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from rdkit import Chem
from rdkit.Chem import AllChem
from joblib import Parallel, delayed
import multiprocessing
num_bits = 2048
input_filename = '../../data/csv_files/logSolubilityTest.csv'
output_filename = '../../data/temp/solubility_control_fingerprints_'+str(num_bits)+'.csv'
def getFingerprint(smiles):
mol ... | debbiemarkslab/neural-fingerprint-theano | code/rdkit_preprocessing/ecfpFingerprintGenThreaded.py | Python | mit | 997 | [
"RDKit"
] | 71b5dc573e86cc3e04599ecaad1d5ef0a854803f5217ccb07629be157f90dc72 |
"""Density-based baselines for imitation learning.
Each of these algorithms learns a density estimate on some aspect of the demonstrations,
then rewards the agent for following that estimate.
"""
from typing import Sequence
import numpy as np
from gym.spaces.utils import flatten
from sklearn.neighbors import KernelD... | humancompatibleai/imitation | src/imitation/algorithms/density_baselines.py | Python | mit | 13,177 | [
"Gaussian"
] | b57e6b14126dbb15d7f30b60834c65eca581195608ecec15416152d6ac74b1f8 |
#!/usr/bin/env python
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Main Madpack installation executable.
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
import sys
import getpass
import re
import os
import glob
import traceback
import subprocess
import datetime
import tempfile
import shutil... | njayaram2/madlib | src/madpack/madpack.py | Python | apache-2.0 | 58,972 | [
"ORCA"
] | 2cb79627ae282d9b0fb03a1b91853699a6c46fddb33e20fcd648353eeda97f95 |
""" The SystemAdministratorClient is a class representing the client of the DIRAC
SystemAdministrator service. It has also methods to update the Configuration
Service with the DIRAC components options
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_functio... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/Client/SystemAdministratorClient.py | Python | gpl-3.0 | 818 | [
"DIRAC"
] | 9d522cff20f8a79c113c055fcb19179ce9fd95a805b46403ef0eb28981018b75 |
#!/usr/bin/env python
# Copyright (c) 2015, 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 | Splunk_TA_paloalto/bin/lib/common.py | Python | isc | 13,115 | [
"Brian"
] | 691f8db6967ce2c45c8eaa67596869b6e574f084d7a8f70d592297fcd4d91061 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/saveepg.py | Python | gpl-2.0 | 5,151 | [
"VisIt"
] | a753161f5f6ff6b53282afd1c28db22991bb15c3422097cf0cf6e8eb3030134f |
import ast
from unittest import TestCase
from darglint.analysis.argument_visitor import (
ArgumentVisitor,
)
from .utils import (
reindent,
require_python,
)
class ArgumentVisitorTests(TestCase):
def assertFound(self, program, *args):
"""Assert that the given arguments were found.
... | terrencepreilly/darglint | tests/test_argument_visitor.py | Python | mit | 3,374 | [
"VisIt"
] | a45698eca1dd50cd31b2ee240172e090fd04db7b3d2fb3f8c640ad87cf4b7934 |
#!/usr/bin/env python
"""
Created on Mon Jun 15 21:49:32 2015
@author: Harald Voehringer
"""
from __future__ import print_function
import sys, os, glob, gzip, textwrap, itertools
from optparse import OptionParser
from collections import defaultdict
from os.path import splitext
from pdbx.reader.PdbxReader import Pdbx... | soedinglab/hh-suite | scripts/cif2fasta.py | Python | gpl-3.0 | 28,734 | [
"CRYSTAL"
] | d4bc9ab1492326bd93c5555ec1c849fff95e194b68191fb3685f97a323c1a7b7 |
from django.db import models
from edc_base.model_managers import HistoricalRecords
from edc_base.model_validators import datetime_not_future
from edc_constants.choices import YES_NO_NA
from edc_constants.constants import NOT_APPLICABLE
from ..choices import HIV_RESULT, WHY_NO_HIV_TESTING_CHOICE, BLOOD_DRAW_TYPES
fro... | botswana-harvard/bcpp-subject | bcpp_subject/models/hiv_result.py | Python | gpl-3.0 | 1,961 | [
"VisIt"
] | e62a257140558ceeabc85511507de1f1f726ef82b258d3e00458fc93897fb9bd |
"""
The vis module provides support for generic vtk file writing, basic mesh
writing (unstructured triangular and tetrahedral meshes), visualization of
aggregate groupings in 2d and in 3d, and C/F splittings.
"""
| huahbo/pyamg | pyamg/vis/info.py | Python | mit | 213 | [
"VTK"
] | 0670f054e3276fa02fbcfc07eff6174a1b2500065868b4043e1f3eb07ccf70bd |
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2015-2018 Canonical Ltd
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation.
#
# This program is distributed in ... | elopio/snapcraft | tests/unit/commands/test_list_plugins.py | Python | gpl-3.0 | 3,146 | [
"GULP"
