Merge pull request #154697 from mweinelt/python2-byebye

nixos/doc/manual/from_md/release-notes/rl-2205.section.xml

···
       </listitem>
       <listitem>
         <para>
+          The <literal>mailpile</literal> email webclient
+          (<literal>services.mailpile</literal>) has been removed due to
+          its reliance on python2.
+        </para>
+      </listitem>
+      <listitem>
+        <para>
           The MoinMoin wiki engine
           (<literal>services.moinmoin</literal>) has been removed,
           because Python 2 is being retired from nixpkgs.

nixos/doc/manual/release-notes/rl-2205.section.md

···
 
 - `services.kubernetes.addons.dashboard` was removed due to it being an outdated version.
 
+- The `mailpile` email webclient (`services.mailpile`) has been removed due to its reliance on python2.
+
 - The MoinMoin wiki engine (`services.moinmoin`) has been removed, because Python 2 is being retired from nixpkgs.
 
 - The `wafHook` hook now honors `NIX_BUILD_CORES` when `enableParallelBuilding` is not set explicitly. Packages can restore the old behaviour by setting `enableParallelBuilding=false`.

nixos/modules/misc/ids.nix

···
       yandexdisk = 143;
       mxisd = 144; # was once collectd
       #consul = 145;# dynamically allocated as of 2021-09-03
-      mailpile = 146;
+      #mailpile = 146; # removed 2022-01-12
       redmine = 147;
       #seeks = 148; # removed 2020-06-21
       prosody = 149;
···
       #yandexdisk = 143; # unused
       mxisd = 144; # was once collectd
       #consul = 145; # unused
-      mailpile = 146;
+      #mailpile = 146; # removed 2022-01-12
       redmine = 147;
       #seeks = 148; # removed 2020-06-21
       prosody = 149;

nixos/modules/module-list.nix

···
   ./services/networking/lldpd.nix
   ./services/networking/logmein-hamachi.nix
   ./services/networking/lxd-image-server.nix
-  ./services/networking/mailpile.nix
   ./services/networking/magic-wormhole-mailbox-server.nix
   ./services/networking/matterbridge.nix
   ./services/networking/mjpg-streamer.nix

nixos/modules/rename.nix

···
     (mkRemovedOptionModule [ "services" "fourStoreEndpoint" ] "The fourStoreEndpoint module has been removed")
     (mkRemovedOptionModule [ "services" "frab" ] "The frab module has been removed")
     (mkRemovedOptionModule [ "services" "kippo" ] "The corresponding package was removed from nixpkgs.")
+    (mkRemovedOptionModule [ "services" "mailpile" ] "The corresponding package was removed from nixpkgs.")
     (mkRemovedOptionModule [ "services" "marathon" ] "The corresponding package was removed from nixpkgs.")
     (mkRemovedOptionModule [ "services" "mathics" ] "The Mathics module has been removed")
     (mkRemovedOptionModule [ "services" "meguca" ] "Use meguca has been removed from nixpkgs")

nixos/modules/services/networking/mailpile.nix

···
-{ config, lib, pkgs, ... }:
-
-with lib;
-
-let
-
-  cfg = config.services.mailpile;
-
-  hostname = cfg.hostname;
-  port = cfg.port;
-
-in
-
-{
-
-  ###### interface
-
-  options = {
-
-    services.mailpile = {
-      enable = mkEnableOption "Mailpile the mail client";
-
-      hostname = mkOption {
-        type = types.str;
-        default = "localhost";
-        description = "Listen to this hostname or ip.";
-      };
-      port = mkOption {
-        type = types.port;
-        default = 33411;
-        description = "Listen on this port.";
-      };
-    };
-
-  };
-
-
-  ###### implementation
-
-  config = mkIf config.services.mailpile.enable {
-
-    users.users.mailpile =
-      { uid = config.ids.uids.mailpile;
-        description = "Mailpile user";
-        createHome = true;
-        home = "/var/lib/mailpile";
-      };
-
-    users.groups.mailpile =
-      { gid = config.ids.gids.mailpile;
-      };
-
-    systemd.services.mailpile =
-      {
-        description = "Mailpile server.";
-        after = [ "network.target" ];
-        wantedBy = [ "multi-user.target" ];
-        serviceConfig = {
-          User = "mailpile";
-          ExecStart = "${pkgs.mailpile}/bin/mailpile --www ${hostname}:${port} --wait";
-          # mixed - first send SIGINT to main process,
-          # then after 2min send SIGKILL to whole group if neccessary
-          KillMode = "mixed";
-          KillSignal = "SIGINT";  # like Ctrl+C - safe mailpile shutdown
-          TimeoutSec = 120;  # wait 2min untill SIGKILL
-        };
-        environment.MAILPILE_HOME = "/var/lib/mailpile/.local/share/Mailpile";
-      };
-
-    environment.systemPackages = [ pkgs.mailpile ];
-
-  };
-
-}

pkgs/applications/graphics/displaycal/default.nix

···
-{ python2
-, lib
-, fetchurl
-, pkg-config
-, libXext
-, libXxf86vm
-, libX11
-, libXrandr
-, libXinerama
-, libXScrnSaver
-, argyllcms
- }:
-
-let
-  inherit (python2.pkgs) buildPythonApplication wxPython numpy dbus-python;
-in buildPythonApplication rec {
-  pname = "displaycal";
-  version = "3.8.9.3";
-
-  enableParallelBuilding = true;
-
-  src = fetchurl {
-    url = "mirror://sourceforge/project/dispcalgui/release/${version}/DisplayCAL-${version}.tar.gz";
-    sha256 = "1sivi4q7sqsrc95qg5gh37bsm2761md4mpl89hflzwk6kyyxyd3w";
-  };
-
-  propagatedBuildInputs = [
-    libXext
-    libXxf86vm
-    libX11
-    libXrandr
-    libXinerama
-    libXScrnSaver
-    argyllcms
-    wxPython
-    numpy
-    dbus-python
-  ];
-
-  nativeBuildInputs = [
-    pkg-config
-  ];
-
-  preConfigure = ''
-    mkdir dist
-    cp {misc,dist}/net.displaycal.DisplayCAL.appdata.xml
-    touch dist/copyright
-    mkdir -p $out
-    ln -s $out/share/DisplayCAL $out/Resources
-  '';
-
-  # no idea why it looks there - symlink .json lang (everything)
-  postInstall = ''
-    for x in $out/share/DisplayCAL/*; do
-      ln -s $x $out/lib/python2.7/site-packages/DisplayCAL
-    done
-
-    for prog in "$out/bin/"*; do
-      wrapProgram "$prog" \
-        --prefix PYTHONPATH : "$PYTHONPATH" \
-        --prefix PATH : ${argyllcms}/bin
-    done
-  '';
-
-  meta = {
-    description = "Display Calibration and Characterization powered by Argyll CMS";
-    homepage = "https://displaycal.net/";
-    license = lib.licenses.gpl3;
-    maintainers = [lib.maintainers.marcweber];
-    platforms = lib.platforms.linux;
-  };
-}

