Merge commit '7e567a3d092b7de69cdf5deaeb8d9526de230916'

# Conflicts:
#	nixpkgs/pkgs/top-level/all-packages.nix

6 files changed, 263 insertions, 17 deletions

diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/xcfun/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/xcfun/default.nix
new file mode 100644
index 000000000000..7f8ef3dc47d7
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/xcfun/default.nix
@@ -0,0 +1,30 @@
+{ stdenv, lib, fetchFromGitHub, cmake, gfortran, python3 } :
+
+stdenv.mkDerivation rec {
+  pname = "xcfun";
+  version = "2.1.1";
+
+  src = fetchFromGitHub  {
+    owner = "dftlibs";
+    repo = pname;
+    rev = "v${version}";
+    sha256= "1bj70cnhbh6ziy02x988wwl7cbwaq17ld7qwhswqkgnnx8rpgxid";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    gfortran
+  ];
+
+  propagatedBuildInputs = [ (python3.withPackages (p: with p; [ pybind11 ])) ];
+
+  cmakeFlags = [ "-DXCFUN_MAX_ORDER=3" ];
+
+  meta = with lib; {
+    description = "A library of exchange-correlation functionals with arbitrary-order derivatives";
+    homepage = "https://github.com/dftlibs/xcfun";
+    license = licenses.mpl20;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix b/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix
index 87b5835aa9ef..efbd071ecd79 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix
@@ -18,7 +18,7 @@ let
   # this derivation. However, we should ensure on version bumps
   # that the CUDA toolkit for `passthru.tests` is still
   # up-to-date.
-  version = "1.8.1";
+  version = "1.9.0";
   device = if cudaSupport then "cuda" else "cpu";
   srcs = import ./binary-hashes.nix version;
   unavailable = throw "libtorch is not available for this platform";
diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix b/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix
index ec4522a75592..6ded62fb87c3 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix
@@ -1,14 +1,14 @@
 version: {
   x86_64-darwin-cpu = {
     url = "https://download.pytorch.org/libtorch/cpu/libtorch-macos-${version}.zip";
-    hash = "sha256-FYgnd5zlycjCYnP5bZcjpMdGYXrRERwhFFBYo/SJgzs=";
+    hash = "sha256-TOJ+iQpqazta46y4IzIbfEGMjz/fz+pRDV8fKqriB6Q=";
   };
   x86_64-linux-cpu = {
     url = "https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-${version}%2Bcpu.zip";
-    hash = "sha256-xneCcVrY25Whgbs/kPbwdS1Lc0e6RxsDRpA5lHTZigc=";
+    hash = "sha256-gZMNLCzW3j+eplBqWo6lVvuHS5iRqtMD8NL3MoszsVg=";
   };
   x86_64-linux-cuda = {
     url = "https://download.pytorch.org/libtorch/cu111/libtorch-cxx11-abi-shared-with-deps-${version}%2Bcu111.zip";
-    hash = "sha256-VW+TW00nD49GBztCyxHE4dTyy81aN/kfYE3hKQOIm50=";
+    hash = "sha256-dRu4F8k2SAbtghwrPJNyX0u3tsODCbXfi9EqUdf4xYc=";
   };
 }
diff --git a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
index f464a755f6e4..ccb37d295bff 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, fetchpatch, perl, which
+{ lib, stdenv, fetchFromGitHub, perl, which
 # Most packages depending on openblas expect integer width to match
 # pointer width, but some expect to use 32-bit integers always
 # (for compatibility with reference BLAS).
@@ -116,7 +116,7 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "openblas";
-  version = "0.3.13";
+  version = "0.3.15";
 
   outputs = [ "out" "dev" ];
 
@@ -124,19 +124,9 @@ stdenv.mkDerivation rec {
     owner = "xianyi";
     repo = "OpenBLAS";
     rev = "v${version}";
-    sha256 = "14jxh0v3jfbw4mfjx4mcz4dd51lyq7pqvh9k8dg94539ypzjr2lj";
+    sha256 = "1qjr02cqncv20abdp1yzr55n7smhx6h9chqvb0xbp18byynvj87w";
   };
 
-  # apply https://github.com/xianyi/OpenBLAS/pull/3060 to fix a crash on arm
-  # remove this when updating to 0.3.14 or newer
-  patches = [
-    (fetchpatch {
-      name = "label-get_cpu_ftr-as-volatile.patch";
-      url = "https://github.com/xianyi/OpenBLAS/commit/6fe0f1fab9d6a7f46d71d37ebb210fbf56924fbc.diff";
-      sha256 = "06gwh73k4sas1ap2fi3jvpifbjkys2vhmnbj4mzrsvj279ljsfdk";
-    })
-  ];
-
   inherit blas64;
 
