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#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | HiroIshikawa/21playground | visualizer/_app_boilerplate/venv/lib/python3.5/site-packages/setuptools/command/easy_install.py | Python | mit | 87,460 | [
"VisIt"
] | de3e1018799a3d56ca89e29213c32f71d9f42b2c541469e06b2e181509745344 |
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#
# Okinawa Institute of Science and Technology, Japan.
#
# This script runs on STEPS 2.x http://steps.sourceforge.net
#
# H Anwar, I Hepburn, H Nedelescu, W Chen and E De Schutter
# Stochastic calcium mechanisms cause dendritic calcium spike... | CNS-OIST/STEPS_Example | publication_models/API_1/Anwar_J Neurosci_2013/StochasticCaburst_cluster.py | Python | gpl-2.0 | 35,247 | [
"Avogadro"
] | 877111e3a60b9cac38e3eece856c4c439cc042fb3f269c1c75e89d25cfe1b7f5 |
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code for the ... | greglandrum/rdkit | rdkit/Chem/Pharm2D/UnitTestGobbi.py | Python | bsd-3-clause | 6,235 | [
"RDKit"
] | c3942a7538666b36989ed61d961a267d479fd19ec3a6422e8fc3634d646250bb |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import product
import numpy as np
from sklearn.utils.testing im... | soulmachine/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 27,885 | [
"Brian"
] | 7c70bf77f0edd08583a001d580c38e7ef4a6d5a7bfb7b5279938562ba3171e78 |
import os
import inspect
import getpass
import subprocess
import sys
import re
import shutil
import cutlass
import anadama.pipelines
from collections import OrderedDict
from . import workflows
from . import PrepProt
def get_proteomes(preps):
def _ps():
for prep in preps:
proteome_list=list()
for proteome in... | ihmpdcc/anadama-pride | pride/pipeline.py | Python | mit | 11,032 | [
"VisIt"
] | 61b1fb77a247a88b3559c268ec9511a730f996189fe23343e7930778479263f5 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from ma... | sujitmhj/document_similarity_based_on_bloom_filter | config/urls.py | Python | mit | 1,590 | [
"VisIt"
] | 29b514822874b39b5759b1203a0b04e8f26b516270f4bfbdbe0d13262b26cb72 |
from .base import SOLAR, EARTH, WATER, FIRE, AIR, LUNAR, Spell
from .. import effects
from .. import targetarea
from .. import enchantments
from .. import animobs
from .. import stats
from .. import invocations
# CIRCLE 1
BLESSING = Spell( "Blessing",
"Increases the physical and magic attack scores of all allies ... | jwvhewitt/dmeternal | old_game/spells/solarspells.py | Python | gpl-2.0 | 5,480 | [
"BLAST"
] | cd357e37daeff20b7d41d4fbd6137dd9dbe73c8ab0bef37abc4082aea12fc981 |
# Jackie's Map
# CMDR Jackie Silver, DISC
# Kay Johnston 2017 / 3303
# Thanks are due to everyone who's collected data for the various source lists, and particularly to edsm.
version = '3r2'
# Standard Python imports. Might need to change PIL to pillow on some versions of Python?
from tkinter import *
impor... | KayJohnston/jackies-map | jmap3r2.py | Python | bsd-3-clause | 76,060 | [
"Galaxy"
] | 48ecaaa316f1be6f2a21bb20aaafc800873d5989b65ee72ef0c4f1aad947b9c1 |
#!/usr/bin/env python
""" Functions and Constants common to all the executables."""
from __future__ import print_function
import redhawk
import redhawk.utils.util as U
import logging
import os
import string
import sys
import tempfile
PYGRAPHVIZ_NOT_FOUND = """This feature requires the pygraphviz, which does not
seem... | JordanMilne/Redhawk | redhawk/scripts/script_util.py | Python | bsd-2-clause | 3,082 | [
"VisIt"
] | d89e28213d18965074182471b2ff76a621c4f7866c46df1876dd3f8f4ad5f5d9 |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributio... | jrwilliams/gif-hook | images2gif.py | Python | mit | 29,501 | [
"NEURON"
] | c0efbb397c7bf948229ec48084d80416a766141f2e6cbda064ebbc45983bb4b1 |
from __future__ import absolute_import
from typing import Any, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import QuerySet
from dja... | niftynei/zulip | zerver/models.py | Python | apache-2.0 | 57,696 | [
"VisIt"
] | fbd96b63aca1547771bf617e6e09125ff7662601a48a6448bf8d196d2eb37f20 |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.common.action_chains import ActionChains
from .course_p... | wwj718/ANALYSE | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 23,238 | [
"VisIt"
] | bf0929ce4e361d1f4b45c6747b2040d698385b11ef3c4c0adc487501286978bd |
# Copyright (c) 2015-2016 Claudiu Popa <pcmanticore@gmail.com>
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/COPYING
"""Micro reports objects.
A micro report is a tree of layout and content objects.
"""
from six import str... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/reporters/ureports/nodes.py | Python | apache-2.0 | 4,643 | [
"VisIt"
] | 9e38310354ebfd5a43d2f79c129dddfcd5655fb8e905a2b608698ed0f9584f35 |
# https://www.hackerrank.com/challenges/ctci-connected-cell-in-a-grid
def DFS(grid, i, j):
# If coordinates exceed bounds, return 0.
if i >= len(grid) or j >= len(grid[0]) or i < 0 or j < 0:
return 0
# If coordinates are empty or already visited, return 0.
if grid[i][j] == -1 or grid[i][j] == 0... | zubie7a/Algorithms | HackerRank/Cracking_The_Coding_Interview/Algorithms/05_DFS_Connected_Cells_In_A_Grid.py | Python | mit | 1,102 | [
"VisIt"
] | 897ffea74daf8322b74039b120a85698451d8af08ac9555f11713227252229fa |
from sfepy.base.testing import TestCommon
import numpy as nm
from sfepy import data_dir
def tetravolume(cells, vertices):
vol = 0.0
c1 = nm.ones((4,4), dtype=nm.float64)
mul = 1.0 / 6.0
for ic in cells:
c1[:,:3] = vertices[ic,:]
vol += mul * nm.linalg.det(c1)
return -vol
expected_... | RexFuzzle/sfepy | tests/test_splinebox.py | Python | bsd-3-clause | 1,843 | [
"VTK"
] | e67feca950b3ee601f451468d8021f91277fbadaeb520c3325d4e10fb47ae37b |
"""
An estimator for modelling data from a mixture of Gaussians,
using an objective function based on minimum message length.
