From e936cee0b58bb979059218433eebeb8faed321da Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Sat, 11 Dec 2021 23:09:13 +0100
Subject: [PATCH 01/36] wafw00f: migrate to new Python app style

---
 pkgs/tools/security/wafw00f/default.nix | 14 ++++++++------
 pkgs/top-level/all-packages.nix         |  2 +-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/pkgs/tools/security/wafw00f/default.nix b/pkgs/tools/security/wafw00f/default.nix
index dae4f5a5ad0c..0e363b608fd4 100644
--- a/pkgs/tools/security/wafw00f/default.nix
+++ b/pkgs/tools/security/wafw00f/default.nix
@@ -1,13 +1,12 @@
 { lib
-, buildPythonApplication
 , fetchFromGitHub
-, pluginbase
-, requests
+, python3
 }:
 
-buildPythonApplication rec {
+python3.pkgs.buildPythonApplication rec {
   pname = "wafw00f";
   version = "2.1.0";
+  format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "EnableSecurity";
@@ -16,14 +15,17 @@ buildPythonApplication rec {
     sha256 = "0526kz6ypww9nxc2vddkhpn1gqvn25mzj3wmi91wwxwxjjb6w4qj";
   };
 
-  propagatedBuildInputs = [
+  propagatedBuildInputs = with python3.pkgs; [
     requests
     pluginbase
   ];
 
   # Project has no tests
   doCheck = false;
-  pythonImportsCheck = [ "wafw00f" ];
+
+  pythonImportsCheck = [
+    "wafw00f"
+  ];
 
   meta = with lib; {
     description = "Tool to identify and fingerprint Web Application Firewalls (WAF)";
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index a698cf8fb640..430e7e74fb71 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -29149,7 +29149,7 @@ with pkgs;
 
   wad = python3Packages.callPackage ../tools/security/wad { };
 
-  wafw00f = python3Packages.callPackage ../tools/security/wafw00f { };
+  wafw00f = callPackage ../tools/security/wafw00f { };
 
   waon = callPackage ../applications/audio/waon { };
 

From 3abb28c6cb12e5bc37fbdeb617e307ef229fbaff Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Sun, 12 Dec 2021 22:11:49 +0100
Subject: [PATCH 02/36] udduup: migrate to new Python app style

---
 pkgs/tools/security/uddup/default.nix | 15 ++++++++-------
 pkgs/top-level/all-packages.nix       |  2 +-
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/pkgs/tools/security/uddup/default.nix b/pkgs/tools/security/uddup/default.nix
index 60c3609738d9..5cde218bacfe 100644
--- a/pkgs/tools/security/uddup/default.nix
+++ b/pkgs/tools/security/uddup/default.nix
@@ -1,13 +1,12 @@
 { lib
-, buildPythonApplication
-, colorama
 , fetchFromGitHub
-, pytestCheckHook
+, python3
 }:
 
-buildPythonApplication rec {
+python3.pkgs.buildPythonApplication rec {
   pname = "uddup";
   version = "0.9.3";
+  format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "rotemreiss";
@@ -16,15 +15,17 @@ buildPythonApplication rec {
     sha256 = "1f5dm3772hiik9irnyvbs7wygcafbwi7czw3b47cwhb90b8fi5hg";
   };
 
-  propagatedBuildInputs = [
+  propagatedBuildInputs = with python3.pkgs; [
     colorama
   ];
 
-  checkInputs = [
+  checkInputs = with python3.pkgs; [
     pytestCheckHook
   ];
 
-  pythonImportsCheck = [ "uddup" ];
+  pythonImportsCheck = [
+    "uddup"
+  ];
 
   meta = with lib; {
     description = "Tool for de-duplication URLs";
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index a698cf8fb640..392fd1b91f95 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15479,7 +15479,7 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) CoreFoundation;
   };
 
-  uddup = python3Packages.callPackage ../tools/security/uddup { };
+  uddup = callPackage ../tools/security/uddup { };
 
   udis86 = callPackage  ../development/tools/udis86 { };
 

From b681bf22a035a1818f1cd396ec03788e610824fc Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 15 Dec 2021 09:01:11 +0100
Subject: [PATCH 03/36] python3Packages.readme_renderer: 30.0 -> 32.0

---
 .../python-modules/readme_renderer/default.nix    | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/pkgs/development/python-modules/readme_renderer/default.nix b/pkgs/development/python-modules/readme_renderer/default.nix
index 43d1494a58b0..ee2599a8fb75 100644
--- a/pkgs/development/python-modules/readme_renderer/default.nix
+++ b/pkgs/development/python-modules/readme_renderer/default.nix
@@ -12,13 +12,16 @@
 }:
 
 buildPythonPackage rec {
-  pname = "readme_renderer";
-  version = "30.0";
+  pname = "readme-renderer";
+  version = "32.0";
+  format = "setuptools";
+
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
-    inherit pname version;
-    sha256 = "sha256-gplwDXqRDDBAcqdgHq+tpnEqWwEaIBOUF+Gx6fBGRdg=";
+    pname = "readme_renderer";
+    inherit version;
+    sha256 = "sha256-tRK+r6Z5gmDH1a8+Gx8Jfli/zZpXXafE3dXgN0kKW4U=";
   };
 
   propagatedBuildInputs = [
@@ -34,7 +37,9 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
-  pythonImportsCheck = [ "readme_renderer" ];
+  pythonImportsCheck = [
+    "readme_renderer"
+  ];
 
   meta = with lib; {
     description = "Python library for rendering readme descriptions";

From 7df866f152e48a1874e82551b99c2a8311198f03 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Sun, 19 Dec 2021 16:54:51 +0100
Subject: [PATCH 04/36] python3Packages.yalexs: 1.1.13 -> 1.1.15

---
 pkgs/development/python-modules/yalexs/default.nix | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/yalexs/default.nix b/pkgs/development/python-modules/yalexs/default.nix
index a97ebe947af9..9b9ef513f70d 100644
--- a/pkgs/development/python-modules/yalexs/default.nix
+++ b/pkgs/development/python-modules/yalexs/default.nix
@@ -16,14 +16,16 @@
 
 buildPythonPackage rec {
   pname = "yalexs";
-  version = "1.1.13";
+  version = "1.1.15";
+  format = "setuptools";
+
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "bdraco";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0938540n60xv7kxam3azszn3nj0mnhhgh5p4hgbfxj43bkwpqz4n";
+    sha256 = "sha256-EK9jmbU3A2rNx/H8WOsZiGA7tqzg/XJkW/DV5s+2Y3U=";
   };
 
   propagatedBuildInputs = [
@@ -44,10 +46,13 @@ buildPythonPackage rec {
 
   postPatch = ''
     # Not used requirement
-    substituteInPlace setup.py --replace '"vol",' ""
+    substituteInPlace setup.py \
+      --replace '"vol",' ""
   '';
 
-  pythonImportsCheck = [ "yalexs" ];
+  pythonImportsCheck = [
+    "yalexs"
+  ];
 
   meta = with lib; {
     description = "Python API for Yale Access (formerly August) Smart Lock and Doorbell";

