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# met.py
# HYSPLITm - HYSPLIT Manager
# The HYSPLIT model is maintained by the NOAA Air Resources Lab. Users of this
# program should properly credit and reference NOAA ARL.
# For more information please visit:
# http://www.arl.noaa.gov/HYSPLIT_info.php
# http://www.arl.noaa.gov/disclaimer.php
# See th... | samatwood/HYSPLITm | met.py | Python | mit | 842 | [
"VisIt"
] | 3d7cf9f96f621339b308c0d699a93771c9b8fb788b9673e2bf741354d969f9d0 |
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License Version
# 1.1 (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.mozilla.org/MPL/
#
# Softwa... | centrumholdings/buildbot | buildbot/db/schema/v1.py | Python | gpl-2.0 | 13,680 | [
"Brian"
] | 3f387480288f649388e99c6f95860946a42d6832a94f898e615d55e98ac3b8a7 |
#!/usr/bin/env python
# Mesher
# Copyright (C) 2017 Christopher Marsh
# 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.
... | Chrismarsh/mesher | mesher.py | Python | gpl-3.0 | 59,549 | [
"VTK"
] | b10b04df74a2c5dd488fff132113f1fa89c24ed1da5d1a9327ed8911b237d265 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | eric-haibin-lin/mxnet | python/mxnet/symbol/numpy_extension/random.py | Python | apache-2.0 | 10,479 | [
"Gaussian"
] | d25eeee95487d85098cc08e42c9943f06e9ddfffb35cf392fa191dd85ad0568c |
import re
import json
import time
import logging
import itertools
from ndex2.nice_cx_network import NiceCXNetwork
from collections import OrderedDict
from indra.statements import *
from indra.databases import context_client, ndex_client
from indra.databases.identifiers import get_identifiers_url, url_prefixes
logger ... | sorgerlab/belpy | indra/assemblers/cx/assembler.py | Python | mit | 27,828 | [
"Cytoscape"
] | 9b1a64f085e3bc0bea9fed68c0eb5a51b0f9b204fca655327af2beb457674928 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2010-2014, Georgios Is. Detorakis (gdetor@gmail.com)
# Nicolas P. Rougier (nicolas.rougier@inria.fr)
# All rights reserved.
#
# Redistribution and use in... | gdetor/SITopMaps | src/DNF-2D-REF-Response.py | Python | gpl-3.0 | 5,881 | [
"Gaussian"
] | 8b65b915649b348222dfbd3b0e5123d5a40d2b1196a7958be8b6d83f01e74c31 |
#
# Copyright 2017 Russell Smiley
#
# This file is part of timetools.
#
# timetools 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.
#
#... | blueskyjunkie/timeTools | timetools/synchronization/analysis/tests/testTdev.py | Python | gpl-3.0 | 9,992 | [
"Gaussian"
] | df7fefcccb3f80fcf793a51069d9e628eb2992faaa372df47e7bec8ed419979b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
## Copyright 2015 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## 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 ... | scholer/na_strand_model | bin/sim_stats_plotting.py | Python | gpl-3.0 | 35,499 | [
"Gaussian"
] | 864ec60ecd92b97c5286abe9be3cc891bb170d3c5cbef081ae6810640f523aeb |
#!/usr/bin/python
import statsmodels.formula.api as sm
import pandas as pd
import numpy as np
def df_impute_values_ols(adf,outvar,model, verbose=True):
"""Specify a Pandas DataFrame with some null (eg. np.nan) values in column <outvar>.
Specify a string model (in statsmodels format, which is like R) to use to... | cpbl/cpblUtilities | stats.py | Python | gpl-3.0 | 2,784 | [
"ADF"
] | 6ad14996101e909b0625fcbeabe8b6ea0d0c41e068c9e80d06bfc38d29bb2ee5 |
__author__ = 'Shin'
"""
This is Django unit test example code.
Django unit test run with command,
"manage.py test target_app_name"
if you want test all app, let target_app_name blank
"manage.py test"
and then coverage run, report with command,
"python -m coverage run --source='.' manage.py test ta... | ShinJJang/django-unit-test-example | test_Exam.py | Python | gpl-2.0 | 3,803 | [
"VisIt"
] | 51c5c7cb75fbe049056cd9227aa8de94b9b83e96170ada76858cbbb572fdcd47 |
import calendar
import datetime
import hashlib
import itertools
import json
import logging
import os
import random
import re
import types
import uuid
from collections import Counter, OrderedDict, defaultdict, namedtuple
from copy import deepcopy
from distutils.version import LooseVersion
from functools import wraps
fro... | dimagi/commcare-hq | corehq/apps/app_manager/models.py | Python | bsd-3-clause | 234,253 | [
"VisIt"
] | a2ff518099d4e66a7b9876b0ea601ebb695780d280bd1a3ca71ee92f11f4bc9e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Find stop codons and longuest ORF from blastx results
__authors__ = "Eric Normandeau"
__program_name__ = "stop_codons_find"
__version_info__ = ('0', '0', '1')
__version__ = '.'.join(__version_info__)
__revision_date__ = "2011-01-14"
# Importing modules
import os
import ... | wkh124/wkh124 | stop_codons_find.py | Python | gpl-3.0 | 7,639 | [
"Biopython"
] | 80a6adfdb944964cd295d4e5673f3573b0e64d9660eabd7cc5e1662896e89f10 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/procrouting/findif_response_utils/db_helper.py | Python | lgpl-3.0 | 6,347 | [
"Psi4"
] | 3004c32fb39c5f46e82040df1a9f6c24b09fce09ee92d4858221c3cdd35077f1 |
#!/usr/bin/env python
import sys
import os
import math
# ensure that the kicad-footprint-generator directory is available
#sys.path.append(os.environ.get('KIFOOTPRINTGENERATOR')) # enable package import from parent directory
#sys.path.append("D:\hardware\KiCAD\kicad-footprint-generator") # enable package im... | pointhi/kicad-footprint-generator | scripts/Crystals_Resonators_SMD/make_crystal_smd.py | Python | gpl-3.0 | 34,432 | [
"CRYSTAL"