   # Some hardening features are disabled due to sporadic failures in
diff --git a/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix b/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix
new file mode 100644
index 000000000000..cf2346bad271
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix
@@ -0,0 +1,181 @@
+{ stdenv
+, bash
+, abseil-cpp
+, fetchFromGitHub
+, fetchFromGitLab
+, fetchpatch
+, fetchurl
+, flatbuffers
+, hostPlatform
+, lib
+, zlib
+}:
+let
+  tflite-eigen = fetchFromGitLab {
+    owner = "libeigen";
+    repo = "eigen";
+    rev = "3d9051ea84a5089b277c88dac456b3b1576bfa7f";
+    sha256 = "1y3f2jvimb5i904f4n37h23cv2pkdlbz8656s0kga1y7c0p50wif";
+  };
+
+  gemmlowp-src = fetchFromGitHub {
+    owner = "google";
+    repo = "gemmlowp";
+    rev = "fda83bdc38b118cc6b56753bd540caa49e570745";
+    sha256 = "1sbp8kmr2azwlvfbzryy1frxi99jhsh1nc93bdbxdf8zdgpv0kxl";
+  };
+
+  neon-2-sse-src = fetchFromGitHub {
+    owner = "intel";
+    repo = "ARM_NEON_2_x86_SSE";
+    rev = "1200fe90bb174a6224a525ee60148671a786a71f";
+    sha256 = "0fhxch711ck809dpq1myxz63jiiwfcnxvj45ww0kg8s0pqpn5kv6";
+  };
+
+  farmhash-src = fetchFromGitHub {
+    owner = "google";
+    repo = "farmhash";
+    rev = "816a4ae622e964763ca0862d9dbd19324a1eaf45";
+    sha256 = "1mqxsljq476n1hb8ilkrpb39yz3ip2hnc7rhzszz4sri8ma7qzp6";
+  };
+
+  fft2d-src = fetchurl {
+    url = "http://www.kurims.kyoto-u.ac.jp/~ooura/fft2d.tgz";
+    sha256 = "ada7e99087c4ed477bfdf11413f2ba8db8a840ba9bbf8ac94f4f3972e2a7cec9";
+  };
+
+  fp16-src = fetchFromGitHub {
+    owner = "Maratyszcza";
+    repo = "FP16";
+    rev = "4dfe081cf6bcd15db339cf2680b9281b8451eeb3";
+    sha256 = "06a8dfl3a29r93nxpp6hpywsajz5d555n3sqd3i6krybb6swnvh7";
+  };
+
+  ruy-src = fetchFromGitHub {
+    owner = "google";
+    repo = "ruy";
+    rev = "23633b37099b614a2f836ef012cafc8087fdb98c";
+    sha256 = "14k9hz6ss8qy8nsajk6lrq25f6qxrldxky31ijw0dpqnfnnswrx4";
+  };
+
+  cpuinfo-src = fetchFromGitHub {
+    owner = "pytorch";
+    repo = "cpuinfo";
+    rev = "5916273f79a21551890fd3d56fc5375a78d1598d";
+    sha256 = "0q6760xdxsg18acdv8vq3yrq7ksr7wsm8zbyan01zf2khnb6fw4x";
+  };
+in
+stdenv.mkDerivation rec {
+  pname = "tensorflow-lite";
+  version = "2.5.0";
+
+  src = fetchFromGitHub {
+    owner = "tensorflow";
+    repo = "tensorflow";
+    rev = "v${version}";
+    sha256 = "1jdw2i1rq06zqd6aabh7bbm0avsg4pygnfmd7gviv0blhih9054l";
+  };
+
+  patches = [
+    # TODO: remove on the next version bump
+    (fetchpatch {
+      name = "include-schema-conversion-utils-source.patch";
+      url = "https://github.com/tensorflow/tensorflow/commit/f3c4f4733692150fd6174f2cd16438cfaba2e5ab.patch";
+      sha256 = "0zx4hbz679kn79f30159rl1mq74dg45cvaawii0cyv48z472yy4k";
+    })
+    # TODO: remove on the next version bump
+    (fetchpatch {
+      name = "cxxstandard-var.patch";
+      url = "https://github.com/tensorflow/tensorflow/commit/9b128ae4200e10b4752f903492d1e7d11957ed5c.patch";
+      sha256 = "1q0izdwdji5fbyqll6k4dmkzfykyvvz5cvc6hysdj285nkn2wy6h";
+    })
+  ];
+
+  buildInputs = [ zlib flatbuffers ];
+
+  dontConfigure = true;
+
+  postPatch = ''
+    substituteInPlace ./tensorflow/lite/tools/make/Makefile \
+      --replace /bin/bash ${bash}/bin/bash \
+      --replace /bin/sh ${bash}/bin/sh
+  '';
+
+  makefile = "tensorflow/lite/tools/make/Makefile";
+
+  preBuild =
+    let
+      includes =
+        lib.concatMapStringsSep
+          " "
+          (subdir: "-I $PWD/tensorflow/lite/tools/make/downloads/${subdir}")
+          [
+            "neon_2_sse"
+            "gemmlowp"
+            "absl"
+            "fp16/include"
+            "farmhash/src"
+            "ruy"
+            "cpuinfo"
+            "cpuinfo/src"
+            "cpuinfo/include"
