Merge branch 'master' into staging-next

This commit is contained in:
Weijia Wang 2023-11-10 16:25:02 +01:00
commit d8ebb73023
33 changed files with 436 additions and 101 deletions

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@ -8,7 +8,7 @@ stdenv.mkDerivation rec {
src = fetchgit {
url = "https://git.launchpad.net/lifeograph";
rev = "v${version}";
sha256 = "sha256-RotbTdTtpwXmo+UKOyp93IAC6CCstv++KtnX2doN+nM=";
hash = "sha256-RotbTdTtpwXmo+UKOyp93IAC6CCstv++KtnX2doN+nM=";
};
nativeBuildInputs = [
@ -36,6 +36,7 @@ stdenv.mkDerivation rec {
description = "Lifeograph is an off-line and private journal and note taking application";
license = licenses.gpl3Only;
maintainers = with maintainers; [ wolfangaukang ];
mainProgram = "lifeograph";
platforms = platforms.linux;
};
}

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@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);
stdenv.mkDerivation (finalAttrs: {
pname = "R";
version = "4.3.1";
version = "4.3.2";
src = let
inherit (finalAttrs) pname version;
in fetchurl {
url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
sha256 = "sha256-jdC/JPECPG9hjDsxc4PSkbSklPQNc7mDrCL/6pnkupk=";
sha256 = "sha256-s/V2CsLu6AJqPw7vyyW0dyPZeAOO7o6ER2IJTIYMRSo=";
};
outputs = [ "out" "tex" ];

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@ -22,7 +22,7 @@
}:
stdenv.mkDerivation (finalAttrs: {
pname = "triton-llvm";
pname = "openai-triton-llvm";
version = "14.0.6-f28c006a5895";
outputs = [

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@ -93,12 +93,12 @@ let
# To avoid confusion later in passthru
allPkgs = pkgs;
in stdenv.mkDerivation (finalAttrs: {
version = "8.3.0";
version = "8.4.0";
pname = "octave";
src = fetchurl {
url = "mirror://gnu/octave/octave-${finalAttrs.version}.tar.gz";
sha256 = "sha256-K0gRHLZ7MSgX5dHz4XH1utFRK7Bn4WdLnEspKBiVuXo=";
sha256 = "sha256-azjdl1FnhCSus6nWZkMrHzeOs5caISkKkM09NRGdVq0=";
};
buildInputs = [

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@ -0,0 +1,35 @@
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 11c1b04c..762eaa75 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -1,20 +1,14 @@
-find_package(GTestSrc)
+enable_testing()
-IF(GTESTSRC_FOUND)
- enable_testing()
+if (WIN32 AND (NOT CYGWIN) AND (NOT MINGW))
+ set(gtest_disable_pthreads ON)
+ set(gtest_force_shared_crt ON)
+endif()
- if (WIN32 AND (NOT CYGWIN) AND (NOT MINGW))
- set(gtest_disable_pthreads ON)
- set(gtest_force_shared_crt ON)
- endif()
+include_directories(SYSTEM ${GTEST_INCLUDE_DIR})
- add_subdirectory(${GTEST_SOURCE_DIR} ${CMAKE_BINARY_DIR}/googletest)
- include_directories(SYSTEM ${GTEST_INCLUDE_DIR})
+set(TEST_LIBRARIES gtest gtest_main)
- set(TEST_LIBRARIES gtest gtest_main)
-
- add_custom_target(tests ALL)
- add_subdirectory(perftest)
- add_subdirectory(unittest)
-
-ENDIF(GTESTSRC_FOUND)
+add_custom_target(tests ALL)
+add_subdirectory(perftest)
+add_subdirectory(unittest)

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@ -0,0 +1,36 @@
diff --git a/test/valgrind.supp b/test/valgrind.supp
index c9d3d226..63af7bf9 100644
--- a/test/valgrind.supp
+++ b/test/valgrind.supp
@@ -24,3 +24,31 @@
fun:*Uri*Parse_UTF16_Std*
}
+{
+ Suppress memcpy_chk valgrind report 5
+ Memcheck:Overlap
+ fun:__memcpy_chk
+ fun:*dtoa_normal*
+}
+
+{
+ Suppress memcpy_chk valgrind report 6
+ Memcheck:Overlap
+ fun:__memcpy_chk
+ fun:*dtoa_maxDecimalPlaces*
+}
+
+{
+ Suppress memcpy_chk valgrind report 7
+ Memcheck:Overlap
+ fun:__memcpy_chk
+ ...
+ fun:*Reader*ParseDoubleHandler*
+}
+
+{
+ Suppress memcpy_chk valgrind report 8
+ Memcheck:Overlap
+ fun:__memcpy_chk
+ fun:*Reader*ParseNumber_NormalPrecisionError*
+}