pkgs/applications/misc/curabydagoma/default.nix

···
-{ stdenv, runtimeShell, lib, fetchurl, python2Packages, unzip }:
-
-# This package uses a precompiled "binary" distribution of CuraByDagoma,
-# distributed by the editor.
-#
-# To update the package, follow the links on https://dist.dagoma.fr/:
-# * Cura By Dagoma
-# * Linux
-# * 64 bits
-# * Genric archive
-#
-# I made the arbitrary choice to compile this package only for x86_64.
-# I guess people owning a 3D printer generally don't use i686.
-# If, however, someone needs it, we certainly can find a solution.
-
-let
-  pythonPackages = python2Packages;
-in stdenv.mkDerivation rec {
-  pname = "curabydagoma";
-  # Version is the date, UNIX format
-  version = "1520506579";
-  # Hash of the user's choice: os, arch, package type...
-  hash = "58228cce5bbdcf764b7116850956f1e5";
-
-  src = fetchurl {
-    url = "https://dist.dagoma.fr/get/zip/CuraByDagoma/${version}/${hash}";
-    sha256 = "16wfipdyjkf6dq8awjzs4zgkmqk6230277mf3iz8swday9hns8pq";
-  };
-  unpackCmd = "unzip $curSrc && tar zxf CuraByDagoma_amd64.tar.gz";
-  nativeBuildInputs = [ unzip ];
-  buildInputs = [ pythonPackages.python pythonPackages.pyopengl pythonPackages.wxPython pythonPackages.pyserial pythonPackages.numpy ];
-
-  # Compile all pyc files because the included pyc files may be older than the
-  # py files. However, Python doesn't realize that because the packages
-  # have all dates set to epoch.
-  buildPhase = ''
-    python -m compileall -f curabydago
-  '';
-
-  # * Simply copy the stuff there
-  # * Create an executable with the correct path etc
-  # * Create a .desktop file to have a launcher in the desktop environments
-  installPhase = ''
-    mkdir $out
-    cp -r * $out/
-
-    mkdir $out/bin
-    cat > $out/bin/curabydago <<EOF
-    #!${runtimeShell}
-    export PYTHONPATH=$PYTHONPATH
-    ${pythonPackages.python.interpreter} $out/curabydago/cura.py
-    EOF
-    chmod a+x $out/bin/curabydago
-
-    mkdir -p $out/share/applications
-    cat > $out/share/applications/curabydago.desktop <<EOF
-    [Desktop Entry]
-    Type=Application
-    Name=Cura-by-dagoma
-    Comment=CuraByDagoma is a fork of Legacy Cura made by Dagoma for its own printers.
-    Icon=$out/curabydago/resources/images/cura.ico
-    Exec=$out/bin/curabydago
-    Path=$out/
-    StartupNotify=true
-    Terminal=false
-    Categories=GNOME;GTK;Utility;
-    EOF
-
-  '';
-
-  meta = with lib; {
-    description = "Slicer for 3D printers built by Dagoma";
-    homepage = "https://dagoma.fr/cura-by-dagoma.html";
-    license = licenses.agpl3;
-    platforms = [ "x86_64-linux" ];
-    maintainers = with maintainers; [ tiramiseb ];
-  };
-}

pkgs/applications/misc/metamorphose2/default.nix

···
-{ lib, stdenv, fetchgit, makeWrapper, gettext
-, python27, python2Packages
-}:
-
-stdenv.mkDerivation {
-  pname = "metamorphose2";
-  version = "0.9.0beta";
-
-  # exif-py vendored via submodule
-  # mutagen vendored via copy
-  src = fetchgit {
-    url = "https://github.com/metamorphose/metamorphose2.git";
-    #rev = "refs/tags/v2.${version}"; #for when wxPython3 support is released
-    rev = "d2bdd6a86340b9668e93b35a6a568894c9909d68";
-    sha256 = "0ivcb3c8hidrff0ivl4dnwa2p3ihpqjdbvdig8dhg9mm5phdbabn";
-  };
-
-  postPatch = ''
-    substituteInPlace messages/Makefile \
-      --replace "\$(shell which msgfmt)" "${gettext}/bin/msgfmt"
-  '';
-
-  postInstall = ''
-    rm $out/bin/metamorphose2
-    makeWrapper ${python27}/bin/python $out/bin/metamorphose2 \
-      --prefix PYTHONPATH : $PYTHONPATH:$(toPythonPath "$out") \
-      --add-flags "-O $out/share/metamorphose2/metamorphose2.py -w=3"
-  '';
-
-  buildInput = [ gettext python27 ];
-  nativeBuildInputs = [ makeWrapper ];
-  propagatedBuildInputs = [ python2Packages.wxPython python2Packages.pillow ];
-
-  makeFlags = [ "PREFIX=$(out)" ];
-
-  meta = with lib; {
-    description = "a graphical mass renaming program for files and folders";
-    homepage    = "https://github.com/metamorphose/metamorphose2";
-    license     = with licenses; gpl3Plus;
-    maintainers = with maintainers; [ ramkromberg ];
-    platforms   = with platforms; linux;
-  };
-}

pkgs/applications/misc/neap/default.nix

···
-{ lib, stdenv, fetchFromGitHub, python2Packages }:
-
-stdenv.mkDerivation rec {
-  pname = "neap";
-  version = "0.7.2";
-
-  src = fetchFromGitHub {
-    owner = "vzxwco";
-    repo = "neap";
-    rev = "v${version}";
-    sha256 = "04da8rq23rl1qcvrdm5m3l90xbwyli7x601sckv7hmkip2q3g1kz";
-  };
-
-  nativeBuildInputs = [
-    python2Packages.wrapPython
-  ];
-
-  buildInputs = [
-    python2Packages.python
-  ];
-
-  pythonPath = [
-    python2Packages.xlib
-    python2Packages.pygtk
-  ];
-
-  installPhase = ''
-    install -D -t $out/bin neap
-    install -D -t $out/share/man/man1 neap.1
-    install -D -t $out/share/applications neap.desktop
-  '';
-
-  postFixup = ''
-    wrapPythonPrograms
-  '';
-
-  meta = with lib; {
-    description = "Systray workspace pager";
-    homepage = "https://github.com/vzxwco/neap";
-    license = licenses.bsd2;
-    platforms = platforms.unix;
-    maintainers = [ maintainers.romildo ];
-  };
-}

