Merge master into haskell-updates

19 files changed, 302 insertions, 129 deletions

diff --git a/pkgs/development/arduino/platformio/core.nix b/pkgs/development/arduino/platformio/core.nix
index ee8bbeabbfe..344835b831b 100644
--- a/pkgs/development/arduino/platformio/core.nix
+++ b/pkgs/development/arduino/platformio/core.nix
@@ -1,30 +1,74 @@
-{ stdenv, lib, buildPythonApplication
-, ajsonrpc
-, bottle
-, click
-, click-completion
-, colorama
+{ stdenv, lib, python3
+, fetchFromGitHub
 , git
-, jsondiff
-, lockfile
-, marshmallow
-, pyelftools
-, pyserial
-, pytest
-, requests
-, semantic-version
 , spdx-license-list-data
-, starlette
-, tabulate
-, tox
-, uvicorn
-, wsproto
-, zeroconf
 , version, src
 }:
 
 let
-  args = lib.concatStringsSep " " ((map (e: "--deselect tests/${e}") [
+  python = python3.override {
+    packageOverrides = self: super: {
+      aiofiles = super.aiofiles.overridePythonAttrs (oldAttrs: rec {
+        version = "0.6.0";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "e0281b157d3d5d59d803e3f4557dcc9a3dff28a4dd4829a9ff478adae50ca092";
+        };
+      });
+
+      click = super.click.overridePythonAttrs (oldAttrs: rec {
+        version = "7.1.2";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "06kbzd6sjfkqan3miwj9wqyddfxc2b6hi7p5s4dvqjb3gif2bdfj";
+        };
+      });
+
+      uvicorn = super.uvicorn.overridePythonAttrs (oldAttrs: rec {
+        version = "0.13.2";
+        src = fetchFromGitHub {
+          owner = "encode";
+          repo = "uvicorn";
+          rev = version;
+          sha256 = "04zgmp9z46k72ay6cz7plga6d3w3a6x41anabm7ramp7jdqf6na9";
+        };
+      });
+    };
+  };
+in
+with python.pkgs; buildPythonApplication rec {
+  pname = "platformio";
+  inherit version src;
+
+  propagatedBuildInputs = [
+    ajsonrpc
+    bottle
+    click
+    click-completion
+    colorama
+    git
+    lockfile
+    marshmallow
+    pyelftools
+    pyserial
+    requests
+    semantic-version
+    starlette
+    tabulate
+    uvicorn
+    wsproto
+    zeroconf
+  ];
+
+  HOME = "/tmp";
+
+  checkInputs = [
+    jsondiff
+    pytestCheckHook
+    tox
+  ];
+
+  pytestFlagsArray = (map (e: "--deselect tests/${e}") [
     "commands/test_ci.py::test_ci_boards"
     "commands/test_ci.py::test_ci_build_dir"
     "commands/test_ci.py::test_ci_keep_build_dir"
@@ -88,44 +132,10 @@ let
     "commands/test_update.py"
     "test_maintenance.py"
     "test_ino2cpp.py"
-  ]));
-
-in buildPythonApplication rec {
-  pname = "platformio";
-  inherit version src;
-
-  propagatedBuildInputs = [
-    ajsonrpc
-    bottle
-    click
-    click-completion
-    colorama
-    git
-    lockfile
-    marshmallow
-    pyelftools
-    pyserial
-    requests
-    semantic-version
-    starlette
-    tabulate
-    uvicorn
-    wsproto
-    zeroconf
+  ]) ++ [
+    "tests"
   ];
 
-  HOME = "/tmp";
-
-  checkInputs = [ pytest tox jsondiff ];
-
-  checkPhase = ''
-    runHook preCheck
-
-    py.test -v tests ${args}
-
-    runHook postCheck
-  '';
-
   patches = [
     ./fix-searchpath.patch
     ./use-local-spdx-license-list.patch
diff --git a/pkgs/development/compilers/gcc-arm-embedded/10/default.nix b/pkgs/development/compilers/gcc-arm-embedded/10/default.nix
index 943ddd100a2..441ce6cdcd5 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/10/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/10/default.nix
@@ -6,7 +6,8 @@
 