] | aaf31ef5129cce00ae29b40e4659a5fa2e3585904b664610b14f80581977dd8f |
# -*- coding: utf-8 -*-
# HiPart is a program to analyze the electronic structure of molecules with
# fuzzy-atom partitioning methods.
# Copyright (C) 2007 - 2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>
#
# This file is part of HiPart.
#
# HiPart is free software; you can redistribute it and/or
# modify it under t... | molmod/hipart | hipart/opts.py | Python | gpl-3.0 | 4,371 | [
"Gaussian"
] | b288a592070e6e7be0701965ca14945e3edc010f09b8b67eeac9874122067d4a |
# pylint: disable=missing-docstring
import urllib
from django.apps import apps
from django.contrib.auth import get_user_model
from lettuce import world
from xmodule.contentstore.django import _CONTENTSTORE
@world.absorb
def create_user(uname, password):
# If the user already exists, don't try to create it aga... | BehavioralInsightsTeam/edx-platform | common/djangoapps/terrain/course_helpers.py | Python | agpl-3.0 | 2,570 | [
"VisIt"
] | ea22e838356545c9579c074774c591a5736733e718eff487c6fecf647ac4c2b2 |
# Copyright 2015 Isotoma Limited
#
# 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... | yaybu/touchdown | touchdown/core/goals.py | Python | apache-2.0 | 3,422 | [
"VisIt"
] | cda4d3c6d8fd46e9267a550b6cba3eddc58defe1d1c0512c5eceaf98f8304eb2 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2016, 2016, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | rschatz/mx | mx_benchmark.py | Python | gpl-2.0 | 70,556 | [
"VisIt"
] | bd0e59b9aa91eb842fc9ebe7afc1d8749079f7d65507e7a3285c95046d18058a |
'''
NeuroLearn Simulator Tools
==========================
Tools to simulate multivariate data.
'''
__all__ = ['Simulator']
__author__ = ["Sam Greydanus","Luke Chang"]
__license__ = "MIT"
import os
import time
import sys
import warnings
from distutils.version import LooseVersion
import random
import cP... | burnash/neurolearn | nltools/simulator.py | Python | mit | 18,310 | [
"Gaussian"
] | 456b74728c9fdc41e2c7eeb4323b92c6fe931d50e23147d7941b300c0b37dcdb |
#
# Copyright (C) 2004-2006 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.
#
class ExcludedVolume(object):
def __init__... | bp-kelley/rdkit | rdkit/Chem/Pharm3D/ExcludedVolume.py | Python | bsd-3-clause | 930 | [
"RDKit"
] | 32b938b6969623b0a27eccfdbe0b1867deec523d031ee5c097c0b11d3a150a0f |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ghutchis/cclib | src/cclib/parser/utils.py | Python | lgpl-2.1 | 4,573 | [
"GAMESS",
"cclib"
] | 12a57163982ebd24772fb2a6c89ec3d7f28b21046f08592caf53144fc8592d69 |
"""
Python code for calculating non-parametric morphological diagnostics
of galaxy images.
"""
# Author: Vicente Rodriguez-Gomez <v.rodriguez@irya.unam.mx>
# Licensed under a 3-Clause BSD License.
from pkg_resources import parse_version
import warnings
import time
import numpy as np
import scipy.optimize as opt
import ... | vrodgom/statmorph | statmorph/statmorph.py | Python | bsd-3-clause | 92,972 | [
"Galaxy",
"Gaussian"
] | d54aea97ac27d1f48ef2bb1a7e38023c9dbfd96f183be43a8ef9e37b56775d4d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Foundati... | andrebellafronte/stoq | stoqlib/domain/test/test_system.py | Python | gpl-2.0 | 1,624 | [
"VisIt"
] | 3bde11dbf92be6813e8bcd0555b067ebae8f4e0e1436b267537106f2bdaf4eaa |
import numpy as np
def Hbeta(D = np.array([]), beta = 1.0):
"""Compute the perplexity and the P-row for a specific value of the precision of a Gaussian distribution."""
# Compute P-row and corresponding perplexity
P = np.exp(-D.copy() * beta);
sumP = sum(P);
H = np.log(sumP) + beta * np.sum(D * P)... | gviejo/ThalamusPhysio | python/TSNE.py | Python | gpl-3.0 | 4,917 | [
"Gaussian"
] | eac2a64af289e4f15a620427dc23b4e0e7dea153271f2cb4d25185c737b9e6c3 |
'''Various extensions to distributions
* skew normal and skew t distribution by Azzalini, A. & Capitanio, A.
* Gram-Charlier expansion distribution (using 4 moments),
* distributions based on non-linear transformation
- Transf_gen
- ExpTransf_gen, LogTransf_gen
- TransfTwo_gen
(defines as examples: square, n... | hlin117/statsmodels | statsmodels/sandbox/distributions/extras.py | Python | bsd-3-clause | 39,483 | [
"Gaussian"
] | 0be4e98a6bdcf869c2d23d51536dc2f05c845f430d6168599dc7f22a7645b496 |
# -*- coding: utf-8 -*-
"""
This awkward set of tests tries to make Grako bang its head against iself.
"""
from __future__ import print_function, division, absolute_import, unicode_literals
import sys
sys.path.append('tmp')
import os
import json
import pickle
from grako.rendering import NodeVisitor
from grako.semantics... | swayf/grako | grako/test/bootstrap_tests.py | Python | bsd-2-clause | 4,674 | [
"VisIt"
] | 68f30e0d67140801b7cfab5464ebd8ef602bb638f24703b1177bcfbdf46c126e |
from collections import OrderedDict
from django.contrib import admin
from copy import copy
from edc_base.modeladmin.admin import BaseModelAdmin
from edc_export.actions import export_as_csv_action
from edc_visit_tracking.admin import VisitAdminMixin
from microbiome.apps.mb_lab.models import MaternalRequisition
from .... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/admin/maternal_visit_admin.py | Python | gpl-2.0 | 1,479 | [
"VisIt"
] | 292f8efc187067ed90525d81d7f8c2868e6dead3bd8b1e10781242943ff9f34f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# oneclick - One-click MiG resource frontend
# 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 of the GNU General Public L... | heromod/migrid | mig/cgi-bin/oneclick.py | Python | gpl-2.0 | 1,118 | [
"Brian"
] | fe497eb9c09ecdb5c2ffd1d96ade7d19f6cdbef014324c7b41e35e4f056c5974 |
"""
This module contains submodules used to mine Interaction data from `Kegg`,
`Hprd`, `InnateDB`, `BioPlex` and `Pina2` along with other data processing
modules.