From a76dcd5293dcb110f14e05f312fa86b19a2def56 Mon Sep 17 00:00:00 2001
From: Ashish SHUKLA <ashish.is@lostca.se>
Date: Mon, 20 Dec 2021 19:34:01 +0530
Subject: [PATCH 05/36] cinny: init at 1.6.1

---
 .../instant-messengers/cinny/default.nix      | 31 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 33 insertions(+)
 create mode 100644 pkgs/applications/networking/instant-messengers/cinny/default.nix

diff --git a/pkgs/applications/networking/instant-messengers/cinny/default.nix b/pkgs/applications/networking/instant-messengers/cinny/default.nix
new file mode 100644
index 000000000000..4c8f356cdf47
--- /dev/null
+++ b/pkgs/applications/networking/instant-messengers/cinny/default.nix
@@ -0,0 +1,31 @@
+{ lib, stdenv, fetchurl, writeText, jq, conf ? {} }:
+
+let
+  configOverrides = writeText "cinny-config-overrides.json" (builtins.toJSON conf);
+in stdenv.mkDerivation rec {
+  pname = "cinny";
+  version = "1.6.1";
+
+  src = fetchurl {
+    url = "https://github.com/ajbura/cinny/releases/download/v${version}/cinny-v${version}.tar.gz";
+    sha256 = "sha256-RJpLK16bedpqo/JJf3atpiuL5spHJNowomcusjZtEWA=";
+  };
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/
+    cp -R . $out/
+    ${jq}/bin/jq -s '.[0] * .[1]' "config.json" "${configOverrides}" > "$out/config.json"
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Yet another Matrix client for the web";
+    homepage = "https://cinny.in/";
+    maintainers = with maintainers; [ abbe ];
+    license = licenses.mit;
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index c057511d2cb9..12ff76396923 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -2473,6 +2473,8 @@ with pkgs;
 
   cht-sh = callPackage ../tools/misc/cht.sh { };
 
+  cinny = callPackage ../applications/networking/instant-messengers/cinny {};
+
   ckbcomp = callPackage ../tools/X11/ckbcomp { };
 
   clac = callPackage ../tools/misc/clac {};

From 02f5a25a790fc040ff2ce86d43a46201cf789634 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 28 Dec 2021 00:41:59 +0100
Subject: [PATCH 06/36] python3Packages.rich: 10.14.0 -> 10.16.1

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

diff --git a/pkgs/development/python-modules/rich/default.nix b/pkgs/development/python-modules/rich/default.nix
index 98c26c7a7ff3..6517d15df579 100644
--- a/pkgs/development/python-modules/rich/default.nix
+++ b/pkgs/development/python-modules/rich/default.nix
@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "rich";
-  version = "10.14.0";
+  version = "10.16.1";
   format = "pyproject";
   disabled = pythonOlder "3.6";
 
@@ -21,7 +21,7 @@ buildPythonPackage rec {
     owner = "willmcgugan";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1j1m1064gmy07ah4crds5sd0k7dcwvf2b1z6rvjfvq4v9fx962qv";
+    sha256 = "sha256-smeRZTMIDbK9pZRRj42BGj8ifQw9bTTE90rGaV/Up/4=";
   };
 
   nativeBuildInputs = [ poetry-core ];

From e06ee07eabb1deec8b4583ad57c29e7d7ebeeb18 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 28 Dec 2021 00:42:25 +0100
Subject: [PATCH 07/36] python3Packages.censys: 2.0.9 -> 2.1.0

---
 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 38653306eefb..4262efb1a317 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 = "2.0.9";
+  version = "2.1.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.6";
@@ -24,7 +24,7 @@ buildPythonPackage rec {
     owner = "censys";
     repo = "censys-python";
     rev = "v${version}";
-    sha256 = "sha256-qh3Z8Gza8J3OEM94GguJ+oEdVle01Gx1m/7+LCOErKY=";
+    sha256 = "sha256-zQoG7clqDAxwJIt0AQcj8kKGODL61ODc4inP2Ll+Jt8=";
   };
 
   nativeBuildInputs = [

From c1b7880d1a203312225c5d7d1a6250c72d485017 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 31 Dec 2021 18:45:07 +0000
Subject: [PATCH 08/36] python38Packages.pyatmo: 6.2.0 -> 6.2.2

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

diff --git a/pkgs/development/python-modules/pyatmo/default.nix b/pkgs/development/python-modules/pyatmo/default.nix
index c039ff16b80e..d35a574029a4 100644
--- a/pkgs/development/python-modules/pyatmo/default.nix
+++ b/pkgs/development/python-modules/pyatmo/default.nix
@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "pyatmo";
-  version = "6.2.0";
+  version = "6.2.2";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
@@ -25,7 +25,7 @@ buildPythonPackage rec {
     owner = "jabesq";
     repo = "pyatmo";
     rev = "v${version}";
-    sha256 = "sha256-VBc2avJiIFQW1LYXQEvIZ/wZKMFJsCF9DDrxwL8dDnk=";
+    sha256 = "1cd6g5vix8k45ndx4aq4pvyyisqdp38gd2466jrlg8z9byandj0i";
   };
 
   SETUPTOOLS_SCM_PRETEND_VERSION = version;

From ce8f41643bf2d4eaf92680eb384b197e561671f1 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Sun, 2 Jan 2022 21:38:31 +0100
Subject: [PATCH 09/36] python3Packages.cmarkgfm: 0.6.0 -> 0.7.0

---
 .../python-modules/cmarkgfm/default.nix       | 24 ++++++++++++++-----
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/pkgs/development/python-modules/cmarkgfm/default.nix b/pkgs/development/python-modules/cmarkgfm/default.nix
index 1085f4030c1e..c0863a5b3945 100644
--- a/pkgs/development/python-modules/cmarkgfm/default.nix
+++ b/pkgs/development/python-modules/cmarkgfm/default.nix
@@ -3,24 +3,36 @@
 , cffi
 , fetchPypi
 , pytestCheckHook
+, pythonOlder
 }:
 
 buildPythonPackage rec {
   pname = "cmarkgfm";
-  version = "0.6.0";
+  version = "0.7.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ec2bf8d5799c4b5bbfbae30a4a1dfcb06512f2e17e9ee60ba7e1d390318582fc";
+    sha256 = "sha256-plwVL52ov4JxTxnCh/4JaO6Of4mejZRQPXPQ/lcinBk=";
   };
 
-  propagatedNativeBuildInputs = [ cffi ];
+  propagatedNativeBuildInputs = [
+    cffi
+  ];
 
-  propagatedBuildInputs = [ cffi ];
+  propagatedBuildInputs = [
+    cffi
+  ];
 
-  checkInputs = [ pytestCheckHook ];
+  checkInputs = [
+    pytestCheckHook
+  ];
 
