Merge staging-next into staging

nixos/modules/programs/command-not-found/command-not-found.pl

···
         exec("nix-shell", "-p", $package, "--run", shell_quote("exec", @ARGV));
     } else {
         print STDERR <<EOF;
-The program '$program' is not in your PATH. You can make it available in a
+The program '$program' is not in your PATH. You can make it available in an
 ephemeral shell by typing:
   nix-shell -p $package
 EOF
···
 } else {
     print STDERR <<EOF;
 The program '$program' is not in your PATH. It is provided by several packages.
-You can make it available in a ephemeral shell by typing one of the following:
+You can make it available in an ephemeral shell by typing one of the following:
 EOF
     print STDERR "  nix-shell -p $_->{package}\n" foreach @$res;
 }

pkgs/applications/editors/joe/default.nix

···
 { stdenv, fetchurl } :
 
 stdenv.mkDerivation rec {
-  version = "4.6";
   pname = "joe";
+  version = "4.6";
 
   src = fetchurl {
     url = "mirror://sourceforge/joe-editor/${pname}-${version}.tar.gz";
···
 
   meta = with stdenv.lib; {
     description = "A full featured terminal-based screen editor";
+    longDescription = ''
+      JOE (Joe's Own Editor) is a full featured terminal-based screen editor
+      which is distributed under the GNU General Public License (GPL). JOE has
+      been around since 1988 and comes standard with many Linux distributions.
+
+      JOE is being maintained by its original author Joseph Allen, plus all of
+      the people who send bug reports, feature suggestions and patches to the
+      project web site. JOE is hosted by SourceForge.net and its source code is
+      controlled under Mercurial.
+
+      JOE is a blending of MicroPro's venerable microcomputer word processor
+      WordStar and Richard Stallman's famous LISP based text editor GNU-EMACS
+      (but it does not use code from either program): most of the basic editing
+      keys are the same as in WordStar as is the overall feel of the editor. JOE
+      also has some of the key bindings and many of the powerful features of
+      EMACS.
+
+      JOE is written in C and its only dependency is libc. This makes JOE very
+      easy to build (just "configure" and "make install"), making it feasible to
+      include on small systems and recovery disks. The compiled binary is about
+      300K in x86. Note that JOE can use either the termcap or terminfo terminal
+      capabilities databases (or a built-in termcap entry for ANSI
+      terminals). The choice is controlled by a "configure" option. If terminfo
+      is used, a library is required to access the database (on some systems
+      this library is ncurses, but JOE does not use curses to control the
+      terminal - it has its own code for this).
+    '';
     homepage = "https://joe-editor.sourceforge.io";
-    license = licenses.gpl2;
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ AndersonTorres ];
     platforms = platforms.unix;
   };
 }

pkgs/applications/networking/cluster/nomad/0.11.nix

···
-{ callPackage, buildGoPackage }:
+{ callPackage
+, buildGoPackage
+, nvidia_x11
+, nvidiaGpuSupport
+}:
 
 callPackage ./generic.nix {
-  inherit buildGoPackage;
+  inherit buildGoPackage nvidia_x11 nvidiaGpuSupport;
   version = "0.11.8";
   sha256 = "1dhh07bifr02jh2lls8fv1d9ra67ymgh8qxqvpvm0cd0qdd469z1";
 }

pkgs/applications/networking/cluster/nomad/0.12.nix

···
-{ callPackage, buildGoPackage }:
+{ callPackage
+, buildGoPackage
+, nvidia_x11
+, nvidiaGpuSupport
+}:
 
 callPackage ./generic.nix {
-  inherit buildGoPackage;
+  inherit buildGoPackage nvidia_x11 nvidiaGpuSupport;
   version = "0.12.9";
   sha256 = "1a0ig6pb0z3qp7zk4jgz3h241bifmjlyqsfikyy3sxdnzj7yha27";
 }

pkgs/applications/networking/cluster/nomad/1.0.nix

···
-{ callPackage, buildGoPackage }:
+{ callPackage
+, buildGoPackage
+, nvidia_x11
+, nvidiaGpuSupport
+}:
 
 callPackage ./generic.nix {
-  inherit buildGoPackage;
+  inherit buildGoPackage nvidia_x11 nvidiaGpuSupport;
   version = "1.0.1";
   sha256 = "07k81csyxhgc7bgn297zlqyvc55qb5fmiavi7dk81rdpg5m2zjvv";
 }

pkgs/applications/networking/cluster/nomad/generic.nix

···
-{ stdenv, buildGoPackage, fetchFromGitHub, version, sha256 }:
+{ lib
+, buildGoPackage
+, fetchFromGitHub
+, version
+, sha256
+, nvidiaGpuSupport
+, patchelf
+, nvidia_x11
+}:
 
 buildGoPackage rec {
   pname = "nomad";
···
     inherit rev sha256;
   };
 