The `features` module contains a function to compute the features based on
two `:class:`.database.models.Protein`s. The `uniprot` module contains s... | daniaki/pyPPI | pyppi/data_mining/__init__.py | Python | mit | 1,091 | [
"Biopython"
] | d312e1255ebf181fbfada4885f69b69f6f260113dcabd3afcdde6c69c5cfed58 |
from random import randint
from stdnet import odm, QuerySetError
from stdnet.utils import test
from stdnet.odm.search import UpdateSE
from stdnet.utils import test, to_string, range
from stdnet.apps.searchengine import SearchEngine, processors
from examples.wordsearch.basicwords import basic_english_words
from exampl... | lsbardel/python-stdnet | tests/all/apps/searchengine/meta.py | Python | bsd-3-clause | 7,675 | [
"Brian"
] | f0438fdfed6de5f3c6bd0bacb97605b3eac7021f6e0c25b3961e279baa3df61a |
import random
class Creature(object):
"""This is the basic melee creature"""
def __init__(self, name, probability, strength,
defense, speed, resist, alignment):
self.name = name
self.probability = probability
self.strength = strength
self.defense = defense
... | blakebye/cyberbattles | cards.py | Python | mit | 59,189 | [
"VisIt"
] | 4123a5e3526742ced50806a152f66b13c4726bd42eeea144b966087c1c96702a |
# -*- coding: utf-8 -*-
# Copyright JS Foundation and other contributors, https://js.foundation/
#
# 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
# ... | mp-coder/translate-dev-tools | esprima/comment_handler.py | Python | mit | 6,492 | [
"VisIt"
] | 817030ad3c92815f6d30f070b3de32c48f68128627bb0c355edbc5896db57fef |
#
# Copyright 2011-2013 Blender Foundation
#
# 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... | pyrochlore/cycles | src/blender/addon/properties.py | Python | apache-2.0 | 37,894 | [
"Gaussian"
] | ad532e1e0e5c95355ea5981ac8f6c92bafffa05d82cfdaf58898af2935bfce42 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageGradient(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.... | nagyistoce/devide | modules/vtk_basic/vtkImageGradient.py | Python | bsd-3-clause | 489 | [
"VTK"
] | f934f393782a643bea7ea33257a917175be10701867246dac51577fb0a52b41e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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
# ... | adityacs/ansible | lib/ansible/modules/network/lenovo/cnos_facts.py | Python | gpl-3.0 | 4,754 | [
"VisIt"
] | e8760211a90f56a56c296a8fdaf8cac2b4fc136edc9c16dda5806b5c260f919f |
#!/usr/bin/env python
import sys
import os
import shutil
from netCDF4 import Dataset
if __name__=='__main__':
variable_name = 'sftof'
if len(sys.argv)!=2:
raise RuntimeError('Need exactly one netcdf file as argument!')
if not os.path.isfile(sys.argv[1]):
raise RuntimeError('"{}" is... | goord/ece2cmor3 | ece2cmor3/scripts/data-qa/scripts/sftof.py | Python | apache-2.0 | 900 | [
"NetCDF"
] | 3d0e7102de95211399a52db39504bd6d6f53395c079de28e837178f114c86b0e |
#!/usr/bin/env python
"""Parsers for XML output of blast, psi-blast and blat.
"""
__author__ = "Kristian Rother"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Micah Hamady"]
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Kristian Rother"
__emai... | sauloal/cnidaria | scripts/venv/lib/python2.7/site-packages/cogent/parse/blast_xml.py | Python | mit | 7,648 | [
"BLAST"
] | ce0bd15a9b28ccdcdfb776f65f4917a5153ed24ed8bf21e5a1507de01d0f232d |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authen... | defance/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 100,562 | [
"VisIt"
] | 583bf29033008a9cde5d2a797aca67caeeb8bbe0068946fd6b2ae1d2e304468a |
from collections import deque
import time
import requests
# Constants
BRAZIL = 'br'
EUROPE_NORDIC_EAST = 'eune'
EUROPE_WEST = 'euw'
KOREA = 'kr'
LATIN_AMERICA_NORTH = 'lan'
LATIN_AMERICA_SOUTH = 'las'
NORTH_AMERICA = 'na'
OCEANIA = 'oce'
RUSSIA = 'ru'
TURKEY = 'tr'
# Platforms
platforms = {
BRAZIL: 'BR1',
EUR... | chenwardT/Riot-Watcher | riotwatcher/riotwatcher.py | Python | mit | 23,170 | [
"CRYSTAL"
] | c262960cc41e04798ae61a27428b40f50151ee1fe607db0943f83d414ea3be3d |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import copy
import json
import os
import py... | amenonsen/ansible | test/units/galaxy/test_collection_install.py | Python | gpl-3.0 | 32,014 | [
"Galaxy"
] | 0f08c17e736116fe4c9ff2ae85221b64fc6d7951c8f92ef22a922e206adfaefe |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/soap/Soap.py | Python | gpl-3.0 | 1,603 | [
"ESPResSo"
] | 70b3d2e282dd5e5502d54fb6fb8ea4fe37a462189e7b4e90c3f1abe88a0c63f0 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/android/android_Vibrate.py | Python | gpl-3.0 | 2,154 | [
"ORCA"
] | 4f09747fb3148e1677f5e9fca09c7af18a787c1d1c20e686181519b2ca365ccb |
# Version: 0.20
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
* [![Latest Version][pyp... | sjsrey/pysal | versioneer.py | Python | bsd-3-clause | 78,254 | [
"Brian"
] | 439815ae46c6c69e1239ba75b7b1f643d76f387c4f96ace82dcc154a7c09f839 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# Redistribution and use in ... | Nikea/scikit-xray | skbeam/core/spectroscopy.py | Python | bsd-3-clause | 13,050 | [
"Gaussian"
] | 63db64e7290852ae025f2a4dd14b367d134c7448c5a021c942e92349e0198755 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/mobile/timeradded.py | Python | gpl-2.0 | 9,111 | [
"VisIt"
] | 601ab0313b0548a4a026db943812c94d4e1e3fce6c6d2e81407dad40e7eee201 |
#!/usr/bin/python
import sys,os,getopt
OUTFILEPART2 = 'tmp.orf.part2.fasta'
#==============================================================================
def usage():
print """Hello!