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@ -1,17 +1,30 @@
{ lib
, stdenv
, fetchFromGitHub
, fetchpatch
, pkg-config
, cmake
, doxygen
, graphviz
, gtest
, valgrind
# One of "11" or "17"; default in source is CXX 11
, cxxStandard ? "11"
, buildDocs ? true
, buildTests ? !stdenv.hostPlatform.isStatic && !stdenv.isDarwin
, buildExamples ? true
}:
stdenv.mkDerivation rec {
stdenv.mkDerivation (finalAttrs: {
pname = "rapidjson";
version = "unstable-2023-09-28";
outputs = [
"out"
] ++ lib.optionals buildDocs [
"doc"
] ++ lib.optionals buildExamples [
"example"
];
src = fetchFromGitHub {
owner = "Tencent";
repo = "rapidjson";
@ -19,26 +32,44 @@ stdenv.mkDerivation rec {
hash = "sha256-rl7iy14jn1K2I5U2DrcZnoTQVEGEDKlxmdaOCF/3hfY=";
};
patches = lib.optionals buildTests [
./0000-unstable-use-nixpkgs-gtest.patch
# https://github.com/Tencent/rapidjson/issues/2214
./0001-unstable-valgrind-suppress-failures.patch
];
nativeBuildInputs = [
pkg-config
cmake
] ++ lib.optionals buildDocs [
doxygen
graphviz
];
patches = [
(fetchpatch {
name = "do-not-include-gtest-src-dir.patch";
url = "https://git.alpinelinux.org/aports/plain/community/rapidjson/do-not-include-gtest-src-dir.patch?id=9e5eefc7a5fcf5938a8dc8a3be8c75e9e6809909";
hash = "sha256-BjSZEwfCXA/9V+kxQ/2JPWbc26jQn35CfN8+8NW24s4=";
})
cmakeFlags = [
(lib.cmakeBool "RAPIDJSON_BUILD_DOC" buildDocs)
(lib.cmakeBool "RAPIDJSON_BUILD_TESTS" buildTests)
(lib.cmakeBool "RAPIDJSON_BUILD_EXAMPLES" buildExamples)
(lib.cmakeBool "RAPIDJSON_BUILD_CXX11" (cxxStandard == "11"))
(lib.cmakeBool "RAPIDJSON_BUILD_CXX17" (cxxStandard == "17"))
] ++ lib.optionals buildTests [
(lib.cmakeFeature "GTEST_INCLUDE_DIR" "${lib.getDev gtest}")
];
# for tests, adding gtest to checkInputs does not work
# https://github.com/NixOS/nixpkgs/pull/212200
buildInputs = [ gtest ];
cmakeFlags = [ "-DGTEST_SOURCE_DIR=${gtest.dev}/include" ];
doCheck = buildTests;
nativeCheckInputs = [ valgrind ];
doCheck = !stdenv.hostPlatform.isStatic && !stdenv.isDarwin;
nativeCheckInputs = [
gtest
valgrind
];
postInstall = lib.optionalString buildExamples ''
mkdir -p $example/bin
find bin -type f -executable \
-not -name "perftest" \
-not -name "unittest" \
-exec cp -a {} $example/bin \;
'';
meta = with lib; {
description = "Fast JSON parser/generator for C++ with both SAX/DOM style API";
@ -46,5 +77,6 @@ stdenv.mkDerivation rec {
license = licenses.mit;
platforms = platforms.unix;
maintainers = with maintainers; [ Madouura ];
broken = (cxxStandard != "11" && cxxStandard != "17");
};
}
})

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@ -28,6 +28,7 @@
, pyro-ppl
#, pystan (not packaged)
, numpyro
, bokeh
}:
buildPythonPackage rec {
@ -72,6 +73,7 @@ buildPythonPackage rec {
pytestCheckHook
torchvision
zarr
bokeh
];
preCheck = ''
@ -97,6 +99,8 @@ buildPythonPackage rec {
# An issue has been opened upstream: https://github.com/arviz-devs/arviz/issues/2282
"test_plot_ppc_discrete"
"test_plot_ppc_discrete_save_animation"
# Assertion error
"test_data_zarr"
];
pythonImportsCheck = [

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@ -69,6 +69,10 @@ buildPythonPackage rec {
disabledTests = [
# exact comparison of floating points
"test_optimize_l0_homotopy"
# AssertionError: 5 != 2
"test_get_standard_plots_moo"
# AssertionError: Expected 'warning' to be called once. Called 3 times
"test_validate_kwarg_typing"
];
pythonImportsCheck = [ "ax" ];

