Merge branch 'master' into fix-release-notes

2020-10-27 23:29:09 +01:00 · 2020-10-27 23:29:09 +01:00 · 86a265b460
parent 4166a767de f08a5cc832
commit 86a265b460
21 changed files with 566 additions and 85 deletions
--- a/pkgs/applications/editors/glow/default.nix
+++ b/pkgs/applications/editors/glow/default.nix
@ -2,16 +2,16 @@

 buildGoModule rec {
  pname = "glow";
-  version = "1.0.2";
+  version = "1.1.0";

  src = fetchFromGitHub {
    owner = "charmbracelet";
    repo = "glow";
    rev = "v${version}";
-    sha256 ="0jyl5ln7c2naawmw7bljzrldr96xyb5rbis6y6blmyghr0vx07zb";
+    sha256 = "016psbm93ni81k87i9gx3cjr59j1fmpq5x8vz0ydabczzdshd1py";
  };

-  vendorSha256 = "0z3r8fvpy36ybgb18sr0lril1sg8z7s99xv1a6g1v3zdnj3zimav";
+  vendorSha256 = "0gvlbj8b5sqk93ahg4b2krwrmr8ljz7cah77fxaxcd98apap0pw6";

  doCheck = false;

--- a/pkgs/applications/networking/nym/default.nix
+++ b/pkgs/applications/networking/nym/default.nix
@ -9,16 +9,25 @@

 rustPlatform.buildRustPackage rec {
  pname = "nym";
-  version = "0.7.0";
+  version = "0.8.1";

  src = fetchFromGitHub {
    owner = "nymtech";
    repo = "nym";
    rev = "v${version}";
-    sha256 = "05bxrpqwwf9spydac0q8sly65q8f1nk13i5fy3p5adr1phzxdnr8";
+    sha256 = "0wzk9qzjyax73lfjbbag412vw1fgk2wmhhry5hdlvdbkim42m5bn";
  };

-  cargoSha256 = "0mh8cwia86bm68b0wcrmnsq1af5cp6kj1j81nwxb03awnqpxc34n";
+  # fix outdated Cargo.lock
+  cargoPatches = [ (writeText "fix-nym-cargo-lock.patch" ''
+    --- a/Cargo.lock
+    +++ b/Cargo.lock
+    @@ -1826 +1826 @@
+    -version = "0.8.0"
+    +version = "0.8.1"
+  '') ];
+
+  cargoSha256 = "0zr5nzmglmvn6xfqgvipbzy8nw5cl3nf7zjmghkqdwi6zj9p9272";

  nativeBuildInputs = [ pkgconfig ];

@ -26,20 +35,6 @@ rustPlatform.buildRustPackage rec {

  checkType = "debug";

-  /*
-  Nym's test presence::converting_mixnode_presence_into_topology_mixnode::it_returns_resolved_ip_on_resolvable_hostname tries to resolve nymtech.net.
-  Since there is no external DNS resolution available in the build sandbox, we point cargo and its children (that's what we remove the 'unsetenv' call for) to a hosts file in which we statically resolve nymtech.net.
-  */
-  preCheck = ''
-    export LD_PRELOAD=${libredirect.overrideAttrs (drv: {
-      postPatch = "sed -i -e /unsetenv/d libredirect.c";
-    })}/lib/libredirect.so
-    export NIX_REDIRECTS=/etc/hosts=${writeText "nym_resolve_test_hosts" "127.0.0.1 nymtech.net"}
-  '';
-
-  postCheck = "unset NIX_REDIRECTS LD_PRELOAD";
-
-
  passthru.updateScript = ./update.sh;

