flake.lock: Update

Flake lock file updates:

• Updated input 'flake-utils':
    'github:numtide/flake-utils/cfacdce06f30d2b68473a46042957675eebb3401' (2023-04-11)
  → 'github:numtide/flake-utils/1ef2e671c3b0c19053962c07dbda38332dcebf26' (2024-01-15)
• Updated input 'nixpkgs':
    'github:NixOS/nixpkgs/daa7efafc2cf6e5efa7ff1c1d24f91127a2d8da4' (2023-05-23)
  → 'github:NixOS/nixpkgs/9a333eaa80901efe01df07eade2c16d183761fa3' (2024-01-22)

README.md

@@ -6,6 +6,10 @@ additional packages to create a repository suitable for use on Compute
 Canada HPC clusters.  It is available to use by default on Compute
 Canada clusters.  It's layout is modelled after the upstream one.
 
+:note: This Edition uses flake overlays for integration into flake
+erivations readily, as well as hydraJobs specified for integration
+into caches
+
 
 # Using
 

default.nix

@@ -1,149 +1,2 @@
-with builtins;
-
-# This duplicates the overlay code in nixpkgs/pkgs/top-level/impure.nix (may require periodic resyncing).
-#
-# It has to be done this way because passing overlays to nixpkgs (required to insert our packages) disables all the
-# default overlay mechanisms (required to pickup any user or system overlays).
-
-let
-
-  # overlaysDefault - List of overlay functions nixpkgs would normally use if not provided.
-  #
-  # This is the order overlays are searched for in accordance to what is done in nixpkgs.  If an overlay is found
-  # at a given level (the leading number) the search is stopped and they are used.  If multiple overlays are found
-  # at a given level then an error is generated.
-  #
-  # 1. <nixpkgs-overlays> (i.e., nixpkgs-overlays.nix or nixpkgs-overlays/default.nix in NIX_PATH)
-  # 2. ~/.config/nixpkgs/overlays.nix
-  # 2. ~/.config/nixpkgs/overlays
-  #
-  # This code is lifted directly from nixpkgs/pkgs/top-level/impure.nix to ensure consistency.
-  #
-  overlaysDefault =
-    let
-
-      # try expression default - Replace expression with default on exception.
-      try = x: def: let res = tryEval x; in if res.success then res.value else def;
-
-      # isDir path - Is path a directory (requires access).
-      isDir = path: pathExists (path + "/.");
-
-      # overlaysRetrieve path - Retrieve a list of the overlay functions from path.
-      #   path is file - import the file itself (should give a list of overlay functions)
-      #   path is directory - list of imports of all the *.nix files in the directory (each should give an overlay function)
-      #
-      overlaysRetrieve = path:
-        if isDir path then 
-          let content = readDir path; in
-            map (n: import (path + ("/" + n)))
-              (builtins.filter (n: builtins.match ".*\\.nix" n != null || pathExists (path + ("/" + n + "/default.nix")))
-                (attrNames content))
-        else 
-          import path;
-
-      # pathOverlays - NIX_PATH nixpkgs-overlays file or "" if not found
-      pathOverlays = try <nixpkgs-overlays> "";
-
-      # homeDir          - ~/
-      # homeOverlaysFile - ~/.config/nixpkgs/overlays.nix
-      # homeOverlaysDir  - ~/.config/nixpkgs/overlays
-      #
-      homeDir = builtins.getEnv "HOME";
-      homeOverlaysFile = homeDir + "/.config/nixpkgs/overlays.nix";
-      homeOverlaysDir = homeDir + "/.config/nixpkgs/overlays";
-
-    in 
-
-      if pathOverlays != "" && pathExists pathOverlays then overlaysRetrieve pathOverlays
-      else if pathExists homeOverlaysFile && pathExists homeOverlaysDir then 
-        throw ''
-          Nixpkgs overlays can be specified with ${homeOverlaysFile} or ${homeOverlaysDir}, but not both.
-          Please remove one of them and try again.
-        ''
-      else if pathExists homeOverlaysFile then 
-        if isDir homeOverlaysFile then 
-          throw (homeOverlaysFile + " should be a file")
-        else overlaysRetrieve homeOverlaysFile
-      else if pathExists homeOverlaysDir then
-        if !(isDir homeOverlaysDir) then 
-          throw (homeOverlaysDir + " should be a directory")
-        else overlaysRetrieve homeOverlaysDir
-      else [];
-
-
-  # overlaysAlways - List of overlay functions provide by this package.
-  #
-  # The naming in this function is misleading but consistent with nixpkgs.
-  #
-  # self - final package set (stack fully closed) (-> pkgs in all-packages.nix)
-  # super - prior package set (stack closed up to us)
-  # res - next package set (stack closed up to and over us) (-> self in all-packages.nix)
-  #
-  overlaysAlways =
-    let
-      # knot - Feed final and up to and over us overlay results into overlay
-      #
-      # This matches what is done in nixpkgs (see pkgs/top-level/stage.nix).
-      #
-      knot = path: self: super:
-        let res = import path res super self; in res;
-    in
-      map knot [
-        ./temporary/all-packages.nix
-        ./pkgs/all-packages.nix
-      ];
-
-  # nixpkgs - The underlying nixpkg to use.
-  #
-  # Get a usable nixpkgs, that is, one with a version that matches ours, or die.
-  # 
-  nixpkgs =
-    let
-
-      # first check list - Return first element of list that passes check list otherwise aborts.
-      #
-      first = check: list:
-        if   list == []
-        then builtins.throw ''
-               Unable to locate a suitable nixpkgs directory.
-               Most likely you want to git clone one into the top of the repo as 'upstream'.
-             ''
-        else if   check ( builtins.head list )
-             then builtins.head list
-             else first check ( builtins.tail list );
-
-      # okay path - Check if path exist and match our version number and otherwise print a warning.
-      #
-      # Version numbers are taken from ./version files.
-      #
-      okay =
-        let
-          version = builtins.readFile ./.version;
-        in
-          path:
-            (    builtins.pathExists (path + /.version)
-              && (    builtins.readFile (path + /.version) == version
-                   || builtins.trace ''
-                        Skipping ${toString path} as not version ${version}.
-                      '' false ) );
-
-      # paths - Paths to search for nixpkgs.
-      #
-      paths = [
-        ./upstream          # 1. build channel or git cloned one directly associated with us takes priority
-        <nixpkgs/upstream>  # 2. if the channel is a version of ourselves the real one will be in a subdirectory
-        <nixpkgs>           # 3. otherwise maybe the channel is a nixpkgs proper
-      ];
-
-    in
-
-      first okay paths;
-
-in
-
-  { overlays ? overlaysDefault
-  , upstream ? nixpkgs
-  , ... } @ args: 
-
-    import upstream (    builtins.removeAttrs args [ "upstream" ]
-                      // { overlays = overlaysAlways ++ overlays; } )
+self: super:
+import ./pkgs/all-packages.nix self super

