text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | jiobert/python | Smith_Ben/Assignments/flaskolympics/olympics7/server.py | Python | mit | 964 | [
"CASINO"
] | cca23293ec4e3b102e4619d551806f083c9c4d12d6dcaaff9421602202bdedae |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2010-2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2017 Francois Beaune, The appleseedhq Organi... | aytekaman/appleseed | scripts/appleseed.benchmark.py | Python | mit | 5,824 | [
"VisIt"
] | 42dd31c482fcad0f176756f4579bf5344feb1ec1f98b63b52fbb05d0de51664e |
# -*- coding: utf-8 -*-
"""
End-to-end tests related to the cohort management on the LMS Instructor Dashboard
"""
import csv
import os
import os.path
import uuid
from datetime import datetime
import six
import unicodecsv
from bok_choy.promise import EmptyPromise
from pytz import UTC, utc
from common.test.acceptance... | appsembler/edx-platform | common/test/acceptance/tests/discussion/test_cohort_management.py | Python | agpl-3.0 | 41,806 | [
"VisIt"
] | 1c1aa29fcb6897ebd6aa4b4e96622db0eaec818499cabe440f7b03416ba18ae0 |
"""Tests that :class:`aflow.entries.Entry` objects have the correct
attributes and that lazy fetching works correctly.
"""
import pytest
def test_eq_hash(paper):
"""Tests equality and hashing of database entries.
"""
paper.reset_iter()
a = paper[0]
assert a == a
assert hash(a) == hash(a.auid)
... | rosenbrockc/aflow | tests/test_entries.py | Python | mit | 4,263 | [
"ASE"
] | 73041dfe2dc689c6b588f4ec934a258f8ab8f109d1d4293349e22545ed115274 |
#!/bin/python
import vtk
import vtk.util.colors
points = vtk.vtkPoints()
points.InsertNextPoint(0, 0, 0)
points.InsertNextPoint(0, 1, 0)
points.InsertNextPoint(1, 0, 0)
points.InsertNextPoint(0, 0, 1)
unstructuredGrid = vtk.vtkUnstructuredGrid()
unstructuredGrid.SetPoints(points)
unstructuredGrid.InsertNextCell(vtk.... | trianam/tests | python/vtkInteractorStyles.py | Python | gpl-2.0 | 1,935 | [
"VTK"
] | 9f79456e709e2760e69271eba36542b78529a36ce3851c42ac68eeb111589079 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
from gi import require_version
require_version('Gtk', '3.0')
from gi.repository import Gtk
require_version('AppIndicator3', '0.1')
from gi.repository import AppIndicator3 as appIndicator
require_version('Notify', '0.7')
from gi.repository import Notify
require_version('... | slytomcat/yandex-disk-indicator | indicator.py | Python | gpl-3.0 | 40,489 | [
"VisIt"
] | f123ea576011dde0817be938ff1754f6db6abab9101c856cc587f823b8ecb034 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016 Wil Clouser <clouserw@micropipes.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the ri... | MatthewCox/dotfiles | weechat/python/emoji2alias.py | Python | mit | 41,709 | [
"FLEUR",
"Octopus"
] | 9e32fbb856b817d1b7d647ac42c4ec3f097e77f46f1dd4aa7525fb04d322bd2f |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
# import iris tests first so that some things can be initialised before importing anything else
import iris.tests as tests # ... | SciTools/iris | lib/iris/tests/test_pp_cf.py | Python | lgpl-3.0 | 6,429 | [
"NetCDF"
] | 5a6a70aa3832c91ff0869c16b5919443ac1e385f4c0ec8d6da5d7c868624ba7d |
#!/usr/bin/env python
# This server validates as of 4/23/01 when run with UserLand's SOAP validator
# (http://validator.soapware.org/).
import getopt
import sys
sys.path.insert (1, '..')