  meta = with lib; {
--- a/pkgs/development/java-modules/maven-minimal.nix
+++ b/pkgs/development/java-modules/maven-minimal.nix
@ -83,6 +83,7 @@ in {
      apache_10
      apache_11
      apache_13
+      apache_14
      backportUtilConcurrent_3_1
      commonsParent_22
      doxia_1_0_alpha7
@ -98,9 +99,11 @@ in {
      mavenParent_21
      mavenParent_22
      mavenParent_23
+      mavenParent_24
      mavenPlugins_22
      mavenPlugins_23
      mavenPlugins_24
+      mavenPlugins_25
      mavenPluginTools_3_1
      mavenReporting_2_0_6
      mavenReporting_2_0_9
@ -121,7 +124,9 @@ in {
      plexus_3_3_1
      plexusCipher_1_4
      plexusCompiler_2_2
+      plexusCompiler_2_4
      plexusCompilers_2_2
+      plexusCompilers_2_4
      plexusComponents_1_1_7
      plexusComponents_1_1_14
      plexusComponents_1_1_15
--- a/pkgs/development/java-modules/maven/compiler-plugin.nix
+++ b/pkgs/development/java-modules/maven/compiler-plugin.nix
@ -0,0 +1,14 @@
+{ fetchMaven }:
+
+{
+  mavenCompiler_3_2 = map (obj: fetchMaven {
+    version = "3.2";
+    artifactId = "maven-compiler-plugin";
+    groupId = "org.apache.maven.plugins";
+    sha512 = obj.sha512;
+    type = obj.type;
+  }) [
+    { type = "jar"; sha512 = "15lncacbgsbkp6m4fb1hv41nxn0w8lxgpjcpghw3znbh909d2y5h70q2nw3fyhd7kqsjwpvwpilkgyd5b35vi1smj5hhapmakqjk28r"; }
+    { type = "pom"; sha512 = "0a9pnb9rscsc32gpjr257k1pnydpskcs4jx8bs88vikxbdgc5sppllmqhi7k00i19azy2vjj59b3m9dcklcspmy9caxv2l7vjyr2lm0"; }
+  ];
+}
--- a/pkgs/development/java-modules/plexus/compiler-api.nix
+++ b/pkgs/development/java-modules/plexus/compiler-api.nix
@ -11,4 +11,15 @@
    { type = "jar"; sha512 = "3by7icjfiymp7g2v1ci5dqwml6ibzh2njyg2w43kvaz3ydcxkzmfg5s97wsdqjsii7vdgqyhr16ydsn6mr90wbjvsi6wasaq1rqa812"; }
    { type = "pom"; sha512 = "0pdl78hp921lgkfya54wl8hxgm1c5474j1p921q5ix1knx1rlr4klpjwx212wy2m7b6bxq0bkf8n66mqjr72rh2rh308qij00ymrga8"; }
  ];
+
+  plexusCompilerApi_2_4 = map (obj: fetchMaven {
+    version = "2.4";
+    artifactId = "plexus-compiler-api";
+    groupId = "org.codehaus.plexus";
+    sha512 = obj.sha512;
+    type = obj.type;
+  }) [
+    { type = "jar"; sha512 = "1xm0lv43dbg33prr0vc7g3vv0r07qc7kxjjbpqkxyh60vryd9q2wj3r656z4x8fwwqjrpr9xb4lmn4nm0c1cn85xzhfpxiq13rnl8cr"; }
+    { type = "pom"; sha512 = "0mqghnfagrmws585bvdwbpf1c719jvbmhwb318vw661cjfzj1b55nvjxza49bx5y38kwnwk0cqk9f26pv323ng09iifyjxgzafqq479"; }
+  ];
 }
--- a/pkgs/development/java-modules/plexus/compiler-javac.nix
+++ b/pkgs/development/java-modules/plexus/compiler-javac.nix
@ -11,4 +11,15 @@
    { type = "jar"; sha512 = "12xsiaqd1q6mmmkcsxf4nr4wdjl8fa1nwz32yqwrrbj9cgakph0368cnk1apjzngsmnl6bws87nlxcz64sg0rb7i2vdzggplj0a41br"; }
    { type = "pom"; sha512 = "1fv2ij4h9xmzv3f5mvs0ilhkw7khkw5v8n1d97a2canfn254fipz7pd9nkmkqzjvy3cqwiczyh2nzibvcii624p8ggwl4s3yjw92jx4"; }
  ];
+
+  plexusCompilerJavac_2_4 = map (obj: fetchMaven {
+    version = "2.4";
+    artifactId = "plexus-compiler-javac";
+    groupId = "org.codehaus.plexus";
+    sha512 = obj.sha512;
+    type = obj.type;
+  }) [
+    { type = "jar"; sha512 = "272iaf7mgmhjssj0k4a9r8rzb3c8pskb4aqypcdvj217l8hbih6rsqhh9nd2xmwrwa1ifvc336b8ihz6f419lj74gp4p1za6mp0nps3"; }
+    { type = "pom"; sha512 = "1g16i5w610nsh9h0yyhw25fpr2lx562c4v8y17lw53imi4rhm0m709ysrbrh71rhv6f8g4i5d6wgps77jmdb5kn2h5k1n4n644wrd12"; }
+  ];
 }
--- a/pkgs/development/java-modules/plexus/compiler-manager.nix
+++ b/pkgs/development/java-modules/plexus/compiler-manager.nix
@ -11,4 +11,15 @@
    { type = "jar"; sha512 = "1r1sdj784x4zcnkaz840vsz36jn1p2j98c21nia56kcdl1njydjn714bsmdy816l6sdinkz4s196mm3hshmxhq8mkmf16wgxx8jnq94"; }
    { type = "pom"; sha512 = "3cpfnbgil6g0bgq0cjbq2ysfjdpl05fh72d9l9cnwbilcsaxcmzn1hgmmkvam2ih222nl82dy7n5020is3y05kiv0i4n4lcs5m0ia48"; }
  ];
+
+  plexusCompilerManager_2_4 = map (obj: fetchMaven {
+    version = "2.4";
+    artifactId = "plexus-compiler-manager";
+    groupId = "org.codehaus.plexus";
+    sha512 = obj.sha512;
+    type = obj.type;
+  }) [
+    { type = "jar"; sha512 = "2al10188nwrdmi9zk3bid4ijjfsa8ymh6m9hin5jsja7hx7anbvs3i2y7kall56h4qn7j1rj73f8499x3i2k6x53kszmksvd2a1pkd4"; }
+    { type = "pom"; sha512 = "2bb2yrvjxci7wx7ira5cnnzdmlzdx4fk59fddpnmvdgh06dmg7fbnjlyx73pn6b13ajjrjl7rgj26mqs2hid3c0p3ni6x1qsg9w3ip0"; }
+  ];
 }
--- a/pkgs/development/java-modules/poms.nix
+++ b/pkgs/development/java-modules/poms.nix
@ -105,6 +105,14 @@
    type = "pom";
  };