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@ -6,23 +6,27 @@
, termcolor
, tqdm
, pandas
, setuptools
# test dependencies
, pytestCheckHook
, pytest-lazy-fixture
, tensorflow
, torch
, datasets
, torchvision
, keras
, fasttext
, hypothesis
, wget
, matplotlib
, skorch
}:
let
buildPythonPackage rec {
pname = "cleanlab";
version = "2.5.0";
in
buildPythonPackage {
inherit pname version;
format = "setuptools";
disabled = pythonOlder "3.8";
pyproject = true;
disabled = pythonOlder "3.7";
src = fetchFromGitHub {
owner = "cleanlab";
@ -31,11 +35,7 @@ buildPythonPackage {
hash = "sha256-5XQQVrhjpvjwtFM79DqttObmw/GQLkMQVXb5jhiC8e0=";
};
# postPatch = ''
# substituteInPlace pyproject.toml \
# --replace '"rich <= 13.0.1"' '"rich"' \
# --replace '"numpy < 1.24.0"' '"numpy"'
# '';
nativeBuildInputs = [ setuptools ];
propagatedBuildInputs = [
scikit-learn
@ -44,13 +44,38 @@ buildPythonPackage {
pandas
];
# This is ONLY turned off when we have testing enabled.
# The reason we do this is because of duplicate packages in the enclosure
# when using the packages in nativeCheckInputs.
# Affected packages: grpcio protobuf tensorboard tensorboard-plugin-profile
catchConflicts = (!doCheck);
doCheck = true;
nativeCheckInputs = [
pytestCheckHook
pytest-lazy-fixture
tensorflow
torch
datasets
torchvision
keras
fasttext
hypothesis
wget
matplotlib
skorch
];
disabledTests = [
# Requires the datasets we prevent from downloading
"test_create_imagelab"
];
disabledTestPaths = [
# Requires internet
"tests/test_dataset.py"
# Requires the datasets we just prevented from downloading
"tests/datalab/test_cleanvision_integration.py"
];
meta = with lib; {

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@ -12,19 +12,20 @@
, scs
, setuptools
, wheel
, pybind11
, useOpenmp ? (!stdenv.isDarwin)
}:
buildPythonPackage rec {
pname = "cvxpy";
version = "1.3.2";
version = "1.4.1";
format = "pyproject";
disabled = pythonOlder "3.7";
src = fetchPypi {
inherit pname version;
hash = "sha256-C2heUEDxmfPXA/MPXSLR+GVZdiNFUVPR3ddwJFrvCXU=";
hash = "sha256-ep7zTjxX/4yETYbwo4NPtVda8ZIzlHY53guld8YSLj4=";
};
# we need to patch out numpy version caps from upstream
@ -35,6 +36,7 @@ buildPythonPackage rec {
nativeBuildInputs = [
setuptools
wheel
pybind11
];
propagatedBuildInputs = [
@ -44,7 +46,6 @@ buildPythonPackage rec {
osqp
scipy
scs
setuptools
];
nativeCheckInputs = [

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@ -2,6 +2,7 @@
, buildPythonPackage
, pythonOlder
, fetchFromGitHub
, fetchpatch
# Native build inputs
, cython
@ -27,12 +28,12 @@
, hypothesis
, pytestCheckHook
}:
let
buildPythonPackage rec {
pname = "fairseq";
version = "0.12.3";
in
buildPythonPackage rec {
inherit version pname;
pyproject = true;
disabled = pythonOlder "3.7";
src = fetchFromGitHub {
owner = "pytorch";
@ -41,17 +42,25 @@ buildPythonPackage rec {
hash = "sha256-XX/grU5ljQCwx33miGoFc/7Uj9fZDtmhm4Fz7L4U+Bc=";
};
disabled = pythonOlder "3.7";
patches = [
# https://github.com/facebookresearch/fairseq/pull/5359
(fetchpatch {
url = "https://github.com/facebookresearch/fairseq/commit/2fa0768c2115b0a4c207cfa3e1b3e4ff3ad9a00c.patch";
hash = "sha256-aYYP/knQX6q6vhyA6q9uOOYfRhDAuJCo9QJWfFEDuuA=";
})
];
nativeBuildInputs = [
cython
pythonRelaxDepsHook
which
];
pythonRelaxDeps = [
"hydra-core"
"omegaconf"
];
propagatedBuildInputs = [
cffi
hydra-core
@ -74,6 +83,7 @@ buildPythonPackage rec {
];
pythonImportsCheck = [ "fairseq" ];
preCheck = ''
export HOME=$TMPDIR
cd tests
@ -82,6 +92,7 @@ buildPythonPackage rec {
pytestFlagsArray = [
"--import-mode append"
];
disabledTests = [
# this test requires xformers
"test_xformers_single_forward_parity"
@ -96,6 +107,11 @@ buildPythonPackage rec {
"test_librispeech_s2t_conformer_s_checkpoint"
];
disabledTestPaths = [
# ValueError: mutable default ... for field bar is not allowed: use default_factory
"test_dataclass_utils.py"
];
meta = with lib; {
description = "Facebook AI Research Sequence-to-Sequence Toolkit";
homepage = "https://github.com/pytorch/fairseq";