] | b2f70e32f93e30279cc4653ee06edea689effba7494f35dfc556f8cbb24f27b9 |
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# 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
# ... | rvianello/rdkit | Contrib/fraggle/fraggle.py | Python | bsd-3-clause | 2,674 | [
"RDKit"
] | e7639ce9f742a842d672dac671dd67bf4ef1bb1e99ac5ac19a138c512a0d3162 |
""" test
"""
import unittest
import types
import importlib
from DIRAC import S_OK
from mock import MagicMock
from DIRAC.RequestManagementSystem.Client.Request import Request
from DIRAC.TransformationSystem.Client.TaskManager import TaskBase, WorkflowTasks, RequestTasks
from DIRAC.Transformati... | coberger/DIRAC | TransformationSystem/Client/test/test_Client.py | Python | gpl-3.0 | 20,376 | [
"DIRAC"
] | 29633bea80e41ab4c2cbfc3fa14005d4a1b867ba57f79f1dd8607fb7c9dd09b9 |
# deadlock_bug.py ---
#
# Filename: deadlock_bug.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Mon Jul 16 22:34:26 2012 (+0530)
# Version:
# Last-Updated: Mon Jul 16 23:07:27 2012 (+0530)
# By: Subhasis Ray
# Update #: 18
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:... | dilawar/moose-full | moose-examples/traub_2005/py/deadlock_bug.py | Python | gpl-2.0 | 8,312 | [
"MOOSE"
] | 44a7d98b8912bc10223de843d4a341402feb7d05b6e8dafcf7cc6edcd625af65 |
#!/usr/bin/env python
"""
splinter
http://splinter.cobrateam.info
"""
def main():
from splinter.browser import Browser
browser = Browser()
browser.visit('http://google.com')
browser.fill('q', 'splinter - python acceptance testing for web applications')
browser.find_by_css('.lsb').first.click()
... | jabbalaci/jabbapylib | demos/browser_automation/splinter_demo.py | Python | gpl-3.0 | 958 | [
"VisIt"
] | 812eb01625fe2cd4847a3c548303ea9f9b758f10f74452d7102d52662a22de78 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | roadmapper/ansible | lib/ansible/modules/network/avi/avi_virtualservice.py | Python | gpl-3.0 | 31,152 | [
"VisIt"
] | 662edb7cfd13912a5b2c956e718ae5662fd59438e398c01eac84315a04bb0170 |
#!/usr/bin/env python
'''
Description:
OWTF imap agent daemon plugin, to emulate user clicks via email
'''
import re, subprocess
URL_REGEX = 'http[:0-9a-zA-Z\.\/]+'
#TODO: Play with below and see if it is better or not
# http://daringfireball.net/2009/11/liberal_regex_for_matching_urls
#url_regex = re.compile(r'\b(([\w... | sharad1126/owtf | agents/imap/payloads/link_clicker.py | Python | bsd-3-clause | 727 | [
"VisIt"
] | f36e5c979caeda34dd673f5da37894932d524433ffba02a6af49b1488d91bb95 |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | kushalbhola/MyStuff | Practice/PythonApplication/env/Lib/site-packages/numpy/core/_add_newdocs.py | Python | apache-2.0 | 201,718 | [
"Brian"
] | 056a9b13f15c8e1bfd62bca69b91f1eb719206f3c97c83390cd1ac7b9c0c3bf8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
From a taxonomy ID retrieves all the nucleotide sequences
It returns a multiFASTA nuc/prot file
Entrez Database UID common name E-utility Database Name
Nucleotide GI number nuccore
Protein GI number protein
Retrieve strategy:
esearch to... | chamaelj/tools-artbio | tools/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI.py | Python | mit | 17,584 | [
"BLAST"
] | cf111844a9bbcc3a12473069ed2e76aa0f6d52589dbd24cd13b61903a463d7bb |
#-----------------------------------------------------------------------------
# Copyright (c) 2012 - 2018, Anaconda, Inc. All rights reserved.
#
# Powered by the Bokeh Development Team.
#
# The full license is in the file LICENSE.txt, distributed with this software.
#---------------------------------------------------... | mindriot101/bokeh | bokeh/model.py | Python | bsd-3-clause | 26,517 | [
"VisIt"
] | 3d4befd81eaafae26f347e3c6525fd274b2676f52f8ff9628232feb282489fcd |
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/qmcpack/package.py | Python | lgpl-2.1 | 9,626 | [
"ESPResSo",
"QMCPACK",
"Quantum ESPRESSO"
] | e86319e896ce5e9e0e01bf520171b3888419c348bf70fc8781a4320748910b86 |
import subprocess
import sys
subprocess.call(['npm', 'install'])
subprocess.call(['node_modules/gulp/bin/gulp.js'])
subprocess.call([sys.executable, 'manage.py', 'collectstatic', '--noinput']) | hamtamtots/sweetshopwebsite | sweetshop_site/restore.py | Python | mit | 196 | [
"GULP"
] | 9c94fad9e5df027d1d9d7e699582e8f17695a158009c404b6a3abca630617e1e |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo 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 versio... | psci2195/espresso-ffans | testsuite/scripts/samples/test_MDAnalysisIntegration.py | Python | gpl-3.0 | 1,234 | [
"ESPResSo",
"MDAnalysis"
] | 56847294621e1a31050f3392d74f7923a73019cfbb6c1b7df3eb782f79c63b90 |
# Copyright (c) 2019 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""Test the simplified plotting interface."""
from datetime import datetime, timedelta
from io import BytesIO
import warnings
import numpy as np
import pandas as pd
import pytes... | Unidata/MetPy | tests/plots/test_declarative.py | Python | bsd-3-clause | 50,818 | [
"Galaxy"
] | 21ce47088cc887aaf9a3a990c632caacf8e72997c16865391599960e3b63f7cd |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# 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 requi... | googleapis/python-service-management | scripts/fixup_servicemanagement_v1_keywords.py | Python | apache-2.0 | 6,796 | [
"VisIt"
] | ee7c6fd694420069e65d12472cc95738246d2016d2aa3f12c0cbba4bf2a5a332 |
"""
Compute the zero-point broadening (ZPB)
using the dynamical AHC theory (ieig2rf=5).