+  nativeBuildInputs = lib.optionals nvidiaGpuSupport [
+    patchelf
+  ];
+
   # ui:
   #  Nomad release commits include the compiled version of the UI, but the file
   #  is only included if we build with the ui tag.
-  # nonvidia:
-  #  We disable Nvidia GPU scheduling on Linux, as it doesn't work there:
-  #  Ref: https://github.com/hashicorp/nomad/issues/5535
-  preBuild = let
-    tags = ["ui"]
-      ++ stdenv.lib.optional stdenv.isLinux "nonvidia";
-    tagsString = stdenv.lib.concatStringsSep " " tags;
-  in ''
-    export buildFlagsArray=(
-      -tags="${tagsString}"
-    )
- '';
+  preBuild =
+    let
+      tags = [ "ui" ] ++ lib.optional (!nvidiaGpuSupport) "nonvidia";
+      tagsString = lib.concatStringsSep " " tags;
+    in
+    ''
+      export buildFlagsArray=(
+        -tags="${tagsString}"
+      )
+    '';
+
+  # The dependency on NVML isn't explicit. We have to make it so otherwise the
+  # binary will not know where to look for the relevant symbols.
+  postFixup = lib.optionalString nvidiaGpuSupport ''
+    for bin in $out/bin/*; do
+      patchelf --add-needed "${nvidia_x11}/lib/libnvidia-ml.so" "$bin"
+    done
+  '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://www.nomadproject.io/";
     description = "A Distributed, Highly Available, Datacenter-Aware Scheduler";
     platforms = platforms.unix;

pkgs/development/haskell-modules/configuration-common.nix

···
   # https://github.com/Gabriel439/Haskell-Nix-Derivation-Library/pull/10
   nix-derivation = doJailbreak super.nix-derivation;
 
+  # Break out of overspecified constraint on QuickCheck.
+  # Fixed by https://github.com/haskell-servant/servant/commit/08579ca0039410e04d6c36c975ddc20165819db6
+  servant-client      = doJailbreak super.servant-client;
+  servant-client-core = doJailbreak super.servant-client-core;
+
 } // import ./configuration-tensorflow.nix {inherit pkgs haskellLib;} self super

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

···
   pname = "csv";
 	version = "2.4";
 
+	useDune2 = true;
+
 	src = fetchurl {
 		url = "https://github.com/Chris00/ocaml-${pname}/releases/download/${version}/csv-${version}.tbz";
 		sha256 = "13m9n8mdss6jfbiw7d5bybxn4n85vmg4zw7dc968qrgjfy0w9zhk";

pkgs/development/ocaml-modules/csv/lwt.nix

···
 
 buildDunePackage {
   pname = "csv-lwt";
-  inherit (csv) src version meta;
+  inherit (csv) src version useDune2 meta;
 
   propagatedBuildInputs = [ csv ocaml_lwt ];
 

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

···
-{ lib, fetchurl, buildDunePackage, ocaml, alcotest, ocaml-migrate-parsetree }:
+{ lib, fetchurl, buildDunePackage, ocaml, alcotest, ppxlib }:
 
 buildDunePackage rec {
   pname = "ppx_blob";
-  version = "0.7.1";
+  version = "0.7.2";
 
   useDune2 = true;
 
   src = fetchurl {
     url = "https://github.com/johnwhitington/${pname}/releases/download/${version}/ppx_blob-${version}.tbz";
-    sha256 = "0m616ri6kmawflphiwm6j4djds27v0fjvi8xjz1fq5ydc1sq8d0l";
+    sha256 = "00haz1cmplk3j9ysh6j656zrldy60585fmlndmfhpd5332mxrfdw";
   };
 
   checkInputs = [ alcotest ];
-  buildInputs = [ ocaml-migrate-parsetree ];
+  propagatedBuildInputs = [ ppxlib ];
   doCheck = lib.versionAtLeast ocaml.version "4.05";
 
   meta = with lib; {

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

···
 { stdenv
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , isPy27
-, pytest
 , pytestrunner
 , pytestCheckHook
 , numpy
 , pillow
 }:
 
