From 3225decddf3965f95410c95ee01a6dfb512a1b99 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 21 Jan 2021 01:37:23 +0000
Subject: [PATCH 01/41] pugixml: 1.11.1 -> 1.11.4

---
 pkgs/development/libraries/pugixml/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/libraries/pugixml/default.nix b/pkgs/development/libraries/pugixml/default.nix
index 14ef8130431a..57335fa3d970 100644
--- a/pkgs/development/libraries/pugixml/default.nix
+++ b/pkgs/development/libraries/pugixml/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "pugixml";
-  version = "1.11.1";
+  version = "1.11.4";
 
   src = fetchFromGitHub {
     owner = "zeux";
     repo = "pugixml";
     rev = "v${version}";
-    sha256 = "0iwn627wynrqrwb2ddm38p6y6cpgcavgbkrrxwxa0d26m9v2avpr";
+    sha256 = "sha256-pXadPs2Dlht3BMNYDVxWZqnVv0umDgYVcqH5YVxr+uA=";
   };
 
   outputs = if shared then [ "out" "dev" ] else [ "out" ];

From 0c2c7038919a0e4a5802ab04a12302d4c73b13b2 Mon Sep 17 00:00:00 2001
From: sophrosyne97 <joshuaortiz@tutanota.com>
Date: Mon, 31 May 2021 18:11:13 -0400
Subject: [PATCH 02/41] vhd2vl: fix build error

---
 pkgs/applications/science/electronics/vhd2vl/default.nix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pkgs/applications/science/electronics/vhd2vl/default.nix b/pkgs/applications/science/electronics/vhd2vl/default.nix
index adce30551071..83657d729f6f 100644
--- a/pkgs/applications/science/electronics/vhd2vl/default.nix
+++ b/pkgs/applications/science/electronics/vhd2vl/default.nix
@@ -4,6 +4,7 @@
 , bison
 , flex
 , verilog
+, which
 }:
 
 stdenv.mkDerivation rec {
@@ -33,6 +34,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     verilog
+    which
   ];
 
   installPhase = ''

From e7235d863c397c51715a1588865f1996ecc63608 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= <joerg@thalheim.io>
Date: Tue, 1 Jun 2021 07:29:13 +0200
Subject: [PATCH 03/41] vhd2vl: apply linting suggestions

---
 pkgs/applications/science/electronics/vhd2vl/default.nix | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/electronics/vhd2vl/default.nix b/pkgs/applications/science/electronics/vhd2vl/default.nix
index 83657d729f6f..f0dd990a35bc 100644
--- a/pkgs/applications/science/electronics/vhd2vl/default.nix
+++ b/pkgs/applications/science/electronics/vhd2vl/default.nix
@@ -30,16 +30,17 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [
     bison
     flex
+    which
   ];
 
   buildInputs = [
     verilog
-    which
   ];
 
   installPhase = ''
-    mkdir -p $out/bin
-    cp src/vhd2vl $out/bin/
+    runHook preInstall
+    install -D -m755 src/vhd2vl $out/bin/vdh2vl
+    runHook postInstall
   '';
 
   meta = with lib; {

From 045d6f35d92e932541ef4f1ab53062c01fb867ef Mon Sep 17 00:00:00 2001
From: Mauricio Collares <mauricio@collares.org>
Date: Sun, 25 Jul 2021 13:24:58 -0300
Subject: [PATCH 04/41] polymake: 3.2.rc4 -> 4.4

---
 .../science/math/polymake/default.nix         | 31 +++++++++++--------
 pkgs/top-level/all-packages.nix               |  4 +--
 2 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/pkgs/applications/science/math/polymake/default.nix b/pkgs/applications/science/math/polymake/default.nix
index b1abb31c7650..9566801479a3 100644
--- a/pkgs/applications/science/math/polymake/default.nix
+++ b/pkgs/applications/science/math/polymake/default.nix
@@ -1,27 +1,32 @@
 { lib, stdenv, fetchurl
-, ninja, libxml2, libxslt, readline, perl, gmp, mpfr, boost
+, perl, gmp, mpfr, flint, boost
 , bliss, ppl, singular, cddlib, lrs, nauty
-, ant, openjdk
+, ninja, ant, openjdk
 , perlPackages
 , makeWrapper
 }:
 
+# polymake compiles its own version of sympol and atint because we
+# don't have those packages. other missing optional dependencies:
+# javaview, libnormaliz, scip, soplex, jreality.
+
 stdenv.mkDerivation rec {
   pname = "polymake";
-  version = "3.2.rc4";
+  version = "4.4";
 
   src = fetchurl {
-    url = "https://polymake.org/lib/exe/fetch.php/download/polymake-3.2r4.tar.bz2";
-    sha256 = "02jpkvy1cc6kc23vkn7nkndzr40fq1gkb3v257bwyi1h5d37fyqy";
+    # "The minimal version is a packager friendly version which omits
+    # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality."
+    url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2";
+    sha256 = "sha256-2nF5F2xznI77pl2TslrxA8HLpw4fmzVnPOM8N3kOwJE=";
   };
 
   buildInputs = [
-    libxml2 libxslt readline perl gmp mpfr boost
+    perl gmp mpfr flint boost
     bliss ppl singular cddlib lrs nauty
     openjdk
-  ] ++
-  (with perlPackages; [
-    XMLLibXML XMLLibXSLT XMLWriter TermReadLineGnu TermReadKey
+  ] ++ (with perlPackages; [
+    JSON TermReadLineGnu TermReadKey XMLSAX
   ]);
 
   nativeBuildInputs = [
@@ -36,11 +41,11 @@ stdenv.mkDerivation rec {
     done
   '';
 
-  meta = {
+  meta = with lib; {
     description = "Software for research in polyhedral geometry";
-    license = lib.licenses.gpl2 ;
-    maintainers = [lib.maintainers.raskin];
-    platforms = lib.platforms.linux;
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+    platforms = platforms.linux;
     homepage = "https://www.polymake.org/doku.php";
   };
 }
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 107722e6e102..2d54dbd596fc 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -26547,9 +26547,7 @@ in
 
   polylith = callPackage ../development/tools/misc/polylith { };
 
-  polymake = callPackage ../applications/science/math/polymake {
-    openjdk = openjdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
+  polymake = callPackage ../applications/science/math/polymake { };
 
   pond = callPackage ../applications/networking/instant-messengers/pond { };
 

From a54c0b9503e35e08fa6eef5dae87fda164267fa8 Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@googlemail.com>
Date: Thu, 22 Jul 2021 23:26:37 +0200
Subject: [PATCH 05/41] libmsym: init at 0.2.3

libmsym: code-review stuff
---
 .../science/chemistry/libmsym/default.nix     | 23 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 25 insertions(+)
 create mode 100644 pkgs/development/libraries/science/chemistry/libmsym/default.nix

diff --git a/pkgs/development/libraries/science/chemistry/libmsym/default.nix b/pkgs/development/libraries/science/chemistry/libmsym/default.nix
new file mode 100644
index 000000000000..8c605f3e07d4
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/libmsym/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, lib, fetchFromGitHub, cmake } :
+
+stdenv.mkDerivation rec {
+  pname = "libmsym";
+  version = "0.2.3";
+
+  src = fetchFromGitHub  {
+    owner = "mcodev31";
+    repo = pname;
+    rev = "v${version}";
+    sha256= "k+OEwrA/saupP/wX6Ii5My0vffiJ0X9xMCTrliMSMik=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with lib; {
+    description = " molecular point group symmetry lib";
+    homepage = "https://github.com/rcsb/mmtf-cpp";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 5ab47db86f9e..2fc5aa5764e9 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -6813,6 +6813,8 @@ in
 
   libmesode = callPackage ../development/libraries/libmesode {};
 
+  libmsym = callPackage ../development/libraries/science/chemistry/libmsym { };
+
   libnabo = callPackage ../development/libraries/libnabo { };
 
   libngspice = callPackage ../development/libraries/libngspice { };

From 3ea182f32180abbb0bfd8896d812609f5a8c137a Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@googlemail.com>
Date: Fri, 16 Jul 2021 11:33:14 +0200
Subject: [PATCH 06/41] mmtf-cpp: init at 1.0.0

---
 .../science/chemistry/mmtf-cpp/default.nix    | 25 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 27 insertions(+)
 create mode 100644 pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix

diff --git a/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix b/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix
new file mode 100644
index 000000000000..ec1fed68ff93
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, lib, fetchFromGitHub, cmake, msgpack } :
+
+stdenv.mkDerivation rec {
+  pname = "mmtf-cpp";
+  version = "1.0.0";
+
+  src = fetchFromGitHub  {
+    owner = "rcsb";
+    repo = pname;
+    rev = "v${version}";
+    sha256= "17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ msgpack ];
+
+  meta = with lib; {
+    description = "A library of exchange-correlation functionals with arbitrary-order derivatives";
+    homepage = "https://github.com/rcsb/mmtf-cpp";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 2fc5aa5764e9..6a780abd1971 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -13957,6 +13957,8 @@ in
 
   mkdocs = callPackage ../development/tools/documentation/mkdocs { };
 
+  mmtf-cpp = callPackage ../development/libraries/science/chemistry/mmtf-cpp { };
+
   mockgen = callPackage ../development/tools/mockgen { };
 
   modd = callPackage ../development/tools/modd { };

From b5bf1346c0e1379561029b0252742b7dc3b68856 Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@googlemail.com>
Date: Tue, 27 Jul 2021 18:42:50 +0200
Subject: [PATCH 07/41] molequeue: init at 0.9.0

molequeue: review comments
---
 .../science/chemistry/molequeue/default.nix   | 33 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 35 insertions(+)
 create mode 100644 pkgs/development/libraries/science/chemistry/molequeue/default.nix

diff --git a/pkgs/development/libraries/science/chemistry/molequeue/default.nix b/pkgs/development/libraries/science/chemistry/molequeue/default.nix
new file mode 100644
index 000000000000..1e8ca2d961d3
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/molequeue/default.nix
@@ -0,0 +1,33 @@
+{ lib, stdenv, fetchFromGitHub, cmake, qttools, wrapQtAppsHook }:
+
+stdenv.mkDerivation rec {
+  pname = "molequeue";
+  version = "0.9.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = pname;
+    rev = version;
+    sha256 = "+NoY8YVseFyBbxc3ttFWiQuHQyy1GN8zvV1jGFjmvLg=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [ qttools ];
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/molequeue/MoleQueueConfig.cmake \
+      --replace "''${MoleQueue_INSTALL_PREFIX}/$out" "''${MoleQueue_INSTALL_PREFIX}"
+  '';
+
+  meta = with lib; {
+    description = "Desktop integration of high performance computing resources";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/molequeue";
+    platforms = platforms.linux;
+    license = licenses.bsd3;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 6a780abd1971..99de1b448a81 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -29850,6 +29850,8 @@ in
     eigen = eigen2;
   };
 