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
-  version = "10-2020-q4-major";
+  version = "10.2.1";
+  release = "10-2020-q4-major";
   subdir = "10-2020q4";
 
   suffix = {
@@ -16,7 +17,7 @@ stdenv.mkDerivation rec {
   }.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
 
   src = fetchurl {
-    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${version}-${suffix}.tar.bz2";
+    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${release}-${suffix}.tar.bz2";
     sha256 = {
       aarch64-linux = "0spkbh7vnda1w0nvavk342nb24nqxn8kln3k9j85mzil560qqg9l";
       x86_64-darwin = "1h5xn0npwkilqxg7ifrymsl7kjpafr9r9gjqgcpb0kjxavijvldy";
diff --git a/pkgs/development/compilers/gcc-arm-embedded/6/default.nix b/pkgs/development/compilers/gcc-arm-embedded/6/default.nix
index 266863d95b2..bab73948ace 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/6/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/6/default.nix
@@ -6,7 +6,8 @@
 
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
-  version = "6-2017-q2-update";
+  version = "6.3.1";
+  release = "6-2017-q2-update";
   subdir = "6-2017q2";
 
   suffix = {
@@ -15,7 +16,7 @@ stdenv.mkDerivation rec {
   }.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
 
   src = fetchurl {
-    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${version}-${suffix}.tar.bz2";
+    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${release}-${suffix}.tar.bz2";
     sha256 = {
       x86_64-darwin = "0019ylpq4inq7p5gydpmc9m8ni72fz2csrjlqmgx1698998q0c3x";
       x86_64-linux  = "1hvwi02mx34al525sngnl0cm7dkmzxfkb1brq9kvbv28wcplp3p6";
diff --git a/pkgs/development/compilers/gcc-arm-embedded/7/default.nix b/pkgs/development/compilers/gcc-arm-embedded/7/default.nix
index 4f2135446f6..ccd99e096f8 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/7/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/7/default.nix
@@ -6,7 +6,8 @@
 
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
-  version = "7-2018-q2-update";
+  version = "7.3.1";
+  release = "7-2018-q2-update";
   subdir = "7-2018q2";
 
   suffix = {
@@ -15,7 +16,7 @@ stdenv.mkDerivation rec {
   }.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
 
   src = fetchurl {
-    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${version}-${suffix}.tar.bz2";
+    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${release}-${suffix}.tar.bz2";
     sha256 = {
       x86_64-darwin = "0nc7m0mpa39qyhfyydxkkyqm7spfc27xf6ygi2vd2aym4r9azi61";
       x86_64-linux  = "0sgysp3hfpgrkcbfiwkp0a7ymqs02khfbrjabm52b5z61sgi05xv";
diff --git a/pkgs/development/compilers/gcc-arm-embedded/8/default.nix b/pkgs/development/compilers/gcc-arm-embedded/8/default.nix
index 2d85113527c..363e87ecb65 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/8/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/8/default.nix
@@ -6,7 +6,8 @@
 
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
-  version = "8-2019-q3-update";
+  version = "8.3.1";
+  release = "8-2019-q3-update";
   subdir = "8-2019q3/RC1.1";
 
   suffix = {
@@ -15,7 +16,7 @@ stdenv.mkDerivation rec {
   }.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
 
   src = fetchurl {
-    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${version}-${suffix}.tar.bz2";
+    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${release}-${suffix}.tar.bz2";
     sha256 = {
       x86_64-darwin = "fc235ce853bf3bceba46eff4b95764c5935ca07fc4998762ef5e5b7d05f37085";
       x86_64-linux  = "b50b02b0a16e5aad8620e9d7c31110ef285c1dde28980b1a9448b764d77d8f92";
diff --git a/pkgs/development/compilers/gcc-arm-embedded/9/default.nix b/pkgs/development/compilers/gcc-arm-embedded/9/default.nix
index 944d7c7b159..6ff1567286d 100644
--- a/pkgs/development/compilers/gcc-arm-embedded/9/default.nix
+++ b/pkgs/development/compilers/gcc-arm-embedded/9/default.nix
@@ -6,7 +6,8 @@
 