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@ -11,6 +11,8 @@
, traitlets
, isPyPy
, py
, pythonOlder
, importlib-metadata
}:
buildPythonPackage rec {
@ -35,6 +37,8 @@ buildPythonPackage rec {
pyzmq
tornado
traitlets
] ++ lib.optionals (pythonOlder "3.10") [
importlib-metadata
] ++ lib.optional isPyPy py;
# Circular dependency with ipykernel

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@ -9,6 +9,7 @@
, pygments
, pyqt5
, pythonOlder
, pythonAtLeast
, traitsui
, vtk
, wrapQtAppsHook
@ -18,8 +19,7 @@ buildPythonPackage rec {
pname = "mayavi";
version = "4.8.1";
format = "setuptools";
disabled = pythonOlder "3.8";
disabled = pythonOlder "3.8" || pythonAtLeast "3.11";
src = fetchPypi {
inherit pname version;

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@ -0,0 +1,21 @@
diff --git a/omegaconf/omegaconf.py b/omegaconf/omegaconf.py
index efde14a..a2a050e 100644
--- a/omegaconf/omegaconf.py
+++ b/omegaconf/omegaconf.py
@@ -7,6 +7,7 @@ import pathlib
import sys
import warnings
from collections import defaultdict
+from dataclasses import _MISSING_TYPE
from contextlib import contextmanager
from enum import Enum
from textwrap import dedent
@@ -828,6 +829,8 @@ class OmegaConf:
if obj is _DEFAULT_MARKER_:
obj = {}
+ if isinstance(obj, _MISSING_TYPE):
+ return OmegaConf.create({}, parent=parent, flags=flags)
if isinstance(obj, str):
obj = yaml.load(obj, Loader=get_yaml_loader())
if obj is None:

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@ -3,6 +3,7 @@
, antlr4-python3-runtime
, buildPythonPackage
, fetchFromGitHub
, setuptools
, jre_minimal
, pydevd
, pytest-mock
@ -15,8 +16,7 @@
buildPythonPackage rec {
pname = "omegaconf";
version = "2.3.0";
format = "setuptools";
pyproject = true;
disabled = pythonOlder "3.6";
src = fetchFromGitHub {
@ -31,6 +31,9 @@ buildPythonPackage rec {
src = ./antlr4.patch;
antlr_jar = "${antlr4.out}/share/java/antlr-${antlr4.version}-complete.jar";
})
# https://github.com/omry/omegaconf/pull/1137
./0000-add-support-for-dataclasses_missing_type.patch
];
postPatch = ''
@ -42,6 +45,7 @@ buildPythonPackage rec {
'';
nativeBuildInputs = [
setuptools
jre_minimal
];

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@ -0,0 +1,39 @@
diff --git a/python/setup.py b/python/setup.py
index 2ac3accd2..f26161c72 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -101,25 +101,6 @@ def get_thirdparty_packages(triton_cache_path):
# ---- package data ---
-def download_and_copy_ptxas():
- base_dir = os.path.dirname(__file__)
- src_path = "bin/ptxas"
- url = "https://conda.anaconda.org/nvidia/label/cuda-12.0.0/linux-64/cuda-nvcc-12.0.76-0.tar.bz2"
- dst_prefix = os.path.join(base_dir, "triton")
- dst_suffix = os.path.join("third_party", "cuda", src_path)
- dst_path = os.path.join(dst_prefix, dst_suffix)
- if not os.path.exists(dst_path):
- print(f'downloading and extracting {url} ...')
- ftpstream = urllib.request.urlopen(url)
- file = tarfile.open(fileobj=ftpstream, mode="r|*")
- with tempfile.TemporaryDirectory() as temp_dir:
- file.extractall(path=temp_dir)
- src_path = os.path.join(temp_dir, src_path)
- os.makedirs(os.path.split(dst_path)[0], exist_ok=True)
- shutil.copy(src_path, dst_path)
- return dst_suffix
-
-
# ---- cmake extension ----
@@ -200,8 +181,6 @@ class CMakeBuild(build_ext):
subprocess.check_call(["cmake", "--build", "."] + build_args, cwd=self.build_temp)
-download_and_copy_ptxas()
-
setup(
name="triton",
version="2.0.0",