+  molequeue = libsForQt5.callPackage ../development/libraries/science/chemistry/molequeue { };
+
   chemtool = callPackage ../applications/science/chemistry/chemtool { };
 
   d-seams = callPackage ../applications/science/chemistry/d-seams {};

From 43e749aa76d28a28d3153ddeff6bf75204d71de1 Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@googlemail.com>
Date: Tue, 27 Jul 2021 18:42:36 +0200
Subject: [PATCH 08/41] avogadrolibs: init at 1.94.0

avogadrolibs: review comments
---
 .../chemistry/avogadrolibs/default.nix        | 68 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 70 insertions(+)
 create mode 100644 pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix

diff --git a/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix b/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix
new file mode 100644
index 000000000000..1130f5c44e70
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix
@@ -0,0 +1,68 @@
+{ lib, stdenv, fetchFromGitHub, cmake, zlib, eigen, libGL, doxygen, spglib
+, mmtf-cpp, glew, python3, libarchive, libmsym, msgpack, qttools, wrapQtAppsHook
+}:
+
+let
+  pythonWP = python3.withPackages (p: with p; [ openbabel-bindings numpy ]);
+
+  # Pure data repositories
+  moleculesRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "molecules";
+    rev = "1.0.0";
+    sha256 = "guY6osnpv7Oqt+HE1BpIqL10POp+x8GAci2kY0bLmqg=";
+  };
+  crystalsRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "crystals";
+    rev = "1.0.1";
+    sha256 = "sH/WuvLaYu6akOc3ssAKhnxD8KNoDxuafDSozHqJZC4=";
+  };
+
+in stdenv.mkDerivation rec {
+  pname = "avogadrolibs";
+  version = "1.94.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = pname;
+    rev = version;
+    sha256 = "6bChJhqrjOxeEWZBNToq3JExHPu7DUMsEHWBDe75zAo=";
+  };
+
+  postUnpack = ''
+    cp -r ${moleculesRepo} molecules
+    cp -r ${crystalsRepo} crystals
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    eigen
+    zlib
+    libGL
+    spglib
+    mmtf-cpp
+    glew
+    libarchive
+    libmsym
+    msgpack
+    qttools
+  ];
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/${pname}/AvogadroLibsConfig.cmake \
+      --replace "''${AvogadroLibs_INSTALL_PREFIX}/$out" "''${AvogadroLibs_INSTALL_PREFIX}"
+  '';
+
+  meta = with lib; {
+    description = "Molecule editor and visualizer";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/avogadrolibs";
+    platforms = platforms.linux;
+    license = licenses.gpl2Only;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 99de1b448a81..527e2cc22984 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -29850,6 +29850,8 @@ in
     eigen = eigen2;
   };
 
+  avogadrolibs = libsForQt5.callPackage ../development/libraries/science/chemistry/avogadrolibs { };
+
   molequeue = libsForQt5.callPackage ../development/libraries/science/chemistry/molequeue { };
 
   chemtool = callPackage ../applications/science/chemistry/chemtool { };

From 9504a98c3266c247d47c0f56ee2c239863b2319b Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@googlemail.com>
Date: Tue, 27 Jul 2021 18:42:25 +0200
Subject: [PATCH 09/41] avogadro2: init at 1.94.0

avogadro2: code-review suggestions


avogadro2: review comments
---
 .../science/chemistry/avogadro2/default.nix   | 37 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 39 insertions(+)
 create mode 100644 pkgs/applications/science/chemistry/avogadro2/default.nix

diff --git a/pkgs/applications/science/chemistry/avogadro2/default.nix b/pkgs/applications/science/chemistry/avogadro2/default.nix
new file mode 100644
index 000000000000..437123faafd8
--- /dev/null
+++ b/pkgs/applications/science/chemistry/avogadro2/default.nix
@@ -0,0 +1,37 @@
+{ lib, stdenv, fetchFromGitHub, cmake, eigen, avogadrolibs, molequeue, hdf5
+, openbabel, qttools, wrapQtAppsHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "avogadro2";
+  version = "1.94.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "avogadroapp";
+    rev = version;
+    sha256 = "6RaiX23YUMfTYAuSighcLGGlJtqeydNgi3PWGF77Jp8=";
+  };
+
+  nativeBuildInputs = [ cmake wrapQtAppsHook ];
+
+  buildInputs = [
+    avogadrolibs
+    molequeue
+    eigen
+    hdf5
+    qttools
+  ];
+
+  propagatedBuildInputs = [ openbabel ];
+
+  qtWrapperArgs = [ "--prefix PATH : ${openbabel}/bin" ];
+
+  meta = with lib; {
+    description = "Molecule editor and visualizer";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/avogadroapp";
+    platforms = platforms.mesaPlatforms;
+    license = licenses.bsd3;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 527e2cc22984..0c3cb6e783b9 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -29854,6 +29854,8 @@ in
 
   molequeue = libsForQt5.callPackage ../development/libraries/science/chemistry/molequeue { };
 
+  avogadro2 = libsForQt5.callPackage ../applications/science/chemistry/avogadro2 { };
+
   chemtool = callPackage ../applications/science/chemistry/chemtool { };
 
   d-seams = callPackage ../applications/science/chemistry/d-seams {};

From afb908bfbdc66dbf8892b862a04b18c6142225c3 Mon Sep 17 00:00:00 2001
From: figsoda <figsoda@pm.me>
Date: Tue, 27 Jul 2021 23:58:33 -0400
Subject: [PATCH 10/41] tree-sitter-comment: init at 2021-04-27

---
 .../tools/parsing/tree-sitter/grammars/default.nix     |  1 +
 .../tree-sitter/grammars/tree-sitter-comment.json      | 10 ++++++++++
 pkgs/development/tools/parsing/tree-sitter/update.nix  |  4 ++++
 3 files changed, 15 insertions(+)
 create mode 100644 pkgs/development/tools/parsing/tree-sitter/grammars/tree-sitter-comment.json

diff --git a/pkgs/development/tools/parsing/tree-sitter/grammars/default.nix b/pkgs/development/tools/parsing/tree-sitter/grammars/default.nix
index 2671e4148b1d..96a376545fa5 100644
--- a/pkgs/development/tools/parsing/tree-sitter/grammars/default.nix
+++ b/pkgs/development/tools/parsing/tree-sitter/grammars/default.nix
@@ -3,6 +3,7 @@
   tree-sitter-bash = (builtins.fromJSON (builtins.readFile ./tree-sitter-bash.json));
   tree-sitter-c = (builtins.fromJSON (builtins.readFile ./tree-sitter-c.json));
   tree-sitter-c-sharp = (builtins.fromJSON (builtins.readFile ./tree-sitter-c-sharp.json));
+  tree-sitter-comment = (builtins.fromJSON (builtins.readFile ./tree-sitter-comment.json));
   tree-sitter-cpp = (builtins.fromJSON (builtins.readFile ./tree-sitter-cpp.json));
   tree-sitter-css = (builtins.fromJSON (builtins.readFile ./tree-sitter-css.json));
   tree-sitter-embedded-template = (builtins.fromJSON (builtins.readFile ./tree-sitter-embedded-template.json));
diff --git a/pkgs/development/tools/parsing/tree-sitter/grammars/tree-sitter-comment.json b/pkgs/development/tools/parsing/tree-sitter/grammars/tree-sitter-comment.json
new file mode 100644
index 000000000000..54e275adf6ec
--- /dev/null
+++ b/pkgs/development/tools/parsing/tree-sitter/grammars/tree-sitter-comment.json
@@ -0,0 +1,10 @@
+{
+  "url": "https://github.com/stsewd/tree-sitter-comment",
+  "rev": "894b61d68a31d93c33ed48dcc7f427174b440abe",
+  "date": "2021-04-27T15:25:48-05:00",
+  "path": "/nix/store/w0yz9imzi33glwk6ilm0jqipcyzl8hgm-tree-sitter-comment",
+  "sha256": "1vfayzzcv6lj63pgcxr8f7rcd81jkgnfdlmhs39i7w3m0s6dv1qg",
+  "fetchSubmodules": false,
+  "deepClone": false,
+  "leaveDotGit": false
+}
diff --git a/pkgs/development/tools/parsing/tree-sitter/update.nix b/pkgs/development/tools/parsing/tree-sitter/update.nix
index 55237b298d2a..d3be42cb3307 100644
--- a/pkgs/development/tools/parsing/tree-sitter/update.nix
+++ b/pkgs/development/tools/parsing/tree-sitter/update.nix
@@ -70,6 +70,10 @@ let
   # If you need a grammar that already exists in the official orga,
   # make sure to give it a different name.
   otherGrammars = {
+    "tree-sitter-comment" = {
+      orga = "stsewd";
+      repo = "tree-sitter-comment";
+    };
     "tree-sitter-nix" = {
       orga = "cstrahan";
       repo = "tree-sitter-nix";

From 90b7de20ac46928d14b5f8c3f2b95dc8638f415e Mon Sep 17 00:00:00 2001
From: Tae Sandoval <tssm@users.noreply.github.com>
Date: Sat, 31 Jul 2021 17:49:21 +0200
Subject: [PATCH 11/41] tree-sitter-fish: init at HEAD