+  apache_14 = fetchMaven {
+    version = "14";
+    artifactId = "apache";
+    groupId = "org.apache";
+    sha512 = "08y5k9lny2z171c78l4j70miylj2xy8w48amqwcghy3p9pc1p19qx6146s4mxc2z4wx4z9gpi9agham46m5hqa6k6v2s16v80phi7xi";
+    type = "pom";
+  };
+
  asmParent_4_0 = fetchMaven {
    version = "4.0";
    artifactId = "asm-parent";
@ -345,6 +353,14 @@
    type = "pom";
  };

+  mavenParent_24 = fetchMaven {
+    version = "24";
+    artifactId = "maven-parent";
+    groupId = "org.apache.maven";
+    sha512 = "0w1v36qx53xv5m8kag6wakzy7rjrp4gzfp7zfmrp5kw13ik6k42fnfkknslqc2g2c5dyxra2vpbvz1z9bcqslyaljd4r1rj3qbh5vl7";
+    type = "pom";
+  };
+
  mavenPlugins_22 = fetchMaven {
    version = "22";
    artifactId = "maven-plugins";
@ -369,6 +385,14 @@
    type = "pom";
  };

+  mavenPlugins_25 = fetchMaven {
+    version = "25";
+    artifactId = "maven-plugins";
+    groupId = "org.apache.maven.plugins";
+    sha512 = "38zx1im9qnblr5p9r4ln91d2280x48n9a11j4476skrgh97l3iqxs5ggqc22wis7r53g4j8ya4dvzqhxx6gymfbz3cn6a6hcmdqbng5";
+    type = "pom";
+  };
+
  mavenPluginTools_3_1 = fetchMaven {
    version = "3.1";
    artifactId = "maven-plugin-tools";
@ -593,6 +617,14 @@
    type = "pom";
  };

+  plexusCompiler_2_4 = fetchMaven {
+    version = "2.4";
+    artifactId = "plexus-compiler";
+    groupId = "org.codehaus.plexus";
+    sha512 = "0v89a5kbgyphmvgmdf6kb7zi4fvq16l435cxsp7grc5jy4ir9d0dv5g7xwhsk9ajp1lcy9kp4l4bk2h93g4kvj3bhk548wv284y36bf";
+    type = "pom";
+  };
+
  plexusCompilers_2_2 = fetchMaven {
    version = "2.2";
    artifactId = "plexus-compilers";
@ -601,6 +633,14 @@
    type = "pom";
  };

+  plexusCompilers_2_4 = fetchMaven {
+    version = "2.4";
+    artifactId = "plexus-compilers";
+    groupId = "org.codehaus.plexus";
+    sha512 = "1zalxaqycaykdn6q6pnxki6yvlpaf5qap1903hcylhbi1gcwmpqys39xg4pah9giy9iis350w2dmsab2prib9lihz4s9z6s6adqcss2";
+    type = "pom";
+  };
+
  plexusComponents_1_1_4 = fetchMaven {
    version = "1.1.4";
    artifactId = "plexus-components";
--- a/pkgs/development/ocaml-modules/mirage-block/default.nix
+++ b/pkgs/development/ocaml-modules/mirage-block/default.nix
@ -0,0 +1,24 @@
+{ lib, fetchurl, buildDunePackage
+, cstruct, lwt, mirage-device
+}:
+
+buildDunePackage rec {
+  pname = "mirage-block";
+  version = "2.0.1";
+
+  useDune2 = true;
+
+  src = fetchurl {
+    url = "https://github.com/mirage/mirage-block/releases/download/v${version}/mirage-block-v${version}.tbz";
+    sha256 = "1wp8wmixaz9i2sbvq6nkx903lbnpdgb2w404pz1wk8kcg9p3ilcc";
+  };
+
+  propagatedBuildInputs = [ cstruct lwt mirage-device ];
+
+  meta = with lib; {
+    description = "Block signatures and implementations for MirageOS";
+    homepage = "https://github.com/mirage/mirage-block";
+    license = licenses.isc;
+    maintainers = with maintainers; [ vbgl ];
+  };
+}
--- a/pkgs/development/python-modules/pc-ble-driver-py/default.nix
+++ b/pkgs/development/python-modules/pc-ble-driver-py/default.nix
@ -1,9 +1,10 @@
-{ stdenv, fetchFromGitHub, cmake, git, swig, boost, udev, pc-ble-driver
+{ stdenv, fetchFromGitHub, cmake, git, swig, boost, udev, pc-ble-driver, pythonOlder
 , buildPythonPackage, enum34, wrapt, future, setuptools, scikit-build }:

 buildPythonPackage rec {
  pname = "pc-ble-driver-py";
  version = "0.14.2";
+  disabled = pythonOlder "3.6";

  src = fetchFromGitHub {
    owner = "NordicSemiconductor";
--- a/pkgs/development/tools/sourcetrail/default.nix
+++ b/pkgs/development/tools/sourcetrail/default.nix
@ -1,77 +1,213 @@
-{ stdenv, fetchurl, autoPatchelfHook
-, zlib, expat, dbus, openssl, python3 }:
+{ stdenv, fetchFromGitHub, callPackage, writeScript, cmake, wrapQtAppsHook
+, boost, qt5, llvmPackages, gcc, jdk, pythonPackages, desktop-file-utils
+, shared-mime-info, imagemagick, which, coreutils, maven, fetchpatch }:

+let
+  # TODO: remove when version incompatibility issue with python3Packages.jedi is
+  # resolved
+  parso = pythonPackages.callPackage ./parso.nix {};
+  jedi = pythonPackages.callPackage ./jedi.nix { inherit parso; };
+
+  pythonIndexer = pythonPackages.callPackage ./python.nix { inherit jedi parso; };
+  javaIndexer = callPackage ./java.nix {};
+
+  # Upstream script:
+  # https://github.com/CoatiSoftware/Sourcetrail/blob/master/script/update_java_indexer.sh
+  installJavaIndexer = writeScript "update_java_indexer.sh" ''
+    #!${stdenv.shell}
+
+    cd "$(dirname "$0")/.."
+    dst="$out/opt/sourcetrail/share/data/java/lib"
+
+    mkdir -p "$dst"
+    cp "${javaIndexer}/target/java-indexer-1.0.jar" "$dst/java-indexer.jar"
+    cp -r java_indexer/lib/*.jar "$dst"
+  '';
+
+  # Upstream script:
+  # https://github.com/CoatiSoftware/Sourcetrail/blob/master/script/download_python_indexer.sh
+  installPythonIndexer = writeScript "download_python_indexer.sh" ''
+    #!${stdenv.shell}
+
+    mkdir -p $out/opt/sourcetrail/share/data
+    ln -s "${pythonIndexer}/bin" "$out/opt/sourcetrail/share/data/python"
+  '';
+in
 stdenv.mkDerivation rec {
  pname = "sourcetrail";
-  version = "2019.3.46";
+  version = "2020.2.43";

-  src = fetchurl {
-    name = "sourtrail.tar.gz";
-    url = "https://www.sourcetrail.com/downloads/${version}/linux/64bit";
-    sha256 = "0dnkxr3fijcsbn6pd20lyxhr9ns6ji1c4dffly9s16yq4x9ad5r4";
+  src = fetchFromGitHub {
+    owner = "CoatiSoftware";
+    repo = "Sourcetrail";
+    rev = "${version}";
+    sha256 = "0jp9y86xzkcxikc1cn4f6gqgg6zdssck08677ldagw25p1zadvzw";
  };

-  nativeBuildInputs = [ autoPatchelfHook ];
-  buildInputs = [ zlib expat dbus stdenv.cc.cc openssl python3 ];
+  patches = let
+    url = commit: "https://github.com/CoatiSoftware/Sourcetrail/commit/${commit}.patch";
+  in [
+    ./disable-updates.patch
+    ./disable-failing-tests.patch # FIXME: 5 test cases failing due to sandbox
+    # TODO: remove on next release
+    (fetchpatch {
+      name = "fix-filecopy.patch";
+      url = url "d079d1787c9e5cadcf41a003666dc0746cc1cda0";
+      sha256 = "0mixy2a4s16kv2q89k7y4dv21wnv2zd86i4gdwn3xz977y8hf92b";
+    })
+    (fetchpatch {
+      name = "fix-broken-test.patch";
+      url = url "85329174bac8a301733100dc4540258f977e2c5a";
+      sha256 = "17l4417sbmkrgr6v3fbazlmkzl9774zrpjv2n9zwfrz52y30f7b9";
+    })
+  ];

-  installPhase = ''
-    runHook preInstall
+  nativeBuildInputs = [
+    cmake
+    jdk
+    wrapQtAppsHook
+    desktop-file-utils
+    imagemagick
+    javaIndexer # the resulting jar file is copied by our install script
+  ] ++ stdenv.lib.optionals doCheck testBinPath;
+  buildInputs = [
+    boost pythonIndexer shared-mime-info
+  ] ++ (with qt5; [ qtbase qtsvg ])
+    ++ (with llvmPackages; [ libclang llvm ]);
+  binPath = [ gcc jdk.jre maven which ];
+  testBinPath = binPath ++ [ coreutils ];

-    mkdir -p $out/bin $out/opt
+  cmakeFlags = [
+    "-DBoost_USE_STATIC_LIBS=OFF"
+    "-DBUILD_CXX_LANGUAGE_PACKAGE=ON"
+    "-DCMAKE_PREFIX_PATH=${llvmPackages.clang-unwrapped}"
+    "-DBUILD_JAVA_LANGUAGE_PACKAGE=ON"
+    "-DBUILD_PYTHON_LANGUAGE_PACKAGE=ON"
+  ];

