From a1d9d4ea21ce9b134931d6387c824ec3d73042b7 Mon Sep 17 00:00:00 2001
From: sternenseemann <0rpkxez4ksa01gb3typccl0i@systemli.org>
Date: Sat, 20 Mar 2021 15:26:41 +0100
Subject: [PATCH 01/30] sks: 1.1.6 -> unstable-2021-02-04

The 1.1.6 release is from 2016 and only supports old OCaml version.
Updating to current master allows us to use nixpkgs' default ocaml
version.

It also no longer vendors in an old version of cryptokit.
---
 pkgs/servers/sks/default.nix    | 32 +++++++++++++++++++++++---------
 pkgs/top-level/all-packages.nix |  2 +-
 2 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/pkgs/servers/sks/default.nix b/pkgs/servers/sks/default.nix
index 8e0ce6bedac5..7a9836e1142f 100644
--- a/pkgs/servers/sks/default.nix
+++ b/pkgs/servers/sks/default.nix
@@ -1,22 +1,36 @@
-{ lib, stdenv, fetchFromBitbucket, ocaml, zlib, db, perl, camlp4 }:
+{ lib, stdenv, fetchFromGitHub, ocamlPackages, perl
+, zlib, db
+}:
+
+let
+  inherit (ocamlPackages)
+    ocaml
+    findlib
+    cryptokit
+    num
+    ;
+in
 
 stdenv.mkDerivation rec {
   pname = "sks";
-  version = "1.1.6";
+  version = "unstable-2021-02-04";
 
-  src = fetchFromBitbucket {
-    owner = "skskeyserver";
+  src = fetchFromGitHub {
+    owner = "SKS-Keyserver";
     repo = "sks-keyserver";
-    rev = version;
-    sha256 = "00q5ma5rvl10rkc6cdw8d69bddgrmvy0ckqj3hbisy65l4idj2zm";
+    rev = "c3ba6d5abb525dcb84745245631c410c11c07ec1";
+    sha256 = "0fql07sc69hv6jy7x5svb19977cdsz0p1j8wv53k045a6v7rw1jw";
   };
 
   # pkgs.db provides db_stat, not db$major.$minor_stat
-  patches = [ ./adapt-to-nixos.patch ];
+  patches = [
+    ./adapt-to-nixos.patch
+  ];
 
   outputs = [ "out" "webSamples" ];
 
-  buildInputs = [ ocaml zlib db perl camlp4 ];
+  nativeBuildInputs = [ ocaml findlib perl ];
+  buildInputs = [ zlib db cryptokit num ];
 
   makeFlags = [ "PREFIX=$(out)" "MANDIR=$(out)/share/man" ];
   preConfigure = ''
@@ -44,7 +58,7 @@ stdenv.mkDerivation rec {
       spotty connectivity, can fully synchronize with rest of the system.
     '';
     inherit (src.meta) homepage;
-    license = licenses.gpl2;
+    license = licenses.gpl2Plus;
     platforms = platforms.linux;
     maintainers = with maintainers; [ primeos fpletz globin ];
   };
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 3ff14e23fbe9..64bf6b05ceea 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -8087,7 +8087,7 @@ in
 
   skippy-xd = callPackage ../tools/X11/skippy-xd {};
 
-  sks = callPackage ../servers/sks { inherit (ocaml-ng.ocamlPackages_4_02) ocaml camlp4; };
+  sks = callPackage ../servers/sks { };
 
   skydns = callPackage ../servers/skydns { };
 

From e71db19e2bce12dbf5f510ac127f9a51b4962ea8 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Sat, 4 Sep 2021 12:09:58 +0000
Subject: [PATCH 02/30] python38Packages.pefile: 2021.9.2 -> 2021.9.3

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

diff --git a/pkgs/development/python-modules/pefile/default.nix b/pkgs/development/python-modules/pefile/default.nix
index 508ba27b2943..1a793644fb29 100644
--- a/pkgs/development/python-modules/pefile/default.nix
+++ b/pkgs/development/python-modules/pefile/default.nix
@@ -8,14 +8,14 @@
 
 buildPythonPackage rec {
   pname = "pefile";
-  version = "2021.9.2";
+  version = "2021.9.3";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "erocarrera";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1pgsw84i9r6ydkfzqifgl5lvcz3cf3xz5c2543kl3q8mgb21wxaz";
+    sha256 = "0sr17rmqpr874m8rpkp8xdz8kjshhimbfgq13qy4lscaiznmlf0d";
   };
 
   nativeBuildInputs = [

From ef98e15e38d715382b7b3bc3eb814d726458b5af Mon Sep 17 00:00:00 2001
From: Samuel Ainsworth <skainsworth@gmail.com>
Date: Sun, 12 Sep 2021 02:15:19 +0000
Subject: [PATCH 03/30] python3Packages.adjustText: init at 0.7.3

---
 .../python-modules/adjustText/default.nix     | 29 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 31 insertions(+)
 create mode 100644 pkgs/development/python-modules/adjustText/default.nix

diff --git a/pkgs/development/python-modules/adjustText/default.nix b/pkgs/development/python-modules/adjustText/default.nix
new file mode 100644
index 000000000000..56f0fa930521
--- /dev/null
+++ b/pkgs/development/python-modules/adjustText/default.nix
@@ -0,0 +1,29 @@
+{ buildPythonPackage
+, numpy
+, matplotlib
+, fetchFromGitHub
+, lib
+}:
+
+buildPythonPackage rec {
+  pname = "adjustText";
+  version = "0.7.3";
+
+  src = fetchFromGitHub {
+    owner = "Phlya";
+    repo = pname;
+    rev = version;
+    sha256 = "02apaznnnmwmrn342f22dj5dldn56gdl9v5qix07ah6kgp9503yw";
+  };
+
+  propagatedBuildInputs = [ matplotlib numpy ];
+
+  pythonImportsCheck = [ "adjustText" ];
+
+  meta = with lib; {
+    description = "Iteratively adjust text position in matplotlib plots to minimize overlaps";
+    homepage    = "https://github.com/Phlya/adjustText";
+    license     = licenses.mit;
+    maintainers = with maintainers; [ samuela ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index cce7d2dab0f9..0d49c4611c1f 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -209,6 +209,8 @@ in {
 
   adguardhome = callPackage ../development/python-modules/adguardhome { };
 
+  adjustText = callPackage ../development/python-modules/adjustText { };
+
   advantage-air = callPackage ../development/python-modules/advantage-air { };
 
   aemet-opendata = callPackage ../development/python-modules/aemet-opendata { };