---
 .../tools/parsing/tree-sitter/grammars/default.nix     |  1 +
 .../parsing/tree-sitter/grammars/tree-sitter-fish.json | 10 ++++++++++
 pkgs/development/tools/parsing/tree-sitter/update.nix  |  4 ++++
 3 files changed, 15 insertions(+)
 create mode 100644 pkgs/development/tools/parsing/tree-sitter/grammars/tree-sitter-fish.json

diff --git a/pkgs/development/tools/parsing/tree-sitter/grammars/default.nix b/pkgs/development/tools/parsing/tree-sitter/grammars/default.nix
index 2671e4148b1d..2407fd86b1fa 100644
--- a/pkgs/development/tools/parsing/tree-sitter/grammars/default.nix
+++ b/pkgs/development/tools/parsing/tree-sitter/grammars/default.nix
@@ -7,6 +7,7 @@
   tree-sitter-css = (builtins.fromJSON (builtins.readFile ./tree-sitter-css.json));
   tree-sitter-embedded-template = (builtins.fromJSON (builtins.readFile ./tree-sitter-embedded-template.json));
   tree-sitter-fennel = (builtins.fromJSON (builtins.readFile ./tree-sitter-fennel.json));
+  tree-sitter-fish = (builtins.fromJSON (builtins.readFile ./tree-sitter-fish.json));
   tree-sitter-fluent = (builtins.fromJSON (builtins.readFile ./tree-sitter-fluent.json));
   tree-sitter-go = (builtins.fromJSON (builtins.readFile ./tree-sitter-go.json));
   tree-sitter-haskell = (builtins.fromJSON (builtins.readFile ./tree-sitter-haskell.json));
diff --git a/pkgs/development/tools/parsing/tree-sitter/grammars/tree-sitter-fish.json b/pkgs/development/tools/parsing/tree-sitter/grammars/tree-sitter-fish.json
new file mode 100644
index 000000000000..4dc81284db91
--- /dev/null
+++ b/pkgs/development/tools/parsing/tree-sitter/grammars/tree-sitter-fish.json
@@ -0,0 +1,10 @@
+{
+  "url": "https://github.com/ram02z/tree-sitter-fish",
+  "rev": "db7139393e50765520618fa469f41dfbb0b3822b",
+  "date": "2021-07-06T21:05:19+02:00",
+  "path": "/nix/store/k67b4bn67zd3dj9yg0q7jywy3vnkv8gw-tree-sitter-fish",
+  "sha256": "09l5myivlq3z53nqlx8x8c45sww2k7vmjp8z0rvwzv08rnym0fah",
+  "fetchSubmodules": false,
+  "deepClone": false,
+  "leaveDotGit": false
+}
diff --git a/pkgs/development/tools/parsing/tree-sitter/update.nix b/pkgs/development/tools/parsing/tree-sitter/update.nix
index 55237b298d2a..81b7da41642e 100644
--- a/pkgs/development/tools/parsing/tree-sitter/update.nix
+++ b/pkgs/development/tools/parsing/tree-sitter/update.nix
@@ -106,6 +106,10 @@ let
       orga = "GrayJack";
       repo = "tree-sitter-zig";
     };
+    "tree-sitter-fish" = {
+      orga = "ram02z";
+      repo = "tree-sitter-fish";
+    };
   };
 
   allGrammars =

From 2c588e0edde3d439988af84315a845df4f7e2bb0 Mon Sep 17 00:00:00 2001
From: Stefan Frijters <sfrijters@gmail.com>
Date: Mon, 2 Aug 2021 21:19:43 +0200
Subject: [PATCH 12/41] wine{Unstable,Staging}: 6.13 -> 6.14

---
 pkgs/misc/emulators/wine/sources.nix | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/pkgs/misc/emulators/wine/sources.nix b/pkgs/misc/emulators/wine/sources.nix
index 6accb486d57c..7e278684cef4 100644
--- a/pkgs/misc/emulators/wine/sources.nix
+++ b/pkgs/misc/emulators/wine/sources.nix
@@ -44,16 +44,16 @@ in rec {
 
   unstable = fetchurl rec {
     # NOTE: Don't forget to change the SHA256 for staging as well.
-    version = "6.13";
+    version = "6.14";
     url = "https://dl.winehq.org/wine/source/6.x/wine-${version}.tar.xz";
-    sha256 = "sha256-4DohoBHUXSrp8iIED7dpC5cVY3bnQx+GHyAHPq8k8oo=";
+    sha256 = "sha256-ZLRxk5lDvAjjUQJ9tvvCRlwTllCjv/65Flf/DujCUgI=";
     inherit (stable) gecko32 gecko64;
 
     ## see http://wiki.winehq.org/Mono
     mono = fetchurl rec {
-      version = "6.2.0";
+      version = "6.3.0";
       url = "https://dl.winehq.org/wine/wine-mono/${version}/wine-mono-${version}-x86.msi";
-      sha256 = "sha256-zY1TUT2DV7KHama6sIllTvmUH0LvaQ+1VcZJP1OB28o=";
+      sha256 = "sha256-pfAtMqAoNpKkpiX1Qc+7tFGIMShHTFyANiOFMXzQmfA=";
     };
 
     patches = [
@@ -65,7 +65,7 @@ in rec {
   staging = fetchFromGitHub rec {
     # https://github.com/wine-staging/wine-staging/releases
     inherit (unstable) version;
-    sha256 = "sha256-3IpO+eQ/+DiQZH6en5Q/p+j441LDvjn4i9Ex7PY8KCk=";
+    sha256 = "sha256-yzpRWNx/e3BDCh1dyf8VdjLgvu6yZ/CXre/cb1roaVs=";
     owner = "wine-staging";
     repo = "wine-staging";
     rev = "v${version}";

From 579c17d7bcbe500b26cbacaa445608289f32ddd9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebasti=C3=A1n=20Mancilla?= <smancill@smancill.dev>
Date: Sat, 31 Jul 2021 15:29:25 -0400
Subject: [PATCH 13/41] pympress: 1.5.1 -> 1.6.3

This also makes the application ready to work on Darwin (but still not
working until #113777 is fixed).

Version 1.5.1 did not build on Darwin because libcanberra-gtk3 is
broken, and python-vlc is required but only works on Linux.

Version 1.6.x fixed the python-vlc requirement to make it optional, so
now both libcanberra-gtk3 and python-vlc inputs can be made optional,
and enabled by default on Linux. This means that on Darwin there is no
support for media, but it is still better than not having the
application at all.

Unfortunately, until watchdog 2.x is fixed, the Darwin build will be
still broken.

-----

The setup.py file now parses the setuptools version, so it needs to be
patched to fix an error with the 'post0' suffix in the version.

Also, setuptools is needed in propagatedBuildInputs to fix the
`ModuleNotFoundError: No module named 'pkg_resources'` error.
---
 pkgs/applications/office/pympress/default.nix | 24 ++++++++++++++-----
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/pkgs/applications/office/pympress/default.nix b/pkgs/applications/office/pympress/default.nix
index ebc93edba6ef..2a97de6ca5b8 100644
--- a/pkgs/applications/office/pympress/default.nix
+++ b/pkgs/applications/office/pympress/default.nix
@@ -1,21 +1,34 @@
 { lib
+, stdenv
+, fetchpatch
 , python3Packages
 , wrapGAppsHook
 , gtk3
 , gobject-introspection
 , libcanberra-gtk3
 , poppler_gi
+, withGstreamer ? stdenv.isLinux
+, withVLC ? stdenv.isLinux
  }:
 
 python3Packages.buildPythonApplication rec {
   pname = "pympress";
-  version = "1.5.1";
+  version = "1.6.3";
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "173d9scf2z29qg279jf33zcl7sgc3wp662fgpm943bn9667q18wf";
+    sha256 = "sha256-f+OjE0x/3yfJYHCLB+on7TT7MJ2vNu87SHRi67qFDCM=";
   };
 
+  patches = [
+    # Should not be needed once v1.6.4 is released
+    (fetchpatch {
+      name = "fix-setuptools-version-parsing.patch";
+      url = "https://github.com/Cimbali/pympress/commit/474514d71396ac065e210fd846e07ed1139602d0.diff";
+      sha256 = "sha256-eiw54sjMrXrNrhtkAXxiSTatzoA0NDA03L+HpTDax58=";
+    })
+  ];
+
   nativeBuildInputs = [
     wrapGAppsHook
   ];
@@ -23,16 +36,15 @@ python3Packages.buildPythonApplication rec {
   buildInputs = [
     gtk3
     gobject-introspection
-    libcanberra-gtk3
     poppler_gi
-  ];
+  ] ++ lib.optional withGstreamer libcanberra-gtk3;
 
   propagatedBuildInputs = with python3Packages; [
     pycairo
     pygobject3
-    python-vlc
+    setuptools
     watchdog
-  ];
+  ] ++ lib.optional withVLC python-vlc;
 
   doCheck = false; # there are no tests
 

From a1371d3e523a067edb2d0470bc32fa3c594d6535 Mon Sep 17 00:00:00 2001
From: Felix Buehler <account@buehler.rocks>
Date: Tue, 3 Aug 2021 14:02:34 +0200
Subject: [PATCH 14/41] wavrsocvt: remove phases

---
 pkgs/applications/misc/audio/wavrsocvt/default.nix | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pkgs/applications/misc/audio/wavrsocvt/default.nix b/pkgs/applications/misc/audio/wavrsocvt/default.nix
index 3b32f0d7f30b..6b09a2e38d8c 100644
--- a/pkgs/applications/misc/audio/wavrsocvt/default.nix
+++ b/pkgs/applications/misc/audio/wavrsocvt/default.nix
@@ -8,8 +8,6 @@ stdenv.mkDerivation {
     sha256 = "15qlvdfwbiclljj7075ycm78yzqahzrgl4ky8pymix5179acm05h";
   };
 
-  phases = [ "unpackPhase" "installPhase" ];
-
   unpackPhase = ''
     tar -zxf $src
     '';

From 4660bf1d1b450a87aa1ac8b1ddb8d4944a457a11 Mon Sep 17 00:00:00 2001
From: Felix Buehler <account@buehler.rocks>
Date: Tue, 3 Aug 2021 14:02:45 +0200
Subject: [PATCH 15/41] avrdudess: deprecate phases

---
 pkgs/applications/misc/avrdudess/default.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/applications/misc/avrdudess/default.nix b/pkgs/applications/misc/avrdudess/default.nix
index 14b372d91e59..61cab2b6a2a4 100644
--- a/pkgs/applications/misc/avrdudess/default.nix
+++ b/pkgs/applications/misc/avrdudess/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation {
 
   nativeBuildInputs = [ unzip ];
 
-  phases = [ "buildPhase" ];
+  dontUnpack = true;
+  dontInstall = true;
 
   buildPhase = ''
     mkdir -p "$out/avrdudess"

From 9a6357c736071ca5636f9818cfeb29dbbd14077c Mon Sep 17 00:00:00 2001
From: Felix Buehler <account@buehler.rocks>
Date: Tue, 3 Aug 2021 14:03:13 +0200
Subject: [PATCH 16/41] azuredatastudio: deprecate phases

---
 pkgs/applications/misc/azuredatastudio/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/applications/misc/azuredatastudio/default.nix b/pkgs/applications/misc/azuredatastudio/default.nix
index 56894a29a662..fca1ad12fd1c 100644
--- a/pkgs/applications/misc/azuredatastudio/default.nix
+++ b/pkgs/applications/misc/azuredatastudio/default.nix
@@ -38,7 +38,7 @@ stdenv.mkDerivation rec {
     at-spi2-atk
   ];
 
-  phases = "unpackPhase fixupPhase";
+  dontInstall = true;
 
   # change this to azuredatastudio-insiders for insiders releases
   edition = "azuredatastudio";

From 5f6fa38b58a67b47e50152083a87f383ae62a07e Mon Sep 17 00:00:00 2001
From: Felix Buehler <account@buehler.rocks>
Date: Tue, 3 Aug 2021 14:03:30 +0200
Subject: [PATCH 17/41] emem: deprecate phases