"""
__all__ = [
"GaussianMixture",
"kullback_leibler_for_multivariate_normals",
"responsibility_matrix",
"split_component", "merge_component", "delete_component",
]
import ... | andycasey/snob | snob/nips_search.py | Python | mit | 67,954 | [
"Gaussian"
] | 003cdd5571d90a2412475250750b20e30ba1abdcc40a14bf8bece7d677b6e40d |
from os.path import join, dirname, abspath
from os import makedirs
''' dir variables'''
PATH_ROOT = dirname(dirname(abspath(__file__)))
PATH_TEST = join(PATH_ROOT, 'test_data')
PATH_SCRIPTS = join(PATH_ROOT, 'scripts')
PATH_DATABASES = join(PATH_ROOT, 'databases')
PATH_DATABASE_LOGS = join(PATH_DATABASES, 'log_files'... | bluegenes/MakeMyTranscriptome | scripts/mmt_defaults.py | Python | bsd-3-clause | 8,123 | [
"BLAST"
] | b920beac1cabea2ef2b37c098cc1b4233ef7044edce9d73cebdc6eb835d60078 |
'''
txBOM lets you integrate asynchronous weather forecast and
observations retrieval from the Australian Bureau of Meteorology
into your Twisted application.
Data definitions extracted from http://www.bom.gov.au/inside/itb/dm/idcodes/struc.shtml
'''
version = (0, 0, 2)
# General form of the ID Code
#
# The gener... | claws/txBOM | txbom/__init__.py | Python | mit | 4,089 | [
"NetCDF"
] | 8047506b3312ccd89a10d4be4eb3f5684c9b2cd4d2a79897daaabb8f967f5bee |
from moose import *
SIMDT = 1e-5
PLOTDT = 1e-4
GLDT = 1e-2
RUNTIME = 0.05
context = PyMooseBase.getContext()
container = Neutral("/test")
proto_file_name = "../../../DEMOS/gbar/myelin2.p"
context.readCell(proto_file_name, "/test/axon")
gl0 = GLview("GLview", container)
gl0.vizpath = '/test/axon/##[CLASS=Compartment]... | BhallaLab/moose-thalamocortical | pymoose/tests/gl/testGLview.py | Python | lgpl-2.1 | 688 | [
"MOOSE"
] | 33efea074711257dc288791d2cb18b53af0f666e4d7c0429e0250aef033db83d |
#!/usr/bin/env python
import sys
from setuptools import find_packages, setup
import versioneer
DISTNAME = 'xarray'
LICENSE = 'Apache'
AUTHOR = 'xarray Developers'
AUTHOR_EMAIL = 'xarray@googlegroups.com'
URL = 'https://github.com/pydata/xarray'
CLASSIFIERS = [
'Development Status :: 4 - Beta',
'License :: O... | jcmgray/xarray | setup.py | Python | apache-2.0 | 2,580 | [
"NetCDF"
] | e467e7bc6853e219ee0cfffed85961c6c2a315084f15e11642739380ab7323f2 |
import pytest
import os
from fontTools.ttLib import TTFont
from fontbakery.checkrunner import (DEBUG, INFO, WARN, ERROR,
SKIP, PASS, FAIL, ENDCHECK)
from fontbakery.codetesting import (assert_results_contain,
assert_PASS,
... | moyogo/fontbakery | tests/profiles/googlefonts_test.py | Python | apache-2.0 | 170,205 | [
"Galaxy"
] | f3fbf814f906bbfb09ee94e8545368f3113136931c3de2297e4b1bc6066f8f9a |
from tao.models import Simulation, StellarModel, DustModel, BandPassFilter
from tao.settings import PROJECT_DIR
from tao.tests.integration_tests.helper import LiveServerTest
from tao.tests.support.factories import UserFactory, SimulationFactory, GalaxyModelFactory, DataSetFactory, JobFactory, DataSetPropertyFactory, Du... | IntersectAustralia/asvo-tao | web/tao/tests/forms/job_type_form_tests.py | Python | gpl-3.0 | 10,308 | [
"VisIt"