Following options are possible:
-i:\tparsed BLASTX best hit definitions
-j:\tinput sequences in FASTA format
-t:\tminim... | lotharwissler/bioinformatics | python/openreadingframe/ORFPREDICTORRR.py | Python | mit | 2,774 | [
"BLAST"
] | 031dc4b418304d1e38a4c00f545b37844cc8071542476c408d05e9d0d2a97774 |
import sys
from subprocess import Popen, PIPE
from mne.utils import run_tests_if_main, requires_version
run_script = """
from __future__ import print_function
import sys
import mne
out = []
# check scipy
ok_scipy_submodules = set(['scipy', 'numpy', # these appear in old scipy
'fftpack'... | jaeilepp/mne-python | mne/tests/test_import_nesting.py | Python | bsd-3-clause | 1,739 | [
"Mayavi"
] | 33bd92d694df8e5a1508f51be394803f826def86e26c0b9761690a8271e6e90d |
# 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... | KaiSzuttor/espresso | testsuite/scripts/samples/test_object_in_fluid__motivation.py | Python | gpl-3.0 | 1,712 | [
"ESPResSo",
"VTK"
] | 0f66f9a357a7057a0c4c1846c976fc813105d0dcefe9164f41f4db648d2bde32 |
#!/usr/bin/env python
# -*- coding:utf-8 -*-
# @author:Hieda no Chiaki <i@wind.moe>
| forblackking/PyBiu | src/__init__.py | Python | apache-2.0 | 86 | [
"MOE"
] | b1faf339f6551c8de973193b7ee980e268e6745fce85f0d0959b66dcf79ccde5 |
##############################################################################
# Copyright (c) 2013-2017, 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... | lgarren/spack | var/spack/repos/builtin/packages/ncl/package.py | Python | lgpl-2.1 | 10,762 | [
"NetCDF"
] | 7dc13b5f33b9a624f83d0ba128c5670e2017222f245c751a60245b4ff5d3374c |
""" The LSF TimeLeft utility interrogates the LSF batch system for the
current CPU and Wallclock consumed, as well as their limits.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import re
import time
from DIRAC import S_OK, S_ERROR
from ... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/LSFResourceUsage.py | Python | gpl-3.0 | 11,615 | [
"DIRAC"
] | 578b5724d6cafb920a79d3856c1e42753f1055a0bf9369fccb6126759ebf143e |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2013 Oleh Petriv <olehsbox[at]yahoo.com>
# Copyright (C) 2013 Fedir Zinchuk <fedikw[at]gmail.com>
#
# This program is free s... | SNoiraud/gramps | gramps/plugins/rel/rel_uk.py | Python | gpl-2.0 | 35,495 | [
"Brian"
] | 60db0a64f06edea14ef59652f165e8b77fdb3eb53ed05cd9202264bbb969557b |
#
# Copyright (C) 2016 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed in the hope that it will be ... | jhdulaney/dnf | dnf/cli/commands/check.py | Python | gpl-2.0 | 7,068 | [
"ASE"
] | e9cf71c99beabeba9b6d4d7acaebac921198a9757694ce75e30d697df785b692 |
""" Recipes on how to create job plots
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK
from DIRAC.AccountingSystem.Client.Types.Job import Job
from DIRAC.AccountingSystem.private.Plotters.BaseReporter import BaseReporter
class J... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/private/Plotters/JobPlotter.py | Python | gpl-3.0 | 34,723 | [
"DIRAC"
] | 34bf747346945ca00b82dd2ec0ba7c51bb7f2e42fff5c5bb04f5b6a4e889e6a5 |
'''
Created on Aug 1, 2011
@author: mkiyer
'''
import logging
import os
import collections
import subprocess
import pysam
from chimerascan.lib import config
from chimerascan.lib.chimera import Chimera
from chimerascan.bx.intersection import IntervalTree, Interval
def get_mapped_read_intervals(c, min_isize, max_isiz... | tectronics/chimerascan | chimerascan/deprecated/filter_homologous_genes_v1.py | Python | gpl-3.0 | 6,500 | [
"Bowtie",
"pysam"
] | 273cf898c8e387c656d8b4d33ba0d3c91679e67453bbfd506b9b57d6d1afb675 |
"""
# Notes:
- This simulation seeks to emulate the CUBA benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008).