---
 pkgs/applications/misc/emem/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/applications/misc/emem/default.nix b/pkgs/applications/misc/emem/default.nix
index ab718cdffcf2..f82ce53d9746 100644
--- a/pkgs/applications/misc/emem/default.nix
+++ b/pkgs/applications/misc/emem/default.nix
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "18x3s3jrph8k3pc75jgwkfqazygpsx93zjxx68zms58my17cybh1";
   };
 
-  phases = [ "buildPhase" "installPhase" ];
+  dontUnpack = true;
 
   buildPhase = ''
     mkdir -p $out/bin $out/share/java

From 2bd399b9daca383bc0501ce6dc7e0347280f245f Mon Sep 17 00:00:00 2001
From: Felix Buehler <account@buehler.rocks>
Date: Tue, 3 Aug 2021 14:03:47 +0200
Subject: [PATCH 18/41] ganttproject-bin: remove phases

---
 pkgs/applications/misc/ganttproject-bin/default.nix | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pkgs/applications/misc/ganttproject-bin/default.nix b/pkgs/applications/misc/ganttproject-bin/default.nix
index 2b4504a1dce2..76a19f5188c8 100644
--- a/pkgs/applications/misc/ganttproject-bin/default.nix
+++ b/pkgs/applications/misc/ganttproject-bin/default.nix
@@ -15,8 +15,6 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ makeWrapper ];
   buildInputs = [ jre ];
 
-  phases = [ "unpackPhase" "installPhase" "fixupPhase" ];
-
   installPhase = let
 
     desktopItem = makeDesktopItem {

From bd52b05ad2c666bcfc73c48b49806fff35e00bb1 Mon Sep 17 00:00:00 2001
From: Felix Buehler <account@buehler.rocks>
Date: Tue, 3 Aug 2021 14:04:03 +0200
Subject: [PATCH 19/41] gollum: deprecate phases

---
 pkgs/applications/misc/gollum/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/applications/misc/gollum/default.nix b/pkgs/applications/misc/gollum/default.nix
index 59bb05f85ced..cc9f9df0c608 100644
--- a/pkgs/applications/misc/gollum/default.nix
+++ b/pkgs/applications/misc/gollum/default.nix
@@ -8,7 +8,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ makeWrapper ];
 
-  phases = [ "installPhase" ];
+  dontUnpack = true;
 
   installPhase = let
     env = bundlerEnv {

From d947fc3f3cb47b7e286d177ec0508491210b393a Mon Sep 17 00:00:00 2001
From: Felix Buehler <account@buehler.rocks>
Date: Tue, 3 Aug 2021 14:04:36 +0200
Subject: [PATCH 20/41] hello-unfree: deprecate phases

---
 pkgs/applications/misc/hello-unfree/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/applications/misc/hello-unfree/default.nix b/pkgs/applications/misc/hello-unfree/default.nix
index 7c54c3201111..5c9a507fc071 100644
--- a/pkgs/applications/misc/hello-unfree/default.nix
+++ b/pkgs/applications/misc/hello-unfree/default.nix
@@ -4,7 +4,7 @@ stdenv.mkDerivation {
   pname = "example-unfree-package";
   version = "1.0";
 
-  phases = [ "installPhase" "fixupPhase" ];
+  dontUnpack = true;
 
   installPhase = ''
     mkdir -p $out/bin

From 91b7879feda05962f6ba914a2f03a81539c7a9f7 Mon Sep 17 00:00:00 2001
From: Felix Buehler <account@buehler.rocks>
Date: Tue, 3 Aug 2021 14:06:02 +0200
Subject: [PATCH 21/41] smos: deprecate phases

---
 pkgs/applications/misc/smos/default.nix | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/misc/smos/default.nix b/pkgs/applications/misc/smos/default.nix
index 7d994a749bd4..aa2f53b5a2c7 100644
--- a/pkgs/applications/misc/smos/default.nix
+++ b/pkgs/applications/misc/smos/default.nix
@@ -4,7 +4,7 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "smos-${version}";
+  pname = "smos";
   version = "0.1.0";
 
   src = fetchurl {
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "sha256:07yavk7xl92yjwwjdig90yq421n8ldv4fjfw7izd4hfpzw849a12";
   };
 
-  phases = [ "unpackPhase" ];
+  dontInstall = true;
+
   unpackCmd = "${unzip}/bin/unzip -d $out $curSrc";
   sourceRoot = ".";
 

From 926fb9396881202e727e5ec1fbf609b64455b388 Mon Sep 17 00:00:00 2001
From: David Arnold <dar@xoe.solutions>
Date: Sun, 6 Jun 2021 12:00:12 -0500
Subject: [PATCH 22/41] nixos/tests/test-driver: normalise test driver
 entrypoint(s)

Previously the driver was configured exclusively through convoluted
environment variables.

Now the driver's defaults are configured through env variables.

Some additional concerns are in the github comments of this PR.
---
 ...nning-nixos-tests-interactively.section.md |  13 +--
 ...ning-nixos-tests-interactively.section.xml |  15 +--
 nixos/lib/test-driver/test-driver.py          | 101 +++++++++++++-----
 nixos/lib/testing-python.nix                  |  23 ++--
 4 files changed, 89 insertions(+), 63 deletions(-)
 mode change 100644 => 100755 nixos/lib/test-driver/test-driver.py

diff --git a/nixos/doc/manual/development/running-nixos-tests-interactively.section.md b/nixos/doc/manual/development/running-nixos-tests-interactively.section.md
index 3ba4e16e77f4..f87298201791 100644
--- a/nixos/doc/manual/development/running-nixos-tests-interactively.section.md
+++ b/nixos/doc/manual/development/running-nixos-tests-interactively.section.md
@@ -5,7 +5,7 @@ when developing or debugging a test:
 
 ```ShellSession
 $ nix-build nixos/tests/login.nix -A driverInteractive
-$ ./result/bin/nixos-test-driver
+$ ./result/bin/nixos-test-driver --interactive
 starting VDE switch for network 1
 >
 ```
@@ -24,20 +24,11 @@ back into the test driver command line upon its completion. This allows
 you to inspect the state of the VMs after the test (e.g. to debug the
 test script).
 
-To just start and experiment with the VMs, run:
-
-```ShellSession
-$ nix-build nixos/tests/login.nix -A driverInteractive
-$ ./result/bin/nixos-run-vms
-```
-
-The script `nixos-run-vms` starts the virtual machines defined by test.
-
 You can re-use the VM states coming from a previous run by setting the
 `--keep-vm-state` flag.
 
 ```ShellSession
-$ ./result/bin/nixos-run-vms --keep-vm-state
+$ ./result/bin/nixos-test-driver --interactive --keep-vm-state
 ```
 
 The machine state is stored in the `$TMPDIR/vm-state-machinename`
diff --git a/nixos/doc/manual/from_md/development/running-nixos-tests-interactively.section.xml b/nixos/doc/manual/from_md/development/running-nixos-tests-interactively.section.xml
index a2030e9c0739..17003cbcbfdc 100644
--- a/nixos/doc/manual/from_md/development/running-nixos-tests-interactively.section.xml
+++ b/nixos/doc/manual/from_md/development/running-nixos-tests-interactively.section.xml
@@ -6,7 +6,7 @@
   </para>
   <programlisting>
 $ nix-build nixos/tests/login.nix -A driverInteractive
-$ ./result/bin/nixos-test-driver
+$ ./result/bin/nixos-test-driver --interactive
 starting VDE switch for network 1
 &gt;
 </programlisting>
@@ -25,23 +25,12 @@ starting VDE switch for network 1
     completion. This allows you to inspect the state of the VMs after
     the test (e.g. to debug the test script).
   </para>
-  <para>
-    To just start and experiment with the VMs, run:
-  </para>
-  <programlisting>
-$ nix-build nixos/tests/login.nix -A driverInteractive
-$ ./result/bin/nixos-run-vms
-</programlisting>
-  <para>
-    The script <literal>nixos-run-vms</literal> starts the virtual
-    machines defined by test.
-  </para>
   <para>
     You can re-use the VM states coming from a previous run by setting
     the <literal>--keep-vm-state</literal> flag.
   </para>
   <programlisting>
-$ ./result/bin/nixos-run-vms --keep-vm-state
+$ ./result/bin/nixos-test-driver --interactive --keep-vm-state
 </programlisting>
   <para>
     The machine state is stored in the
diff --git a/nixos/lib/test-driver/test-driver.py b/nixos/lib/test-driver/test-driver.py
old mode 100644
new mode 100755
index 2a3e4d94b948..1720e553d733
--- a/nixos/lib/test-driver/test-driver.py
+++ b/nixos/lib/test-driver/test-driver.py
@@ -24,7 +24,6 @@ import sys
 import telnetlib
 import tempfile
 import time
-import traceback
 import unicodedata
 
 CHAR_TO_KEY = {
@@ -930,29 +929,16 @@ def join_all() -> None:
             machine.wait_for_shutdown()
 
 
-def test_script() -> None:
-    exec(os.environ["testScript"])
-
-
-def run_tests() -> None:
+def run_tests(interactive: bool = False) -> None:
     global machines
-    tests = os.environ.get("tests", None)
-    if tests is not None:
-        with log.nested("running the VM test script"):
-            try:
-                exec(tests, globals())
-            except Exception as e:
-                eprint("error: ")
-                traceback.print_exc()
-                sys.exit(1)
+    if interactive:
+        ptpython.repl.embed(globals(), locals())
     else:
-        ptpython.repl.embed(locals(), globals())
-
-    # TODO: Collect coverage data
-
-    for machine in machines:
-        if machine.is_up():
-            machine.execute("sync")
+        test_script()
+        # TODO: Collect coverage data
+        for machine in machines:
+            if machine.is_up():
+                machine.execute("sync")
 
 
 def serial_stdout_on() -> None:
@@ -965,6 +951,31 @@ def serial_stdout_off() -> None:
     log._print_serial_logs = False
 