"""
from ElectronPhononCoupling import compute
# Lists of files used
# ===================
ddb_fnames = """
Calculations/01-LiF-dynamical/odat_calc_DS5_DDB.nc
Calculations/01-LiF-dynamical/odat_calc_DS9_DDB.nc
Calculations/01-Li... | jmbeuken/abinit | scripts/post_processing/ElectronPhononCoupling/Examples/1-3-dynamical-zpb.py | Python | gpl-3.0 | 1,956 | [
"ABINIT"
] | 4f538277e8e860096e4a5a1dbf351a129595afbe8251fffc59d1659e4f63910b |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
#... | dictoon/blenderseed | ui/meshes.py | Python | mit | 2,263 | [
"VisIt"
] | a2081a647dc02814401cfd462efc77c18df0f2824320574b2b6df4b29519eb1b |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/vasp/incar/test_incar_algo.py | Python | gpl-3.0 | 3,510 | [
"CRYSTAL",
"VASP"
] | 2af5106fd27be65022bfb1029e9f69bbd44f2bb4bc3710f0cb7817fe6db659ae |
import dateparser
from datetime import datetime, timedelta, timezone
import demistomock as demisto
from CommonServerPython import *
from FeedCyjax import INDICATORS_LAST_FETCH_KEY, DATE_FORMAT, INDICATORS_LIMIT, Client, main, \
test_module as module_test, get_indicators_last_fetch_date, set_indicators_last_fetch_... | demisto/content | Packs/FeedCyjax/Integrations/FeedCyjax/FeedCyjax_test.py | Python | mit | 25,920 | [
"Amber"
] | e19cc348f888be8228c8fba63d8baa8e26a194514d395a6f4def3237c34dbc96 |
__all__ = [
'AddCellConnToPoints',
'PointsToTube',
'LonLatToUTM',
'RotatePoints',
'ExtractPoints',
'RotationTool',
'ExtractCellCenters',
'AppendCellCenters',
'IterateOverPoints',
'ConvertUnits',
'BuildSurfaceFromPoints',
]
__displayname__ = 'Point/Line Sets'
from datetime i... | banesullivan/ParaViewGeophysics | PVGeo/filters/xyz.py | Python | bsd-3-clause | 36,851 | [
"ParaView",
"VTK"
] | 92a3c5bb3f1734fdc57b43ccaf5994d2bd1b433bf990b45e9a0a4cf3632d78f0 |
# --------------
# USER INSTRUCTIONS
#
# Now you will put everything together.
#
# First make sure that your sense and move functions
# work as expected for the test cases provided at the
# bottom of the previous two programming assignments.
# Once you are satisfied, copy your sense and move
# definitions into the robo... | orsenthil/coursedocs | gatech/cs8803-O01/final_quiz.py | Python | apache-2.0 | 11,482 | [
"Gaussian"
] | f8a5129493b68e44e893b44ff6590e669081cc16243b4c8677bd724cc85f9a3b |
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 04 14:56:12 2016
@author: jpeacock
Gui to transform model data into vtk
"""
#==============================================================================
# Imports
#==============================================================================
# standard packages
impo... | MTgeophysics/mtpy | mtpy/gui/convert_model_to_vtk_qt5.py | Python | gpl-3.0 | 7,832 | [
"VTK"
] | 65e496f2b3e4c24235f198f1b81a93920662f250ad03bc11d198d01f14e1ecc6 |
"""
Copyright (C) 2016 Quinn D Granfor <spootdev@gmail.com>
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
version 2, as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but
... | MediaKraken/MediaKraken_Deployment | source/db_update_version.py | Python | gpl-3.0 | 30,791 | [
"Elk"
