Merge staging-next into staging

pkgs/applications/audio/musly/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake, eigen, libav_all }:
+{ stdenv, fetchFromGitHub, cmake, eigen, libav }:
 stdenv.mkDerivation {
   pname = "musly";
   version = "unstable-2017-04-26";
@@ -9,7 +9,7 @@ stdenv.mkDerivation {
     sha256 = "1q42wvdwy2pac7bhfraqqj2czw7w2m33ms3ifjl8phm7d87i8825";
   };
   nativeBuildInputs = [ cmake ];
-  buildInputs = [ eigen (libav_all.override { vaapiSupport = stdenv.isLinux; }).libav_11 ];
+  buildInputs = [ eigen (libav.override { vaapiSupport = stdenv.isLinux; }) ];
   fixupPhase = if stdenv.isDarwin then ''
     install_name_tool -change libmusly.dylib $out/lib/libmusly.dylib $out/bin/musly
     install_name_tool -change libmusly_resample.dylib $out/lib/libmusly_resample.dylib $out/bin/musly

pkgs/applications/audio/ncmpc/default.nix

@@ -10,13 +10,13 @@ assert pcreSupport -> pcre != null;
 
 stdenv.mkDerivation rec {
   pname = "ncmpc";
-  version = "0.38";
+  version = "0.39";
 
   src = fetchFromGitHub {
     owner  = "MusicPlayerDaemon";
     repo   = "ncmpc";
     rev    = "v${version}";
-    sha256 = "1kidpd1xrfax3v31q93r9g9b7jd841476q47wgd94h1a86b70gs9";
+    sha256 = "08xrcinfm1a7hjycf8la7gnsxbp3six70ks987dr7j42kd42irfq";
   };
 
   buildInputs = [ glib ncurses mpd_clientlib boost ]

pkgs/applications/science/chemistry/marvin/default.nix

@@ -4,12 +4,12 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   pname = "marvin";
-  version = "20.16.0";
+  version = "20.17.0";
 
   src = fetchurl {
     name = "marvin-${version}.deb";
     url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb";
-    sha256 = "0wfg5zd8dvjy6x6al58jd5d53gar3ds326q3b6771h5p5jzv0x2g";
+    sha256 = "0ip6ma9ivk5b74s9najn2rrkiha7hya1rjhgyrc71kwsj5gqgli0";
   };
 
   nativeBuildInputs = [ dpkg makeWrapper ];

pkgs/development/compilers/openjdk/openjfx/14.nix

@@ -96,7 +96,7 @@ in makePackage {
   postFixup = ''
     # Remove references to bootstrap.
     find "$out" -name \*.so | while read lib; do
-      new_refs="$(patchelf --print-rpath "$lib" | sed -E 's,:?${openjdk11_headless}[^:]*,,')"
+      new_refs="$(patchelf --print-rpath "$lib" | sed -E 's,:?${lib.escape ["+"] openjdk11_headless.outPath}[^:]*,,')"
       patchelf --set-rpath "$new_refs" "$lib"
     done
   '';

pkgs/development/libraries/gdal/default.nix

@@ -7,13 +7,14 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   pname = "gdal";
-  version = "3.0.4";
+  # broken with poppler 20.08, however, can't fetch patches cleanly
+  version = "3.1.2.post2020-08-26";
 
   src = fetchFromGitHub {
     owner = "OSGeo";
     repo = "gdal";
-    rev = "v${version}";
-    sha256 = "00a7q9wv8s1bmdhqxvixkq2afr8aibg3pkc76gg50r8lavf6j84c";
+    rev = "9a8df672204a8b3b33c36e09a32f747e21166fe9";
+    sha256 = "1n25jma4x1l7slwxk702q77r84vxr90fyn4c3zpkr07q1b8wqql9";
   };
 