pkgs/applications/networking/instant-messengers/blink/default.nix

···
-{ lib, fetchdarcs, python2Packages, libvncserver, zlib
-, gnutls, libvpx, makeDesktopItem, mkDerivationWith }:
-
-mkDerivationWith python2Packages.buildPythonApplication rec {
-
-  pname = "blink";
-  version = "3.2.0";
-
-  src = fetchdarcs {
-    url = "http://devel.ag-projects.com/repositories/blink-qt";
-    rev = "release-${version}";
-    sha256 = "19rcwr5scw48qnj79q1pysw95fz9h98nyc3161qy2kph5g7dwkc3";
-  };
-
-  patches = [ ./pythonpath.patch ];
-  postPatch = ''
-    sed -i 's|@out@|'"''${out}"'|g' blink/resources.py
-  '';
-
-  propagatedBuildInputs = with python2Packages; [
-    pyqt5_with_qtwebkit
-    cjson
-    sipsimple
-    twisted
-    google-api-python-client
-  ];
-
-  buildInputs = [
-    python2Packages.cython
-    zlib
-    libvncserver
-    libvpx
-  ];
-
-  desktopItem = makeDesktopItem {
-    name = "Blink";
-    exec = "blink";
-    comment = meta.description;
-    desktopName = "Blink";
-    icon = "blink";
-    genericName = "Instant Messaging";
-    categories = "Internet;";
-  };
-
-  dontWrapQtApps = true;
-
-  postInstall = ''
-    mkdir -p "$out/share/applications"
-    mkdir -p "$out/share/pixmaps"
-    cp "$desktopItem"/share/applications/* "$out/share/applications"
-    cp "$out"/share/blink/icons/blink.* "$out/share/pixmaps"
-  '';
-
-  preFixup = ''
-    makeWrapperArgs+=(
-      --prefix "LD_LIBRARY_PATH" ":" "${gnutls.out}/lib"
-      "''${qtWrapperArgs[@]}"
-    )
-  '';
-
-  meta = with lib; {
-    homepage = "https://icanblink.com/";
-    description = "A state of the art, easy to use SIP client for Voice, Video and IM";
-    platforms = platforms.linux;
-    license = licenses.gpl3;
-    maintainers = with maintainers; [ pSub ];
-  };
-}

pkgs/applications/networking/instant-messengers/blink/pythonpath.patch

···
---- blink-2.0.0/blink/resources.py	2016-03-09 14:39:07.000000000 +0100
-+++ blink-2.0.0/blink/resources-patched.py	2016-03-12 21:34:14.965476623 +0100
-@@ -1,7 +1,10 @@
-+# Copyright (C) 2010-2013 AG Projects. See LICENSE for details.
-+#
- 
- """Provide access to Blink's resources"""
- 
--import __main__
-+__all__ = ['ApplicationData', 'Resources', 'IconManager']
-+
- import imghdr
- import os
- import platform
-@@ -19,14 +22,10 @@
- from blink.util import run_in_gui_thread
- 
- 
--__all__ = ['ApplicationData', 'Resources', 'IconManager']
--
--
- class DirectoryContextManager(unicode):
-     def __enter__(self):
-         self.directory = os.getcwdu()
-         os.chdir(self)
--
-     def __exit__(self, type, value, traceback):
-         os.chdir(self.directory)
- 
-@@ -61,18 +60,7 @@
-     @classproperty
-     def directory(cls):
-         if cls._cached_directory is None:
--            try:
--                binary_directory = os.path.dirname(os.path.realpath(__main__.__file__))
--            except AttributeError:
--                if hasattr(sys, 'frozen'):
--                    application_directory = os.path.dirname(os.path.realpath(sys.executable))
--                else:
--                    application_directory = os.path.realpath('')  # executed in interactive interpreter
--            else:
--                if os.path.basename(binary_directory) == 'bin':
--                    application_directory = os.path.dirname(binary_directory)
--                else:
--                    application_directory = binary_directory
-+            application_directory = '@out@'
-             if os.path.exists(os.path.join(application_directory, 'resources', 'blink.ui')):
-                 cls._cached_directory = os.path.join(application_directory, 'resources').decode(sys.getfilesystemencoding())
-             else:

pkgs/applications/networking/mailreaders/mailpile/default.nix

···
-{ lib, fetchFromGitHub, python2Packages, gnupg1orig, openssl, git }:
-
-python2Packages.buildPythonApplication rec {
-  pname = "mailpile";
-  version = "1.0.0rc2";
-
-  src = fetchFromGitHub {
-    owner = "mailpile";
-    repo = "Mailpile";
-    rev = version;
-    sha256 = "1z5psh00fjr8gnl4yjcl4m9ywfj24y1ffa2rfb5q8hq4ksjblbdj";
-  };
-
-  postPatch = ''
-    patchShebangs scripts
-  '';
-
-  nativeBuildInputs = with python2Packages; [ pbr git ];
-  PBR_VERSION=version;
-
-  propagatedBuildInputs = with python2Packages; [
-    appdirs
-    cryptography
-    fasteners
-    gnupg1orig
-    jinja2
-    pgpdump
-    pillow
-    python2Packages.lxml
-    spambayes
-  ];
-
-  postInstall = ''
-    wrapProgram $out/bin/mailpile \
-      --prefix PATH ":" "${lib.makeBinPath [ gnupg1orig openssl ]}" \
-      --set-default MAILPILE_SHARED "$out/share/mailpile"
-  '';
-
-  # No tests were found
-  doCheck = false;
-
-  meta = with lib; {
-    description = "A modern, fast web-mail client with user-friendly encryption and privacy features";
-    homepage = "https://www.mailpile.is/";
-    license = [ licenses.asl20 licenses.agpl3 ];
-    platforms = platforms.linux;
-    maintainers = [ ];
-    knownVulnerabilities = [
-      "Numerous and uncounted, upstream has requested we not package it. See more: https://github.com/NixOS/nixpkgs/pull/23058#issuecomment-283515104"
-    ];
-  };
-}