-  pythonImportsCheck = [ "cmarkgfm" ];
+  pythonImportsCheck = [
+    "cmarkgfm"
+  ];
 
   meta = with lib; {
     description = "Minimal bindings to GitHub's fork of cmark";

From 340076689f44d49a5d7183cb076cad5e25b4fea3 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Mon, 3 Jan 2022 21:36:07 +0100
Subject: [PATCH 10/36] python3Packages.ephem: 4.1.1 -> 4.1.3

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

diff --git a/pkgs/development/python-modules/ephem/default.nix b/pkgs/development/python-modules/ephem/default.nix
index 1e5db008dea9..a5a87f908d4f 100644
--- a/pkgs/development/python-modules/ephem/default.nix
+++ b/pkgs/development/python-modules/ephem/default.nix
@@ -7,12 +7,12 @@
 
 buildPythonPackage rec {
   pname = "ephem";
-  version = "4.1.1";
+  version = "4.1.3";
   format = "setuptools";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-26ngXHjOkQrnWgY1GlWSR5GRqNxXCsDNbRinfpgTiHM=";
+    sha256 = "sha256-f6GGhZgbpSjt1QQFKp1SEqCapb8VwRpzTtxqhuiotWo=";
   };
 
   checkInputs = [

From 3aae5c9376711c8cc64b940677668bc6a4ba781b Mon Sep 17 00:00:00 2001
From: Vladyslav M <dywedir@gra.red>
Date: Mon, 3 Jan 2022 23:27:37 +0200
Subject: [PATCH 11/36] pijul: 1.0.0-alpha.56 -> 1.0.0-alpha.57

---
 pkgs/applications/version-management/pijul/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/version-management/pijul/default.nix b/pkgs/applications/version-management/pijul/default.nix
index 03659e0ba40f..ac3beb54f6ec 100644
--- a/pkgs/applications/version-management/pijul/default.nix
+++ b/pkgs/applications/version-management/pijul/default.nix
@@ -13,14 +13,14 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "pijul";
-  version = "1.0.0-alpha.56";
+  version = "1.0.0-alpha.57";
 
   src = fetchCrate {
     inherit version pname;
-    sha256 = "zV4F4dbjJ58yGiupUwj5Z0HrKR78Mzch8Zs98YfxSTQ=";
+    sha256 = "sha256-HhGUoO8UHJkfQ5QQ/H+PT8mqvdPb8Ok4D3j7QArLBeA=";
   };
 
-  cargoSha256 = "JQGBTCNu9U2Kq6tc7VT07LEbzLW+jdVWrK5e2qjzGRA=";
+  cargoSha256 = "sha256-SyyJqUC7bCUJf53/+GJ/7+huab8hycNABwAFaHHmJtY=";
 
   doCheck = false;
   nativeBuildInputs = [ pkg-config ];

From 4606c0e5c6f55e0d0e34e15b631c0c76f248dc90 Mon Sep 17 00:00:00 2001
From: Mathieu Post <mathieupost@gmail.com>
Date: Tue, 4 Jan 2022 15:20:27 +0100
Subject: [PATCH 12/36] golangci-lint: add fish completion

---
 pkgs/development/tools/golangci-lint/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/tools/golangci-lint/default.nix b/pkgs/development/tools/golangci-lint/default.nix
index a142d9a9d9bf..706d8e428ff9 100644
--- a/pkgs/development/tools/golangci-lint/default.nix
+++ b/pkgs/development/tools/golangci-lint/default.nix
@@ -24,7 +24,7 @@ buildGoModule rec {
   ];
 
   postInstall = ''
-    for shell in bash zsh; do
+    for shell in bash zsh fish; do
       HOME=$TMPDIR $out/bin/golangci-lint completion $shell > golangci-lint.$shell
       installShellCompletion golangci-lint.$shell
     done

From 8bedcacaf137c71bbc7096c88d37229e73c8e48c Mon Sep 17 00:00:00 2001
From: Vincent Haupert <mail@vincent-haupert.de>
Date: Wed, 5 Jan 2022 00:19:09 +0100
Subject: [PATCH 13/36] linux: enable X86_SGX{_KVM} on x86_64 only

The config option X86_SGX is available on x86_64-linux only; i686-linux
is not supported.

https://github.com/torvalds/linux/blob/55a677b/arch/x86/Kconfig#L1914
---
 pkgs/os-specific/linux/kernel/common-config.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/os-specific/linux/kernel/common-config.nix b/pkgs/os-specific/linux/kernel/common-config.nix
index b127ec9197cb..82de6a96e745 100644
--- a/pkgs/os-specific/linux/kernel/common-config.nix
+++ b/pkgs/os-specific/linux/kernel/common-config.nix
@@ -473,7 +473,7 @@ let
 
       # Detect buffer overflows on the stack
       CC_STACKPROTECTOR_REGULAR = {optional = true; tristate = whenOlder "4.18" "y";};
-    } // optionalAttrs stdenv.hostPlatform.isx86 {
+    } // optionalAttrs stdenv.hostPlatform.isx86_64 {
       # Enable Intel SGX
       X86_SGX     = whenAtLeast "5.11" yes;
       # Allow KVM guests to load SGX enclaves

From c5c1b337e52b99d92d8330f48a544e0f48ca7889 Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Mon, 3 Jan 2022 23:35:33 -0800
Subject: [PATCH 14/36] python3Packages.gcsfs.src: fix sha

---
 pkgs/development/python-modules/gcsfs/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/python-modules/gcsfs/default.nix b/pkgs/development/python-modules/gcsfs/default.nix
index c6e0dc18356b..9eeb13b8f97f 100644
--- a/pkgs/development/python-modules/gcsfs/default.nix
+++ b/pkgs/development/python-modules/gcsfs/default.nix
@@ -26,7 +26,7 @@ buildPythonPackage rec {
     owner = "dask";
     repo = pname;
     rev = version;
-    sha256 = "sha256-BME40kyxZHx9+XrMCqWYp8+q6tjeYwAw/zISMNpQxDU=";
+    sha256 = "sha256-cpV+HKE39Yct1yu5xW9HZftx2Wy9ydFL2YLvPD3YM2M=";
   };
 
   propagatedBuildInputs = [

From dcc20d7c1710cd043554378fd1b04dc819361108 Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Mon, 3 Jan 2022 23:22:25 -0800
Subject: [PATCH 15/36] firebird_4.src: fix sha256

---
 pkgs/servers/firebird/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/servers/firebird/default.nix b/pkgs/servers/firebird/default.nix
index 5a975205a245..7924f6e6ab4a 100644
--- a/pkgs/servers/firebird/default.nix
+++ b/pkgs/servers/firebird/default.nix
@@ -75,7 +75,7 @@ let base = {
       owner = "FirebirdSQL";
       repo = "firebird";
       rev = "v${version}";
-      sha256 = "sha256-a4ex19FMfiJsUEhWUYd2YXKgJ24Jnpoab2t6x9sUuyQ=";
+      sha256 = "sha256-Pc3hUAhXgpa6VOkjidfh/vS/60Gtjenid8nHnIH7s0E=";
     };
 
     buildInputs = base.buildInputs ++ [ zlib unzip libtommath libtomcrypt ];