-    mv -v setup/share $out
-    mv -v data/gui/icon/logo_1024_1024.png $out/share/icons/sourcetrail.png
-    mv -v data/gui/icon/project_256_256.png $out/share/icons/project-sourcetrail.png
-
-    mkdir -p $out/share/sourcetrail/doc
-    mv -v README EULA.txt $out/share/sourcetrail/doc
-    mv -v plugin $out/share/sourcetrail
-
-    cp -rv . $out/opt
-
-    rm $out/opt/lib/libssl.so
-    rm $out/opt/lib/platforms/{libqeglfs.so,libqwebgl.so}
-    ln -s ${openssl}/lib/libssl.so $out/opt/lib/libssl.so
-
-    substituteInPlace \
-      $out/share/applications/sourcetrail.desktop \
-      --replace /usr/bin/ $out/bin/
-
-    cat <<EOF > $out/bin/sourcetrail
-    #! ${stdenv.shell} -e
-
-    # XXX: Sourcetrail somehow copies the initial config files into the home
-    # directory without write permissions. We currently just copy them
-    # ourselves to work around this problem.
-    setup_config() {
-      local src dst
-
-      [ ! -d ~/.config/sourcetrail ] && mkdir -p ~/.config/sourcetrail
-      for src in $out/opt/data/fallback/*; do
-        dst=~/.config/sourcetrail/"\$(basename "\$src")"
-        if [ ! -e "\$dst" ]; then
-          cp -r "\$src" "\$dst"
-        fi
-      done
-
-      chmod -R u+w ~/.config/sourcetrail
-    }
-
-    [ -d "\$HOME" ] && setup_config
-    export PATH="\$PATH:${python3}/bin"
-    exec "$out/opt/Sourcetrail.sh" "\$@"
+  postPatch = let
+    major = stdenv.lib.versions.major version;
+    minor = stdenv.lib.versions.minor version;
+    patch = stdenv.lib.versions.patch version;
+  in ''
+    # Upstream script obtains it's version from git:
+    # https://github.com/CoatiSoftware/Sourcetrail/blob/master/cmake/version.cmake
+    cat > cmake/version.cmake <<EOF
+    set(GIT_BRANCH "")
+    set(GIT_COMMIT_HASH "")
+    set(GIT_VERSION_NUMBER "")
+    set(VERSION_YEAR "${major}")
+    set(VERSION_MINOR "${minor}")
+    set(VERSION_COMMIT "${patch}")
+    set(BUILD_TYPE "Release")
+    set(VERSION_STRING "${major}.${minor}.${patch}")
    EOF

-    chmod +x $out/bin/sourcetrail
+    # Sourcetrail attempts to copy clang headers from the LLVM store path
+    substituteInPlace CMakeLists.txt \
+      --replace "\''${LLVM_BINARY_DIR}" '${llvmPackages.clang-unwrapped}'

-    runHook postInstall
+    patchShebangs script
+    ln -sf ${installJavaIndexer} script/update_java_indexer.sh
+    ln -sf ${installPythonIndexer} script/download_python_indexer.sh
  '';

