python_code stringlengths 0 679k | repo_name stringlengths 9 41 | file_path stringlengths 6 149 |
|---|---|---|
import logging
import dask
from cuchemcommon.data.helper.chembldata import IMP_PROPS
from cuchemcommon.data.cluster_wf import ChemblClusterWfDao
from cuchemcommon.fingerprint import MorganFingerprint, TransformationDefaults
logger = logging.getLogger(__name__)
def test_dataframe():
"""
Verify fetching data ... | cheminformatics-master | cuchem/tests/test_chembl.py |
cheminformatics-master | cuchem/tests/__init__.py | |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/tests/test_benchmark.py |
import os
import dask
import time
import inspect
import tempfile
import logging
from locust import events
from cuchem.utils.dask import initialize_cluster
from cuchemcommon.context import Context
logger = logging.getLogger(__name__)
def _fetch_chembl_test_dataset(n_molecules=None):
if n_molecules is None:
... | cheminformatics-master | cuchem/tests/utils.py |
import os
import logging
import tempfile
import dask
from cuchemcommon.data.helper.chembldata import ChEmblData
from cuchemcommon.data.cluster_wf import FINGER_PRINT_FILES
from cuchemcommon.fingerprint import MorganFingerprint, Embeddings
logger = logging.getLogger(__name__)
def test_cache_morganfingerprint():
... | cheminformatics-master | cuchem/tests/test_fp_cache.py |
import logging
from cuchem.benchmark.data import TrainingData
logger = logging.getLogger(__name__)
def test_training_data():
training_data = TrainingData()
cursor = training_data.conn.cursor()
cursor.execute('SELECT smiles FROM train_data limit 10')
smiles_strs = cursor.fetchall()
for smiles in... | cheminformatics-master | cuchem/tests/test_benchmark_data.py |
# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions a... | cheminformatics-master | cuchem/tests/perf_triton.py |
import logging
from cuchem.decorator import LipinskiRuleOfFiveDecorator, MolecularStructureDecorator
from cuchem.wf.generative import MolBART, Cddd
logger = logging.getLogger(__name__)
def interpolation(wf, num_points=20, force_unique=False):
"""
Verify fetching data from chemblDB when the input is a pandas... | cheminformatics-master | cuchem/tests/test_generative_wf.py |
cheminformatics-master | cuchem/cuchem/__init__.py | |
#!/usr/bin/env python3
import glob
import os
import sys
import matplotlib.pyplot as plt
import argparse
import numpy as np
import textwrap
import pandas as pd
def parse_args():
parser = argparse.ArgumentParser(description='Plot Results')
parser.add_argument('-i', '--input_dir',
dest=... | cheminformatics-master | cuchem/cuchem/benchmark/plot.py |
cheminformatics-master | cuchem/cuchem/benchmark/__init__.py | |
import os
import time
import logging
import hydra
import pandas as pd
from datetime import datetime
import os
import logging
import argparse
from cuml.ensemble.randomforestregressor import RandomForestRegressor
from cuml import LinearRegression, ElasticNet
from cuml.svm import SVR
from cuchem.wf.generative.megatronmo... | cheminformatics-master | cuchem/cuchem/benchmark/megamolbart.py |
import os
import pickle
import sqlite3
import logging
from typing import List
from cuchemcommon.utils.singleton import Singleton
from cuchemcommon.context import Context
logger = logging.getLogger(__name__)
class TrainingData(object, metaclass=Singleton):
def __init__(self):
context = Context()
... | cheminformatics-master | cuchem/cuchem/benchmark/data.py |
cheminformatics-master | cuchem/cuchem/metrics/__init__.py | |
#!/usr/bin/env python3
import logging
import pickle
import cupy
import numpy as np
import pandas as pd
from cuml.metrics import pairwise_distances
from sklearn.model_selection import ParameterGrid, KFold
from cuml.metrics.regression import mean_squared_error