- The time taken to si... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_CUBA_nosyn_compiled_4000.py | Python | gpl-3.0 | 2,140 | [
"Brian"
] | a3254b3d2b564fc2da7d78535123abdc5276c72a95f9e8bf053a99e80028b21f |
# onetoonemsg.py ---
#
# Filename: onetoonemsg.py
# Description:
# Author:
# Maintainer:
# Created: Wed May 1 11:05:30 2013 (+0530)
# Version:
# Last-Updated: Wed May 1 11:12:07 2013 (+0530)
# By: subha
# Update #: 24
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Chan... | dilawar/moose-full | moose-examples/snippets/onetoonemsg.py | Python | gpl-2.0 | 1,752 | [
"MOOSE"
] | 148c5b784a5376e0341fe40d1ba4fb6f7dbc8725a0ab94875d578b60a19bf4bc |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
####################################################################################
### Copyright (C) 2015-2019 by ABLIFE
####################################################################################
########################################################... | ablifedev/ABLIRC | ABLIRC/bin/public/expression_quantity_calculation_v2.2.py | Python | mit | 32,586 | [
"HTSeq"
] | a42ada22b7eb119d64dd436314fe7bc67822fdda5ced1173ec8e2eb260dd41a8 |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | testsuite/python/tabulated.py | Python | gpl-3.0 | 3,589 | [
"ESPResSo"
] | 022cea73c9f987a496aef66a2d30f498b9ff07e92d8b58b5309a3a67793449ed |
"""DataBase models for raspapreco mod1"""
import os
from collections import OrderedDict
from sqlalchemy import (Column, DateTime, ForeignKey, Integer, LargeBinary,
Numeric, PickleType, String, Table, create_engine)
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm impo... | IvanBrasilico/raspa-preco | raspapreco/models/models.py | Python | gpl-3.0 | 6,326 | [
"RASPA"
] | 0924092b94f82cc5218f497d3e93d70e45c7dc3f29ba01667e5e1126bbe40cc4 |
# Based on code Created by Laurens van der Maaten on 20-12-08.
# see point #4
import sys
import numpy
from . import compiled
version = getattr(compiled, 'version_info', (0, 0))
if version < (2, 0):
raise ImportError('Cython module "compiled" is too old, try "python setup.py build_ext -i"')
cythonTSNE = compiled... | utunga/hashmapd | hashmapd/tsne.py | Python | agpl-3.0 | 11,474 | [
"Gaussian"
] | e3182d786ca02bee41bafcbcbde665a081e9d71012ded8db144ab196096325a8 |
#Copyright ReportLab Europe Ltd. 2000-2012
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/platypus/paraparser.py
__version__=''' $Id$ '''
__doc__='''The parser used to process markup within paragraphs'''
import string
import re
import sys
im... | Microvellum/Fluid-Designer | win64-vc/2.78/python/lib/reportlab/platypus/paraparser.py | Python | gpl-3.0 | 45,904 | [
"VisIt"
] | 3ba6304cc14905f4f3ef94a816819f2c8dc3feb6a86e543670274671e6d1ae44 |
r"""
Empirical Power Estimation (:mod:`skbio.stats.power`)
=====================================================
.. currentmodule:: skbio.stats.power
The purpose of this module is to provide empirical, post-hoc power estimation
of normally and non-normally distributed data. It also provides support to
subsample data ... | jairideout/scikit-bio | skbio/stats/power.py | Python | bsd-3-clause | 51,714 | [
"scikit-bio"
] | 654060bb3024a421d45e981ca02a49432f754383fd645d39227f7c5c87fdc4a8 |
# Copyright (C) 2006, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Wrappers for PSEA, a program for secondary structure assignment.
See this citation for... | bryback/quickseq | genescript/Bio/PDB/PSEA.py | Python | mit | 2,755 | [
"Biopython"
] | e4c8ed805e276b4f1319b2e9341cd5ad2848823eded6af23df762e263fbd36b1 |
from django.core.management.base import NoArgsCommand
# from dropbox import rest, session
# from django_dropbox.settings import CONSUMER_KEY, CONSUMER_SECRET, ACCESS_TYPE
from django.conf import settings
from datetime import datetime
import dropbox
import glob, os
_now = datetime.now()
_local = '/RootAir/%s/%s/%s/' %(... | rootAir/rootAir | utils/dropbox.py | Python | gpl-2.0 | 2,765 | [
"VisIt"
] | f10ded3626ed33f6c5bd403e7499f22108e4ad3a26c44ee7d7f8a7fd5defdf9c |
# ==================================================================================================
#
# Copyright (c) 2016, Chen Kian Wee (chenkianwee@gmail.com)
#
# This file is part of py4design
#
# py4design is free software: you can redistribute it and/or modify
# it under the terms of the GNU General ... | chenkianwee/envuo | py4design/urbanformeval.py | Python | gpl-3.0 | 86,231 | [
"EPW"
] | 05dd304cb955f0ad2ad61a918c2af213dd818b28f558d916b76afb376da7f3db |
"""
This module implements the default behavior for the FTS3 system for TPC and source SE selection
"""
import random
from DIRAC.DataManagementSystem.Utilities.DMSHelpers import DMSHelpers
class DefaultFTS3Plugin(object):
""""
Default FTS3 plugin.