 stdenv.mkDerivation rec {
   pname = "gcc-arm-embedded";
-  version = "9-2020-q2-update";
+  version = "9.3.1";
+  release = "9-2020-q2-update";
   subdir = "9-2020q2";
 
   suffix = {
@@ -16,7 +17,7 @@ stdenv.mkDerivation rec {
   }.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
 
   src = fetchurl {
-    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${version}-${suffix}.tar.bz2";
+    url = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${release}-${suffix}.tar.bz2";
     sha256 = {
       aarch64-linux = "1b5q2y710hy7lddj8vj3zl54gfl74j30kx3hk3i81zrcbv16ah8z";
       x86_64-darwin = "1ils9z16wrvglh72m428y5irmd36biq79yj86756whib8izbifdv";
diff --git a/pkgs/development/libraries/java/saxon/default.nix b/pkgs/development/libraries/java/saxon/default.nix
index e6f2fcadbe7..da1e6120da6 100644
--- a/pkgs/development/libraries/java/saxon/default.nix
+++ b/pkgs/development/libraries/java/saxon/default.nix
@@ -1,7 +1,7 @@
-{ lib, stdenv, fetchurl, unzip, jre }:
+{ lib, stdenv, fetchurl, unzip, jre, jre8 }:
 
 let
-  common = { pname, version, src, description
+  common = { pname, version, src, description, java ? jre
            , prog ? null, jar ? null, license ? lib.licenses.mpl20 }:
     stdenv.mkDerivation {
       name = "${pname}-${version}";
@@ -45,6 +45,7 @@ in {
     description = "XSLT 1.0 processor";
     # http://saxon.sourceforge.net/saxon6.5.3/conditions.html
     license = lib.licenses.mpl10;
+    java = jre8;
   };
 
   saxonb_8_8 = common {
@@ -56,6 +57,7 @@ in {
       sha256 = "15bzrfyd2f1045rsp9dp4znyhmizh1pm97q8ji2bc0b43q23xsb8";
     };
     description = "Complete and conformant processor of XSLT 2.0, XQuery 1.0, and XPath 2.0";
+    java = jre8;
   };
 
   saxonb_9_1 = common {
diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix
index f06a028fe64..ee495deedc1 100644
--- a/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/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 ];
-
-  # 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 ''
+  mpiSupport = !withp4est || p4est.mpiSupport;
+  withp4est = petsc-withp4est;
+
+  nativeBuildInputs = [ python3 gfortran ];
+  buildInputs = [ blas lapack ]
+    ++ lib.optional mpiSupport mpi
+    ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh
+    ++ lib.optional withp4est p4est
+  ;
+
+  prePatch = 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"
-      "--with-cxx=$CXX"
-      "--with-fc=$FC"
-      "--with-mpi=0"
-      "--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]"
+      ${if !mpiSupport then ''
+        "--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=1"
+      "--with-lapack=1"
     )
   '';
 
+  configureScript = "python ./configure";
+
+  enableParallelBuilding = true;
+  doCheck = stdenv.hostPlatform == stdenv.buildPlatform;
+
   meta = with lib; {
-    description = ''
-      Library of 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 ];
-    platforms = platforms.all;
+    maintainers = with maintainers; [ wucke13 cburstedde ];
   };
 }
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 00000000000..2e4e0518a52
--- /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 00000000000..5048a8fd06a
--- /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 00000000000..6dfea612b10
--- /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/development/python-modules/geopy/default.nix b/pkgs/development/python-modules/geopy/default.nix
index 693a4221ee0..6b05bb72283 100644
--- a/pkgs/development/python-modules/geopy/default.nix
+++ b/pkgs/development/python-modules/geopy/default.nix
@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "geopy";
-  version = "2.1.0";
+  version = "2.2.0";
   disabled = !isPy3k; # only Python 3
 