from SOAPpy import SOAP
ident = '$Id$'
def whichToolkit ():
return SOAP.SOAPUserAgent ()
def countTheEntities (s):
cou... | jjdmol/LOFAR | LTA/LTAIngest/SOAPpy-0.12.0/validate/soapware.py | Python | gpl-3.0 | 3,205 | [
"MOE"
] | a4318ae8a12a34b0db572787d95f20c4d2c6ca8f92e43c114f0dc12c281f7a99 |
# test_readcell.py ---
#
# Filename: test_readcell.py
# Description: test readCell command
# Author: Subhasis Ray
# Maintainer:
# Created: Thu Nov 27 18:08:44 2008 (+0530)
# Version:
# Last-Updated: Fri Nov 28 18:40:09 2008 (+0530)
# By: Subhasis Ray
# Update #: 71
# URL:
# Keywords:
# Compatibility... | BhallaLab/moose-thalamocortical | pymoose/tests/regression/test_readcell.py | Python | lgpl-2.1 | 3,641 | [
"MOOSE"
] | 27c86a43bc569c2b547e4b04a713f23c538b017180c9a4703fd7dfc65f1e947d |
#!/usr/bin/env python
import os
import subprocess
import sys
from distutils.command.build import build
from distutils.command.sdist import sdist
from distutils.errors import DistutilsExecError
from distutils.version import StrictVersion
from setuptools.command.build_ext import build_ext
from setuptools.command.install ... | torcolvin/openbabel | scripts/python/setup.py | Python | gpl-2.0 | 6,107 | [
"Open Babel",
"Pybel"
] | 402c358d78710fe2799517d94cb35df30408e0012e5a852fc13cc61d31a627de |
# pylint: disable=invalid-name,no-init,too-many-arguments,too-many-branches, unused-variable,too-many-return-statements
# This script creates numerous PeaksWorkspaces for different Crystal Types and Centerings. Random errors
# are also introduced into the peak's. Each PeaksWorkspace is sent through the algorithm's Fin... | dymkowsk/mantid | Testing/SystemTests/tests/analysis/Peak2ConvCell_Test.py | Python | gpl-3.0 | 34,952 | [
"CRYSTAL"
] | 71058359cf45988a2ba17fd09aa868851e494980f4430f46b30b1f37152be538 |
import logging
import os
import pytest
import datetime
from os.path import join
from urllib.parse import quote
from sigal.gallery import Album, Media, Image, Video, Gallery
from sigal.video import SubprocessException
CURRENT_DIR = os.path.dirname(__file__)
REF = {
'dir1': {
'title': 'An example gallery',... | t-animal/sigal | tests/test_gallery.py | Python | mit | 9,801 | [
"Galaxy"
] | f086234fb3e1e9a0572d43fcfed66e34800e6016d41f9116040d0b61a36a1a09 |
import numpy as np
import copy
import pele.utils.rotations as rot
import itertools
__all__ = ["alignCoM", "CoMToOrigin", "getAlignRotation", "alignRotation",
"findBestPermutationRBMol", "aa2xyz",
"getDistxyz", "getDistaa"]
def alignCoM( X1, X2):
"""
align the center of mass of X2 with t... | js850/pele | pele/mindist/obsolete/mindistutils.py | Python | gpl-3.0 | 6,992 | [
"Jmol"
] | fe54fce85d16395f41e009e806d6d6cd283842a2f9a2c1ffe8256139600029ba |
# -*- coding: utf-8 -*-
"""
Created on 2017
Author : Edouard Cuvelier
Affiliation : Université catholique de Louvain - ICTEAM - UCL Crypto Group
Address : Place du Levant 3, 1348 Louvain-la-Neuve, BELGIUM
email : firstname.lastname@uclouvain.be
"""
import tools.fingexp as fingexp
from Crypto.Random.random import randi... | ecuvelier/P3MVEOS | pathORAM/ringORAM.py | Python | apache-2.0 | 40,966 | [
"VisIt"
] | 01b2c1a55858e742c686892af1cf023e73535221789f74cf64a7789d723b6796 |
import requests
from bs4 import BeautifulSoup
from colorama import Fore
import csv
dealerships = [
# these ones work well
'subarupacific',
'timmonssubaru',
'subarusantamonica',
'glendale.subaru',
'renicksubaru',
'subarushermanoaks',
'puente-hills.subaru',
'southcoast.subaru',
's... | joshvillbrandt/subi-scrape | subi-scrape.py | Python | mit | 4,281 | [
"CRYSTAL"
] | 90e9a89690bc8168bd4093fe760f9b23dbccc10c4a8976e6b8acc7f580c33c0d |
#!/usr/bin/python
import numpy
import numpy.random
import scipy
import scipy.optimize
import scipy.stats
import matplotlib
import matplotlib.pyplot as plt
#==========================
# HELPER FUNCTIONS
#=========================
def check_twodtype(type): # check if it's a valid type
if (type=='dbeta-dpressure')... | shirtsgroup/pygo | analysis/checkensemble.py | Python | gpl-2.0 | 42,550 | [
"Gromacs"
] | 8c7a09e7af53753e5d9fe1bc645668df91da6a022bca90a29f382a752c18bff0 |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
#
# Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig,RDRandom
import random
import types,os.path,sys
SeqTypes=(types.ListType,types.TupleType)
def SplitIndices(nPts,frac,silent=1,lega... | rdkit/rdkit-orig | rdkit/ML/Data/SplitData.py | Python | bsd-3-clause | 8,679 | [