For the TPC selection, it returns the list configu... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/private/FTS3Plugins/DefaultFTS3Plugin.py | Python | gpl-3.0 | 4,255 | [
"DIRAC"
] | 0cf7642538d014ff7e2dd7f6c087aaa178a0a839b747ec275e79ad6118942080 |
# coding=utf-8
from __future__ import unicode_literals
from seamless_karma.extensions import db, api
from seamless_karma.models import User
import sqlalchemy as sa
from flask import request
import six
from flask.ext.restful import Resource
from decimal import Decimal
from .decorators import handle_sqlalchemy_errors
fr... | singingwolfboy/seamless-karma | seamless_karma/restful/allocation.py | Python | mit | 4,619 | [
"Brian"
] | c6d35517236702734ffcdc69124854643104d4b56f396b4c896c51598b62a5bf |
from __future__ import print_function
import psi4
from psi4.driver import qcdb
#! A test of the basis specification. Various basis sets are specified outright and in blocks, both
#! orbital and auxiliary. Constructs libmints BasisSet objects through the constructor that calls
#! qcdb.BasisSet infrastructure. Checks th... | amjames/psi4 | samples/python/mints9/input.py | Python | lgpl-3.0 | 4,436 | [
"Psi4"
] | f661056e72a207b0518c4904058cd2706ad7ff23c463a55e1e64cfea7ecec7b0 |
# $Id$
#
# importsym.py: Import C symbol decls (structs, enums, etc) and write them
# to another file
#
# Copyright (C)2013 Teluu Inc. (http://www.teluu.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
# t... | nigusgirma/https-svn.pjsip.org-repos-pjproject-trunk- | pjsip-apps/src/swig/importsym.py | Python | gpl-2.0 | 5,062 | [
"VisIt"
] | dd255722ca646fe6c5e6601769cfc680b07244f216047419ada61192e6c85d2e |
#!/usr/bin/env python3
# Python modules
import calendar
from collections import OrderedDict
import copy
import datetime
import gzip
import logging
import os
import sys
# 3rd party modules
from configobj import ConfigObj
import numpy
import pandas
import pytz
import scipy
import scipy.stats
import xlrd
import xlwt
# che... | OzFlux/PyFluxPro | external/process_isd2nc.py | Python | gpl-3.0 | 40,461 | [
"NetCDF"
] | 198754b4cc1f675130d442df2884253635fe21744bf251bcb674c7ce6ddf8140 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008-2010, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License ... | NetNow/wmi-samba | pysamba/test/connect.py | Python | gpl-2.0 | 1,698 | [
"VisIt"
] | 37425eac944788d529552c34d72385155fe479a48deafd1fdb845be63bd27c8c |
from typing import *
import click
import pros.common.ui as ui
if TYPE_CHECKING:
from sentry_sdk import Client, Hub, Scope # noqa: F401, flake8 issue with "if TYPE_CHECKING"
import jsonpickle.handlers # noqa: F401, flake8 issue, flake8 issue with "if TYPE_CHECKING"
from pros.config.cli_config import Cli... | purduesigbots/pros-cli | pros/common/sentry.py | Python | mpl-2.0 | 5,218 | [
"VisIt"
] | 39ec9a0a9bb263158597af00b9cc9ac7d3d32724cb3f1b560eeb451a2f073c66 |
r"""
I/O utils (:mod:`skbio.io.util`)
================================
.. currentmodule:: skbio.io.util
This module provides utility functions to deal with files and I/O in
general.
Functions
---------
.. autosummary::
:toctree: generated/
open_file
open_files
"""
# ----------------------------------... | Achuth17/scikit-bio | skbio/io/util.py | Python | bsd-3-clause | 3,967 | [
"scikit-bio"
] | 7d5fbb678a43291ae0e2cefc52663bac1c462ed5d30a9a2c73d1c3ff0e29ea22 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function
from .utils.visibility import getLogger
logger = getLogger(__name__)
import logging
plainLogger = logging.getLogger(__name__)
import getpass
import gzip
import hashlib
import io
import os
import re
import ruamel
import shutil
import sys
i... | mhumeSF/ansible-container | container/core.py | Python | lgpl-3.0 | 39,437 | [
"Galaxy"
] | 6c2c8becc4ec324e86eff8d86231da3cb33f7c05bbf47d133aee155221c02ae1 |
import os
import re
from datetime import timedelta
from unittest import skipIf
from django.conf import settings
from django.contrib.contenttypes.models import ContentType
from django.core import mail
from django.core.exceptions import ObjectDoesNotExist
from django.core.urlresolvers import reverse
from django.test im... | CroceRossaItaliana/jorvik | formazione/tests.py | Python | gpl-3.0 | 50,932 | [
"VisIt"
] | b953a972292aff73b3bd9c25b52bc32008c2a4a37b308228c82e86aac36691fa |
import copy
import functools
import json
import logging
import random
import tempfile
from collections import namedtuple
from typing import Any, Callable, Generator, Iterable, List, Text, Union, cast
import schema_salad.validate as validate
from ruamel.yaml.comments import CommentedMap, CommentedSeq
from schema_salad.... | SciDAP/cwltool | cwltool/workflow.py | Python | apache-2.0 | 40,379 | [
"VisIt"
] | e9c50be8ea565757c2a4fc2a96ae1087361718480c83778bdcfbeb6ee83fdd6e |
import os
import json
import numpy as np
from typing import Tuple
from deepchem.utils.data_utils import download_url, get_data_dir
from deepchem.utils.typing import PymatgenStructure
from deepchem.feat import MaterialStructureFeaturizer
from deepchem.feat.graph_data import GraphData
ATOM_INIT_JSON_URL = 'https://deep... | deepchem/deepchem | deepchem/feat/material_featurizers/cgcnn_featurizer.py | Python | mit | 6,686 | [
"CRYSTAL",
"Gaussian",
"pymatgen"
] | 5d232ef31d8480667214359cc807a4dad5c9932bb1514fa230d962361eb7f7a0 |
import numpy.random as random
import numpy as np
from ase import Atoms
from ase.calculators.neighborlist import NeighborList
from ase.structure import bulk
atoms = Atoms(numbers=range(10),
cell=[(0.2, 1.2, 1.4),
(1.4, 0.1, 1.6),
(1.3, 2.0, -0.1)])
atoms.set_scaled_... | slabanja/ase | ase/test/neighbor.py | Python | gpl-2.0 | 2,399 | [
"ASE"
] | 6e722f3057b664f04b6d4dfab65338a01bd701486508baf2c8141f9c24f5580b |
"""Commonly used code by tvtk objects.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2004-2008, Enthought, Inc.
