14 files changed, 110 insertions, 112 deletions
diff --git a/pkgs/development/go-modules/generic/default.nix b/pkgs/development/go-modules/generic/default.nix
index f00ca1984ec88..753dcfab37079 100644
--- a/pkgs/development/go-modules/generic/default.nix
+++ b/pkgs/development/go-modules/generic/default.nix
@@ -26,12 +26,10 @@
 , vendorSha256
 # Whether to delete the vendor folder supplied with the source.
 , deleteVendor ? false
-# Whether to run the vend tool to regenerate the vendor directory.
-# This is useful if any dependency contain C files.
-, runVend ? false
 # Whether to fetch (go mod download) and proxy the vendor directory.
-# This is useful if any dependency has case-insensitive conflicts
-# which will produce platform dependant `vendorSha256` checksums.
+# This is useful if your code depends on c code and go mod tidy does not
+# include the needed sources to build or if any dependency has case-insensitive
+# conflicts which will produce platform dependant `vendorSha256` checksums.
 , proxyVendor ? false
 
 # We want parallel builds by default
@@ -43,6 +41,9 @@
 
 , meta ? {}
 
+# disabled
+, runVend ? false
+
 # Not needed with buildGoModule
 , goPackagePath ? ""
 
@@ -54,7 +55,7 @@
 
 with builtins;
 
-assert (runVend == true && proxyVendor == true) -> throw "can't use `runVend` and `proxyVendor` together";
+assert runVend != false -> throw "`runVend` has been replaced by `proxyVendor`";
 
 assert goPackagePath != "" -> throw "`goPackagePath` is not needed with `buildGoModule`";
 
diff --git a/pkgs/development/libraries/LASzip/LASzip2.nix b/pkgs/development/libraries/LASzip/LASzip2.nix
index b080153826ad1..4f63dfe8059c8 100644
--- a/pkgs/development/libraries/LASzip/LASzip2.nix
+++ b/pkgs/development/libraries/LASzip/LASzip2.nix
@@ -1,12 +1,14 @@
-{ lib, stdenv, fetchurl, cmake }:
+{ lib, stdenv, fetchFromGitHub, cmake }:
 
 stdenv.mkDerivation rec {
   version = "2.2.0";
   pname = "LASzip";
 
-  src = fetchurl {
-    url = "https://github.com/LASzip/LASzip/archive/v${version}.tar.gz";
-    sha256 = "b8e8cc295f764b9d402bc587f3aac67c83ed8b39f1cb686b07c168579c61fbb2";
+  src = fetchFromGitHub {
+    owner = "LASzip";
+    repo = "LASzip";
+    rev = "v${version}";
+    sha256 = "sha256-TXzse4oLjNX5R2xDR721iV+gW/rP5z3Zciv4OgxfeqA=";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/development/libraries/graphene-hardened-malloc/default.nix b/pkgs/development/libraries/graphene-hardened-malloc/default.nix
index 35a4d93626802..f3c16c8ac3217 100644
--- a/pkgs/development/libraries/graphene-hardened-malloc/default.nix
+++ b/pkgs/development/libraries/graphene-hardened-malloc/default.nix
@@ -1,12 +1,14 @@
-{ lib, stdenv, fetchurl, python3, runCommand, makeWrapper, stress-ng }:
+{ lib, stdenv, fetchFromGitHub, python3, runCommand, makeWrapper, stress-ng }:
 
 lib.fix (self: stdenv.mkDerivation rec {
   pname = "graphene-hardened-malloc";
   version = "8";
 
-  src = fetchurl {
-    url = "https://github.com/GrapheneOS/hardened_malloc/archive/${version}.tar.gz";
-    sha256 = "0lipyd2pb1bmghkyv9zmg25jwcglj7m281f01zlh3ghz3xlfh0ym";
+  src = fetchFromGitHub {
+    owner = "GrapheneOS";
+    repo = "hardened_malloc";
+    rev = version;
+    sha256 = "sha256-+5kJb3hhuFTto7zsIymIXl3tpKUOm3v1DCY4EkAOCgo=";
   };
 