"RDKit"
] | f2f4f4df582fbeabc3a600f8a29f1cef1ec99dbca3358b431c992c6fc55e2c3a |
from .named import UniqueNamedObjectStore
from openpathsampling.netcdfplus.attribute import PseudoAttribute
from openpathsampling.netcdfplus.stores.value import ValueStore
class PseudoAttributeStore(UniqueNamedObjectStore):
"""
ObjectStore to store additional attributes to an existing store
"""
def __... | openpathsampling/openpathsampling | openpathsampling/netcdfplus/stores/attribute.py | Python | mit | 5,990 | [
"NetCDF"
] | 64b77d0df17bb5eb1d043c7a237a0a6e68ec7d15ce86e556c9d462bc9fc976be |
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
# Berlin, 14195 Berlin, Germany.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistributions of source c... | arokem/PyEMMA | pyemma/coordinates/tests/test_save_trajs.py | Python | bsd-2-clause | 7,260 | [
"MDTraj"
] | 04d0340389aeee3a55de2b30c4a465a88e2162cdbcf472d36d5075cc6180add7 |
# Copyright (C) 2010-2018 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 v... | mkuron/espresso | samples/immersed_boundary/addSoft.py | Python | gpl-3.0 | 1,890 | [
"ESPResSo"
] | 635316f3563f1595eb41a87ab5bca48d73403632169a3f4a7a9a0d8278145da4 |
#
# @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 | psi4/driver/p4const/psifiles.py | Python | gpl-2.0 | 10,802 | [
"Psi4"
] | bb690d2958dedaa7f8b63b32b5432055d4936adaf00f174f68df6f05c92718b6 |
#!/usr/bin/python
# SDE.py: calculate the transition rate of a particle in a well
# COMMAND TO RUN: ./SDE-script.py $Temp $Numt
from math import sqrt # import sqrt function
from sys import argv # command line arguments
import random # random number library
from os import urandom # used to seed... | patrickmalsom/SDE | SDE.py | Python | mit | 1,820 | [
"Gaussian"
] | 2f6161037ade79fe6e4272a557d10f698a8aa93accbf3b6676bd79d44b551ec7 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import unicodedata
from fontTools.misc.py23 import unichr
_scriptsText = """
# Scripts-9.0.0.txt
# Date: 2016-03-02, 18:55:13 GMT
# © 2016 Unicode®, Inc.
# Unicode and the Unicode Logo are registered trademarks of Unicode, Inc. in the U.S. and other count... | anthrotype/defcon | Lib/defcon/tools/unicodeTools.py | Python | mit | 181,143 | [
"FEFF"
] | 1956f49d39954418c1335f13597d8bb15a0e8b8456455e1c47935de74e88f29e |
# -*- 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 publish... | thica/ORCA-Remote | src/ORCA/vars/Helpers.py | Python | gpl-3.0 | 4,527 | [
"ORCA"
] | 96085ce182a353166f9d9ba286608b6b1a9a57ea8ddac96e12d2dab0a9d03d8d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Defines the classes relating to 3D lattices.
"""
import collections
import itertools
import math
import warnings
from fractions import Fraction
from functools import reduce
from typing import Dict, Iterato... | davidwaroquiers/pymatgen | pymatgen/core/lattice.py | Python | mit | 62,529 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | d41f3e9c7f46bfb1a92cac1459d6090d83fc327e035182493edc29a848459e55 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
import re
import time
import csv
import random
from urlparse import urlparse
from collections import defaultdict
import ... | mozilla/pto | pto/apps/dates/tests/test_views.py | Python | mpl-2.0 | 76,732 | [
"VisIt"
] | bc76076748823fc43189de53783841b9975a0159508868ec8babd48797cf4643 |
import numpy as np
import galsim
import os
from .galaxymaker import GalaxyMaker
from .great3_cosmos_gals.galaxies import COSMOSGalaxyBuilder
from .great3_cosmos_gals.noise import PlaceholderNoiseBuilder
from .. import utils
from ..observation import Observation
class GREAT3COSMOSGalaxyMaker(GalaxyMaker):
"""
... | esheldon/egret | egret/galaxymakers/cosmosgalaxymaker.py | Python | bsd-3-clause | 16,339 | [
"Galaxy"
] | e10967666ba4a95f02cb1ecd3597e225ccf12ccf80d7d2a09750867dacf83b73 |
"""TransformationCleaningAgent cleans up finalised transformations.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN TransformationCleaningAgent
:end-before: ##END
:dedent: 2
:caption: TransformationCleaningAgent options
"""
from __future__ import absolute_import
from __future__ import division... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Agent/TransformationCleaningAgent.py | Python | gpl-3.0 | 29,582 | [
"DIRAC"
] | b50eb11caa8821bf6d3710636def5d682becafd41d8dc797bd4d3efbad444387 |
""" Command module contains the base "Command" class, base for all RSS commands
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