From 975d350d51db0bcd956e5f57afd14ba53606144c Mon Sep 17 00:00:00 2001
From: Samuel Ainsworth <skainsworth@gmail.com>
Date: Mon, 13 Sep 2021 00:19:41 +0000
Subject: [PATCH 04/30] python3Packages.{adjustText -> adjusttext}: PEP-503
 naming

---
 .../python-modules/{adjustText => adjusttext}/default.nix   | 6 +++---
 pkgs/top-level/python-packages.nix                          | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)
 rename pkgs/development/python-modules/{adjustText => adjusttext}/default.nix (82%)

diff --git a/pkgs/development/python-modules/adjustText/default.nix b/pkgs/development/python-modules/adjusttext/default.nix
similarity index 82%
rename from pkgs/development/python-modules/adjustText/default.nix
rename to pkgs/development/python-modules/adjusttext/default.nix
index 56f0fa930521..5a1d3f936ec0 100644
--- a/pkgs/development/python-modules/adjustText/default.nix
+++ b/pkgs/development/python-modules/adjusttext/default.nix
@@ -6,7 +6,7 @@
 }:
 
 buildPythonPackage rec {
-  pname = "adjustText";
+  pname = "adjusttext";
   version = "0.7.3";
 
   src = fetchFromGitHub {
@@ -22,8 +22,8 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "Iteratively adjust text position in matplotlib plots to minimize overlaps";
-    homepage    = "https://github.com/Phlya/adjustText";
-    license     = licenses.mit;
+    homepage = "https://github.com/Phlya/adjustText";
+    license = licenses.mit;
     maintainers = with maintainers; [ samuela ];
   };
 }
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 0d49c4611c1f..a08e8d1f79f8 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -209,7 +209,7 @@ in {
 
   adguardhome = callPackage ../development/python-modules/adguardhome { };
 
-  adjustText = callPackage ../development/python-modules/adjustText { };
+  adjusttext = callPackage ../development/python-modules/adjusttext { };
 
   advantage-air = callPackage ../development/python-modules/advantage-air { };
 

From 87b368e637442c87bd1bedac1e4d8ca0b4990543 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Mon, 13 Sep 2021 09:37:05 +0000
Subject: [PATCH 05/30] python38Packages.scp: 0.14.0 -> 0.14.1

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

diff --git a/pkgs/development/python-modules/scp/default.nix b/pkgs/development/python-modules/scp/default.nix
index cba6ddc0acf6..47276ad305c7 100644
--- a/pkgs/development/python-modules/scp/default.nix
+++ b/pkgs/development/python-modules/scp/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "scp";
-  version = "0.14.0";
+  version = "0.14.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ddbdb3ef8c068aa1fd37a5fa65a122a80673c9fd73fdc5668a4604f99ccf5943";
+    sha256 = "b776bd6ce8c8385aa9a025b64a9815b5d798f12d4ef0d712d569503f62aece8b";
   };
 
   propagatedBuildInputs = [

From ac70c0ba3aa1977b628a8fd289b1f9c2c0fca995 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Tue, 14 Sep 2021 15:19:48 +0000
Subject: [PATCH 06/30] libquotient: 0.6.8 -> 0.6.9

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

diff --git a/pkgs/development/libraries/libquotient/default.nix b/pkgs/development/libraries/libquotient/default.nix
index 6264a9de3691..b64e9de9ceed 100644
--- a/pkgs/development/libraries/libquotient/default.nix
+++ b/pkgs/development/libraries/libquotient/default.nix
@@ -2,13 +2,13 @@
 
 mkDerivation rec {
   pname = "libquotient";
-  version = "0.6.8";
+  version = "0.6.9";
 
   src = fetchFromGitHub {
     owner = "quotient-im";
     repo = "libQuotient";
     rev = version;
-    sha256 = "sha256-CrAK0yq1upB1+C2z6mqKkSArCmzI+TDEEHTIBWB29Go=";
+    sha256 = "sha256-1YiS2b4lYknNSB+8LKB/s6AcF0yQVsakrkp6/Sjkczo=";
   };
 
   buildInputs = [ qtbase qtmultimedia ];

From 65be4ada23bfb63b75df0293c31f5c79f1b84ac7 Mon Sep 17 00:00:00 2001
From: Charlotte Van Petegem <charlotte.vanpetegem@ugent.be>
Date: Wed, 22 Sep 2021 09:27:26 +0200
Subject: [PATCH 07/30] gomuks: 0.2.3 -> 0.2.4

---
 .../instant-messengers/gomuks/default.nix     |  6 ++--
 .../gomuks/hardcoded_path.patch               | 28 ++++++++++---------
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/pkgs/applications/networking/instant-messengers/gomuks/default.nix b/pkgs/applications/networking/instant-messengers/gomuks/default.nix
index 0fea57ea9cc7..5f2a094ca36b 100644
--- a/pkgs/applications/networking/instant-messengers/gomuks/default.nix
+++ b/pkgs/applications/networking/instant-messengers/gomuks/default.nix
@@ -13,16 +13,16 @@
 
 buildGoModule rec {
   pname = "gomuks";
-  version = "0.2.3";
+  version = "0.2.4";
 
   src = fetchFromGitHub {
     owner = "tulir";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0g0aa6h6bm00mdgkb38wm66rcrhqfvs2xj9rl04bwprsa05q5lca";
+    sha256 = "bTOfnEmJHTuniewH//SugNNDuKIFMQb1Safs0UVKH1c=";
   };
 
-  vendorSha256 = "14ya5advpv4q5il235h5dxy8c2ap2yzrvqs0sjqgw0v1vm6vpwdx";
+  vendorSha256 = "PuNROoxL7UmcuYDgfnsMUsGk9i1jnQyWtaUmT7vXdKE=";
 
   doCheck = false;
 