+  # Sourcetrail doesn't use the usual cmake install() commands and instead uses
+  # its own bash script for packaging. Since we're not able to reuse the script,
+  # we'll have to roll our own in nixpkgs.
+  #
+  # Sourcetrail currently assumes one of the following two layouts for the
+  # placement of its files:
+  #
+  # AppImage Layout       Traditional Layout
+  # ├── bin/              ├── sourcetrail*
+  # │   └── sourcetrail*  └── data/
+  # └── share/
+  #     └── data/         sourcetrail: application executable
+  #                       data: contains assets exlusive to Sourcetrail
+  #
+  # The AppImage layout is the one currently used by the upstream project for
+  # packaging its Linux port. We can't use this layout as-is for nixpkgs,
+  # because Sourcetrail treating $out/share/data as its own might lead to
+  # conflicts with other packages when linked into a Nix profile.
+  #
+  # On the other hand, the traditional layout isn't used by the upstream project
+  # anymore so there's a risk that it might become unusable at any time in the
+  # future. Since it's hard to detect these problems at build time, it's not a
+  # good idea to use this layout for packaging in nixpkgs.
+  #
+  # Considering the problems with the above layouts, we go with the third
+  # option, a slight variation of the AppImage layout:
+  #
+  # nixpkgs
+  # ├── bin/
+  # │   └── sourcetrail* (wrapper for opt/sourcetrail/bin/sourcetrail)
+  # └── opt/sourcetrail/
+  #     ├── bin/
+  #     │   └── sourcetrail*
+  #     └── share/
+  #         └── data/
+  #
+  # Upstream install script:
+  # https://github.com/CoatiSoftware/Sourcetrail/blob/master/setup/Linux/createPackages.sh
+  installPhase = ''
+    mkdir -p $out/opt/sourcetrail/bin
+    cp app/Sourcetrail $out/opt/sourcetrail/bin/sourcetrail
+    cp app/sourcetrail_indexer $out/opt/sourcetrail/bin/sourcetrail_indexer
+
+    desktop-file-install --dir=$out/share/applications \
+      --set-key Exec --set-value $out/bin/sourcetrail \
+      ../setup/Linux/data/sourcetrail.desktop
+
+    mkdir -p $out/share/mime/packages
+    cp ../setup/Linux/data/sourcetrail-mime.xml $out/share/mime/packages/
+
+    mkdir -p $out/opt/sourcetrail/share
+    cp -R ../bin/app/data $out/opt/sourcetrail/share
+    cp -R ../bin/app/user/projects $out/opt/sourcetrail/share/data/fallback
+    rm $out/opt/sourcetrail/share/data/*_template.xml
+    rm -r $out/opt/sourcetrail/share/data/install
+
+    for size in 48 64 128 256 512; do
+      mkdir -p $out/share/icons/hicolor/''${size}x''${size}/apps/
+      convert app/data/gui/icon/logo_1024_1024.png -resize ''${size}x''${size} \
+        $out/share/icons/hicolor/''${size}x''${size}/apps/sourcetrail.png
+    done
+
+    mkdir -p $out/bin
+    makeQtWrapper $out/opt/sourcetrail/bin/sourcetrail $out/bin/sourcetrail \
+      --prefix PATH : ${stdenv.lib.makeBinPath binPath}
+  '';
+
+  checkPhase = ''
+    rm -rf ../bin/app/data/{python,java/lib}
+    ln -s $out/opt/sourcetrail/share/data/python ../bin/app/data/python
+    ln -s $out/opt/sourcetrail/share/data/java/lib ../bin/app/data/java/lib
+
+    pushd test
+    # shorten PATH to prevent build failures
+    wrapQtApp ./Sourcetrail_test \
+      --set PATH "" \
+      --prefix PATH : ${stdenv.lib.makeBinPath testBinPath} \
+      --set MAVEN_OPTS "-Dmaven.repo.local=$TMPDIR/m2repo"
+    ./Sourcetrail_test
+    popd
+
+    rm ../bin/app/data/{python,java/lib}
+  '';
+
+  # This has to be done manually in the installPhase because the actual binary
+  # lives in $out/opt/sourcetrail/bin, which isn't covered by wrapQtAppsHook
+  dontWrapQtApps = true;
+
+  # FIXME: some test cases are disabled in the patch phase
+  doCheck = true;
+
  meta = with stdenv.lib; {
    homepage = "https://www.sourcetrail.com";
    description = "A cross-platform source explorer for C/C++ and Java";
-    platforms = [ "x86_64-linux" ];
-    license = licenses.unfree;
+    platforms = platforms.all;
+    license = licenses.gpl3;
    maintainers = with maintainers; [ midchildan ];
  };
 }
--- a/pkgs/development/tools/sourcetrail/disable-failing-tests.patch
+++ b/pkgs/development/tools/sourcetrail/disable-failing-tests.patch
@ -0,0 +1,48 @@
+diff --git a/src/test/SourceGroupTestSuite.cpp b/src/test/SourceGroupTestSuite.cpp
+index b5c5562a..d56b83bb 100644
+--- a/src/test/SourceGroupTestSuite.cpp
+++ b/src/test/SourceGroupTestSuite.cpp
+@@ -522,6 +522,7 @@ TEST_CASE("sourcegroup java gradle generates expected output")
+ 
+ TEST_CASE("sourcegroup java maven generates expected output")
+ {
+	return;
+ 	std::vector<FilePath> mavenPaths = utility::getMavenExecutablePathDetector()->getPaths();
+ 
+ 	REQUIRE(!mavenPaths.empty());
+diff --git a/src/test/UtilityMavenTestSuite.cpp b/src/test/UtilityMavenTestSuite.cpp
+index f48fe2b6..363ef64a 100644
+--- a/src/test/UtilityMavenTestSuite.cpp
+++ b/src/test/UtilityMavenTestSuite.cpp
+@@ -17,6 +17,7 @@ TEST_CASE("maven path detector is working")
+ 
+ TEST_CASE("maven wrapper detects source directories of simple projects")
+ {
+	return;
+ 	std::shared_ptr<PathDetector> mavenPathDetector = utility::getMavenExecutablePathDetector();
+ 	REQUIRE(!mavenPathDetector->getPaths().empty());
+ 
+@@ -41,6 +42,7 @@ TEST_CASE("maven wrapper detects source directories of simple projects")
+ 
+ TEST_CASE("maven wrapper detects source and test directories of simple projects")
+ {
+	return;
+ 	std::shared_ptr<PathDetector> mavenPathDetector = utility::getMavenExecutablePathDetector();
+ 	REQUIRE(!mavenPathDetector->getPaths().empty());
+ 
+@@ -65,6 +67,7 @@ TEST_CASE("maven wrapper detects source and test directories of simple projects"
+ 
+ TEST_CASE("maven wrapper detects source directories of nested modules")
+ {
+	return;
