From 72c23a3469732cd0f0d649a85083ce75cc6f5a81 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Wed, 30 Jun 2021 17:54:45 +0200
Subject: [PATCH 01/18] petsc: refactor using mpi and p4est

---
 .../libraries/science/math/petsc/default.nix  | 59 +++++++++++++++----
 1 file changed, 47 insertions(+), 12 deletions(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index f06a028fe64f..e64df8eb51bd 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -1,5 +1,23 @@
-{ lib, stdenv , darwin , fetchurl , blas , gfortran , lapack , python }:
+{ lib
+, stdenv
+, fetchurl
+, darwin
+, gfortran
+, python
+, blas
+, lapack
+, mpi                   # generic mpi dependency
+, openmpi               # to compare against mpi
+, openssh               # required for openmpi tests
+, petsc-withp4est ? true
+, p4est
+, zlib                  # propagated by p4est but required by petsc
+}:
 
+let
+  mpiSupport = !withp4est || p4est.mpiSupport;
+  withp4est = petsc-withp4est;
+in
 stdenv.mkDerivation rec {
   pname = "petsc";
   version = "3.14.2";
@@ -9,7 +27,12 @@ stdenv.mkDerivation rec {
     sha256 = "04vy3qyakikslc58qyv8c9qrwlivix3w6znc993i37cvfg99dch9";
   };
 
-  nativeBuildInputs = [ blas gfortran gfortran.cc.lib lapack python ];
+  nativeBuildInputs = [ python gfortran gfortran.cc.lib ];
+  buildInputs = [ blas lapack ]
+    ++ lib.optional mpiSupport mpi
+    ++ lib.optional (mpiSupport && mpi == openmpi) openssh
+    ++ lib.optional withp4est p4est
+  ;
 
   # Upstream does some hot she-py-bang stuff, this change streamlines that
   # process. The original script in upstream is both a shell script and a
@@ -30,23 +53,35 @@ stdenv.mkDerivation rec {
     patchShebangs .
     configureFlagsArray=(
       $configureFlagsArray
-      "--CC=$CC"
-      "--with-cxx=$CXX"
-      "--with-fc=$FC"
-      "--with-mpi=0"
+      ${if !mpiSupport then ''
+        "--CC=$CC"
+        "--with-cxx=$CXX"
+        "--with-fc=$FC"
+        "--with-mpi=0"
+      '' else ''
+        "--CC=mpicc"
+        "--with-cxx=mpicxx"
+        "--with-fc=mpif90"
+        "--with-mpi=1"
+      ''}
+      ${if withp4est then ''
+        "--with-p4est=1"
+        "--with-zlib-include=${zlib.dev}/include"
+        "--with-zlib-lib=-L${zlib}/lib -lz"
+      '' else ""}
       "--with-blas-lib=[${blas}/lib/libblas.so,${gfortran.cc.lib}/lib/libgfortran.a]"
       "--with-lapack-lib=[${lapack}/lib/liblapack.so,${gfortran.cc.lib}/lib/libgfortran.a]"
     )
   '';
 
+  inherit mpiSupport withp4est;
+  enableParallelBuilding = true;
+  doCheck = stdenv.hostPlatform == stdenv.buildPlatform;
+
   meta = with lib; {
-    description = ''
-      Library of linear algebra algorithms for solving partial differential
-      equations
-    '';
+    description = "Linear algebra algorithms for solving partial differential equations";
     homepage = "https://www.mcs.anl.gov/petsc/index.html";
     license = licenses.bsd2;
-    maintainers = with maintainers; [ wucke13 ];
-    platforms = platforms.all;
+    maintainers = with maintainers; [ wucke13 cburstedde ];
   };
 }

From 8834c5399c218701c36193f2ca11f3ae0298c162 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Thu, 1 Jul 2021 22:16:53 +0200
Subject: [PATCH 02/18] petsc: address couple suggestions

---
 .../libraries/science/math/petsc/default.nix        | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index e64df8eb51bd..2e10df1c9670 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -7,17 +7,12 @@
 , blas
 , lapack
 , mpi                   # generic mpi dependency
-, openmpi               # to compare against mpi
 , openssh               # required for openmpi tests
 , petsc-withp4est ? true
 , p4est
 , zlib                  # propagated by p4est but required by petsc
 }:
 