 
+class EnvDefault(argparse.Action):
+    """An argpars Action that takes values from the specified
+    environment variable as the flags default value.
+    """
+
+    def __init__(self, envvar, required=False, default=None, nargs=None, **kwargs):  # type: ignore
+        if not default and envvar:
+            if envvar in os.environ:
+                if nargs is not None and (nargs.isdigit() or nargs in ["*", "+"]):
+                    default = os.environ[envvar].split()
+                else:
+                    default = os.environ[envvar]
+                kwargs["help"] = (
+                    kwargs["help"] + f" (default from environment: {default})"
+                )
+        if required and default:
+            required = False
+        super(EnvDefault, self).__init__(
+            default=default, required=required, nargs=nargs, **kwargs
+        )
+
+    def __call__(self, parser, namespace, values, option_string=None):  # type: ignore
+        setattr(namespace, self.dest, values)
+
+
 @contextmanager
 def subtest(name: str) -> Iterator[None]:
     with log.nested(name):
@@ -986,18 +997,52 @@ if __name__ == "__main__":
         help="re-use a VM state coming from a previous run",
         action="store_true",
     )
-    (cli_args, vm_scripts) = arg_parser.parse_known_args()
+    arg_parser.add_argument(
+        "-I",
+        "--interactive",
+        help="drop into a python repl and run the tests interactively",
+        action="store_true",
+    )
+    arg_parser.add_argument(
+        "--start-scripts",
+        metavar="START-SCRIPT",
+        action=EnvDefault,
+        envvar="startScripts",
+        nargs="*",
+        help="start scripts for participating virtual machines",
+    )
+    arg_parser.add_argument(
+        "--vlans",
+        metavar="VLAN",
+        action=EnvDefault,
+        envvar="vlans",
+        nargs="*",
+        help="vlans to span by the driver",
+    )
+    arg_parser.add_argument(
+        "testscript",
+        action=EnvDefault,
+        envvar="testScript",
+        help="the test script to run",
+        type=pathlib.Path,
+    )
+
+    args = arg_parser.parse_args()
+    global test_script
+
+    def test_script() -> None:
+        with log.nested("running the VM test script"):
+            exec(pathlib.Path(args.testscript).read_text(), globals())
 
     log = Logger()
 
-    vlan_nrs = list(dict.fromkeys(os.environ.get("VLANS", "").split()))
-    vde_sockets = [create_vlan(v) for v in vlan_nrs]
+    vde_sockets = [create_vlan(v) for v in args.vlans]
     for nr, vde_socket, _, _ in vde_sockets:
         os.environ["QEMU_VDE_SOCKET_{}".format(nr)] = vde_socket
 
     machines = [
-        create_machine({"startCommand": s, "keepVmState": cli_args.keep_vm_state})
-        for s in vm_scripts
+        create_machine({"startCommand": s, "keepVmState": args.keep_vm_state})
+        for s in args.start_scripts
     ]
     machine_eval = [
         "{0} = machines[{1}]".format(m.name, idx) for idx, m in enumerate(machines)
@@ -1017,6 +1062,6 @@ if __name__ == "__main__":
         log.close()
 
     tic = time.time()
-    run_tests()
+    run_tests(args.interactive)
     toc = time.time()
     print("test script finished in {:.2f}s".format(toc - tic))
diff --git a/nixos/lib/testing-python.nix b/nixos/lib/testing-python.nix
index 768f1dc2a170..87a30f7f8b72 100644
--- a/nixos/lib/testing-python.nix
+++ b/nixos/lib/testing-python.nix
@@ -83,7 +83,10 @@ rec {
         ''
           mkdir -p $out
 
-          LOGFILE=/dev/null tests='exec(os.environ["testScript"])' ${driver}/bin/nixos-test-driver
+          # effectively mute the XMLLogger
+          export LOGFILE=/dev/null
+
+          ${driver}/bin/nixos-test-driver
         '';
 
       passthru = driver.passthru // {
@@ -161,7 +164,10 @@ rec {
       ''
         mkdir -p $out/bin
 
+        vmStartScripts=($(for i in ${toString vms}; do echo $i/bin/run-*-vm; done))
         echo -n "$testScript" > $out/test-script
+        ln -s ${testDriver}/bin/nixos-test-driver $out/bin/nixos-test-driver
+
         ${lib.optionalString (!skipLint) ''
           PYFLAKES_BUILTINS="$(
             echo -n ${lib.escapeShellArg (lib.concatStringsSep "," nodeHostNames)},
@@ -169,17 +175,12 @@ rec {
           )" ${python3Packages.pyflakes}/bin/pyflakes $out/test-script
         ''}
 
-        ln -s ${testDriver}/bin/nixos-test-driver $out/bin/
-        vms=($(for i in ${toString vms}; do echo $i/bin/run-*-vm; done))
+        # set defaults through environment
+        # see: ./test-driver/test-driver.py argparse implementation
         wrapProgram $out/bin/nixos-test-driver \
-          --add-flags "''${vms[*]}" \
-          --run "export testScript=\"\$(${coreutils}/bin/cat $out/test-script)\"" \
-          --set VLANS '${toString vlans}'
-        ln -s ${testDriver}/bin/nixos-test-driver $out/bin/nixos-run-vms
-        wrapProgram $out/bin/nixos-run-vms \
-          --add-flags "''${vms[*]}" \
-          --set tests 'start_all(); join_all();' \
-          --set VLANS '${toString vlans}'
+          --set startScripts "''${vmStartScripts[*]}" \
+          --set testScript "$out/test-script" \
+          --set vlans '${toString vlans}'
       '');
 
   # Make a full-blown test

From 303f9b6b4421f3cfcb20f77c1a0f7b11f32a9454 Mon Sep 17 00:00:00 2001
From: Atkins Chang <atkinschang@gmail.com>
Date: Fri, 6 Aug 2021 22:09:02 +0800
Subject: [PATCH 23/41] kind: patch for correct kernal module path

Signed-off-by: Atkins Chang <atkinschang@gmail.com>
---
 pkgs/development/tools/kind/default.nix       |  5 ++
 .../tools/kind/kernel-module-path.patch       | 47 +++++++++++++++++++
 2 files changed, 52 insertions(+)
 create mode 100644 pkgs/development/tools/kind/kernel-module-path.patch

diff --git a/pkgs/development/tools/kind/default.nix b/pkgs/development/tools/kind/default.nix
index 88bc30943c38..e667238b9b09 100644
--- a/pkgs/development/tools/kind/default.nix
+++ b/pkgs/development/tools/kind/default.nix
@@ -13,6 +13,11 @@ buildGoModule rec {
     sha256 = "sha256-pjg52ONseKNw06EOBzD6Elge+Cz+C3llPvjJPHkn1cw=";
   };
 
+  patches = [
+    # fix kernel module path used by kind
+    ./kernel-module-path.patch
+  ];
+
   vendorSha256 = "sha256-HiVdekSZrC/RkMSvcwm1mv6AE4bA5kayUsMdVCbckiE=";
 
   doCheck = false;
diff --git a/pkgs/development/tools/kind/kernel-module-path.patch b/pkgs/development/tools/kind/kernel-module-path.patch
new file mode 100644
index 000000000000..833cd3388ec2
--- /dev/null
+++ b/pkgs/development/tools/kind/kernel-module-path.patch
@@ -0,0 +1,47 @@
+diff --git a/pkg/cluster/internal/providers/common/getmodules.go b/pkg/cluster/internal/providers/common/getmodules.go
+new file mode 100644
+index 00000000..f42a883d
+--- /dev/null
++++ b/pkg/cluster/internal/providers/common/getmodules.go
+@@ -0,0 +1,15 @@
++package common
++
++import "os"
++
++const (
++	fhsKernalModulePath = "/lib/modules"
++	nixKernalModulePath = "/run/booted-system/kernel-modules/lib"
++)
++
++func GetKernelModulePath() string {
++	if _, err := os.Stat(nixKernalModulePath); !os.IsNotExist(err) {
++		return nixKernalModulePath
++	}
++	return fhsKernalModulePath
++}
+diff --git a/pkg/cluster/internal/providers/docker/provision.go b/pkg/cluster/internal/providers/docker/provision.go
+index 50161861..86d5b7b6 100644
+--- a/pkg/cluster/internal/providers/docker/provision.go
++++ b/pkg/cluster/internal/providers/docker/provision.go
+@@ -242,7 +242,7 @@ func runArgsForNode(node *config.Node, clusterIPFamily config.ClusterIPFamily, n
+ 		// (please don't depend on doing this though!)
+ 		"--volume", "/var",
+ 		// some k8s things want to read /lib/modules
+-		"--volume", "/lib/modules:/lib/modules:ro",
++		"--volume", fmt.Sprintf("%s:/lib/modules:ro", common.GetKernelModulePath()),
+ 	},
+ 		args...,
+ 	)
+diff --git a/pkg/cluster/internal/providers/podman/provision.go b/pkg/cluster/internal/providers/podman/provision.go
+index 51dce486..3bc36b42 100644
+--- a/pkg/cluster/internal/providers/podman/provision.go
++++ b/pkg/cluster/internal/providers/podman/provision.go
+@@ -205,7 +205,7 @@ func runArgsForNode(node *config.Node, clusterIPFamily config.ClusterIPFamily, n
+ 		// dev: devices on the volume will be able to be used by processes within the container
+ 		"--volume", fmt.Sprintf("%s:/var:suid,exec,dev", varVolume),
+ 		// some k8s things want to read /lib/modules
+-		"--volume", "/lib/modules:/lib/modules:ro",
++		"--volume", fmt.Sprintf("%s:/lib/modules:ro", common.GetKernelModulePath()),
+ 	},
+ 		args...,
+ 	)

From fceabc3a388456634a3bd690daa03c5e564402d5 Mon Sep 17 00:00:00 2001
From: Jan Tojnar <jtojnar@gmail.com>
Date: Thu, 5 Aug 2021 19:18:55 +0200
Subject: [PATCH 24/41] =?UTF-8?q?teensy-loader-cli:=202.1.20191110=20?=
 =?UTF-8?q?=E2=86=92=202.1+unstable=3D2021-04-10?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Add support for Teensy 4.1.