pkgs/applications/science/biology/lumpy/default.nix

···
-{ lib, stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
-, samtools, hexdump, python2Packages, which }:
-
-let
-  python =
-    python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
-
-in stdenv.mkDerivation rec {
-  pname = "lumpy";
-  version = "0.3.1";
-
-  src = fetchFromGitHub {
-    owner = "arq5x";
-    repo = "lumpy-sv";
-    rev = "v${version}";
-    sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
-    fetchSubmodules = true;
-  };
-
-  nativeBuildInputs = [ which ];
-  buildInputs =
-    [ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
-
-  preConfigure = ''
-    patchShebangs ./.
-
-    # Use Nix htslib over bundled version
-    sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
-    sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
-    # Also make sure we use the includes from Nix's htslib
-    sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
-  '';
-
-  # Upstream's makefile doesn't have an install target
-  installPhase = ''
-    mkdir -p $out
-    cp -r bin $out
-    cp -r scripts $out
-    sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
-  '';
-
-  meta = with lib; {
-    description = "Probabilistic structural variant caller";
-    homepage = "https://github.com/arq5x/lumpy-sv";
-    maintainers = with maintainers; [ jbedo ];
-    license = licenses.mit;
-    platforms = [ "x86_64-linux" ];
-  };
-
-}

pkgs/applications/version-management/git-crecord/default.nix

···
-{ lib, fetchFromGitHub, python2Packages }:
+{ lib, fetchFromGitHub, python3 }:
 
-python2Packages.buildPythonApplication rec {
+python3.pkgs.buildPythonApplication rec {
   pname = "git-crecord";
-  version = "20161216.0";
+  version = "20201025.0";
 
   src = fetchFromGitHub {
     owner = "andrewshadura";
     repo = "git-crecord";
     rev = version;
-    sha256 = "0v3y90zi43myyi4k7q3892dcrbyi9dn2q6xgk12nw9db9zil269i";
+    sha256 = "1rkdmy2d2vsx22fx97nd9afh0g5lq4pns7rdxyl711apq1bhiihn";
   };
 
-  propagatedBuildInputs = with python2Packages; [ docutils ];
+  propagatedBuildInputs = with python3.pkgs; [ docutils ];
+
+  # has no tests
+  doCheck = false;
 
   meta = {
     homepage = "https://github.com/andrewshadura/git-crecord";

pkgs/applications/version-management/gitinspector/default.nix

···
-{ lib, fetchFromGitHub, python2Packages }:
-
-python2Packages.buildPythonApplication rec {
-  pname = "gitinspector";
-  version = "0.4.4";
-  namePrefix = "";
-
-  src = fetchFromGitHub {
-    owner = "ejwa";
-    repo = "gitinspector";
-    rev = "v${version}";
-    sha256 = "sha256-9bChvE5aAZFunu599pH7QKHZFd7aQzv0i9LURrvh2t0=";
-  };
-
-  checkInputs = with python2Packages; [
-    unittest2
-  ];
-
-  meta = with lib; {
-    homepage = "https://github.com/ejwa/gitinspector";
-    description = "Statistical analysis tool for git repositories";
-    license = licenses.gpl3;
-    platforms = platforms.all;
-    maintainers = [ maintainers.bjornfor ];
-  };
-}

pkgs/data/themes/cdetheme/default.nix

···
-{ lib, stdenv, fetchFromGitHub, python2Packages }:
-
-stdenv.mkDerivation rec {
-  pname = "cdetheme";
-  version = "1.3";
-
-  src = fetchFromGitHub {
-    owner = "josvanr";
-    repo = "cde-motif-theme";
-    rev = version;
-    sha256 = "1v5c4db69cmzdci8xxlkx3s3cifg1h5160qq5siwfps0sj7pvggj";
-  };
-
-  dontBuild = true;
-
-  pythonPath = with python2Packages; [ pyqt4 pillow pyxdg pyyaml ];
-  nativeBuildInputs = with python2Packages; [ python wrapPython ];
-
-  installPhase = ''
-    mkdir -p $out/share/themes
-    cp -r cdetheme $out/share/themes
-    patchShebangs $out/share/themes/cdetheme/scripts/switchtheme
-    wrapPythonProgramsIn "$out/share/themes/cdetheme/scripts" "$out $pythonPath"
-  '';
-
-  meta = with lib; {
-    description = "Gtk2 / Gtk3 theme mimicking CDE / Motif";
-    homepage = "https://www.gnome-look.org/p/1231025";
-    license = licenses.gpl3;
-    platforms = platforms.all;
-    maintainers = with maintainers; [ ];
-    hydraPlatforms = [];
-  };
-}

pkgs/development/embedded/arduino/ino/default.nix

···
-{ lib, fetchurl, python2Packages, picocom
-, avrdude, arduino-core }:
-
-python2Packages.buildPythonApplication rec {
-  pname = "ino";
-  version = "0.3.6";
-
-  src = fetchurl {
-    url = "mirror://pypi/i/ino/ino-${version}.tar.gz";
-    sha256 = "0k6lzfcn55favbj0w4afrvnmwyskf7bgzg9javv2ycvskp35srwv";
-  };
-
-  # TODO: add avrgcclibc, it must be rebuild with C++ support
-  propagatedBuildInputs = with python2Packages; [
-    arduino-core
-    avrdude
-    picocom
-    configobj
-    jinja2
-    pyserial
-    six
-  ];
-
-  patchPhase = ''
-    echo "Patching Arduino distribution path"
-    sed -i 's@/usr/local/share/arduino@${arduino-core}/share/arduino@g' \
-        ino/environment.py
-    sed -i -e 's@argparse@@' -e 's@ordereddict@@' \
-        requirements.txt
-    sed -i -e 's@from ordereddict@from collections@' \
-        ino/environment.py ino/utils.py
-
-    # Patch the upload command so it uses the correct avrdude
-    substituteInPlace ino/commands/upload.py \
-      --replace "self.e['avrdude']" "'${avrdude}/bin/avrdude'" \
-      --replace "'-C', self.e['avrdude.conf']," ""
-  '';
-
-  meta = with lib; {
-    description = "Command line toolkit for working with Arduino hardware";
-    homepage = "http://inotool.org/";
-    license = licenses.mit;
-    maintainers = with maintainers; [ antono ];
-    platforms = platforms.linux;
-  };
-}