   sourceRoot = "source/gdal";
@@ -57,7 +58,7 @@ stdenv.mkDerivation rec {
     "--with-proj=${proj.dev}" # optional
     "--with-geos=${geos}/bin/geos-config" # optional
     "--with-hdf4=${hdf4.dev}" # optional
-    "--with-xml2=${libxml2.dev}/bin/xml2-config" # optional
+    "--with-xml2=yes" # optional
     (if netcdfSupport then "--with-netcdf=${netcdf}" else "")
   ];
 

pkgs/development/node-packages/node-packages.json

@@ -122,6 +122,7 @@
 , "mocha"
 , "multi-file-swagger"
 , "neovim"
+, "netlify-cli"
 , "nijs"
 , "node-gyp"
 , "node-gyp-build"

pkgs/development/ocaml-modules/camlpdf/default.nix

@@ -1,20 +1,20 @@
-{ stdenv, fetchFromGitHub, ocaml, findlib }:
+{ stdenv, fetchFromGitHub, which, ocaml, findlib }:
 
 if !stdenv.lib.versionAtLeast ocaml.version "4.02"
 then throw "camlpdf is not available for OCaml ${ocaml.version}"
 else
 
 stdenv.mkDerivation rec {
-  version = "2.3";
+  version = "2.3.1";
   name = "ocaml${ocaml.version}-camlpdf-${version}";
   src = fetchFromGitHub {
     owner = "johnwhitington";
     repo = "camlpdf";
     rev = "v${version}";
-    sha256 = "1z8h6bjzmlscr6h6kdvzj8kspifb4n9dg7zi54z1cv2qi03kr8dk";
+    sha256 = "1q69hhk63z836jbkv4wsng27w35w0qpz01c7ax0mqm8d8kmnr0v4";
   };
 
-  buildInputs = [ ocaml findlib ];
+  buildInputs = [ which ocaml findlib ];
 
   # Version number in META file is wrong
   patchPhase = ''
@@ -26,7 +26,9 @@ stdenv.mkDerivation rec {
     EOF
   '';
 
-  createFindlibDestdir = true;
+  preInstall = ''
+    mkdir -p $out/lib/ocaml/${ocaml.version}/site-lib/stublibs
+  '';
 
   meta = with stdenv.lib; {
     description = "An OCaml library for reading, writing and modifying PDF files";

pkgs/development/ocaml-modules/cpdf/default.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, ocaml, findlib, camlpdf, ncurses }:
 
-let version = "2.3"; in
+let version = "2.3.1"; in
 
 stdenv.mkDerivation {
   name = "ocaml${ocaml.version}-cpdf-${version}";
@@ -9,9 +9,13 @@ stdenv.mkDerivation {
     owner = "johnwhitington";
     repo = "cpdf-source";
     rev = "v${version}";
-    sha256 = "0i976y1v0l7x7k2n8k6v0h4bw9zlxsv04y4fdxss6dzpsfz49w23";
+    sha256 = "1gwz0iy28f67kbqap2q10nf98dalwbi03vv5j893z2an7pb4w68z";
   };
 
+  prePatch = ''
+    substituteInPlace META --replace 'version="1.7"' 'version="${version}"'
+  '';
+
   buildInputs = [ ocaml findlib ncurses ];
   propagatedBuildInputs = [ camlpdf ];
 

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

@@ -1,29 +1,32 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, pythonOlder
 , attrs
 , botocore
 , click
 , enum-compat
+, hypothesis
 , jmespath
+, mock
+, mypy-extensions
 , pip
+, pytest
+, pyyaml
 , setuptools
 , six
 , typing
-, wheel
 , watchdog
-, pytest
-, hypothesis
-, mock
+, wheel
 }:
 
 buildPythonPackage rec {
   pname = "chalice";
-  version = "1.17.0";
+  version = "1.18.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b1ab4197628f4725ac50479aefe61698ea4a5d83ef88bb88978023cdf840a9a2";
+    sha256 = "0zb4xk9b553pnfzh8s909cixfdplqnc3nda0fjwjrryi2nxjxd6a";
   };
 
   checkInputs = [ watchdog pytest hypothesis mock ];
@@ -33,10 +36,13 @@ buildPythonPackage rec {
     click
     enum-compat
     jmespath
+    mypy-extensions
     pip
+    pyyaml
     setuptools
     six
     wheel
+  ] ++ lib.optionals (pythonOlder "3.5") [
     typing
   ];
 