Also clean the expression up a bit.
---
 .../tools/misc/teensy-loader-cli/default.nix  | 29 ++++++++++++++-----
 1 file changed, 22 insertions(+), 7 deletions(-)

diff --git a/pkgs/development/tools/misc/teensy-loader-cli/default.nix b/pkgs/development/tools/misc/teensy-loader-cli/default.nix
index 156e3f7f895d..ccae93770249 100644
--- a/pkgs/development/tools/misc/teensy-loader-cli/default.nix
+++ b/pkgs/development/tools/misc/teensy-loader-cli/default.nix
@@ -1,31 +1,46 @@
-{ lib, stdenv, fetchFromGitHub, go-md2man, installShellFiles, libusb-compat-0_1 }:
+{ stdenv
+, lib
+, fetchFromGitHub
+, go-md2man
+, installShellFiles
+, libusb-compat-0_1
+}:
 
 stdenv.mkDerivation rec {
   pname = "teensy-loader-cli";
-  version = "2.1.20191110";
+  version = "2.1+unstable=2021-04-10";
 
   src = fetchFromGitHub {
     owner = "PaulStoffregen";
     repo = "teensy_loader_cli";
-    rev = "e98b5065cdb9f04aa4dde3f2e6e6e6f12dd97592";
-    sha256 = "1yx8vsh6b29pqr4zb6sx47429i9x51hj9psn8zksfz75j5ivfd5i";
+    rev = "9dbbfa3b367b6c37e91e8a42dae3c6edfceccc4d";
+    sha256 = "lQ1XtaWPr6nvE8NArD1980QVOH6NggO3FlfsntUjY7s=";
   };
 
-  buildInputs = [ libusb-compat-0_1 ];
+  nativeBuildInputs = [
+    go-md2man
+    installShellFiles
+  ];
 
-  nativeBuildInputs = [ go-md2man installShellFiles ];
+  buildInputs = [
+    libusb-compat-0_1
+  ];
 
   installPhase = ''
+    runHook preInstall
+
     install -Dm555 teensy_loader_cli $out/bin/teensy-loader-cli
     install -Dm444 -t $out/share/doc/${pname} *.md *.txt
     go-md2man -in README.md -out ${pname}.1
     installManPage *.1
+
+    runHook postInstall
   '';
 
   meta = with lib; {
     description = "Firmware uploader for the Teensy microcontroller boards";
     homepage = "https://www.pjrc.com/teensy/";
-    license = licenses.gpl3;
+    license = licenses.gpl3Only;
     platforms = platforms.unix;
   };
 }

From 74f86bdb64ec8836f091500ccf26057930521c55 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Lafuente?= <jl@lafuente.me>
Date: Fri, 6 Aug 2021 20:18:49 +0200
Subject: [PATCH 25/41] clojure: 1.10.3.933 expects tools.edn

That's required to use the new -T switch
---
 pkgs/development/interpreters/clojure/default.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/interpreters/clojure/default.nix b/pkgs/development/interpreters/clojure/default.nix
index 77ec74e8c3f5..3fca18f65a6e 100644
--- a/pkgs/development/interpreters/clojure/default.nix
+++ b/pkgs/development/interpreters/clojure/default.nix
@@ -29,6 +29,7 @@ stdenv.mkDerivation rec {
       echo "Installing libs into $clojure_lib_dir"
       install -Dm644 deps.edn "$clojure_lib_dir/deps.edn"
       install -Dm644 example-deps.edn "$clojure_lib_dir/example-deps.edn"
+      install -Dm644 tools.edn "$clojure_lib_dir/tools.edn"
       install -Dm644 exec.jar "$clojure_lib_dir/libexec/exec.jar"
       install -Dm644 clojure-tools-${version}.jar "$clojure_lib_dir/libexec/clojure-tools-${version}.jar"
 
@@ -48,7 +49,7 @@ stdenv.mkDerivation rec {
 
   doInstallCheck = true;
   installCheckPhase = ''
-    CLJ_CONFIG=$out CLJ_CACHE=$out/libexec $out/bin/clojure \
+    CLJ_CONFIG=$TMPDIR CLJ_CACHE=$TMPDIR/.clj_cache $out/bin/clojure \
       -Spath \
       -Sverbose \
       -Scp $out/libexec/clojure-tools-${version}.jar

From 240cf37b505554ba7466993b7b11682ad2dcec74 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sandro=20J=C3=A4ckel?= <sandro.jaeckel@gmail.com>
Date: Sun, 8 Aug 2021 06:44:13 +0200
Subject: [PATCH 26/41] python39Packages.awslambdaric: move depedency patching
 to right phase

---
 pkgs/development/python-modules/awslambdaric/default.nix | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/awslambdaric/default.nix b/pkgs/development/python-modules/awslambdaric/default.nix
index 6bb6702b1e2b..f5d282ac0ee1 100644
--- a/pkgs/development/python-modules/awslambdaric/default.nix
+++ b/pkgs/development/python-modules/awslambdaric/default.nix
@@ -13,6 +13,11 @@ buildPythonPackage rec {
     sha256 = "120qar8iaxj6dmnhjw1c40n2w06f1nyxy57dwh06xdiany698fg4";
   };
 
+  postPatch = ''
+    substituteInPlace requirements/base.txt \
+      --replace 'simplejson==3' 'simplejson~=3'
+  '';
+
   propagatedBuildInputs = [ simplejson ];
 
   nativeBuildInputs = [ autoconf automake cmake libtool perl ];
@@ -21,10 +26,6 @@ buildPythonPackage rec {
 
   dontUseCmakeConfigure = true;
 
-  preBuild = ''
-    substituteInPlace requirements/base.txt --replace 'simplejson==3' 'simplejson~=3'
-  '';
-
   checkInputs = [ pytestCheckHook ];
 
   pythonImportsCheck = [ "awslambdaric" "runtime_client" ];

From 90832a038710a2d925626a4f5230f5ccbead89c5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sandro=20J=C3=A4ckel?= <sandro.jaeckel@gmail.com>
Date: Sun, 8 Aug 2021 06:50:00 +0200
Subject: [PATCH 27/41] python39Packages.xml-marshaller: add pythonImportsCheck

---
 pkgs/development/python-modules/xml-marshaller/default.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/python-modules/xml-marshaller/default.nix b/pkgs/development/python-modules/xml-marshaller/default.nix
index 748b68756208..30300c61045d 100644
--- a/pkgs/development/python-modules/xml-marshaller/default.nix
+++ b/pkgs/development/python-modules/xml-marshaller/default.nix
@@ -10,13 +10,15 @@ buildPythonPackage rec {
   version = "1.0.2";
 
   src = fetchPypi {
-    inherit version;
     pname = "xml_marshaller";
+    inherit version;
     sha256 = "sha256-QvBALLDD8o5nZQ5Z4bembhadK6jcydWKQpJaSmGqqJM=";
   };
 
   propagatedBuildInputs = [ lxml six ];
 
+  pythonImportsCheck = [ "xml_marshaller" ];
+
   meta = with lib; {
     description = "This module allows one to marshal simple Python data types into a custom XML format.";
     homepage = "https://www.python.org/community/sigs/current/xml-sig/";

From 23615cdd9e1a794f7824a925e493be951da3ca85 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Sat, 7 Aug 2021 21:31:18 -0400
Subject: [PATCH 28/41] python3Packages.threadpoolctl: 2.1.0 -> 2.2.0

---
 pkgs/development/python-modules/threadpoolctl/default.nix | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/threadpoolctl/default.nix b/pkgs/development/python-modules/threadpoolctl/default.nix
index 20fad7c18a0a..7ba82aaec296 100644
--- a/pkgs/development/python-modules/threadpoolctl/default.nix
+++ b/pkgs/development/python-modules/threadpoolctl/default.nix
@@ -4,14 +4,13 @@
 , fetchFromGitHub
 , flit
 , pytestCheckHook
-, pytest-cov
 , numpy
 , scipy
 }:
 
 buildPythonPackage rec {
   pname = "threadpoolctl";
-  version = "2.1.0";
+  version = "2.2.0";
 
   disabled = isPy27;
   format = "flit";
@@ -20,10 +19,10 @@ buildPythonPackage rec {
     owner = "joblib";
     repo = pname;
     rev = version;
-    sha256 = "0sl6mp3b2gb0dvqkhnkmrp2g3r5c7clyyyxzq44xih6sw1pgx9df";
+    sha256 = "7UUjbX1IpXtUAgN48Db43Zr1u360UETSUnIHD6rQRLs=";
   };
 
-  checkInputs = [ pytestCheckHook pytest-cov numpy scipy ];
+  checkInputs = [ pytestCheckHook numpy scipy ];
 
   meta = with lib; {
     homepage = "https://github.com/joblib/threadpoolctl";

From 90fcd8e7a948601a7a9c9d5b752aa40bfb5fbec1 Mon Sep 17 00:00:00 2001
From: Atkins Chang <atkinschang@gmail.com>
Date: Sun, 11 Aug 2019 06:30:01 +0800
Subject: [PATCH 29/41] vistafonts-cht: init

Signed-off-by: Atkins Chang <atkinschang@gmail.com>
---
 pkgs/data/fonts/vista-fonts-cht/default.nix | 41 +++++++++++++++++++++
 pkgs/data/fonts/vista-fonts-cht/no-op.conf  |  9 +++++
 pkgs/top-level/all-packages.nix             |  2 +
 3 files changed, 52 insertions(+)
 create mode 100644 pkgs/data/fonts/vista-fonts-cht/default.nix
 create mode 100644 pkgs/data/fonts/vista-fonts-cht/no-op.conf

diff --git a/pkgs/data/fonts/vista-fonts-cht/default.nix b/pkgs/data/fonts/vista-fonts-cht/default.nix
new file mode 100644
index 000000000000..264d5a41bf48
--- /dev/null
+++ b/pkgs/data/fonts/vista-fonts-cht/default.nix
@@ -0,0 +1,41 @@
+{ lib, stdenvNoCC, fetchurl, cabextract }:
+
+stdenvNoCC.mkDerivation {
+  pname = "vista-fonts-cht";
+  version = "1";
+
+  src = fetchurl {
+    url = https://download.microsoft.com/download/7/6/b/76bd7a77-be02-47f3-8472-fa1de7eda62f/VistaFont_CHT.EXE;
+    sha256 = "sha256-fSnbbxlMPzbhFSQyKxQaS5paiWji8njK7tS8Eppsj6g=";
+  };
+
+  nativeBuildInputs = [ cabextract ];
+
+  unpackPhase = ''
+    cabextract --lowercase --filter '*.TTF' $src
+  '';
+
+  installPhase = ''
+    mkdir -p $out/share/fonts/truetype
+    cp *.ttf $out/share/fonts/truetype
+
+    # Set up no-op font configs to override any aliases set up by
+    # other packages.
+    mkdir -p $out/etc/fonts/conf.d
+    substitute ${./no-op.conf} $out/etc/fonts/conf.d/30-msjhenghei.conf \
+      --subst-var-by fontname "Microsoft JhengHei"
+  '';
+
+
+  meta = with lib; {
+    description = "TrueType fonts from Microsoft Windows Vista For Traditional Chinese (Microsoft JhengHei)";
+    homepage = "https://www.microsoft.com/typography/fonts/family.aspx";
+    license = licenses.unfree;
+    maintainers = with maintainers; [ atkinschang ];
+
+    # Set a non-zero priority to allow easy overriding of the
+    # fontconfig configuration files.
+    priority = 5;
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/data/fonts/vista-fonts-cht/no-op.conf b/pkgs/data/fonts/vista-fonts-cht/no-op.conf
new file mode 100644
index 000000000000..3f8a9b9b5444
--- /dev/null
+++ b/pkgs/data/fonts/vista-fonts-cht/no-op.conf
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE fontconfig SYSTEM "urn:fontconfig:fonts.dtd">
+<fontconfig>
+  <!-- This configuation is intentionally left empty in order to
+       override any other font package that may wish to set up an
+       alias for the Microsoft @fontname@ font. If you actually do
+       want to have the alias then please change the priority of that
+       package; see the Nix manual page for nix-env for details. -->
+</fontconfig>
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 6410e89a1bee..2a6164271ae8 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -23120,6 +23120,8 @@ in
 
   vistafonts-chs = callPackage ../data/fonts/vista-fonts-chs { };
 
