NixOS · Feb 12, 2019 · Nov 3, 2019 · Nov 4, 2019 · Nov 4, 2019 · Nov 4, 2019
diff --git a/nixos/modules/virtualisation/qemu-vm.nix b/nixos/modules/virtualisation/qemu-vm.nix
@@ -23,24 +23,56 @@ let
 
   cfg = config.virtualisation;
 
-  qemuGraphics = lib.optionalString (!cfg.graphics) "-nographic";
-
   consoles = lib.concatMapStringsSep " " (c: "console=${c}") cfg.qemu.consoles;
 
-  # XXX: This is very ugly and in the future we really should use attribute
-  # sets to build ALL of the QEMU flags instead of this mixed mess of Nix
-  # expressions and shell script stuff.
-  mkDiskIfaceDriveFlag = idx: driveArgs: let
-    inherit (cfg.qemu) diskInterface;
-    # The drive identifier created by incrementing the index by one using the
-    # shell.
-    drvId = "drive$((${idx} + 1))";
-    # NOTE: DO NOT shell escape, because this may contain shell variables.
-    commonArgs = "index=${idx},id=${drvId},${driveArgs}";
-    isSCSI = diskInterface == "scsi";
-    devArgs = "${diskInterface}-hd,drive=${drvId}";
-    args = "-drive ${commonArgs},if=none -device lsi53c895a -device ${devArgs}";
-  in if isSCSI then args else "-drive ${commonArgs},if=${diskInterface}";
+  driveOpts = { ... }: {
+
+    options = {
+
+      file = mkOption {
+        type = types.str;
+        description = "The file image used for this drive.";
+      };
+
+      driveExtraOpts = mkOption {
+        type = types.attrsOf types.str;
+        default = {};
+        description = "Extra options passed to drive flag.";
+      };
+
+      deviceExtraOpts = mkOption {
+        type = types.attrsOf types.str;
+        default = {};
+        description = "Extra options passed to device flag.";
+      };
+
+    };
+
+  };
+
+  driveCmdline = idx: { file, driveExtraOpts, deviceExtraOpts, ... }:
+    let
+      drvId = "drive${toString idx}";
+      mkKeyValue = generators.mkKeyValueDefault {} "=";
+      mkOpts = opts: concatStringsSep "," (mapAttrsToList mkKeyValue opts);
+      driveOpts = mkOpts (driveExtraOpts // {
+        index = idx;
+        id = drvId;
+        "if" = "none";
+        inherit file;
+      });
+      deviceOpts = mkOpts (deviceExtraOpts // {
+        drive = drvId;
+      });
+      device =
+        if cfg.qemu.diskInterface == "scsi" then
+          "-device lsi53c895a -device scsi-hd,${deviceOpts}"
+        else
+          "-device virtio-blk-pci,${deviceOpts}";
+    in
+      "-drive ${driveOpts} ${device}";
+
+  drivesCmdLine = drives: concatStringsSep " " (imap1 driveCmdline drives);
 
   # Shell script to start the VM.
   startVM =
@@ -77,13 +109,11 @@ let
       ''}
 
       cd $TMPDIR
-      idx=2
-      extraDisks=""
+      idx=0
       ${flip concatMapStrings cfg.emptyDiskImages (size: ''
         if ! test -e "empty$idx.qcow2"; then
             ${qemu}/bin/qemu-img create -f qcow2 "empty$idx.qcow2" "${toString size}M"
         fi
-        extraDisks="$extraDisks ${mkDiskIfaceDriveFlag "$idx" "file=$(pwd)/empty$idx.qcow2,werror=report"}"
         idx=$((idx + 1))
       '')}
 
@@ -97,21 +127,7 @@ let
           -virtfs local,path=/nix/store,security_model=none,mount_tag=store \
           -virtfs local,path=$TMPDIR/xchg,security_model=none,mount_tag=xchg \
           -virtfs local,path=''${SHARED_DIR:-$TMPDIR/xchg},security_model=none,mount_tag=shared \
-          ${if cfg.useBootLoader then ''
-            ${mkDiskIfaceDriveFlag "0" "file=$NIX_DISK_IMAGE,cache=writeback,werror=report"} \
-            ${mkDiskIfaceDriveFlag "1" "file=$TMPDIR/disk.img,media=disk"} \
-            ${if cfg.useEFIBoot then ''
-              -pflash $TMPDIR/bios.bin \
-            '' else ''
-            ''}
-          '' else ''
-            ${mkDiskIfaceDriveFlag "0" "file=$NIX_DISK_IMAGE,cache=writeback,werror=report"} \
-            -kernel ${config.system.build.toplevel}/kernel \
-            -initrd ${config.system.build.toplevel}/initrd \
-            -append "$(cat ${config.system.build.toplevel}/kernel-params) init=${config.system.build.toplevel}/init regInfo=${regInfo}/registration ${consoles} $QEMU_KERNEL_PARAMS" \
-          ''} \
-          $extraDisks \
-          ${qemuGraphics} \
+          ${drivesCmdLine config.virtualisation.qemu.drives} \
           ${toString config.virtualisation.qemu.options} \
           $QEMU_OPTS \
           "$@"
@@ -367,6 +383,12 @@ in
           '';
         };
 