From e604394699d95482f3cf8e792cdb7666ac9407a9 Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Mon, 3 Jan 2022 22:27:08 -0800
Subject: [PATCH 16/36] bitcoin-classic.src: fix sha

---
 pkgs/applications/blockchains/bitcoin-classic/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/applications/blockchains/bitcoin-classic/default.nix b/pkgs/applications/blockchains/bitcoin-classic/default.nix
index 533e3c7dca6e..8aacb50a1b54 100644
--- a/pkgs/applications/blockchains/bitcoin-classic/default.nix
+++ b/pkgs/applications/blockchains/bitcoin-classic/default.nix
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
     owner = "bitcoinclassic";
     repo = "bitcoinclassic";
     rev = "v${version}";
-    sha256 = "sha256-V1cOB5FLotGS5jup/aVaiDiyr/v2KJ2SLcIu/Hrjuwk=";
+    sha256 = "sha256-fVmFD1B4kKoejd2cmPPF5TJJQTAA6AVsGlVY8IIUNK4=";
   };
 
   nativeBuildInputs = [ pkg-config autoreconfHook ];

From 681f18ffa80a55c870cdd721c548676ba5c2eef2 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Wed, 5 Jan 2022 08:21:00 +0000
Subject: [PATCH 17/36] python38Packages.deemix: 3.6.4 -> 3.6.5

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

diff --git a/pkgs/development/python-modules/deemix/default.nix b/pkgs/development/python-modules/deemix/default.nix
index cf54f6facf82..e9bbb8a63773 100644
--- a/pkgs/development/python-modules/deemix/default.nix
+++ b/pkgs/development/python-modules/deemix/default.nix
@@ -12,12 +12,12 @@
 
 buildPythonPackage rec {
   pname = "deemix";
-  version = "3.6.4";
+  version = "3.6.5";
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "268617b3ff9346ae51a063cbdb820c1f591cbadc1cf2fafd201dc671e721c1dd";
+    sha256 = "c56245b2a2142dafb0658d60919ccf34e04e5d87720d5909e0e030521349a65a";
   };
 
   propagatedBuildInputs = [

From 6597f5a27438abcfbe75fa8cbdc33fe686ab9582 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 09:38:24 +0100
Subject: [PATCH 18/36] python3Packages.ansible-runner: disable failing tests

---
 .../python-modules/ansible-runner/default.nix | 61 +++++++++++--------
 1 file changed, 36 insertions(+), 25 deletions(-)

diff --git a/pkgs/development/python-modules/ansible-runner/default.nix b/pkgs/development/python-modules/ansible-runner/default.nix
index f4ec1c184627..92d377d0886c 100644
--- a/pkgs/development/python-modules/ansible-runner/default.nix
+++ b/pkgs/development/python-modules/ansible-runner/default.nix
@@ -1,30 +1,40 @@
 { lib
-, buildPythonPackage
-, fetchPypi
-, psutil
-, pexpect
-, python-daemon
-, pyyaml
-, six
 , stdenv
 , ansible
+, buildPythonPackage
+, fetchPypi
 , mock
 , openssh
+, pexpect
+, psutil
 , pytest-mock
 , pytest-timeout
 , pytest-xdist
 , pytestCheckHook
+, python-daemon
+, pyyaml
+, six
 }:
 
 buildPythonPackage rec {
   pname = "ansible-runner";
   version = "2.1.1";
+  format = "setuptools";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7684612f7543c5f07f3e8135667eeb22a9dbd98f625cc69901ba9924329ef24f";
+    hash = "sha256-doRhL3VDxfB/PoE1Zn7rIqnb2Y9iXMaZAbqZJDKe8k8=";
   };
 
+  propagatedBuildInputs = [
+    ansible
+    psutil
+    pexpect
+    python-daemon
+    pyyaml
+    six
+  ];
+
   checkInputs = [
     ansible # required to place ansible CLI onto the PATH in tests
     pytestCheckHook
@@ -35,44 +45,45 @@ buildPythonPackage rec {
     openssh
   ];
 
-  propagatedBuildInputs = [
-    ansible
-    psutil
-    pexpect
-    python-daemon
-    pyyaml
-    six
-  ];
-
   preCheck = ''
     export HOME=$(mktemp -d)
+    export PATH="$PATH:$out/bin";
   '';
 
   disabledTests = [
-    "test_callback_plugin_task_args_leak" # requires internet
+    # Requires network access
+    "test_callback_plugin_task_args_leak"
     "test_env_accuracy"
-    "test_large_stdout_blob" # times out on slower hardware
-  ]
+    # Times out on slower hardware
+    "test_large_stdout_blob"
+    # Failed: DID NOT RAISE <class 'RuntimeError'>
+    "test_validate_pattern"
+  ] ++ lib.optional stdenv.isDarwin [
     # test_process_isolation_settings is currently broken on Darwin Catalina
     # https://github.com/ansible/ansible-runner/issues/413
-  ++ lib.optional stdenv.isDarwin "process_isolation_settings";
+    "process_isolation_settings"
+  ];
 
   disabledTestPaths = [
-    # these tests unset PATH and then run executables like `bash` (see https://github.com/ansible/ansible-runner/pull/918)
+    # These tests unset PATH and then run executables like `bash` (see https://github.com/ansible/ansible-runner/pull/918)
     "test/integration/test_runner.py"
     "test/unit/test_runner.py"
   ]
   ++ lib.optionals stdenv.isDarwin [
-    # integration tests on Darwin are not regularly passing in ansible-runner's own CI
+    # Integration tests on Darwin are not regularly passing in ansible-runner's own CI
     "test/integration"
-    # these tests write to `/tmp` which is not writable on Darwin
+    # These tests write to `/tmp` which is not writable on Darwin
     "test/unit/config/test__base.py"
   ];
 
+  pythonImportsCheck = [
+    "ansible_runner"
+  ];
+
   meta = with lib; {
     description = "Helps when interfacing with Ansible";
     homepage = "https://github.com/ansible/ansible-runner";
     license = licenses.asl20;
-    maintainers = [ maintainers.costrouc ];
+    maintainers = with maintainers; [ costrouc ];
   };
 }