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@ -1,5 +1,5 @@
{ lib
, callPackage
, config
, buildPythonPackage
, fetchFromGitHub
, addOpenGLRunpath
@ -14,10 +14,12 @@
, ncurses
, libxml2
, lit
, llvm
, filelock
, torchWithRocm
, python
, cudaPackages
, cudaSupport ? config.cudaSupport
}:
let
@ -33,7 +35,6 @@ let
# be executed on the GPU.
# Cf. https://nixos.org/manual/nixpkgs/unstable/#sec-cross-infra
ptxas = "${pkgsTargetTarget.cudaPackages.cuda_nvcc}/bin/ptxas"; # Make sure cudaPackages is the right version each update (See python/setup.py)
llvm = callPackage ./llvm.nix { }; # Use a custom llvm, see llvm.nix for details
in
buildPythonPackage rec {
pname = "triton";
@ -57,6 +58,8 @@ buildPythonPackage rec {
# url = "https://github.com/openai/triton/commit/fc7c0b0e437a191e421faa61494b2ff4870850f1.patch";
# hash = "sha256-f0shIqHJkVvuil2Yku7vuqWFn7VCRKFSFjYRlwx25ig=";
# })
] ++ lib.optionals (!cudaSupport) [
./0000-dont-download-ptxas.patch
];
nativeBuildInputs = [
@ -102,21 +105,18 @@ buildPythonPackage rec {
substituteInPlace bin/CMakeLists.txt \
--replace "add_subdirectory(FileCheck)" ""
# Use our linker flags
substituteInPlace python/triton/compiler.py \
--replace '${oldStr}' '${newStr}'
# Don't fetch googletest
substituteInPlace unittest/CMakeLists.txt \
--replace "include (\''${CMAKE_CURRENT_SOURCE_DIR}/googletest.cmake)" ""\
--replace "include(GoogleTest)" "find_package(GTest REQUIRED)"
'' + lib.optionalString cudaSupport ''
# Use our linker flags
substituteInPlace python/triton/compiler.py \
--replace '${oldStr}' '${newStr}'
'';
# Avoid GLIBCXX mismatch with other cuda-enabled python packages
preConfigure = ''
export CC=${cudaPackages.backendStdenv.cc}/bin/cc;
export CXX=${cudaPackages.backendStdenv.cc}/bin/c++;
# Upstream's setup.py tries to write cache somewhere in ~/
export HOME=$(mktemp -d)
@ -127,6 +127,9 @@ buildPythonPackage rec {
# The rest (including buildPhase) is relative to ./python/
cd python
'' + lib.optionalString cudaSupport ''
export CC=${cudaPackages.backendStdenv.cc}/bin/cc;
export CXX=${cudaPackages.backendStdenv.cc}/bin/c++;
# Work around download_and_copy_ptxas()
mkdir -p $PWD/triton/third_party/cuda/bin
@ -137,7 +140,7 @@ buildPythonPackage rec {
dontUseCmakeConfigure = true;
# Setuptools (?) strips runpath and +x flags. Let's just restore the symlink
postFixup = ''
postFixup = lib.optionalString cudaSupport ''
rm -f $out/${python.sitePackages}/triton/third_party/cuda/bin/ptxas
ln -s ${ptxas} $out/${python.sitePackages}/triton/third_party/cuda/bin/ptxas
'';

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@ -8,6 +8,7 @@
, torch
, torchvision
, typing-extensions
, pythonAtLeast
}:
buildPythonPackage rec {
@ -41,6 +42,7 @@ buildPythonPackage rec {
"tests/pytorch_pfn_extras_tests/onnx_tests/test_export.py"
"tests/pytorch_pfn_extras_tests/onnx_tests/test_torchvision.py"
"tests/pytorch_pfn_extras_tests/onnx_tests/utils.py"
"tests/pytorch_pfn_extras_tests/onnx_tests/test_lax.py"
# RuntimeError: No Op registered for Gradient with domain_version of 9
"tests/pytorch_pfn_extras_tests/onnx_tests/test_grad.py"
@ -53,13 +55,15 @@ buildPythonPackage rec {
"tests/pytorch_pfn_extras_tests/nn_tests/modules_tests/test_lazy.py"
"tests/pytorch_pfn_extras_tests/profiler_tests/test_record.py"
"tests/pytorch_pfn_extras_tests/runtime_tests/test_to.py"
"tests/pytorch_pfn_extras_tests/test_handler.py"
"tests/pytorch_pfn_extras_tests/test_logic.py"
"tests/pytorch_pfn_extras_tests/handler_tests/test_handler.py"
"tests/pytorch_pfn_extras_tests/test_reporter.py"
"tests/pytorch_pfn_extras_tests/training_tests/test_trainer.py"
"tests/pytorch_pfn_extras_tests/utils_tests/test_checkpoint.py"
"tests/pytorch_pfn_extras_tests/utils_tests/test_comparer.py"
"tests/pytorch_pfn_extras_tests/utils_tests/test_new_comparer.py"
] ++ lib.optionals (pythonAtLeast "3.11") [
# Remove this when https://github.com/NixOS/nixpkgs/pull/259068 is merged
"tests/pytorch_pfn_extras_tests/dynamo_tests/test_compile.py"
];
meta = with lib; {