from cuchem.utils.metrics import spearmanr
from cuchem.uti... | cheminformatics-master | cuchem/cuchem/metrics/model.py |
import base64
import logging
from typing import Union
import cudf
import pandas
from cuchem.decorator import BaseMolPropertyDecorator
from rdkit import Chem
from rdkit.Chem import Draw
logger = logging.getLogger(__name__)
class MolecularStructureDecorator(BaseMolPropertyDecorator):
ERROR_VALUE = 'Error interpr... | cheminformatics-master | cuchem/cuchem/decorator/mol_structure.py |
import logging
from typing import Union
import cudf
import pandas
from numpy.core.numeric import NaN
from cuchem.decorator import BaseMolPropertyDecorator
from rdkit import Chem
from rdkit.Chem import QED, Descriptors, Lipinski
logger = logging.getLogger(__name__)
class LipinskiRuleOfFiveDecorator(BaseMolPropertyDe... | cheminformatics-master | cuchem/cuchem/decorator/lipinski.py |
from typing import Union
import cudf
import pandas
class BaseMolPropertyDecorator(object):
def decorate(self,
df: Union[cudf.DataFrame, pandas.DataFrame],
smile_cols: int = 0):
NotImplemented
from .lipinski import LipinskiRuleOfFiveDecorator as LipinskiRuleOfFiveDecor... | cheminformatics-master | cuchem/cuchem/decorator/__init__.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/datasets/create_ZINC15_trie_multiprocessing.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/datasets/prepare_ChEMBL_tanimoto.py |
import logging
import os
import pathlib
import cudf
logger = logging.getLogger(__name__)
class GenericCSVDataset():
def __init__(self):
self.name = None
self.index_col = None
self.index = None
self.max_len = None
self.data_path = None
self.data = None
def _lo... | cheminformatics-master | cuchem/cuchem/datasets/loaders.py |
cheminformatics-master | cuchem/cuchem/datasets/__init__.py | |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/datasets/prepare_ChEMBL_approved_drugs_data.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/datasets/create_ZINC15_test_split.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/utils/metrics.py |
import logging
import sys
import traceback
from functools import wraps
# import dask
# import dask_cudf
import dash
import numpy as np
logger = logging.getLogger(__name__)
# DELAYED_DF_TYPES = Union[dask.dataframe.core.DataFrame, dask_cudf.core.DataFrame]
def generate_colors(num_colors):
"""
Generates eve... | cheminformatics-master | cuchem/cuchem/utils/__init__.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/utils/distance.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/utils/dataset.py |
import logging
import cupy
from dask.distributed import Client, LocalCluster
from dask_cuda import initialize, LocalCUDACluster
from dask_cuda.local_cuda_cluster import cuda_visible_devices
from dask_cuda.utils import get_n_gpus
logger = logging.getLogger(__name__)
def initialize_cluster(use_gpu=True, n_cpu=None, n... | cheminformatics-master | cuchem/cuchem/utils/dask.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/utils/plot_benchmark_results.py |
import logging
import os
import shutil
from subprocess import run
from cuchemcommon.context import Context
CDDD_MODEL_SCRIPT = 'https://raw.githubusercontent.com/jrwnter/cddd/master/download_default_model.sh'
logger = logging.getLogger(__name__)
def download_cddd_models():
"""
Downloads CDDD model
"""
... | cheminformatics-master | cuchem/cuchem/utils/data_peddler.py |
# Copyright 2020 NVIDIA Corporation
# SPDX-License-Identifier: Apache-2.0
import base64
import json
import logging
from io import StringIO
from pydoc import locate
import cupy
import dash
import dash_bootstrap_components as dbc
import dash_core_components as dcc
import dash_html_components as html
import plotly.graph... | cheminformatics-master | cuchem/cuchem/interactive/chemvisualize.py |