-let
-  mpiSupport = !withp4est || p4est.mpiSupport;
-  withp4est = petsc-withp4est;
-in
 stdenv.mkDerivation rec {
   pname = "petsc";
   version = "3.14.2";
@@ -27,10 +22,13 @@ stdenv.mkDerivation rec {
     sha256 = "04vy3qyakikslc58qyv8c9qrwlivix3w6znc993i37cvfg99dch9";
   };
 
+  mpiSupport = !withp4est || p4est.mpiSupport;
+  withp4est = petsc-withp4est;
+
   nativeBuildInputs = [ python gfortran gfortran.cc.lib ];
   buildInputs = [ blas lapack ]
     ++ lib.optional mpiSupport mpi
-    ++ lib.optional (mpiSupport && mpi == openmpi) openssh
+    ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh
     ++ lib.optional withp4est p4est
   ;
 
@@ -74,12 +72,11 @@ stdenv.mkDerivation rec {
     )
   '';
 
-  inherit mpiSupport withp4est;
   enableParallelBuilding = true;
   doCheck = stdenv.hostPlatform == stdenv.buildPlatform;
 
   meta = with lib; {
-    description = "Linear algebra algorithms for solving partial differential equations";
+    description = "Portable Extensible Toolkit for Scientific computation";
     homepage = "https://www.mcs.anl.gov/petsc/index.html";
     license = licenses.bsd2;
     maintainers = with maintainers; [ wucke13 cburstedde ];

From dbf58984625ca1e2e35c40cb89cd4ee41d0fdc8a Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Thu, 1 Jul 2021 22:27:03 +0200
Subject: [PATCH 03/18] petsc: simplify blas, lapack dependencies

---
 pkgs/development/libraries/science/math/petsc/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index 2e10df1c9670..426a4a8f9159 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
   mpiSupport = !withp4est || p4est.mpiSupport;
   withp4est = petsc-withp4est;
 
-  nativeBuildInputs = [ python gfortran gfortran.cc.lib ];
+  nativeBuildInputs = [ python gfortran ];
   buildInputs = [ blas lapack ]
     ++ lib.optional mpiSupport mpi
     ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh
@@ -67,8 +67,8 @@ stdenv.mkDerivation rec {
         "--with-zlib-include=${zlib.dev}/include"
         "--with-zlib-lib=-L${zlib}/lib -lz"
       '' else ""}
-      "--with-blas-lib=[${blas}/lib/libblas.so,${gfortran.cc.lib}/lib/libgfortran.a]"
-      "--with-lapack-lib=[${lapack}/lib/liblapack.so,${gfortran.cc.lib}/lib/libgfortran.a]"
+      "--with-blas=1"
+      "--with-lapack=1"
     )
   '';
 

From ce30d367c1427ac39d583daf814f0a23eaf4afd4 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Thu, 1 Jul 2021 22:37:52 +0200
Subject: [PATCH 04/18] petsc: assert requirement for p4est.mpiSupport

---
 pkgs/development/libraries/science/math/petsc/default.nix | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index 426a4a8f9159..900ea76e2840 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -13,6 +13,9 @@
 , zlib                  # propagated by p4est but required by petsc
 }:
 
+# This version of PETSc does not support a non-MPI p4est build
+assert petsc-withp4est -> p4est.mpiSupport;
+
 stdenv.mkDerivation rec {
   pname = "petsc";
   version = "3.14.2";

From bcf9629def740946f74e56d0cf0fd1dfd6772d9a Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Thu, 1 Jul 2021 22:50:54 +0200
Subject: [PATCH 05/18] petsc: remove unnecessary configure options

---
 pkgs/development/libraries/science/math/petsc/default.nix | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index 900ea76e2840..921ac859b1bd 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -55,9 +55,6 @@ stdenv.mkDerivation rec {
     configureFlagsArray=(
       $configureFlagsArray
       ${if !mpiSupport then ''
-        "--CC=$CC"
-        "--with-cxx=$CXX"
-        "--with-fc=$FC"
         "--with-mpi=0"
       '' else ''
         "--CC=mpicc"

From 870b2847a42822384b55e13ed6317d9714e20407 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Thu, 1 Jul 2021 22:31:19 +0200
Subject: [PATCH 06/18] getdp: align with latest petsc dependency