   doCheck = true;
diff --git a/pkgs/development/libraries/grib-api/default.nix b/pkgs/development/libraries/grib-api/default.nix
deleted file mode 100644
index 1f7097dc4a3f5..0000000000000
--- a/pkgs/development/libraries/grib-api/default.nix
+++ /dev/null
@@ -1,71 +0,0 @@
-{ fetchurl, fetchpatch, lib, stdenv,
-  cmake, netcdf, gfortran, libpng, openjpeg,
-  enablePython ? false, pythonPackages ? null }:
-
-stdenv.mkDerivation rec {
-  pname = "grib-api";
-  version = "1.28.0";
-
-  src = fetchurl {
-    url = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-${version}-Source.tar.gz";
-    sha256 = "0qbj12ap7yy2rl1pq629chnss2jl73wxdj1lwzv0xp87r6z5qdfl";
-  };
-
-  patches = [
-    (fetchpatch {
-      url = "https://salsa.debian.org/science-team/grib-api/raw/debian/1.28.0-2/debian/patches/openjpeg2.patch";
-      sha256 = "05faxh51vlidiazxq1ssd3k4cjivk1adyn30k94mxqa1xnb2r2pc";
-    })
-  ];
-
-  preConfigure = ''
-    # Fix "no member named 'inmem_' in 'jas_image_t'"
-    substituteInPlace "src/grib_jasper_encoding.c" --replace "image.inmem_    = 1;" ""
-  '';
-
-  nativeBuildInputs = [ cmake gfortran ];
-  buildInputs = [ netcdf
-                  libpng
-                  openjpeg
-                ] ++ lib.optionals enablePython [
-                  pythonPackages.python
-                ];
-
-  propagatedBuildInputs = lib.optionals enablePython [
-                  pythonPackages.numpy
-                ];
-
-  cmakeFlags = [ "-DENABLE_PYTHON=${if enablePython then "ON" else "OFF"}"
-                 "-DENABLE_PNG=ON"
-                 "-DENABLE_FORTRAN=ON"
-                 "-DOPENJPEG_INCLUDE_DIR=${openjpeg.dev}/include/${openjpeg.incDir}"
-               ];
-
-  doCheck = true;
-
-  # Only do tests that don't require downloading 120MB of testdata
-  # We fix the darwin checkPhase, which searches for libgrib_api.dylib
-  # in /nix/store by setting DYLD_LIBRARY_PATH
-  checkPhase = lib.optionalString (stdenv.isDarwin) ''
-    substituteInPlace "tests/include.sh" --replace "set -ea" "set -ea; export DYLD_LIBRARY_PATH=$(pwd)/lib"
-  '' + ''
-    ctest -R "t_definitions|t_calendar|t_unit_tests" -VV
-  '';
-
-
-  meta = with lib; {
-    homepage = "https://software.ecmwf.int/wiki/display/GRIB/Home";
-    license = licenses.asl20;
-    platforms = with platforms; linux ++ darwin;
-    description = "ECMWF Library for the GRIB file format -- DEPRECATED";
-    longDescription = ''
-      The ECMWF GRIB API is an application program interface accessible from C,
-      FORTRAN and Python programs developed for encoding and decoding WMO FM-92
-      GRIB edition 1 and edition 2 messages.
-
-      Please note: GRIB-API support is being discontinued at the end of 2018.
-      After which there will be no further releases. Please upgrade to ecCodes
-    '';
-    maintainers = with maintainers; [ knedlsepp ];
-  };
-}
diff --git a/pkgs/development/libraries/keybinder/default.nix b/pkgs/development/libraries/keybinder/default.nix
index fb481c19d05f7..95eb0ce4de0a1 100644
--- a/pkgs/development/libraries/keybinder/default.nix
+++ b/pkgs/development/libraries/keybinder/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, autoconf, automake, libtool, pkg-config, gnome
+{ lib, stdenv, fetchFromGitHub, autoconf, automake, libtool, pkg-config, gnome
 , gtk-doc, gtk2, python2Packages, lua, gobject-introspection
 }:
 
@@ -8,10 +8,11 @@ in stdenv.mkDerivation rec {
   pname = "keybinder";
   version = "0.3.0";
 
-  src = fetchurl {
-    name = "${pname}-${version}.tar.gz";
-    url = "https://github.com/engla/keybinder/archive/v${version}.tar.gz";
-    sha256 = "0kkplz5snycik5xknwq1s8rnmls3qsp32z09mdpmaacydcw7g3cf";
+  src = fetchFromGitHub {
+    owner = "engla";
+    repo = "keybinder";
+    rev = "v${version}";
+    sha256 = "sha256-q/+hqhvXIknT+/5oENcWSr1OuF00kaZlXFUP1fdCMlk=";
   };
 
   nativeBuildInputs = [ pkg-config ];
diff --git a/pkgs/development/libraries/libcangjie/default.nix b/pkgs/development/libraries/libcangjie/default.nix
index c6bbbcdb61ab0..b0c02eaa6bcf3 100644
--- a/pkgs/development/libraries/libcangjie/default.nix
+++ b/pkgs/development/libraries/libcangjie/default.nix
@@ -1,13 +1,15 @@
-{ lib, stdenv, autoconf, automake, libtool, m4, fetchurl, bash, pkg-config, sqlite }:
+{ lib, stdenv, autoconf, automake, libtool, m4, fetchFromGitLab, bash, pkg-config, sqlite }:
 
 stdenv.mkDerivation rec {
   pname = "libcangjie";
   version = "1.4_rev_${rev}";
   rev = "a73c1d8783f7b6526fd9b2cc44a669ffa5518d3d";
 