from DIRAC import gLogger, S_OK
class Command(object):
"""
The Command class is a simple base cla... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Command/Command.py | Python | gpl-3.0 | 2,541 | [
"DIRAC"
] | 719f011fdfd5620600ad881e0f1646f30f691be90423460813a856028d5f4f1f |
##########################################################################
#
# Copyright (C) 2001-2014, Michele Cappellari
# E-mail: cappellari_at_astro.ox.ac.uk
#
# Updated versions of the software are available from my web page
# http://purl.org/cappellari/software
#
# If you have found this software useful for your ... | zpace/MaNGA-fitting | ppxf.py | Python | mit | 59,335 | [
"Galaxy",
"Gaussian"
] | dcbf5a18bbbc62a5275e490c03ed4500df6a529d1c5a5525b22f2d6529e2b973 |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2012 OpenPlans
#
# 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 versio... | IMIO/imio.geonode.portal | geonode/base/enumerations.py | Python | gpl-3.0 | 14,433 | [
"BWA"
] | c79852f833e1495165437c4e3e16bd61690211ad1d453cb87327f67f76c938af |
""" Base class for plugins as used in the transformation system
"""
import re
from DIRAC import S_ERROR, gLogger
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
class PluginBase( object ):
def __init__( self, plugin, operationsHelper = None ):
""" plugin name has to be passed in: it... | vmendez/DIRAC | TransformationSystem/Client/PluginBase.py | Python | gpl-3.0 | 1,204 | [
"DIRAC"
] | 87309701c8a23ff20173c6fe294413c91d95d69c6056729e3e0de0378fd748ba |
"""
Tools for density estimation
See also:
- sklearn.mixture.gmm : gaussian mixture models
- sklearn.neighbors.KernelDensity : Kernel Density Estimation (version 0.14+)
- astroML.density_estimation.XDGMM : extreme deconvolution
- scipy.spatial.gaussian_kde : a gaussian KDE implementation
"""
import warnings
import num... | nhuntwalker/astroML | astroML/density_estimation/density_estimation.py | Python | bsd-2-clause | 7,788 | [
"Gaussian"
] | 82070142ab491442d5ca1671819ce6e7a99011b1d9c6016628eb9ca243743cfb |
import numpy as np
from ase.calculators.eam import EAM
from ase.lattice import bulk
# test to generate an EAM potential file using a simplified
# approximation to the Mishin potential Al99.eam.alloy data
from scipy.interpolate import InterpolatedUnivariateSpline as spline
cutoff = 6.28721
n = 21
rs = np.arange(0, ... | grhawk/ASE | tools/ase/test/eam_test.py | Python | gpl-2.0 | 3,119 | [
"ASE"
] | d864660f6b19b79c90474c62908eccda6b29438425a54765b1cc0138a7024e86 |
########################################################################
# $HeadURL$
# File: Operation.py
# Date: 2012/07/24 12:12:05
########################################################################
"""
:mod: Operation
.. module: Operation
:synopsis: Operation implementation
Operation implementation
"""
# ... | fibbo/DIRAC | RequestManagementSystem/Client/Operation.py | Python | gpl-3.0 | 10,200 | [
"DIRAC"
] | 609f707186daf446af6da814b3563b4a8f3d2580a2a6bcb4fcaf7621a5b8810d |
import gzip
import csv
import os
import operator
from collections import defaultdict
from sklearn.feature_extraction import DictVectorizer
from sklearn.preprocessing import MultiLabelBinarizer
from sklearn.feature_selection.variance_threshold import VarianceThreshold
def openAny(inPath, mode):
return gzip.open(inP... | TurkuNLP/CAFA3 | learning/loading.py | Python | lgpl-3.0 | 14,780 | [
"BLAST"
] | 6c89156ee3358fc95d853ea744d085144ceacf5df7786610104453f7411a2bdb |
""" Utility Class for threaded agents (e.g. TransformationAgent)
Mostly for logging
"""
import time
from DIRAC import gLogger
__RCSID__ = "$Id$"
AGENT_NAME = ''
class TransformationAgentsUtilities(object):
""" logging utilities for threaded TS agents
"""
def __init__(self):
""" c'tor
"""
sel... | arrabito/DIRAC | TransformationSystem/Agent/TransformationAgentsUtilities.py | Python | gpl-3.0 | 3,139 | [
"DIRAC"
] | 686a424a5b766be18140cbaf147f0b449ddcb384399232d0ef7e8126707810d5 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | scripts/AbinsModules/Instruments/Instrument.py | Python | gpl-3.0 | 3,960 | [
"Gaussian"
] | 827cc18b16cfe5a6228621fb9ca6d2c68b1c794ea98ed0c635864abb47980568 |
# -*- coding: utf-8 -*-
"""Load py_pRF_mapping config file."""
import os
import csv
import ast
# Get path of this file:
strDir = os.path.dirname(os.path.abspath(__file__))
def load_config(strCsvCnfg, lgcTest=False, lgcPrint=True):
"""
Load py_pRF_mapping config file.