+            "cpuinfo/deps/clog/include"
+            "eigen"
+          ];
+    in
+    ''
+      # enter the vendoring lair of doom
+
+      prefix="$PWD/tensorflow/lite/tools/make/downloads"
+
+      mkdir -p "$prefix"
+
+      tar xzf ${fft2d-src} -C "$prefix"
+
+      ln -s ${ruy-src} "$prefix/ruy"
+      ln -s ${gemmlowp-src} "$prefix/gemmlowp"
+      ln -s ${neon-2-sse-src} "$prefix/neon_2_sse"
+      ln -s ${farmhash-src} "$prefix/farmhash"
+      ln -s ${cpuinfo-src} "$prefix/cpuinfo"
+      ln -s ${fp16-src} "$prefix/fp16"
+      ln -s ${tflite-eigen} "$prefix/eigen"
+
+      # tensorflow lite is using the *source* of flatbuffers
+      ln -s ${flatbuffers.src} "$prefix/flatbuffers"
+
+      # tensorflow lite expects to compile abseil into `libtensorflow-lite.a`
+      ln -s ${abseil-cpp.src} "$prefix/absl"
+
+      # set CXXSTANDARD=c++17 here because abseil-cpp in nixpkgs is set as
+      # such and would be used in dependents like libedgetpu
+      buildFlagsArray+=(
+        INCLUDES="-I $PWD ${includes}"
+        CXXSTANDARD="-std=c++17"
+        TARGET_TOOLCHAIN_PREFIX=""
+        -j$NIX_BUILD_CORES
+        all)
+    '';
+
+  installPhase = ''
+    mkdir "$out"
+
+    # copy the static lib and binaries into the output dir
+    cp -r ./tensorflow/lite/tools/make/gen/linux_${hostPlatform.uname.processor}/{bin,lib} "$out"
+
+    find ./tensorflow/lite -type f -name '*.h' | while read f; do
+      path="$out/include/''${f/.\//}"
+      install -D "$f" "$path"
+
+      # remove executable bit from headers
+      chmod -x "$path"
+    done
+  '';
+
+  meta = with lib; {
+    description = "An open source deep learning framework for on-device inference.";
+    homepage = "https://www.tensorflow.org/lite";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ cpcloud ];
+    platforms = [ "x86_64-linux" "aarch64-linux" ];
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/eigen_include_dir.patch b/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/eigen_include_dir.patch
new file mode 100644
index 000000000000..6fa3c703efa9
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/eigen_include_dir.patch
@@ -0,0 +1,45 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 28103856e..a36909c0e 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -449,13 +449,6 @@ install(FILES
+   DESTINATION ${INCLUDE_INSTALL_DIR} COMPONENT Devel
+   )
+ 
+-if(EIGEN_BUILD_PKGCONFIG)
+-    configure_file(eigen3.pc.in eigen3.pc @ONLY)
+-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/eigen3.pc
+-        DESTINATION ${PKGCONFIG_INSTALL_DIR}
+-        )
+-endif()
+-
+ install(DIRECTORY Eigen DESTINATION ${INCLUDE_INSTALL_DIR} COMPONENT Devel)
+ 
+ add_subdirectory(doc EXCLUDE_FROM_ALL)
+@@ -570,8 +563,15 @@ set ( EIGEN_VERSION_MAJOR  ${EIGEN_WORLD_VERSION} )
+ set ( EIGEN_VERSION_MINOR  ${EIGEN_MAJOR_VERSION} )
+ set ( EIGEN_VERSION_PATCH  ${EIGEN_MINOR_VERSION} )
+ set ( EIGEN_DEFINITIONS "")
+-set ( EIGEN_INCLUDE_DIR "${CMAKE_INSTALL_PREFIX}/${INCLUDE_INSTALL_DIR}" )
+ set ( EIGEN_ROOT_DIR ${CMAKE_INSTALL_PREFIX} )
++GNUInstallDirs_get_absolute_install_dir(EIGEN_INCLUDE_DIR INCLUDE_INSTALL_DIR)
++
++if(EIGEN_BUILD_PKGCONFIG)
++    configure_file(eigen3.pc.in eigen3.pc @ONLY)
++    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/eigen3.pc
++        DESTINATION ${PKGCONFIG_INSTALL_DIR}
++        )
++endif()
+ 
+ # Interface libraries require at least CMake 3.0
+ if (NOT CMAKE_VERSION VERSION_LESS 3.0)
+diff --git a/eigen3.pc.in b/eigen3.pc.in
+index 3368a3aa1..d6778bf06 100644
+--- a/eigen3.pc.in
++++ b/eigen3.pc.in
+@@ -6,4 +6,4 @@ Description: A C++ template library for linear algebra: vectors, matrices, and r
+ Requires:
+ Version: @EIGEN_VERSION_NUMBER@
+ Libs:
+-Cflags: -I${prefix}/@INCLUDE_INSTALL_DIR@
++Cflags: -I@EIGEN_INCLUDE_DIR@