flake.lock

@@ -0,0 +1,61 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1705309234,
+        "narHash": "sha256-uNRRNRKmJyCRC/8y1RqBkqWBLM034y4qN7EprSdmgyA=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "1ef2e671c3b0c19053962c07dbda38332dcebf26",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1705957679,
+        "narHash": "sha256-Q8LJaVZGJ9wo33wBafvZSzapYsjOaNjP/pOnSiKVGHY=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "9a333eaa80901efe01df07eade2c16d183761fa3",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "release-23.05",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

flake.nix

@@ -0,0 +1,39 @@
+{
+  description = "Compute Canada Flake Packages (Overlay)";
+
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs/release-23.05";
+  inputs.flake-utils.url = "github:numtide/flake-utils";
+
+  outputs = { self, nixpkgs, flake-utils }: {
+    overlays = {
+      default = final: prev: import ./pkgs/all-packages.nix final prev;
+    };
+  } // (flake-utils.lib.eachDefaultSystem (system:
+    let
+      pkgs = import nixpkgs {
+        inherit system;
+        config.allowAliases = false;
+        config.permittedInsecurePackages = [
+          "python-2.7.18.6"
+          "python-2.7.18.6-env"
+        ];
+        overlays = [ self.overlays.default ];
+      };
+      inherit (pkgs) lib;
+      overlayAttributes = lib.pipe (import ./. pkgs pkgs) [
+        builtins.attrNames
+        (lib.partition (n: lib.isDerivation pkgs.${n}))
+      ];
+      attributesToAttrset = attributes: lib.pipe attributes [
+        (map (n: lib.nameValuePair n pkgs.${n}))
+        lib.listToAttrs
+      ];
+    in {
+      lib = attributesToAttrset overlayAttributes.wrong;
+      packages = pkgs.lib.optionalAttrs
+        (system == "x86_64-linux" ) (attributesToAttrset overlayAttributes.right);
+      hydraJobs = pkgs.lib.optionalAttrs
+        (system == "x86_64-linux" ) self.packages;
+    }
+  ));
+}

pkgs/all-packages.nix

@@ -1,8 +1,7 @@
-# self  - next package set (after our additions)
-# super - prior package set (before our additions)
-# pkgs  - final package set (after everyone's additions)
+# final  - next package set (after our additions)
+# prev - prior package set (before our additions)
 #
-self: super: pkgs: with pkgs; {
+final: prev: with prev; {
 
   fastqc = callPackage ./fastqc.nix { };
 