-buildPythonPackage rec {
-  version = "2.1.1";
+let
   pname = "pydicom";
-  disabled = isPy27;
+  version = "2.1.2";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "72a11086f6a277c1529a552583fde73e03256a912173f15e9bc256e5b28f28f1";
+  src = fetchFromGitHub {
+    owner = "${pname}";
+    repo = "${pname}";
+    rev = "v${version}";
+    sha256 = "sha256-iExy+mUs1uqs/u9N6btlqyP6/TvoPVsuOuzs56zZAS8=";
   };
 
+  # Pydicom needs pydicom-data to run some tests. If these files are downloaded
+  # before the package creation, it'll try to download during the checkPhase.
+  test_data = fetchFromGitHub {
+    owner = "${pname}";
+    repo = "${pname}-data";
+    rev = "bbb723879690bb77e077a6d57657930998e92bd5";
+    sha256 = "sha256-dCI1temvpNWiWJYVfQZKy/YJ4ad5B0e9hEKHJnEeqzk=";
+  };
+
+in
+buildPythonPackage {
+  inherit pname version src;
+  disabled = isPy27;
+
   propagatedBuildInputs = [ numpy pillow ];
 
-  checkInputs = [ pytest pytestrunner pytestCheckHook ];
-  disabledTests = [ "test_invalid_bit_depth_raises" ];
-  # harmless failure; see https://github.com/pydicom/pydicom/issues/1119
+  checkInputs = [ pytestrunner pytestCheckHook ];
+
+  # Setting $HOME to prevent pytest to try to create a folder inside
+  # /homeless-shelter which is read-only.
+  # Linking pydicom-data dicom files to $HOME/.pydicom/data
+  preCheck = ''
+    export HOME=$TMP/test-home
+    mkdir -p $HOME/.pydicom/
+    ln -s ${test_data}/data_store/data $HOME/.pydicom/data
+  '';
+
+  # This test try to remove a dicom inside $HOME/.pydicom/data/ and download it again.
+  disabledTests = [
+    "test_fetch_data_files"
+  ];
 
   meta = with stdenv.lib; {
     homepage = "https://pydicom.github.io";

pkgs/development/tools/sourcetrail/python.nix

···
     owner = "CoatiSoftware";
     repo = pname;
     rev = version;
-    sha256 = "05hlpd3am029pv1wi6mys3q0ggp64axmg8bdf1fabl9cl9jffscq";
+    sha256 = "01jaigxigq6dvfwq018gn9qw7i6p4jm0y71lqzschfv9vwf6ga45";
     fetchSubmodules = true;
   };
 
···
     description = "Python indexer for Sourcetrail";
     homepage = "https://github.com/CoatiSoftware/SourcetrailPythonIndexer";
     license = licenses.gpl3;
+    broken = stdenv.isDarwin;
+    # https://github.com/NixOS/nixpkgs/pull/107533#issuecomment-751063675
   };
 }

pkgs/shells/zsh/default.nix

···
     "--with-tcsetpgrp"
     "--enable-pcre"
     "--enable-zprofile=${placeholder "out"}/etc/zprofile"
+    "--disable-site-fndir"
   ];
 
   # the zsh/zpty module is not available on hydra

pkgs/tools/backup/duplicity/default.nix

···
   propagatedBuildInputs = with pythonPackages; [
     b2sdk
     boto
+    boto3
     cffi
     cryptography
     ecdsa

pkgs/tools/misc/hdf4/default.nix

···
 , fixDarwinDylibNames
 , cmake
 , libjpeg
+, libtirpc
 , zlib
 , szip ? null
 }:
···
     sha256 = "04nbgfxyj5jg4d6sr28162cxbfwqgv0sa7vz1ayzvm8wbbpkbq5x";
   };
 
