Merge staging-next into staging

12 files changed, 257 insertions, 20 deletions

diff --git a/pkgs/development/interpreters/picolisp/default.nix b/pkgs/development/interpreters/picolisp/default.nix
index 058a83b6b43..a7e6f6e2dc7 100644
--- a/pkgs/development/interpreters/picolisp/default.nix
+++ b/pkgs/development/interpreters/picolisp/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, jdk, makeWrapper }:
+{ stdenv, fetchurl, jdk, w3m, makeWrapper }:
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
@@ -33,6 +33,7 @@ stdenv.mkDerivation rec {
 
 
     makeWrapper $out/bin/picolisp $out/bin/pil \
+      --prefix PATH : ${w3m}/bin \
       --add-flags "$out/lib/picolisp/lib.l" \
       --add-flags "@lib/misc.l" \
       --add-flags "@lib/btree.l" \
diff --git a/pkgs/development/libraries/flatpak/default.nix b/pkgs/development/libraries/flatpak/default.nix
index aff5737432f..4ea17e588a9 100644
--- a/pkgs/development/libraries/flatpak/default.nix
+++ b/pkgs/development/libraries/flatpak/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, autoreconfHook, docbook_xml_dtd_412, docbook_xml_dtd_42, docbook_xml_dtd_43, docbook_xsl, which, libxml2
 , gobject-introspection, gtk-doc, intltool, libxslt, pkgconfig, xmlto, appstream-glib, substituteAll, glibcLocales, yacc, xdg-dbus-proxy, p11-kit
 , bubblewrap, bzip2, dbus, glib, gpgme, json-glib, libarchive, libcap, libseccomp, coreutils, gettext, python2, hicolor-icon-theme
-, libsoup, lzma, ostree, polkit, python3, systemd, xorg, valgrind, glib-networking, wrapGAppsHook, gnome3, gsettings-desktop-schemas }:
+, libsoup, lzma, ostree, polkit, python3, systemd, xorg, valgrind, glib-networking, wrapGAppsHook, gnome3, gsettings-desktop-schemas, librsvg }:
 
 stdenv.mkDerivation rec {
   pname = "flatpak";
@@ -33,6 +33,7 @@ stdenv.mkDerivation rec {
     ./respect-xml-catalog-files-var.patch
     ./use-flatpak-from-path.patch
     ./unset-env-vars.patch
+    ./validate-icon-pixbuf.patch
   ];
 
   nativeBuildInputs = [
@@ -44,6 +45,7 @@ stdenv.mkDerivation rec {
     bubblewrap bzip2 dbus gnome3.dconf glib gpgme json-glib libarchive libcap libseccomp
     libsoup lzma ostree polkit python3 systemd xorg.libXau
     gsettings-desktop-schemas glib-networking
+    librsvg # for flatpak-validate-icon
   ];
 
   checkInputs = [ valgrind ];
diff --git a/pkgs/development/libraries/flatpak/validate-icon-pixbuf.patch b/pkgs/development/libraries/flatpak/validate-icon-pixbuf.patch
new file mode 100644
index 00000000000..5b8cc2d0383
--- /dev/null
+++ b/pkgs/development/libraries/flatpak/validate-icon-pixbuf.patch
@@ -0,0 +1,13 @@
+diff --git a/icon-validator/validate-icon.c b/icon-validator/validate-icon.c
+index 6e23d9f2..f0659a78 100644
+--- a/icon-validator/validate-icon.c
++++ b/icon-validator/validate-icon.c
+@@ -193,6 +193,8 @@ rerun_in_sandbox (const char *arg_width,
+     add_args (args, "--setenv", "G_MESSAGES_DEBUG", g_getenv ("G_MESSAGES_DEBUG"), NULL);
+   if (g_getenv ("G_MESSAGES_PREFIXED"))
+     add_args (args, "--setenv", "G_MESSAGES_PREFIXED", g_getenv ("G_MESSAGES_PREFIXED"), NULL);
++  if (g_getenv ("GDK_PIXBUF_MODULE_FILE"))
++    add_args (args, "--setenv", "GDK_PIXBUF_MODULE_FILE", g_getenv ("GDK_PIXBUF_MODULE_FILE"), NULL);
+ 
+   add_args (args, validate_icon, arg_width, arg_height, filename, NULL);
+   g_ptr_array_add (args, NULL);
diff --git a/pkgs/development/libraries/liburing/default.nix b/pkgs/development/libraries/liburing/default.nix
index 4564bab227b..cce10a761d3 100644
--- a/pkgs/development/libraries/liburing/default.nix
+++ b/pkgs/development/libraries/liburing/default.nix
@@ -3,12 +3,12 @@
 
