text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# coding: utf-8
# (c) 2015-05-02 Teruhisa Okada
"""
2015/05/02 okada create this file.
2015/06/30 okada update.
# (c) 2015-11-24 Teruhisa Okada
"""
import netCDF4
import numpy as np
from numpy import dtype
from datetime import datetime
import pandas as pd
import romspy
def make_obs_file(ncfile, csvfile, stafile=Non... | okadate/romspy | romspy/make/make_obs_file.py | Python | mit | 9,106 | [
"NetCDF"
] | 9e88546b34ef7ae755afbbcc5317cfff11bbd56f71156233088a0e162aab5420 |
from __future__ import print_function, division, absolute_import
from george import kernels, GP
import numpy as np
from kglib import fitters
from scipy.integrate import quad
from scipy.optimize import minimize
class HistFitter(fitters.Bayesian_LS):
def __init__(self, mcmc_samples, bin_edges):
"""
... | kgullikson88/gullikson-scripts | kglib/fitters/histogram.py | Python | mit | 5,838 | [
"Gaussian"
] | a21cbe6b41efef8700f8be48c915e48abfabc27858fe35f2484dc46e4a89941c |
# MolMod is a collection of molecular modelling tools for python.
# Copyright (C) 2007 - 2008 Toon Verstraelen <Toon.Verstraelen@UGent.be>
#
# This file is part of MolMod.
#
# MolMod 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... | woutersmet/Molmodsummer | lib/molmod/io/dlpoly.py | Python | gpl-3.0 | 9,363 | [
"DL_POLY"
] | 85cbfa274690f56fa53644ef60e69cd996e6d09c706c39e2fcff9bdc4a3ff56e |
#!/usr/bin/env python3
#
# Script to convert DFTB+ MD output to ASE ext-xyz trajectory
# by Patrick Melix
# 2018/02/13
#
# You can import the module and then call .main() or use it as a script
import os
from ase import io
from ase.io.dftb import read_dftb_lattice
def main():
if not os.path.isfile('geo_end.xyz'):
... | patrickmelix/Python4ChemistryTools | dftb+2traj.py | Python | mit | 893 | [
"ASE"
] | f2e7d3118e3a5fd65ab8d645b773662ca48c7146e5bcb14586e02b7cfeb82fcf |
# $Id$
#
# Copyright (C) 2003-2006 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 ... | soerendip42/rdkit | rdkit/Chem/Suppliers/UnitTestSmilesMolSupplier.py | Python | bsd-3-clause | 3,046 | [
"RDKit"
] | 4067bb3f0008c794ae24d2c1213e0e15a75f947aa2beec8aab48ae4e63947be8 |
# Copyright 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Runs Mozilla's Kraken JavaScript benchmark."""
import os
from metrics import power
from telemetry import benchmark
from telemetry.page import page_set
f... | sencha/chromium-spacewalk | tools/perf/benchmarks/kraken.py | Python | bsd-3-clause | 4,952 | [
"Brian",
"Gaussian"
] | 08a53af7a7a6ff10f011384a04b8b2840d3ccd59a5335f18e30d3445500edffb |
#!/usr/bin/env python
CopyRight = '''
/**************************************************************************
*
* Copyright 2010 VMware, Inc.
* All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a
* copy of this software and associated documentation files (the
* "... | execunix/vinos | xsrc/external/mit/MesaLib/dist/src/util/format_srgb.py | Python | apache-2.0 | 4,744 | [
"Brian"
] | 0bb51dfa1d126b930ff6f9a8683cd82c0bbd14e9b47baeb21d1789f5a469d35f |
#%%
from SimPEG import np, Mesh
import SimPEG as simpeg
import time as tm
import vtk, vtk.util.numpy_support as npsup
import re, sys, os
def read_GOCAD_ts(tsfile):
"""Read GOCAD triangulated surface (*.ts) file
INPUT:
tsfile: Triangulated surface
OUTPUT:
vrts : Array of vertices in XYZ coordinates... | simpeg/presentations | SciPy2016/Geological_model/GKR_gocadUtils.py | Python | mit | 6,519 | [
"VTK"
] | 2d6b967432d0f3c6536b432cf3724072eeae72c86dcfead69fe40974c15b6d4c |
# coding: utf-8
from sqlalchemy import (
BINARY,
DECIMAL,
TIMESTAMP,
Column,
Computed,
Date,
DateTime,
Enum,
Float,
ForeignKey,
Index,
LargeBinary,
String,
Table,
Text,
Time,
text,
)
from sqlalchemy.dialects.mysql import (
BIGINT,
INTEGER,
... | DiamondLightSource/ispyb-api | src/ispyb/sqlalchemy/_auto_db_schema.py | Python | apache-2.0 | 191,002 | [
"CRYSTAL"
] | 2b20e027a77a13bb6c7d759603ab2d6f1318308e4d13fd418a301f1f7892db9b |
# -*- coding: utf-8 -*-
import datetime
import re
from PyQt5.QtCore import pyqtSignal, QThread, QMutex
from .xn_page_cache import XNovaPageCache
from .xn_page_dnl import XNovaPageDownload
from .xn_data import XNAccountInfo, XNCoords, XNFlight, XNPlanet, XNPlanetBuildingItem
from .xn_techtree import XNTechTree_instanc... | minlexx/xnovacmd | ui/xnova/xn_world.py | Python | gpl-2.0 | 61,963 | [
"Galaxy"
] | 3602cfcbdb74608d26ff465350429bb26ae1abc17b783faeec3e0ed2a026fa0c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from .errors import GitQLError
class NodeVisitor(object):
@staticmethod
def get_method_name(node):
name = type(node).__name__.lower() # lower() make PEP happy.