@@ -16,20 +15,21 @@ self: super: pkgs: with pkgs; {
 
   #meraculous = callPackage ./meraculous.nix { let stdenv49 = overrideCC stdenv gcc49; in stdenv = stdenv49; boost = boost159.override { stdenv = stdenv49 }; };
 
-  mfixgui = python36Packages.callPackage ./mfix/mfixgui.nix { };
+  mfixgui = python38Packages.callPackage ./mfix/mfixgui.nix { };
+  
   mfixsolver = callPackage ./mfix/mfixsolver.nix { };
 
-  inherit (callPackage ./opengl/default.nix { inherit super; }) libGL mesa_glxgallium;
+  # inherit (callPackage ./opengl/default.nix { inherit prev; }) libGL mesa_glxgallium;
 
   openfoam = callPackage ./openfoam.nix { };
 
   openslide = callPackage ./openslide { };
 
-  ovito = libsForQt5.callPackage ./ovito.nix { };
+  ovito = qt6Packages.callPackage ./ovito.nix { };
 
-  pythonOverrides = lib.composeExtensions super.pythonOverrides (import ./python-packages.nix pkgs);
+  pythonOverrides = lib.composeExtensions prev.pythonOverrides (import ./python-packages.nix pkgs);
 
-  rOverrides = lib.composeExtensions super.rOverrides (import ./r-modules.nix pkgs);
+  rOverrides = lib.composeExtensions prev.rOverrides (import ./r-modules.nix pkgs);
 
   smoove = callPackage ./smoove { };
 
@@ -41,12 +41,12 @@ self: super: pkgs: with pkgs; {
 
   samblaster = callPackage ./samblaster.nix { };
 
-  svtyper = pythonPackages.callPackage ./svtyper.nix { };
+  svtyper = python38Packages.callPackage ./svtyper.nix { };
 
   idba = callPackage ./idba.nix { };
 
-  nixStable = ( super.nixStable.override { confDir= "/nix/etc"; } ).overrideAttrs
-    ( attrs: { patches = attrs.patches or [] ++ [ ./nix/remote.patch ./nix/cvmfs.patch ]; } );
-  nix = ( super.nix.override { confDir = "/nix/etc"; } ).overrideAttrs
+  # nixStable = ( prev.nixStable.override { confDir= "/nix/etc"; } ).overrideAttrs
+    # ( attrs: { patches = attrs.patches or [] ++ [ ./nix/remote.patch ./nix/cvmfs.patch ]; } );
+  nix = ( prev.nix.override { confDir = "/nix/etc"; } ).overrideAttrs
     ( attrs: { patches = attrs.patches or [] ++ [ ./nix/remote.patch ./nix/cvmfs.patch ]; } );
 }

pkgs/fastqc.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub
+{ stdenv, lib, fetchFromGitHub
 , jdk, ant, makeWrapper
 , jre, perl }:
 
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
     makeWrapper $out/share/FastQC/fastqc $out/bin/fastqc --add-flags --java=${jre}/bin/java
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://www.bioinformatics.babraham.ac.uk/projects/fastqc/;
     description = "A quality control tool for high throughput sequence data";
     longDescription = ''

pkgs/firedrake/exodus.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, cmake, gfortran
+{ stdenv, lib, fetchurl, cmake, gfortran
 , netcdf, hdf5 }:
 
 stdenv.mkDerivation rec {
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
   patches = ./exodus-include.patch;
   sourceRoot = "${name}/exodus";
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "http://gsjaardema.github.io/seacas";
     description = "A model developed to store and retrieve data for finite element analyses.";
     license = licenses.bsd3;

pkgs/firedrake/hypre.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake
+{ stdenv, lib, fetchFromGitHub, cmake
 , openmpi }:
 
 stdenv.mkDerivation rec {
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
 
   makeFlags = [ "VERBOSE=1" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "http://www.llnl.gov/casc/hypre";
     description = "Parallel solvers for sparse linear systems featuring multigrid methods.";
     license = licenses.gpl2;

pkgs/firedrake/metis.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromBitbucket, cmake }:
+{ stdenv, lib, fetchFromBitbucket, cmake }:
 
 stdenv.mkDerivation rec {
   version = "5.1.0-p4";
@@ -17,7 +17,7 @@ stdenv.mkDerivation rec {
 
   makeFlags = [ "VERBOSE=1" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://bitbucket.org/petsc/metis";
     description = "A set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.";
   };

pkgs/firedrake/parmetis.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromBitbucket, cmake
+{ stdenv, lib, fetchFromBitbucket, cmake
 , openmpi
 , metis }:
 