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

@@ -1,8 +1,9 @@
-{ stdenv, fetchPypi, buildPythonPackage, sphinx }:
+{ stdenv, fetchPypi, buildPythonPackage, isPy27, sphinx }:
 
 buildPythonPackage rec {
   pname = "hieroglyph";
   version = "2.1.0";
+  disabled = isPy27; # python2 compatible sphinx is too low
 
   src = fetchPypi {
     inherit pname version;

pkgs/development/python-modules/jupyterlab-git/default.nix

@@ -0,0 +1,37 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pythonOlder
+, notebook
+, nbdime
+, git
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "jupyterlab_git";
+  version = "0.20.0";
+  disabled = pythonOlder "3.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0qs3wrcils07xlz698xr7giqf9v63n2qb338mlh7wql93rmjg45i";
+  };
+
+  propagatedBuildInputs = [ notebook nbdime git ];
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    pytest jupyterlab_git/ --ignore=jupyterlab_git/tests/test_handlers.py
+  '';
+
+  pythonImportsCheck = [ "jupyterlab_git" ];
+
+  meta = with lib; {
+    description = "Jupyter lab extension for version control with Git.";
+    license = with licenses; [ bsd3 ];
+    homepage = "https://github.com/jupyterlab/jupyterlab-git";
+    maintainers = with maintainers; [ chiroptical ];
+  };
+}

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

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "sphinx_rtd_theme";
-  version = "0.5.0";
+  version = "0.4.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "22c795ba2832a169ca301cd0a083f7a434e09c538c70beb42782c073651b707d";
+    sha256 = "728607e34d60456d736cc7991fd236afb828b21b82f956c5ea75f94c8414040a";
   };
 
   propagatedBuildInputs = [ sphinx ];

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

@@ -1,8 +1,9 @@
-{ stdenv, buildPythonPackage, fetchPypi, coverage, pytest, pytestcov }:
+{ stdenv, buildPythonPackage, fetchPypi, isPy27, coverage, pytest, pytestcov }:
 
 buildPythonPackage rec {
   pname = "vulture";
   version = "2.0";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;

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

@@ -3,6 +3,7 @@
 , fetchPypi
 , xorg
 , cffi
+, nose
 , six
 }:
 
@@ -22,6 +23,10 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ cffi six ];
 
+  checkInputs = [ nose ];
+
+  pythonImportsCheck = [ "xcffib" ];
+
   meta = with stdenv.lib; {
     description = "A drop in replacement for xpyb, an XCB python binding";
     homepage = "https://github.com/tych0/xcffib";

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchFromGitHub, xcffib, pillow }:
+{ lib, buildPythonPackage, fetchFromGitHub, xcffib, pillow, nose }:
 
 buildPythonPackage rec {
   pname = "xpybutil";
@@ -15,6 +15,8 @@ buildPythonPackage rec {
   # pillow is a dependency in image.py which is not listed in setup.py
   propagatedBuildInputs = [ xcffib pillow ];
 
+  checkInputs = [ nose ];
+
   meta = with lib; {
     homepage = "https://github.com/BurntSushi/xpybutil";
     description = "An incomplete xcb-util port plus some extras";