From 893ffee2866dbf9f2aa6e3128368e0cd5729e4b9 Mon Sep 17 00:00:00 2001
From: kraem <ebrin.ronnie@protonmail.com>
Date: Wed, 5 Jan 2022 12:36:54 +0100
Subject: [PATCH 19/36] Revert "nixos/documentation: avoid copying nixpkgs
 subpaths"

builtins.storePath is not allowed in pure evaluation mode

This reverts commit 1511e72b75b49cdeeee68def0c203f997d01bafa.
---
 nixos/modules/misc/documentation.nix | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/nixos/modules/misc/documentation.nix b/nixos/modules/misc/documentation.nix
index 70152c5d6624..7d8fc08b60e3 100644
--- a/nixos/modules/misc/documentation.nix
+++ b/nixos/modules/misc/documentation.nix
@@ -67,15 +67,11 @@ let
               (t == "directory" -> baseNameOf n != "tests")
               && (t == "file" -> hasSuffix ".nix" n)
             );
-        pull = dir:
-          if isStorePath pkgs.path
-          then "${builtins.storePath pkgs.path}/${dir}"
-          else filter "${toString pkgs.path}/${dir}";
       in
         pkgs.runCommand "lazy-options.json" {
-          libPath = pull "lib";
-          pkgsLibPath = pull "pkgs/pkgs-lib";
-          nixosPath = pull "nixos";
+          libPath = filter "${toString pkgs.path}/lib";
+          pkgsLibPath = filter "${toString pkgs.path}/pkgs/pkgs-lib";
+          nixosPath = filter "${toString pkgs.path}/nixos";
           modules = map (p: ''"${removePrefix "${modulesPath}/" (toString p)}"'') docModules.lazy;
         } ''
           export NIX_STORE_DIR=$TMPDIR/store

From a173e35a9e624423dce0b42f566c1e922e1735d9 Mon Sep 17 00:00:00 2001
From: 0x4A6F <0x4A6F@users.noreply.github.com>
Date: Wed, 5 Jan 2022 14:15:49 +0100
Subject: [PATCH 20/36] zellij: 0.23.0 -> 0.24.0 (#153587)

---
 pkgs/tools/misc/zellij/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/tools/misc/zellij/default.nix b/pkgs/tools/misc/zellij/default.nix
index 2fb985c79162..6a09ba4e0ec5 100644
--- a/pkgs/tools/misc/zellij/default.nix
+++ b/pkgs/tools/misc/zellij/default.nix
@@ -12,16 +12,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "zellij";
-  version = "0.23.0";
+  version = "0.24.0";
 
   src = fetchFromGitHub {
     owner = "zellij-org";
     repo = "zellij";
     rev = "v${version}";
-    sha256 = "sha256-DJ7FGtcsWGk4caS22aXo+8chCcvEdRlVrSRmIHsETD4=";
+    sha256 = "sha256-GYbRu2ZEFswyOBUbg6jdAZQRogIDT/YolEElZT8h744=";
   };
 
-  cargoSha256 ="sha256-dWdFBSZwTEvxrPiXtTWcYLtC+4XFb5R7Wu4r1YpHQRk=";
+  cargoSha256 = "sha256-ogWFAO3xMH4vho9SRjyeHCDxRtAx6exGkMpNhz2VOLA";
 
   nativeBuildInputs = [
     installShellFiles

From 492a4bd35757398939cff434a1fa2a7cec50f400 Mon Sep 17 00:00:00 2001
From: Vladimir Serov <me@cab404.ru>
Date: Wed, 5 Jan 2022 16:19:19 +0300
Subject: [PATCH 21/36] super-slicer: 2.3.57.8 -> 2.3.57.9

---
 pkgs/applications/misc/prusa-slicer/super-slicer.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/misc/prusa-slicer/super-slicer.nix b/pkgs/applications/misc/prusa-slicer/super-slicer.nix
index 384ca820d505..72941e3f23e5 100644
--- a/pkgs/applications/misc/prusa-slicer/super-slicer.nix
+++ b/pkgs/applications/misc/prusa-slicer/super-slicer.nix
@@ -5,8 +5,8 @@ let
   description = "PrusaSlicer fork with more features and faster development cycle";
 
   versions = {
-    stable = { version = "2.3.57.8"; sha256 = "sha256-k1G9sFukYyCqVeJIbYgjJX9T8zqmFTmjmj9OXZ78+LY="; };
-    latest = { version = "2.3.57.8"; sha256 = "sha256-k1G9sFukYyCqVeJIbYgjJX9T8zqmFTmjmj9OXZ78+LY="; };
+    stable = { version = "2.3.57.9"; sha256 = "sha256-JWZ6PdzKwxdyp7StYuW69XGbTPoxaIJ2R4Ynmc65hvE="; };
+    latest = { version = "2.3.57.9"; sha256 = "sha256-JWZ6PdzKwxdyp7StYuW69XGbTPoxaIJ2R4Ynmc65hvE="; };
   };
 
   override = { version, sha256 }: super: {

From b65eb7ec84816acba5b6b5721fd6a3cdddf160a3 Mon Sep 17 00:00:00 2001
From: Will Cohen <willcohen@users.noreply.github.com>
Date: Wed, 5 Jan 2022 08:35:16 -0500
Subject: [PATCH 22/36] obb: switch to fetchFromGitHub

---
 pkgs/development/interpreters/clojure/obb.nix | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/interpreters/clojure/obb.nix b/pkgs/development/interpreters/clojure/obb.nix
index 3e0a63b5e28c..2b37428b25ba 100644
--- a/pkgs/development/interpreters/clojure/obb.nix
+++ b/pkgs/development/interpreters/clojure/obb.nix
@@ -7,6 +7,7 @@
 , git
 , jdk
 , callPackage
+, fetchFromGitHub
 , makeWrapper
 , runCommand }:
 
@@ -14,9 +15,11 @@ stdenv.mkDerivation rec {
   pname = "obb";
   version = "0.0.1";
 
-  src = fetchurl {
-    url = "https://github.com/babashka/${pname}/archive/refs/tags/v${version}.tar.gz";
-    sha256 = "sha256-ZVd3VCJ7vdQGQ7iY5v2b+gRX/Ni0/03hzqBElqpPvpI=";
+  src = fetchFromGitHub {
+    owner = "babashka";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-WxQjBg6el6XMiHTurmSo1GgZnTdaJjRmcV3+3X4yohc=";
   };
 
   nativeBuildInputs = [ makeWrapper ];

From 3dd76988673bd6a67ab43567963ead57030af355 Mon Sep 17 00:00:00 2001
From: Will Cohen <willcohen@users.noreply.github.com>
Date: Wed, 5 Jan 2022 08:39:26 -0500
Subject: [PATCH 23/36] obb: switch to passthru.tests

---
 pkgs/development/interpreters/clojure/obb.nix | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/pkgs/development/interpreters/clojure/obb.nix b/pkgs/development/interpreters/clojure/obb.nix
index 2b37428b25ba..9583be923939 100644
--- a/pkgs/development/interpreters/clojure/obb.nix
+++ b/pkgs/development/interpreters/clojure/obb.nix
@@ -6,7 +6,7 @@
 , clojure
 , git
 , jdk
-, callPackage
+, obb
 , fetchFromGitHub
 , makeWrapper
 , runCommand }:
@@ -64,11 +64,12 @@ stdenv.mkDerivation rec {
     runHook postInstall
   '';
 