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@ -1,9 +1,8 @@
{ lib
, buildPythonPackage
, fetchFromGitHub
, fetchpatch
, pythonOlder
, pytestCheckHook
, setuptools
, gym
, gymnasium
, torch
@ -11,13 +10,13 @@
, tqdm
, wandb
, packaging
, pytestCheckHook
}:
buildPythonPackage rec {
pname = "skrl";
version = "1.0.0";
format = "setuptools";
pyproject = true;
disabled = pythonOlder "3.6";
src = fetchFromGitHub {
@ -27,14 +26,7 @@ buildPythonPackage rec {
hash = "sha256-89OoJanmaB74SLF1qMI8WFBdN1czS7Yr7BmojaRdo4M=";
};
patches = [
# remove after next release:
(fetchpatch {
name = "fix-python_requires-specification";
url = "https://github.com/Toni-SM/skrl/pull/62/commits/9b554adfe2da6cd97cccbbcd418a349cc8f1de80.patch";
hash = "sha256-GeASMU1Pgy8U1zaIAVroBDjYaY+n93XP5uFyP4U9lok=";
})
];
nativeBuildInputs = [ setuptools ];
propagatedBuildInputs = [
gym

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@ -197,6 +197,30 @@
"sha256": "0dmhv1fa46hi78jgv562v4x3mfl7svchs6kiz35s63ph9ik5r6f2",
"license": "cc-by-sa-40"
},
{
"pname": "ja_core_news_lg",
"version": "3.7.0",
"sha256": "1nb77kivzy0wixsw8ijmw78fffkpqa63kykqph04jzmh75ra4wvg",
"license": "cc-by-sa-40"
},
{
"pname": "ja_core_news_md",
"version": "3.7.0",
"sha256": "0p22bwc24q76cl7ndszvhqgllvq3ws3i3vbjsp5xvhxxls6p49x9",
"license": "cc-by-sa-40"
},
{
"pname": "ja_core_news_sm",
"version": "3.7.0",
"sha256": "0bfvkds4dqynjshk2lxfya9yfcnbvwjfhc6n7yh0852ms1ycicaw",
"license": "cc-by-sa-40"
},
{
"pname": "ja_core_news_trf",
"version": "3.7.0",
"sha256": "0n2lqql4flnilgf671n5mcdp8vi5pdjfz3vymxsapc1gyp29jykk",
"license": "cc-by-sa-30"
},
{
"pname": "it_core_news_lg",
"version": "3.7.0",
@ -377,6 +401,30 @@
"sha256": "11mh1rd0q024xfagdqkly1n4nndksrlq650n51jl1x1pmzlsdgzl",
"license": "mit"
},
{
"pname": "sl_core_news_lg",
"version": "3.7.0",
"sha256": "128ayhp21szc31ckiq3i8vib42i9xnz4lpi1709gjdc38cpmpnlp",
"license": "cc-by-sa-40"
},
{
"pname": "sl_core_news_md",
"version": "3.7.0",
"sha256": "07gx174gw5q1zgyyg1xhfplihhnr311f9562ri5pdd2hgjyz58yb",
"license": "cc-by-sa-40"
},
{
"pname": "sl_core_news_sm",
"version": "3.7.0",
"sha256": "005xwsnh5y3pf8y64lhvrzcbh8y34yr3in204as6hv7krsfg8bxa",
"license": "cc-by-sa-40"
},
{
"pname": "sl_core_news_trf",
"version": "3.7.0",
"sha256": "0x97lwm1i2dq4kdg6rvarh9mnlcx45cnwq80qpjwv3b7zmviyq8c",
"license": "cc-by-sa-40"
},
{
"pname": "sv_core_news_lg",
"version": "3.7.0",

View File

@ -0,0 +1,26 @@
diff --git a/stytra/gui/fishplots.py b/stytra/gui/fishplots.py
index 49ef1fe..fd1cc50 100644
--- a/stytra/gui/fishplots.py
+++ b/stytra/gui/fishplots.py
@@ -13,7 +13,7 @@ from lightparam.gui import ParameterGui
from scipy.ndimage.filters import gaussian_filter1d
-class StreamingPositionPlot(pg.GraphicsWindow):
+class StreamingPosition(pg.GraphicsView):
"""Plot that displays the virtual position of the fish"""
def __init__(self, *args, data_accumulator, n_points=500, **kwargs):
diff --git a/stytra/utilities.py b/stytra/utilities.py
index f79c4db..feaa7ef 100644
--- a/stytra/utilities.py
+++ b/stytra/utilities.py
@@ -239,7 +239,7 @@ def recursive_update(d, u):
:return:
"""
for k, v in u.items():
- if isinstance(v, collections.Mapping):
+ if isinstance(v, collections.ChainMap):
d[k] = recursive_update(d.get(k, {}), v)
else:
d[k] = v