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
   cmakeFlags = [ "-DGKLIB_PATH=../headers" ];
   makeFlags = [ "VERBOSE=1" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "http://glaros.dtc.umn.edu/gkhome/metis/parmetis";
     description = "An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.";
   };

pkgs/firedrake/petsc.nix

@@ -1,4 +1,4 @@
-{ stdenv, callPackage, writeText, fetchFromGitHub, python, gfortran
+{ stdenv, lib, callPackage, writeText, fetchFromGitHub, python, gfortran
 , openmpi, blas, liblapack, hdf5, netcdf, eigen
 , sowing, metis, hypre, parmetis, exodus }:
 
@@ -45,7 +45,7 @@ stdenv.mkDerivation rec {
 
   setupHook = writeText "setupHook.sh" "export PETSC_DIR=@out@";
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/firedrakeproject/petsc";
     description = "A suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.";
     license = licenses.bsd2;

pkgs/firedrake/sowing.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromBitbucket, ghostscript }:
+{ stdenv, lib, fetchFromBitbucket, ghostscript }:
 
 stdenv.mkDerivation rec {
   version = "1.1.25-p1";
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
     ghostscript
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://bitbucket.org/petsc/pkg-sowing";
     description = "Tools that are part of the petsc program development and maintenance environment.";
   };

pkgs/ghmm/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchsvn, autoreconfHook, pkgconfig
+{ stdenv, lib, fetchsvn, autoreconfHook, pkg-config
 , libxml2, python2Packages, swig }:
 
 stdenv.mkDerivation rec {
@@ -37,7 +37,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     autoreconfHook
-    pkgconfig
+    pkg-config
     libxml2
     python2Packages.python
     swig
@@ -45,7 +45,7 @@ stdenv.mkDerivation rec {
 
   hardeningDisable = [ "format" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "The General Hidden Markov Model library (GHMM) is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions.";
     homepage = http://ghmm.sourceforge.net;
     platforms = platforms.all;

pkgs/gsort/default.nix

@@ -1,5 +1,5 @@
 # This file was generated by https://github.com/kamilchm/go2nix v1.3.0
-{ stdenv, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn }:
+{ stdenv, lib, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn }:
 
 buildGoPackage rec {
   name = "gsort-${version}";
@@ -15,7 +15,7 @@ buildGoPackage rec {
 
   goDeps = ./deps.nix;
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://github.com/brentp/gsort;
     description = "A tool to sort genomic files according to a genomefile.";
     platforms = platforms.all;

pkgs/idba.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl
+{ stdenv, lib, fetchurl
 , bash }:
 
 stdenv.mkDerivation rec {
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
   #   stdenv
   # ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://github.com/loneknightpy/idba/;
     description = "Basic iterative de Bruijn graph assembler for second-generation sequencing reads";
     longDescription = "IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data.";

pkgs/lumpy.nix

@@ -1,8 +1,27 @@
-{ stdenv, fetchFromGitHub, which, autoconf, automake
+{ stdenv, lib, fetchFromGitHub, which, autoconf, automake
 , zlib, curl
-, python, hexdump, sambamba, samblaster, samtools }:
-
-stdenv.mkDerivation rec {
+, python2, fetchPypi, hexdump, sambamba, samblaster, samtools }: let
+  python = python2.override {
+    packageOverrides = final: prev: {
+      numpy = prev.numpy.overridePythonAttrs(old: rec {
+        version = "1.16.6";
+        disabled = false;
+        src = fetchPypi {
+          inherit version;
+          pname = "numpy";
+          extension = "zip";
+          sha256 = "e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff";
+        };
+        nativeCheckInputs = [
+          prev.pytest
+          # "hypothesis" indirectly depends on numpy to build its documentation.
+          prev.hypothesis
+          prev.typing-extensions
+        ];
+      });
+    };
+  };
+in stdenv.mkDerivation rec {
   version = "0.3.0";
   name = "lumpy-${version}";
 
@@ -39,14 +58,19 @@ stdenv.mkDerivation rec {
     automake
     zlib
     curl
-    (python.withPackages (packages: with packages; [ numpy pysam ]))
+    (python.withPackages (packages: with packages;
+      [
+        numpy
+        pysam
+      ]
+    ))
     hexdump
     sambamba
     samblaster
     samtools
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A probabilistic framework for structural variant discovery.";
     homepage = https://github.com/arq5x/lumpy-sv;
     platforms = platforms.all;

pkgs/meraculous.nix

@@ -1,4 +1,4 @@
-{ stdenv, overrideCC, gcc49, fetchurl, makeWrapper, gzip, cmake
+{ stdenv, lib, overrideCC, gcc49, fetchurl, makeWrapper, gzip, cmake
 , boost, perl, perlPackages, gnuplot }:
 