+ 	std::shared_ptr<PathDetector> mavenPathDetector = utility::getMavenExecutablePathDetector();
+ 	REQUIRE(!mavenPathDetector->getPaths().empty());
+ 
+@@ -101,6 +104,7 @@ TEST_CASE("maven wrapper detects source directories of nested modules")
+ 
+ TEST_CASE("maven wrapper detects source and test directories of nested modules")
+ {
+	return;
+ 	std::shared_ptr<PathDetector> mavenPathDetector = utility::getMavenExecutablePathDetector();
+ 	REQUIRE(!mavenPathDetector->getPaths().empty());
+ 
--- a/pkgs/development/tools/sourcetrail/disable-updates.patch
+++ b/pkgs/development/tools/sourcetrail/disable-updates.patch
@ -0,0 +1,13 @@
+diff --git a/src/lib/settings/ApplicationSettings.cpp b/src/lib/settings/ApplicationSettings.cpp
+index 1be13ccd..db6098e1 100644
+--- a/src/lib/settings/ApplicationSettings.cpp
+++ b/src/lib/settings/ApplicationSettings.cpp
+@@ -593,7 +593,7 @@ void ApplicationSettings::setUserToken(std::string token)
+ 
+ bool ApplicationSettings::getAutomaticUpdateCheck() const
+ {
+-	return getValue<bool>("user/update_check/automatic", true);
+	return false;
+ }
+ 
+ void ApplicationSettings::setAutomaticUpdateCheck(bool automaticUpdates)
--- a/pkgs/development/tools/sourcetrail/java.nix
+++ b/pkgs/development/tools/sourcetrail/java.nix
@ -0,0 +1,27 @@
+{ pkgs, javaPackages }:
+
+let
+  javaIndexer = javaPackages.mavenbuild {
+    name = "sourcetrail-java-indexer-${pkgs.sourcetrail.version}";
+    src = pkgs.sourcetrail.src;
+    m2Path = "com/sourcetrail/java-indexer";
+
+    # This doesn't include all required dependencies. We still rely on binary
+    # copies of maven packages included in the source repo for building.
+    mavenDeps = with javaPackages; [
+      mavenCompiler_3_2
+      plexusCompilerApi_2_4
+      plexusCompilerJavac_2_4
+      plexusCompilerManager_2_4
+    ];
+
+    meta = {
+      description = "Java indexer for Sourcetrail";
+    };
+  };
+in
+javaIndexer.overrideAttrs (drv: {
+  postUnpack = ''
+    export sourceRoot=''${sourceRoot}/java_indexer
+  '';
+})
--- a/pkgs/development/tools/sourcetrail/jedi.nix
+++ b/pkgs/development/tools/sourcetrail/jedi.nix
@ -0,0 +1,36 @@
+# Taken from a past commit of nixpkgs
+
+{ stdenv, buildPythonPackage, fetchPypi, pytest, glibcLocales, tox, pytestcov, parso }:
+
+buildPythonPackage rec {
+  pname = "jedi";
+
+  # TODO: Remove this package when version incompatibility issue with
+  # python3Packages.jedi is resolved.
+  #
+  # Upstream requirements:
+  # https://github.com/CoatiSoftware/SourcetrailPythonIndexer#requirements
+  version = "0.17.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "86ed7d9b750603e4ba582ea8edc678657fb4007894a12bcf6f4bb97892f31d20";
+  };
+
+  checkInputs = [ pytest glibcLocales tox pytestcov ];
+
+  propagatedBuildInputs = [ parso ];
+
+  checkPhase = ''
+    LC_ALL="en_US.UTF-8" py.test test
+  '';
+
+  # tox required for tests: https://github.com/davidhalter/jedi/issues/808
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/davidhalter/jedi";
+    description = "An autocompletion tool for Python that can be used for text editors";
+    license = licenses.lgpl3Plus;
+  };
+}
--- a/pkgs/development/tools/sourcetrail/parso.nix
+++ b/pkgs/development/tools/sourcetrail/parso.nix
@ -0,0 +1,29 @@
+# Taken from a past commit of nixpkgs
+
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "parso";
+
+  # TODO: Remove along with ./jedi.nix when version compatiblity issue is
+  # resolved.
+  version = "0.7.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c";
+  };
+
+  checkInputs = [ pytest ];
+
+  meta = {
+    description = "A Python Parser";
+    homepage = "https://github.com/davidhalter/parso";
+    license = lib.licenses.mit;
+  };
+
+}
--- a/pkgs/development/tools/sourcetrail/python.nix
+++ b/pkgs/development/tools/sourcetrail/python.nix
@ -0,0 +1,68 @@
+{ stdenv, lib, fetchFromGitHub, wrapPython, python, jedi, parso, cmake, swig }:
+
+stdenv.mkDerivation rec {
+  pname = "SourcetrailPythonIndexer";
+  version = "v1_db25_p5";
+
+  src = fetchFromGitHub {
+    owner = "CoatiSoftware";
+    repo = pname;
+    rev = version;
+    sha256 = "05hlpd3am029pv1wi6mys3q0ggp64axmg8bdf1fabl9cl9jffscq";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [ wrapPython cmake swig ];
+  buildInputs = [ python ];
+  pythonPath = [ jedi parso ];
+
+  dontUseCmakeConfigure = true;
+  cmakeFlags = [
+    "-DBUILD_BINDINGS_PYTHON=1"
+    "-DPYTHON_VERSION=${lib.versions.majorMinor python.version}"
+  ];
+
+  buildPhase = ''
+    pushd SourcetrailDB
+    cmake -Bbuild $cmakeFlags .
+    pushd build
+    make -j $NIX_BUILD_CORES
+    popd
+    popd
+  '';
+
+  checkPhase = ''
+    buildPythonPath "$pythonPath"
+
+    # FIXME: some tests are failing
+    # PYTHONPATH="$program_PYTHONPATH:SourcetrailDB/build/bindings_python" \
+    #   ${python}/bin/python test.py
+    PYTHONPATH="$program_PYTHONPATH:SourcetrailDB/build/bindings_python" \
+      ${python}/bin/python test_shallow.py
+  '';
+
+  installPhase = ''
+    shopt -s extglob
+    mkdir -p $out/{bin,libexec}
+
+    cp !(run).py $out/libexec # copy *.py excluding run.py (needs extglob)
+    cat <(echo '#!/usr/bin/env python') run.py > $out/libexec/run.py
+    chmod +x $out/libexec/run.py
+    ln -s $out/libexec/run.py $out/bin/SourcetrailPythonIndexer
+
+    pushd SourcetrailDB/build/bindings_python
+    cp sourcetraildb.py $out/libexec
+    cp _sourcetraildb* $out/libexec/_sourcetraildb.so
+    popd
+
+    wrapPythonProgramsIn "$out/libexec" "$pythonPath"
+  '';
+
+  doCheck = true;
+
+  meta = with lib; {
+    description = "Python indexer for Sourcetrail";
+    homepage = "https://github.com/CoatiSoftware/SourcetrailPythonIndexer";
+    license = licenses.gpl3;
+  };
+}
--- a/pkgs/tools/text/mdbook/default.nix
+++ b/pkgs/tools/text/mdbook/default.nix
@ -2,16 +2,16 @@