pkgs/development/interpreters/pyrex/0.9.5.nix

···
-{ lib, fetchurl, python2Packages }:
-
-python2Packages.buildPythonPackage rec {
-  pname = "pyrex";
-  version = "0.9.5.1.1";
-
-  src = fetchurl {
-    url = "https://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/oldtar/Pyrex-${version}.tar.gz";
-    sha256 = "0lxxvn4mjfb83swcbqb5908q4iy53w4ip5i0f9angm2va1jyhd3z";
-  };
-
-  doCheck = false;
-
-  meta = {
-    homepage = "http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/";
-    description = "A language for writing Python extension modules";
-    license = lib.licenses.asl20;
-  };
-}

pkgs/development/interpreters/pyrex/0.9.6.nix

···
-{ lib, fetchurl, python2Packages }:
-
-python2Packages.buildPythonPackage rec {
-  pname = "pyrex";
-  version = "0.9.6.4";
-
-  src = fetchurl {
-    url = "https://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/oldtar/Pyrex-${version}.tar.gz";
-    sha256 = "18pd9f8al3l6i27cc0ddhgg7hxf28lnfs75x4a8jzscydxgiq5a8";
-  };
-
-  doCheck = false;
-
-  meta = {
-    homepage = "http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/";
-    description = "A language for writing Python extension modules";
-    license = lib.licenses.asl20;
-  };
-}

pkgs/development/interpreters/renpy/default.nix

···
-{ lib, stdenv, fetchurl, python2Packages, pkg-config, SDL2
-, libpng, ffmpeg, freetype, glew, libGL, libGLU, fribidi, zlib
-, glib
-}:
-
-with python2Packages;
-
-stdenv.mkDerivation rec {
-  pname = "renpy";
-  version = "7.3.5";
-
-  meta = with lib; {
-    description = "Ren'Py Visual Novel Engine";
-    homepage = "https://renpy.org/";
-    license = licenses.mit;
-    platforms = platforms.linux;
-  };
-
-  src = fetchurl {
-    url = "https://www.renpy.org/dl/${version}/renpy-${version}-source.tar.bz2";
-    sha256 = "1anr5cfbvbsbik4v4rvrkdkciwhg700k4lydfbs4n85raimz9mw4";
-  };
-
-  patches = [
-    ./launcherenv.patch
-  ];
-
-  postPatch = ''
-    substituteInPlace launcher/game/choose_directory.rpy --replace /usr/bin/python ${python.interpreter}
-  '';
-
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [
-    python cython wrapPython tkinter
-    SDL2 libpng ffmpeg freetype glew libGLU libGL fribidi zlib pygame_sdl2 glib
-  ];
-
-  pythonPath = [ pygame_sdl2 tkinter ];
-
-  RENPY_DEPS_INSTALL = lib.concatStringsSep "::" (map (path: path) [
-    SDL2 SDL2.dev libpng ffmpeg ffmpeg.out freetype glew.dev glew.out libGLU libGL fribidi zlib
-  ]);
-
-  buildPhase = ''
-    python module/setup.py build
-  '';
-
-  installPhase = ''
-    mkdir -p $out/share/renpy
-    cp -vr * $out/share/renpy
-    rm -rf $out/share/renpy/module
-
-    python module/setup.py install --prefix=$out --install-lib=$out/share/renpy/module
-
-    makeWrapper ${python}/bin/python $out/bin/renpy \
-      --set PYTHONPATH $PYTHONPATH \
-      --set RENPY_BASE $out/share/renpy \
-      --add-flags "-O $out/share/renpy/renpy.py"
-  '';
-
-  NIX_CFLAGS_COMPILE = "-I${pygame_sdl2}/include/${python.libPrefix}";
-}

pkgs/development/interpreters/renpy/launcherenv.patch

···
-# The launcher game starts projects in a separate python process
-# with the -E flag, which prevents the nix set PYTHONPATH envvar
-# from taking effect, preventing the loading of pygame_sdl2
---- a/launcher/game/project.rpy
-+++ b/launcher/game/project.rpy
-@@ -239,7 +239,7 @@
-                 raise Exception("Python interpreter not found: %r", executables)
- 
-             # Put together the basic command line.
--            cmd = [ executable, "-EO", sys.argv[0] ]
-+            cmd = [ executable, "-O", sys.argv[0] ]
- 
-             cmd.append(self.path)
-             cmd.extend(args)

pkgs/development/libraries/gdal/2.4.nix

···
 { lib, stdenv, fetchurl, libjpeg, libtiff, zlib
-, postgresql, libmysqlclient, libgeotiff, python2Packages, proj, geos, openssl
+, postgresql, libmysqlclient, libgeotiff, python3Packages, proj, geos, openssl
 , libpng, sqlite, libspatialite, poppler, hdf4, qhull, giflib, expat
 , libiconv, libxml2
 , netcdfSupport ? true, netcdf, hdf5, curl
···
 
   buildInputs = [ libjpeg libtiff libgeotiff libpng proj openssl sqlite
     libspatialite poppler hdf4 qhull giflib expat libxml2 proj ]
-  ++ (with python2Packages; [ python numpy wrapPython ])
+  ++ (with python3Packages; [ python numpy wrapPython ])
   ++ lib.optional stdenv.isDarwin libiconv
   ++ lib.optionals netcdfSupport [ netcdf hdf5 curl ];
 

pkgs/development/libraries/opae/default.nix

···
 { lib, stdenv, fetchFromGitHub, cmake
 , libuuid, json_c
-, doxygen, perl, python2, python2Packages
+, doxygen, perl, python3
 }:
 
 stdenv.mkDerivation rec {
···
   NIX_CFLAGS_COMPILE = [
     "-Wno-error=format-truncation"
     "-Wno-error=address-of-packed-member"
+    "-Wno-array-bounds"
   ];
 
-  nativeBuildInputs = [ cmake doxygen perl python2Packages.sphinx ];
-  buildInputs = [ libuuid json_c python2 ];
+  nativeBuildInputs = [ cmake doxygen perl python3.pkgs.sphinx ];
+  buildInputs = [ libuuid json_c python3 ];
 
   # Set the Epoch to 1980; otherwise the Python wheel/zip code
   # gets very angry

pkgs/development/libraries/quickder/default.nix

···
-{ lib, stdenv, fetchFromGitHub, python2Packages, hexio
+{ lib, stdenv, fetchFromGitHub, python3Packages, hexio
 , cmake, bash, arpa2cm, git, asn2quickder }:
 
 stdenv.mkDerivation rec {
···
 
   nativeBuildInputs = [ cmake ];
 