 # gcc 5.x c++11 requires istream to be explicitly cast to bool
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
     gnuplot
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = http://jgi.doe.gov/data-and-tools/meraculous;
     description = "Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes.";
     platforms = platforms.all;

pkgs/mfix/mfixgui.nix

@@ -1,4 +1,4 @@
-{ lib, fetchurl, fetchFromGitHub, buildPythonApplication, sphinx, sphinx_rtd_theme
+{ lib, fetchurl, fetchFromGitHub, buildPythonApplication, sphinx, sphinx-rtd-theme
 , mfixsolver
 , numpy, psutil, pyqtgraph, qtpy, pyqt5, vtk, requests, simpleeval, simplejson }:
 
@@ -65,7 +65,7 @@ buildPythonApplication rec {
   '';
 
   nativeBuildInputs = [
-    sphinx sphinx_rtd_theme
+    sphinx sphinx-rtd-theme
   ];
 
   buildInputs = [

pkgs/mfix/mfixsolver.nix

@@ -1,5 +1,5 @@
-{ stdenv, fetchurl, fetchFromGitHub
-, cmake, gfortran, python, pkgconfig
+{ stdenv, lib, fetchurl, fetchFromGitHub
+, cmake, gfortran, python38, pkg-config
 , openmpi, netcdf, boost }:
 
 stdenv.mkDerivation rec {
@@ -55,8 +55,8 @@ stdenv.mkDerivation rec {
   ];
 
   nativeBuildInputs = [
-    python
-    pkgconfig
+    python38
+    pkg-config
   ];
 
   buildInputs = [
@@ -67,7 +67,7 @@ stdenv.mkDerivation rec {
     # netcdf
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://mfix.netl.doe.gov;
     description = "An open-source multiphase flow solver";
     platforms = platforms.all;

pkgs/openfoam.nix

@@ -1,4 +1,4 @@
-{ stdenv, bashInteractive, fetchFromGitHub, makeWrapper, flex, bison
+{ stdenv, lib, bashInteractive, fetchFromGitHub, makeWrapper, flex, bison
 , zlib, boost, openmpi, readline, gperftools, cgal, metis, scotch, mpfr }:
 
 
@@ -84,7 +84,7 @@ stdenv.mkDerivation rec {
     mpfr
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = http://www.openfoam.com;
     description = "Free open-source CFD software";
     platforms = platforms.linux;

pkgs/opengl/default.nix

@@ -3,8 +3,8 @@
 # Add a setup hook to the mesa package that automatically adds a
 # libvglfaker.so dependency to executables that depend on libGL.so.
 
-{ super, stdenv, buildEnv, substituteAll, bash
-, autoreconfHook, pkgconfig, python2
+{ prev, stdenv, buildEnv, substituteAll, bash
+, autoreconfHook, pkg-config, python2
 , xorg, llvmPackages, expat, mesa_glxgallium, mesa, libglvnd }:
 
 let
@@ -13,23 +13,23 @@ let
       # Ugliness required to break the loop created by the fact that
       # the libGL hook requires VirtualGL which requires libGL.
       #
-      # This would be clean if super was closed on itself (nixpkgs #15280)
+      # This would be clean if prev was closed on itself (nixpkgs #15280)
 
-      libGL = super.libGL;
-      libGLU = super.libGLU.override { inherit libGL; };
+      libGL = prev.libGL;
+      libGLU = prev.libGLU.override { inherit libGL; };
       libGLU_combined = buildEnv {
         name = "libGLU-combined";
         paths = [ libGL libGLU ];
         extraOutputsToInstall = [ "dev" ];
       };
 
-      virtualglLib = (super.virtualglLib.override { inherit libGL libGLU fltk; }).overrideAttrs (attrs: {
+      virtualglLib = (prev.virtualglLib.override { inherit libGL libGLU fltk; }).overrideAttrs (attrs: {
         postFixup = attrs.postFixup or "" + ''
           patchelf --set-rpath /usr/lib${stdenv.lib.optionalString stdenv.is64bit "64"}/nvidia:"$(patchelf --print-rpath $out/lib/libvglfaker.so)" $out/lib/libvglfaker.so
         '';
       } );
-      fltk = super.fltk.override { inherit libGL libGLU freeglut; };
-      freeglut = super.freeglut.override { inherit libGL libGLU; };
+      fltk = prev.fltk.override { inherit libGL libGLU; };
+      freeglut = prev.freeglut.override { inherit libGL libGLU; };
     in
       substituteAll {
         src = ./insert-virtualgl.sh;

pkgs/openslide/default.nix

@@ -1,5 +1,5 @@
-{ stdenv, autoreconfHook, pkgconfig, fetchFromGitHub
-, zlib, openjpeg, libtiff, cairo, libpng, gdk_pixbuf, libxml2, sqlite }:
+{ stdenv, lib, autoreconfHook, pkg-config, fetchFromGitHub
+, zlib, openjpeg, libtiff, cairo, libpng, gdk-pixbuf, libxml2, sqlite }:
 