] | bc8f26d5355a130c69828130b36a1ad8cf6c36db1dbef2bcde9d24c1bdd96a06 |
from pylab import *
from math import exp, sqrt
import numpy
import Image
# return the energy measure of the transformation from image I to J.
# Works for d-dimensional images I and J
def transformation_energy(I, J):
s = image_similarity(I, J)
r = image_regularity(J)
return (s, r, s + r)
# return the simi... | facundoq/ipim | tp1/py/image.py | Python | gpl-3.0 | 2,196 | [
"Gaussian"
] | 296919795fa00687f4de59825d9e5021edc2abc6f48d4dbd085868377f606ea9 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | pierrelapointe/scancode-toolkit | src/licensedcode/index.py | Python | apache-2.0 | 18,939 | [
"VisIt"
] | 0e8c6fd6e5d543cb68238287ee8ec82ec19b64c709e63d0d923b6d7e60037867 |
from django.contrib.auth.models import User
from lettuce import step, world
from notification_prefs import NOTIFICATION_PREF_KEY
from user_api.models import UserPreference
USERNAME = "robot"
UNSUB_TOKEN = "av9E-14sAP1bVBRCPbrTHQ=="
@step(u"I have notifications enabled")
def enable_notifications(step_):
user = U... | yokose-ks/edx-platform | lms/djangoapps/notification_prefs/features/unsubscribe.py | Python | agpl-3.0 | 829 | [
"VisIt"
] | fc50ccea07f53d5af3d3f2336111d1b7f60a2c709cdf6c9e2e871cb48001c1bb |
# 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... | espressomd/espresso | testsuite/scripts/tutorials/test_ferrofluid_2.py | Python | gpl-3.0 | 1,566 | [
"ESPResSo"
] | 21738e2d291d71df2ee3cd9028a517a451631b575a0b110d4d82f64e60fb9fc2 |
"""Provides utilities for creating and working with Databases in ESPEI
"""
import logging
from typing import Dict, Union
from pycalphad import Database, variables as v
import espei.refdata
from espei.utils import extract_aliases
_log = logging.getLogger(__name__)
def _get_ser_data(element, ref_state, fallback_ref_st... | PhasesResearchLab/ESPEI | espei/database_utils.py | Python | mit | 5,678 | [
"pycalphad"
] | 54b66c18e2afce300dbaa951daa3f8998c5fcfd78e86b6004f76ae1ecac68230 |
#
# This file is part of GNU Enterprise.
#
# GNU Enterprise 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 2, or (at your option) any later version.
#
# GNU Enterprise is distributed in the h... | HarmonyEnterpriseSolutions/harmony-platform | src/gnue/common/utils/GMimeTypes.py | Python | gpl-2.0 | 30,650 | [
"NetCDF"
] | 77f09e36e378eeed6ecfe701bf56e9dd9ceeea266e85bb749d628c21b00534e2 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
SYNOPSIS
.
DESCRIPTION
EXAMPLES
python inverse_document.py
EXIT STATUS
0 program exit normal
1 program had problem on execution
AUTHOR
Theofilis George <theofilis.g@gmail.com>
LICENSE
This program is free software: you ca... | theofilis/tutorial-information-retrieval | inverse_document.py | Python | gpl-3.0 | 3,502 | [
"TINKER"
] | d3759458ed2c20a1b6212f37c60baab07158b7e7a20c9af6f47fed060f5031c1 |
ITEMS = [
"An unfavorable wind blowing the ship towards shore. Sailing into the wind means tacking, which is hard and exhausting work for the crew and navigator.",
"A Blue sea dragon demands tribute, Gold, Valuables, or Blood",
"A Crate with a cures Crown made of blue scales and golden thorns",
"A Float... | d2emon/generator-pack | src/sample_data/dndspeak/sailing_conditions.py | Python | gpl-3.0 | 9,755 | [
"VisIt"
] | fbfc7b6c9b7b11ccff45b9e1a34cef6350cd8c78ae960c8cfee5cf8f54a93002 |
###############################
# 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 | src/pylada/config/ipython.py | Python | gpl-3.0 | 1,425 | [
"CRYSTAL",
"VASP"
] | 26ef81844f0676dcbb6530c6baafeb000737708637e45c0f6dc4419948499662 |
# Licensed under GPL version 3 - see LICENSE.rst
'''Add additional scattering to processed photons.
Classes in this file add additional scattering in a statistical sense.
The classes in this module do not trace the photon to a specific location, they
just add the scatter at the point of the last interaction. For exa... | Chandra-MARX/marxs | marxs/optics/scatter.py | Python | gpl-3.0 | 6,432 | [
"Gaussian"
] | 13b5fb8968806c866046b777c62e9d35c53e2d6b82b41492fbd71ab6cf63e82c |
'''
CMEMS module
Builds copernicus formatted daily netCDFs from a single pandas dataframe/csv.
Originally written by Steve Jones.
Modified to better interact with export routine
Maren K. Karlsen 2020.10.29
'''
import sys, os
import tempfile
import datetime
import pandas as pd
import numpy as np
import numpy.ma as... | BjerknesClimateDataCentre/QuinCe | external_scripts/export/modules/CMEMS/Export_CMEMS_netCDF_builder.py | Python | gpl-3.0 | 12,637 | [
"NetCDF"
] | 5240050eb9d5193a9e22e7587fc2a670b815a47ee65659cbc05d83d6cf6841e9 |
#!/usr/bin/env python
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2015, Numenta, Inc. Unless you have purchased from
# Numenta, Inc. a separate commercial license for this software code, the
# following terms and conditio... | neuroidss/nupic.rogue | tools/convert_key_data.py | Python | agpl-3.0 | 4,972 | [
"Avogadro"