Parameters
----------
strCs... | MSchnei/py_pRF_motion | pyprf_feature/analysis/load_config.py | Python | gpl-3.0 | 10,909 | [
"Gaussian"
] | cc8f493b524af7b0c5511aa9f6b222980d69daf18b88169495489e57c6153760 |
# -*- coding: utf-8 -*-
## Copyright 2015 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## This file is part of Nascent.
##
## Nascent is free software: you can redistribute it and/or modify
## it under the terms of the GNU Affero General Public License as
## published by the Free Software Foundati... | scholer/na_strand_model | nascent/graph_visualization/cytoscape.py | Python | gpl-3.0 | 13,046 | [
"Cytoscape"
] | d61cbcb5a973cc9ba96bb4f521c4ab583029eea6d0a4db7d76bf38cdeda46465 |
#!/usr/bin/env python
""" refresh CS
"""
import DIRAC
DIRAC.initialize() # Initialize configuration
from DIRAC.ConfigurationSystem.private.Refresher import gRefresher
res = gRefresher.forceRefresh()
if not res["OK"]:
print(res["Message"])
| DIRACGrid/DIRAC | tests/Jenkins/dirac-refresh-cs.py | Python | gpl-3.0 | 247 | [
"DIRAC"
] | c4aed1ad56b2ada65bef2067c5af866c1ddc57582cbcca1efb5b5c6a26fdd4fb |
# Copyright 2004-2012 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, m... | MSEMJEJME/Get-Dumped | renpy/display/imagelike.py | Python | gpl-2.0 | 10,715 | [
"VisIt"
] | a365738a07b7d740ef013190203ea710cf3ff6cebfb048ddd490cd7a5ab19ebe |
#!/usr/bin/env python
"""
Parse to BLASTn tabular output format 6 to get sequences in fasta format from database.
BLASTn tabular output format 6 - Column headers:
qseqid **sseqid** pident length mismatch gapopen **qstart** **qend** sstart send evalue bitscore
author: A. Zyla - azyla
.. warning:: Tested only on fasta... | mmagnus/rna-pdb-tools | rna_tools/tools/rna_seq_search_BLASTn_outfmt-6/select_seq_fromBLAStn_6outfm.py | Python | gpl-3.0 | 3,958 | [
"Biopython"
] | 7706c8ea9def27fb0d180060b2ff5eb2019ee59eef64fb3b2b3bee3749b5036f |
# Import the PyQt and QGIS libraries
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from qgis.core import * #this is not currently working either due to qgis version or file location
# Initialize Qt resources from file resources.py
import resources
# Import the code for the dialog
from meshnetcdfdialog import Mes... | janhui/test_engine | dev/plugins/mesh_netcdf/StandardModules.py | Python | lgpl-2.1 | 776 | [
"NetCDF"
] | 17f3f3a27b5048aeb22f660a2882ccc9662a190f9ab9a296456b57450743df86 |
"""
baserawio
======
Classes
-------
BaseRawIO
abstract class which should be overridden to write a RawIO.
