Now Passing

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 { };
 
@@ -16,10 +15,11 @@ 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 { };
 
@@ -27,9 +27,9 @@ self: super: pkgs: with pkgs; {
 
   ovito = libsForQt5.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/ghmm/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchsvn, autoreconfHook, pkgconfig
+{ stdenv, 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

pkgs/lumpy.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, which, autoconf, automake
 , zlib, curl
-, python, hexdump, sambamba, samblaster, samtools }:
+, python2, hexdump, sambamba, samblaster, samtools }:
 
 stdenv.mkDerivation rec {
   version = "0.3.0";
@@ -39,7 +39,7 @@ stdenv.mkDerivation rec {
     automake
     zlib
     curl
-    (python.withPackages (packages: with packages; [ numpy pysam ]))
+    (python2.withPackages (packages: with packages; [ numpy pysam ]))
     hexdump
     sambamba
     samblaster

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
+, 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 = [

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; };
+      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, 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
   ];

pkgs/ovito.nix

@@ -1,5 +1,5 @@
 { mkDerivation, lib, fetchFromGitLab, cmake
-, boost, netcdf, hdf5, fftwSinglePrec, muparser, openssl, ffmpeg, python
+, boost, netcdf, hdf5, fftwSinglePrec, muparser, openssl, ffmpeg, python38
 , qtbase, qtsvg, qttools, qscintilla }:
 
 mkDerivation rec {
@@ -21,7 +21,7 @@ mkDerivation rec {
     muparser
     openssl
     ffmpeg
-    python
+    python38
     qtbase qtsvg qttools qscintilla
   ];
 

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 ];