 stdenv.mkDerivation rec {
   name = "liburing-${version}";
-  version = "1.0.0pre132_${builtins.substring 0 7 src.rev}";
+  version = "1.0.0pre137_${builtins.substring 0 7 src.rev}";
 
   src = fetchgit {
     url    = "http://git.kernel.dk/liburing";
-    rev    = "f8865bc65feced660a3075175200a60968187bba";
-    sha256 = "13l6s5iyrhqa0yj272qax0261cfw3nz09hq5hpf0f0kb2952d4rc";
+    rev    = "91dde5c956b1af491bc6c16ee230daa4b4b66706";
+    sha256 = "0rk1ikrn3s6sp3gx7kc4y6msx7yncr3845m67vhk8lxvhd90sgza";
   };
 
   separateDebugInfo = true;
diff --git a/pkgs/development/libraries/opencv/3.x.nix b/pkgs/development/libraries/opencv/3.x.nix
index 676666d7f47..b0652176c94 100644
--- a/pkgs/development/libraries/opencv/3.x.nix
+++ b/pkgs/development/libraries/opencv/3.x.nix
@@ -35,20 +35,20 @@
 }:
 
 let
-  version = "3.4.5";
+  version = "3.4.6";
 
   src = fetchFromGitHub {
     owner  = "opencv";
     repo   = "opencv";
     rev    = version;
-    sha256 = "0hz9316ys2qi0lx9dcbsk3mkn8cn08q12hc96p6zz2d4is6d5wsc";
+    sha256 = "1gf0rbgd5s13q46bdna0bqn4yz9rxfhvlhbp5ds9hs326q8zprg8";
   };
 
   contribSrc = fetchFromGitHub {
     owner  = "opencv";
     repo   = "opencv_contrib";
     rev    = version;
-    sha256 = "1fw7qwgibiznqal2dg4alkw8hrrrpjc0jaicf2406604rjm2lx6h";
+    sha256 = "115qcq0k2wmvhxw5lyv14yrd8m6xq3qy0pdby90ml2yl1caymbfy";
   };
 
   # Contrib must be built in order to enable Tesseract support:
@@ -147,6 +147,12 @@ stdenv.mkDerivation rec {
     cp --no-preserve=mode -r "${contribSrc}/modules" "$NIX_BUILD_TOP/opencv_contrib"
   '';
 
+  patches = lib.optional stdenv.isDarwin
+    (fetchpatch {
+      url = "https://github.com/opencv/opencv/commit/7621b91769098359e893e68ad474040ca7940fa1.patch";
+      sha256 = "12qb14yd5934ig61lzs4pg29gak9wjyhnj7nmfx5r213jj1a4m21";
+    });
+
   # This prevents cmake from using libraries in impure paths (which
   # causes build failure on non NixOS)
   # Also, work around https://github.com/NixOS/nixpkgs/issues/26304 with
diff --git a/pkgs/development/libraries/opencv/4.x.nix b/pkgs/development/libraries/opencv/4.x.nix
index a21cd6d079b..b4ad2bcb867 100644
--- a/pkgs/development/libraries/opencv/4.x.nix
+++ b/pkgs/development/libraries/opencv/4.x.nix
@@ -35,20 +35,20 @@
 }:
 
 let
-  version = "4.0.1";
+  version = "4.1.0";
 
   src = fetchFromGitHub {
     owner  = "opencv";
     repo   = "opencv";
     rev    = version;
-    sha256 = "1f0n2a57sn47w55vaxlwhr3g6xgchvr3gxicxbkyzai3pvj55k48";
+    sha256 = "0m1f51m11iz4vxfrmnhawksd669ld247rlfdq5fhkvfk3r7aidw6";
   };
 
   contribSrc = fetchFromGitHub {
     owner  = "opencv";
     repo   = "opencv_contrib";
     rev    = version;
-    sha256 = "0svw8f6nvnzmrc0baj6priq4hbijla4kl6gzy8yif1jfvcwb1syy";
+    sha256 = "1phmmba96m5znjf3wxwhxavgzgp3bs5qqsjk9ay1i63rdacz4vlf";
   };
 