cheminformatics-master | cuchem/cuchem/interactive/__init__.py | |
import logging
import os
import werkzeug
werkzeug.cached_property = werkzeug.utils.cached_property
from flask import Blueprint, Flask, send_file, json
from flask.globals import current_app
from flask.helpers import safe_join
from flask_restplus import Api
from werkzeug.exceptions import HTTPException
from werkzeug.ht... | cheminformatics-master | cuchem/cuchem/api/__init__.py |
import logging
from flask import jsonify
from flask_restplus import Resource
from cuchem.api import api_rest
from cuchem.wf.generative import Cddd, MolBART
logger = logging.getLogger(__name__)
@api_rest.route('/interpolator/<string:model>/<string:smiles>/<int:num_requested>')
class Interpolator(Resource):
"""
... | cheminformatics-master | cuchem/cuchem/api/interpolator.py |
cheminformatics-master | cuchem/cuchem/wf/__init__.py | |
from typing import List
import cupy
import numpy
from cuchemcommon.data.helper.chembldata import ADDITIONAL_FEILD, IMP_PROPS
from cuml.metrics import pairwise_distances
from cuchem.utils.distance import tanimoto_calculate
from cuchem.utils.metrics import spearmanr
class BaseClusterWorkflow:
def __init__(self):
... | cheminformatics-master | cuchem/cuchem/wf/cluster/__init__.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/wf/cluster/gpurandomprojection.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/wf/cluster/cpukmeansumap.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | cuchem/cuchem/wf/cluster/gpukmeansumap.py |
import logging
from typing import List
import numpy as np
import pandas as pd
from cuchemcommon.data import GenerativeWfDao
from cuchemcommon.data.generative_wf import ChemblGenerativeWfDao
from cuchemcommon.fingerprint import Embeddings
from cuchemcommon.utils.singleton import Singleton
from cuchemcommon.workflow imp... | cheminformatics-master | cuchem/cuchem/wf/generative/cddd.py |
import logging
import os
import grpc
import pandas as pd
from typing import List
from generativesampler_pb2_grpc import GenerativeSamplerStub
from generativesampler_pb2 import GenerativeSpec, EmbeddingList, GenerativeModel, google_dot_protobuf_dot_empty__pb2
from cuchemcommon.data import GenerativeWfDao
from cuchemc... | cheminformatics-master | cuchem/cuchem/wf/generative/megatronmolbart.py |
from cuchem.wf.generative.cddd import Cddd as Cddd
from cuchem.wf.generative.megatronmolbart import MegatronMolBART as MegatronMolBART | cheminformatics-master | cuchem/cuchem/wf/generative/__init__.py |
import logging
from cuchemcommon.data import GenerativeWfDao
from cuchemcommon.data.generative_wf import ChemblGenerativeWfDao
from cuchemcommon.utils.singleton import Singleton
from cuchemcommon.workflow import BaseGenerativeWorkflow
logger = logging.getLogger(__name__)
class MolBART(BaseGenerativeWorkflow, metacl... | cheminformatics-master | cuchem/cuchem/wf/generative/molbart.py |
import os
from setuptools import setup, find_packages
requirementPath = 'requirements.txt'
install_requires = []
if os.path.isfile(requirementPath):
with open(requirementPath) as f:
install_requires = f.read().splitlines()
setup(
name='cuchem-commons',
version='0.1',
packages=find_packages()... | cheminformatics-master | common/setup.py |
# -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: generativesampler.proto
"""Generated protocol buffer code."""
from google.protobuf.internal import enum_type_wrapper
from google.protobuf import descriptor as _descriptor
from google.protobuf import message as _message
from goo... | cheminformatics-master | common/generated/generativesampler_pb2.py |
# Generated by the gRPC Python protocol compiler plugin. DO NOT EDIT!
"""Client and server classes corresponding to protobuf-defined services."""