if name.endswith('node'):
name = name[:-4]
return 'visit_' + name
... | mackong/gitql | gitql/visitor.py | Python | mit | 612 | [
"VisIt"
] | 2c4ff6ea6bb04e8a31613cb697b57eacb2807e78e9575cde2e77100386da975e |
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, Calour development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------... | RNAer/Calour | calour/_testing.py | Python | bsd-3-clause | 6,427 | [
"OpenMS"
] | 80e312bcdf3e5fc51764e2df426efa2d352460c0d9bc789da5b3dfd774f56f6d |
"""
Neuron Models
"""
import numpy as np
def HodgekinHuxley(x, param):
"""
Computes the differential of the HH states given the current states and the model parameters
:param x: Current state [v(t); m(t); n(t); h(t)]
:type x: np.array
:param param: Hodgkin-Huxley model parameters [I... | cpsnowden/ComputationalNeurodynamics | HH_Braitenberg/NeuronModels.py | Python | gpl-3.0 | 1,536 | [
"NEURON"
] | 882cbea445d9a89fe5f73b10c5a314178323fd519da6e9488ae40131e6322b64 |
""" ComponentMonitoring class is a front-end to the Component monitoring Database
"""
import random
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Utilities import Time, List, Network
__RCSID__ = "$Id$"
class ComponentMonitoringDB(DB):
def __init__(self, requireVoms=F... | fstagni/DIRAC | FrameworkSystem/DB/ComponentMonitoringDB.py | Python | gpl-3.0 | 20,017 | [
"DIRAC"
] | 37d61e09ac239022d15124271270bc5a2e95be579348c5de69206d83b99aa4fb |
#
# ast_body.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, or
# (at your option) any lat... | kperun/nestml | pynestml/meta_model/ast_body.py | Python | gpl-2.0 | 2,508 | [
"NEURON"
] | 6ce59b41d8658a7827d49988344123a2a500993fb74610d4358971b89dc090a0 |
# First-Visit MC Policy Improvement with Exploring Starts
# Author: Yiheng Zhu
# Date: 13th/Dec/2017
import numpy as np
import Gridworld
########################
# Deterministic Policy #
########################
# hyperparameters
GAMMA = 0.9 # discount rate
NUM_EPISODES = 100 # number of episodes
ACTIONS = ('U', 'D'... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/policy_improvement_exploring_starts.py | Python | mit | 5,056 | [
"VisIt"
] | f60be862e40ac2adb65703a448ae2ec23558e1096363a352bb8c2d92c4de55c3 |
# Copyright (C) 2010-2019 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 v... | psci2195/espresso-ffans | samples/visualization_poiseuille.py | Python | gpl-3.0 | 2,161 | [
"ESPResSo"
] | 74e2f0d3960540f482f751ac89f71436abcd5168f64d801d615aa560230caee4 |
# 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.Wise contains modules for running and processing the output of
# some of the models in the Wise2 package by Ewan Birney available from:
# ftp:/... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Wise/__init__.py | Python | apache-2.0 | 3,993 | [
"Biopython"
] | 4251a78b07fc6a67f1daf725837410e569609ba64d2ea360f503fa8a94108854 |
# -*- coding: utf-8 -*-
#The following code assumes that Biopython is installed
from Bio.Seq import Seq
from Bio import motifs
from Bio.Alphabet import IUPAC
#imports the NCBI_utils lib containing the functions for GI accession and BLAST
import MG_synth_lib as MGlib
#random number generation
import random
#mean and s... | ErillLab/CogsNormalizedPosteriorProbabilityThetas | MGtest/permutation_test.py | Python | gpl-3.0 | 11,301 | [
"BLAST",
"Biopython"
] | f995e5e042a60740363053388d53539c374c64c138eaf32d31763e88219defcc |
#!/usr/bin/python2
import optparse
import subprocess
import sys
from builds import GporcaBuild, GpcodegenBuild, GporcacodegenBuild
def make(num_cpus):
return subprocess.call("make -j %d" % (num_cpus), cwd="gpdb_src", shell=True)
def install(output_dir):
subprocess.call("make install", cwd="gpdb_src", shell=T... | CraigHarris/gpdb | concourse/scripts/build_gpdb.py | Python | apache-2.0 | 1,806 | [
"ORCA"
] | 468ef80559a964e56df575ea7f7bb4e509d8a701a4d71dc43d76945246e645ee |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | si618/pi-time | node_modules/grunt-pylint/tasks/lib/pylint/checkers/design_analysis.py | Python | gpl-3.0 | 14,322 | [
"VisIt"
] | 895737fcd4c0e97c1f94fc74a8ac5a07f9086fe14ff7be5b78303c8bd307dd68 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | doc/sphinxman/source/psi4doc/ext/psidomain.py | Python | gpl-2.0 | 1,221 | [
"Psi4"
] | 8fa3d94ff0fe31434539907be3948d69f2d306ad203b14e944d9f73e8d5316bb |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/sources/extractor.py | Python | agpl-3.0 | 34,804 | [
"Galaxy"
] | 931ee6f9934fd33c79a85cf318f329cab7ca5b9443f141ad02a7e816fce51772 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.web_app_test import WebAppTest
from ...pages.lms.account_settings import AccountSettingsPage
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.da... | xingyepei/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 17,287 | [
"VisIt"
] | 91a1ab8bf59abcfb5ebdfdeb428d51a9ad5c576dfdf362ee58f252f46e706b81 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
r"""
This module contains classes useful for analyzing ferroelectric candidates.
The Polarization class can recover the spontaneous polarization using
multiple calculations along a nonpolar to polar ferroelectr... | gmatteo/pymatgen | pymatgen/analysis/ferroelectricity/polarization.py | Python | mit | 19,826 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | 1d30bb5d26ea77e67c47e3a3b79b38767dd8ac53f00289dcdc4d997606c9400d |
#!C:\Python33\python.exe -u
# -*- coding: UTF-8 -*-
# enable debugging
import cgi
import cgitb
cgitb.enable()
import struct
import array
import uuid
import mysql.connector
from mysql.connector import errorcode
import configparser
import re
import http.cookies
import os
def getCharsAndDeaths():
chars = []
form = cgi... | RKYates/Dark-Souls-Death-Count-cgi-page | cgi-bin/results.py | Python | gpl-3.0 | 4,756 | [
"VisIt"
] | 6d211f65f090ce252fa4964c71da4a4322166810295c7657d70d80944217d659 |
"""
Mask R-CNN
The main Mask R-CNN model implementation.