---
 pkgs/applications/science/math/getdp/default.nix | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/math/getdp/default.nix b/pkgs/applications/science/math/getdp/default.nix
index 39d9c866caef..5ea3550d08a4 100644
--- a/pkgs/applications/science/math/getdp/default.nix
+++ b/pkgs/applications/science/math/getdp/default.nix
@@ -1,15 +1,19 @@
 { lib, stdenv, fetchurl, cmake, gfortran, blas, lapack, mpi, petsc, python3 }:
 
 stdenv.mkDerivation rec {
-  name = "getdp-${version}";
+  pname = "getdp";
   version = "3.3.0";
   src = fetchurl {
     url = "http://getdp.info/src/getdp-${version}-source.tgz";
     sha256 = "1pfviy2bw8z5y6c15czvlvyjjg9pvpgrj9fr54xfi2gmvs7zkgpf";
   };
 
-  nativeBuildInputs = [ cmake gfortran ];
-  buildInputs = [ blas lapack mpi petsc python3 ];
+  inherit (petsc) mpiSupport;
+  nativeBuildInputs = [ cmake python3 ];
+  buildInputs = [ gfortran blas lapack petsc ]
+    ++ lib.optional mpiSupport mpi
+  ;
+  cmakeFlags = lib.optional mpiSupport "-DENABLE_MPI=1";
 
   meta = with lib; {
     description = "A General Environment for the Treatment of Discrete Problems";

From 87da2a041474a275c1ed6838916a700cd045df05 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Mon, 5 Jul 2021 15:39:02 +0200
Subject: [PATCH 07/18] petsc: do not build with p4est on aarch64

---
 pkgs/development/libraries/science/math/petsc/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index 921ac859b1bd..87689ddb827c 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
   };
 
   mpiSupport = !withp4est || p4est.mpiSupport;
-  withp4est = petsc-withp4est;
+  withp4est = !stdenv.isAarch64 && petsc-withp4est;
 
   nativeBuildInputs = [ python gfortran ];
   buildInputs = [ blas lapack ]

From c99a5b9a60ae5c5204a3f41f5d65b642093d1b82 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Mon, 5 Jul 2021 16:58:59 +0200
Subject: [PATCH 08/18] petsc: do not build with p4est on darwin

---
 pkgs/development/libraries/science/math/petsc/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index 87689ddb827c..8cea4026d9eb 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
   };
 
   mpiSupport = !withp4est || p4est.mpiSupport;
-  withp4est = !stdenv.isAarch64 && petsc-withp4est;
+  withp4est = !(stdenv.isAarch64 || stdenv.isDarwin) && petsc-withp4est;
 
   nativeBuildInputs = [ python gfortran ];
   buildInputs = [ blas lapack ]

From 27b512299f1a9e5e1fb5801d195f9cb98e75dc73 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Tue, 6 Jul 2021 07:13:59 +0200
Subject: [PATCH 09/18] petsc: restrict patchSheBang; use configureScript

The configure script can be called with python via configureScript.
This leaves only ./lib/petsc/bin to be patched.
---
 pkgs/development/libraries/science/math/petsc/default.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index 8cea4026d9eb..e72b2912f4d6 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -51,7 +51,7 @@ stdenv.mkDerivation rec {
 
   preConfigure = ''
     export FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
-    patchShebangs .
+    patchShebangs ./lib/petsc/bin
     configureFlagsArray=(
       $configureFlagsArray
       ${if !mpiSupport then ''
@@ -71,6 +71,7 @@ stdenv.mkDerivation rec {
       "--with-lapack=1"
     )
   '';
+  configureScript = "python ./configure";
 
   enableParallelBuilding = true;
   doCheck = stdenv.hostPlatform == stdenv.buildPlatform;

From 80697bfb8e32b9169ee6db4079dff88da733c0f9 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Tue, 6 Jul 2021 07:20:21 +0200
Subject: [PATCH 10/18] petsc: build with p4est for all platforms

Recent master updates make p4est build on aarch64 and darwin.
Undo their deactivation in the petsc build.
---
 pkgs/development/libraries/science/math/petsc/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index e72b2912f4d6..3fed81fa34a4 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
   };
 
   mpiSupport = !withp4est || p4est.mpiSupport;
-  withp4est = !(stdenv.isAarch64 || stdenv.isDarwin) && petsc-withp4est;
+  withp4est = petsc-withp4est;
 
   nativeBuildInputs = [ python gfortran ];
   buildInputs = [ blas lapack ]