+  vistafonts-cht = callPackage ../data/fonts/vista-fonts-cht { };
+
   vollkorn = callPackage ../data/fonts/vollkorn { };
 
   weather-icons = callPackage ../data/fonts/weather-icons { };

From 0429b202a32022f1626b08f00aaca9d3c31c03a6 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Sun, 8 Aug 2021 02:10:36 -0400
Subject: [PATCH 30/41] python3Packages.ignite: 0.4.5 -> 0.4.6

---
 pkgs/development/python-modules/ignite/default.nix | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/ignite/default.nix b/pkgs/development/python-modules/ignite/default.nix
index 72a607505cdc..177fd8915607 100644
--- a/pkgs/development/python-modules/ignite/default.nix
+++ b/pkgs/development/python-modules/ignite/default.nix
@@ -3,6 +3,7 @@
 , fetchFromGitHub
 , pytestCheckHook
 , pytest-xdist
+, torchvision
 , pythonOlder
 , matplotlib
 , mock
@@ -14,16 +15,16 @@
 
 buildPythonPackage rec {
   pname = "ignite";
-  version = "0.4.5";
+  version = "0.4.6";
 
   src = fetchFromGitHub {
     owner = "pytorch";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-FGFpaqq7InwRqFmQTmXGpJEjRUB69ZN/l20l42L2BAA=";
+    sha256 = "sha256-dlKGXjUUnyYmPDilo0LQg9OkSkBnMYNgzlFLIfI0T6I=";
   };
 
-  checkInputs = [ pytestCheckHook matplotlib mock pytest-xdist ];
+  checkInputs = [ pytestCheckHook matplotlib mock pytest-xdist torchvision ];
   propagatedBuildInputs = [ pytorch scikit-learn tqdm pynvml ];
 
   # runs succesfully in 3.9, however, async isn't correctly closed so it will fail after test suite.
@@ -38,6 +39,7 @@ buildPythonPackage rec {
     "--ignore=tests/ignite/contrib/handlers/test_trains_logger.py"
     "--ignore=tests/ignite/metrics/nlp/test_bleu.py"
     "--ignore=tests/ignite/metrics/nlp/test_rouge.py"
+    "--ignore=tests/ignite/metrics/gan" # requires pytorch_fid; tries to download model to $HOME
     "--ignore=tests/ignite/metrics/test_dill.py"
     "--ignore=tests/ignite/metrics/test_psnr.py"
     "--ignore=tests/ignite/metrics/test_ssim.py"

From 79031751b9586a9b74c773d06148f82904a45c57 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Sun, 8 Aug 2021 02:22:19 -0400
Subject: [PATCH 31/41] python3Packages.pynvml: 8.0.4 -> 11.0.0

---
 pkgs/development/python-modules/pynvml/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/pynvml/default.nix b/pkgs/development/python-modules/pynvml/default.nix
index 75d8056fa557..59698fa18767 100644
--- a/pkgs/development/python-modules/pynvml/default.nix
+++ b/pkgs/development/python-modules/pynvml/default.nix
@@ -7,12 +7,12 @@
 
 buildPythonPackage rec {
   pname = "pynvml";
-  version = "8.0.4";
+  version = "11.0.0";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0pfykj1amqh1rixp90rg85v1nj6qmx89fahqr6ii4zlcckffmm68";
+    sha256 = "sha256-1fxKItNVtAw0HWugqoiKLU0iUxd9JDkA+EAbfmyssbs=";
   };
 
   propagatedBuildInputs = [ cudatoolkit ];

From 3015c82ecad73712579db990c2878980db72b1dd Mon Sep 17 00:00:00 2001
From: Angus Trau <me@angus.ws>
Date: Sun, 8 Aug 2021 16:54:17 +1000
Subject: [PATCH 32/41] etcher: fix desktop file

---
 pkgs/tools/misc/etcher/default.nix | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pkgs/tools/misc/etcher/default.nix b/pkgs/tools/misc/etcher/default.nix
index d0fae336d9d3..6834179cfe9a 100644
--- a/pkgs/tools/misc/etcher/default.nix
+++ b/pkgs/tools/misc/etcher/default.nix
@@ -59,6 +59,9 @@ stdenv.mkDerivation rec {
     cp -a usr/share/* $out/share
     cp -a opt/balenaEtcher/{locales,resources} $out/share/${pname}
 
+    substituteInPlace $out/share/applications/balena-etcher-electron.desktop \
+      --replace /opt/balenaEtcher/balena-etcher-electron ${pname}
+
     runHook postInstall
   '';
 

From 9ec3ed91b88835db42d14b0df69e6d1a2a105349 Mon Sep 17 00:00:00 2001
From: Vladyslav M <dywedir@gra.red>
Date: Sun, 8 Aug 2021 10:03:03 +0300
Subject: [PATCH 33/41] mdbook: 0.4.10 -> 0.4.12

---
 pkgs/tools/text/mdbook/default.nix | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/pkgs/tools/text/mdbook/default.nix b/pkgs/tools/text/mdbook/default.nix
index 29007dd1282d..d3a136d6bf75 100644
--- a/pkgs/tools/text/mdbook/default.nix
+++ b/pkgs/tools/text/mdbook/default.nix
@@ -2,22 +2,22 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "mdbook";
-  version = "0.4.10";
+  version = "0.4.12";
 
   src = fetchFromGitHub {
-    owner = "rust-lang-nursery";
+    owner = "rust-lang";
     repo = "mdBook";
     rev = "v${version}";
-    sha256 = "sha256-1Ddy/kb2Q7P+tzyEr3EC3qWm6MGSsDL3/vnPJLAm/J0=";
+    sha256 = "sha256-2lxotwL3Dc9jRA12iKO5zotO80pa+RfUZucyDRgFOsI=";
   };
 
-  cargoSha256 = "sha256-x2BwnvEwTqz378aDE7OHWuEwNEsUnRudLq7sUJjHRpA=";
+  cargoSha256 = "sha256-TNd4pj4qSKgmmVtSCSKFCxNtv96xD7+24BPsLXPgiEI=";
 
   buildInputs = lib.optionals stdenv.isDarwin [ CoreServices ];
 
   meta = with lib; {
     description = "Create books from MarkDown";
-    homepage = "https://github.com/rust-lang-nursery/mdbook";
+    homepage = "https://github.com/rust-lang/mdBook";
     license = [ licenses.mpl20 ];
     maintainers = [ maintainers.havvy ];
   };

From e1012bc6f1ed0a9ad7b99d9fa9d7f8187e8530a2 Mon Sep 17 00:00:00 2001
From: Kid <44045911+kidonng@users.noreply.github.com>
Date: Sun, 8 Aug 2021 16:53:43 +0800
Subject: [PATCH 34/41] yarn: 1.22.10 -> 1.22.11

---
 pkgs/development/tools/yarn/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/tools/yarn/default.nix b/pkgs/development/tools/yarn/default.nix
index 1868bdaf2c32..10012e552ced 100644
--- a/pkgs/development/tools/yarn/default.nix
+++ b/pkgs/development/tools/yarn/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "yarn";
-  version = "1.22.10";
+  version = "1.22.11";
 
   src = fetchzip {
     url = "https://github.com/yarnpkg/yarn/releases/download/v${version}/yarn-v${version}.tar.gz";
-    sha256 = "0pdimll8lhsnqfafhdaxd6h6mgxhj1c7h56r111cmxhzw462y3mr";
+    sha256 = "0gmk46b9gd6q0zi3a2adgf8c1y05c2lf34k5wrw7alnlwy8iqvvp";
   };
 
   buildInputs = [ nodejs ];

From 90d14641289b1d18c9919bef32afd84472231efc Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Sun, 8 Aug 2021 09:07:28 +0000
Subject: [PATCH 35/41] cloudflared: 2021.7.4 -> 2021.8.1

---
 pkgs/applications/networking/cloudflared/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/networking/cloudflared/default.nix b/pkgs/applications/networking/cloudflared/default.nix
index 9026738133b0..61e2063f2cb2 100644
--- a/pkgs/applications/networking/cloudflared/default.nix
+++ b/pkgs/applications/networking/cloudflared/default.nix
@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "cloudflared";
-  version = "2021.7.4";
+  version = "2021.8.1";
 
   src = fetchFromGitHub {
     owner  = "cloudflare";
     repo   = "cloudflared";
     rev    = version;
-    sha256 = "sha256-3HK7QLUhU6MUayRYec4LP2BfbwEsvtjtCf++o1cQsQw=";
+    sha256 = "sha256-92Uq7hSqfsiES6dSCw4cotfLJ8TLRRO6QPkwQ8iv124=";
   };
 
   vendorSha256 = null;

From 9ccb5859fba07e105931c9527f059ada0ca6fdea Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Sun, 8 Aug 2021 10:05:40 +0000
Subject: [PATCH 36/41] dnsproxy: 0.39.1 -> 0.39.2

---
 pkgs/tools/networking/dnsproxy/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/networking/dnsproxy/default.nix b/pkgs/tools/networking/dnsproxy/default.nix
index 7a49af85d39d..3debf67f81a9 100644
--- a/pkgs/tools/networking/dnsproxy/default.nix
+++ b/pkgs/tools/networking/dnsproxy/default.nix
@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "dnsproxy";
-  version = "0.39.1";
+  version = "0.39.2";
 
   src = fetchFromGitHub {
     owner = "AdguardTeam";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-3ixWiY7gJaavJw3WuK3aTYE6lb328VgWSPCuf5PN8Ds=";
+    sha256 = "sha256-FuPNWoLsqPvz4J+ymfEKBjPmLlxwDUp/196REDnGPmQ=";
   };
 
   vendorSha256 = null;

From cc3a5e1e45c15221431cb1a16ce84bef1fb1eaee Mon Sep 17 00:00:00 2001
From: Alyssa Ross <hi@alyssa.is>
Date: Sun, 25 Jul 2021 11:28:20 +0000
Subject: [PATCH 37/41] pantheon.granite: propagate dependencies

All of these dependencies are pkg-config Requires, so dependent
packages have to depend on all of them, or they'll get messages like
this:

meson.build:17:0: ERROR: Could not generate cargs for granite:
Package gee-0.8 was not found in the pkg-config search path.
Perhaps you should add the directory containing `gee-0.8.pc'
to the PKG_CONFIG_PATH environment variable
Package 'gee-0.8', required by 'granite', not found