Copyright (c) 2017 Matterport, Inc.
Licensed under the MIT License (see LICENSE for details)
Written by Waleed Abdulla
"""
import os
import random
import datetime
import re
import math
import logging
from collections import OrderedDict
import multiprocessing
im... | agiovann/Constrained_NMF | caiman/source_extraction/volpy/mrcnn/model.py | Python | gpl-2.0 | 127,322 | [
"Gaussian"
] | 553a3c9517649d25aaa5434bd4c17bdc02cb18eb31b5214d61706d375f6451f0 |
#!/usr/bin/env python
'''
Use geomeTRIC library to optimize the molecular geometry.
'''
from pyscf import gto, scf
from pyscf.geomopt.geometric_solver import optimize
mol = gto.M(atom='N 0 0 0; N 0 0 1.2', basis='ccpvdz')
mf = scf.RHF(mol)
#
# geometry optimization for HF. There are two entries to invoke the geome... | gkc1000/pyscf | examples/geomopt/01-geomeTRIC.py | Python | apache-2.0 | 1,061 | [
"PySCF"
] | c98144eb9d3c6ac75ecc6b1f49dc64421afdae442e8637ff01163aeb62248bb4 |
from __future__ import print_function
import unittest
import sys
import os
import numpy as np
import macrodensity as md
import pkg_resources
from os.path import join as path_join
try:
import pandas
has_pandas = True
except ImportError:
has_pandas = False
test_dir = os.path.abspath(os.path.dirname(__file_... | WMD-group/MacroDensity | tests/unit_tests.py | Python | mit | 9,944 | [
"GULP"
] | 066afdc4bd5e22819f88da3dc278f188388865f48b23a216163644356d684ab4 |
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 22 13:22:26 2015
@author: agiovann
"""
#%%
from scipy.ndimage.filters import gaussian_filter
from scipy.ndimage import label
import pylab as pl
import numpy as np
#%%
def extractROIsFromPCAICA(spcomps, numSTD=4, gaussiansigmax=2 , gaussiansigmay=2,thresh=None):
"... | agiovann/CalBlitz | calblitz/rois.py | Python | gpl-3.0 | 2,284 | [
"Gaussian"
] | 8af0c1812bf205500827cdee1cad39ee1710d0030b119c72dc6b21a81d6bfac9 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | eagle/extractor.py | Python | agpl-3.0 | 39,415 | [
"Galaxy",
"Gaussian"
] | 8c5840088af1baec10333e3d1d9603ba77fee319c2a5369e4a9a149c0b5ef15f |
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | GNOME/orca | src/orca/pronunciation_dict.py | Python | lgpl-2.1 | 2,668 | [
"ORCA"
] | c14fd857d8dce249859fdad59ace432101896efbc4b0927bf0e44f78cb6d87bc |
"""
Module to set up run time parameters for Clawpack -- classic code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='classic'):
#--------------------------... | amath574w2015/am574-class | labs/lab4/chap6/wavepacket/setrun.py | Python | bsd-3-clause | 7,233 | [
"Gaussian",
"NetCDF"
] | 0b532fc19c6475fbde34b5309217c284c40fb71f85ac294e9cda6279208ec32f |
#!/usr/bin/env python3
# Copyright 2020 Efabless Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | efabless/openlane | scripts/pfg.py | Python | apache-2.0 | 106,511 | [
"Galaxy"
] | 924c61ae0e275292cd21a8c2cd2366101090671dbd2e736da8a2cacfa1cd0dde |
import numpy as np
from unittest import TestCase
from os import sep, remove, rmdir
from tempfile import mkdtemp
import tarfile
from glob import glob
from exatomic.base import resource
from exatomic.va import VA, get_data, gen_delta
from exatomic.gaussian import Fchk, Output as gOutput
from exatomic.nwchem import Output... | exa-analytics/atomic | exatomic/va/tests/test_va.py | Python | apache-2.0 | 24,233 | [
"Gaussian",
"NWChem"
] | 6b1e6f0c6a58301eb9eb0ad159381afdca0de58d64f81dd0d3375fada98bf516 |
import string
import numpy
from os import path
from orbkit.units import u_to_me
nist_mass = None
# Standard atomic masses as "Linearized ASCII Output", see http://physics.nist.gov
nist_file = path.join(path.dirname(path.realpath(__file__)),
'supporting_data/Atomic_Weights_NIST.html')
# see http:... | orbkit/orbkit | orbkit/tools.py | Python | lgpl-3.0 | 10,554 | [
"Gaussian",
"Molpro"
] | e769b3781adae15d69e5e0c2751aea0f0194030d22e386c7646b74e981a272e8 |
from __future__ import division, print_function, absolute_import
import numpy as np
import warnings
from scipy._lib._util import check_random_state
def rvs_ratio_uniforms(pdf, umax, vmin, vmax, size=1, c=0, random_state=None):
"""
Generate random samples from a probability density function using the
rati... | arokem/scipy | scipy/stats/_rvs_sampling.py | Python | bsd-3-clause | 7,146 | [
"Gaussian"
] | 9b8b1bb0416299aab11c034e82df903c7db127661c9aa4785d7f357444d23303 |
import hashlib
from tango.ast import *
from tango.builtin import Int, Double, String
from tango.types import FunctionType, NominalType, TypeUnion
def transpile(module, header_stream, source_stream):
transpiler = Transpiler(header_stream, source_stream)
transpiler.visit(module)
def compatibilize(name):
... | kyouko-taiga/tango | tango/transpilers/cpp.py | Python | apache-2.0 | 8,789 | [
"VisIt"
] | 7068fa2b5c19e2d9e6720e3e789bef7c32ee591782622a4835166b69a7cca1d5 |
#!/usr/bin/env python
import argparse
from dataclasses import dataclass
import os
from pathlib import Path
import shutil
import sys
import time
import traceback
import orjson
import numpy as np
import psutil
from pysisyphus.calculators import XTB
from pysisyphus.constants import AU2KJPERMOL
from pysisyphus.cos.Growi... | eljost/pysisyphus | scripts/crest_gnts.py | Python | gpl-3.0 | 7,690 | [
"xTB"
] | db46fa656b4ddbbb084669ac0cb5c39841c0579ded86a73a3aded8158034eec6 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for CMS Video Module.