From cf4b4bdbeafdae01ba309b0fc3cbba7aa3df1593 Mon Sep 17 00:00:00 2001
From: Carsten Burstedde <burstedde@ins.uni-bonn.de>
Date: Tue, 6 Jul 2021 23:10:19 +0200
Subject: [PATCH 11/18] petsc: specify python3 and remove unneeded patch

---
 .../libraries/science/math/petsc/default.nix     | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index 3fed81fa34a4..ee495deedc1e 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/pkgs/development/libraries/science/math/petsc/default.nix
@@ -3,7 +3,7 @@
 , fetchurl
 , darwin
 , gfortran
-, python
+, python3
 , blas
 , lapack
 , mpi                   # generic mpi dependency
@@ -28,23 +28,14 @@ stdenv.mkDerivation rec {
   mpiSupport = !withp4est || p4est.mpiSupport;
   withp4est = petsc-withp4est;
 
-  nativeBuildInputs = [ python gfortran ];
+  nativeBuildInputs = [ python3 gfortran ];
   buildInputs = [ blas lapack ]
     ++ lib.optional mpiSupport mpi
     ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh
     ++ lib.optional withp4est p4est
   ;
 
-  # Upstream does some hot she-py-bang stuff, this change streamlines that
-  # process. The original script in upstream is both a shell script and a
-  # python script, where the shellscript just finds a suitable python
-  # interpreter to execute the python script. See
-  # https://github.com/NixOS/nixpkgs/pull/89299#discussion_r450203444
-  # for more details.
-  prePatch = ''
-    substituteInPlace configure \
-      --replace /bin/sh /usr/bin/python
-  '' + lib.optionalString stdenv.isDarwin ''
+  prePatch = lib.optionalString stdenv.isDarwin ''
     substituteInPlace config/install.py \
       --replace /usr/bin/install_name_tool ${darwin.cctools}/bin/install_name_tool
   '';
@@ -71,6 +62,7 @@ stdenv.mkDerivation rec {
       "--with-lapack=1"
     )
   '';
+
   configureScript = "python ./configure";
 
   enableParallelBuilding = true;

From 64f17e13328add755ac7149d65cbe2b774515cae Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Sat, 10 Jul 2021 17:41:22 +0200
Subject: [PATCH 12/18] python3Packages.pre-commit-hooks: 3.4.0 -> 4.0.1

---
 .../pre-commit-hooks/default.nix              | 27 ++++++++++++-------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/pkgs/development/python-modules/pre-commit-hooks/default.nix b/pkgs/development/python-modules/pre-commit-hooks/default.nix
index f664d9c6d25e..212fdf6a721a 100644
--- a/pkgs/development/python-modules/pre-commit-hooks/default.nix
+++ b/pkgs/development/python-modules/pre-commit-hooks/default.nix
@@ -1,9 +1,8 @@
-{ buildPythonPackage
+{ lib
+, buildPythonPackage
 , fetchFromGitHub
-, fetchPypi
 , git
-, isPy27
-, lib
+, pythonOlder
 , pytestCheckHook
 , ruamel_yaml
 , toml
@@ -11,19 +10,25 @@
 
 buildPythonPackage rec {
   pname = "pre-commit-hooks";
-  version = "3.4.0";
-  disabled = isPy27;
+  version = "4.0.1";
+  disabled = pythonOlder "3.6";
 
-  # fetchPypi does not provide tests
   src = fetchFromGitHub {
     owner = "pre-commit";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1aqkmprdc2lhds9c59pkkf2js65j63197flanaggk7cm8k0kz7zs";
+    sha256 = "sha256-Rg2I79r0Pp3AUgT6mD+kEdm+5CEGgdmFn6G3xcU6fnk=";
   };
 
-  propagatedBuildInputs = [ toml ruamel_yaml ];
-  checkInputs = [ git pytestCheckHook ];
+  propagatedBuildInputs = [
+    ruamel_yaml
+    toml
+  ];
+
+  checkInputs = [
+    git
+    pytestCheckHook
+  ];
 
   # the tests require a functional git installation which requires a valid HOME
   # directory.
@@ -34,6 +39,8 @@ buildPythonPackage rec {
     git config --global user.email "nix-builder@nixos.org"
   '';
 