   # Contrib must be built in order to enable Tesseract support:
diff --git a/pkgs/development/python-modules/matchpy/default.nix b/pkgs/development/python-modules/matchpy/default.nix
index dcac40b873c..a9f37b52c1b 100644
--- a/pkgs/development/python-modules/matchpy/default.nix
+++ b/pkgs/development/python-modules/matchpy/default.nix
@@ -3,7 +3,7 @@
 , fetchPypi
 , hopcroftkarp
 , multiset
-, pytest
+, pytest_3
 , pytestrunner
 , hypothesis
 , setuptools_scm
@@ -12,16 +12,20 @@
 
 buildPythonPackage rec {
   pname = "matchpy";
-  version = "0.4.6";
+  version = "0.5.1";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "eefa1e50a10e1255db61bc2522a6768ad0701f8854859f293ebaa442286faadd";
+    sha256 = "1vvf1cd9kw5z1mzvypc9f030nd18lgvvjc8j56b1s9b7dyslli2r";
   };
 
+  postPatch = ''
+    substituteInPlace setup.cfg --replace "hypothesis>=3.6,<4.0" "hypothesis"
+  '';
+
   buildInputs = [ setuptools_scm pytestrunner ];
-  checkInputs = [ pytest hypothesis ];
+  checkInputs = [ pytest_3 hypothesis ];
   propagatedBuildInputs = [ hopcroftkarp multiset ];
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/pygraphviz/default.nix b/pkgs/development/python-modules/pygraphviz/default.nix
index 835cdbaa6be..706284b56db 100644
--- a/pkgs/development/python-modules/pygraphviz/default.nix
+++ b/pkgs/development/python-modules/pygraphviz/default.nix
@@ -3,11 +3,12 @@
 
 buildPythonPackage rec {
   pname = "pygraphviz";
-  version = "1.3.1";
+  version = "1.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7c294cbc9d88946be671cc0d8602aac176d8c56695c0a7d871eadea75a958408";
+    sha256 = "179i3mjprhn200gcj6jq7c4mdrzckyqlh1srz78hynnw0nijka2h";
+    extension = "zip";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/development/tools/build-managers/bmake/default.nix b/pkgs/development/tools/build-managers/bmake/default.nix
new file mode 100644
index 00000000000..e101eea0cd3
--- /dev/null
+++ b/pkgs/development/tools/build-managers/bmake/default.nix
@@ -0,0 +1,37 @@
+{ stdenv, fetchurl
+, gnugrep, coreutils, getopt
+}:
+
+stdenv.mkDerivation rec {
+  name    = "bmake-${version}";
+  version = "20121212";
+
+  src = fetchurl {
+    # really wish this URL was versioned. if this changes for some
+    # update in the future, we'll have to backport those updates to
+    # any stable branches so builds can continue to work. :(
+    url    = "http://www.crufty.net/ftp/pub/sjg/bmake.tar.gz";
+    sha256 = "0zp6yy27z52qb12bgm3hy1dwal2i570615pqqk71zwhcxfs4h2gw";
+  };
+
+  nativeBuildInputs =
+    [ gnugrep coreutils getopt
+    ];
+
+  # unexport-env sets PATH to a bogus value that won't be
+  # possible to use inside the build sandbox. nuke that test;
+  # we could also re-construct the PATH variable a bit based on
+  # nativeBuildInputs, but not for now
+  patchPhase = ''
+    substituteInPlace ./unit-tests/Makefile.in \
+      --replace "unexport-env" ""
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Portable version of NetBSD 'make'";
+    homepage    = "http://www.crufty.net/help/sjg/bmake.html";
+    license     = licenses.bsd3;
+    platforms   = platforms.unix;
+    maintainers = with maintainers; [ thoughtpolice ];
+  };
+}
diff --git a/pkgs/development/tools/flatpak-builder/default.nix b/pkgs/development/tools/flatpak-builder/default.nix
index 5f8aaf07d73..fa00b8e5f89 100644
--- a/pkgs/development/tools/flatpak-builder/default.nix
+++ b/pkgs/development/tools/flatpak-builder/default.nix
@@ -24,6 +24,9 @@
 , flatpak
 , gitMinimal
 , glib
+, glibcLocales
+, gnumake
+, gnupg
 , gnutar
 , json-glib
 , libcap
@@ -32,20 +35,23 @@
 , libyaml
 , ostree
 , patch
+, python2
 , rpm
 , unzip
 }:
 
 let
-  version = "1.0.6";
+  installed_testdir = "${placeholder "installedTests"}/libexec/installed-tests/flatpak-builder";
+  installed_test_metadir = "${placeholder "installedTests"}/share/installed-tests/flatpak-builder";
+  version = "1.0.7";
 in stdenv.mkDerivation rec {
   name = "flatpak-builder-${version}";
 