] | 15de39dbd795ab633d21f7767a805630ed526d37a77e3076fa8fa1040ac965f8 |
#!/usr/bin/env python
# Copyright (c) 2014, Palo Alto Networks
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" A... | PaloAltoNetworks-BD/SplunkforPaloAltoNetworks | SplunkforPaloAltoNetworks/bin/lib/pandevice/examples/userid.py | Python | isc | 4,289 | [
"Brian"
] | 58133d3218914bc676d63a26aab7c2eed0d7f243cd201f1d19f402f67dbb8785 |
# (c) 2012-2016, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/main/management/commands/reimport_role.py | Python | apache-2.0 | 1,725 | [
"Galaxy"
] | a2a57563b537d000fd43ad482704897ef045d8ce59feadf127ff0fc3bc0d6aa3 |
# -*- coding: utf-8 -*-
{
'!langcode!': 'nl',
'!langname!': 'Nederlands',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN',
'%(nrows)s rec... | zvolsky/zv | languages/nl.py | Python | agpl-3.0 | 17,128 | [
"Elk"
] | 3c48c44678a1e1faa5095d1a5d4eede43fbbc0361ed68d1c1f197c8792ac912d |
import gen_utils
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
import module_utils
import vtk
class transformPolyData(NoConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
... | nagyistoce/devide | modules/filters/transformPolyData.py | Python | bsd-3-clause | 1,855 | [
"VTK"
] | 4f604ab61ebe8b895856799ce344729ce35abf949da0ec1a27f6ae39ed66323f |
#!/usr/bin/python
#
# Copyright 2015 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/licenses/LICENSE-2.0
#
# Unless required b... | coxmediagroup/googleads-python-lib | examples/adwords/v201502/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,880 | [
"VisIt"
] | 237f8e73c493cb9fded6d4409e2855c0eb1bf4dc66fb9048cf18a981866bdc68 |
from copy import deepcopy
from decimal import Decimal
from collections import OrderedDict
from collections import Iterable
from enum import Enum
from my_visitor import NodeVisitor
from my_ast import FuncDecl
from my_ast import VarDecl
from my_ast import Else
from my_grammar import *
# The Interpreter has been abandone... | Ayehavgunne/Mythril | my_interpreter.py | Python | unlicense | 8,348 | [
"VisIt"
] | e8dcc9ce4cfd0bac1728add808217265452f61f7128c1427fc92cb62b28892ca |
# -*- coding: utf-8 -*-
#
# test_refractory.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 2 of the License... | heplesser/nest-simulator | testsuite/pytests/test_refractory.py | Python | gpl-2.0 | 8,170 | [
"NEURON"
] | ea8005a9133cc06faeb0ad3ee35410650ee6b19095989f38cb1749309f9e1f91 |
# Example for: topology.make(), topology.write()
# This creates a topology library for heavy atoms from the
# CHARMM all-atom topology library:
from modeller import *
env = environ()
tpl = env.libs.topology
# Read CHARMM all-atom topology library:
tpl.read(file='${LIB}/top.lib')
# Keep only heavy atoms (TOPOLOGY_M... | bjornwallner/proq2-server | apps/modeller9v8/examples/commands/make_topology_model.py | Python | gpl-3.0 | 437 | [
"CHARMM"
] | 23a3e3345709095b2e87a7ecc50f3bd2ef4c282f0d37e1fbb3099f381d6e1dce |
# -*- coding: utf-8 -*-
#
# structural_plasticity.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 2 of the L... | lekshmideepu/nest-simulator | pynest/examples/structural_plasticity.py | Python | gpl-2.0 | 13,940 | [
"Gaussian",
"NEURON"
] | adba6929d5fccb010f36ad9c5f09b53a837b2ec5929fdb02a3976acea309a6ca |
###############################################################################
##
## Copyright (C) 2014-2015, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | hjanime/VisTrails | vistrails/packages/ImageMagick/init.py | Python | bsd-3-clause | 11,223 | [
"Gaussian"
] | 0c6703938f44bd908b6bb92cb81e362d3e5de527c59a0bb17262b2ba5a58762b |
# -*- coding: utf-8 -*-
import logging
from pybel.utils import ensure_quotes
def write_metabolites_proteins_bel(manager, file=None):
"""Writes the metabolite-protein association relations found in HMDB into a BEL document.
:param bio2bel_hmdb.Manager manager: Manager object connected to the local HMDB data... | bio2bel/hmdb | src/bio2bel_hmdb/to_bel.py | Python | mit | 3,904 | [
"Pybel"
] | d9ec025efbd10a651fcfeb94155cf3bf863298ccf3e241b25ef7831338c95703 |
"""
This file contain all test for the GalaxyConnector class.
This test need a Galaxy instance to be executed
"""
import os
import time
import unittest
from shutil import copyfile
from bioblend import galaxy
from pyramid.paster import get_appsettings
from pyramid import testing
from askomics.libaskomics.ParamManager ... | ofilangi/askomics | askomics/test/GalaxyConnector_test.py | Python | agpl-3.0 | 6,011 | [
"Galaxy"
] | bd7349c2bad5cccd1c82e6b1b2c2ace3b721d6e0dda1742667e3d28662c636d4 |
import ase.db
from ase.lattice import bulk
from gpaw import GPAW, PW
from gpaw.response.g0w0 import G0W0
data = {
'C': ['diamond', 3.553],
'Si': ['diamond', 5.421],
'Ge': ['diamond', 5.644],
'SiC': ['zincblende', 4.346],
'AlN': ['zincblende', 4.368],
'AlP': ['zincblende', 5.451],
'AlAs': ... | robwarm/gpaw-symm | gpaw/test/big/gw/gw.py | Python | gpl-3.0 | 1,426 | [
"ASE",
"GPAW"