+  pythonImportsCheck = [ "pre_commit_hooks" ];
+
   meta = with lib; {
     description = "Some out-of-the-box hooks for pre-commit";
     homepage = "https://github.com/pre-commit/pre-commit-hooks";

From 46f213b36d22481bf50070d25442f2d009d649b7 Mon Sep 17 00:00:00 2001
From: Mica Semrick <mica@silentumbrella.com>
Date: Sat, 10 Jul 2021 23:46:32 -0700
Subject: [PATCH 13/18] darktable: add some optional packages

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

diff --git a/pkgs/applications/graphics/darktable/default.nix b/pkgs/applications/graphics/darktable/default.nix
index cc15b96b4b6e..540a74e6524f 100644
--- a/pkgs/applications/graphics/darktable/default.nix
+++ b/pkgs/applications/graphics/darktable/default.nix
@@ -3,7 +3,7 @@
 , ilmbase, gtk3, intltool, lcms2, lensfun, libX11, libexif, libgphoto2, libjpeg
 , libpng, librsvg, libtiff, openexr, osm-gps-map, pkg-config, sqlite, libxslt
 , openjpeg, lua, pugixml, colord, colord-gtk, libwebp, libsecret, gnome
-, ocl-icd, pcre, gtk-mac-integration, isocodes, llvmPackages
+, ocl-icd, pcre, gtk-mac-integration, isocodes, llvmPackages, gmic, libavif, icu
 }:
 
 stdenv.mkDerivation rec {
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
     cairo curl exiv2 glib gtk3 ilmbase lcms2 lensfun libexif
     libgphoto2 libjpeg libpng librsvg libtiff openexr sqlite libxslt
     libsoup graphicsmagick json-glib openjpeg lua pugixml
-    libwebp libsecret gnome.adwaita-icon-theme osm-gps-map pcre isocodes
+    libwebp libsecret gnome.adwaita-icon-theme osm-gps-map pcre isocodes gmic libavif icu
   ] ++ lib.optionals stdenv.isLinux [
     colord colord-gtk libX11 ocl-icd
   ] ++ lib.optional stdenv.isDarwin gtk-mac-integration

From 99bc203025a0ff1265eedc6ff3d6c7aa1f320c09 Mon Sep 17 00:00:00 2001
From: Robert Hensing <robert@roberthensing.nl>
Date: Mon, 12 Jul 2021 07:23:45 +0200
Subject: [PATCH 14/18] Partially revert "lib/modules: Drop mkStrict and
 mkFixStrictness"

mkFixStrictness was never properly deprecated and should only be
removed after warning for some time.

This partially reverts commit 8fb9984690c878fcd768e967190957441de05d11.
---
 lib/default.nix | 4 ++--
 lib/modules.nix | 4 ++++
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/default.nix b/lib/default.nix
index ccfee2ebe303..ccae0bbc3ab4 100644
--- a/lib/default.nix
+++ b/lib/default.nix
@@ -115,8 +115,8 @@ let
       mergeModules' mergeOptionDecls evalOptionValue mergeDefinitions
       pushDownProperties dischargeProperties filterOverrides
       sortProperties fixupOptionType mkIf mkAssert mkMerge mkOverride
-      mkOptionDefault mkDefault mkForce mkVMOverride
-      mkOrder mkBefore mkAfter mkAliasDefinitions
+      mkOptionDefault mkDefault mkForce mkVMOverride mkStrict
+      mkFixStrictness mkOrder mkBefore mkAfter mkAliasDefinitions
       mkAliasAndWrapDefinitions fixMergeModules mkRemovedOptionModule
       mkRenamedOptionModule mkMergedOptionModule mkChangedOptionModule
       mkAliasOptionModule doRename;
diff --git a/lib/modules.nix b/lib/modules.nix
index 58c6cda58e49..99b9a8a31eac 100644
--- a/lib/modules.nix
+++ b/lib/modules.nix
@@ -713,6 +713,10 @@ rec {
   mkForce = mkOverride 50;
   mkVMOverride = mkOverride 10; # used by ‘nixos-rebuild build-vm’
 
+  mkStrict = builtins.trace "`mkStrict' is obsolete; use `mkOverride 0' instead." (mkOverride 0);
+
+  mkFixStrictness = id; # obsolete, no-op
+
   mkOrder = priority: content:
     { _type = "order";
       inherit priority content;