-  buildInputs = with python2Packages; [
+  buildInputs = with python3Packages; [
     arpa2cm
     asn1ate
     hexio

pkgs/development/libraries/vigra/default.nix

···
 , libpng
 , libtiff
 , openexr
-, python2Packages
+, python3
 }:
 
 let
-  inherit (python2Packages) python numpy;
-  # Might want to use `python2.withPackages(ps: [ps.numpy]);` here...
+  python = python3.withPackages (py: with py; [ numpy ]);
 in
 stdenv.mkDerivation rec {
   pname = "vigra";
···
     libjpeg
     libpng
     libtiff
-    numpy
     openexr
     python
   ];

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

···
-{ lib, buildPythonPackage, fetchPypi, isPy3k, isPyPy }:
-
-buildPythonPackage rec {
-  pname = "python-cjson";
-  version = "1.2.2";
-  disabled = isPy3k || isPyPy;
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "3006c2c218297be3448dc793218e0b15d20fe9839775521bfc294fc6aa24972b";
-  };
-
-  meta = with lib; {
-    description = "A very fast JSON encoder/decoder for Python";
-    homepage = "https://ag-projects.com/";
-    license = licenses.lgpl2;
-  };
-}

pkgs/development/tools/profiling/systemtap/default.nix

···
 { lib, fetchgit, pkg-config, gettext, runCommand, makeWrapper
-, elfutils, kernel, gnumake, python2, python2Packages
+, cpio, elfutils, kernel, gnumake, python3
 }:
 
 let
···
     pname = "systemtap";
     inherit version;
     src = fetchgit { inherit url rev sha256; };
-    nativeBuildInputs = [ pkg-config ];
-    buildInputs = [ elfutils gettext python2 python2Packages.setuptools ];
+    nativeBuildInputs = [ pkg-config cpio ];
+    buildInputs = [ elfutils gettext python3 python3.pkgs.setuptools ];
     enableParallelBuilding = true;
   };
 
···
     done
   '';
 
-  pypkgs = with python2Packages; makePythonPath [ pyparsing ];
+  pypkgs = with python3.pkgs; makePythonPath [ pyparsing ];
 
 in runCommand "systemtap-${kernel.version}-${version}" {
   inherit stapBuild kernelBuildDir;

pkgs/tools/audio/mididings/default.nix

···
-{ lib, python2Packages, fetchFromGitHub, pkg-config, glib, alsa-lib, libjack2  }:
-
-python2Packages.buildPythonApplication {
-  version = "2015-11-17";
-  pname = "mididings";
-
-  src = fetchFromGitHub {
-    owner = "dsacre";
-    repo = "mididings";
-    rev = "bbec99a8c878a2a7029e78e84fc736e4a68ed5a0";
-    sha256 = "1pdf5mib87zy7yjh9vpasja419h28wvgq6x5hw2hkm7bg9ds4p2m";
-  };
-
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ glib alsa-lib libjack2 python2Packages.boost ];
-  propagatedBuildInputs = with python2Packages; [ decorator ]
-    # for livedings
-    ++ [ tkinter pyliblo ]
-    # for mididings.extra
-    ++ [ dbus-python pyinotify ]
-    # to read/write standard MIDI files
-    ++ [ pysmf ]
-    # so mididings knows where to look for config files
-    ++ [ pyxdg ];
-
-  preBuild = with lib.versions; ''
-    substituteInPlace setup.py \
-      --replace boost_python "boost_python${major python2Packages.python.version}${minor python2Packages.python.version}"
-  '';
-
-  meta = with lib; {
-    description = "A MIDI router and processor based on Python, supporting ALSA and JACK MIDI";
-    homepage = "http://das.nasophon.de/mididings";
-    license = licenses.gpl2;
-    maintainers = [ ];
-    platforms = platforms.linux;
-  };
-}

pkgs/tools/networking/getmail/default.nix

···
-{ lib, fetchurl, python2Packages }:
-
-python2Packages.buildPythonApplication rec {
-  pname = "getmail";
-  version = "5.14";
-
-  src = fetchurl {
-    url = "http://pyropus.ca/software/getmail/old-versions/${pname}-${version}.tar.gz";
-    sha256 = "1hcrd9h4g12f5gvl1djsbchcjry02ghq4icdr897s8v48pkrzagk";
-  };
-
-  doCheck = false;
-
-  postPatch = ''
-    # getmail spends a lot of effort to build an absolute path for
-    # documentation installation; too bad it is counterproductive now
-    sed -e '/datadir or prefix,/d' -i setup.py
-  '';
-
-  meta = {
-    description = "A program for retrieving mail";
-    maintainers = [ lib.maintainers.raskin ];
-    platforms = lib.platforms.linux;
-
-    homepage = "http://pyropus.ca/software/getmail/";
-    updateWalker = true;
-    license = lib.licenses.gpl2Plus;
-  };
-}

pkgs/top-level/aliases.nix

···
   bitwarden_rs-postgresql = vaultwarden-postgresql;
   bitwarden_rs-vault = vaultwarden-vault;
 