-  src = fetchurl {
-    url = "https://github.com/Cangjians/libcangjie/archive/${rev}.tar.gz";
-    sha256 = "0i5svvcx099fc9hh5dvr3gpb1041v6vn5fnylxy82zjy239114lg";
+  src = fetchFromGitLab {
+    owner = "Cangjians";
+    repo = "libcangjie";
+    inherit rev;
+    sha256 = "sha256-R7WqhxciaTxhTiwPp2EUNTOh477gi/Pj3VpMtat5qXw=";
   };
 
   nativeBuildInputs = [ pkg-config ];
@@ -26,7 +28,7 @@ stdenv.mkDerivation rec {
     longDescription = ''
       libcangjie is a library implementing the Cangjie input method.
     '';
-    homepage = "http://cangjians.github.io/projects/libcangjie/";
+    homepage = "https://gitlab.freedesktop.org/cangjie/libcangjie";
     license = lib.licenses.lgpl3Plus;
 
     maintainers = [ lib.maintainers.linquize ];
diff --git a/pkgs/development/libraries/libcec/default.nix b/pkgs/development/libraries/libcec/default.nix
index b0de959234774..e03416a221c19 100644
--- a/pkgs/development/libraries/libcec/default.nix
+++ b/pkgs/development/libraries/libcec/default.nix
@@ -1,12 +1,14 @@
-{ lib, stdenv, fetchurl, cmake, pkg-config, udev, libcec_platform, libraspberrypi ? null }:
+{ lib, stdenv, fetchFromGitHub, cmake, pkg-config, udev, libcec_platform, libraspberrypi ? null }:
 
 stdenv.mkDerivation rec {
   pname = "libcec";
   version = "6.0.2";
 
-  src = fetchurl {
-    url = "https://github.com/Pulse-Eight/libcec/archive/libcec-${version}.tar.gz";
-    sha256 = "0xrkrcgfgr5r8r0854bw3i9jbq4jmf8nzc5vrrx2sxzvlkbrc1h9";
+  src = fetchFromGitHub {
+    owner = "Pulse-Eight";
+    repo = "libcec";
+    rev = "libcec-${version}";
+    sha256 = "sha256-OWqCn7Z0KG8sLlfMWd0btJIFJs79ET3Y1AV/y/Kj2TU=";
   };
 
   nativeBuildInputs = [ pkg-config cmake ];
diff --git a/pkgs/development/libraries/libcrafter/default.nix b/pkgs/development/libraries/libcrafter/default.nix
index 37ac9bf7f171d..22543972c1e6c 100644
--- a/pkgs/development/libraries/libcrafter/default.nix
+++ b/pkgs/development/libraries/libcrafter/default.nix
@@ -1,12 +1,14 @@
-{ lib, stdenv, fetchzip, autoconf, automake, libtool, libpcap }:
+{ lib, stdenv, fetchFromGitHub, autoconf, automake, libtool, libpcap }:
 
 stdenv.mkDerivation rec {
   pname = "libcrafter";
   version = "1.0";
 
-  src = fetchzip {
-    url = "https://github.com/pellegre/libcrafter/archive/version-${version}.zip";
-    sha256 = "1d2vgxawdwk2zg3scxclxdby1rhghmivly8azdjja89kw7gls9xl";
+  src = fetchFromGitHub {
+    owner = "pellegre";
+    repo = "libcrafter";
+    rev = "version-${version}";
+    sha256 = "sha256-tCdN3+EzISVl+wp5umOFD+bgV+uUdabH+2LyxlV/W7Q=";
   };
 
   preConfigure = "cd libcrafter";
diff --git a/pkgs/development/libraries/wolfssl/default.nix b/pkgs/development/libraries/wolfssl/default.nix
index 619f41eb33f25..d2735f34b7f08 100644
--- a/pkgs/development/libraries/wolfssl/default.nix
+++ b/pkgs/development/libraries/wolfssl/default.nix
@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   pname = "wolfssl";
-  version = "5.1.0";
+  version = "5.1.1";
 
   src = fetchFromGitHub {
     owner = "wolfSSL";
     repo = "wolfssl";
     rev = "v${version}-stable";
-    sha256 = "sha256-PkuYXDL04LbUiY+O/4EilZn2+hTbwbRXPDE3B5d/4pQ=";
+    sha256 = "sha256-/noS5cn8lllWoGyZ9QyjRmdiR6LXzfT4lYGEt+0+Bdw=";
   };
 