] | fc9c42910d7f5c3d7c189de16959c69428835ff9b1993af2ffc185a9e2d7678a |
import pytest
# TODO: Remove this once bioarchive is up again.
from datetime import datetime
from functools import partial
SKIP_DUE_TO_BIOARCHIVE_OUTAGE = partial(
pytest.mark.skipif,
datetime.now() < datetime(2020, 6, 22),
reason='temporarily skipped due to bioarchive.galaxyproject.org outage',
)
from bi... | bioconda/bioconda-utils | test/test_bioconductor_skeleton.py | Python | mit | 8,543 | [
"Bioconda",
"Bioconductor"
] | 968b599c4a37018c66d7b042a4af00a6261de154ec2136ed8f3be52f2eeacab6 |
import functools
from firefly.common import pixlib
from firefly.widgets import ToolBarStretcher
from firefly.qt import (
QToolBar,
QMenu,
QIcon,
QAction,
)
def preview_toolbar(wnd):
toolbar = QToolBar(wnd)
action_poster = QMenu("Set poster", wnd)
action_poster.menuAction().setIcon(QIcon(... | immstudios/firefly | firefly/modules/detail_toolbars.py | Python | gpl-3.0 | 3,363 | [
"Firefly"
] | 567ce76722baac169fa6faf139e6f2a665929ee9f84291a6118df7f1dfbc55bf |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/qcdb/subsetgenerator.py | Python | lgpl-3.0 | 4,294 | [
"Psi4"
] | 27144927daf434f9609169768c60bff7b27b193d11aa5443d19e9d75b0152888 |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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 y... | mazaclub/electrum-nmc | plugins/trustedcoin.py | Python | gpl-3.0 | 25,424 | [
"VisIt"
] | 8002b49e7dc6328aadc7bed0e10290d604d4d0ff1607052559fdd98ca476c18f |
"""
Reference: https://en.wikipedia.org/wiki/Gaussian_function
"""
from numpy import exp, pi, sqrt
def gaussian(x, mu: float = 0.0, sigma: float = 1.0) -> int:
"""
>>> gaussian(1)
0.24197072451914337
>>> gaussian(24)
3.342714441794458e-126
>>> gaussian(1, 4, 2)
0.06475879783294587
>... | TheAlgorithms/Python | maths/gaussian.py | Python | mit | 1,598 | [
"Gaussian"
] | 742188d6ab2fbbba9fa4c7849d3ae3ca052aabf845d7ef67af517b8d59dd541d |
# -*- coding:utf-8 -*-
# Author: hankcs
# Date: 2020-07-16 18:44
import os
from hanlp.utils.io_util import get_resource, get_exitcode_stdout_stderr, run_cmd
def official_conll_05_evaluate(pred_path, gold_path):
script_root = get_resource('http://www.lsi.upc.edu/~srlconll/srlconll-1.1.tgz')
lib_path = f'{scri... | hankcs/HanLP | hanlp/metrics/srl/srlconll.py | Python | apache-2.0 | 1,701 | [
"MOOSE"
] | 08f7bc53b7b8fa2d3a97f0b613beaf356ce6c6562798b704c48f64c6cccca40e |
# Site Model
import networkx as nx
from gen_model import *
from random import *
import datetime
import pickle
import datetime
import os
BLOG_TEST = 1
WIKI_TEST = 0
if BLOG_TEST:
VISIT_RATE = 4
VISIT_UNIT = "days"
NUM_USERS = 20
PERCENT_NEW = 0.3
FROM_DATE = datetime.datetime(2010, 05, 01)
... | eob/synckit-research | perf/usage_generator_2010_02_01.py | Python | bsd-3-clause | 7,731 | [
"VisIt"
] | 08a9ca761d09b08ffcdb934ed9b8e28e2ce33b3ad34da20369af123409a20994 |
#### PATTERN | VECTOR ####################################################
# -*- coding: utf-8 -*-
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
######################################... | shubhangiKishore/pattern | pattern/vector/__init__.py | Python | bsd-3-clause | 138,418 | [
"NEURON",
"VisIt"
] | 6330c1a8d93ffb34cf19648b230a2eb74ad201a9a7838d118830665f5da059b3 |
import os,sys
#sys.path.append(os.path.join(os.path.dirname(os.path.abspath(__file__)),'requests/'))
import requests
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import json
class ClusterpostLib(object):
def __init__(self, parent=None):
if parent:
parent.title = " "
... | ClementMirabel/DatabaseInteractorExtension | DatabaseInteractor/ClusterpostLib.py | Python | apache-2.0 | 4,777 | [
"VTK"
] | acbdb965e134d88ea0a23ee3ba15096db1d49af6e9738547420fa863ba98d87f |
from docopt import docopt
from IPython import embed
from ilxutils.cli import Client
import json
import os
import requests as r
from sys import exit
import time
import unittest
VERSION = '0.0.2'
# ILX:0108124 == "Organ" | term
# ILX:0101431 == "brain" | term
# ILX:0107497 == "Neuron" | term
# ILX:0112772 == "Afferent pr... | tgbugs/pyontutils | ilxutils/tests/cli_test.py | Python | mit | 3,750 | [
"NEURON"
] | ad1afd3ee809fed0ecabddaef0b0eb4d324d80420ddd5a6757881838c0f8bb44 |
from __future__ import nested_scopes
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without... | marco-mariotti/selenoprofiles | libraries/SOAPpy/Types.py | Python | gpl-2.0 | 51,871 | [
"Brian"
] | 516f6b678818a92bc4b7444ea4e1e0c517cbf1200d086c78fff4ddb973a963f6 |
# (C) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import hashlib
import json
import os
import t... | BondAnthony/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 26,029 | [
"Galaxy"
] | fb3fc17ed8958c1ef30d20adbc08acea51d8833a0eef04462ba90790ee8ca055 |
# -*- coding: utf-8 -*-
"""
================
Vocal separation
================
This notebook demonstrates a simple technique for separating vocals (and
other sporadic foreground signals) from accompanying instrumentation.
This is based on the "REPET-SIM" method of `Rafii and Pardo, 2012
<http://www.cs.northwestern.ed... | librosa/librosa | docs/examples/plot_vocal_separation.py | Python | isc | 4,721 | [
"Brian"
] | 6419d3f41d2e6fb39ffee063bcbefea7decb5149101c6582a5225bbf79f186c4 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.metrics.pairwise` submodule implements utilities to evaluate
pairwise distances, paired distances or affinity of sets of samples.
This module contains both distance metrics and kernels. A brief summary is
given on the two here.