RawIO is a new API in neo that is supposed to acces as fast as possible
raw data. All IO with theses characteristics should/could be rewritten:
* internally use of memmap (or hdf5)
* reading header is quite... | JuliaSprenger/python-neo | neo/rawio/baserawio.py | Python | bsd-3-clause | 26,231 | [
"NEURON"
] | 602538bb3846bb241c1cc8fd615e7d5e82e7e7a9872466c81f2573e38f1a10de |
"""
Helper scripts for running galfit
"""
import os
import glob
from collections import OrderedDict
import numpy as np
import astropy.io.fits as pyfits
import astropy.wcs as pywcs
from grizli import utils
try:
from .psf import DrizzlePSF
except:
from grizli.galfit.psf import DrizzlePSF
# Constraints
# see ... | gbrammer/grizli | grizli/galfit/galfit.py | Python | mit | 25,223 | [
"Gaussian"
] | 770972d2dd0990adb1e9e7882ef4d584fafb21ca48987c785deefb0eced94b9f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
"""
.. currentmodule:: pylayers.simul.simultraj
.. autosummary::
"""
import doctest
import numpy as np
import copy
import matplotlib.pylab as plt
import pylayers.util.pyutil as pyu
import pylayers.signal.waveform as wvf
from pylayers.signal.device import Device
# Handle La... | dialounke/pylayers | pylayers/simul/simultraj.py | Python | mit | 43,629 | [
"Mayavi"
] | 2697905fb2683fd7f3e74b16424c0378221a09ab364aad2dd2de17994aeffc3a |
#!/usr/bin/env python
#Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.intervals.io
assert sys.version_info[:2] >= ( 2, 4 )
def stop_err( msg ):
sys.stderr.write( msg )
sys.exit()
def __main__():
output_name = sys.argv[1]
input_... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/converters/interval_to_bed_converter.py | Python | gpl-3.0 | 2,212 | [
"Galaxy"
] | 3a023c655da194abf08c907ca799b99c1329f4c6333149c31665df086d873ebe |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/remindor-qt | remindor_qt/scheduler_qt.py | Python | gpl-3.0 | 4,060 | [
"Brian"
] | f6a0710650d6c94246ad3db24e6e44cddbd94b3a0d8eb143f24bced07d3fdba3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Visualization
==================
This is module contains a simple visualizer to show event lists along with the audio.
The visualizer can show multiple event lists for the same reference audio allowing the
comparison of the reference and estimated event lists.
.. imag... | TUT-ARG/sed_vis | sed_vis/visualization.py | Python | mit | 54,744 | [
"Gaussian"
] | 9d086b98509fbe8f04f9c3036d8c714bd23f8963e9f561e7cc8db41a1091405e |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/diversity/_driver.py | Python | bsd-3-clause | 15,329 | [
"scikit-bio"
] | c2524213496a4d3f865e158502efbc2a68418a95175ec1f55c1bdfd9b8d9158a |
"""
SystemLoggingHandler is the implementation of the Logging service
in the DISET framework.
The following methods are available in the Service interface::
addMessages()
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Framew... | andresailer/DIRAC | FrameworkSystem/Service/SystemLoggingHandler.py | Python | gpl-3.0 | 2,129 | [
"DIRAC"
] | e932694ef0b55ba21b03338ebb29f947c21e1cc8058461d9e1dbc97249a51ed6 |
import mdtraj as md
import numpy as np
from . import Featurizer
class BaseSubsetFeaturizer(Featurizer):
"""Base class for featurizers that have a subset of active features.
n_features refers to the number of active features. n_max refers to the
number of possible features.
Parameters
----------... | msultan/msmbuilder | msmbuilder/featurizer/subset.py | Python | lgpl-2.1 | 4,979 | [
"MDTraj"
] | f5fb974773c3578f92529b9fb853dc0feabd42a01b512a4b94bb5ec335a3db00 |
""" FileManager for ... ?
"""
import six
import os
import datetime
from DIRAC import S_OK, S_ERROR
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.FileManager.FileManagerBase import FileManagerBase
from DIRAC.Core.Utilities.List import stringListToString, intListToString, breakListIntoChunks
# The logic of s... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/FileManager/FileManagerPs.py | Python | gpl-3.0 | 33,895 | [
"DIRAC"
] | ff9b01e1917c634d5a6bb08003235b84c228b5f367de2022b2de17bac3e1f189 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgeexamples/exset2_singlecell_simulations/singlecell_simulation050.py | Python | bsd-2-clause | 3,177 | [
"NEURON"
] | e556cc39d1b714ae6427cfdd7a42224c9b7eb3c2eb13150034cad3c8f8db4d62 |
'''
Tratihubis converts Trac tickets to Github issues by using the following steps:
1. The user manually exports the Trac tickets to convert to a CSV file.
2. Tratihubis reads the CSV file and uses the data to create Github issues and milestones.
Installation
============
To install tratihubis, use ``pip`` or ``eas... | i-rabot/tractogithub | tratihubis.py | Python | bsd-3-clause | 38,635 | [
"VisIt"
] | d25d0ea68aa7acba0f0acbea940cf0a5478119b66d8b944e53b154fc215cc0c6 |
#!/usr/bin/python
import argparse
import re
import pysam
import pickle
import os
import string
from pysam import VariantFile
import itertools
from marker_util import Marker
"""
vcf_to_ldheatmap_format.py outputs vcf snps in a format acceptable for LDheatmap R package
https://cran.r-project.org/web/packages/LDheatmap/... | christopher-gillies/VCFScripts | vcf_to_ldheatmap_format.py | Python | apache-2.0 | 4,257 | [
"pysam"
] | 90bf5e48144ee65cb71eeccb8711ec655a00396b6359814dc790be578e7a1b64 |
# State Capitals Game
import random
def main():
state_capitals={"Washington":"Olympia","Oregon":"Salem",\
"California":"Sacramento","Ohio":"Columbus",\
"Nebraska":"Lincoln","Colorado":"Denver",\
"Michigan":"Lansing","Massachusetts":"Boston",\
... | ActiveState/code | recipes/Python/576783_State_Capitals_Quiz/recipe-576783.py | Python | mit | 2,687 | [
"COLUMBUS"
] | e10a5676924dc8f712e014ca988d5d42b9ecd2f4b6506146f41217ace1cf48c7 |
# 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, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | src/cclib/bridge/cclib2biopython.py | Python | lgpl-2.1 | 1,395 | [
"Biopython",
"cclib"
] | 11bb4878d0b9e1b657399efc31eca34a1801a9868a9a0565c3dbe41b5c7dc53e |
import time
from dominate import document, tags as dom
from authlib.oauth2 import OAuth2Error
from authlib.oauth2.rfc6749.grants import AuthorizationEndpointMixin
from authlib.oauth2.rfc6749.errors import InvalidClientError, UnauthorizedClientError
from authlib.oauth2.rfc8628 import (
DeviceAuthorizationEndpoint as... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/private/authorization/grants/DeviceFlow.py | Python | gpl-3.0 | 6,415 | [
"DIRAC"
] | 6a48e3de2cce476840f94784877848a1b10c4ca5fcaffce146e4fa471bd5f56d |
#!/usr/bin/env python
"""
Created on March 1, 2016
@author: Alan L. Hutchison, alanlhutchison@uchicago.edu, Aaron R. Dinner Group, University of Chicago
Use ./CalcP.py -h to see usage
Credit for the arbfit code goes to Nablaquabla
"""
import numpy as np
import matplotlib.pylab as plt
from mpfit import mpfit
VERSION=... | alanlhutchison/empirical-JTK_CYCLE-with-asymmetry | bin/CalcP.py | Python | mit | 8,530 | [
"Gaussian"
] | 01961149264e3e95b54ffb4e0701c2f69b05127c135bf32139aabb49d2206b43 |
"""Make supplementary PDB enrichment figures.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
import os
import logging
from matplotlib import pyplot as plt
import seaborn as sns
from python_utilities.scripting import setup_logging
from e3fp_paper.plotting.defaults import DefaultColors
from e3fp_paper.plotting.util... | keiserlab/e3fp-paper | project/analysis/comparison/make_pdb_supp_plot.py | Python | lgpl-3.0 | 5,449 | [
"RDKit"
] | f143d61b0342c6acb95fd9e946c58e115766ddf260e779b68ecd07ea08c09c1c |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2004-2009 Edgewall Software
# Copyright (C) 2004 Daniel Lundin <daniel@edgewall.com>
# Copyright (C) 2004-2006 Christopher Lenz <cmlenz@gmx.de>
# Copyright (C) 2006 Jonas Borgström <jonas@edgewall.com>
# Copyright (C) 2008 Matt Good <matt@matt-good.net>
# All rights reserved.
#... | jun66j5/trac-ja | trac/web/session.py | Python | bsd-3-clause | 20,875 | [
"VisIt"
] | c5057a654408f6882d8a808ae2bb0832cd4623059fe6c455583c9da29c37d17b |
"""Perform regional de-novo assembly calling with cortex_var.
Using a pre-mapped set of reads and BED file of regions, performs de-novo
assembly and variant calling against the reference sequence in each region.
This avoids whole genome costs while gaining the advantage of de-novo
prediction.
http://cortexassembler.s... | vladsaveliev/bcbio-nextgen | bcbio/variation/cortex.py | Python | mit | 15,497 | [
"pysam"
] | c198b6d518be47151333fd37c8be6dde76d3b40982f38b79167225f7d2d36503 |
"""Produce custom labelling for a colorbar.
Contributed by Scott Sinclair
"""
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import cm
from numpy.random import randn
# Make plot with vertical (default) colorbar
fig = plt.figure()
ax = fig.add_subplot(111)
data = np.clip(randn(250, 250), -1, 1)
... | lthurlow/Network-Grapher | proj/external/matplotlib-1.2.1/lib/mpl_examples/pylab_examples/colorbar_tick_labelling_demo.py | Python | mit | 1,036 | [
"Gaussian"
] | 72992c59101f3c1965d9247b1bd40b0b6f2bee05894ab42cf67ba2b2871f9730 |
"""
======================
Working with ECoG data
======================
MNE supports working with more than just MEG and EEG data. Here we show some
of the functions that can be used to facilitate working with
electrocorticography (ECoG) data.
