Merge master into staging-next

lib/default.nix

@@ -116,7 +116,7 @@ let
       pushDownProperties dischargeProperties filterOverrides
       sortProperties fixupOptionType mkIf mkAssert mkMerge mkOverride
       mkOptionDefault mkDefault mkForce mkVMOverride
-      mkOrder mkBefore mkAfter mkAliasDefinitions
+      mkFixStrictness mkOrder mkBefore mkAfter mkAliasDefinitions
       mkAliasAndWrapDefinitions fixMergeModules mkRemovedOptionModule
       mkRenamedOptionModule mkMergedOptionModule mkChangedOptionModule
       mkAliasOptionModule doRename;

lib/modules.nix

@@ -713,6 +713,8 @@ rec {
   mkForce = mkOverride 50;
   mkVMOverride = mkOverride 10; # used by ‘nixos-rebuild build-vm’
 
+  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";
       inherit priority content;

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

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 ];

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 ];
+  inherit (petsc) mpiSupport;
-  buildInputs = [ blas lapack mpi petsc python3 ];
+  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";

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 = {

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 = {

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 = {

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 = {

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 = {

pkgs/development/libraries/science/math/petsc/default.nix

@@ -1,4 +1,20 @@
-{ lib, stdenv , darwin , fetchurl , blas , gfortran , lapack , python }:
+{ lib
+, stdenv
+, fetchurl
+, darwin
+, gfortran
+, python3
+, blas
+, lapack
+, mpi                   # generic mpi dependency
+, openssh               # required for openmpi tests
+, petsc-withp4est ? true
+, p4est
+, 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";
@@ -9,44 +25,53 @@ stdenv.mkDerivation rec {
     sha256 = "04vy3qyakikslc58qyv8c9qrwlivix3w6znc993i37cvfg99dch9";
   };
 
-  nativeBuildInputs = [ blas gfortran gfortran.cc.lib lapack python ];
+  mpiSupport = !withp4est || p4est.mpiSupport;
+  withp4est = petsc-withp4est;
 
-  # Upstream does some hot she-py-bang stuff, this change streamlines that
+  nativeBuildInputs = [ python3 gfortran ];
-  # process. The original script in upstream is both a shell script and a
+  buildInputs = [ blas lapack ]
-  # python script, where the shellscript just finds a suitable python
+    ++ lib.optional mpiSupport mpi
-  # interpreter to execute the python script. See
+    ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh
-  # https://github.com/NixOS/nixpkgs/pull/89299#discussion_r450203444
+    ++ lib.optional withp4est p4est
-  # for more details.
+  ;
-  prePatch = ''
+
-    substituteInPlace configure \
+  prePatch = lib.optionalString stdenv.isDarwin ''
-      --replace /bin/sh /usr/bin/python
-  '' + lib.optionalString stdenv.isDarwin ''
     substituteInPlace config/install.py \
       --replace /usr/bin/install_name_tool ${darwin.cctools}/bin/install_name_tool
   '';
 
   preConfigure = ''
     export FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
-    patchShebangs .
+    patchShebangs ./lib/petsc/bin
     configureFlagsArray=(
       $configureFlagsArray
-      "--CC=$CC"
+      ${if !mpiSupport then ''
-      "--with-cxx=$CXX"
+        "--with-mpi=0"
-      "--with-fc=$FC"
+      '' else ''
-      "--with-mpi=0"
+        "--CC=mpicc"
-      "--with-blas-lib=[${blas}/lib/libblas.so,${gfortran.cc.lib}/lib/libgfortran.a]"
+        "--with-cxx=mpicxx"
-      "--with-lapack-lib=[${lapack}/lib/liblapack.so,${gfortran.cc.lib}/lib/libgfortran.a]"
+        "--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=1"
+      "--with-lapack=1"
     )
   '';
 
+  configureScript = "python ./configure";
+
+  enableParallelBuilding = true;
+  doCheck = stdenv.hostPlatform == stdenv.buildPlatform;
+
   meta = with lib; {
-    description = ''
+    description = "Portable Extensible Toolkit for Scientific computation";
-      Library of linear algebra algorithms for solving partial differential
-      equations
-    '';
     homepage = "https://www.mcs.anl.gov/petsc/index.html";
     license = licenses.bsd2;
-    maintainers = with maintainers; [ wucke13 ];
+    maintainers = with maintainers; [ wucke13 cburstedde ];
-    platforms = platforms.all;
   };
 }

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 ];
+  };
+}

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)";
+  };
+}

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 ];
+  };
+}

pkgs/development/python-modules/pre-commit-hooks/default.nix

@@ -1,9 +1,8 @@
-{ buildPythonPackage
+{ lib
+, buildPythonPackage
 , fetchFromGitHub
-, fetchPypi
 , git
-, isPy27
+, pythonOlder
-, lib
 , pytestCheckHook
 , ruamel_yaml
 , toml
@@ -11,19 +10,25 @@
 
 buildPythonPackage rec {
   pname = "pre-commit-hooks";
-  version = "3.4.0";
+  version = "4.0.1";
-  disabled = isPy27;
+  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 ];
+  propagatedBuildInputs = [
-  checkInputs = [ git pytestCheckHook ];
+    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";

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 { };