# License: BSD Style.
import types
import sys
import weakref
import os
import logging
import vtk
from traits import api as traits
from traitsui.api import BooleanEditor, RGBCo... | liulion/mayavi | tvtk/tvtk_base.py | Python | bsd-3-clause | 18,274 | [
"VTK"
] | ff856f468ac5a58b3e522cfe843255e92aef2969586970ebe484e294c76ab415 |
from setuptools import setup, find_packages
with open('README.rst') as f:
readme = f.read()
with open('LICENSE') as f:
license = f.read()
setup(
name='isodatetimehandler',
version='1.0.2',
description='An alternate jsonpickle handler for datetime objects.',
long_description=readme,
author='Brian Hammon... | fictorial/jsonpickle-isodatetimehandler | setup.py | Python | mit | 503 | [
"Brian"
] | 61c7e0ee7abb1757f3d2a4f93d0b2516913af52fb5dc5040dc2bb468abdd5483 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
filenames = list()
uGrids = list()
uGrids.append(MakeUnstructuredGrid(vtk.vtkVertex()))
filenames.append("Vertex.vtk")
uGrids.append(MakePolyVertex())
filenames.append("PolyVertex.vtk")
uGrids.append(MakeUnstructuredG... | lorensen/VTKExamples | src/Python/IO/WriteLegacyLinearCells.py | Python | apache-2.0 | 5,185 | [
"VTK"
] | 7eb2c2819b1df6b793438302792b00961c36676bb68a185f544684626d097433 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# restartstore - Back end to restart one or more resource store units
# 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 of... | heromod/migrid | mig/shared/functionality/restartstore.py | Python | gpl-2.0 | 5,626 | [
"Brian"
] | 3abff5d3668b60d4f559d07d57bc7cde29477adb6931da27a2832037666f07ae |
import os
import sys
import subprocess
import pprint
SYS_PATHS = ["/System/", "/usr/lib/"]
class LibraryNotFound(Exception):
pass
class Node:
"""
self.path should be an absolute path to self.name
"""
def __init__(self, name, path="", children=None):
self.name = name
... | yantrabuddhi/FreeCAD | src/Tools/MakeMacBundleRelocatable.py | Python | lgpl-2.1 | 9,205 | [
"VisIt"
] | 164dc4009e3bae3bbb6aa77422f49585a465e74ad6723d7de702182d5094db2e |
import collections
import django_tables2 as tables
from django_tables2.utils import A
from django.db import connection
from django.utils import timezone
from .models import PatientVisit, BillingCode, Provider
TABLE_ATTRIBUTES = {"class": "paleblue"}
TABLE_ATTRIBUTES = {"class": "table table-striped"}
class PatientVis... | craighagan/rvumanager | rvusite/rvu/tables.py | Python | apache-2.0 | 2,775 | [
"VisIt"
] | eee50c325dd938617b585c6963eee99156c7ccd8b3018606dc8c194688902c89 |
""" Unit tests for PathFinder only for functions that I added
"""
import pytest
from diraccfg import CFG
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client import PathFinder
from DIRAC.ConfigurationSystem.Client.Helpers import Operations
from DIRAC.ConfigurationSystem.private.ConfigurationData... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/Client/test/Test_PathFinder.py | Python | gpl-3.0 | 8,432 | [
"DIRAC"
] | f396d5e214b5f1cacb40af2cbf6323985a6fc38053c1d9370d1387fed1d79fe2 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-attributes
# Author : Stuart Paterson
########################################################################
"""
Retrieve attributes associated with the given DIRAC job
Example:
$ dirac-wms-job... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_attributes.py | Python | gpl-3.0 | 2,169 | [
"DIRAC"
] | 78d02a0a8131939693349ceefd27416d5660b3c683819fe3b8623d1b96b8bf97 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | brianmay/python-tldap-debian | tldap/transaction.py | Python | gpl-3.0 | 8,015 | [
"Brian"
] | f205258abcb2c0c6683b49b79bbcfad3744b2de5a7bf399dbbb33f7912a5b10a |
import sys
import hashlib
import pytest
import numpy as np
from numpy.linalg import LinAlgError
from numpy.testing import (
assert_, assert_raises, assert_equal, assert_allclose,
assert_warns, assert_no_warnings, assert_array_equal,
assert_array_almost_equal, suppress_warnings)
from numpy.random import G... | pdebuyl/numpy | numpy/random/tests/test_generator_mt19937.py | Python | bsd-3-clause | 112,949 | [
"Gaussian"
] | ee7d0d04fee099759ae29ce0bf996d4e4e3b5a523e2699f103b7db7d9a49ab3f |
import numpy as np
import os
import pandas as pd
import time
import math
from itertools import chain
import bifacial_radiance
from dask.distributed import Client
from math import sin, cos, radians
# Run simulation using the given timestamp
def simulate_single(clearance_height=None, xgap=None,
tilt... | NREL/bifacial_radiance | bifacial_radiance/HPCScripts/Other Examples (unorganized)/PuertoRico_Original.py | Python | bsd-3-clause | 6,873 | [
"EPW"
] | 1ae09e2dce458019596c1fe4b99140b257219e79ce4a911b73c9ebecb9b6ab61 |
import json
START_CHARACTER = u"Woobeewoo Villagers"
dict_characters = json.loads(open('../problem/graph_nodes.json','rb').read())
dict_episodes = json.loads(open('../problem/graph_vertices.json','rb').read())
def adj(for_character):
return [(character, episode) for episode in dict_characters[for_character] for... | dborzov/practicin | 05 BFS with Finn and Jake/solution/bfs.py | Python | mit | 1,156 | [
"VisIt"