diff --git a/pkgs/applications/networking/instant-messengers/gomuks/hardcoded_path.patch b/pkgs/applications/networking/instant-messengers/gomuks/hardcoded_path.patch
index 0e0d4e28b0a1..dd89c92fd3d4 100644
--- a/pkgs/applications/networking/instant-messengers/gomuks/hardcoded_path.patch
+++ b/pkgs/applications/networking/instant-messengers/gomuks/hardcoded_path.patch
@@ -1,13 +1,15 @@
-diff --git a/lib/notification/notify_linux.go b/lib/notification/notify_linux.go
-index f93a95f..da6a61d 100644
---- a/lib/notification/notify_linux.go
-+++ b/lib/notification/notify_linux.go
-@@ -32,7 +32,7 @@ func Send(title, text string, critical, sound bool) error {
- 		if critical {
- 			soundName = "complete"
- 		}
--		exec.Command("paplay", "/usr/share/sounds/freedesktop/stereo/"+soundName+".oga").Run()
-+		exec.Command("paplay", "@soundTheme@/share/sounds/freedesktop/stereo/"+soundName+".oga").Run()
- 	}
- 	return exec.Command("notify-send", args...).Run()
- }
+diff --git a/lib/notification/notify_xdg.go b/lib/notification/notify_xdg.go
+index 7f102b8..996c15f 100644
+--- a/lib/notification/notify_xdg.go
++++ b/lib/notification/notify_xdg.go
+@@ -26,8 +26,8 @@ import (
+ var notifySendPath string
+ var audioCommand string
+ var tryAudioCommands = []string{"ogg123", "paplay"}
+-var soundNormal = "/usr/share/sounds/freedesktop/stereo/message-new-instant.oga"
+-var soundCritical = "/usr/share/sounds/freedesktop/stereo/complete.oga"
++var soundNormal = "@soundTheme@/share/sounds/freedesktop/stereo/message-new-instant.oga"
++var soundCritical = "@soundTheme@/share/sounds/freedesktop/stereo/complete.oga"
+ 
+ func getSoundPath(env, defaultPath string) string {
+ 	if path, ok := os.LookupEnv(env); ok {

From bbcd0887bdf180f3b9fe1d63c48402ea636fbe53 Mon Sep 17 00:00:00 2001
From: Sergei Trofimovich <slyich@gmail.com>
Date: Sun, 12 Sep 2021 08:17:28 +0100
Subject: [PATCH 08/30] gpm: pull upstream fix for -fno-common compiler

Fixes build failure against upstream gcc (defaults -fno-common).
---
 pkgs/servers/gpm/default.nix | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pkgs/servers/gpm/default.nix b/pkgs/servers/gpm/default.nix
index 4337820683d0..206ac6131e42 100644
--- a/pkgs/servers/gpm/default.nix
+++ b/pkgs/servers/gpm/default.nix
@@ -37,6 +37,11 @@ stdenv.mkDerivation rec {
       url = "https://raw.githubusercontent.com/gentoo/musl/5aed405d87dfa92a5cab1596f898e9dea07169b8/sys-libs/gpm/files/gpm-1.20.7-sysmacros.patch";
       sha256 = "0lg4l9phvy2n8gy17qsn6zn0qq52vm8g01pgq5kqpr8sd3fb21c2";
     })
+    (fetchpatch {
+      # upstream build fix against -fno-common compilers like >=gcc-10
+      url = "https://github.com/telmich/gpm/commit/f04f24dd5ca5c1c13608b144ab66e2ccd47f106a.patch";
+      sha256 = "1q5hl5m61pci2f0x7r5in99rmqh328v1k0zj2693wdlafk9dabks";
+    })
   ];
   preConfigure = ''
     ./autogen.sh

From a98087d710aa7b874ac0686f7ae02fdb8790169f Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 22 Sep 2021 23:04:33 +0200
Subject: [PATCH 09/30] python3Packages.marshmallow-polyfield: 5.9 -> 5.10

---
 .../marshmallow-polyfield/default.nix         | 29 +++++++++++++------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/python-modules/marshmallow-polyfield/default.nix b/pkgs/development/python-modules/marshmallow-polyfield/default.nix
index aa2784cd1dbb..6b5394ac2770 100644
--- a/pkgs/development/python-modules/marshmallow-polyfield/default.nix
+++ b/pkgs/development/python-modules/marshmallow-polyfield/default.nix
@@ -1,32 +1,43 @@
-{ buildPythonPackage
+{ lib
+, buildPythonPackage
 , fetchFromGitHub
-, lib
 , marshmallow
-  # Check Inputs
+, pythonOlder
 , pytestCheckHook
-, pytest-cov
 }:
 
 buildPythonPackage rec {
   pname = "marshmallow-polyfield";
-  version = "5.9";
+  version = "5.10";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "Bachmann1234";
     repo = pname;
     rev = "v${version}";
-    sha256 = "15yx8ib5yx1xx6kq8wnfdmv9zm43k7y33c6zpq5rba6a30v4lcnd";
+    sha256 = "sha256-oF5LBuDK4kqsAcKwidju+wFjigjy4CNbJ6bfWpGO1yQ=";
   };
 
   propagatedBuildInputs = [
     marshmallow
   ];
 
-  # setuptools check can run, but won't find tests
-  checkInputs = [ pytestCheckHook pytest-cov ];
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  postPatch = ''
+    substituteInPlace setup.cfg \
+      --replace "--cov=marshmallow_polyfield" ""
+  '';
+
+  pythonImportsCheck = [
+    "marshmallow"
+  ];
 
   meta = with lib; {
-    description = "An unofficial extension to Marshmallow to allow for polymorphic fields";
+    description = "Extension to Marshmallow to allow for polymorphic fields";
     homepage = "https://github.com/Bachmann1234/marshmallow-polyfield";
     license = licenses.asl20;
     maintainers = with maintainers; [ drewrisinger ];

From f89bdb5bc362e33c28b6bb42a06637ad7a5cb31a Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 22 Sep 2021 23:07:19 +0200
Subject: [PATCH 10/30] python3Packages.marshmallow: 3.11.1 -> 3.13.0

---
 .../python-modules/marshmallow/default.nix       | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/pkgs/development/python-modules/marshmallow/default.nix b/pkgs/development/python-modules/marshmallow/default.nix
index 3de64fea37fa..a4f60d8202a4 100644
--- a/pkgs/development/python-modules/marshmallow/default.nix
+++ b/pkgs/development/python-modules/marshmallow/default.nix
@@ -9,26 +9,27 @@
 
 buildPythonPackage rec {
   pname = "marshmallow";
-  version = "3.11.1";
-  disabled = pythonOlder "3.5";
+  version = "3.13.0";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "marshmallow-code";
     repo = pname;
     rev = version;
-    sha256 = "1ypm142y3giaqydc7fkigm9r057yp2sd1ng5zr2x3w3wbbj5yfm6";
+    sha256 = "sha256-tP/RKo2Hzxz2bT7ybRs9wGzq7TpsmzmOPi3BGuSLDA0=";
   };
 
-  pythonImportsCheck = [
-    "marshmallow"
-  ];
-
   checkInputs = [
     pytestCheckHook
     pytz
     simplejson
   ];
 