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
     rev = version;
-    sha256 = "0239a4achk49ngagb6aqy6cgzfwgbxir07vwi13ysbpx78y0l4g9";
+    sha256 = "sha256-zFz0T/M/CABKkChuiKsFkWj2pphZuFeE5gz0HxZYaz8=";
   };
 
   propagatedBuildInputs = [ geographiclib ];
diff --git a/pkgs/development/python-modules/langdetect/default.nix b/pkgs/development/python-modules/langdetect/default.nix
index 57fee2664cd..2b9f87fdd81 100644
--- a/pkgs/development/python-modules/langdetect/default.nix
+++ b/pkgs/development/python-modules/langdetect/default.nix
@@ -1,16 +1,28 @@
-{ lib, buildPythonPackage, fetchPypi, six }:
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytestCheckHook
+, six
+}:
 
 buildPythonPackage rec {
   pname = "langdetect";
-  version = "1.0.7";
+  version = "1.0.9";
 
   src = fetchPypi {
     inherit pname version;
-    extension = "zip";
-    sha256 = "0c5zm6c7xzsigbb9c7v4r33fcpz911zscfwvh3dq1qxdy3ap18ci";
+    sha256 = "1805svvb7xjm4sf1j7b6nc3409x37pd1xmabfwwjf1ldkzwgxhfb";
   };
 
-  propagatedBuildInputs = [ six ];
+  propagatedBuildInputs = [
+    six
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [ "langdetect" ];
 
   meta = with lib; {
     description = "Python port of Google's language-detection library";
diff --git a/pkgs/development/python-modules/libsass/default.nix b/pkgs/development/python-modules/libsass/default.nix
index 9feb5b1d242..5cc36906610 100644
--- a/pkgs/development/python-modules/libsass/default.nix
+++ b/pkgs/development/python-modules/libsass/default.nix
@@ -1,14 +1,21 @@
-{ lib, buildPythonPackage, fetchFromGitHub, libsass, six, pytest, werkzeug }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, libsass
+, six
+, pytestCheckHook
+, werkzeug
+}:
 
 buildPythonPackage rec {
   pname = "libsass";
-  version = "0.20.1";
+  version = "0.21.0";
 
   src = fetchFromGitHub {
     owner = "sass";
     repo = "libsass-python";
     rev = version;
-    sha256 = "1r0kgl7i6nnhgjl44sjw57k08gh2qr7l8slqih550dyxbf1akbxh";
+    sha256 = "sha256-4doz3kkRlyfVfeUarYw2tcybeDVeE2jpgmHxFJsPiVc=";
   };
 
   buildInputs = [ libsass ];
@@ -20,16 +27,16 @@ buildPythonPackage rec {
   '';
 
   checkInputs = [
-    pytest
+    pytestCheckHook
     werkzeug
   ];
 
-  checkPhase = ''
-    pytest sasstests.py
-  '';
+  pytestFlagsArray = [ "sasstests.py" ];
+
+  pythonImportsCheck = [ "sass" ];
 
   meta = with lib; {
-    description = "A straightforward binding of libsass for Python. Compile Sass/SCSS in Python with no Ruby stack at all!";
+    description = "Python binding for libsass to compile Sass/SCSS";
     homepage = "https://sass.github.io/libsass-python/";
     license = licenses.mit;
     maintainers = with maintainers; [ SuperSandro2000 ];
diff --git a/pkgs/development/python-modules/pre-commit-hooks/default.nix b/pkgs/development/python-modules/pre-commit-hooks/default.nix
index f664d9c6d25..212fdf6a721 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";
diff --git a/pkgs/development/tools/analysis/frama-c/default.nix b/pkgs/development/tools/analysis/frama-c/default.nix
index ab82aed8e5e..9d87cb30520 100644
--- a/pkgs/development/tools/analysis/frama-c/default.nix
+++ b/pkgs/development/tools/analysis/frama-c/default.nix
@@ -31,12 +31,12 @@ in
 
 stdenv.mkDerivation rec {
   pname = "frama-c";
-  version = "23.0-rc1";
+  version = "23.0";
   slang   = "Vanadium";
 
   src = fetchurl {
-    url    = "http://frama-c.com/download/frama-c-${version}-${slang}.tar.gz";
-    sha256 = "1z9f9a217bav3vfc99kq57d5rza6j7hr91ndviwkgcaib6wc5hcv";
+    url    = "https://frama-c.com/download/frama-c-${version}-${slang}.tar.gz";
+    sha256 = "0pdm3y2nfyjhpnicv1pg9j48llq86dmb591d2imnafp4xfqani0s";
   };
 