+      drives =
+        mkOption {
+          type = types.listOf (types.submodule driveOpts);
+          description = "Drives passed to qemu.";
+        };
+
       diskInterface =
         mkOption {
           default = "virtio";
@@ -476,8 +498,49 @@ in
 
     # FIXME: Consolidate this one day.
     virtualisation.qemu.options = mkMerge [
-      (mkIf (pkgs.stdenv.isi686 || pkgs.stdenv.isx86_64) [ "-vga std" "-usb" "-device usb-tablet,bus=usb-bus.0" ])
-      (mkIf (pkgs.stdenv.isAarch32 || pkgs.stdenv.isAarch64) [ "-device virtio-gpu-pci" "-device usb-ehci,id=usb0" "-device usb-kbd" "-device usb-tablet" ])
+      (mkIf (pkgs.stdenv.isi686 || pkgs.stdenv.isx86_64) [
+        "-vga std" "-usb" "-device usb-tablet,bus=usb-bus.0"
+      ])
+      (mkIf (pkgs.stdenv.isAarch32 || pkgs.stdenv.isAarch64) [
+        "-device virtio-gpu-pci" "-device usb-ehci,id=usb0" "-device usb-kbd" "-device usb-tablet"
+      ])
+      (mkIf (!cfg.useBootLoader) [
+        "-kernel ${config.system.build.toplevel}/kernel"
+        "-initrd ${config.system.build.toplevel}/initrd"
+        ''-append "$(cat ${config.system.build.toplevel}/kernel-params) init=${config.system.build.toplevel}/init regInfo=${regInfo}/registration ${consoles} $QEMU_KERNEL_PARAMS"''
+      ])
+      (mkIf cfg.useEFIBoot [
+        "-pflash $TMPDIR/bios.bin"
+      ])
+      (mkIf (!cfg.graphics) [
+        "-nographic"
+      ])
+    ];
+
+    virtualisation.qemu.drives = mkMerge [
+      (mkIf cfg.useBootLoader [
+        {
+          file = "$NIX_DISK_IMAGE";
+          driveExtraOpts.cache = "writeback";
+          driveExtraOpts.werror = "report";
+        }
+        {
+          file = "$TMPDIR/disk.img";
+          driveExtraOpts.media = "disk";
+          deviceExtraOpts.bootindex = "1";
+        }
+      ])
+      (mkIf (!cfg.useBootLoader) [
+        {
+          file = "$NIX_DISK_IMAGE";
+          driveExtraOpts.cache = "writeback";
+          driveExtraOpts.werror = "report";
+        }
+      ])
+      (imap0 (idx: _: {
+        file = "$(pwd)/empty${toString idx}.qcow2";
+        driveExtraOpts.werror = "report";
+      }) cfg.emptyDiskImages)
     ];
 
     # Mount the host filesystem via 9P, and bind-mount the Nix store

diff --git a/pkgs/applications/office/paperwork/default.nix b/pkgs/applications/office/paperwork/default.nix
@@ -61,7 +61,7 @@ python3Packages.buildPythonApplication rec {
   '';
 
   propagatedBuildInputs = with python3Packages; [
-    paperwork-backend pypillowfight gtk3 cairo pyxdg dateutil setuptools
+    paperwork-backend pypillowfight gtk3 cairo pyxdg dateutil setuptools pandas
   ];
 
   makeWrapperArgs = [

diff --git a/pkgs/applications/radio/sdrangel/default.nix b/pkgs/applications/radio/sdrangel/default.nix
@@ -39,7 +39,7 @@ let
 
 in mkDerivation rec {
   pname = "sdrangel";
-  version = "4.11.7";
+  version = "4.11.12";
 
   src = fetchFromGitHub {
     owner = "f4exb";

diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix
@@ -0,0 +1,42 @@
+{ lib
+, python
+}:
+with python.pkgs;
+buildPythonApplication rec {
+  pname = "deepTools";
+  version = "3.3.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "08p36p9ncj5s8qf1r7h83x4rnmi63l3yk6mnr3wgpg2qgvwl0hji";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    numpydoc
+    scipy
+    py2bit
+    pybigwig
+    pysam
+    matplotlib
+    plotly
+    deeptoolsintervals
+  ];
+
+  checkInputs = [ pytest ];
+
+  meta = with lib; {
+    homepage = "https://deeptools.readthedocs.io/en/develop";
+    description = "Tools for exploring deep DNA sequencing data";
+    longDescription = ''
+      deepTools contains useful modules to process the mapped reads data for multiple
+      quality checks, creating normalized coverage files in standard bedGraph and bigWig
+      file formats, that allow comparison between different files (for example, treatment and control).
+      Finally, using such normalized and standardized files, deepTools can create many
+      publication-ready visualizations to identify enrichments and for functional
+      annotations of the genome.
+    '';
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ scalavision ];
+  };
+}
diff --git a/pkgs/applications/version-management/sourcehut/builds.nix b/pkgs/applications/version-management/sourcehut/builds.nix
@@ -4,7 +4,7 @@
 , srht, redis, celery, pyyaml, markdown }:
 
 let
-  version = "0.47.9";
+  version = "0.48.0";
 
   buildWorker = src: buildGoModule {
     inherit src version;
@@ -20,7 +20,7 @@ in buildPythonPackage rec {
   src = fetchgit {
     url = "https://git.sr.ht/~sircmpwn/builds.sr.ht";
     rev = version;
-    sha256 = "1zgaba58svhksxb1pzz8bym9p0pm7fnxsj5k6jz86095xmfijp34";
+    sha256 = "1z5bxsn67cqffixqsrnska86mw0a6494650wbi6dbp10z03870bs";
   };
 
   patches = [

diff --git a/pkgs/applications/version-management/sourcehut/core.nix b/pkgs/applications/version-management/sourcehut/core.nix
@@ -1,17 +1,18 @@
 { stdenv, fetchgit, fetchNodeModules, buildPythonPackage
 , pgpy, flask, bleach, misaka, humanize, markdown, psycopg2, pygments, requests
 , sqlalchemy, flask_login, beautifulsoup4, sqlalchemy-utils, celery, alembic
+, importlib-metadata
 , sassc, nodejs
 , writeText }:
 
 buildPythonPackage rec {
   pname = "srht";
-  version = "0.54.3";
+  version = "0.54.4";
 
   src = fetchgit {
     url = "https://git.sr.ht/~sircmpwn/core.sr.ht";
     rev = version;
-    sha256 = "1f4srhp5g6652anifs1vyijzi2v23l2rnfpf3x96j9r8rdap42rq";
+    sha256 = "0flxvn178hqd8ljz89ddis80zfnmzgimv4506w4dg2flbwzywy7z";
   };
 
   node_modules = fetchNodeModules {
@@ -47,6 +48,7 @@ buildPythonPackage rec {
     # Unofficial runtime dependencies?
     celery
     alembic
+    importlib-metadata
   ];
 
   PKGVER = version;

diff --git a/pkgs/applications/version-management/sourcehut/dispatch.nix b/pkgs/applications/version-management/sourcehut/dispatch.nix
@@ -4,12 +4,12 @@
 
 buildPythonPackage rec {
   pname = "dispatchsrht";
-  version = "0.11.1";
+  version = "0.12.3";
 
   src = fetchgit {
     url = "https://git.sr.ht/~sircmpwn/dispatch.sr.ht";
     rev = version;
-    sha256 = "1bi7vn0yr326mf2c63f2fahdlrx2c6a8d6p6bzy2ym2835qfcc0v";
+    sha256 = "0lpc8jpyz1rg3g98546wlhr27b15g32lds77hl42aixv5f5b8lc9";
   };
 
   patches = [

diff --git a/pkgs/applications/version-management/sourcehut/git.nix b/pkgs/applications/version-management/sourcehut/git.nix
@@ -4,11 +4,19 @@
 , srht, pygit2, scmsrht }:
 