-  doInstallCheck = true;
-  installCheckPhase = ''
-    [ $($out/bin/obb -e '(+ 1 2)') = '3' ]
-  '';
-
+  passthru.tests = {
+    simple = runCommand "${pname}-test" {} ''
+      [ $(${obb}/bin/obb -e '(+ 1 2)') = '3' ]
+      touch $out
+    '';
+  };
 
   meta = with lib; {
     description = "Ad-hoc ClojureScript scripting of Mac applications via Apple's Open Scripting Architecture";

From 50284bd7c0e621c43c93f415f228213c0a029bcb Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 14:50:01 +0100
Subject: [PATCH 24/36] python3Packages.sqlobject: disable failing test

---
 .../python-modules/sqlobject/default.nix      | 26 ++++++++++++++++---
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/sqlobject/default.nix b/pkgs/development/python-modules/sqlobject/default.nix
index c645a850f497..817ba2dfc706 100644
--- a/pkgs/development/python-modules/sqlobject/default.nix
+++ b/pkgs/development/python-modules/sqlobject/default.nix
@@ -9,17 +9,35 @@
 }:
 
 buildPythonPackage rec {
-  pname = "SQLObject";
+  pname = "sqlobject";
   version = "3.9.1";
+  format = "setuptools";
 
   src = fetchPypi {
-    inherit pname version;
+    pname = "SQLObject";
+    inherit version;
     sha256 = "45064184decf7f42d386704e5f47a70dee517d3e449b610506e174025f84d921";
   };
 
-  propagatedBuildInputs = [ FormEncode pastedeploy paste pydispatcher ];
+  propagatedBuildInputs = [
+    FormEncode
+    paste
+    pastedeploy
+    pydispatcher
+  ];
 
-  checkInputs = [ pytestCheckHook ];
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  disabledTests = [
+    # https://github.com/sqlobject/sqlobject/issues/179
+    "test_fail"
+  ];
+
+  pythonImportsCheck = [
+    "sqlobject"
+  ];
 
   meta = with lib; {
     description = "Object Relational Manager for providing an object interface to your database";

From 07db5d29809b0e30084c769c3c49ba2cf9a50c82 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 15:24:38 +0100
Subject: [PATCH 25/36] python3Packages.pycm: disable failing test

---
 .../python-modules/pycm/default.nix           | 49 ++++++++++++++-----
 1 file changed, 38 insertions(+), 11 deletions(-)

diff --git a/pkgs/development/python-modules/pycm/default.nix b/pkgs/development/python-modules/pycm/default.nix
index 9e3b711718c3..878e36e5c07a 100644
--- a/pkgs/development/python-modules/pycm/default.nix
+++ b/pkgs/development/python-modules/pycm/default.nix
@@ -1,28 +1,55 @@
-{ lib, buildPythonPackage, fetchFromGitHub, isPy3k, matplotlib, numpy, pytestCheckHook, seaborn }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, matplotlib
+, numpy
+, pytestCheckHook
+, pythonOlder
+, seaborn
+}:
 
 buildPythonPackage rec {
   pname = "pycm";
   version = "3.3";
+  format = "setuptools";
 
-  disabled = !isPy3k;
+  disabled = pythonOlder "3.5";
 
   src = fetchFromGitHub {
-    owner  = "sepandhaghighi";
-    repo   = pname;
-    rev    = "v${version}";
+    owner = "sepandhaghighi";
+    repo = pname;
+    rev = "v${version}";
     sha256 = "0i3qpb20mnc22qny1ar3yvxb1dac7njwi8bvi5sy5kywz10c5dkw";
   };
 
-  # remove a trivial dependency on the author's `art` Python ASCII art library
+  propagatedBuildInputs = [
+    matplotlib
+    numpy
+    seaborn
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
   postPatch = ''
+    # Remove a trivial dependency on the author's `art` Python ASCII art library
     rm pycm/__main__.py
-    rm Otherfiles/notebook_check.py  # also depends on python3Packages.notebook
-    substituteInPlace setup.py --replace '=get_requires()' '=[]'
+    # Also depends on python3Packages.notebook
+    rm Otherfiles/notebook_check.py
+    substituteInPlace setup.py \
+      --replace '=get_requires()' '=[]'
   '';
 
-  checkInputs = [ pytestCheckHook ];
-  disabledTests = [ "pycm.pycm_compare.Compare" ];  # output formatting error
-  propagatedBuildInputs = [ matplotlib numpy seaborn ];
+  disabledTests = [
+    # Output formatting error
+    "pycm.pycm_compare.Compare"
+    "plot_test"
+  ];
+
+  pythonImportsCheck = [
+    "pycm"
+  ];
 
   meta = with lib; {
     description = "Multiclass confusion matrix library";

From ea6b995da5dea47ebd38db11133ee9a2ba357749 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 15:28:16 +0100
Subject: [PATCH 26/36] python3Packages.flux-led: 0.27.36 -> 0.27.40

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

diff --git a/pkgs/development/python-modules/flux-led/default.nix b/pkgs/development/python-modules/flux-led/default.nix
index a898520f5992..bb271807a7b3 100644
--- a/pkgs/development/python-modules/flux-led/default.nix
+++ b/pkgs/development/python-modules/flux-led/default.nix
@@ -8,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "flux-led";
-  version = "0.27.36";
+  version = "0.27.40";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "Danielhiversen";
     repo = "flux_led";
     rev = version;
-    sha256 = "sha256-Q84hDb7YnYU5L2IyL3aZ/16yRxViGlt8VX4vlMcykDA=";
+    sha256 = "sha256-imfdLomMjeGAyVBSygx+TV0DA9OrMreeSlzzrJ2B9cc=";
   };
 
   propagatedBuildInputs = [

From a2fa741467689446957b968a20b28d6f5126ba25 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 15:33:07 +0100
Subject: [PATCH 27/36] python3Packages.pyebus: 1.2.4 -> 1.4.0

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

diff --git a/pkgs/development/python-modules/pyebus/default.nix b/pkgs/development/python-modules/pyebus/default.nix
index d4c8658673a0..5506c1fbf36e 100644
--- a/pkgs/development/python-modules/pyebus/default.nix
+++ b/pkgs/development/python-modules/pyebus/default.nix
@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "pyebus";
-  version = "1.2.4";
+  version = "1.4.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "i+p40s9SXey1lfXWW+PiXsA1kUF4o6Rk7QLmQ2ljN6g=";
+    sha256 = "sha256-6ooOSJAIi8vYmCjDHnbMGQJfPqPmzA5thDSg+iM7T+8=";
   };
 
   nativeBuildInputs = [

From e01959e3cefd016dc271ef8985831c012dc46fd7 Mon Sep 17 00:00:00 2001
From: deltadelta <contact@libellules.eu>
Date: Tue, 4 Jan 2022 17:47:10 +0100
Subject: [PATCH 28/36] maintainers: add deltadelta

---
 maintainers/maintainer-list.nix | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index a03d2e4b9318..ec48bd7dc206 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -2812,6 +2812,11 @@
     email = "d4delta@outlook.fr";
     name = "Delta";
   };
+  deltadelta = {
+    email = "contact@libellules.eu";
+    name = "Dara Ly";
+    github = "tournemire";
+  };
   deltaevo = {
     email = "deltaduartedavid@gmail.com";
     github = "DeltaEvo";