+  blink = throw "blink has been removed from nixpkgs, it was unmaintained and required python2 at the time of removal."; # added 2022-01-12
   bs1770gain = throw "bs1770gain has been removed from nixpkgs, as it had no maintainer or reverse dependencies."; # added 2021-01-02
   bsod = throw "bsod has been removed: deleted by upstream"; # added 2022-01-07
   btc1 = throw "btc1 has been removed, it was abandoned by upstream"; # added 2020-11-03
···
   casperjs = throw "casperjs has been removed, it was abandoned by upstream and broken.";
   catfish = xfce.catfish; # added 2019-12-22
   ccnet = throw "ccnet has been removed because seafile does not depend on it anymore"; # added 2021-03-25
+  cde-gtk-theme = throw "cde-gtk-theme has been removed from nixpkgs as it shipped with python2 scripts that didn't work anymore."; # added 2022-01-12
   cgmanager = throw "cgmanager was deprecated by lxc and therefore removed from nixpkgs."; # added 2020-06-05
   checkbashism = checkbashisms; # added 2016-08-16
   chronos = throw "chronos has been removed from nixpkgs, as it was unmaintained"; # added 2020-08-15
···
   cups_filters = cups-filters; # added 2016-08
   cups-googlecloudprint = throw "Google Cloudprint is officially discontinued since Jan 2021, more info https://support.google.com/chrome/a/answer/9633006";
   cloud-print-connector = throw "Google Cloudprint is officially discontinued since Jan 2021, more info https://support.google.com/chrome/a/answer/9633006";
+  curaByDagoma = throw "curaByDagoma has been removed from nixpkgs, because it was unmaintained and dependent on python2 packages."; # added 2022-01-12
   curaLulzbot = throw "curaLulzbot has been removed due to insufficient upstream support for a modern dependency chain"; # added 2021-10-23
   cquery = throw "cquery has been removed because it is abandoned by upstream. Consider switching to clangd or ccls instead."; # added 2020-06-15
   cv = progress; # added 2015-09-06
···
   desktop_file_utils = desktop-file-utils; # added 2018-02-25
   devicemapper = lvm2; # added 2018-04-25
   digikam5 = digikam; # added 2017-02-18
+  displaycal = throw "displaycal has been removed from nixpkgs, as it hasn't migrated to python3."; # added 2022-01-12
   dmtx = dmtx-utils; # added 2018-04-25
   dnnl = oneDNN; # added 2020-04-22
   docbook5_xsl = docbook_xsl_ns; # added 2018-04-25
···
   gdb-multitarget = gdb; # added 2017-11-13
   gdk_pixbuf = gdk-pixbuf; # added 2019-05-22
   gettextWithExpat = gettext; # 2016-02-19
+  getmail = throw "getmail has been removed from nixpkgs, migrate to getmail6."; # added 2022-01-12
   giflib_4_1 = throw "giflib_4_1 has been removed; use giflib instead"; # 2020-02-12
   git-bz = throw "giz-bz has been removed from nixpkgs as it is stuck on python2."; # added 2022-01-01
   gitAndTools = self // { # added 2021-01-14
···
     topGit = top-git;
   };
   gitin = throw "gitin has been remove because it was unmaintained and depended on an insecure version of libgit2"; # added 2021-12-07
+  gitinspector = throw "gitinspector has been removed because it doesn't work with python3."; # added 2022-01-12
   glib_networking = glib-networking; # added 2018-02-25
   gmailieer = lieer; # added 2020-04-19
   gmvault = throw "gmvault has been removed because it is unmaintained, mostly broken, and insecure"; # added 2021-03-08
···
   kodiGBM = kodi-gbm;
   kodiPlain = kodi;
   kodiPlainWayland = kodi-wayland;
+  ino = throw "ino has been removed from nixpkgs, the project is stuck on python2 and upstream has archived the project."; # added 2022-01-12
   jellyfin_10_5 = throw "Jellyfin 10.5 is no longer supported and contains a security vulnerability. Please upgrade to a newer version."; # added 2021-04-26
   julia_07 = throw "julia_07 has been deprecated in favor of the latest LTS version"; # added 2020-09-15
   julia_1 = throw "julia_1 has been deprecated in favor of julia_10 as it was ambiguous"; # added 2021-03-13
···
   lua5_1_sockets = lua51Packages.luasocket; # added 2017-05-02
   lua5_expat = luaPackages.luaexpat; # added 2017-05-02
   lua5_sec = luaPackages.luasec; # added 2017-05-02
+  lumpy = throw "lumpy has been removed from nixpkgs, as it is stuck on python2."; # added 2022-01-12
   lxappearance-gtk3 = throw "lxappearance-gtk3 has been removed. Use lxappearance instead, which now defaults to Gtk3";  # added 2020-06-03
   lzma = xz; # moved from top-level 2021-03-14
   m3d-linux = m33-linux; # added 2016-08-13
   mail-notification = throw "mail-notification has been removed from nixpkgs, as it's unmaintained and has dependencies on old gnome libraries we want to remove"; # added 2021-08-21
+  mailpile = throw "mailpile was removed from nixpkgs, as it is stuck on python2."; # added 2022-01-12
   man_db = man-db; # added 2016-05
   manpages = man-pages; # added 2015-12-06
   marathon = throw "marathon has been removed from nixpkgs, as it's unmaintained"; # added 2020-08-15
···
   mbedtls_1_3 = throw "mbedtls_1_3 is end of life, see https://tls.mbed.org/kb/how-to/upgrade-2.0"; # added 2019-12-08
   meme = meme-image-generator; # added 2021-04-21
   mess = mame; # added 2019-10-30
+  metamorphose2 = throw "metamorphose2 has been removed from nixpkgs, as it was stuck on python2."; # added 2022-01-12
   mcgrid = throw "mcgrid has been removed from nixpkgs, as it's not compatible with rivet 3"; # added 2020-05-23
   mcomix = throw "mcomix has been removed from nixpkgs, as it's unmaintained; try mcomix3 a Python 3 fork"; # added 2019-12-10, modified 2020-11-25
+  mididings = throw "mididings has been removed from nixpkgs as it doesn't support recent python3 versions and its upstream stopped maintaining it."; # added 2022-01-12
   mimms = throw "mimms has been removed from nixpkgs as the upstream project is stuck on python2."; # added 2022-01-01
   mirage = throw "mirage has been removed from nixpkgs, as it's unmaintained"; # added 2019-12-10
   minergate = throw "minergate has been removed from nixpkgs, because the package is unmaintained and the site has a bad reputation"; # added 2021-08-13
···
   nagiosPluginsOfficial = monitoring-plugins;
   navit = throw "navit has been removed from nixpkgs, due to being unmaintained"; # added 2021-06-07
   ncat = nmap;  # added 2016-01-26
+  neap = throw "neap was removed from nixpkgs, as it relies on python2"; # added 2022-01-12
   netcat-openbsd = libressl.nc; # added 2018-04-25
   netease-cloud-music = throw "netease-cloud-music has been removed together with deepin"; # added 2020-08-31
   networkmanager_fortisslvpn = networkmanager-fortisslvpn; # added 2018-02-25
···
   pybind11 = throw "pybind11 was removed because pythonPackages.pybind11 for the appropriate version of Python should be used"; # added 2021-05-14
   pybitmessage = throw "pybitmessage was removed from nixpkgs as it is stuck on python2."; # added 2022-01-01
   pynagsystemd = throw "pynagsystemd was removed as it was unmaintained and incompatible with recent systemd versions. Instead use its fork check_systemd."; # added 2020-10-24
+  pyrex = throw "pyrex has been removed from nixpkgs as the project is still stuck on python2."; # added 2022-01-12
+  pyrex095 = throw "pyrex has been removed from nixpkgs as the project is still stuck on python2."; # added 2022-01-12
+  pyrex096 = throw "pyrex has been removed from nixpkgs as the project is still stuck on python2."; # added 2022-01-12
   pyrit = throw "pyrit has been removed from nixpkgs as the project is still stuck on python2."; # added 2022-01-01
   python2nix = throw "python2nix has been removed as it is outdated. Use e.g. nixpkgs-pytools instead."; # added 2021-03-08
   python-swiftclient = swiftclient; # added 2021-09-09
···
   radare2-cutter = cutter; # added 2021-03-30
   redkite = throw "redkite was archived by upstream"; # added 2021-04-12
   redshift-wlr = throw "redshift-wlr has been replaced by gammastep"; # added 2021-12-25
+  renpy = throw "renpy has been removed from nixpkgs, it was unmaintained and the latest packaged version required python2."; # added 2022-01-12
   retroArchCores = throw "retroArchCores has been removed. Please use overrides instead, e.g.: `retroarch.override { cores = with libretro; [ ... ]; }`"; # added 2021-11-19
   rkt = throw "rkt was archived by upstream"; # added 2020-05-16
   rpiboot-unstable = rpiboot; # added 2021-07-30