import grpc
import generativesampler_pb2 as generativesampler__pb2
from google.protobuf import empty_pb2 as google_dot_protobuf_dot_empty__pb2
class GenerativeSamplerStub(... | cheminformatics-master | common/generated/generativesampler_pb2_grpc.py |
import logging
import os
from abc import ABC
from enum import Enum
import numpy as np
import pandas as pd
from cddd.inference import InferenceModel
from cuchem.utils.data_peddler import download_cddd_models
from rdkit import Chem
from rdkit.Chem import AllChem
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
logger = logging... | cheminformatics-master | common/cuchemcommon/fingerprint.py |
cheminformatics-master | common/cuchemcommon/__init__.py | |
import logging
import os
from configparser import RawConfigParser
from io import StringIO
from cuchemcommon.utils.singleton import Singleton
logger = logging.getLogger(__name__)
CONFIG_FILE = '.env'
class Context(metaclass=Singleton):
def __init__(self):
self.dask_client = None
self.compute_t... | cheminformatics-master | common/cuchemcommon/context.py |
# import os
# os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
# import logging
# from abc import ABC
# from rdkit.Chem.SaltRemover import SaltRemover
# from cddd.preprocessing import remove_salt_stereo, filter_smiles
# logger = logging.getLogger(__name__)
# class BaseTransformation(ABC):
# def __init__(self):
# ... | cheminformatics-master | common/cuchemcommon/smiles.py |
import logging
# import torch
from functools import singledispatch
from typing import List
import numpy as np
from cuchemcommon.data import GenerativeWfDao
from rdkit.Chem import PandasTools, CanonSmiles
logger = logging.getLogger(__name__)
@singledispatch
def add_jitter(embedding, radius, cnt, shape):
return N... | cheminformatics-master | common/cuchemcommon/workflow.py |
from cuchemcommon.utils.singleton import Singleton | cheminformatics-master | common/cuchemcommon/utils/__init__.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | common/cuchemcommon/utils/logger.py |
# singleton.py
import logging
"""
Metaclass for singletons.
"""
logger = logging.getLogger(__name__)
class Singleton(type):
"""
Ensures single instance of a class.
Example Usage:
class MySingleton(metaclass=Singleton)
pass
"""
_instances = {}
def __call__(cls, *args, *... | cheminformatics-master | common/cuchemcommon/utils/singleton.py |
#!/opt/conda/envs/rapids/bin/python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | cheminformatics-master | common/cuchemcommon/utils/sysinfo.py |
from typing import List
class ClusterWfDAO(object):
"""
Base class for all DAO for fetching data for Clustering Workflows
"""
def meta_df(self):
"""
Returns df with dtype set for structure without any column filter.
"""
return NotImplemented
def fetch_molecular_em... | cheminformatics-master | common/cuchemcommon/data/__init__.py |
import logging
from typing import List
from cuchemcommon.data.helper.chembldata import ChEmblData
from cuchemcommon.utils.singleton import Singleton
from . import GenerativeWfDao
logger = logging.getLogger(__name__)
class ChemblGenerativeWfDao(GenerativeWfDao, metaclass=Singleton):
def __init__(self, fp_type)... | cheminformatics-master | common/cuchemcommon/data/generative_wf.py |
import logging
import math
import os
from typing import List
import cudf
import dask
import dask_cudf
from cuchemcommon.context import Context
from cuchemcommon.data.helper.chembldata import BATCH_SIZE, ChEmblData
from cuchemcommon.utils.singleton import Singleton
from . import ClusterWfDAO
logger = logging.getLogge... | cheminformatics-master | common/cuchemcommon/data/cluster_wf.py |
cheminformatics-master | common/cuchemcommon/data/helper/__init__.py | |
import os
import warnings
import pandas
import sqlite3
import logging
from typing import List
from dask import delayed, dataframe
from contextlib import closing
from cuchemcommon.utils.singleton import Singleton
from cuchemcommon.context import Context
warnings.filterwarnings("ignore", message=r"deprecated", categor... | cheminformatics-master | common/cuchemcommon/data/helper/chembldata.py |
#!/usr/bin/env python3