+  pythonImportsCheck = [
+    "marshmallow"
+  ];
+
   meta = with lib; {
     description = ''
       A lightweight library for converting complex objects to and from
@@ -38,5 +39,4 @@ buildPythonPackage rec {
     license = licenses.mit;
     maintainers = with maintainers; [ cript0nauta ];
   };
-
 }

From a74a864b0fc5f1194e13c6e84ec9099cdaa5ad2d Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 23 Sep 2021 00:52:50 +0000
Subject: [PATCH 11/30] iotop-c: 1.18 -> 1.19

---
 pkgs/os-specific/linux/iotop-c/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/os-specific/linux/iotop-c/default.nix b/pkgs/os-specific/linux/iotop-c/default.nix
index ca0eddac6664..ea40ff79f64a 100644
--- a/pkgs/os-specific/linux/iotop-c/default.nix
+++ b/pkgs/os-specific/linux/iotop-c/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "iotop-c";
-  version = "1.18";
+  version = "1.19";
 
   src = fetchFromGitHub {
     owner = "Tomas-M";
     repo = "iotop";
     rev = "v${version}";
-    sha256 = "sha256-5RbxryvRKWJvjuJJwDK6GYnwdtHGfW7XEc75q4omxIA=";
+    sha256 = "sha256-CuZwOIhjl6fpEvfw/4CTjKQkxazLL/NGujmNcx1Jrbc=";
   };
 
   nativeBuildInputs = [ pkg-config ];

From 68a8d86415c3de64a9ba311058bdb8fda7f930dd Mon Sep 17 00:00:00 2001
From: Robert Hensing <robert@roberthensing.nl>
Date: Thu, 23 Sep 2021 18:42:29 +0200
Subject: [PATCH 12/30] es *beat6: Fix build on aarch64

---
 pkgs/misc/logging/beats/6.x.nix | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/pkgs/misc/logging/beats/6.x.nix b/pkgs/misc/logging/beats/6.x.nix
index 81b8ba0ab5bf..1808197498b5 100644
--- a/pkgs/misc/logging/beats/6.x.nix
+++ b/pkgs/misc/logging/beats/6.x.nix
@@ -1,4 +1,4 @@
-{ lib, fetchFromGitHub, elk6Version, buildGoPackage, libpcap, nixosTests, systemd }:
+{ lib, fetchFromGitHub, fetchpatch, elk6Version, buildGoPackage, libpcap, nixosTests, systemd }:
 
 let beat = package : extraArgs : buildGoPackage (rec {
       name = "${package}-${version}";
@@ -15,6 +15,14 @@ let beat = package : extraArgs : buildGoPackage (rec {
 
       subPackages = [ package ];
 
+      patches = [
+        (fetchpatch {
+          # Build fix for aarch64, possibly other systems, merged in beats 7.x https://github.com/elastic/beats/pull/9493
+          url = "https://github.com/elastic/beats/commit/5d796571de1aa2a299393d2045dacc2efac41a04.diff";
+          sha256 = "sha256:0b79fljbi5xd3h8iiv1m38ad0zhmj09f187asc0m9rxlqrz2l9r2";
+        })
+      ];
+
       meta = with lib; {
         homepage = "https://www.elastic.co/products/beats";
         license = licenses.asl20;

From 6219c9b363e2c06378cbca5b55e0acd109540864 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 23 Sep 2021 19:12:05 +0000
Subject: [PATCH 13/30] python38Packages.parts: 1.1.0 -> 1.1.2

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

diff --git a/pkgs/development/python-modules/parts/default.nix b/pkgs/development/python-modules/parts/default.nix
index 95f7ea9a6df2..c615fe5a0307 100644
--- a/pkgs/development/python-modules/parts/default.nix
+++ b/pkgs/development/python-modules/parts/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "parts";
-  version = "1.1.0";
+  version = "1.1.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-Xtcu/0ZO+6L7RiVfq/Jog4f7LOtZo4QUD1qi7UdPO7g=";
+    sha256 = "2212129476f6d285c3aaab309b80b83664d13dca5a42c5ca3500bd32130af7ec";
   };
 
   # Project has no tests

From 75fec7494be462a771e5697af71b8644cb8521c6 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 23 Sep 2021 20:07:11 +0000
Subject: [PATCH 14/30] python38Packages.pybullet: 3.1.8 -> 3.1.9

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

diff --git a/pkgs/development/python-modules/pybullet/default.nix b/pkgs/development/python-modules/pybullet/default.nix
index 4d97b535606f..3a5d68f37e4a 100644
--- a/pkgs/development/python-modules/pybullet/default.nix
+++ b/pkgs/development/python-modules/pybullet/default.nix
@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "pybullet";
-  version = "3.1.8";
+  version = "3.1.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "a7e6c7c77cab39e1559c98e4290c5138247b15d3a26a76a23b2737c159f3f905";
+    sha256 = "6fb4d48d5ba9c09cdd1ed732e8a1d48b41bca379e072268af3831774d8391300";
   };
 
   buildInputs = [

From 4b321e220446ca7ab05805a1e84f54d8d82bc357 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 24 Sep 2021 00:07:09 +0200
Subject: [PATCH 15/30] python3Packages.censys: 2.0.7 -> 2.0.8

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

diff --git a/pkgs/development/python-modules/censys/default.nix b/pkgs/development/python-modules/censys/default.nix
index 09dc32c6b698..0d14441932e3 100644
--- a/pkgs/development/python-modules/censys/default.nix
+++ b/pkgs/development/python-modules/censys/default.nix
@@ -15,7 +15,7 @@
 
 buildPythonPackage rec {
   pname = "censys";
-  version = "2.0.7";
+  version = "2.0.8";
   format = "pyproject";
 
   disabled = pythonOlder "3.6";
@@ -24,7 +24,7 @@ buildPythonPackage rec {
     owner = "censys";
     repo = "censys-python";
     rev = "v${version}";
-    sha256 = "0s9y9956awl26rnrp5l78rbrjcwliqdijnmm7k6xm4hh7iak4q6z";
+    sha256 = "sha256-2qMUQ+MRrPzXlH+WUJ8DSXtrgaZp4OD36X8cX7cNIks=";
   };
 
   nativeBuildInputs = [

From 24a855097a7632e967852b1cbb70bb4b392acc2f Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 24 Sep 2021 01:03:30 +0200
Subject: [PATCH 16/30] python3Packages.hiyapyco: allow later Jinja2 releases