-  outputs = [ "out" "doc" "man" ];
+  outputs = [ "out" "doc" "man" "installedTests" ];
 
   src = fetchurl {
     url = "https://github.com/flatpak/flatpak-builder/releases/download/${version}/${name}.tar.xz";
-    sha256 = "1fw9lzf9cy3fnnvn9q3g0schxcj7kaj6kjijhrmcmsfcnzbjlmrv";
+    sha256 = "04z9i2kahj4mffzq8ny0jvc4g3ah8kv8ilqv2rx9r1l8fhbq30jj";
   };
 
   nativeBuildInputs = [
@@ -95,8 +101,38 @@ in stdenv.mkDerivation rec {
       eustrip = "${elfutils}/bin/eu-strip";
       euelfcompress = "${elfutils}/bin/eu-elfcompress";
     })
+
+    # The test scripts in Flatpak repo were updated so we are basing
+    # this on our patch for Flatpak 0.99.
+    (substituteAll {
+      src = ./fix-test-paths.patch;
+      inherit glibcLocales python2;
+    })
   ];
 
+  configureFlags = [
+    "--enable-installed-tests"
+  ];
+
+  makeFlags = [
+    "installed_testdir=${installed_testdir}"
+    "installed_test_metadir=${installed_test_metadir}"
+  ];
+
+  # Some scripts used by tests  need to use shebangs that are available in Flatpak runtimes.
+  dontPatchShebangs = true;
+
+  # Installed tests
+  postFixup = ''
+    for file in ${installed_testdir}/{test-builder.sh,test-builder-python.sh}; do
+      patchShebangs $file
+    done
+  '';
+
+  passthru = {
+    installedTestsDependencies = [ gnupg ostree python2 gnumake ];
+  };
+
   meta = with stdenv.lib; {
     description = "Tool to build flatpaks from source";
     homepage = https://flatpak.org/;
diff --git a/pkgs/development/tools/flatpak-builder/fix-test-paths.patch b/pkgs/development/tools/flatpak-builder/fix-test-paths.patch
new file mode 100644
index 00000000000..96212a30fcf
--- /dev/null
+++ b/pkgs/development/tools/flatpak-builder/fix-test-paths.patch
@@ -0,0 +1,111 @@
+--- a/tests/libtest.sh
++++ b/tests/libtest.sh
+@@ -301,7 +301,7 @@
+ }
+ 
+ skip_without_python2 () {
+-    if ! test -f /usr/bin/python2 || ! /usr/bin/python2 -c "import sys; sys.exit(0 if sys.version_info >= (2, 7) else 1)" ; then
++    if ! test -f @python2@/bin/python2 || ! @python2@/bin/python2 -c "import sys; sys.exit(0 if sys.version_info >= (2, 7) else 1)" ; then
+         echo "1..0 # SKIP this test requires /usr/bin/python2 (2.7) support"
+         exit 0
+     fi
+--- a/tests/make-test-runtime.sh
++++ b/tests/make-test-runtime.sh
+@@ -26,6 +26,7 @@
+ PATH="$PATH:/usr/sbin:/sbin"
+ 
+ # Add bash and dependencies
++mkdir -p ${DIR}/nix/store
+ mkdir -p ${DIR}/usr/bin
+ mkdir -p ${DIR}/usr/lib
+ ln -s ../lib ${DIR}/usr/lib64
+@@ -35,73 +36,28 @@
+ else
+     cp `which ldconfig` ${DIR}/usr/bin
+ fi
+-LIBS=`mktemp`
+-BINS=`mktemp`
+-
+-add_bin() {
+-    local f=$1
+-    shift
+-
+-    if grep -qFe "${f}" $BINS; then
+-        # Already handled
+-        return 0
+-    fi
+-
+-    echo $f >> $BINS
+-
+-    # Add library dependencies
+-    (ldd "${f}" | sed "s/.* => //"  | awk '{ print $1}' | grep ^/ | sort -u -o $LIBS $LIBS -)  || true
+-
+-    local shebang=$(sed -n '1s/^#!\([^ ]*\).*/\1/p' "${f}")
+-    if [ x$shebang != x ]; then
+-        add_bin "$shebang"
+-    fi
+-}
+ 
+ for i in $@; do
+-    I=`which $i`
+-    add_bin $I
+-    if test $i == python2; then
+-        mkdir -p ${DIR}/usr/lib/python2.7/lib-dynload
+-        # This is a hardcoded minimal set of modules we need in the current tests.
+-        # Pretty hacky stuff. Add modules as needed.
+-        PYDIR=/usr/lib/python2.7
+-        if test -d /usr/lib64/python2.7; then PYDIR=/usr/lib64/python2.7; fi
+-        for py in site os stat posixpath genericpath warnings \