#
# Copyright (c) 2020, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | cheminformatics-master | megamolbart/launch.py |
# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions a... | cheminformatics-master | megamolbart/tests/perf_grpc.py |
import sys
import grpc
import logging
from concurrent import futures
from contextlib import contextmanager
from megamolbart.service import GenerativeSampler
import generativesampler_pb2
import generativesampler_pb2_grpc
from util import (DEFAULT_NUM_LAYERS, DEFAULT_D_MODEL, DEFAULT_NUM_HEADS, CHECKPOINTS_DIR)
logger... | cheminformatics-master | megamolbart/tests/test_grpc.py |
#!/usr/bin/env python3
import pandas as pd
import torch
from megamolbart.inference import MegaMolBART
if __name__ == '__main__':
num_interp = 3
smiles1 = 'CC(=O)Nc1ccc(O)cc1'
smiles2 = 'CC(=O)Oc1ccccc1C(=O)O'
with torch.no_grad():
wf = MegaMolBART()
# Test each of the major functi... | cheminformatics-master | megamolbart/tests/test_megamolbart.py |
#!/usr/bin/env python3
import os
import sys
import math
import time
import random
import argparse
from subprocess import run
from rdkit import Chem
from pathlib import Path
from concurrent.futures import ProcessPoolExecutor
MAX_LENGTH = 150
VAL_TEST_SPLIT = 0.005
def process_line(line):
if line is None or lin... | cheminformatics-master | megamolbart/scripts/process_file.py |
import logging
from generativesampler_pb2 import EmbeddingList, SmilesList, IterationVal
import generativesampler_pb2_grpc
from megamolbart.inference import MegaMolBART
from cuchemcommon.utils import Singleton
logger = logging.getLogger(__name__)
class GenerativeSampler(generativesampler_pb2_grpc.GenerativeSampler... | cheminformatics-master | megamolbart/megamolbart/service.py |
cheminformatics-master | megamolbart/megamolbart/__init__.py | |
#!/usr/bin/env python3
import logging
from functools import partial
from pathlib import Path
from typing import List
from rdkit import Chem
import torch
import pandas as pd
from checkpointing import load_checkpoint
from cuchemcommon.workflow import BaseGenerativeWorkflow, add_jitter
from decoder import DecodeSampler
... | cheminformatics-master | megamolbart/megamolbart/inference.py |
#!/usr/bin/env python
# Generate set of projects mk files.
# Usage: python generate_mk.py PROJECTS_MK_DIR THRUST_SOURCE_DIR
# The program scans through unit tests and examples in THRUST_SOURCE_DIR
# and generates project mk for each of the tests and examples in PROJECTS_MK_DIR
# A single example or unit test so... | thrust-master | generate_mk.py |
#! /usr/bin/env python
# Copyright (c) 2022 NVIDIA Corporation
# Reply-To: Allison Vacanti <alliepiper16@gmail.com>
# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
# Released under the Apache License v2.0 with LLVM Exceptions.
# See https://llvm.org/LICENSE.txt for license information.
help_text = """%(prog... | thrust-master | ci/common/memmon.py |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c) 2012-7 Bryce Adelstein Lelbach aka wash <brycelelbach@gmail.com>
#
# Distributed under the Boost Software License, Version 1.0. (See accompanying
# file LICENSE_1_0.txt or copy... | thrust-master | internal/benchmark/combine_benchmark_results.py |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c) 2012-7 Bryce Adelstein Lelbach aka wash <brycelelbach@gmail.com>
#
# Distributed under the Boost Software License, Version 1.0. (See accompanying
# file LICENSE_1_0.txt or copy... | thrust-master | internal/benchmark/compare_benchmark_results.py |
'''
Convert Google Code .wiki files into .tex formatted files.
Output is designed to be included within a larger TeX project, it is
not standalone.
'''
import sys
import re
import codecs
print(sys.argv)
'''
A "rule" is a begin tag, an end tag, and how to reformat the inner text
(function)
'''
def encase(pre, post... | thrust-master | internal/scripts/wiki2tex.py |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c) 2018 NVIDIA Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain ... | thrust-master | internal/scripts/eris_perf.py |
'''
Helper script for creating a header file that includes all of Thrust's
public headers. This is useful for instance, to quickly check that
all the thrust headers obey proper syntax or are warning free.