Hence, they should be propagated.
---
 pkgs/desktops/pantheon/granite/default.nix | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/pkgs/desktops/pantheon/granite/default.nix b/pkgs/desktops/pantheon/granite/default.nix
index 2397dd8ffcf5..7f3a6dc0983e 100644
--- a/pkgs/desktops/pantheon/granite/default.nix
+++ b/pkgs/desktops/pantheon/granite/default.nix
@@ -46,16 +46,13 @@ stdenv.mkDerivation rec {
     wrapGAppsHook
   ];
 
-  buildInputs = [
+  propagatedBuildInputs = [
     glib
+    gsettings-desktop-schemas # is_clock_format_12h uses "org.gnome.desktop.interface clock-format"
     gtk3
     libgee
   ];
 
-  propagatedBuildInputs = [
-    gsettings-desktop-schemas # is_clock_format_12h uses "org.gnome.desktop.interface clock-format"
-  ];
-
   postPatch = ''
     chmod +x meson/post_install.py
     patchShebangs meson/post_install.py

From fbaa499c62958e5576ec81a04b7e233c15333b30 Mon Sep 17 00:00:00 2001
From: Alyssa Ross <hi@alyssa.is>
Date: Sun, 25 Jul 2021 11:30:44 +0000
Subject: [PATCH 38/41] cozy: 0.7.2 -> 1.0.3

---
 pkgs/applications/audio/cozy-audiobooks/default.nix | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/pkgs/applications/audio/cozy-audiobooks/default.nix b/pkgs/applications/audio/cozy-audiobooks/default.nix
index 5eb71cbe04f3..88ac8002140e 100644
--- a/pkgs/applications/audio/cozy-audiobooks/default.nix
+++ b/pkgs/applications/audio/cozy-audiobooks/default.nix
@@ -8,11 +8,13 @@
 , gtk3
 , gst_all_1
 , gobject-introspection
+, libhandy
 , python3Packages
 , file
 , cairo
 , gettext
 , gnome
+, pantheon
 }:
 
 python3Packages.buildPythonApplication rec {
@@ -20,7 +22,7 @@ python3Packages.buildPythonApplication rec {
   format = "other"; # no setup.py
 
   pname = "cozy";
-  version = "0.7.2";
+  version = "1.0.3";
 
   # Temporary fix
   # See https://github.com/NixOS/nixpkgs/issues/57029
@@ -31,7 +33,7 @@ python3Packages.buildPythonApplication rec {
     owner = "geigi";
     repo = pname;
     rev = version;
-    sha256 = "0fmbddi4ga0bppwg3rm3yjmf7jgqc6zfslmavnr1pglbzkjhy9fs";
+    sha256 = "0m0xiqpb87pwr3fhy0a4qxg67yjhwchcxj3x2anyy0li4inryxag";
   };
 
   nativeBuildInputs = [
@@ -47,6 +49,8 @@ python3Packages.buildPythonApplication rec {
     cairo
     gettext
     gnome.adwaita-icon-theme
+    libhandy
+    pantheon.granite
   ] ++ (with gst_all_1; [
     gstreamer
     gst-plugins-good
@@ -70,8 +74,7 @@ python3Packages.buildPythonApplication rec {
   ];
 
   postPatch = ''
-    chmod +x meson/post_install.py
-    patchShebangs meson/post_install.py
+    patchShebangs meson/*.py
   '';
 
   postInstall = ''

From 3d59c44dfda83b00b57f047e35cd67fe2b37ea2c Mon Sep 17 00:00:00 2001
From: misuzu <bakalolka@gmail.com>
Date: Sun, 8 Aug 2021 13:16:12 +0300
Subject: [PATCH 39/41] nix-simple-deploy: 0.1.1 -> 0.2.1 (#133104)

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
---
 .../nix-simple-deploy/default.nix                | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/pkgs/tools/package-management/nix-simple-deploy/default.nix b/pkgs/tools/package-management/nix-simple-deploy/default.nix
index 75f47d35ce2c..bd16ecc6f3fc 100644
--- a/pkgs/tools/package-management/nix-simple-deploy/default.nix
+++ b/pkgs/tools/package-management/nix-simple-deploy/default.nix
@@ -1,21 +1,29 @@
-{ lib, fetchFromGitHub, rustPlatform }:
+{ lib, fetchFromGitHub, rustPlatform, makeWrapper, openssh, nix-serve }:
 
 rustPlatform.buildRustPackage rec {
   pname = "nix-simple-deploy";
-  version = "0.1.1";
+  version = "0.2.1";
 
   src = fetchFromGitHub {
     owner = "misuzu";
     repo = pname;
     rev = version;
-    sha256 = "12g0sbgs2dfnk0agp1kagfi1yhk26ga98zygxxrjhjxrqb2n5w80";
+    sha256 = "0vkgs3ffb5vdzhrqdnd54vbi36vrgd3408zvjn0rmqlnwi3wwhnk";
   };
 
-  cargoSha256 = "1wp8wdv25j8ybq2j04z3nl4yc95wkj5h740lzpyps08yaxj8bncr";
+  cargoSha256 = "0z4d4cazl6qvigyqzdayxqfjc1ki1rhrpm76agc8lkrxrvhyay2h";
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  postInstall = ''
+    wrapProgram "$out/bin/nix-simple-deploy" \
+      --prefix PATH : "${lib.makeBinPath [ openssh nix-serve ]}"
+  '';
 
   meta = with lib; {
     description = "Deploy software or an entire NixOS system configuration to another NixOS system";
     homepage = "https://github.com/misuzu/nix-simple-deploy";
+    platforms = platforms.unix;
     license = with licenses; [ asl20 /* OR */ mit ];
     maintainers = with maintainers; [ misuzu ];
   };

From 0f572158bb08182b1400bab92a14a49a3b9dd11d Mon Sep 17 00:00:00 2001
From: Bobby Rong <rjl931189261@126.com>
Date: Sun, 8 Aug 2021 18:33:15 +0800
Subject: [PATCH 40/41] rtv: drop package (#133085)

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
---
 pkgs/applications/misc/rtv/default.nix | 46 --------------------------
 pkgs/top-level/aliases.nix             |  1 +
 pkgs/top-level/all-packages.nix        |  2 --
 3 files changed, 1 insertion(+), 48 deletions(-)
 delete mode 100644 pkgs/applications/misc/rtv/default.nix

diff --git a/pkgs/applications/misc/rtv/default.nix b/pkgs/applications/misc/rtv/default.nix
deleted file mode 100644
index be539a37a301..000000000000
--- a/pkgs/applications/misc/rtv/default.nix
+++ /dev/null
@@ -1,46 +0,0 @@
-{ lib, fetchFromGitHub, python3Packages }:
-
-with python3Packages;
-buildPythonApplication rec {
-  version = "1.27.0";
-  pname = "rtv";
-
-  src = fetchFromGitHub {
-    owner = "michael-lazar";
-    repo = "rtv";
-    rev = "v${version}";
-    sha256 = "1hw7xy2kjxq7y3wcibcz4l7zj8icvigialqr17l362xry0y17y5j";
-  };
-
-  # Tests try to access network
-  doCheck = false;
-
-  checkPhase = ''
-    py.test
-  '';
-
-  checkInputs = [
-    coverage
-    coveralls
-    docopt
-    mock
-    pylint
-    pytest
-    vcrpy
-  ];
-
-  propagatedBuildInputs = [
-    beautifulsoup4
-    decorator
-    kitchen
-    requests
-    six
-  ];
-
-  meta = with lib; {
-    homepage = "https://github.com/michael-lazar/rtv";
-    description = "Browse Reddit from your Terminal";
-    license = licenses.mit;
-    maintainers = with maintainers; [ matthiasbeyer wedens ];
-  };
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index a91db037114c..ae0194850666 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -709,6 +709,7 @@ mapAliases ({
   redkite = throw "redkite was archived by upstream"; # added 2021-04-12
   rkt = throw "rkt was archived by upstream"; # added 2020-05-16
   rpiboot-unstable = rpiboot; # added 2021-07-30
+  rtv = throw "rtv was archived by upstream. Consider using tuir, an actively maintained fork"; # added 2021-08-08
   ruby_2_0_0 = throw "ruby_2_0_0 was deprecated on 2018-02-13: use a newer version of ruby";
   ruby_2_1_0 = throw "ruby_2_1_0 was deprecated on 2018-02-13: use a newer version of ruby";
   ruby_2_2_9 = throw "ruby_2_2_9 was deprecated on 2018-02-13: use a newer version of ruby";
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b47b378e52e1..a922dae9246d 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -27117,8 +27117,6 @@ in
   rtl-sdr = callPackage ../applications/radio/rtl-sdr { };
   librtlsdr = callPackage ../development/libraries/librtlsdr { };
 
-  rtv = callPackage ../applications/misc/rtv { };
-
   rubyripper = callPackage ../applications/audio/rubyripper {};
 
   runc = callPackage ../applications/virtualization/runc {};

From 7a0c6cdd396521b2d0207bd97bf7b119fbd8e3ea Mon Sep 17 00:00:00 2001
From: erdnaxe <erdnaxe@users.noreply.github.com>
Date: Sun, 8 Aug 2021 13:58:30 +0200
Subject: [PATCH 41/41] nixos/miniflux: systemd unit hardening (#133123)

---
 nixos/modules/services/web-apps/miniflux.nix | 23 ++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/nixos/modules/services/web-apps/miniflux.nix b/nixos/modules/services/web-apps/miniflux.nix
index 01710b1bd59c..1bbadafa2078 100644
--- a/nixos/modules/services/web-apps/miniflux.nix
+++ b/nixos/modules/services/web-apps/miniflux.nix
@@ -98,6 +98,29 @@ in
         EnvironmentFile = if cfg.adminCredentialsFile == null
         then defaultCredentials
         else cfg.adminCredentialsFile;
+        # Hardening
+        CapabilityBoundingSet = [ "" ];
+        DeviceAllow = [ "" ];
+        LockPersonality = true;
+        MemoryDenyWriteExecute = true;
+        PrivateDevices = true;
+        PrivateUsers = true;
+        ProcSubset = "pid";
+        ProtectClock = true;
+        ProtectControlGroups = true;
+        ProtectHome = true;
+        ProtectHostname = true;
+        ProtectKernelLogs = true;
+        ProtectKernelModules = true;
+        ProtectKernelTunables = true;
+        ProtectProc = "invisible";
+        RestrictAddressFamilies = [ "AF_INET" "AF_INET6" ];
+        RestrictNamespaces = true;
+        RestrictRealtime = true;
+        RestrictSUIDSGID = true;
+        SystemCallArchitectures = "native";
+        SystemCallFilter = [ "@system-service" "~@privileged" "~@resources" ];
+        UMask = "0077";
       };
 
       environment = cfg.config;