"""
import os
from mock import patch
from nose.plugins.attrib import attr
from unittest import skipIf
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.studio.video.video import Vid... | adoosii/edx-platform | common/test/acceptance/tests/video/test_studio_video_module.py | Python | agpl-3.0 | 11,604 | [
"VisIt"
] | 9d1597fd77a90b0a27240e696796b46cefae770b3689a12ce5163f83b8e4b071 |
"""
"""
import numpy
import theano
import theano.tensor as T
from pythonDnn.layers.logistic_sgd import LogisticRegression
from pythonDnn.layers.mlp import HiddenLayer
from pythonDnn.layers.rbm import RBM, GBRBM
from pythonDnn.models import nnet
class DBN(nnet):
"""Deep Belief Network
A deep belief network ... | IITM-DONLAB/python-dnn | src/pythonDnn/models/dbn.py | Python | apache-2.0 | 8,684 | [
"Gaussian"
] | a56e200639f49f3b92d841d01f862ca13e2b81ffb161539c59a5f28f223ed231 |
#!/usr/bin/env python
#Schedule is Call, Long, Short, MVSC, Vacation
import numpy as np
import itertools
import random
import sys
import math
import logging
def gen_permutations(n, mvsc_list): #Generate all possible combinations for a week's schedule
p = itertools.permutations(list(range(1,n+1)))
temp = np.a... | jbolinge/scheduler | scheduler.py | Python | lgpl-3.0 | 6,098 | [
"Brian"
] | 58adb3d69f0f12d22ffa7993cd331d04f0af75beb56153a5b4f26c66d6153546 |
#!/usr/bin/env python3
"""
Smooth one or more labels within an integer atlas volume
Usage
----
smooth_labels.py -i <input label image> -o <output label image> [label numbers]
smooth_labels.py -h
Example
----
>>> smooth_labels.py -i atlas.nii.gz -o atlas_smooth_5.nii.gz 5 10 11
Authors
----
Mike Tyszka, Caltech Brain... | jmtyszka/atlaskit | smooth_labels.py | Python | gpl-3.0 | 3,435 | [
"Gaussian"
] | e9c654ec9c7b2bc6248f3be708a62af0b32bba9f46a7b8e72e086d0d5b9c366e |
import requests
from lxml import html
import datetime
import inflect
from docx import Document
from docx.shared import Inches
from PyQt4 import QtGui, uic
from PyQt4.QtGui import QTableWidgetItem, QApplication, QColor, QIcon, QPushButton, QHBoxLayout, QAction
from PyQt4.QtCore import QDate, QTimer, QSize, Qt
import sys... | CoronalRain/Saga | saga.py | Python | gpl-3.0 | 20,417 | [
"VisIt"
] | f1346c8eeb2694d9a3cb28ffd90d3cc9bb1722250df290e57a0efad008925346 |
# -*- coding: utf-8 -*-
"""
General class for parsing different DEMs
Created on Mon Sep 10 14:43:26 2012
@author: mrayson
"""
import numpy as np
from netCDF4 import Dataset
from scipy import spatial
import matplotlib.pyplot as plt
from interpXYZ import tile_vector
import time
import shutil
import gda... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/GIS/dem.py | Python | mit | 12,866 | [
"NetCDF"
] | 9f39541c1688548e0b5899aa29b06abe14a3a0a068e9fabe1b50fca359a3903c |
#!/usr/bin/env python
#
# This file is part of OpenDrift.
#
# OpenDrift 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, version 2
#
# OpenDrift is distributed in the hope that it will be useful,
# but WITHOU... | knutfrode/opendrift | opendrift/scripts/readerinfo.py | Python | gpl-2.0 | 4,321 | [
"NetCDF"
] | b358595a4b7ec6e64dc957793637252c3a559253d19a37e6e36fc3a17ab24337 |
#!/bin/env python
"""
Tests for Bdii2CSAgent module
"""
import unittest
from mock import MagicMock as Mock, patch
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Agent import Bdii2CSAgent
MODNAME= "DIRAC.ConfigurationSystem.Agent.Bdii2CSAgent"
MAINBDII = { 'site1': {'CEs': { 'ce1': { 'Queues': { 'que... | fstagni/DIRAC | ConfigurationSystem/Agent/test/Test_Bdii2CS.py | Python | gpl-3.0 | 5,058 | [
"DIRAC"
] | fac53fa97ad6119df5057a6636ae3c5fcaeda0fae71c0a16a7b5f71f7ac63a5a |
# 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, software
# d... | openstack/rally | tests/unit/test_mock.py | Python | apache-2.0 | 12,518 | [
"VisIt"
] | d43c80152a03699bfb04e979e326d94dfa990efef9f240a13e6b5e7fb97670ae |
# -*- coding: utf-8 -*-
#
# glif_psc_neuron.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... | hakonsbm/nest-simulator | pynest/examples/glif_psc_neuron.py | Python | gpl-2.0 | 9,614 | [
"NEURON"
] | affc5edaa644144f9ffd12953f5b9d88b46318a05070a32198bfae0ba3aebeae |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
import os, sys, time
from PyQt5.QtCore import Qt, QThread, QObject, pyqtSignal, pyqtSlot, QObjectCleanupHandler
from PyQt5.QtWidgets import QApplication, QWidget, QGridLayout, QStackedLayout, QLayout, QTextEdit
from PyQt5.QtGui import QPixmap, QPalette, QBrush
from fsSocket... | neksysinfo/fspanel | fsPanel.py | Python | gpl-3.0 | 7,462 | [
"ADF"
] | 1cdf3fe9b0c7f8fd0b550f4cf46db2bba586beb070829f51e59255cd042eec59 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
sessions2trash.py
Run this script in a web2py environment shell e.g. python web2py.py -S app
If models are loaded (-M option) auth.settings.expiration is assumed
for sessions without an expiration. If models are not loaded, sessions older