---
 .../python-modules/hiyapyco/default.nix       | 20 +++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/hiyapyco/default.nix b/pkgs/development/python-modules/hiyapyco/default.nix
index f443c58723e8..79693747cfac 100644
--- a/pkgs/development/python-modules/hiyapyco/default.nix
+++ b/pkgs/development/python-modules/hiyapyco/default.nix
@@ -6,7 +6,7 @@
 }:
 
 buildPythonPackage rec {
-  pname = "HiYaPyCo";
+  pname = "hiyapyco";
   version = "0.4.16";
 
   src = fetchFromGitHub {
@@ -16,17 +16,29 @@ buildPythonPackage rec {
     sha256 = "1ams9dp05yhgbg6255wrjgchl2mqg0s34d8b8prvql9lsh59s1fj";
   };
 
-  propagatedBuildInputs = [ pyyaml jinja2 ];
+  propagatedBuildInputs = [
+    pyyaml
+    jinja2
+  ];
+
+  postPatch = ''
+    # Should no longer be needed with the next release
+    # https://github.com/zerwes/hiyapyco/pull/42
+    substituteInPlace setup.py \
+      --replace "Jinja2>1,<3" "Jinja2>1"
+  '';
 
   checkPhase = ''
     set -e
     find test -name 'test_*.py' -exec python {} \;
   '';
 
+  pythonImportsCheck = [ "hiyapyco" ];
+
   meta = with lib; {
-    description = "A simple python lib allowing hierarchical overlay of config files in YAML syntax, offering different merge methods and variable interpolation based on jinja2.";
+    description = "Python library allowing hierarchical overlay of config files in YAML syntax";
     homepage = "https://github.com/zerwes/hiyapyco";
-    license = licenses.gpl3;
+    license = licenses.gpl3Plus;
     maintainers = with maintainers; [ veehaitch ];
   };
 }

From 1f2047b3fa4ac99da16be1d286d7c5fbee589ec5 Mon Sep 17 00:00:00 2001
From: figsoda <figsoda@pm.me>
Date: Thu, 23 Sep 2021 21:09:27 -0400
Subject: [PATCH 17/30] cargo-supply-chain: 0.0.2 -> 0.2.0

---
 .../tools/rust/cargo-supply-chain/default.nix      | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/pkgs/development/tools/rust/cargo-supply-chain/default.nix b/pkgs/development/tools/rust/cargo-supply-chain/default.nix
index d8b9788dc32c..d5876f240a93 100644
--- a/pkgs/development/tools/rust/cargo-supply-chain/default.nix
+++ b/pkgs/development/tools/rust/cargo-supply-chain/default.nix
@@ -1,17 +1,15 @@
-{ lib, rustPlatform, fetchFromGitHub, stdenv, Security }:
+{ lib, rustPlatform, fetchCrate, stdenv, Security }:
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-supply-chain";
-  version = "0.0.2";
+  version = "0.2.0";
 
-  src = fetchFromGitHub {
-    owner = "rust-secure-code";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "0kpm842p7l0vwbfa99zq3w3nsasy5sp1b99si7brjjvq99bad9gr";
+  src = fetchCrate {
+    inherit pname version;
+    sha256 = "sha256-zjDZJOUjnEQ03rmo5CdSY1emE6YohOPlf7SKuvNLuV0=";
   };
 
-  cargoSha256 = "sha256-Mn5s6pfTHoFXtHqn6ii8PtAIBz/RJaR0zO5U5jS3UDU=";
+  cargoSha256 = "sha256-xSJ5rx8k+my0NeGYHZyvDzbM7uMdbViT7Ou9a9JACfs=";
 
   buildInputs = lib.optional stdenv.isDarwin Security;
 

From 346117904c6b2167ea602d47fd87a75063646cb2 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Fri, 24 Sep 2021 01:13:57 +0000
Subject: [PATCH 18/30] python38Packages.tinydb: 4.5.1 -> 4.5.2

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

diff --git a/pkgs/development/python-modules/tinydb/default.nix b/pkgs/development/python-modules/tinydb/default.nix
index 118317781281..958624f80935 100644
--- a/pkgs/development/python-modules/tinydb/default.nix
+++ b/pkgs/development/python-modules/tinydb/default.nix
@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "tinydb";
-  version = "4.5.1";
+  version = "4.5.2";
   disabled = pythonOlder "3.5";
   format = "pyproject";
 
@@ -18,7 +18,7 @@ buildPythonPackage rec {
     owner = "msiemens";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1p0whrljjh7cpigr1glszssxsi6adi4cj7y3976q8sj9z47bdx8a";
+    sha256 = "0gyc9rk1adw4gynwnv4kfas0hxv1cql0sm5b3fsms39088ha894l";
   };
 
   nativeBuildInputs = [

From 24cd58440a06e79b7f8cd019f897c83abf56ddc9 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Fri, 24 Sep 2021 01:19:24 +0000
Subject: [PATCH 19/30] python38Packages.toonapi: 0.2.0 -> 0.2.1

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

diff --git a/pkgs/development/python-modules/toonapi/default.nix b/pkgs/development/python-modules/toonapi/default.nix
index 003670989920..8df8fa89a2ca 100644
--- a/pkgs/development/python-modules/toonapi/default.nix
+++ b/pkgs/development/python-modules/toonapi/default.nix
@@ -8,13 +8,13 @@
 
 buildPythonPackage rec {
   pname = "toonapi";
-  version = "0.2.0";
+  version = "0.2.1";
 
   src = fetchFromGitHub {
     owner = "frenck";
     repo = "python-toonapi";
     rev = "v${version}";
-    sha256 = "1d4n615vlcgkvmchrfjw4h3ndav3ljmcfydxr2b41zn83mzizqdf";
+    sha256 = "10jh6p0ww51cb9f8amd9jq3lmvby6n2k08qwcr2n8ijbbgyp0ibf";
   };
 
   propagatedBuildInputs = [

From e31a829e26d63cda34aaabe0fb6d6074cf05e58f Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Fri, 24 Sep 2021 04:20:45 +0000
Subject: [PATCH 20/30] python38Packages.hvac: 0.11.0 -> 0.11.2

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

diff --git a/pkgs/development/python-modules/hvac/default.nix b/pkgs/development/python-modules/hvac/default.nix
index 5eaf6f1199eb..c30566a45109 100644
--- a/pkgs/development/python-modules/hvac/default.nix
+++ b/pkgs/development/python-modules/hvac/default.nix
@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "hvac";
-  version = "0.11.0";
+  version = "0.11.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9d5504e35388e665db5086edf75d2425831573c6569bb0bf3c2c6eaff30e034e";
+    sha256 = "f905c59d32d88d3f67571fe5a8a78de4659e04798ad809de439f667247d13626";
   };
 
   propagatedBuildInputs = [

From 2588a5f650dfa43c30f81a5c00ed2cc396c65c9a Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 24 Sep 2021 08:34:49 +0200
Subject: [PATCH 21/30] python3Packages.python-http-client: 3.3.2 -> 3.3.3