 rustPlatform.buildRustPackage rec {
  pname = "mdbook";
-  version = "0.4.3";
+  version = "0.4.4";

  src = fetchFromGitHub {
    owner = "rust-lang-nursery";
    repo = "mdBook";
    rev = "v${version}";
-    sha256 = "1566jabmvafv6aiw5nvb6y2zcnxc7pbb9dl3s4vi6mx21kqp68ag";
+    sha256 = "0nqr5a27i91m71fhpycf60q54qplc920y1fmk9hav3pbb9wcc5dl";
  };

-  cargoSha256 = "0sa1h3qzdhgk2h3wrc0kg0ajq6zbkvn1ry4672gfn3j9gpgvy2bb";
+  cargoSha256 = "1p72iwl9ca7a92nf6wyjjbn0qns0xxb4xrbz2r2nmd83cxs0fplg";

  buildInputs = stdenv.lib.optionals stdenv.isDarwin [ CoreServices ];

--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -23480,7 +23480,11 @@ in

  libspotify = callPackage ../development/libraries/libspotify (config.libspotify or {});

-  sourcetrail = callPackage ../development/tools/sourcetrail { };
+  sourcetrail = libsForQt5.callPackage ../development/tools/sourcetrail {
+    jdk = jdk8;
+    llvmPackages = llvmPackages_10;
+    pythonPackages = python3Packages;
+  };

  spotifywm = callPackage ../applications/audio/spotifywm { };

--- a/pkgs/top-level/java-packages.nix
+++ b/pkgs/top-level/java-packages.nix
@ -89,6 +89,9 @@ in {
    mavenCommonArtifactFilters_1_3
    mavenCommonArtifactFilters_1_4;

+  inherit (callPackage ../development/java-modules/maven/compiler-plugin.nix { inherit fetchMaven; })
+    mavenCompiler_3_2;
+
  inherit (callPackage ../development/java-modules/maven/core.nix { inherit fetchMaven; })
    mavenCore_2_0_1
    mavenCore_2_0_6
@ -243,13 +246,16 @@ in {
    plexusClassworlds_2_4;

  inherit (callPackage ../development/java-modules/plexus/compiler-api.nix { inherit fetchMaven; })
-    plexusCompilerApi_2_2;
+    plexusCompilerApi_2_2
+    plexusCompilerApi_2_4;

  inherit (callPackage ../development/java-modules/plexus/compiler-javac.nix { inherit fetchMaven; })
-    plexusCompilerJavac_2_2;
+    plexusCompilerJavac_2_2
+    plexusCompilerJavac_2_4;

  inherit (callPackage ../development/java-modules/plexus/compiler-manager.nix { inherit fetchMaven; })
-    plexusCompilerManager_2_2;
+    plexusCompilerManager_2_2
+    plexusCompilerManager_2_4;

  inherit (callPackage ../development/java-modules/plexus/component-annotations.nix { inherit fetchMaven; })
    plexusComponentAnnotations_1_5_5;
--- a/pkgs/top-level/ocaml-packages.nix
+++ b/pkgs/top-level/ocaml-packages.nix
@ -539,6 +539,8 @@ let

    minisat = callPackage ../development/ocaml-modules/minisat { };

+    mirage-block = callPackage ../development/ocaml-modules/mirage-block { };
+
    mirage-bootvar-unix = callPackage ../development/ocaml-modules/mirage-bootvar-unix { };

    mirage-clock = callPackage ../development/ocaml-modules/mirage-clock { };