From cad20d8983a547c19e914ec5a2a6093b0c8e5a16 Mon Sep 17 00:00:00 2001
From: Robert Hensing <robert@roberthensing.nl>
Date: Mon, 12 Jul 2021 07:31:20 +0200
Subject: [PATCH 15/18] lib.mkFixStrictness: Deprecate

---
 lib/default.nix | 2 +-
 lib/modules.nix | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/lib/default.nix b/lib/default.nix
index ccae0bbc3ab4..8e29ef5c4201 100644
--- a/lib/default.nix
+++ b/lib/default.nix
@@ -115,7 +115,7 @@ let
       mergeModules' mergeOptionDecls evalOptionValue mergeDefinitions
       pushDownProperties dischargeProperties filterOverrides
       sortProperties fixupOptionType mkIf mkAssert mkMerge mkOverride
-      mkOptionDefault mkDefault mkForce mkVMOverride mkStrict
+      mkOptionDefault mkDefault mkForce mkVMOverride
       mkFixStrictness mkOrder mkBefore mkAfter mkAliasDefinitions
       mkAliasAndWrapDefinitions fixMergeModules mkRemovedOptionModule
       mkRenamedOptionModule mkMergedOptionModule mkChangedOptionModule
diff --git a/lib/modules.nix b/lib/modules.nix
index 99b9a8a31eac..ab2bc4f7f8e2 100644
--- a/lib/modules.nix
+++ b/lib/modules.nix
@@ -713,9 +713,7 @@ rec {
   mkForce = mkOverride 50;
   mkVMOverride = mkOverride 10; # used by ‘nixos-rebuild build-vm’
 
-  mkStrict = builtins.trace "`mkStrict' is obsolete; use `mkOverride 0' instead." (mkOverride 0);
-
-  mkFixStrictness = id; # obsolete, no-op
+  mkFixStrictness = lib.warn "lib.mkFixStrictness has no effect and will be removed. It returns its argument unmodified, so you can just remove any calls." id;
 
   mkOrder = priority: content:
     { _type = "order";

From bdf42f22df5400659c55b5238d67ec65a80bf442 Mon Sep 17 00:00:00 2001
From: Sumner Evans <me@sumnerevans.com>
Date: Mon, 12 Jul 2021 00:23:00 -0600
Subject: [PATCH 16/18] mako: 1.5 -> 1.6

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

diff --git a/pkgs/applications/misc/mako/default.nix b/pkgs/applications/misc/mako/default.nix
index f28292cb2f16..8f984db7df52 100644
--- a/pkgs/applications/misc/mako/default.nix
+++ b/pkgs/applications/misc/mako/default.nix
@@ -5,13 +5,13 @@
 
 stdenv.mkDerivation rec {
   pname = "mako";
-  version = "1.5";
+  version = "1.6";
 
   src = fetchFromGitHub {
     owner = "emersion";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0f92krcgybl4113g2gawf7lcbh1fss7bq4cx81h1zyn7yvxlwx2b";
+    sha256 = "sha256-RcPwZ5NeO9vxwPWfgj5x3wVdCYGKumnYT3ngHEAWfW0=";
   };
 
   nativeBuildInputs = [ meson ninja pkg-config scdoc wayland-protocols wrapGAppsHook ];

From a164e1d0a17549cc4c238cfe9c32a0bac97b24e1 Mon Sep 17 00:00:00 2001
From: Ulrik Strid <ulrik.strid@outlook.com>
Date: Mon, 12 Jul 2021 11:29:43 +0200
Subject: [PATCH 17/18] ocamlPackages.json-data-encoding: init at 0.8,
 ocamlPackages.data-encoding: init at 0.2.0 (#129444)