+-                       linecache types UserDict abc _abcoll \
+-                       _weakrefset copy_reg traceback sysconfig \
+-                       re sre_compile sre_parse sre_constants \
+-                       _sysconfigdata ; do
+-            cp ${PYDIR}/$py.py ${DIR}/usr/lib/python2.7
+-        done
+-        # These might not exist, depending how Python was configured; and the
+-        # part after ${so} might be "module" or ".x86_64-linux-gnu" or
+-        # something else
+-        for so in _locale strop ; do
+-            cp ${PYDIR}/lib-dynload/${so}*.so ${DIR}/usr/lib/python2.7/lib-dynload || :
+-        done
+-        for plat in $( cd ${PYDIR} && echo plat-* ); do
+-            test -e ${PYDIR}/${plat} || continue
+-            mkdir -p ${DIR}/usr/lib/python2.7/${plat}
+-            cp ${PYDIR}/${plat}/*.py ${DIR}/usr/lib/python2.7/${plat}/
+-        done
+-    fi
+-done
+-for i in `cat $BINS`; do
+-    echo Adding binary $i 1>&2
+-    cp "$i" ${DIR}/usr/bin/
+-done
+-for i in `cat $LIBS`; do
+-    echo Adding library $i 1>&2
+-    cp "$i" ${DIR}/usr/lib/
++    I=$(readlink -f $(which $i))
++    requisites=$(nix-store --query --requisites "$I")
++    for r in $requisites; do
++        # a single store item can be needed by multiple paths, no need to copy it again
++        if [ ! -e ${DIR}/$r ]; then
++            cp -r $r ${DIR}/$r
++        fi
++    done
++    ln -s $I ${DIR}/usr/bin/$i
+ done
+ ln -s bash ${DIR}/usr/bin/sh
+ 
+-# We copy the C.UTF8 locale and call it en_US. Its a bit of a lie, but
+-# the real en_US locale is often not available, because its in the
+-# local archive.
++mv ${DIR}/nix/store ${DIR}/usr/store # files outside /usr are not permitted, we will have to replace /nix/store with /usr/store
++chmod -R u+w ${DIR} # nix store has read-only directories which would cause problems during clean-up, files need to be writable for sed
++find ${DIR} -type f -print0 | xargs -0 sed -i 's~/nix/store/~/usr/store/~g' # replace hardcoded paths
++find ${DIR} -type l | xargs -I '{}' sh -c 'tg="$(readlink "$1")"; newtg="${tg#/nix/store/}"; if [ "$tg" != "$newtg" ]; then ln -fs "/usr/store/$newtg" "$1"; fi' -- '{}' # replace symlink targets
++
++# We copy the whole locale archive because we do not have C.UTF8 locale
+ mkdir -p ${DIR}/usr/lib/locale/
+-cp -r /usr/lib/locale/C.* ${DIR}/usr/lib/locale/en_US
++cp @glibcLocales@/lib/locale/locale-archive ${DIR}/usr/lib/locale/locale-archive
+ 
+ if [ x$COLLECTION_ID != x ]; then
+     collection_args=--collection-id=${COLLECTION_ID}
diff --git a/pkgs/development/tools/misc/reviewdog/default.nix b/pkgs/development/tools/misc/reviewdog/default.nix
new file mode 100644
index 00000000000..65a7c9eef39
--- /dev/null
+++ b/pkgs/development/tools/misc/reviewdog/default.nix
@@ -0,0 +1,26 @@
+{ lib, buildGoModule, fetchFromGitHub }:
+
+buildGoModule rec {
+  pname = "reviewdog";
+  version = "0.9.12";
+
+  src = fetchFromGitHub {
+    owner = pname;
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0r7y8nbpwfbvinpapv6lgnlc93kwn4b6722cp5ihyf361fklcd02";
+  };
+
+  modSha256 = "1ydfirjhw238zbia5mk90fx9rrg3kvm2h54zjhiimlvnpls5y8c9";
+
+  subPackages = [ "cmd/reviewdog" ];
+
+  buildFlagsArray = [ "-ldflags=-X github.com/reviewdog/reviewdog/commands.Version=${version}" ];
+
+  meta = with lib; {
+    description = "Automated code review tool integrated with any code analysis tools regardless of programming language";
+    homepage = "https://github.com/reviewdog/reviewdog";
+    maintainers = [ maintainers.marsam ];
+    license = licenses.mit;
+  };
+}