+  patches = [
+    # Note that the PPC, SPARC and s390 patches are only needed so the aarch64 patch applies cleanly
+    (fetchpatch {
+      url = "https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-ppc.patch";
+      sha256 = "0dbbfpsvvqzy9zyfv38gd81zzc44gxjib9sd8scxqnkkqprj6jq0";
+    })
+    (fetchpatch {
+      url = "https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-4.2.4-sparc.patch";
+      sha256 = "0ip4prcjpa404clm87ib7l71605mws54x9492n9pbz5yb51r9aqh";
+    })
+    (fetchpatch {
+      url = "https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-s390.patch";
+      sha256 = "0aiqbr4s1l19y3r3y4wjd5fkv9cfc8rlr4apbh1p0d57wyvqa7i3";
+    })
+    (fetchpatch {
+      url = "https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-arm.patch";
+      sha256 = "157k1avvkpf3x89m1fv4a1kgab6k3jv74rskazrmjivgzav4qaw3";
+    })
+    (fetchpatch {
+      url = "https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-aarch64.patch";
+      sha256 = "112svcsilk16ybbsi8ywnxfl2p1v44zh3rfn4ijnl8z08vfqrvvs";
+    })
+  ];
+
   nativeBuildInputs = [
     cmake
   ] ++ stdenv.lib.optionals stdenv.isDarwin [
···
 
   buildInputs = [
     libjpeg
+    libtirpc
     szip
     zlib
   ];
 
-  preConfigure = stdenv.lib.optionalString (szip != null) "export SZIP_INSTALL=${szip}";
+  preConfigure = ''
+    # Make tirpc discovery work with CMAKE_PREFIX_PATH
+    substituteInPlace config/cmake/FindXDR.cmake \
+      --replace 'find_path(XDR_INCLUDE_DIR NAMES rpc/types.h PATHS "/usr/include" "/usr/include/tirpc")' \
+                'find_path(XDR_INCLUDE_DIR NAMES rpc/types.h PATH_SUFFIXES include/tirpc)'
+  '' + stdenv.lib.optionalString (szip != null) ''
+    export SZIP_INSTALL=${szip}
+  '';
 
   cmakeFlags = [
     "-DBUILD_SHARED_LIBS=ON"

pkgs/tools/misc/ipxe/default.nix

···
 
 stdenv.mkDerivation rec {
   pname = "ipxe";
-  version = "1.20.1";
+  version = "1.21.1";
 
   nativeBuildInputs = [ perl cdrkit syslinux xz openssl gnu-efi mtools ];
 
···
     owner = "ipxe";
     repo = "ipxe";
     rev = "v${version}";
-    sha256 = "0w7h7y97gj9nqvbmsg1zp6zj5mpbbpckqbbx7bpp6k3ahy5fk8zp";
+    sha256 = "1pkf1n1c0rdlzfls8fvjvi1sd9xjd9ijqlyz3wigr70ijcv6x8i9";
   };
 
   # not possible due to assembler code

pkgs/top-level/all-packages.nix

···
   # with different versions we pin Go for all versions.
   nomad_0_11 = callPackage ../applications/networking/cluster/nomad/0.11.nix {
     buildGoPackage = buildGo114Package;
+    inherit (linuxPackages) nvidia_x11;
+    nvidiaGpuSupport = config.cudaSupport or (!stdenv.isLinux);
   };
   nomad_0_12 = callPackage ../applications/networking/cluster/nomad/0.12.nix {
     buildGoPackage = buildGo114Package;
+    inherit (linuxPackages) nvidia_x11;
+    nvidiaGpuSupport = config.cudaSupport or (!stdenv.isLinux);
   };
   nomad_1_0 = callPackage ../applications/networking/cluster/nomad/1.0.nix {
     buildGoPackage = buildGo115Package;
+    inherit (linuxPackages) nvidia_x11;
+    nvidiaGpuSupport = config.cudaSupport or (!stdenv.isLinux);
   };
 
   notable = callPackage ../applications/misc/notable { };

pkgs/top-level/ocaml-packages.nix

···
 
     pprint = callPackage ../development/ocaml-modules/pprint { };
 
-    ppx_blob =
-      if lib.versionAtLeast ocaml.version "4.02"
-      then callPackage ../development/ocaml-modules/ppx_blob {}
-      else null;
+    ppx_blob = callPackage ../development/ocaml-modules/ppx_blob { };
 
     ppx_cstruct = callPackage ../development/ocaml-modules/cstruct/ppx.nix {};