Distance metrics are a function d(a, b) such... | soulmachine/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 43,059 | [
"Gaussian"
] | 0299f68938247d2f385e59cc90ddcc44acc7af0b021186b5d314201f94c48b0d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Charge Decomposition Analysis (CDA)"""
import random
import numpy
from cclib.method.fragments import FragmentAnalysi... | ATenderholt/cclib | cclib/method/cda.py | Python | bsd-3-clause | 4,422 | [
"cclib"
] | be3aa7e1261792b6fd58fc392f919eedf988e30eda37c3e8427b867ba2ee5628 |
import dropbox
class DropboxMixin(object):
def setup(self):
self.name = 'dropbox'
self.pretty_name = 'Dropbox'
self.addConfig('app_key', 'App Key', default='1ykd6aqi5m05m0t', internal=True)
self.addConfig('app_secret', 'App Secret', default='qs5ga0gd61fxuz3', internal=True)
self.addConfig('use... | theduke/mycloudbackup | mcb/utils/dropbo.py | Python | bsd-3-clause | 1,685 | [
"VisIt"
] | 6b6abac31dcee0991aaa52138e2b9dd2251fe4ae5e2934271fecd351362f353c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains some math utils that are used in the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__credits__ = "Geoffroy Hautier"
__ve... | gmatteo/pymatgen | pymatgen/analysis/chemenv/utils/math_utils.py | Python | mit | 11,244 | [
"pymatgen"
] | bbb04a71febb4aa0007c92937e00cfba5ed206d80d2d90dc57e28faa55d8d50e |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from .posterior import Posterior
from ...util.linalg import pdinv, dpotrs, tdot
from ...util import diag
import numpy as np
from . import LatentFunctionInference
log_2_pi = np.log(2*np.pi)
class Exac... | jameshensman/GPy | GPy/inference/latent_function_inference/exact_gaussian_inference.py | Python | bsd-3-clause | 2,785 | [
"Gaussian"
] | b4e1016e53c2647ce57bc5edf26d3a1d9d2863cde73ff4ce115f9651ef9fac15 |
import cairo, math, sys
import cairoplot
from series import Series
# non-random data for needs of visual comparison of changes
if '--non-random' in sys.argv:
random = lambda : 1.0
print('Plotting nonrandom data')
else:
import random
random = random.random
# Line plotting
test_scatter_plot = 1
test_do... | m-labs/cairoplot3 | seriestests.py | Python | lgpl-2.1 | 15,371 | [
"Gaussian"
] | 42ce4a4a5cc75b92c6c46b4b8c5f8086e51f588c7a05fecfce857587f0cac94c |
from __future__ import division
import numpy as np
from keras import initializations, regularizers, constraints
from keras import backend as K
from keras.layers.core import Layer, Dense
from .backend import random_binomial
import theano
class RBM(Layer):
"""
Bernoulli-Bernoulli Restricted Boltzmann Machi... | wuaalb/keras_extensions | keras_extensions/rbm.py | Python | mit | 17,177 | [
"Gaussian"
] | 92def0a5ba0ba2450c3035bc8e1fc8e8f7297942d991747994e95ffd3b77d9b1 |
import logging
from pywps import ComplexInput, ComplexOutput
from pywps import Format
from pywps import LiteralInput
from pywps import Process
from pywps.app.Common import Metadata
from flyingpigeon import plt_ncdata
from flyingpigeon.utils import extract_archive
from flyingpigeon.nc_utils import get_variable
# from ... | bird-house/flyingpigeon | flyingpigeon/processes/wps_plot_uncertainty.py | Python | apache-2.0 | 6,758 | [
"NetCDF"
] | c3268494ce49a989b48d8002f5bf825f67728412495bc97b76e7c030e5a2a848 |
################################################################################
# Copyright (C) 2013 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Unit tests for bayespy.utils.linalg module.
"""
import warnings
w... | SalemAmeen/bayespy | bayespy/utils/tests/test_linalg.py | Python | mit | 6,248 | [
"Gaussian"
] | 20a4b039e0669ac1324214fa4d6fa4713bb6519ce6ae87dee574080554195792 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
SHA Query Tool
--------------
:Author: Brian Svoboda (svobodb@email.arizona.edu)
This package is for querying the Spitzer Heritage Archive (SHA)
found at: http://sha.ipac.caltech.edu/applications/Spitzer/SHA.
"""
from .core import *
import warnings
... | imbasimba/astroquery | astroquery/sha/__init__.py | Python | bsd-3-clause | 446 | [
"Brian"
] | 650330a0db7c5160e378a57becad5a382a205f155b1418d24794cbcdb0799214 |
""" NormalizeMethodCalls turns built in method calls into function calls. """
from pythran.analyses import Globals, Ancestors
from pythran.passmanager import Transformation
from pythran.syntax import PythranSyntaxError
from pythran.tables import attributes, functions, methods, MODULES
from pythran.tables import duplic... | pombredanne/pythran | pythran/transformations/normalize_method_calls.py | Python | bsd-3-clause | 11,301 | [
"VisIt"
] | 9ae4ac478ad1571705575753b0cf568971df399aa51c1c4529c8a5923f9a4baf |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2017-08-17
# @Filename: structs.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: 2... | sdss/marvin | python/marvin/utils/general/structs.py | Python | bsd-3-clause | 9,001 | [
"Brian"
] | 8de3b6f1f2c96b11656177eaabd4d72c9b1540826763e572384e2f4f22d7a163 |
#!/usr/bin/env python
# Author: Greg Caporaso (gregcaporaso@gmail.com)
# formatdb.py
""" Description
File created on 16 Sep 2009.
"""
from __future__ import division
from optparse import OptionParser
from os.path import split, splitext
from os import remove
from glob import glob
from cogent.app.util import CommandLin... | sauloal/cnidaria | scripts/venv/lib/python2.7/site-packages/cogent/app/formatdb.py | Python | mit | 8,701 | [
"BLAST"
] | 8db75904e9955ce29bce09b4ddf12f1a1e2d4b4a33acf170a812e7cbe5d62e41 |
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
import sys
print 'Number of arguments:', len(sys.argv), 'arguments.'