] | 42cb3734f38130c081f94c2558ae39566ec0cafb3268c41f588958b46b1c9c5e |
# Copyright 2008-2010 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SeqIO support for the "ace" file format.
You are expected to use this module via... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SeqIO/AceIO.py | Python | gpl-2.0 | 4,689 | [
"Biopython"
] | bfb20e567975cc7955b3a6894f7a8b975312d72d7af78a2e5aae2a6daffa18da |
import json
from coalib.bearlib import deprecate_settings
from coalib.bearlib.abstractions.Linter import linter
from dependency_management.requirements.NpmRequirement import NpmRequirement
from coala_utils.param_conversion import negate
def bool_or_str(value):
try:
return bool(value)
except ValueErro... | coala-analyzer/coala-bears | bears/js/JSHintBear.py | Python | agpl-3.0 | 20,717 | [
"VisIt"
] | 6c31cb6a2dce33a89c61af9083140fbd85478b94158984a21202e0d2ad6e223b |
import numpy as np
from compliance_checker.base import check_has, Result
from compliance_checker.defined_base import DefinedNCBaseCheck
from netCDF4 import Dataset
from compliance_checker import DTExportFormat
#from docutils.math.math2html import LimitsProcessor
##
## UR-TODO - simple copy from ROMS, needs adjusting ... | webtrike/compliance-checker | compliance_checker/shoc.py | Python | apache-2.0 | 28,288 | [
"NetCDF"
] | 7fe05b86a99a2faaefb37798d43601014f4745a0e7b8d3bf00ceba45159c4990 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""
Main pro... | harterj/moose | python/MooseDocs/main.py | Python | lgpl-2.1 | 2,810 | [
"MOOSE"
] | e8e53b26d5d458752f4e8a14f85cbc7ff670c82d0934788909d337b41977a3b3 |
'''
synbiochem (c) University of Manchester 2015
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
from setuptools import find_packages, setup
setup(name='synbiochem-py',
version='0.6.35',
description='... | synbiochem/synbiochem-py | setup.py | Python | mit | 1,269 | [
"Biopython",
"VisIt"
] | 442a8f159d2431068527a9e6843b2dc6a8884d9cfce6c28c5edd176bccc4f456 |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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
#
# ... | viggates/nova | nova/tests/network/test_manager.py | Python | apache-2.0 | 144,833 | [
"FEFF"
] | 0edf8440b061ae72d1485f7d225c5602450bbfd49a478a1385e64673e90017e5 |
import vtkAll as vtk
from vtkNumpy import addNumpyToVtk
from shallowCopy import shallowCopy
import numpy as np
class DebugData(object):
def __init__(self):
self.append = vtk.vtkAppendPolyData()
def write(self, filename):
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInputConnection(s... | mitdrc/director | src/python/director/debugVis.py | Python | bsd-3-clause | 7,129 | [
"VTK"
] | d1561a85e947f35a62674cf31c7fd6edb5e7952c0cc7eccedf2161ae1f3c6ccd |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_request_plan_find_drug_package.py | Python | apache-2.0 | 10,123 | [
"VisIt"
] | 0c2345c120c9d70e1e4f9553247a3d26389ddc0101befa5765fac685907f508a |
# -*- coding: utf-8 -*-
#
# hl_api_connections.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 2 of the Lice... | zifeo/nest-simulator | pynest/nest/lib/hl_api_connections.py | Python | gpl-2.0 | 25,062 | [
"NEURON"
] | d7d7174bb2a3504d2aef1a989b6a942246c3ea4e7a0e233906eb5fee855449e9 |
import os
import subprocess
import sys
import numpy
import argparse
import pysam
import vcf
import pybedtools
import logging
from collections import defaultdict, OrderedDict
from utils import makedirs
def uint(value):
if not value.isdigit(): raise argparse.ArgumentTypeError("%s is not digit-only" % value)
ret = in... | bioinform/varsim | generate_small_test_ref.py | Python | bsd-2-clause | 7,472 | [
"pysam"
] | ef3f48193e260f31bb14d77f1b59740b1d7f3231ea4e43a98e080ea3c423a79c |
# -*- coding: utf-8 -*-
# MD-Tracks is a trajectory analysis toolkit for molecular dynamics
# and monte carlo simulations.
# Copyright (C) 2007 - 2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
#... | molmod/md-tracks | tracks/convert.py | Python | gpl-3.0 | 17,763 | [
"CP2K",
"CPMD"
] | 24acb3106b169ae019d11af33d5bf0e53ee6d05ca468bb0f1e8e774798095d7e |
import unittest
import numpy as np
import cpnest.model
class GaussianModel(cpnest.model.Model):
"""
A simple 2 dimensional gaussian
"""
def __init__(self):
pass
names=['x','y']
bounds=[[-10,10],[-10,10]]
analytic_log_Z=0.0 - np.log(bounds[0][1]-bounds[0][0]) - np.log(bounds[1][1]-bo... | johnveitch/cpnest | tests/test_2d.py | Python | mit | 1,488 | [
"Gaussian"
] | 39c1cde73fba021203d29bf60f553e229efbee779e55054aea7529cb2cf3a689 |
'''apport package hook for foomatic-db-engine
(c) 2009 Canonical Ltd.
Author: Brian Murray <brian@ubuntu.com>
'''
from apport.hookutils import *
def add_info(report):
attach_hardware(report)
attach_printing(report)
| Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/apport/package-hooks/source_foomatic-db-engine.py | Python | gpl-3.0 | 226 | [
"Brian"
] | 3d3f84ed7de5d7f126cf87a5ed883fb16dc3e162fca301ddb24938f260261951 |
"""
Accounting agent to consume perfSONAR network metrics received via a message queue.
"""
from datetime import datetime
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.AccountingSystem.Client.Types.Network import Network
from DIRAC.ConfigurationSystem.Client.C... | fstagni/DIRAC | AccountingSystem/Agent/NetworkAgent.py | Python | gpl-3.0 | 9,794 | [
"DIRAC"
] | 73847ff85e8d9d44994e634766302d87997d14b5de383b11668ab1f52facda5e |
# Copyright 2012 Brian Waldon
#
# 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 applicable law or agreed to in writing,... | bcwaldon/warlock | warlock/model.py | Python | apache-2.0 | 3,900 | [
"Brian"
] | efd3aae27edd64400cc8ca5db540606450a72e0639f350feb2849bb67c6a5d22 |
#
# Copyright (C) 2000 greg Landrum
#
""" unit tests for the Neural network trainer implementation
this basically works out **all** of the network code
"""
import unittest
from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH
from rdkit.ML.Neural.NetNode import NetNode
from rdkit.ML.Neural.Network import Network... | ptosco/rdkit | rdkit/ML/Neural/UnitTestOther.py | Python | bsd-3-clause | 2,461 | [
"RDKit"
] | 1fe712156a7ecd4d82a3bda2d10936eaa08ba6007c8ccd28023d1b0d791a2c48 |
#!/usr/bin/env python
from setuptools import setup, find_packages
import os
# Utility function to read the README file. Used for the long_description.
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name='netcdf_extended_utils',
version='0.1',
description='E... | socib/netcdf_extended_utils | setup.py | Python | gpl-3.0 | 689 | [
"NetCDF"
] | 4a86a94e157ea6f95f57421acafb4ae5e9aeda628cbce00e827ff2c621d726ee |
"""
Base implementation of the Page Object pattern.