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

diff --git a/pkgs/development/python-modules/python-http-client/default.nix b/pkgs/development/python-modules/python-http-client/default.nix
index 8eece2ed4fee..b69c478ef27d 100644
--- a/pkgs/development/python-modules/python-http-client/default.nix
+++ b/pkgs/development/python-modules/python-http-client/default.nix
@@ -7,13 +7,13 @@
 
 buildPythonPackage rec {
   pname = "python_http_client";
-  version = "3.3.2";
+  version = "3.3.3";
 
   src = fetchFromGitHub {
     owner = "sendgrid";
     repo = "python-http-client";
     rev = version;
-    sha256 = "0z7nvfq9wdcprwh88xn9p3vm15gb3ijdc8pxn0a133ini9hxxlpx";
+    sha256 = "sha256-cZqyu67xP0UIKYbhYYTNL5kLiPjjMjayde75sqkHZhg=";
   };
 
   checkInputs = [

From 5b1ce387db813d0378a6f9c4e096ebf280a01bcc Mon Sep 17 00:00:00 2001
From: Fabian Affolter <fabian@affolter-engineering.ch>
Date: Fri, 24 Sep 2021 08:55:46 +0200
Subject: [PATCH 22/30] python3Packages.adjusttext: add doCheck

---
 pkgs/development/python-modules/adjusttext/default.nix | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pkgs/development/python-modules/adjusttext/default.nix b/pkgs/development/python-modules/adjusttext/default.nix
index 5a1d3f936ec0..82613ffa52aa 100644
--- a/pkgs/development/python-modules/adjusttext/default.nix
+++ b/pkgs/development/python-modules/adjusttext/default.nix
@@ -18,6 +18,9 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ matplotlib numpy ];
 
+  # Project has no tests
+  doCheck = false;
+
   pythonImportsCheck = [ "adjustText" ];
 
   meta = with lib; {

From affa5e384f151cf79aa935397f4d56d64bf86f8f Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 24 Sep 2021 09:32:51 +0200
Subject: [PATCH 23/30] python3Packages.pysyncobj: 0.3.8 -> 0.3.10

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

diff --git a/pkgs/development/python-modules/pysyncobj/default.nix b/pkgs/development/python-modules/pysyncobj/default.nix
index 3afdacd18034..13936ba090c2 100644
--- a/pkgs/development/python-modules/pysyncobj/default.nix
+++ b/pkgs/development/python-modules/pysyncobj/default.nix
@@ -5,13 +5,13 @@
 
 buildPythonPackage rec {
   pname = "pysyncobj";
-  version = "0.3.8";
+  version = "0.3.10";
 
   src = fetchFromGitHub {
     owner = "bakwc";
     repo = "PySyncObj";
     rev = version;
-    sha256 = "sha256-T7ecy5/1eF0pYaOv74SBEp6V6Z23E2b9lo5Q/gig3Cw=";
+    sha256 = "sha256-tcoG0KZewPRYPwDSV7aqrAGw3NF4yj/Ukc+I7HHI9+I=";
   };
 
   # Tests require network features

From 39e8ec2db68b863543bd377e44fbe02f8d05864e Mon Sep 17 00:00:00 2001
From: Sergei Trofimovich <slyich@gmail.com>
Date: Fri, 24 Sep 2021 08:06:57 +0000
Subject: [PATCH 24/30] maintainers/scripts/rebuild-amount.sh: report
 parallelism, add example, cleanup (#137695)

* maintainers/scripts/rebuild-amount.sh: report parallelism setting

This slightly helps discovering parallelism support.

* maintainers/scripts/rebuild-amount.sh: add basic example

It's not clear if script should be used against HEAD or HEAD^.
Let's have a copyable example.

* maintainers/scripts/rebuild-amount.sh: convert tabs to four spaces

One notable change is here-document conversion.
Before:

  <TAB>cat <<-FOO
  <TAB>...
  <TAB>FOO

After:

  <sp><sp><sp><sp>cat <<FOO
  <sp><sp><sp><sp>...
  FOO

Note seemingly misaligned 'FOO': '-FOO' understands leading tabs,
but not spaces.
---
 maintainers/scripts/rebuild-amount.sh | 147 ++++++++++++++------------
 1 file changed, 77 insertions(+), 70 deletions(-)

diff --git a/maintainers/scripts/rebuild-amount.sh b/maintainers/scripts/rebuild-amount.sh
index ca89e08073e8..bedd352db5f3 100755
--- a/maintainers/scripts/rebuild-amount.sh
+++ b/maintainers/scripts/rebuild-amount.sh
@@ -4,123 +4,130 @@ set -e
 # --print: avoid dependency on environment
 optPrint=
 if [ "$1" == "--print" ]; then
-	optPrint=true
-	shift
+    optPrint=true
+    shift
 fi
 
 if [ "$#" != 1 ] && [ "$#" != 2 ]; then
-	cat <<-EOF
-	Usage: $0 [--print] commit-spec [commit-spec]
-	    You need to be in a git-controlled nixpkgs tree.
-	    The current state of the tree will be used if the second commit is missing.
-	EOF
-	exit 1
+    cat <<EOF
+    Usage: $0 [--print] from-commit-spec [to-commit-spec]
+        You need to be in a git-controlled nixpkgs tree.
+        The current state of the tree will be used if the second commit is missing.
+
+        Examples:
+          effect of latest commit:
+              $ $0 HEAD^
+              $ $0 --print HEAD^
+          effect of the whole patch series for 'staging' branch:
+              $ $0 origin/staging staging
+EOF
+    exit 1
 fi
 
 # A slightly hacky way to get the config.
 parallel="$(echo 'config.rebuild-amount.parallel or false' | nix-repl . 2>/dev/null \
-			| grep -v '^\(nix-repl.*\)\?$' | tail -n 1 || true)"
+            | grep -v '^\(nix-repl.*\)\?$' | tail -n 1 || true)"
 
-echo "Estimating rebuild amount by counting changed Hydra jobs."
+echo "Estimating rebuild amount by counting changed Hydra jobs (parallel=${parallel:-unset})."
 