print 'Argument List:', str(sys.argv)
print sys.argv[1]
#smiles = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
smiles = sys.argv[1]
file=sys.argv[2]
x=int(sys.argv[3])
y=int(sys.argv[4])
print smiles
mol = ... | BielStela/eTOXlabWS | scripts/generate_img.py | Python | gpl-3.0 | 387 | [
"RDKit"
] | 740af7bb4a25cf8396cf7b1d6431712ffdf39d559865e053db4a6853eea554fe |
"""MSMBuilder: Statistical models for Biomolecular Dynamics
"""
from __future__ import print_function, absolute_import
DOCLINES = __doc__.split("\n")
import sys
import traceback
import numpy as np
from os.path import join as pjoin
from setuptools import setup, Extension, find_packages
try:
sys.dont_write_byteco... | cxhernandez/msmbuilder | setup.py | Python | lgpl-2.1 | 7,479 | [
"Gaussian",
"MDTraj"
] | bab578c664d102f7133ae04e5efcc918aa872ea34eaf1cf7e44976fc78b1e327 |
import sklearn.grid_search
import scipy.stats.distributions
import lb_loader
import simtk.openmm.app as app
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
n_steps = 1500
temperature =... | kyleabeauchamp/HMCNotes | code/optimize/old/test_optimize_respa.py | Python | gpl-2.0 | 3,950 | [
"OpenMM"
] | bc05a802211842bae7c730327c3ce0def76ba08b30f1720c3e81acc7b3fdac94 |
"""Steps to test the demonstration Cockpit plugin"""
from behave import given, when, then
from hamcrest import (
assert_that, equal_to, greater_than, greater_than_or_equal_to
)
@given("Cockpit is installed on the testing host")
def check_cockpit_is_installed(context):
"""Checks for the `cockpit-bridge` command... | vmindru/prototype | integration-tests/features/steps/cockpit_demo.py | Python | lgpl-2.1 | 14,754 | [
"VisIt"
] | d4d2bfd8ed6c70435a278686bd2771727ea4e62ca41f2c48507e97bbd2f54839 |
# -*- coding: utf-8 -*-
import numpy as np
import parabem
from parabem.vtk_export import VtkWriter
from parabem.pan2d import *
from parabem import PanelVector2, Vector2, Panel2
from parabem.airfoil.conformal_mapping import *
from parabem.pan2d import DirichletDoublet0Source0Case2 as Case
from parabem.utils import chec... | booya-at/paraBEM | examples/vtk/vtk_coordinates_not_aligned.py | Python | gpl-3.0 | 2,119 | [
"VTK"
] | 74f8033501e25d27773048dc42020a5daab1cd1b40aba61586fb6be3c53b6dc1 |
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy.dual import eig
from scipy.special import comb
from scipy import linspace, pi, exp
from scipy.signal import convolve
__all__ = ['daub', 'qmf', 'cascade', 'morlet', 'ricker', 'cwt']
def daub(p):
"""
The coefficient... | mgaitan/scipy | scipy/signal/wavelets.py | Python | bsd-3-clause | 10,472 | [
"Gaussian"
] | f283a3ebba8b08073d07f9e09f47b09fbb9bd6597aee53510e9282d7df494453 |
"""
Definition of default parameters (and hence, standard parameter names) for
standard current source models.
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
from pyNN.standardmodels import StandardCurrentSource
from pyNN.parameters import Sequence
clas... | anupkdas-nus/global_synapses | pyNN-dispackgaes/standardmodels/electrodes.py | Python | gpl-3.0 | 3,347 | [
"Gaussian"
] | f3dcaacaf4cd651929b23e3bb23de7d910045f9c91677e9845f9a37a67c6092c |
import numpy as np
from scipy import stats
from scipy.special import expit
def exp_cosh(H, beta=1.0):
return np.exp(beta * H) / (2. * np.cosh(beta * H))
def kinetic_ising_model(S, J, no_spike):
""" Returns probabilities of S[t+1,:] being one.
:param S: numpy.ndarray (T,N)
Binary data where an e... | noashin/Ising_model_gibbs_sampler | network_simulator.py | Python | mit | 2,687 | [
"NEURON"
] | 1a38705b5ec6f4856d0b936e4a0dab976f5c4e2662b6deb34a07141e55952efb |
import _bct as bct
""" Generator function for synthetic connection networks
and graph randomization algorithms
Synthetic Connection Networks
* makerandCIJ_dir.m. (BD networks)
Generates a random, directed network with a specified number of nodes and links.
Contributor: OS.
.
* makerandCIJ_... | unidesigner/pyconto | pyconto/bct/generators.py | Python | gpl-3.0 | 14,595 | [
"Gaussian"
] | c688065acce6fea3ae0a8d2845dbb6abab00d541ab81476f2b2d6073621be670 |
'''test_filterbyobjectmeasurements.py: Test FilterByObjectMeasurements module
CellProfiler is distributed under the GNU General Public License.
See the accompanying file LICENSE for details.
Copyright (c) 2003-2009 Massachusetts Institute of Technology
Copyright (c) 2009-2015 Broad Institute
All rights reserved.
Plea... | LeeKamentsky/CellProfiler | cellprofiler/modules/tests/test_filterobjects.py | Python | gpl-2.0 | 91,690 | [
"Gaussian"
] | a42328129e0e552fee4c1c9a5a80a9109f2d176c8fa0955d5a1948ff756d82ed |
import logging
from random import Random
from math import sin, cos, pi, atan2, sqrt, exp
from collections import deque
class NothingFoundError(Exception):
pass
class NotInThatSpotError(Exception):
pass
class ConnectionRefusedError(Exception):
pass
class Map(object):
def __init__(self, width, height):
sel... | evuez/mutations | mutations.py | Python | mit | 9,837 | [
"Gaussian"
] | 270f48334f10e202cfbfcec5f2f725fa42abc5a967a545bdae7192fc8edd16a8 |
# -*- encoding: utf-8 -*-
"""
General helper functions that don't fit neatly under any given category.
They provide some useful string and conversion methods that might
be of use when designing your own game.