] | 5fe10c66605bd277cd51fde6176ea3f6c5b20ceb8107ef90910636a1f8a794bd |
# -*- 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.
"""Test the MBO method in cclib"""
import sys
import os
import logging
import unittest
import numpy
fro... | cclib/cclib | test/method/testmbo.py | Python | bsd-3-clause | 1,685 | [
"Gaussian",
"cclib"
] | e774b942565280dda52efcaf3ef870f4c2f1830b31c89b6cc3a757f5d03cbe4f |
from django.conf.urls import url, include
from crystal_dashboard.dashboards.crystal.filters import views
from crystal_dashboard.dashboards.crystal.filters.dependencies import urls as dependencies_urls
from crystal_dashboard.dashboards.crystal.filters.filters import urls as filter_urls
urlpatterns = [
url(r'^$', vi... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/filters/urls.py | Python | gpl-3.0 | 508 | [
"CRYSTAL"
] | 9c2916c0df056cee25c07250f86ae77ac92385f0b68d1f3613e906a83ff77cc9 |
# Translation table for Unicode symbols to LaTeX math commands
# for use with the translate() method of unicode objects.
# Includes commands from: standard LaTeX, amssymb, amsmath
uni2tex_table = {
160: u'~',
163: u'\\pounds ',
165: u'\\yen ',
172: u'\\neg ',
174: u'\\circledR ',
177: u'\\pm ',
215: u'\\times ',
240:... | chirilo/remo | vendor-local/lib/python/docutils/math/unimathsymbols2tex.py | Python | bsd-3-clause | 17,496 | [
"Bowtie"
] | e664ae73c973c3acd84c980edcd66b415a90cf67ddfa5c88bb87c6880746de64 |
from __future__ import print_function
# Copyright (C) 2008 CSC - Scientific Computing Ltd.
"""This module defines an ASE interface to VASP.
Developed on the basis of modules by Jussi Enkovaara and John
Kitchin. The path of the directory containing the pseudopotential
directories (potpaw,potpaw_GGA, potpaw_PBE, ...) s... | suttond/MODOI | ase/calculators/vasp.py | Python | lgpl-3.0 | 76,855 | [
"ASE",
"VASP",
"Wannier90"
] | f4e27884f1aa79a70f981f1311df84087a45b623e3e59772ce103071f655b5d4 |
# -*- coding: utf-8 -*-
#----------------------------------------------------------------------------
# Copyright 2017 Marcel Paffrath (Ruhr-Universitaet Bochum, Germany)
#
# This file is part of ActiveSeismoPick3D
#----------------------------------------------------------------------------
import matplotlib.pypl... | seismology-RUB/ASP3D | asp3d/core/seismicArrayPreparation.py | Python | gpl-3.0 | 44,913 | [
"VTK"
] | 1b87c61d1ae615e8b81868b1a7dd5b085109ea5d709f8f23f33e7cff245a7e73 |
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... | ortylp/scipy | scipy/signal/wavelets.py | Python | bsd-3-clause | 10,480 | [
"Gaussian"
] | 3360b27f0ec6893f5be664ab81cccd15f83c9bb8fa2f59fd948f7a1a244c959b |
"""DBF header definition.
TODO:
- handle encoding of the character fields
(encoding information stored in the DBF header)
"""
"""History (most recent first):
16-sep-2010 [als] fromStream: fix century of the last update field
11-feb-2007 [als] added .ignoreErrors
10-feb-2007 [als] added __getitem__: return... | 171121130/SWI | venv/Lib/site-packages/tablib/packages/dbfpy/header.py | Python | mit | 9,388 | [
"VisIt"
] | a0512cae44cdf1b41e7361b816bc540b02530b664fb2805a5cef4eebe1a2d3ed |
import threading
# Because eval(valenc) might require it
import datetime
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import DEncode, List
from DIRAC.Core.Utilities.ReturnValues import isReturnStructure
from DIRAC.Core.Base.ExecutorModule import ExecutorModule
from DIRAC.WorkloadManagementSystem.C... | Sbalbp/DIRAC | WorkloadManagementSystem/Executor/Base/OptimizerExecutor.py | Python | gpl-3.0 | 8,046 | [
"DIRAC"
] | 119acffa4b38c4c16d3f4433c7838fcfb742d13428614157b0eabe56ec318213 |
#!/usr/bin/env python
# Copyright (C) 2014 Open Data ("Open Data" refers to
# one or more of the following companies: Open Data Partners LLC,
# Open Data Research LLC, or Open Data Capital LLC.)
#
# This file is part of Hadrian.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this... | opendatagroup/hadrian | titus/test/lib/model/testNaive.py | Python | apache-2.0 | 11,462 | [
"Gaussian"
] | 3636eed5fff2a2336993725ef7dd91d79318288cf61518cd08c99625fe25cee0 |
# Copyright 2002, 2003 Ben Escoto
#
# This file is part of rdiff-backup.
#
# rdiff-backup is free software; you can redistribute it and/or modify
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2 of the License, or (at your
# option) any later version.
... | Christoph-D/rdiff-backup | rdiff_backup/FilenameMapping.py | Python | gpl-2.0 | 9,067 | [
"VisIt"
] | 219703f8cf8c87bf29f1b78f310277a2fdf39902e16fb6b5fdf2a4e5be9e3055 |
#!/usr/bin/env python
"""Extract start end positions of sequences that blast on transposons
Usage:
program_name <tblastx_result_file>
"""
# Importing modules
import sys
import re
# Parsing user input
try:
infile = sys.argv[1]
except:
print __doc__
sys.exit(1)
# Defining functions
def blastplus(raw... | wkh124/wkh124 | blast_parser_generic.py | Python | gpl-3.0 | 2,491 | [
"BLAST"
] | 39f8bf0543f5287d9162bbe9b8e038efcc22496a0c09cdfa09a38bb053b3a4cb |
#!/usr/bin/env python
"""moose_sim.py:
A cable with 1000 compartments with HH-type channels in it.
Last modified: Wed May 21, 2014 09:51AM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__... | dilawar/moose-full | moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/moose_sim.py | Python | gpl-2.0 | 10,305 | [
"MOOSE"
] | ad473f65299cd3b41703dd1269768e94991748ddd9e433e2be2f93c0f4e44eff |
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