---
 .../ocaml-modules/data-encoding/default.nix   | 46 +++++++++++++++++++
 .../ocaml-modules/json-data-encoding/bson.nix | 20 ++++++++
 .../json-data-encoding/default.nix            | 31 +++++++++++++
 pkgs/top-level/ocaml-packages.nix             |  6 +++
 4 files changed, 103 insertions(+)
 create mode 100644 pkgs/development/ocaml-modules/data-encoding/default.nix
 create mode 100644 pkgs/development/ocaml-modules/json-data-encoding/bson.nix
 create mode 100644 pkgs/development/ocaml-modules/json-data-encoding/default.nix

diff --git a/pkgs/development/ocaml-modules/data-encoding/default.nix b/pkgs/development/ocaml-modules/data-encoding/default.nix
new file mode 100644
index 000000000000..2e4e0518a522
--- /dev/null
+++ b/pkgs/development/ocaml-modules/data-encoding/default.nix
@@ -0,0 +1,46 @@
+{ lib
+, fetchFromGitLab
+, buildDunePackage
+, ezjsonm
+, zarith
+, hex
+, json-data-encoding
+, json-data-encoding-bson
+, alcotest
+, crowbar
+}:
+
+buildDunePackage {
+  pname = "data-encoding";
+  version = "0.2.0";
+
+  src = fetchFromGitLab {
+    owner = "nomadic-labs";
+    repo = "data-encoding";
+    rev = "0.2";
+    sha256 = "0d9c2ix2imqk4r0jfhnwak9laarlbsq9kmswvbnjzdm2g0hwin1d";
+  };
+  useDune2 = true;
+
+  propagatedBuildInputs = [
+    ezjsonm
+    zarith
+    hex
+    json-data-encoding
+    json-data-encoding-bson
+  ];
+
+  checkInputs = [
+    alcotest
+    crowbar
+  ];
+
+  doCheck = true;
+
+  meta = {
+    homepage = "https://gitlab.com/nomadic-labs/data-encoding";
+    description = "Library of JSON and binary encoding combinators";
+    license = lib.licenses.mit;
+    maintainers = [ lib.maintainers.ulrikstrid ];
+  };
+}
diff --git a/pkgs/development/ocaml-modules/json-data-encoding/bson.nix b/pkgs/development/ocaml-modules/json-data-encoding/bson.nix
new file mode 100644
index 000000000000..5048a8fd06a7
--- /dev/null
+++ b/pkgs/development/ocaml-modules/json-data-encoding/bson.nix
@@ -0,0 +1,20 @@
+{ lib, buildDunePackage, json-data-encoding, ocplib-endian, crowbar }:
+
+buildDunePackage {
+  pname = "json-data-encoding-bson";
+
+  inherit (json-data-encoding) version src useDune2 doCheck;
+
+  propagatedBuildInputs = [
+    json-data-encoding
+    ocplib-endian
+  ];
+
+  checkInputs = [
+    crowbar
+  ];
+
+  meta = json-data-encoding.meta // {
+    description = "Type-safe encoding to and decoding from JSON (bson support)";
+  };
+}
diff --git a/pkgs/development/ocaml-modules/json-data-encoding/default.nix b/pkgs/development/ocaml-modules/json-data-encoding/default.nix
new file mode 100644
index 000000000000..6dfea612b10a
--- /dev/null
+++ b/pkgs/development/ocaml-modules/json-data-encoding/default.nix
@@ -0,0 +1,31 @@
+{ lib, fetchFromGitLab, buildDunePackage, uri, crowbar }:
+
+buildDunePackage rec {
+  pname = "json-data-encoding";
+  version = "0.8";
+
+  src = fetchFromGitLab {
+    owner = "nomadic-labs";
+    repo = "json-data-encoding";
+    rev = "v${version}";
+    sha256 = "1c6m2qvi9bm6qjxc38p6cia1f66r0rb9xf6b8svlj3jjymvqw889";
+  };
+  useDune2 = true;
+
+  propagatedBuildInputs = [
+    uri
+  ];
+
+  checkInputs = [
+    crowbar
+  ];
+
+  doCheck = true;
+
+  meta = {
+    homepage = "https://gitlab.com/nomadic-labs/json-data-encoding";
+    description = "Type-safe encoding to and decoding from JSON";
+    license = lib.licenses.lgpl3;
+    maintainers = [ lib.maintainers.ulrikstrid ];
+  };
+}
diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix
index 977d70e7ef15..31ef92e42048 100644
--- a/pkgs/top-level/ocaml-packages.nix
+++ b/pkgs/top-level/ocaml-packages.nix
@@ -242,6 +242,8 @@ let
 
     dap =  callPackage ../development/ocaml-modules/dap { };
 