   preConfigure = lib.optionalString stdenv.cc.isClang "configureFlagsArray=(\"--with-cpp=clang -E -C\")";
diff --git a/pkgs/development/tools/pandoc/default.nix b/pkgs/development/tools/pandoc/default.nix
index 4f65d5fa5db..7c286218d8e 100644
--- a/pkgs/development/tools/pandoc/default.nix
+++ b/pkgs/development/tools/pandoc/default.nix
@@ -8,6 +8,14 @@ in
     configureFlags = drv.configureFlags or [] ++ ["-fembed_data_files"];
     buildDepends = drv.buildDepends or [] ++ [haskellPackages.file-embed];
     buildTools = (drv.buildTools or []) ++ [ removeReferencesTo ];
+    patches = (drv.patches or []) ++ [
+      # Support citerefentry DocBook element.
+      # https://github.com/jgm/pandoc/pull/7437
+      (fetchpatch {
+        url = "https://github.com/jgm/pandoc/commit/06408d08e5ccf06a6a04c9b77470e6a67d98e52c.patch";
+        sha256 = "gOtrWVylzwgu0YLD4SztqlXxtaXXGOf8nTqLwUBS7qs=";
+      })
+    ];
   })).overrideAttrs (drv: {
 
     # These libraries are still referenced, because they generate
diff --git a/pkgs/development/tools/rust/cargo-make/default.nix b/pkgs/development/tools/rust/cargo-make/default.nix
index d5fd7ee4a83..01173474db6 100644
--- a/pkgs/development/tools/rust/cargo-make/default.nix
+++ b/pkgs/development/tools/rust/cargo-make/default.nix
@@ -13,11 +13,11 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-make";
-  version = "0.34.0";
+  version = "0.35.0";
 
   src = fetchCrate {
     inherit pname version;
-    sha256 = "sha256-/9v9nedLoXwuFuqw3W4RjTwvNIlisbiPCcVF/0oH4fw=";
+    sha256 = "sha256-pC3iX5jAPBArxs+YECDyUW5+MP+/f2HMLZNjo+BoKOE=";
   };
 
   nativeBuildInputs = [ pkg-config ];
@@ -25,7 +25,7 @@ rustPlatform.buildRustPackage rec {
   buildInputs = [ openssl ]
     ++ lib.optionals stdenv.isDarwin [ Security SystemConfiguration libiconv ];
 
-  cargoSha256 = "sha256-clav4lGDuWvwzq78Kw+vtz+boNcZnNH+NHH7ZaZYSC4=";
+  cargoSha256 = "sha256-Zp2LoeCnpYupi/QY3Ft1VQ+O/y3I96UaouEFs9QpbLg=";
 
   # Some tests fail because they need network access.
   # However, Travis ensures a proper build.
diff --git a/pkgs/development/tools/stylua/default.nix b/pkgs/development/tools/stylua/default.nix
index 7394b402cfe..86ab951bb9d 100644
--- a/pkgs/development/tools/stylua/default.nix
+++ b/pkgs/development/tools/stylua/default.nix
@@ -8,16 +8,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "stylua";
-  version = "0.9.3";
+  version = "0.10.0";
 
   src = fetchFromGitHub {
     owner = "johnnymorganz";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1xpl3nxiln6hxxjd9nx99h4qijjym3afxm5nalw40p152h8zgig4";
+    sha256 = "03w976fghqs2kswab5bridpr2p6hgldjyfd3l4kz0p5h98f3wzvf";
   };
 
-  cargoSha256 = "012zv1myackwk0x73l6ri7zzrzwdkd970hh4p30b590bmsam6sb9";
+  cargoSha256 = "1311ly02r6c2rqx0ssd6hpbw3sp0ffrf37bzdm66chxnh8cr83sj";
 
   cargoBuildFlags = lib.optionals lua52Support [ "--features" "lua52" ]
     ++ lib.optionals luauSupport [ "--features" "luau" ];