View File

@ -33,8 +33,7 @@
buildPythonPackage rec {
pname = "stytra";
version = "0.8.34";
format = "setuptools";
pyproject = true;
disabled = pythonOlder "3.7";
src = fetchPypi {
@ -42,10 +41,10 @@ buildPythonPackage rec {
sha256 = "aab9d07575ef599a9c0ae505656e3c03ec753462df3c15742f1f768f2b578f0a";
};
# crashes python
preCheck = ''
rm stytra/tests/test_z_experiments.py
'';
patches = [
# https://github.com/portugueslab/stytra/issues/87
./0000-workaround-pyqtgraph.patch
];
propagatedBuildInputs = [
opencv4
@ -79,6 +78,11 @@ buildPythonPackage rec {
pyserial
];
disabledTestPaths = [
# Crashes python
"stytra/tests/test_z_experiments.py"
];
meta = with lib; {
description = "A modular package to control stimulation and track behaviour";
homepage = "https://github.com/portugueslab/stytra";

View File

@ -305,7 +305,7 @@ in buildPythonPackage rec {
])
++ lib.optionals rocmSupport [ rocmtoolkit_joined ];
buildInputs = [ blas blas.provider pybind11 ]
buildInputs = [ blas blas.provider ]
++ lib.optionals cudaSupport (with cudaPackages; [
cuda_cccl.dev # <thrust/*>
cuda_cudart # cuda_runtime.h and libraries
@ -357,17 +357,15 @@ in buildPythonPackage rec {
# the following are required for tensorboard support
pillow six future tensorboard protobuf
# ROCm build and `torch.compile` requires openai-triton
openai-triton
# torch/csrc requires `pybind11` at runtime
pybind11
]
++ lib.optionals MPISupport [ mpi ]
++ lib.optionals rocmSupport [ rocmtoolkit_joined ]
# rocm build requires openai-triton;
# openai-triton currently requires cuda_nvcc,
# so not including it in the cpu-only build;
# torch.compile relies on openai-triton,
# so we include it for the cuda build as well
++ lib.optionals (rocmSupport || cudaSupport) [
openai-triton
];
++ lib.optionals rocmSupport [ rocmtoolkit_joined ];
# Tests take a long time and may be flaky, so just sanity-check imports
doCheck = false;

View File

@ -53,6 +53,8 @@ buildPythonPackage rec {
"test_flan_t5_small"
# AssertionError in output
"test_google"
# "addmm_impl_cpu_" not implemented for 'Half'
"test_input_size_half_precision"
];
disabledTestPaths = [

View File

@ -14,6 +14,8 @@
, pytestCheckHook
, torchmetrics
, pytorch-lightning
, pytest-doctestplus
, pytest-xdist
}:
let
@ -22,10 +24,11 @@ let
in
buildPythonPackage {
inherit pname version;
pyproject = true;
src = fetchFromGitHub {
owner = "PyTorchLightning";
repo = "metrics";
owner = "Lightning-AI";
repo = "torchmetrics";
rev = "refs/tags/v${version}";
hash = "sha256-g5JuTbiRd8yWx2nM3UE8ejOhuZ0XpAQdS5AC9AlrSFY=";
};
@ -51,22 +54,33 @@ buildPythonPackage {
cloudpickle
psutil
pytestCheckHook
pytest-doctestplus
pytest-xdist
];
# A cyclic dependency in: integrations/test_lightning.py
doCheck = false;
passthru.tests.check = torchmetrics.overridePythonAttrs (_: {
pname = "${pname}-check";
doCheck = true;
# We don't have to install because the only purpose
# of this passthru test is to, well, test.
# This fixes having to set `catchConflicts` to false.
dontInstall = true;
});
disabledTests = [
# `IndexError: list index out of range`
"test_metric_lightning_log"
];
disabledTestPaths = [
# These require too many "leftpad-level" dependencies
"tests/text"
"tests/audio"
"tests/image"
# Also too cross-dependent
"tests/unittests"
# A few non-deterministic things like test_check_compute_groups_is_faster
"tests/bases/test_collections.py"
# A trillion import path mismatch errors
"src/torchmetrics"
];
pythonImportsCheck = [
@ -75,11 +89,10 @@ buildPythonPackage {
meta = with lib; {
description = "Machine learning metrics for distributed, scalable PyTorch applications (used in pytorch-lightning)";
homepage = "https://torchmetrics.readthedocs.io";
homepage = "https://lightning.ai/docs/torchmetrics/";
license = licenses.asl20;
maintainers = with maintainers; [
SomeoneSerge
];
};
}