pkgs/top-level/all-packages.nix

···
 
   bitbucket-server-cli = callPackage ../applications/version-management/git-and-tools/bitbucket-server-cli { };
 
-  blink = libsForQt5.callPackage ../applications/networking/instant-messengers/blink { };
-
   blitz = callPackage ../development/libraries/blitz { };
 
   blockbook = callPackage ../servers/blockbook { };
···
   metabase = callPackage ../servers/metabase { };
 
   midicsv = callPackage ../tools/audio/midicsv { };
-
-  mididings = callPackage ../tools/audio/mididings { };
 
   miniscript = callPackage ../applications/blockchains/miniscript { };
 
···
   gerrit = callPackage ../applications/version-management/gerrit { };
 
   geteltorito = callPackage ../tools/misc/geteltorito { };
-
-  getmail = callPackage ../tools/networking/getmail { };
 
   getmail6 = callPackage ../tools/networking/getmail6 { };
 
···
 
   github-runner = callPackage ../development/tools/continuous-integration/github-runner { };
 
-  gitinspector = callPackage ../applications/version-management/gitinspector { };
-
   gitkraken = callPackage ../applications/version-management/gitkraken { };
 
   gitlab = callPackage ../applications/version-management/gitlab { };
···
 
   mailsend = callPackage ../tools/networking/mailsend { };
 
-  mailpile = callPackage ../applications/networking/mailreaders/mailpile { };
-
   mailutils = callPackage ../tools/networking/mailutils {
     sasl = gsasl;
   };
···
   memo = callPackage ../applications/misc/memo { };
 
   mencal = callPackage ../applications/misc/mencal { } ;
-
-  metamorphose2 = callPackage ../applications/misc/metamorphose2 { };
 
   metar = callPackage ../applications/misc/metar { };
 
···
 
   pyradio = callPackage ../applications/audio/pyradio {};
 
-  pyrex = pyrex095;
-
-  pyrex095 = callPackage ../development/interpreters/pyrex/0.9.5.nix { };
-
-  pyrex096 = callPackage ../development/interpreters/pyrex/0.9.6.nix { };
-
   racket = callPackage ../development/interpreters/racket {
     # racket 6.11 doesn't build with gcc6 + recent glibc:
     # https://github.com/racket/racket/pull/1886
···
   regina = callPackage ../development/interpreters/regina { };
 
   inherit (ocamlPackages) reason;
-
-  renpy = callPackage ../development/interpreters/renpy { };
 
   pixie = callPackage ../development/interpreters/pixie { };
   dust = callPackage ../development/interpreters/pixie/dust.nix { };
···
   };
 
   indent = callPackage ../development/tools/misc/indent { };
-
-  ino = callPackage ../development/embedded/arduino/ino { };
 
   inotify-tools = callPackage ../development/tools/misc/inotify-tools { };
 
···
   carlito = callPackage ../data/fonts/carlito {};
 
   cascadia-code = callPackage ../data/fonts/cascadia-code { };
-
-  cde-gtk-theme = callPackage ../data/themes/cdetheme { };
 
   charis-sil = callPackage ../data/fonts/charis-sil { };
 
···
 
   n8n = callPackage ../applications/networking/n8n {};
 
-  neap = callPackage ../applications/misc/neap { };
-
   neomutt = callPackage ../applications/networking/mailreaders/neomutt { };
 
   natron = callPackage ../applications/video/natron { };
···
   cura = libsForQt5.callPackage ../applications/misc/cura { };
 
   curaPlugins = callPackage ../applications/misc/cura/plugins.nix { };
-
-  curaByDagoma = callPackage ../applications/misc/curabydagoma { };
 
   peru = callPackage ../applications/version-management/peru {};
 
···
 
   digikam = libsForQt5.callPackage ../applications/graphics/digikam {};
 
-  displaycal = callPackage ../applications/graphics/displaycal {};
-
   drumkv1 = libsForQt5.callPackage ../applications/audio/drumkv1 { };
 
   ### GAMES
···
   kssd = callPackage ../applications/science/biology/kssd { };
 
   last = callPackage ../applications/science/biology/last { };
-
-  lumpy = callPackage ../applications/science/biology/lumpy { };
 
   macse = callPackage ../applications/science/biology/macse { };
 

pkgs/top-level/python-packages.nix

···
 
   cjkwrap = callPackage ../development/python-modules/cjkwrap { };
 
-  cjson = callPackage ../development/python-modules/cjson { };
-
   ckcc-protocol = callPackage ../development/python-modules/ckcc-protocol { };
 
   claripy = callPackage ../development/python-modules/claripy { };
···
 
   fints = callPackage ../development/python-modules/fints { };
 
-  fiona = callPackage ../development/python-modules/fiona {
-    gdal = pkgs.gdal_2;
-  };
+  fiona = callPackage ../development/python-modules/fiona { };
 
   fipy = callPackage ../development/python-modules/fipy { };
 
···
     inherit (pkgs) libarchive;
   };
 
-  rasterio = callPackage ../development/python-modules/rasterio {
-    gdal = pkgs.gdal_2;
-  };
+  rasterio = callPackage ../development/python-modules/rasterio { };
 
   ratelim = callPackage ../development/python-modules/ratelim { };