This script simply outputs a list of C-style #include's to the standard
output--this should be redirected to a he... | thrust-master | internal/build/warningstester_create_uber_header.py |
import gdb
import sys
if sys.version_info[0] > 2:
Iterator = object
else:
# "Polyfill" for Python2 Iterator interface
class Iterator:
def next(self):
return self.__next__()
class ThrustVectorPrinter(gdb.printing.PrettyPrinter):
"Print a thrust::*_vector"
class _host_accessibl... | thrust-master | scripts/gdb-pretty-printers.py |
#!/usr/bin/env python3
# Copyright (C) 2013-2022 Free Software Foundation, Inc.
#
# This file is part of GDB.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, ... | cuda-gdb-master | gdb/make-target-delegates.py |
#! /usr/bin/env python3
# Copyright (C) 2011-2022 Free Software Foundation, Inc.
#
# This file is part of GDB.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License,... | cuda-gdb-master | gdb/copyright.py |
# Dynamic architecture support for GDB, the GNU debugger.
# Copyright (C) 1998-2022 Free Software Foundation, Inc.
# This file is part of GDB.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; ... | cuda-gdb-master | gdb/gdbarch-components.py |
# Copyright constant for Python code to use.
#
# Copyright (C) 2022 Free Software Foundation, Inc.
#
# This file is part of GDB.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version ... | cuda-gdb-master | gdb/gdbcopyright.py |
#!/usr/bin/env python3
# Generate Unicode case-folding table for Ada.
# Copyright (C) 2022 Free Software Foundation, Inc.
# This file is part of GDB.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foun... | cuda-gdb-master | gdb/ada-unicode.py |
#!/usr/bin/env python3
# Architecture commands for GDB, the GNU debugger.
#
# Copyright (C) 1998-2022 Free Software Foundation, Inc.
#
# This file is part of GDB.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free S... | cuda-gdb-master | gdb/gdbarch.py |
# Program to fetch python compilation parameters.
# Copied from python-config of the 2.7 release.
import sys
import os
import getopt
import sysconfig
valid_opts = ["prefix", "exec-prefix", "includes", "libs", "cflags", "ldflags", "help"]
def exit_with_usage(code=1):
sys.stderr.write(
"Usage: %s [%s]\n" ... | cuda-gdb-master | gdb/python/python-config.py |
# Copyright (C) 2013-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | cuda-gdb-master | gdb/python/lib/gdb/FrameIterator.py |
# Copyright (C) 2015-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | cuda-gdb-master | gdb/python/lib/gdb/unwinder.py |
# Copyright (C) 2021-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | cuda-gdb-master | gdb/python/lib/gdb/disassembler.py |
# Styling related hooks.
# Copyright (C) 2010-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any late... | cuda-gdb-master | gdb/python/lib/gdb/styling.py |
# Copyright (C) 2010-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | cuda-gdb-master | gdb/python/lib/gdb/__init__.py |
# Python side of the support for xmethods.
# Copyright (C) 2013-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at you... | cuda-gdb-master | gdb/python/lib/gdb/xmethod.py |
# Type utilities.
# Copyright (C) 2010-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later versi... | cuda-gdb-master | gdb/python/lib/gdb/types.py |
# Frame-filter commands.
# Copyright (C) 2013-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any late... | cuda-gdb-master | gdb/python/lib/gdb/frames.py |
# Extended prompt utilities.
# Copyright (C) 2011-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any ... | cuda-gdb-master | gdb/python/lib/gdb/prompt.py |
# Copyright (C) 2013-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | cuda-gdb-master | gdb/python/lib/gdb/FrameDecorator.py |
# Pretty-printer utilities.
# Copyright (C) 2010-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any l... | cuda-gdb-master | gdb/python/lib/gdb/printing.py |
# Pretty-printers for bounds registers.
# Copyright (C) 2013-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your o... | cuda-gdb-master | gdb/python/lib/gdb/printer/bound_registers.py |
# Copyright (C) 2014-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | cuda-gdb-master | gdb/python/lib/gdb/printer/__init__.py |
# Copyright (C) 2012-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | cuda-gdb-master | gdb/python/lib/gdb/function/__init__.py |
# Useful gdb string convenience functions.
# Copyright (C) 2012-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at you... | cuda-gdb-master | gdb/python/lib/gdb/function/strfns.py |
# Copyright (C) 2016-2022 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | cuda-gdb-master | gdb/python/lib/gdb/function/as_string.py |
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