 let
-  version = "0.34.2";
+  version = "0.35.6";
+
+  buildShell = src: buildGoModule {
+    inherit src version;
+    pname = "git-srht-shell";
+    goPackagePath = "git.sr.ht/~sircmpwn/git.sr.ht/gitsrht-shell";
+
+    modSha256 = "1v4npijqgv09ssrxf1y1b3syb2fs7smy7k9rcj3ynsfrn9xgfd9y";
+  };
 
   buildDispatcher = src: buildGoModule {
     inherit src version;
-    pname = "git-sr-ht-dispatcher";
+    pname = "git-srht-dispatcher";
     goPackagePath = "git.sr.ht/~sircmpwn/git.sr.ht/gitsrht-dispatch";
 
     modSha256 = "1lmgmlin460g09dph2hw6yz25d4agqwjhrjv0qqsis7df9qpf3i1";
@@ -20,7 +28,7 @@ in buildPythonPackage rec {
   src = fetchgit {
     url = "https://git.sr.ht/~sircmpwn/git.sr.ht";
     rev = version;
-    sha256 = "1z10r2d9x71n1n36g55j4cswh0dqnzmgj2qiy1h92wwgq8azpiyy";
+    sha256 = "0j8caqbzdqkgc1bdhzz4k5hgh8lhsghfgwf46d19ryf83d8ggxqc";
   };
 
   patches = [
@@ -42,6 +50,7 @@ in buildPythonPackage rec {
 
   postInstall = ''
     mkdir -p $out/bin
+    cp ${buildShell "${src}/gitsrht-shell"}/bin/gitsrht-shell $out/bin/gitsrht-shell
     cp ${buildDispatcher "${src}/gitsrht-dispatch"}/bin/gitsrht-dispatch $out/bin/gitsrht-dispatch
   '';
 

diff --git a/pkgs/applications/version-management/sourcehut/hg.nix b/pkgs/applications/version-management/sourcehut/hg.nix
@@ -4,12 +4,12 @@
 
 buildPythonPackage rec {
   pname = "hgsrht";
-  version = "0.16.0";
+  version = "0.16.2";
 
   src = fetchhg {
     url = "https://hg.sr.ht/~sircmpwn/hg.sr.ht";
     rev = version;
-    sha256 = "0ncrj1cbls9ix2ig3qqwbzs6q6cmpqy3zs21p9fw3idfw703j3g0";
+    sha256 = "02bzy31zplnlqg8rcls5n65q1h920lhy6f51w89w1kskdw7r2mhy";
   };
 
   patches = [

diff --git a/pkgs/applications/version-management/sourcehut/meta.nix b/pkgs/applications/version-management/sourcehut/meta.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "metasrht";
-  version = "0.35.3";
+  version = "0.37.0";
 
   src = fetchgit {
     url = "https://git.sr.ht/~sircmpwn/meta.sr.ht";
     rev = version;
-    sha256 = "1kcmlmdk9v59fr3r0g2q2gfkb735xza0wni9s942wh418dr66x2f";
+    sha256 = "1jf3h2v27cbam8bwiw3x35319pzp0r651p8mfhw150jvskyvmkmr";
   };
 
   nativeBuildInputs = srht.nativeBuildInputs;

diff --git a/pkgs/applications/version-management/sourcehut/paste.nix b/pkgs/applications/version-management/sourcehut/paste.nix
@@ -4,12 +4,12 @@
 
 buildPythonPackage rec {
   pname = "pastesrht";
-  version = "0.7.1";
+  version = "0.7.3";
 
   src = fetchgit {
     url = "https://git.sr.ht/~sircmpwn/paste.sr.ht";
     rev = version;
-    sha256 = "19y9ghhi4llyg7kd3a888gbjc698vdamin4hb8dk1j6pd2f0qmjp";
+    sha256 = "15689gk37djcwdjb636d97k0il2zpdpksb95l9l4d43wipd7x5qi";
   };
 
   patches = [

diff --git a/pkgs/applications/version-management/sourcehut/scm.nix b/pkgs/applications/version-management/sourcehut/scm.nix
@@ -4,12 +4,12 @@
 
 buildPythonPackage rec {
   pname = "scmsrht";
-  version = "0.15.3";
+  version = "0.16.0";
 
   src = fetchgit {
     url = "https://git.sr.ht/~sircmpwn/scm.sr.ht";
     rev = version;
-    sha256 = "1rzm3r280211w51sjngm5a3pdlzg07c64324k99bqs1fkc2yrfy6";
+    sha256 = "0jny8ihn49n7bpw5nhdrfha78yzpxp277l50y1lj142r59kwmh22";
   };
 
   nativeBuildInputs = srht.nativeBuildInputs;