 stdenv.mkDerivation rec {
   version = "3.4.1";
@@ -14,13 +14,13 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     autoreconfHook
-    pkgconfig
+    pkg-config
     zlib
     openjpeg
     libtiff
     cairo
     libpng
-    gdk_pixbuf
+    gdk-pixbuf
     libxml2
     sqlite
   ];
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
     sed -i -e 's|AM_CONDITIONAL(\[WINDOWS_RESOURCES\], \[test x$RC != x\])|AM_CONDITIONAL([WINDOWS_RESOURCES], [false])|' configure.ac
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = http://openslide.org;
     description = "A C library that provides a simple interface to read whole-slide images.";
     platforms = platforms.all;

pkgs/ovito.nix

@@ -1,30 +1,55 @@
-{ mkDerivation, lib, fetchFromGitLab, cmake
-, boost, netcdf, hdf5, fftwSinglePrec, muparser, openssl, ffmpeg, python
-, qtbase, qtsvg, qttools, qscintilla }:
+{ stdenv
+, lib
+, fetchFromGitLab
+, cmake
+, ninja
+, wrapQtAppsHook
+, qtbase
+, qtnetworkauth
+, qtscxml
+, qtsvg
+, ffmpeg
+, netcdf
+, libssh
+, boost
+, hdf5
+, python3 ? python3
+}:
 
-mkDerivation rec {
+stdenv.mkDerivation rec {
   pname = "ovito";
-  version = "3.4.0";
+  version = "3.8.4";
 
   src = fetchFromGitLab {
     owner = "stuko";
     repo = "ovito";
     rev = "v${version}";
-    sha256 = "1y3wr6yzpsl0qm7cicp2mppfszxd0fgx8hm99in9wff9qd0r16b5";
+    sha256 = "Vw9mB+huQHLg8OqyGo9KEg55ag3NQG+nTJj3tB++eQk=";
   };
 
-  buildInputs = [
+  nativeBuildInputs = [
     cmake
-    boost
-    netcdf hdf5
-    fftwSinglePrec
-    muparser
-    openssl
-    ffmpeg
-    python
-    qtbase qtsvg qttools qscintilla
+    ninja
+    wrapQtAppsHook
   ];
 
+  buildInputs = [
+    qtbase
+    qtnetworkauth
+    qtscxml
+    qtsvg
+    ffmpeg
+    netcdf
+    libssh
+    boost
+    hdf5
+    python3
+  ];
+
+  cmakeFlags = [
+    "-DOVITO_BUILD_PYPI=${if python3 != null then "ON" else "OFF"}"
+  ];
+  
   meta = with lib; {
     description = "Scientific visualization and analysis software for atomistic and particle simulation data";
     homepage = https://ovito.org;

pkgs/sambamba.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, ldc
+{ stdenv, lib, fetchFromGitHub, ldc
 , python3, glibc, which, zlib }:
 
 stdenv.mkDerivation rec {
@@ -27,7 +27,7 @@ stdenv.mkDerivation rec {
     zlib
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://github.com/lomereiter/sambamba/wiki;
     description = "Sambamba is a set of command-line tools for working with SAM/BAM file formats which are used for storing next generation sequencing (NGS) datasets.";
     platforms = platforms.all;

pkgs/samblaster.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub }:
+{ stdenv, lib, fetchFromGitHub }:
 
 stdenv.mkDerivation rec {
   version = "0.1.24";
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.";
     homepage = https://github.com/GregoryFaust/samblaster;
     platforms = platforms.all;

pkgs/smoove/default.nix

@@ -1,5 +1,5 @@
 # This file was generated by https://github.com/kamilchm/go2nix v1.3.0
-{ stdenv, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn, makeWrapper
+{ stdenv, lib, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn, makeWrapper
 , gzip, gsort, htslib, lumpy, samtools, svtyper, mosdepth }:
 
 buildGoPackage rec {
@@ -31,7 +31,7 @@ buildGoPackage rec {
     makeWrapper
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://github.com/brentp/smoove;
     description = "Wrap existing software and adds some internal read-filtering to simplify calling and genotyping structural variants.";
     platforms = platforms.all;

pkgs/sumo.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, unzip
+{ stdenv, lib, fetchurl, unzip
 , lzma, bzip2, zlib, libjpeg, libtiff, openssl
 , mesa, xorg
 , fox, xercesc, proj, gdal, hdf5, curl }:
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
     curl
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = http://software.dlr.de/p/sumo/home;
     description = "SUMO is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks";
     platforms = platforms.all;

pkgs/svtyper.nix

@@ -1,6 +1,6 @@
 { lib, fetchPypi, buildPythonApplication
 , scipy, cytoolz, pysam
-, pytest, pytestrunner }:
+, pytest, pytest-runner }:
 
 buildPythonApplication rec {
   version = "0.7.1";
@@ -16,7 +16,7 @@ buildPythonApplication rec {
       --replace o"pytest==4.6.4" "pytest"
   '';
 