"""
from __future__ import division, print_function
from builtins import object, range
from future.utils impo... | titeuf87/evennia | evennia/utils/utils.py | Python | bsd-3-clause | 59,783 | [
"VisIt"
] | 9fc9b93aff5c04d833add52422afa1799c9b93b1cffdcacfcbf3d1e5f47aee20 |
# -*- coding: utf-8 -*-
# Generated by Django 1.10.2 on 2017-07-05 01:00
from __future__ import unicode_literals
from django.db import migrations
PLATFORM_MAP = {
'3DO': '3do',
'Arcade': 'arcade',
'Amiga': 'amiga',
'Apple II': 'apple-e',
'Atari 2600': 'atari-2600',
'Atari 5200': 'atari-5200',... | lutris/website | platforms/migrations/0006_populate_tgdb_names.py | Python | agpl-3.0 | 1,918 | [
"Jaguar"
] | d80bd01be5f8a704d6ebed1a8b2609f78a112c2df89a9bc2e6b9fe38b258b8c4 |
# Copyright (C) 2012, Christof Buchbender
# BSD Licencse
import math
import sys
import scipy
from scipy.optimize import leastsq as least
from numpy import asarray, mean, std, where, exp, log, sqrt, arange, float64, floor
from copy import deepcopy as copy
import random as rnd
import astrolyze.functions.constants as co... | buchbend/astrolyze | build/lib/astrolyze/functions/astro_functions.py | Python | bsd-3-clause | 46,095 | [
"Gaussian"
] | 18aa752eabcaaf90c018f243492d80652d79d58a12cd64b5c375a73435001d43 |
#!/usr/bin/env python
#filename: pca.py
import os
import sys
import time
import re
import math
import argparse
from time import sleep, gmtime, strftime
from datetime import datetime
import mdtraj as md
import numpy as np
from sklearn.decomposition import PCA, KernelPCA, IncrementalPCA
from sklearn.metrics import euclid... | RUBi-ZA/MODE-TASK | pca.py | Python | gpl-3.0 | 17,248 | [
"MDTraj"
] | 3de452d8f779e724a3a78170b82759885c8979897212fd37aa116a6abc896d13 |
r"""
I/O Registry (:mod:`skbio.io.registry`)
=======================================
.. currentmodule:: skbio.io.registry
Classes
-------
.. autosummary::
:toctree: generated/
IORegistry
Format
Functions
---------
.. autosummary::
:toctree: generated/
create_format
Exceptions
----------
.. autos... | anderspitman/scikit-bio | skbio/io/registry.py | Python | bsd-3-clause | 42,339 | [
"scikit-bio"
] | 5a5b90158b74902eda75e75f56f9d5f80a23a11932e4a80385e612b899d09cbb |
"""Gaussian processes regression. """
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
import warnings
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve_triangular
from scipy.optimize import fmin_l_bfgs_b
from sklearn.base im... | waterponey/scikit-learn | sklearn/gaussian_process/gpr.py | Python | bsd-3-clause | 18,747 | [
"Gaussian"
] | 4ede303192657be7912ef14efb65ff53306b35b3516985236c314ac33c205ab6 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | dmlc/tvm | python/tvm/relay/backend/contrib/ethosu/tir/compiler.py | Python | apache-2.0 | 6,772 | [
"VisIt"
] | 90e19db164bae8b8dae7f8c48965d58550073ad1950a720800434880972a40b2 |
from setuptools import setup
import versioneer
commands = versioneer.get_cmdclass()
setup(name="magic-wormhole-transit-relay",
version=versioneer.get_version(),
description="Transit Relay server for Magic-Wormhole",
author="Brian Warner",
author_email="warner-magic-wormhole@lothar.com",
... | warner/magic-wormhole-transit-relay | setup.py | Python | mit | 922 | [
"Brian"
] | cded4045538efe1567481d93c98cc2cf51967ce60f9bad00172fb74423323cdc |
#==============================================================================
# analytical.py
# Contains all python classes for computing analytical solutions for key
# test problems for plotting or analysis.
#
# This file is part of GANDALF :
# Graphical Astrophysics code for N-body Dynamics And Lagrangian Flui... | gandalfcode/gandalf | analysis/analytical.py | Python | gpl-2.0 | 19,743 | [
"BLAST"
] | 5b624ffe2d5b01fe13cf64afff20b29868ab4d251d400bb2e1f331b9d86de2ae |
from common import Modules, data_strings_wide, load_yara_rules, PEParseModule, ModuleMetadata
from string import lowercase, uppercase, punctuation, digits
class projecthook(PEParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="projecthook",
bot_name="ProjectHook",
... | bwall/bamfdetect | BAMF_Detect/modules/projecthook.py | Python | mit | 1,350 | [
"Brian"
] | 08e31f285a9a5c0b2a6b5ece8cbf8d820e37442b1b4f104f25d352bffeebc37c |
import os
import shutil
from datetime import datetime
import tempfile
import tarfile
import random
import threading
import uuid
import shutil
from GangaCore import _gangaVersion
from GangaCore.Core.exceptions import ApplicationConfigurationError, ApplicationPrepareError, GangaException, GangaFileError
from GangaCore.GP... | ganga-devs/ganga | ganga/GangaLHCb/Lib/RTHandlers/GaudiExecRTHandlers.py | Python | gpl-3.0 | 34,456 | [
"DIRAC"
] | a1073585e464eebe7acab26d5c8e74fe9bb2620e9287217b37ec214f4beeb37d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# v1.0: se permite argumento "-w" para escribir la salida en el archivo brutefir_config
# v1.1: incorpora un coeff de xover "dirac pulse" para poder cargarlo en una vía full range"
# v1.2: se permiten nuevos argumentos:
# - un archivo brutefir.ini alternativo
# - u... | rripio/FIRtro | bin/brutefir_config.py | Python | gpl-3.0 | 15,776 | [
"DIRAC"
] | 9d45b3e099e0dc773232ac843db5edc07351f7ec4aaa559b9d11440d3939af74 |
# Natural Language Toolkit: Conditional Random Fields
#
# Copyright (C) 2001-2013 NLTK Project
# Author: Edward Loper <edloper@gmail.com>
# URL: <http://nltk.org/>
# For license information, see LICENSE.TXT
"""
An interface to Mallet <http://mallet.cs.umass.edu/>'s Linear Chain
Conditional Random Field (LC-CRF) implem... | TeamSPoon/logicmoo_workspace | packs_sys/logicmoo_nlu/ext/pldata/nltk_3.0a3/nltk/tag/crf.py | Python | mit | 31,278 | [
"Gaussian"
] | e26cb12a9e5764f896acd471715cc7fc9fad9424627719e50f3dfb46305d66be |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible 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) an... | brokenjacobs/ansible | lib/ansible/utils/color.py | Python | gpl-3.0 | 3,891 | [
"Brian"
] | eb3d8d354747fa49ec1e05571fe6459ba3275e5a8cb06a35a343764391c3b1f2 |
import json
import os
from shutil import copy
from pynit.tools import messages
from pynit.tools import methods
from pynit.handler.project import Project
from pynit.pipelines import pipelines
from pynit.process import Process
from ..tools import progressbar, display, clear_output, HTML as title, display_html
class Pip... | dvm-shlee/pynit | pynit/pipelines/base.py | Python | gpl-3.0 | 22,604 | [
"VisIt"