From a207408aa280e2dbf1db0bbc23a01a25237b911b Mon Sep 17 00:00:00 2001
From: deltadelta <contact@libellules.eu>
Date: Tue, 4 Jan 2022 17:51:12 +0100
Subject: [PATCH 29/36] ocamlPackages.dbf: init at 1.1.0

---
 maintainers/maintainer-list.nix               |  1 +
 .../development/ocaml-modules/dbf/default.nix | 28 +++++++++++++++++++
 pkgs/top-level/ocaml-packages.nix             |  2 ++
 3 files changed, 31 insertions(+)
 create mode 100644 pkgs/development/ocaml-modules/dbf/default.nix

diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index ec48bd7dc206..1a950838ab0c 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -2816,6 +2816,7 @@
     email = "contact@libellules.eu";
     name = "Dara Ly";
     github = "tournemire";
+    githubId = 20159432;
   };
   deltaevo = {
     email = "deltaduartedavid@gmail.com";
diff --git a/pkgs/development/ocaml-modules/dbf/default.nix b/pkgs/development/ocaml-modules/dbf/default.nix
new file mode 100644
index 000000000000..d2dad611bf46
--- /dev/null
+++ b/pkgs/development/ocaml-modules/dbf/default.nix
@@ -0,0 +1,28 @@
+{ lib, buildDunePackage, fetchFromGitHub, ppx_cstruct, rresult, cstruct-unix
+, core_kernel }:
+
+buildDunePackage rec {
+  pname = "dbf";
+  version = "0.1.1";
+
+  minimalOCamlVersion = "4.08";
+
+  useDune2 = true;
+
+  src = fetchFromGitHub {
+    owner = "pveber";
+    repo = "dbf";
+    rev = "${version}";
+    sha256 = "sha256-h1K5YDLbXGEJi/quKXvSR0gZ+WkBzut7AsVFv+Bm8/g=";
+  };
+
+  buildInputs = [ ppx_cstruct ];
+  propagatedBuildInputs = [ rresult cstruct-unix core_kernel ];
+
+  meta = with lib; {
+    description = "DBF format parsing";
+    homepage = "https://github.com/pveber/dbf";
+    license = licenses.isc;
+    maintainers = [ maintainers.deltadelta ];
+  };
+}
diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix
index aed626868651..ab1c8704fbb0 100644
--- a/pkgs/top-level/ocaml-packages.nix
+++ b/pkgs/top-level/ocaml-packages.nix
@@ -254,6 +254,8 @@ let
 
     data-encoding = callPackage ../development/ocaml-modules/data-encoding { };
 
+    dbf =  callPackage ../development/ocaml-modules/dbf { };
+
     decompress =  callPackage ../development/ocaml-modules/decompress { };
 
     diet =  callPackage ../development/ocaml-modules/diet { };

From 43a1e275c44395751c3ff5af09d2b1cc1b79e331 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 15:50:32 +0100
Subject: [PATCH 30/36] python3Packages.parsy: switch to pytestCheckHook

---
 .../python-modules/parsy/default.nix          | 22 +++++++++++++------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/pkgs/development/python-modules/parsy/default.nix b/pkgs/development/python-modules/parsy/default.nix
index 53743052f4e4..149eea715dbd 100644
--- a/pkgs/development/python-modules/parsy/default.nix
+++ b/pkgs/development/python-modules/parsy/default.nix
@@ -1,21 +1,29 @@
-{ lib, buildPythonPackage, fetchPypi, pythonOlder, pytest }:
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pythonOlder
+, pytestCheckHook
+}:
 
 buildPythonPackage rec {
   pname = "parsy";
   version = "1.4.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "7c411373e520e97431f0b390db9d2cfc5089bc1d33f4f1584d2cdc9e6368f302";
   };
 
-  checkInputs = [ pytest ];
+  checkInputs = [
+    pytestCheckHook
+  ];
 
-  checkPhase = ''
-    py.test test/
-  '';
-
-  disabled = pythonOlder "3.4";
+  pythonImportsCheck = [
+    "parsy"
+  ];
 
   meta = with lib; {
     homepage = "https://github.com/python-parsy/parsy";

From 4c21eb400aa94bb13fa259258cef184f646a9f1d Mon Sep 17 00:00:00 2001
From: Bobby Rong <rjl931189261@126.com>
Date: Wed, 5 Jan 2022 22:57:25 +0800
Subject: [PATCH 31/36] python3Packages.gcsfs: update homepage

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

diff --git a/pkgs/development/python-modules/gcsfs/default.nix b/pkgs/development/python-modules/gcsfs/default.nix
index 9eeb13b8f97f..66d05f2a355b 100644
--- a/pkgs/development/python-modules/gcsfs/default.nix
+++ b/pkgs/development/python-modules/gcsfs/default.nix
@@ -23,7 +23,7 @@ buildPythonPackage rec {
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
-    owner = "dask";
+    owner = "fsspec";
     repo = pname;
     rev = version;
     sha256 = "sha256-cpV+HKE39Yct1yu5xW9HZftx2Wy9ydFL2YLvPD3YM2M=";
@@ -58,7 +58,7 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "Convenient Filesystem interface over GCS";
-    homepage = "https://github.com/dask/gcsfs";
+    homepage = "https://github.com/fsspec/gcsfs";
     license = licenses.bsd3;
     maintainers = with maintainers; [ nbren12 ];
   };

From 4ae1672085bbde9304f80fb2f115788c8732af44 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 16:13:00 +0100
Subject: [PATCH 32/36] python3Packages.sumo: relax castepxbin constraint

---
 .../python-modules/sumo/default.nix           | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/sumo/default.nix b/pkgs/development/python-modules/sumo/default.nix
index 204bb80e5870..299d8446cfb7 100644
--- a/pkgs/development/python-modules/sumo/default.nix
+++ b/pkgs/development/python-modules/sumo/default.nix
@@ -1,4 +1,6 @@
-{ lib, buildPythonPackage, fetchFromGitHub
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
 , pythonOlder
 , h5py
 , matplotlib
@@ -15,10 +17,10 @@
 buildPythonPackage rec {
   pname = "sumo";
   version = "2.2.5";
+  format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
-  # No tests in Pypi tarball
   src = fetchFromGitHub {
     owner = "SMTG-UCL";
     repo = "sumo";
@@ -38,7 +40,18 @@ buildPythonPackage rec {
     castepxbin
   ];
 
-  checkInputs = [ pytestCheckHook ];
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "castepxbin==0.1.0" "castepxbin>=0.1.0"
+  '';
+
+  pythonImportsCheck = [
+    "sumo"
+  ];
 
   meta = with lib; {
     description = "Toolkit for plotting and analysis of ab initio solid-state calculation data";