than 60 minutes are removed. U... | andersonsilvade/python_C | Python32/web2py/scripts/sessions2trash.py | Python | mit | 6,674 | [
"VisIt"
] | 3d152439ac0b36b665316a9c11007f7775c80aa7250e60a987a9cf66cd71f690 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# this script tests vtkImageSlab with various axes permutations,
# in order to cover a nasty set of "if" statements that check
# the intersections of the raster lines with the input b... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestImageProjection.py | Python | gpl-3.0 | 4,660 | [
"VTK"
] | 65232acfcd64a0bcfbf07c6e2a5013981a7231c85d0a5025850ee31d3fcdc61d |
#BEGIN_HEADER
import sys
import os
import glob
import json
#sys.path.insert(0, '/kb/dev_container/modules/genome_util/lib/biokbase/genome_util')
import script_util
#from biokbase.workspace.client import Workspace
#from workspace.client import Workspace
#END_HEADER
class KBaseGenomeUtil:
'''
Module Name:
... | pranjan77/genome_util | lib/biokbase/genome_util/KBaseGenomeUtilImpl.py | Python | mit | 4,192 | [
"BLAST"
] | c5a3f3bb7b8979be04367044b2a196bac2cd1a7050828b86be3937fe71ccedcf |
from flask import Blueprint, make_response, render_template
from octopus.core import app
blueprint = Blueprint('configjs', __name__)
# this allows us to serve our standard javascript config
@blueprint.route("/javascript/config.js")
def javascript_config():
configs = {}
for key, val in app.config.iteritems():... | JiscPER/magnificent-octopus | octopus/modules/clientjs/configjs.py | Python | apache-2.0 | 566 | [
"Octopus"
] | f3eb6d8998e71179d76750bd2279acbcf374baf43e53feb0232f418b48c929e9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__all__ = []
from molecules import Molecule
def plot_maya( mol, key = lambda x: (x[0].r, x[1].r, x[2].r),
copy = True ):
"""Wrapper function to plot quivers of beta
For Residue
at1 is the first atom to center around
at2 is the atom which wi... | fishstamp82/moltools | moltools/plot_functions.py | Python | mit | 1,470 | [
"Mayavi"
] | f2d60d61eabd55c5274c1b3e0670b0a95f96d0770486c63bbedaf4d94dbb4a99 |
#!/usr/bin/python
#
# CCLib_proxy Utilities
# Copyright (c) 2014 Ioannis Charalampidis
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | wavesoft/CCLib | Python/cc_resume.py | Python | gpl-3.0 | 1,430 | [
"cclib"
] | 5ad00fe5793757b0f02bebd6713e94891657ac200b2547e31610c011ca391441 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/__init__.py | Python | lgpl-3.0 | 1,868 | [
"Psi4"
] | 1b838261ad5dd47fafbc3fc989db8332443e6c206470590595ec14e3f38ba0af |
# coding: utf-8
#
# Copyright 2014 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | NAMD/pypln.backend | pypln/backend/workers/word_cloud.py | Python | gpl-3.0 | 1,702 | [
"NAMD"
] | 212d243eb11c69b7f9a3aad04ba63ab47a2e4be0d0edb6855268c5fac7be904c |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.analysis.hhi import HHIModel
class HHIModelTest(unittest.TestCase):
def test_hhi(self):
hhi = HHIModel()
self.assertEqual(hhi.get_hhi("He"), (3200, 3900))
self.asser... | vorwerkc/pymatgen | pymatgen/analysis/tests/test_hhi.py | Python | mit | 874 | [
"pymatgen"
] | 5245d3d0cddcd9dd6e74a893342ea5f33a5a8ca214fe9696abac3d85034666f3 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/tree/_nj.py | Python | bsd-3-clause | 10,946 | [
"scikit-bio"
] | 7fa8f2485f6767dd5ac0171b9542e9a8635989c3c9255b575df4f10d824cf5b9 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk, pango
from zeroinstall import _, translation
from zeroinstall.support import tasks, pretty_size
from zeroinstall.injector import model, reader, download
from zeroinstall.gui import properties
from zeroins... | linuxmidhun/0install | zeroinstall/gui/iface_browser.py | Python | lgpl-2.1 | 18,312 | [
"VisIt"
] | a5bd1f345269e071bdff139efba1119e7a98a1a478d0e5870adbeac87e02d093 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | leezu/mxnet | tests/python/unittest/test_gluon_probability_v1.py | Python | apache-2.0 | 97,927 | [
"Gaussian"
] | 4599ce21c2a4170558d3008816222ce754ba0474bf060cd19fa45f5e988fd957 |
#Purpose: To implement a suite of 3D shape statistics and to use them for point
#cloud classification
#TODO: Fill in all of this code for group assignment 2
import sys
sys.path.append("S3DGLPy")
from Primitives3D import *
from PolyMesh import *
import numpy as np
import matplotlib.pyplot as plt
POINTCLOUD_CLASSES = [... | stevenyy/ShapeGoogle | ShapeStatistics.py | Python | mit | 23,901 | [
"Gaussian"
] | 894a80902a064d334cfdb64a362a714b1be9e1117ac9522d2ed2d91041566ed6 |
#============================================================================
#
# Copyright (c) Kitware Inc.
#
# 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... | agirault/VesselView | Modules/Scripted/InteractiveSegmentTubes/InteractiveSegmentTubesLogic/SegmentTubesLogic.py | Python | apache-2.0 | 5,566 | [
"VTK"
] | 7171d756667e0c390af0fee0d5e83f6d5c9a54f7a0a15fc1a784f10481c9afb0 |
#!/usr/bin/env python
"""Multithreaded interactive interpreter with GTK and Matplotlib support.