View File

@ -58,6 +58,7 @@ stdenv.mkDerivation rec {
sourceProvenance = with sourceTypes; [ binaryNativeCode ];
license = licenses.gpl3Only;
maintainers = with maintainers; [ d-xo ];
mainProgram = "bazarr";
platforms = platforms.all;
};
}

View File

@ -47,6 +47,7 @@ in stdenv.mkDerivation rec {
homepage = "https://lidarr.audio/";
license = licenses.gpl3;
maintainers = [ maintainers.etu ];
mainProgram = "Lidarr";
platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" ];
};
}

View File

@ -52,6 +52,7 @@ in stdenv.mkDerivation rec {
changelog = "https://github.com/Radarr/Radarr/releases/tag/v${version}";
license = licenses.gpl3Only;
maintainers = with maintainers; [ edwtjo purcell ];
mainProgram = "Radarr";
platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ];
};
}

View File

@ -46,6 +46,7 @@ in stdenv.mkDerivation rec {
homepage = "https://readarr.com";
license = licenses.gpl3;
maintainers = [ maintainers.jocelynthode ];
mainProgram = "Readarr";
sourceProvenance = with lib.sourceTypes; [ binaryBytecode ];
platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" ];
};

View File

@ -34,6 +34,7 @@ stdenv.mkDerivation rec {
homepage = "https://sonarr.tv/";
license = lib.licenses.gpl3Only;
maintainers = with lib.maintainers; [ fadenb purcell ];
mainProgram = "NzbDrone";
platforms = lib.platforms.all;
};
}

View File

@ -83,6 +83,7 @@ stdenv.mkDerivation rec {
changelog = "https://github.com/recyclarr/recyclarr/releases/tag/v${version}";
license = licenses.mit;
maintainers = with maintainers; [ josephst ];
mainProgram = "recyclarr";
platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ];
};
}

View File

@ -4160,7 +4160,9 @@ self: super: with self; {
oelint-parser = callPackage ../development/python-modules/oelint-parser { };
openllm = callPackage ../development/python-modules/openllm { };
openllm = callPackage ../development/python-modules/openllm {
openai-triton = self.openai-triton-cuda;
};
openllm-client = callPackage ../development/python-modules/openllm-client { };
@ -6662,8 +6664,7 @@ self: super: with self; {
maya = callPackage ../development/python-modules/maya { };
mayavi = pkgs.libsForQt5.callPackage ../development/python-modules/mayavi {
inherit buildPythonPackage pythonOlder;
inherit (self) pyface pygments numpy packaging vtk traitsui envisage apptools pyqt5;
inherit (self) buildPythonPackage pythonOlder pythonAtLeast pyface pygments numpy packaging vtk traitsui envisage apptools pyqt5;
};
mbddns = callPackage ../development/python-modules/mbddns { };
@ -8424,12 +8425,24 @@ self: super: with self; {
open-meteo = callPackage ../development/python-modules/open-meteo { };
openai-triton = callPackage ../development/python-modules/openai-triton { cudaPackages = pkgs.cudaPackages_12_0; };
openai-triton = callPackage ../development/python-modules/openai-triton {
llvm = pkgs.openai-triton-llvm;
cudaPackages = pkgs.cudaPackages_12_0;
};
openai-triton-cuda = self.openai-triton.override {
cudaSupport = true;
};
openai-triton-no-cuda = self.openai-triton.override {
cudaSupport = false;
};
openai-triton-bin = callPackage ../development/python-modules/openai-triton/bin.nix { };
openai-whisper = callPackage ../development/python-modules/openai-whisper {
inherit (pkgs.config) cudaSupport;
openai-triton = self.openai-triton-cuda;
};
openant = callPackage ../development/python-modules/openant { };
@ -14057,6 +14070,7 @@ self: super: with self; {
torchWithCuda = self.torch.override {
magma = pkgs.magma-cuda-static;
openai-triton = self.openai-triton-cuda;
cudaSupport = true;
rocmSupport = false;
};
@ -14067,6 +14081,7 @@ self: super: with self; {
torchWithRocm = self.torch.override {
magma = pkgs.magma-hip;
openai-triton = self.openai-triton-no-cuda;
rocmSupport = true;
cudaSupport = false;
};
@ -15765,7 +15780,9 @@ self: super: with self; {
inherit (pkgs) graphviz;
};
xformers = callPackage ../development/python-modules/xformers { };
xformers = callPackage ../development/python-modules/xformers {
openai-triton = self.openai-triton-cuda;
};
xgboost = callPackage ../development/python-modules/xgboost {
inherit (pkgs) xgboost;