From 271ca2b032cbf6106ecdabdf191cda0503c0c625 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 16:51:44 +0100
Subject: [PATCH 33/36] python3Packages.environs: 9.3.5 -> 9.4.0

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

diff --git a/pkgs/development/python-modules/environs/default.nix b/pkgs/development/python-modules/environs/default.nix
index 04bb5dda00ea..a0a4fb88e0cd 100644
--- a/pkgs/development/python-modules/environs/default.nix
+++ b/pkgs/development/python-modules/environs/default.nix
@@ -12,7 +12,7 @@
 
 buildPythonPackage rec {
   pname = "environs";
-  version = "9.3.5";
+  version = "9.4.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
@@ -21,7 +21,7 @@ buildPythonPackage rec {
     owner = "sloria";
     repo = pname;
     rev = version;
-    sha256 = "sha256-4jyqdA/xoIEsfouIneGs3A9++sNG2kRUhDzteN0Td6w=";
+    sha256 = "sha256-LPD46kxzQ/oTC7XjJn/SXaLQgX613ZoCrJuaRng57Gw=";
   };
 
   propagatedBuildInputs = [

From ff81162833bf4614766c31f5c3056770817deeec Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Wed, 5 Jan 2022 16:54:30 +0100
Subject: [PATCH 34/36] python3Packages.hahomematic: 0.12.0 -> 0.13.3

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

diff --git a/pkgs/development/python-modules/hahomematic/default.nix b/pkgs/development/python-modules/hahomematic/default.nix
index 9cb116a9a7a2..bf8bed9dd262 100644
--- a/pkgs/development/python-modules/hahomematic/default.nix
+++ b/pkgs/development/python-modules/hahomematic/default.nix
@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "hahomematic";
-  version = "0.12.0";
+  version = "0.13.3";
   format = "setuptools";
 
   disabled = pythonOlder "3.9";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "danielperna84";
     repo = pname;
     rev = version;
-    sha256 = "sha256-A7fuTSrXMTK0oz87htylWKb868+YR7FXYYEC3hSgG7o=";
+    sha256 = "sha256-9dR0qYoHVovD4fwJz6v+/RItMuqr2vA9YHn0nMGHUX0=";
   };
 
   propagatedBuildInputs = [

From fa44da7f5167e2866a2227d55ebf13335d825025 Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Wed, 5 Jan 2022 17:34:34 +0100
Subject: [PATCH 35/36] python3Packages.parsy: fix eval

---
 pkgs/development/python-modules/parsy/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/python-modules/parsy/default.nix b/pkgs/development/python-modules/parsy/default.nix
index 70d10f77d995..9083953009ad 100644
--- a/pkgs/development/python-modules/parsy/default.nix
+++ b/pkgs/development/python-modules/parsy/default.nix
@@ -1,6 +1,6 @@
 { lib
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , pythonOlder
 , pytestCheckHook
 }:

From 115a6f077fc29e7dc846618be86ece84c6d6aea7 Mon Sep 17 00:00:00 2001
From: sternenseemann <sternenseemann@systemli.org>
Date: Tue, 4 Jan 2022 12:30:40 +0100
Subject: [PATCH 36/36] llvmPackages_{12,13,git}.compiler-rt: remove new
 runtimes in useLLVM

LLVM 12 added the memory profiling runtime and LLVM 13 the ORC
runtime. Both need a libc in order to build (or at least headers not
present in clang's resource root), so we'll disable them for any sort of
baremetal-ish build. memprof likely doesn't work in a baremetal
situation at all, orc is unknown. Whether both would compile with musl
is to be checked.
---
 pkgs/development/compilers/llvm/12/compiler-rt/default.nix  | 1 +
 pkgs/development/compilers/llvm/13/compiler-rt/default.nix  | 2 ++
 pkgs/development/compilers/llvm/git/compiler-rt/default.nix | 2 ++
 3 files changed, 5 insertions(+)

diff --git a/pkgs/development/compilers/llvm/12/compiler-rt/default.nix b/pkgs/development/compilers/llvm/12/compiler-rt/default.nix
index 13c611ca8cc6..4b2907ed3078 100644
--- a/pkgs/development/compilers/llvm/12/compiler-rt/default.nix
+++ b/pkgs/development/compilers/llvm/12/compiler-rt/default.nix
@@ -30,6 +30,7 @@ stdenv.mkDerivation {
     "-DCOMPILER_RT_BUILD_XRAY=OFF"
     "-DCOMPILER_RT_BUILD_LIBFUZZER=OFF"
     "-DCOMPILER_RT_BUILD_PROFILE=OFF"
+    "-DCOMPILER_RT_BUILD_MEMPROF=OFF"
   ] ++ lib.optionals ((useLLVM || bareMetal) && !haveLibc) [
     "-DCMAKE_C_COMPILER_WORKS=ON"
     "-DCMAKE_CXX_COMPILER_WORKS=ON"
diff --git a/pkgs/development/compilers/llvm/13/compiler-rt/default.nix b/pkgs/development/compilers/llvm/13/compiler-rt/default.nix
index e30db5fcd954..10b89b91b96f 100644
--- a/pkgs/development/compilers/llvm/13/compiler-rt/default.nix
+++ b/pkgs/development/compilers/llvm/13/compiler-rt/default.nix
@@ -33,6 +33,8 @@ stdenv.mkDerivation {
     "-DCOMPILER_RT_BUILD_SANITIZERS=OFF"
     "-DCOMPILER_RT_BUILD_XRAY=OFF"
     "-DCOMPILER_RT_BUILD_PROFILE=OFF"
+    "-DCOMPILER_RT_BUILD_MEMPROF=OFF"
+    "-DCOMPILER_RT_BUILD_ORC=OFF" # may be possible to build with musl if necessary
   ] ++ lib.optionals ((useLLVM || bareMetal) && !haveLibc) [
     "-DCMAKE_C_COMPILER_WORKS=ON"
     "-DCMAKE_CXX_COMPILER_WORKS=ON"
diff --git a/pkgs/development/compilers/llvm/git/compiler-rt/default.nix b/pkgs/development/compilers/llvm/git/compiler-rt/default.nix
index 5874a91e03c8..019148039d17 100644
--- a/pkgs/development/compilers/llvm/git/compiler-rt/default.nix
+++ b/pkgs/development/compilers/llvm/git/compiler-rt/default.nix
@@ -32,6 +32,8 @@ stdenv.mkDerivation {
     "-DCOMPILER_RT_BUILD_XRAY=OFF"
     "-DCOMPILER_RT_BUILD_LIBFUZZER=OFF"
     "-DCOMPILER_RT_BUILD_PROFILE=OFF"
+    "-DCOMPILER_RT_BUILD_MEMPROF=OFF"
+    "-DCOMPILER_RT_BUILD_ORC=OFF" # may be possible to build with musl if necessary
   ] ++ lib.optionals ((useLLVM || bareMetal) && !haveLibc) [
     "-DCMAKE_C_COMPILER_WORKS=ON"
     "-DCMAKE_CXX_COMPILER_WORKS=ON"