   # Almost same as Debian but for now using --enable-all --enable-reproducible-build instead of --enable-distro to ensure options.h gets installed
diff --git a/pkgs/development/ocaml-modules/uunf/default.nix b/pkgs/development/ocaml-modules/uunf/default.nix
index b71442a6a8b3d..073e6865fcdd0 100644
--- a/pkgs/development/ocaml-modules/uunf/default.nix
+++ b/pkgs/development/ocaml-modules/uunf/default.nix
@@ -22,6 +22,8 @@ stdenv.mkDerivation {
 
   propagatedBuildInputs = [ uchar ];
 
+  prePatch = lib.optionalString stdenv.isAarch64 "ulimit -s 16384";
+
   inherit (topkg) buildPhase installPhase;
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/limnoria/default.nix b/pkgs/development/python-modules/limnoria/default.nix
index 8e2cb3ca366ee..7a4e93f9ddd34 100644
--- a/pkgs/development/python-modules/limnoria/default.nix
+++ b/pkgs/development/python-modules/limnoria/default.nix
@@ -15,14 +15,14 @@
 
 buildPythonPackage rec {
   pname = "limnoria";
-  version = "2022.1.1";
+  version = "2022.1.1.post1";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-tJqUsNRvSipuvOTfxJOFUCojrkRrrrzIgEYNShrTP8c=";
+    hash = "sha256-9p06yD95emBOFKtTZMVR/3ySAB24pB3QRmzVEnqeb9U=";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/optax/default.nix b/pkgs/development/python-modules/optax/default.nix
new file mode 100644
index 0000000000000..bf0383fa15309
--- /dev/null
+++ b/pkgs/development/python-modules/optax/default.nix
@@ -0,0 +1,55 @@
+{ absl-py
+, buildPythonPackage
+, chex
+, dm-haiku
+, fetchFromGitHub
+, jaxlib
+, lib
+, numpy
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "optax";
+  # As of 2022-01-06, the latest stable version (0.1.0) has broken tests that are fixed
+  # in https://github.com/deepmind/optax/commit/d6633365d84eb6f2c0df0c52b630481a349ce562
+  version = "unstable-2022-01-05";
+
+  src = fetchFromGitHub {
+    owner = "deepmind";
+    repo = pname;
+    rev = "5ec5541b3486224b22e950480ff639ceaf5098f7";
+    sha256 = "1q8cxc42a5xais2ll1l238cnn3l7w28savhgiz0lg01ilz2ysbli";
+  };
+
+  propagatedBuildInputs = [
+    absl-py
+    chex
+    jaxlib
+    numpy
+  ];
+
+  checkInputs = [
+    dm-haiku
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "optax"
+  ];
+
+  disabledTestPaths = [
+    # Requires `flax` which depends on `optax` creating circular dependency.
+    "optax/_src/equivalence_test.py"
+    # Require `tensorflow_datasets` which isn't packaged in `nixpkgs`.
+    "examples/datasets_test.py"
+    "examples/lookahead_mnist_test.py"
+  ];
+
+  meta = with lib; {
+    description = "Optax is a gradient processing and optimization library for JAX.";
+    homepage = "https://github.com/deepmind/optax";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ ndl ];
+  };
+}
diff --git a/pkgs/development/python-modules/parfive/default.nix b/pkgs/development/python-modules/parfive/default.nix
index 822ae2113b2a3..5bb1b04439346 100644
--- a/pkgs/development/python-modules/parfive/default.nix
+++ b/pkgs/development/python-modules/parfive/default.nix
@@ -15,14 +15,14 @@
 
 buildPythonPackage rec {
   pname = "parfive";
-  version = "1.5.0";
+  version = "1.5.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f36128e8a93f3494ce3de8af883eeba4bd651ab228682810a46ec4b7897a84b3";
+    sha256 = "c411fd7269a49d1c72a964e97de474ec082115777b363aeed98a6595f90b8676";
   };
 
   buildInputs = [
diff --git a/pkgs/development/tools/go-task/default.nix b/pkgs/development/tools/go-task/default.nix
index 822633982c879..05ffe14dd4ded 100644
--- a/pkgs/development/tools/go-task/default.nix
+++ b/pkgs/development/tools/go-task/default.nix
@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "go-task";
-  version = "3.9.2";
+  version = "3.10.0";
 
   src = fetchFromGitHub {
     owner = pname;
     repo = "task";
     rev = "v${version}";
-    sha256 = "sha256-nlIgX7TV3bWi8vaYQ9kXmNzGlVLgRUDNkNApwrAw3EQ=";
+    sha256 = "sha256-E0wMFdLK8lA8oluFQuq7hPMWh4t6OsoJ14d7ErDjAdA=";
   };
 
-  vendorSha256 = "sha256-Dmn3LJ+TBO/F3N5lgrNXXrFJ5KTp6r45ZwU11LxvQSg=";
+  vendorSha256 = "sha256-ClMvbxDKwwoVUC9+AJPZfBxJ26KKuLueUn9Nz/gh4Fs=";
 
   doCheck = false;