] | 9bd401765f1eb1ca09b4e8cc7bdd0446e13670713de1e1d45d38eb363fd19d8e |
# -*- coding:utf-8; python-indent:2; indent-tabs-mode:nil -*-
# Copyright 2013 Google Inc. All Rights Reserved.
#
# 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/l... | pombredanne/pytype | pytype/pytd/parse/ast_test.py | Python | apache-2.0 | 21,553 | [
"VisIt"
] | 52b4d7bbfddec0a63c5f46d8fd4a5192e690658340f05a6caf66a2fc7a07de84 |
#
# This file is a part of the normalize python library
#
# normalize is free software: you can redistribute it and/or modify
# it under the terms of the MIT License.
#
# normalize is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FI... | tomo-otsuka/normalize | tests/test_visitor.py | Python | mit | 6,923 | [
"VisIt"
] | 448dd629c11d25066290683c0eef49caa7c40c93cf116e6a172a265ffaa048b4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# vgrid - helper functions related to VGrid actions
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General P... | heromod/migrid | mig/shared/vgrid.py | Python | gpl-2.0 | 25,440 | [
"Brian",
"Dalton"
] | 7c79c94cf1fc383729a0d601567f59a45abc5a84d7fc45dc12e8a9a366dd999b |
# BurnMan - a lower mantle toolkit
# Copyright (C) 2012, 2013, Heister, T., Unterborn, C., Rose, I. and Cottaar, S.
# Released under GPL v2 or later.
import warnings
import numpy as np
from burnman.material import Material
import burnman.eos as eos
class Mineral(Material):
"""
This is the base class for al... | QuLogic/burnman | burnman/mineral.py | Python | gpl-2.0 | 10,036 | [
"Avogadro"
] | 889922f8ae7249a0509a62de814b4ff27721ef0ffd1623a091e7fbd4e9598c36 |
#coding=utf-8
"""This module contains the "Viz" objects
These objects represent the backend of all the visualizations that
Caravel can render.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import copy
import has... | wbsljh/caravel-aidp | caravel/viz.py | Python | apache-2.0 | 78,988 | [
"VisIt"
] | 5c4358cd86280528655907529355c232dd2dd764405b4be7b07c2abc433f5cfb |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import gzip
import json
import os
import unittest
import warnings
import xml.etree.cElementTree as ET
from pathlib import Path
from shutil import copyfile, copyfileobj
import numpy as np
import pytest
from mo... | gmatteo/pymatgen | pymatgen/io/vasp/tests/test_outputs.py | Python | mit | 89,380 | [
"VASP",
"Wannier90",
"pymatgen"
] | 92c5275c1fcb54b7c091e7a7178ada5bb3391c8499f1c7732bf5a88b4e808a05 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module provides classes to perform fitting of structures.
"""
import six
from six.moves import filter
from six.moves import zip
__author__ = "William Davidson Richards, Stephen Dacek, Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Mate... | yanikou19/pymatgen | pymatgen/analysis/structure_matcher.py | Python | mit | 38,626 | [
"pymatgen"
] | 61681369351a954bcc2ac8d6dded41e1daa77d27592169d0ac0fbc7429e6790f |
#! /usr/bin/env python
# -*- coding : utf8 -*-
#
# This file is a part of Siesta Help Scripts
#
# (c) Andrey Sobolev, 2011-2015
#
import os
import glob
from calctypes import CalcType
from errors import FileError, UnsupportedError
from evolution import Evolution
from geom import Geom
from options import Options
impor... | ansobolev/shs | shs/calc.py | Python | mit | 6,682 | [
"LAMMPS",
"SIESTA"
] | 430eaeee09d59f00f12bf107dc832714ed1572946210384ef8bbb499a71dc4f9 |
from __future__ import print_function
from distutils.core import setup
from distutils.extension import Extension
import numpy as np
from distutils.ccompiler import new_compiler
import os
import sys
import tempfile
"""
Check for OpenMP based on
https://github.com/MDAnalysis/mdanalysis/tree/develop/package/setup.py
retr... | mindriot101/batman | setup.py | Python | gpl-3.0 | 3,882 | [
"MDAnalysis"
] | 0e24c39bf858568f5af293630a3c588e3d919b1c13d158f8235d536f1f1d2fd3 |
../../../../../../../share/pyshared/orca/scripts/toolkits/Gecko/formatting.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/toolkits/Gecko/formatting.py | Python | gpl-3.0 | 77 | [
"ORCA"
] | 376d4ed00580ce1b520d7670631f70dc5e28bc9696c005e784c56c4563b2a4db |
from ase import Atoms
from ase.visualize import view
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.lattice.surface import fcc111,add_adsorbate
h = 1.85
d = 1.10
slab = fcc111('Cu', size=(4,4,2), vacuum=10.0)
slab.set_calculator(EMT())
e_slab = ... | grhawk/ASE | tools/doc/tutorials/N2Cu.py | Python | gpl-2.0 | 769 | [
"ASE"
] | 13e01e88baf864d8d847216dde8247794b2ada9b02d75879dc5eb1e1c23f8906 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | susilehtola/psi4 | psi4/driver/qcdb/psiutil.py | Python | lgpl-3.0 | 5,058 | [
"Psi4"
] | 9136aaa849a49f89283afd749161900219ef64c717a56ba08658ef3c818775f1 |
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