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

@@ -0,0 +1,27 @@
+{ stdenv, fetchFromGitHub, cmake, asciidoc, libxslt, docbook_xsl }:
+
+stdenv.mkDerivation rec {
+  pname = "kpack";
+
+  version = "1.1.0";
+
+  src = fetchFromGitHub {
+    owner = "KnightOS";
+    repo = "kpack";
+    rev = version;
+    sha256 = "0kakfbzdvq5ldv1gdzl473j73c9nfdyx4xzfkriglkrqmksqc329";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ asciidoc libxslt.bin docbook_xsl ];
+
+  hardeningDisable = [ "fortify" ];
+
+  meta = with stdenv.lib; {
+    homepage    = "https://knightos.org/";
+    description = "A tool to create or extract KnightOS packages";
+    license     = licenses.lgpl2Only;
+    maintainers = with maintainers; [ siraben ];
+  };
+}

pkgs/games/klavaro/default.nix

@@ -37,6 +37,7 @@ stdenv.mkDerivation rec {
   meta = with stdenv.lib; {
     description = "Free touch typing tutor program";
     homepage = "http://klavaro.sourceforge.net/";
+    changelog = "https://sourceforge.net/p/klavaro/code/HEAD/tree/trunk/ChangeLog";
     license = licenses.gpl3Plus;
     platforms = platforms.linux;
     maintainers = with maintainers; [ mimame davidak ];

pkgs/tools/package-management/nfpm/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "nfpm";
-  version = "1.6.0";
+  version = "1.7.0";
 
   src = fetchFromGitHub {
     owner = "goreleaser";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1q4fzjlaiwsm028cwcw7xgcbdkccw18f2mf1vh7lz42l1bxy8bk4";
+    sha256 = "0jmxafvxzqg65zg5cnjd2nsz1mmw06mc7qz3lbs5h2gkxiah8264";
   };
 
-  vendorSha256 = "1bsb05qhr9zm8yar8mdi3mw0i5ak1s5x0i8qkz5fd6wcqnsw2jjw";
+  vendorSha256 = "0yvzwbm0xb1h45x96h658avbjz9w79aaa6z042xpvjqc4wsr8155";
 
   doCheck = false;
 

pkgs/top-level/all-packages.nix

@@ -579,7 +579,10 @@ in
 
   acpica-tools = callPackage ../tools/system/acpica-tools { };
 
-  act = callPackage ../development/tools/misc/act {};
+  act = callPackage ../development/tools/misc/act {
+    # go 1.15 cannot connect to docker-for-mac https://github.com/docker/for-mac/issues/4855
+    buildGoModule = if stdenv.isDarwin then buildGo114Module else buildGoModule;
+  };
 
   actdiag = with python3.pkgs; toPythonApplication actdiag;
 
@@ -5621,6 +5624,8 @@ in
 
   netkittftp = callPackage ../tools/networking/netkit/tftp { };
 
+  netlify-cli = nodePackages.netlify-cli;
+
   netpbm = callPackage ../tools/graphics/netpbm { };
 
   netrw = callPackage ../tools/networking/netrw { };
@@ -11044,6 +11049,8 @@ in
     inherit (darwin.apple_sdk.frameworks) Security;
   };
 
+  kpack = callPackage ../development/tools/misc/kpack { };
+
   kustomize = callPackage ../development/tools/kustomize { };
 
   ktlint = callPackage ../development/tools/ktlint { };
@@ -13094,7 +13101,7 @@ in
   libaudclient = callPackage ../development/libraries/libaudclient { };
 
   libav = libav_11; # branch 11 is API-compatible with branch 10
-  libav_all = callPackage ../development/libraries/libav { };
+  libav_all = callPackages ../development/libraries/libav { };
   inherit (libav_all) libav_0_8 libav_11 libav_12;
 
   libavc1394 = callPackage ../development/libraries/libavc1394 { };

pkgs/top-level/python-packages.nix

@@ -3361,6 +3361,8 @@ in {
 
   jupyterlab = callPackage ../development/python-modules/jupyterlab {};
 
+  jupyterlab-git = callPackage ../development/python-modules/jupyterlab-git {};
+
   jupyter-sphinx = callPackage ../development/python-modules/jupyter-sphinx { };
 
   jupytext = callPackage ../development/python-modules/jupytext { };