See https://code.google.com/p/selenium/wiki/PageObjects
"""
from abc import ABCMeta, abstractmethod, abstractproperty
from collections import defaultdict, namedtuple
from functools import wraps
from contextlib import contextmanager
import json
import logging
import os... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/bok_choy/page_object.py | Python | agpl-3.0 | 23,649 | [
"VisIt"
] | 1a9e87ed0c96621dcedc7fee8fa85e26b31785b85ea9415d1cce12eb8295c46d |
#!/usr/bin/env python
import argparse
import collections
import datetime
import itertools
import logging
import os
import sys
import HTSeq as hts
def assess_bundle(bundle, features):
"""
Takes a bundle of (potentially multiply mapped) paired-end read pairs, and looks to
see how many features map to each... | oxpeter/htseq-transcriptome | htseq-trancriptome.py | Python | gpl-3.0 | 9,943 | [
"HTSeq"
] | f35f952cbc49476fde1f22f459b9000ebf6855babc4b2329ec7fde695d748991 |
""" Test for various numpy_interface modules. Main goal is to test
parallel algorithms in vtk.numpy_interface.algorithms."""
from __future__ import print_function
import sys
try:
import numpy
except ImportError:
print("Numpy (http://numpy.scipy.org) not found.", end=' ')
print("This test requires numpy!")... | SimVascular/VTK | Parallel/MPI4Py/Testing/Python/TestParallelNumpy.py | Python | bsd-3-clause | 9,846 | [
"VTK"
] | 6ea097deffc2449c82971a03348fff73a88d19fcb774ad907060dcf9e923c4fb |
# -*- coding: utf-8 -*-
"""
jinja2.visitor
~~~~~~~~~~~~~~
This module implements a visitor for the nodes.
:copyright: (c) 2017 by the Jinja Team.
:license: BSD.
"""
from jinja2.nodes import Node
class NodeVisitor(object):
"""Walks the abstract syntax tree and call visitor functions for every... | wildchildyn/autism-website | yanni_env/lib/python3.6/site-packages/jinja2/visitor.py | Python | gpl-3.0 | 3,316 | [
"VisIt"
] | 243d47d5c00d036f49727b457cde5f3f2a90c41e1b238c02d3407365af971e4b |
import numpy as np
from assignment2.cs231n.layers import *
from assignment2.cs231n.fast_layers import *
from assignment2.cs231n.layer_utils import *
from assignment2.cs231n.layer_utils import conv_relu_pool_forward,\
affine_relu_forward
from assignment2.cs231n.layers import affine_forward, softmax_loss,\
affin... | machinelearningnanodegree/stanford-cs231 | solutions/levin/assignment2/cs231n/classifiers/cnn.py | Python | mit | 7,062 | [
"Gaussian"
] | e624af09a518fbc2c99bb71b97f784dd3f3f277716ba998f618cd1fc16fa67c0 |
import unicodedata
import numpy as np
from .. import coding
from ..core.variable import Variable
# Special characters that are permitted in netCDF names except in the
# 0th position of the string
_specialchars = '_.@+- !"#$%&\\()*,:;<=>?[]^`{|}~'
# The following are reserved names in CDL and may not be used as name... | shoyer/xarray | xarray/backends/netcdf3.py | Python | apache-2.0 | 3,931 | [
"NetCDF"
] | 2a41559ef0ccd144f567d910ed03215e555abcb085af227a5c6bb11f0fc6b42c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#******************************************************************************
#*
#* Copyright (C) 2015 Kiran Karra <kiran.karra@gmail.com>
#*
#* This program is free software: you can redistribute it and/or modify
#* it under the terms of the GNU General Public Licens... | kkarrancsu/copula-bayesian-networks | copulafit.py | Python | gpl-3.0 | 5,485 | [
"Gaussian"
] | 2a0c320c26ddbf154152ec3ecdc0df0491cffc0b5e1d58489a45e3be4704b2e0 |
from . import moe | bung87/moto-moe | moto/__init__.py | Python | mit | 17 | [
"MOE"
] | 51ce869efa9791369aea30bb25630ba50715aee3f9ac3ab88ea51220fbf41a24 |
#!/usr/bin/env python
""" Virana mapping tool for aligning short read data to human-microbial
reference genomes. Part of the Virana package.
(c) 2013, Sven-Eric Schelhorn, MPI for Informatics.