Usage:
pyint-gtk.py -> starts shell with gtk thread running separately
pyint-gtk.py -pylab [filename] -> initializes matplotlib, optionally running
the named file. The shell starts after the file is executed.
Thre... | sniemi/SamPy | sandbox/src1/examples/interactive.py | Python | bsd-2-clause | 7,867 | [
"Brian"
] | 0680ba0cc9602edaa9e79e436bd8099ad23fe29e43c0bd70982f1f4b40d6de91 |
#########################################################
#
# DO NOT EDIT THIS FILE. IT IS GENERATED AUTOMATICALLY. #
# PLEASE LOOK INTO THE README FOR MORE INFORMATION. #
#
#########################################################
# coding: utf-8
# # Caffe2 Basic Concepts - Operators & Nets
#
# In this tutoria... | Yangqing/caffe2 | caffe2/python/tutorials/py_gen/Basics.py | Python | apache-2.0 | 13,139 | [
"Gaussian"
] | c362eaaa45b0b7bf8adfc0bdde88f9e06cc29d105f4673f347ec1f7e19f7a7c7 |
# ---
# jupyter:
# jupytext:
# formats: ipynb,.pct.py:percent
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.3.3
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
# %% [markdown]
... | GPflow/GPflow | doc/source/notebooks/basics/classification.pct.py | Python | apache-2.0 | 9,219 | [
"Gaussian"
] | 4c4ecbbae563e85407600e6d82b532ba967134e9b10f850e7db28ec651d88146 |
##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | hpcugent/easybuild-easyblocks | easybuild/easyblocks/c/cp2k.py | Python | gpl-2.0 | 39,559 | [
"CP2K"
] | e6880856a8e2e7d51010a63ce8ad1f992bb4bd1ff66526626f5be5d8625a1a79 |
#!/usr/bin/env python
#
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2013, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public v... | Clyde-fare/cclib_bak | setup.py | Python | lgpl-2.1 | 3,486 | [
"ADF",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"ORCA",
"cclib"
] | 0a5382f48b3224d4ac37611aafe11a859975556326ee9c42e23f765f90df8136 |
# -*- coding: utf-8 -*-
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope tha... | AdamWill/bodhi | bodhi/tests/server/services/test_updates.py | Python | gpl-2.0 | 144,771 | [
"VisIt"
] | ef1d62949eb76a1f1cc3f09910aff4793015c9815a78db76b34fbc191386663b |
from itertools import chain
import json
import os
import sys
from core import fasta
json_format_version = 'mdrscan/json/0.4.0'
def get_program(blast_output):
for line in blast_output:
words = line.split()
if words:
return words[0]
def get_database(blast_output):
for line in bla... | BILS/agda | agda/datisca/parse_blast.py | Python | mit | 4,756 | [
"BLAST"
] | 2a1ca59d0838e7b23578b5cb8abcbac677307679dd08d40db99f980452f1102b |
"""Multiple views testing."""
# pylint: disable=unused-argument,redefined-outer-name,invalid-name
from time import sleep
from numpy import random as rng
import pandas as pd
import pytest
from bowtie import App, View
from bowtie.control import Nouislider, Button
from bowtie.visual import Table
from bowtie.tests.utils... | jwkvam/bowtie | bowtie/tests/test_multiple.py | Python | mit | 2,332 | [
"Bowtie"
] | 3bf70eaf81eb0785b7f2228c2f213e2089e2bacd9718102d68937b5a3e5ff6f0 |
# -*- coding: utf-8 -*-
import pytest
from ..helpers.movie_data import Movie,Actor,Director
from .fixtures import backend
from blitzdb.backends.sql.relations import ManyToManyProxy
def prepare_data(backend):
backend.init_schema()
backend.create_schema()
francis_coppola = Director({'name' : 'Francis Co... | M4rtinK/tsubame | core/bundle/blitzdb/tests/sql/test_intersect.py | Python | gpl-3.0 | 2,887 | [
"Brian"
] | c191c96e922266fb2481f9dffbb6b20dba8481fc7367448b482866190cf20507 |
import logging
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
from astropy import units as u
from ipywidgets import fixed, interact
from ._utils import which_epi_janus_resonance
from .meta import get_all_resonances
from .ringcube import RingCube
logger = logging.getLogger(__name__)
res... | michaelaye/pyciss | pyciss/plotting.py | Python | isc | 9,363 | [
"Gaussian"
] | 455a071ad88f3e8131edcc08d7da56653a8b73a0345d841aca36855c563704e3 |
from __future__ import print_function
import os
import sys
from six import StringIO
import unittest2 as unittest
from nose.plugins.attrib import attr
from contextlib import contextmanager
from jnpr.junos import Device
from jnpr.junos.exception import RpcError, SwRollbackError, RpcTimeoutError
from jnpr.junos.utils.sw i... | pklimai/py-junos-eznc | tests/unit/utils/test_sw.py | Python | apache-2.0 | 40,404 | [
"Firefly"
] | 312a85894f1bf4344b29761caad7249b93ee1c750ca241f1d2dfbd798bfb933a |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawLoops(myscreen, loops, loopcolor):
nloop = 0
for lop in loops:
n = 0
N = len(lop)
first_point=ocl.Point(-1,-1,5)
previous=ocl.Point(-1,-1,5)
for p in lop:
if n==0: # don't dra... | aewallin/opencamlib | examples/python/waterline/waterline_7_cavity.py | Python | lgpl-2.1 | 3,896 | [
"VTK"
] | c0e42dc951bf1689c350760c65aa5479a5ff53fd813bc6183c816648034a0891 |
# -*- coding: utf-8 -*-
"""
http://www.astroml.org/sklearn_tutorial/dimensionality_reduction.html
"""
print (__doc__)
import numpy as np
import copy
from sklearn.cluster import k_means
from sklearn.manifold import spectral_embedding
from sklearn.utils import check_random_state
import nslkdd.preprocessing as preproce... | zedoul/AnomalyDetection | test_discretization/test_affinity.py | Python | mit | 1,535 | [
"Gaussian"
] | 6a3348e132511bfa91180ba504637c7210a6cb22372aac28670232d3a87c0c4d |
"""
IO for ADF files.