+    data-encoding = callPackage ../development/ocaml-modules/data-encoding { };
+
     decompress =  callPackage ../development/ocaml-modules/decompress { };
 
     diet =  callPackage ../development/ocaml-modules/diet { };
@@ -548,6 +550,10 @@ let
 
     jsonm = callPackage ../development/ocaml-modules/jsonm { };
 
+    json-data-encoding = callPackage ../development/ocaml-modules/json-data-encoding { };
+
+    json-data-encoding-bson = callPackage ../development/ocaml-modules/json-data-encoding/bson.nix { };
+
     junit = callPackage ../development/ocaml-modules/junit { };
     junit_ounit = callPackage ../development/ocaml-modules/junit/ounit.nix { };
     junit_alcotest = callPackage ../development/ocaml-modules/junit/alcotest.nix { };

From 009668465ed07712a51d0b00e33e2d9e00d203ad Mon Sep 17 00:00:00 2001
From: Sirio Balmelli <sirio@b-ad.ch>
Date: Mon, 12 Jul 2021 11:18:25 +0200
Subject: [PATCH 18/18] gcc-arm-embedded: add numVersion attribute for
 convenience

There are builds which rely on having the numeric version of gcc (eg "10.2.1")
declared in an environment variable.

Running 'arm-none-eabi-gcc --version' returns:
"arm-none-eabi-gcc (GNU Arm Embedded Toolchain 10-2020-q4-major) 10.2.1 20201103 (release)"

However, the attribute arm-none-eabi-gcc.version is "10-2020-q4-major",
from which there is no way to derive "10.2.1".

Contrast this with the attribute gcc.version which (at this time) gives "10.3.0".

By adding a numVersion attribute, consumers of this package can
correctly determine what GCC version is being executed.

Signed-off-by: Sirio Balmelli <sirio@b-ad.ch>
---
 pkgs/development/compilers/gcc-arm-embedded/10/default.nix | 1 +
 pkgs/development/compilers/gcc-arm-embedded/6/default.nix  | 1 +
 pkgs/development/compilers/gcc-arm-embedded/7/default.nix  | 1 +
 pkgs/development/compilers/gcc-arm-embedded/8/default.nix  | 1 +
 pkgs/development/compilers/gcc-arm-embedded/9/default.nix  | 1 +
 5 files changed, 5 insertions(+)

diff --git a/pkgs/development/compilers/gcc-arm-embedded/10/default.nix b/pkgs/development/compilers/gcc-arm-embedded/10/default.nix
index 943ddd100a21..88dd4d37f7b9 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/10/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/10/default.nix
@@ -7,6 +7,7 @@
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
   version = "10-2020-q4-major";
+  numVersion = "10.2.1";
   subdir = "10-2020q4";
 
   suffix = {
diff --git a/pkgs/development/compilers/gcc-arm-embedded/6/default.nix b/pkgs/development/compilers/gcc-arm-embedded/6/default.nix
index 266863d95b2e..6dd6ab027f1a 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/6/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/6/default.nix
@@ -7,6 +7,7 @@
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
   version = "6-2017-q2-update";
+  numVersion = "6.3.1";
   subdir = "6-2017q2";
 
   suffix = {
diff --git a/pkgs/development/compilers/gcc-arm-embedded/7/default.nix b/pkgs/development/compilers/gcc-arm-embedded/7/default.nix
index 4f2135446f61..d2ff1c875508 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/7/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/7/default.nix
@@ -7,6 +7,7 @@
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
   version = "7-2018-q2-update";
+  numVersion = "7.3.1";
   subdir = "7-2018q2";
 
   suffix = {
diff --git a/pkgs/development/compilers/gcc-arm-embedded/8/default.nix b/pkgs/development/compilers/gcc-arm-embedded/8/default.nix
index 2d85113527c0..4fbc58f15a8d 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/8/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/8/default.nix
@@ -7,6 +7,7 @@
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
   version = "8-2019-q3-update";
+  numVersion = "8.3.1";
   subdir = "8-2019q3/RC1.1";
 
   suffix = {
diff --git a/pkgs/development/compilers/gcc-arm-embedded/9/default.nix b/pkgs/development/compilers/gcc-arm-embedded/9/default.nix
index 944d7c7b1593..073dc10dd44c 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/9/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/9/default.nix
@@ -7,6 +7,7 @@
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
   version = "9-2020-q2-update";
+  numVersion = "9.3.1";
   subdir = "9-2020q2";
 
   suffix = {