"""
#from __future__ import print_function
import numpy
import pysam
import sys
import tempfile
import subprocess... | schelhorn/virana | virana/vmap.py | Python | apache-2.0 | 69,616 | [
"BWA",
"HTSeq",
"pysam"
] | 627b742ce237a25d25b819173dbe32ed41c9d53bb2e2a00fea4c56bd96e2373c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# vncsession - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 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 o... | heromod/migrid | mig/cgi-bin/vncsession.py | Python | gpl-2.0 | 1,140 | [
"Brian"
] | b27f057c3615585c3fcca88a36ca56b4eeed22fb072f042dab8130b225265278 |
###############################
# 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 | src/pylada/vasp/incar/_params.py | Python | gpl-3.0 | 45,787 | [
"CRYSTAL",
"DIRAC",
"Gaussian",
"VASP"
] | 0db37bf58836df832e551df7d3106108a846cfe5518dbe1d13a64dc6c199c79c |
#!/usr/bin/python3
#
# Copyright (c) 2012 Mikkel Schubert <MikkelSch@gmail.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
... | MikkelSchubert/paleomix | paleomix/pipelines/bam/pipeline.py | Python | mit | 23,115 | [
"BWA"
] | 077d7ca0f79975e57e34ee812c1cc58dff7f0af7a1b2666c7a84f37f63a3eb13 |
# * Copyright 2020 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 required by applicable la... | google/making_with_ml | instafashion/scripts/utils.py | Python | apache-2.0 | 2,814 | [
"Bowtie"
] | 05fe67058a5494393c15b6f8b9a8925a59428a830990da68acfa5fe488461bbc |
import numpy as np
import math
unit = 2.2
height = 1.6
from chemfiles import Trajectory, UnitCell, Atom, Topology, Frame, Selection
def coordinate_si(ring, column, state):
x = unit * column
y = - unit * ring
if state == 0 or state == 7:
return 0, 0, 0, 0, 0, 0, 0
if state == 1:
return... | lscalfi/imogolite | 5-IsingModel/film.py | Python | mit | 4,077 | [
"Chemfiles"
] | 76bf9d32074de93e86a5bf40d24cf1276cf0ee87915052482d7a98ee1e185c52 |
'''
This script reads snow depth geotiffs and preprocesses them
and stores results to a dict.
Dict structure is src_name (str)
snow with NaN mask (numpy array)
rasterio metadata
Gaussian blurred snow (numpy array)
Normalized (0 to 1... | charparr/tundra-snow | snow_preprocess.py | Python | mit | 2,083 | [
"Gaussian"
] | 0a46f58da57740df202d8860acea620cef00fc20eb0a225fa140249792f1c528 |
""" DIRAC Workload Management System Client class encapsulates all the
methods necessary to communicate with the Workload Management System
"""
import os
import StringIO
import time
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.Utilities.ClassAd.ClassAd... | fstagni/DIRAC | WorkloadManagementSystem/Client/WMSClient.py | Python | gpl-3.0 | 8,338 | [
"DIRAC"
] | 0c69ecbe71545212254978e76459e241edf6222fcc6a75021701332054223cac |
# coding: utf-8
# Copyright 2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergo... | blond-admin/BLonD | unittests/beam_profile/test_sparse_profile.py | Python | gpl-3.0 | 7,221 | [
"Gaussian"
] | 771e441418f5d5623945ac6ff17b55370b148a4c7accb9f88b7240ad627dd592 |
"""
Creates a table with efficiency metrics (running time, peak memory
footprint) from SLURM output generated from sbatch_align.sh.
"""
from __future__ import print_function
import glob
import sys
from collections import defaultdict
nslurm, nsam = 0, 0
sam_names = defaultdict(int)
tab_wrapped = defaultdict(lambda: d... | BenLangmead/qtip-experiments | experiments/real_data/perf_tabulate.py | Python | mit | 3,305 | [
"BWA",
"Bowtie"
] | f8a7abbf4a6a6e38d6225ab92d8e92d3232745b591bb77c3c0ac4f2212bfee0b |
import gzip
import os
import shutil
import socket
import urllib2
from contextlib import closing
import requests
from ftplib import FTP
import settings
from models.conan import CONAN_PIPELINES
from models.soft_mapper import SoftHeaderMapper, SoftTableMapper
from utils.common import execute_command
from utils.conan.cona... | arrayexpress/ae_auto | automation/geo/import_adf.py | Python | apache-2.0 | 6,795 | [
"ADF"
] | 523e6c32d2ef5554eef531a0e3ba05948fa31d385c07d021c2e22d53c168942d |
# Author: Travis Oliphant
# 2003
from numpy import asarray, zeros, place, nan, mod, pi, extract, log, sqrt, \
exp, cos, sin, size, polyval, polyint, log10
def sawtooth(t,width=1):
"""Returns a periodic sawtooth waveform with period 2*pi
which rises from -1 to 1 on the interval 0 to width*2*pi
and dro... | huard/scipy-work | scipy/signal/waveforms.py | Python | bsd-3-clause | 6,637 | [
"Gaussian"
] | 34df022500bbfa229a24adb00c917330d560bb20d8ac542a0b9f22d5ae0583b4 |
#!/usr/bin/env python
"""
Implementation for get_environment CLI.
"""
from pymatgen.analysis.chemenv.utils.scripts_utils import compute_environments, welcome, thankyou
from pymatgen.analysis.chemenv.utils.chemenv_config import ChemEnvConfig
from argparse import ArgumentParser
import logging
__author__ = 'waroquiers... | gVallverdu/pymatgen | pymatgen/cli/get_environment.py | Python | mit | 1,425 | [
"pymatgen"
] | 5208728c91c384a5fa02a793648987e3cc0c93e0f42772ef6b76a0f942d83611 |
# -*- coding: utf-8 -*-
"""Miscellaneous convenience functions.
"""
import ast
import functools
import operator
import os
import shutil
import subprocess
import collections
import itertools
from numbers import Number
import traceback
from warnings import warn
from functools import (partial, wraps)
import xarray
imp... | atmtools/typhon | typhon/utils/common.py | Python | mit | 21,289 | [
"NetCDF"
] | f0f0ca42413bb645370bb347d3e1d1392748db2dcfc2c371db090107bc864e49 |
"""Generate html report from MNE database
"""
# Authors: Alex Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Mainak Jas <mainak@neuro.hut.fi>
# Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import os
import os.path as op
import fnmatch
import re
import codecs
import time
from... | matthew-tucker/mne-python | mne/report.py | Python | bsd-3-clause | 61,163 | [
"Mayavi"
