib64", "lib32", "sbin", "opt", NULL};
 
 int pivot_root(const char *new_root, const char *put_old) {
   return syscall(SYS_pivot_root, new_root, put_old);

pkgs/build-support/build-fhs-userenv/env.nix

@@ -184,7 +184,7 @@ let
     done
     cd ..
 
-    for i in var etc; do
+    for i in var etc opt; do
       if [ -d "${staticUsrProfileTarget}/$i" ]; then
         cp -rsHf "${staticUsrProfileTarget}/$i" "$i"
       fi

pkgs/development/libraries/hyperscan/default.nix

@@ -1,5 +1,5 @@
 { lib, stdenv, fetchFromGitHub, cmake, ragel, python3
-, coreutils, gnused, util-linux
+, coreutils, gnused, util-linux, fetchpatch
 , boost
 , withStatic ? false # build only shared libs by default, build static+shared if true
 }:
@@ -37,6 +37,14 @@ stdenv.mkDerivation rec {
   ++ lib.optional (withStatic) "-DBUILD_STATIC_AND_SHARED=ON"
   ++ lib.optional (!withStatic) "-DBUILD_SHARED_LIBS=ON";
 
+  patches = [
+    (fetchpatch {
+      # part of https://github.com/intel/hyperscan/pull/336
+      url = "https://github.com/intel/hyperscan/commit/e2c4010b1fc1272cab816ba543940b3586e68a0c.patch";
+      sha256 = "sha256-doVNwROL6MTcgOW8jBwGTnxe0zvxjawiob/g6AvXLak=";
+    })
+  ];
+
   postPatch = ''
     sed -i '/examples/d' CMakeLists.txt
     substituteInPlace libhs.pc.in \

pkgs/development/libraries/libyaml-cpp/default.nix

@@ -18,6 +18,12 @@ stdenv.mkDerivation rec {
       url = "https://github.com/jbeder/yaml-cpp/commit/4f48727b365962e31451cd91027bd797bc7d2ee7.patch";
       sha256 = "sha256-jarZAh7NgwL3xXzxijDiAQmC/EC2WYfNMkYHEIQBPhM=";
     })
+    # TODO: Remove with the next release, when https://github.com/jbeder/yaml-cpp/pull/1058 is available
+    (fetchpatch {
+      name = "libyaml-cpp-Fix-pc-paths-for-absolute-GNUInstallDirs.patchj";
+      url = "https://github.com/jbeder/yaml-cpp/commit/328d2d85e833be7cb5a0ab246cc3f5d7e16fc67a.patch";
+      sha256 = "12g5h7lxzd5v16ykay03zww5g28j3k69k228yr3v8fnmyv2spkfl";
+    })
   ];
 
   nativeBuildInputs = [ cmake ];

pkgs/development/python-modules/rdflib-jsonld/default.nix

@@ -1,23 +0,0 @@
-{ buildPythonPackage, fetchPypi, lib, rdflib, nose }:
-
-buildPythonPackage rec {
-  pname = "rdflib-jsonld";
-  version = "0.6.2";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "107cd3019d41354c31687e64af5e3fd3c3e3fa5052ce635f5ce595fd31853a63";
-  };
-
-  nativeBuildInputs = [ nose ];
-  propagatedBuildInputs = [ rdflib ];
-
-  meta = with lib; {
-    homepage = "https://github.com/RDFLib/rdflib-jsonld";
-    license = licenses.bsdOriginal;
-    description = "rdflib extension adding JSON-LD parser and serializer";
-    maintainers = [ maintainers.koslambrou ];
-    # incomptiable with rdflib 6.0.0, half of the test suite fails with import and atrribute errors
-    broken = true;
-  };
-}

pkgs/development/python-modules/schema-salad/default.nix

@@ -6,7 +6,6 @@
 , lockfile
 , mistune
 , rdflib
-, rdflib-jsonld
 , ruamel-yaml
 , pytestCheckHook
 , pythonOlder
@@ -29,7 +28,6 @@ buildPythonPackage rec {
     lockfile
     mistune
     rdflib
-    rdflib-jsonld
     ruamel-yaml
   ];
 

pkgs/top-level/python-aliases.nix

@@ -82,6 +82,7 @@ mapAliases ({
   pytest_xdist = pytest-xdist; # added 2021-01-04
   python_simple_hipchat = python-simple-hipchat; # added 2021-07-21
   qasm2image = throw "qasm2image is no longer maintained (since November 2018), and is not compatible with the latest pythonPackages.qiskit versions."; # added 2020-12-09
+  rdflib-jsonld = throw "rdflib-jsonld is not compatible with rdflib 6"; # added 2021-11-05
   requests_toolbelt = requests-toolbelt; # added 2017-09-26
   rotate-backups = throw "rotate-backups was removed in favor of the top-level rotate-backups"; # added 2021-07-01
   ruamel_base = ruamel-base; # added 2021-11-01

pkgs/top-level/python-packages.nix

@@ -8046,8 +8046,6 @@ in {
 
   rdflib = callPackage ../development/python-modules/rdflib { };
 
-  rdflib-jsonld = callPackage ../development/python-modules/rdflib-jsonld { };
-
   rdkit = callPackage ../development/python-modules/rdkit { };
 
   re-assert = callPackage ../development/python-modules/re-assert { };