-  nativeBuildInputs = [ pytestrunner ];
+  nativeBuildInputs = [ pytest-runner ];
   propagatedBuildInputs = [ scipy cytoolz pysam ];
   checkInputs = [ pytest ];
 

release.nix

@@ -1,167 +0,0 @@
-{ ccpkgs                       # Checked out ccpkgs git repo
-    ? { outPath = ./.;
-        revCount = 1234 + 149;
-        shortRev = "gabcdef";
-      }
-, nixpkgs                      # Checked out nixpkgs git repe
-    ? { outPath = ./upstream;
-        revCount = 5678 + 242760;
-        shortRev = "gfedcba";
-      }
-, nixpkgsArgs ? { config = { allowUnfree = true; inHydra = true; }; }
-, stableBranch ? false
-, supportedSystems ? [ "x86_64-linx" ] }:
-
-
-# Free up the nixpkgs and ccpkgs name for binding to final product.
-#
-let
-  # *Git - git checkout
-  #
-  nixpkgsGit = nixpkgs;
-  ccpkgsGit = ccpkgs;
-
-# Tarball hydra release product for the ccpkgs channel.
-#
-# 1. Generate an unpacked channel for the associated nixpkgs in the store.
-# 2. Symlink this into the top-level directory as upstream (nixpkgs is used).
-# 3. Stick in the standard version files.
-# 4. Let releaseTools.sourceTarball handle the details of exposing it as a hydra product.
-#
-in let
-
-  # pkgs - Packages sucked in from the given ccpkgs git version.
-  #
-  pkgs = import ccpkgsGit ( nixpkgsArgs // { upstream = nixpkgsGit; } );
-
-  # version        - Version number (e.g., "17.09")
-  # version*Suffix - Version suffix (e.g., "5678.gfedcba")
-  #
-  # Code lifted from nixos/release.nix.
-  #
-  version =
-    let
-      versionNixpkgs = pkgs.lib.fileContents (nixpkgsGit + /.version);
-      versionCcpkgs  = pkgs.lib.fileContents ./.version;
-    in
-      assert (versionNixpkgs == versionCcpkgs); versionCcpkgs;
-
-  versionSeparator = if stableBranch then "." else "pre";
-
-  mkVersion = base: git: rec {
-    count = toString (git.revCount - base);
-    commit = git.shortRev;
-    suffix = "${versionSeparator}${count}.${commit}";
-  };
-
-  nixpkgsVersion = mkVersion 242760 nixpkgsGit;
-  ccpkgsVersion  = mkVersion 149 ccpkgsGit;
-
-  versionSuffix = "${versionSeparator}${ccpkgsVersion.count}.${nixpkgsVersion.count}.${ccpkgsVersion.commit}.${nixpkgsVersion.commit}";
-
-  # nixpkgs - The store path containing the unpacked nixpkgs channel.
-  #
-  # 1. Generate a channel tarball from the git repo via the nixos/release.nix expression for hydra.
-  # 2. Unpack this into the store using the nix/unpack-channel.nix expression used by nix-channel.
-  #
-  nixpkgs =
-    let
-      # channel - Store path containing the channel release tarballs.
-      #
-      # The nixos.channel attribute from nixos/release.nix builds the nixpkgs channel tarballs.
-      #
-      channel =
-        ( import (nixpkgsGit + /nixos/release.nix) {
-            inherit stableBranch supportedSystems;
-            nixpkgs = nixpkgsGit;
-          } ).channel;
-
-      # nixpkgs - The store path containing the unpacked nixpkgs channel.
-      #
-      # The nix provided nix/unpack-channel.nix function extracts the nixpkgs from the channel,
-      #
-      nixpkgs =
-        ( pkgs.callPackage ./unpack-channel.nix { } rec {
-           name = "nixos";
-           channelName = "${name}-${version}";
-           src = channel + /tarballs + "/${name}-${version}${nixpkgsVersion.suffix}.tar.xz";
-          } );
-    in
-      nixpkgs;
-
-  # jobs - The jobs hydra is to run.
-  #
-  jobs =
-    let
-      # Extract the valid derivations from an overlay
-      #
-      # nameSet  - the attribute set the uncomposed overlay (just the names are required)
-      # valueSet - the final attribute from the composed overlay (the values are required)
-      #
-      extractDerivations = valueSet: nameSet:
-        builtins.listToAttrs
-          ( builtins.map
-              ( name: { inherit name; value = valueSet.${name}; } )
-              ( pkgs.lib.filter
-                  ( name: ( builtins.tryEval (pkgs.lib.isDerivation valueSet.${name}) ).value )
-                  ( pkgs.lib.attrNames nameSet ) ) );
-
-      # Provided overlays
-      pkgsNamesTopLevel = let self = import ./pkgs/all-packages.nix    self { } self; in self;
-      pkgsNamesPython   = let self = import ./pkgs/python-packages.nix { } self { } ; in self;
-      pkgsNamesR        = let self = import ./pkgs/r-modules.nix       { } self { } ; in self;
-
-      temporaryNamesTopLevel = let self = import ./temporary/all-packages.nix    self { } self; in self;
-      temporaryNamesPython   = let self = import ./temporary/python-packages.nix { } self { } ; in self;
-      temporaryNamesR        = let self = import ./temporary/r-modules.nix       { } self { } ; in self;
-
-    in {
-      # Tweak the nixos make-channel code to include the upstream channel.
-      #
-      # 1. Replace the git repo nixpkgs with a copy of the unpacked nixpkgs channel.
-      #
-      channel =
-        ( import (nixpkgsGit + /nixos/lib/make-channel.nix) {
-            inherit pkgs version versionSuffix;
-            nixpkgs = ccpkgsGit;
-        } ).overrideAttrs ( original: {
-            name = "ccpkgs-channel";
-            distPhase =
-              ''
-                rm -fr upstream
-                cp -rd ${nixpkgs}/nixos-${version} upstream
-              '' + original.distPhase;
-        } );
-
-      # tested - Aggregate package set required to built for automatic channel release
-      #
-      tested = pkgs.lib.hydraJob (pkgs.releaseTools.aggregate {
-        name = "ccpkgs-${version}";
-
-        constituents = builtins.map ( pkgs.lib.collect pkgs.lib.isDerivation ) [ jobs.pkgs jobs.temporary ];
-
-        meta = {
-          description = "Release-critical builds for the ccpkgs channel";
-          maintainers = with pkgs.lib.maintainers; [ ];
-        };
-      });
-
-      # pkgs - Attribute set of overlayed pkgs.
-      #
-      pkgs = extractDerivations pkgs pkgsNamesTopLevel // {
-        python2Packages = extractDerivations pkgs.python2Packages pkgsNamesPython;
-        python3Packages = extractDerivations pkgs.python3Packages pkgsNamesPython;
-        rPackages       = extractDerivations pkgs.rPackages       pkgsNamesR;
-      };
-
-
-      # temporary - Attribute set of overlayed pkgs.
-      #
-      temporary = extractDerivations pkgs temporaryNamesTopLevel // {
-        python2Packages = extractDerivations pkgs.python2Packages temporaryNamesPython;
-        python3Packages = extractDerivations pkgs.python3Packages temporaryNamesPython;
-        rPackages       = extractDerivations pkgs.rPackages       temporaryNamesR;
-      };
-    };
-
-in jobs