] | 91f476b36792ff17da0c6bf0b8d41746fcdf650137a48a4b97e41365e0bf8792 |
# Copyright (c) 2014-2016 Genome Research Ltd.
#
# This file is part of IVA.
#
# IVA 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.
# ... | sanger-pathogens/iva | iva/tests/assembly_test.py | Python | gpl-3.0 | 10,150 | [
"pysam"
] | b7ca9c199d7b932f0e8aefeba5e13924dcd8b912799cfc5311356815bf0fc405 |
# Transformer/IO/StructureIO.py
# -------
# Imports
# -------
import os;
from Transformer.IO import _AIMS, _VASP;
# ---------
# Constants
# ---------
# Tuples of (formatCode, defaultExtension, readSupport, writeSupport).
SupportedFileFormats = [
('aims', '.geometry.in', True, True),
('vasp', '.va... | JMSkelton/Transformer | Transformer/IO/StructureIO.py | Python | gpl-3.0 | 5,218 | [
"VASP"
] | 769e6a58eb08bd4246440fe5e04d5bb8917735d1ba0dd0377b4a10248bbee4d1 |
"""
Unit tests for the atom renderer
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import unittest
import numpy as np
import vtk
from vtk.util import numpy_support
from .. import atomRenderer
from ... import utils
from six.moves import range
###################################... | chrisdjscott/Atoman | atoman/rendering/renderers/tests/test_atomRenderer.py | Python | mit | 2,682 | [
"VTK"
] | f3e05f17d505ccc81316b4ce56ab640a3776958c386e7e8801bb7694f2403c7c |
# -*- coding: utf-8 -*-
# Copyright 2013 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import unittest
import pytest
from .fake_webapp import EXAMPLE_APP
from .base import WebDriverTests, get_browser
class ChromeBrowser... | cobrateam/splinter | tests/test_webdriver_chrome.py | Python | bsd-3-clause | 1,136 | [
"VisIt"
] | 4113c9aa72b785ad409ff042bac6329668ea1caf5bc8b627a83aacc6b7cb61d6 |
import os
import os.path
import shutil
from easybuild.framework.easyblock import EasyBlock
from easybuild.easyblocks.generic.configuremake import ConfigureMake
from easybuild.framework.easyconfig import CUSTOM
from easybuild.tools.build_log import EasyBuildError
from easybuild.tools.run import run_cmd
class EB_LAMM... | qldhpc/eb_local | eb_blocks/l/lammps.py | Python | apache-2.0 | 5,482 | [
"LAMMPS"
] | 41528372b34353fd35a1c9898df204f6548255f0373b7ec5cffae3bf4a0e87cc |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | retrography/scancode-toolkit | tests/commoncode/test_functional.py | Python | apache-2.0 | 2,092 | [
"VisIt"
] | 710870084a2a79e8c5298c25ed0fe990ff1f6ffc265da4592312b51def38aacd |
import vtk
import time
import numpy as np
from director import transformUtils
from director.timercallback import TimerCallback
from director import propertyset
from collections import OrderedDict
class OrbitController(TimerCallback):
def __init__(self, view):
TimerCallback.__init__(self)
self.view... | manuelli/director | src/python/director/cameracontrol.py | Python | bsd-3-clause | 15,095 | [
"VTK"
] | 7f0e3b2334dde1d46f1ee7d5e898f7d85de1f1082145fb9529925af0733575cb |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | qiime2/q2-diversity | q2_diversity/plugin_setup.py | Python | bsd-3-clause | 42,797 | [
"VisIt",
"scikit-bio"
] | c6092ee73d2cb534f077eae4a8324ef9ab7b40346fcf214e967fbbeae804ae3e |
"""
End-to-end test for cohorted courseware. This uses both Studio and LMS.
"""
from bok_choy.page_object import XSS_INJECTION
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.utils imp... | cpennington/edx-platform | common/test/acceptance/tests/test_cohorted_courseware.py | Python | agpl-3.0 | 12,088 | [
"VisIt"
] | 6d635771aaf6b846eb86a7b08e26e2fadd99f09404e5d61947b912cba4cb08e0 |
import numpy as np # type: ignore
from scipy.ndimage.filters import gaussian_filter1d # type: ignore
from pymatgen import Structure # type: ignore
from typing import List, Optional, TypeVar, Type
"""
This module provides classes for calculating radial disitrbution functions
and Van Hove correlation functions.
"""
R... | bjmorgan/vasppy | vasppy/rdf.py | Python | mit | 10,969 | [
"Gaussian",
"pymatgen"
] | 76e19bb92ac4a3c9a800b30da9fba825a0ab90e23ddde3e5ad457bbb8384c93a |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package contains classes to parse input files from the exciting
code package.
"""
from .inputs import ExcitingInput
| materialsproject/pymatgen | pymatgen/io/exciting/__init__.py | Python | mit | 220 | [
"exciting",
"pymatgen"
] | c5179c38fe73a9302b5a1490c441560b56686d1311f5c20b765f38bceb29413f |
import pysam, sys, os, random
from jobTree.src.bioio import fastaRead, fastqRead, \
cigarReadFromString,PairwiseAlignment, fastaWrite, fastqWrite, logger, absSymPath, reverseComplementChar
def pathToBaseNanoporeDir():
"""Returns path to base directory "marginAlign"
"""
import marginAlign
i = absSymPath... | benedictpaten/marginAlign | src/margin/utils.py | Python | mit | 19,174 | [
"BWA",
"pysam"
] | b195f47e86f56f73a6b25fd95709d8379d37461c2824bf0b61fa8be17bfa6d64 |
''' FreeDiskSpaceCommand
The Command gets the free space that is left in a Storage Element
Note: there are, still, many references to "space tokens",
for example ResourceManagementClient().selectSpaceTokenOccupancyCache(token=elementName)
This is for historical reasons, and shoud be fixed one day.
... | arrabito/DIRAC | ResourceStatusSystem/Command/FreeDiskSpaceCommand.py | Python | gpl-3.0 | 4,872 | [
"DIRAC"
] | 564742fcc77fa4633119c00c885751edcc33b32c15b167788625a216edb1ab45 |
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