"""
import os
import re
from monty.io import reverse_readline
from monty.itertools import chunks
from monty.json import MSONable
from pymatgen.core.structure import Molecule
__author__ = "Xin Chen, chenxin13@mails.tsinghua.edu.cn"
def is_numeric(s):
"""
Return True is the string ``s`... | vorwerkc/pymatgen | pymatgen/io/adf.py | Python | mit | 31,369 | [
"ADF",
"Gaussian",
"NWChem",
"pymatgen"
] | 7c568b63766fa3a14a976fbb2374d8c3eb5ad439535fa7144040bd8fc2c00fb2 |
"""Test string and unicode support in VTK-Python
The following string features have to be tested for string and unicode
- Pass a string arg by value
- Pass a string arg by reference
- Return a string arg by value
- Return a string arg by reference
The following features are not supported
- Pointers to strings, arrays... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Common/Core/Testing/Python/TestStrings.py | Python | gpl-3.0 | 3,620 | [
"VTK"
] | 8599af3c0738c74a43cb1b6eaa2aca4052a0559325bb39cd74fd28ab9a2796d0 |
#!/usr/bin/env python
"""
Created on Jun 19, 2012
"""
import unittest
import os
import warnings
from pymongo import MongoClient
from pymongo.errors import ConnectionFailure
from pymatgen.apps.borg.queen import BorgQueen
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.electronic_structure.... | materialsproject/pymatgen-db | pymatgen/db/tests/test_creator_and_query_engine.py | Python | mit | 7,165 | [
"pymatgen"
] | 4402286ba2dc87a4617e7b8420e9401ce4fd36c1ba02985be46fd27efb342e4b |
# coding: utf-8
# In[46]:
##imports
import numpy as np
import networkx as nx
import math
import matplotlib.pyplot as plt
# In[1]:
#function to generate real valued som for graph input
def initialise_network(X, num_neurons, w):
#network will be a one dimensional list
network = nx.Graph()
#dim... | DavidMcDonald1993/ghsom | som_functions.py | Python | gpl-2.0 | 15,610 | [
"NEURON",
"VisIt"
] | beb903436a577964b50887e9a04aaa0e317e81187a2ce056ea5c0ae9f00f4b67 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Nodes for PPAPI IDL AST"""
#
# IDL Node
#
# IDL Node defines the IDLAttribute and IDLNode objects which are constructed
# by th... | GeyerA/android_external_chromium_org | ppapi/generators/idl_node.py | Python | bsd-3-clause | 14,696 | [
"VisIt"
] | 407fe5793af98f6f255c1975d40b153ac6d94e505f7ae01a9b9ac991350ff687 |
#!/usr/local/bin/python -i
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this... | eddiejessup/pizza | src/pizza.py | Python | gpl-2.0 | 13,329 | [
"RasMol"
] | 201019a3f953621232d5ce7816c2fb1e61e5941610c219fdfce3ddee782949e9 |
#!/usr/bin/env python
import os.path
import time
import fitsio
import astropy.io.fits as pyfits
import opscore.protocols.keys as keys
import opscore.protocols.types as types
from opscore.utility.qstr import qstr
import actorcore.utility.fits as actorFits
class HxCmd(object):
def __init__(self, actor):
... | CraigLoomis/ics_hxActor | python/hxActor/Commands/HxCmd.py | Python | mit | 14,461 | [
"VisIt"
] | 1762f3b0798c939e450201f518c8eb121bcf617b298d90e6c0cb0361fdebd769 |
""" Handling of the local glacier map and masks. Defines the first tasks
to be realized by any OGGM pre-processing workflow.
"""
# Built ins
import os
import logging
import warnings
from distutils.version import LooseVersion
from functools import partial
# External libs
import numpy as np
import shapely.ops
import pa... | TimoRoth/oggm | oggm/core/gis.py | Python | bsd-3-clause | 55,626 | [
"Gaussian",
"NetCDF"
] | 8cd35807458690fcd72fa6d852f8b5cd63ac9c5febbe2edb564f9efc2cd940b5 |
# -*- coding: UTF-8 -*-
# Practical 5
# Galaxy Data Structures
gMap = [[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]
name = ""
coords = (0, 0)
data = {}
def recruit(name, coords):
data[name] = coords
row = gMap[coords[1]]
row[coords[0]] = "E"
def retire(name):
... | AlexNewson/UniPracticals | Solutions/Practical 5/Excercise.py | Python | mit | 1,655 | [
"Galaxy"
] | a95c732aac56d32beac86f0e5395d0d8d864b894f02a3fbec4a0dfda2654fb85 |
#!/usr/bin/env python
# An example from scipy cookbook demonstrating the use of numpy arrys in vtk
import vtk
from numpy import *
basename = "output"
infofile = basename+".txt"
filename = basename+".raw"
f = open(infofile,"r")
nx,ny,nz = [int(x) for x in f.readline().split()]
f.close()
print nx,ny,nz
data = fromfil... | egaburov/volren | astra/render.py | Python | apache-2.0 | 5,161 | [
"VTK"
] | 6e14bd77bf694bcc16c6c9a880405cf0dc165eb156aeecaf287240655276493e |
"""
Created on Thurs, 9/04/2014
@author: mdistasio
Uses BioPython
"""
import os
import glob
import math
import random
import re
import numpy as np
import itertools
import subprocess
class Shuffler:
def __init__(self, p):
#p = Paths object (from mmdSetPaths.py)
np.set_printoptions(suppress=True)... | ChellyD65/shoelace | python/shoelace/lib/Shuffler.py | Python | gpl-2.0 | 4,694 | [
"Biopython"
] | a93336772b0a97835ce584c0a8f1fb4e312364bb32f4d0f98dd25ce34f43dbae |
#!/usr/bin/env python
"""
Utilities for using M2Crypto SSL with DIRAC.