 toRemove=()
 
 cleanup() {
-	rm -rf "${toRemove[@]}"
+    rm -rf "${toRemove[@]}"
 }
 trap cleanup EXIT SIGINT SIGQUIT ERR
 
 MKTEMP='mktemp --tmpdir nix-rebuild-amount-XXXXXXXX'
 
 nixexpr() {
-	cat <<-EONIX
-		let
-		  lib = import $1/lib;
-		  hydraJobs = import $1/pkgs/top-level/release.nix
-		    # Compromise: accuracy vs. resources needed for evaluation.
-		    { supportedSystems = cfg.systems or [ "x86_64-linux" "x86_64-darwin" ]; };
-		  cfg = (import $1 {}).config.rebuild-amount or {};
+    cat <<EONIX
+        let
+          lib = import $1/lib;
+          hydraJobs = import $1/pkgs/top-level/release.nix
+            # Compromise: accuracy vs. resources needed for evaluation.
+            { supportedSystems = cfg.systems or [ "x86_64-linux" "x86_64-darwin" ]; };
+          cfg = (import $1 {}).config.rebuild-amount or {};
 
-		  recurseIntoAttrs = attrs: attrs // { recurseForDerivations = true; };
+          recurseIntoAttrs = attrs: attrs // { recurseForDerivations = true; };
 
-		  # hydraJobs leaves recurseForDerivations as empty attrmaps;
-		  # that would break nix-env and we also need to recurse everywhere.
-		  tweak = lib.mapAttrs
-		    (name: val:
-		      if name == "recurseForDerivations" then true
-		      else if lib.isAttrs val && val.type or null != "derivation"
-		              then recurseIntoAttrs (tweak val)
-		      else val
-		    );
+          # hydraJobs leaves recurseForDerivations as empty attrmaps;
+          # that would break nix-env and we also need to recurse everywhere.
+          tweak = lib.mapAttrs
+            (name: val:
+              if name == "recurseForDerivations" then true
+              else if lib.isAttrs val && val.type or null != "derivation"
+                      then recurseIntoAttrs (tweak val)
+              else val
+            );
 
-		  # Some of these contain explicit references to platform(s) we want to avoid;
-		  # some even (transitively) depend on ~/.nixpkgs/config.nix (!)
-		  blacklist = [
-		    "tarball" "metrics" "manual"
-		    "darwin-tested" "unstable" "stdenvBootstrapTools"
-		    "moduleSystem" "lib-tests" # these just confuse the output
-		  ];
+          # Some of these contain explicit references to platform(s) we want to avoid;
+          # some even (transitively) depend on ~/.nixpkgs/config.nix (!)
+          blacklist = [
+            "tarball" "metrics" "manual"
+            "darwin-tested" "unstable" "stdenvBootstrapTools"
+            "moduleSystem" "lib-tests" # these just confuse the output
+          ];
 
-		in
-		  tweak (builtins.removeAttrs hydraJobs blacklist)
-	EONIX
+        in
+          tweak (builtins.removeAttrs hydraJobs blacklist)
+EONIX
 }
 
 # Output packages in tree $2 that weren't in $1.
 # Changing the output hash or name is taken as a change.
 # Extra nix-env parameters can be in $3
 newPkgs() {
-	# We use files instead of pipes, as running multiple nix-env processes
-	# could eat too much memory for a standard 4GiB machine.
-	local -a list
-	for i in 1 2; do
-		local l="$($MKTEMP)"
-		list[$i]="$l"
-		toRemove+=("$l")
+    # We use files instead of pipes, as running multiple nix-env processes
+    # could eat too much memory for a standard 4GiB machine.
+    local -a list
+    for i in 1 2; do
+        local l="$($MKTEMP)"
+        list[$i]="$l"
+        toRemove+=("$l")
 
-		local expr="$($MKTEMP)"
-		toRemove+=("$expr")
-		nixexpr "${!i}" > "$expr"
+        local expr="$($MKTEMP)"
+        toRemove+=("$expr")
+        nixexpr "${!i}" > "$expr"
 
-		nix-env -f "$expr" -qaP --no-name --out-path --show-trace $3 \
-			| sort > "${list[$i]}" &
+        nix-env -f "$expr" -qaP --no-name --out-path --show-trace $3 \
+            | sort > "${list[$i]}" &
 
-		if [ "$parallel" != "true" ]; then
-			wait
-		fi
-	done
+        if [ "$parallel" != "true" ]; then
+            wait
+        fi
+    done
 
-	wait
-	comm -13 "${list[@]}"
+    wait
+    comm -13 "${list[@]}"
 }
 
 # Prepare nixpkgs trees.
 declare -a tree
 for i in 1 2; do
-	if [ -n "${!i}" ]; then # use the given commit
-		dir="$($MKTEMP -d)"
-		tree[$i]="$dir"
-		toRemove+=("$dir")
+    if [ -n "${!i}" ]; then # use the given commit
+        dir="$($MKTEMP -d)"
+        tree[$i]="$dir"
+        toRemove+=("$dir")
 
-		git clone --shared --no-checkout --quiet . "${tree[$i]}"
-		(cd "${tree[$i]}" && git checkout --quiet "${!i}")
-	else #use the current tree
-		tree[$i]="$(pwd)"
-	fi
+        git clone --shared --no-checkout --quiet . "${tree[$i]}"
+        (cd "${tree[$i]}" && git checkout --quiet "${!i}")
+    else #use the current tree
+        tree[$i]="$(pwd)"
+    fi
 done
 
 newlist="$($MKTEMP)"
 toRemove+=("$newlist")
 # Notes:
-#	- the evaluation is done on x86_64-linux, like on Hydra.
-#	- using $newlist file so that newPkgs() isn't in a sub-shell (because of toRemove)
+#    - the evaluation is done on x86_64-linux, like on Hydra.
+#    - using $newlist file so that newPkgs() isn't in a sub-shell (because of toRemove)
 newPkgs "${tree[1]}" "${tree[2]}" '--argstr system "x86_64-linux"' > "$newlist"
 
 # Hacky: keep only the last word of each attribute path and sort.
 sed -n 's/\([^. ]*\.\)*\([^. ]*\) .*$/\2/p' < "$newlist" \
-	| sort | uniq -c
+    | sort | uniq -c
 
 if [ -n "$optPrint" ]; then
-	echo
-	cat "$newlist"
+    echo
+    cat "$newlist"
 fi

From 4f8b48e432d37b4bda1013ca99aab702e6138aac Mon Sep 17 00:00:00 2001
From: Vincenzo Mantova <1962985+xworld21@users.noreply.github.com>
Date: Fri, 24 Sep 2021 10:23:45 +0100
Subject: [PATCH 25/30] texlive.bin.core: remove format -> engine links
 (#136293)