unpack-channel.nix

@@ -1,45 +0,0 @@
-# Hydra runs the newer nix which doesn't have corepkgs/unpack-channel.nix. The nix-daemon runs the older nix which
-# doesn't have builtins:unpack-channel. This means
-#
-#  - for now we need to provide the older corepkgs/unpack-channel.nix
-#  - in the future we should switch to src/nix-channel/unpack-channel.nix
-
-{ bash, coreutils, gnutar, xz, gzip, bzip2 }:
-
-let
-
-  tarFlags = "--warning=no-timestamp";
-
-  builder = builtins.toFile "unpack-channel.sh"
-    ''
-      mkdir $out
-      cd $out
-      xzpat="\.xz\$"
-      gzpat="\.gz\$"
-      if [[ "$src" =~ $xzpat ]]; then
-        xz -d < $src | tar xf - ${tarFlags}
-      elif [[ "$src" =~ $gzpat ]]; then
-        gzip -d < $src | tar xf - ${tarFlags}
-      else
-        bzip2 -d < $src | tar xf - ${tarFlags}
-      fi
-      if [ * != $channelName ]; then
-        mv * $out/$channelName
-      fi
-    '';
-
-in
-
-{ name, channelName, src }:
-
-derivation {
-  system = builtins.currentSystem;
-  builder = "${bash}/bin/sh";
-  args = [ "-e" builder ];
-  inherit name channelName src;
-
-  PATH = "${coreutils}/bin:${gnutar}/bin:${xz}/bin:${gzip}/bin:${bzip2}/bin";
-
-  # No point in doing this remotely.
-  preferLocalBuild = true;
-}