"""
import os
import tempfile
from M2Crypto import SSL, m2, X509
from DIRAC.Core.DISET import DEFAULT_SSL_CIPHERS, DEFAULT_SSL_METHODS
from DIRAC.Core.Security import Locations
from DIRAC.Core.Security.m2crypto.X509Chain import X509Chain
# Verify ... | DIRACGrid/DIRAC | src/DIRAC/Core/DISET/private/Transports/SSL/M2Utils.py | Python | gpl-3.0 | 8,509 | [
"DIRAC"
] | f47da441c2f9e1874e822acfc6a8a47c47c942233180fa9622e6a03138ac78c0 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | modules/geochemistry/python/readers/reader_utils.py | Python | lgpl-2.1 | 5,815 | [
"MOOSE"
] | a0ef1ed7af9e4a5422a9a995c03f6cdcbcc2122712e3552b8912c82120993b82 |
import numpy as np
from DesOptPy.scaling import denormalize
def OptSciPy(self, x0, xL, xU, SysEq):
def ObjFnSciPy(xVal):
if xVal.tolist() in [ list(item) for item in self.xAll ]:
i = np.where((self.xAll == xVal).all(axis=1))[0][0]
fVal = self.fAll[i].copy()
else:
... | e-dub/DesOptPy | DesOptPy/interfaces/SciPy.py | Python | gpl-3.0 | 8,414 | [
"VisIt"
] | 0a27770d9aa4022dcbf836fbce1f49af7d7c07923777fac43d6febfaa3dccc83 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# userscriptgen - Generator backend for user scripts
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General ... | heromod/migrid | mig/shared/userscriptgen.py | Python | gpl-2.0 | 129,151 | [
"Brian"
] | 7443fca7c51a3c50458c8b8728f275d7569bd5a68a2acc75f1951d355d571318 |
# Copyright (C) 2012-2016 Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011 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 the GNU General Public License ... | espressopp/espressopp | src/interaction/LJcos.py | Python | gpl-3.0 | 10,827 | [
"ESPResSo"
] | fe3baca224d5d88f56744b4f0e588e504a8c8d1c7428ed54a130ae78026619c9 |
"""Base classes for parameters of algorithms with biomod functionality"""
from zope.interface import provider
from zope.schema.vocabulary import SimpleVocabulary, SimpleTerm
from zope.schema.interfaces import IVocabularyFactory
brt_var_monotone_vocab = SimpleVocabulary([
SimpleTerm(-1, '-1', u'-1'),
SimpleTe... | BCCVL/org.bccvl.compute | src/org/bccvl/compute/vocabularies.py | Python | gpl-2.0 | 1,461 | [
"Gaussian"
] | d9c67aebeb1c568209529914ff0184664674386b8789d3ff52e59492f717f6a6 |
"""This module defines a linear response TDDFT-class.
"""
from math import sqrt
import sys
import numpy as np
from ase.units import Hartree
import _gpaw
import gpaw.mpi as mpi
MASTER = mpi.MASTER
from gpaw import debug
from gpaw.poisson import PoissonSolver
from gpaw.output import initialize_text_stream
from gpaw.lr... | ajylee/gpaw-rtxs | gpaw/lrtddft/__init__.py | Python | gpl-3.0 | 15,015 | [
"ASE",
"GPAW"
] | a1b0a28dfc325fae0d4bb1a493dc7b6a11f8be2fdec4f0ca5ab0d62efa142187 |
"""
BoltzTraT2 is a python software interpolating band structures and
computing materials properties from dft band structure using Boltzmann
semi-classical transport theory.
This module provides a pymatgen interface to BoltzTraT2.
Some of the code is written following the examples provided in BoltzTraP2
BoltzTraT2 has... | gVallverdu/pymatgen | pymatgen/electronic_structure/boltztrap2.py | Python | mit | 31,894 | [
"ASE",
"BoltzTrap",
"VASP",
"pymatgen"
] | 01f0ee216abedaecc4be5ca501fbd41b138a2e95066c3896c62463a0486865b5 |
'''apport package hook for min12xxw
(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_min12xxw.py | Python | gpl-3.0 | 216 | [
"Brian"
] | 1c8df8337a5f23858bc46aedccb07a2a1d4b14f4c0efbb5da6ee0b76ecdad9b1 |
#! /usr/bin/env python
#import __main__
#__main__.pymol_argv = ['pymol','-qc']
##__main__.pymol_argv = ['pymol','']
#import sys,time,os
#import pymol
#
#pymol.finish_launching()
#pymol.cmd.feedback("disable","all","actions")
#pymol.cmd.feedback("disable","all","results")
#sys.path.append("/home/scratch/software/Pymol-... | demharters/git_scripts | dist_rna_me1.py | Python | apache-2.0 | 1,413 | [
"MDAnalysis",
"PyMOL"
] | 08ca39763f1ae87b7eb88ebe6c73934bbcbf6e4c134550acf7630e851fb32635 |
# Copyright (C) 2004-2008 Paul Cochrane
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distribut... | paultcochrane/pyvisi | examples/imageLoadExample.py | Python | gpl-2.0 | 3,883 | [
"VTK"
] | 1a4736d379c5b464ecd8dcd55f044e22070ad14d6dead292b22dfd6dcd92ccb2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
r""" A JSON data encoder and decoder.
This Python module implements the JSON (http://json.org/) data
encoding format; a subset of ECMAScript (aka JavaScript) for encoding
primitive data types (numbers, strings, booleans, lists, and
associative arrays) in a language-n... | vorburger/mcedit2 | src/mceditlib/util/demjson.py | Python | bsd-3-clause | 247,568 | [
"CDK"
] | 5d04f76a4c2189a6967895fbe94893e058ac6b6e016aa322daf6ff2f218e1fd6 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.