---
 pkgs/tools/typesetting/tex/texlive/bin.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pkgs/tools/typesetting/tex/texlive/bin.nix b/pkgs/tools/typesetting/tex/texlive/bin.nix
index 05c1644c8c7d..9aa2cde0f3c9 100644
--- a/pkgs/tools/typesetting/tex/texlive/bin.nix
+++ b/pkgs/tools/typesetting/tex/texlive/bin.nix
@@ -103,7 +103,9 @@ core = stdenv.mkDerivation rec {
   installTargets = [ "install" "texlinks" ];
 
   # TODO: perhaps improve texmf.cnf search locations
-  postInstall = /* a few texmf-dist files are useful; take the rest from pkgs */ ''
+  postInstall = /* links format -> engine will be regenerated in texlive.combine */ ''
+    PATH="$out/bin:$PATH" ${texlinks} --cnffile "$out/share/texmf-dist/web2c/fmtutil.cnf" --unlink "$out/bin"
+  '' + /* a few texmf-dist files are useful; take the rest from pkgs */ ''
     mv "$out/share/texmf-dist/web2c/texmf.cnf" .
     rm -r "$out/share/texmf-dist"
     mkdir -p "$out"/share/texmf-dist/{web2c,scripts/texlive/TeXLive}

From 74890343e45aac498f881fa8a51e19a9456b5141 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 24 Sep 2021 11:25:05 +0200
Subject: [PATCH 26/30] python3Packages.bitlist: 0.4.0 -> 0.5.1

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

diff --git a/pkgs/development/python-modules/bitlist/default.nix b/pkgs/development/python-modules/bitlist/default.nix
index 42fc3b5460b4..e985dbf28c0f 100644
--- a/pkgs/development/python-modules/bitlist/default.nix
+++ b/pkgs/development/python-modules/bitlist/default.nix
@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "bitlist";
-  version = "0.4.0";
+  version = "0.5.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-IL1tpP/F6O3BvJab6aC6r6PhRgKFpLp9aXmOK1rQXaU=";
+    sha256 = "sha256-bX/Z5FBm21gX4ax/HfqD2bNotZyNFX7dHCEN5uZzQJQ=";
   };
 
   propagatedBuildInputs = [

From bda03add2bcd6ee6406daea4783000d26dcd0c56 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 24 Sep 2021 11:25:26 +0200
Subject: [PATCH 27/30] python3Packages.fountains: 0.2.1 -> 1.0.0

---
 pkgs/development/python-modules/fountains/default.nix | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/fountains/default.nix b/pkgs/development/python-modules/fountains/default.nix
index b706930b3ef3..a5eee78aee33 100644
--- a/pkgs/development/python-modules/fountains/default.nix
+++ b/pkgs/development/python-modules/fountains/default.nix
@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "fountains";
-  version = "0.2.1";
+  version = "1.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0jk5y099g6ggaq5lwp0jlg4asyhcdxnl3him3ibmzc1k9nnknp30";
+    sha256 = "sha256-e4WCO/CS7LBYUziKPuCQIOHEHUlnKE5vDbOsqC8SrA8=";
   };
 
   propagatedBuildInputs = [
@@ -19,6 +19,7 @@ buildPythonPackage rec {
 
   # Project has no test
   doCheck = false;
+
   pythonImportsCheck = [ "fountains" ];
 
   meta = with lib; {

From 25f627eaac5ae4a386b397cb56e5e572c53b2c4c Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Fri, 24 Sep 2021 10:05:57 +0000
Subject: [PATCH 28/30] python38Packages.mypy-boto3-s3: 1.18.46 -> 1.18.47

---
 pkgs/development/python-modules/mypy-boto3-s3/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/mypy-boto3-s3/default.nix b/pkgs/development/python-modules/mypy-boto3-s3/default.nix
index f9c003395182..8a92882ff364 100644
--- a/pkgs/development/python-modules/mypy-boto3-s3/default.nix
+++ b/pkgs/development/python-modules/mypy-boto3-s3/default.nix
@@ -8,12 +8,12 @@
 
 buildPythonPackage rec {
   pname = "mypy-boto3-s3";
-  version = "1.18.46";
+  version = "1.18.47";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4061100ba506866c3ac530733bdefd302acbd67add17daeb22ca02ce3105fcf0";
+    sha256 = "0687354a1970a157f293ff57f8b38379497b606643633912cc28f76e0333b301";
   };
 
   propagatedBuildInputs = [

From e36f885a098825a0228a7967b312873f08a6916e Mon Sep 17 00:00:00 2001
From: Emery Hemingway <ehmry@posteo.net>
Date: Fri, 24 Sep 2021 12:17:20 +0200
Subject: [PATCH 29/30] rstudio: remove ehmry from maintainers

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

diff --git a/pkgs/applications/editors/rstudio/default.nix b/pkgs/applications/editors/rstudio/default.nix
index 76d9c2e594b2..da7047b90254 100644
--- a/pkgs/applications/editors/rstudio/default.nix
+++ b/pkgs/applications/editors/rstudio/default.nix
@@ -135,7 +135,7 @@ mkDerivation rec {
     { description = "Set of integrated tools for the R language";
       homepage = "https://www.rstudio.com/";
       license = licenses.agpl3;
-      maintainers = with maintainers; [ ehmry changlinli ciil ];
+      maintainers = with maintainers; [ changlinli ciil ];
       platforms = platforms.linux;
     };
 }

From 10770653d783ace820726977433e23526bae31e7 Mon Sep 17 00:00:00 2001
From: Michael Weiss <dev.primeos@gmail.com>
Date: Fri, 24 Sep 2021 12:36:19 +0200
Subject: [PATCH 30/30] sks: remove myself as maintainer

I don't use it anymore and, as such, cannot properly test updates/PRs.
---
 pkgs/servers/sks/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/servers/sks/default.nix b/pkgs/servers/sks/default.nix
index 8e0ce6bedac5..05c4c9fcfdad 100644
--- a/pkgs/servers/sks/default.nix
+++ b/pkgs/servers/sks/default.nix
@@ -46,7 +46,7 @@ stdenv.mkDerivation rec {
     inherit (src.meta) homepage;
     license = licenses.gpl2;
     platforms = platforms.linux;
-    maintainers = with maintainers; [ primeos fpletz globin ];
+    maintainers = with maintainers; [ fpletz globin ];
   };
 }