"""
# Authors: Eric Larson <larson.eric.d@gmail.com>
# Chris Hold... | jaeilepp/mne-python | tutorials/plot_ecog.py | Python | bsd-3-clause | 2,696 | [
"Mayavi"
] | 0ff1cf84eb33fc1dc6436a86722e22ecbe0fd859db7991d717ed5137a3f07b8b |
import StringIO
from itertools import chain
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
from ase.vibrations import Vibrations
from ase.vibrations.franck_condon import FranckCondon
from ase.io.xyz import read_xyz
from ase.optimize import FIRE
from gpaw import GPAW
from gpaw.cluster import C... | robwarm/gpaw-symm | gpaw/test/big/fc/fc_butadiene.py | Python | gpl-3.0 | 3,095 | [
"ASE",
"GPAW",
"Gaussian"
] | 9f38e70d6e5fcb38b237f40b45ee29ccf80e5cdf4852518b30340bc51dbaf15d |
"""
Tests for discussion pages
"""
import datetime
from unittest import skip
from uuid import uuid4
from nose.plugins.attrib import attr
from nose.tools import nottest
from pytz import UTC
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.fixtures.discuss... | Edraak/edraak-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 63,157 | [
"VisIt"
] | 7784f2d9e22faf75fc31f2ef566c9ae8f0d50189bbca88d66b8bc4bff6288447 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'IndicatorData.change_from_time'
db.add_column('profiles_indicatordata', 'change_from_time'... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0019_auto__add_field_indicatordata_change_from_time__add_field_indicatordat.py | Python | mit | 11,574 | [
"MOE"
] | 485d07e17dfe0e7a9d0c1b422443091176baee7b89de70d44ff0fb976f27aa5a |
# 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... | indhub/mxnet | python/mxnet/contrib/onnx/onnx2mx/_op_translations.py | Python | apache-2.0 | 25,806 | [
"Gaussian"
] | 4deac7dfb45abadfa0610e6a06d70584471dd8cbcdfa7918dbbcb5aecc3a7133 |
from collections import OrderedDict
import contextlib
import copy
from difflib import SequenceMatcher
import json
import operator
import os
import re
import time
import h5py
import jinja2
import netCDF4
import numpy as np
import pyparsing
import rdflib
import rdflib.collection
import rdflib.namespace
import requests
... | binary-array-ld/bald | lib/bald/__init__.py | Python | bsd-3-clause | 58,220 | [
"NetCDF"
] | 04b286447ef9020a7b0ec711588f74b6573f1e999a77f234e690ea68f13874f3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# 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 Licens... | hryamzik/ansible | lib/ansible/modules/network/cnos/cnos_showrun.py | Python | gpl-3.0 | 5,175 | [
"VisIt"
] | 419c555951523db808d0c0e6f7d3f342ad071682e93f277f24f02bcce21853bf |
import simtk.unit as units
from intermol.decorators import accepts_compatible_units
from intermol.forces.abstract_angle_type import AbstractAngleType
class CosineAngleType(AbstractAngleType):
__slots__ = ['k', 'c']
@accepts_compatible_units(None, None, None,
k=units.kilojoules... | ctk3b/InterMol | intermol/forces/cosine_angle_type.py | Python | mit | 1,109 | [
"LAMMPS"
] | 6a3b0df6b64b71ffdb99572d0fab29712ed34d460f50e55ac65255c88956c159 |
'''
All communication to the neuPrint server is peformed using a
:py:class:`Client` object, which holds your authorization
credentials, the dataset name to use, and other connection settings.
(To obtain your authorization credentials, see the :ref:`quickstart`.)
For commonly used queries, see :ref:`queries`.
Or you c... | connectome-neuprint/neuprint-python | neuprint/client.py | Python | bsd-3-clause | 26,456 | [
"NEURON"
] | 1c396005e8807314c3e454b47899bad358c2eac2b508e9e7f93fe8fd94564f71 |
# Copyright (C) 2013-2019 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# 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... | espressomd/espresso | maintainer/check_features.py | Python | gpl-3.0 | 1,019 | [
"ESPResSo"
] | 92f13c5ea15650caf7d484f9c056810f98603a5459bdedac190112041064e3a4 |
# -*- coding: utf-8 -*-
#
# samtools documentation build configuration file, created by
# sphinx-quickstart on Wed Aug 12 14:43:42 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | daler/pysam | doc/conf.py | Python | mit | 7,394 | [
"pysam"
] | 1e2435232a9dfba08c35c3e5c0579b6b0b63b6b1df76d063863311fd0b15043b |
# 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.
#
"""Generic functions which are useful for working with HMMs.
This just collects general functions which you might like to use in
dealing with HMMs.
... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/HMM/Utilities.py | Python | gpl-2.0 | 2,170 | [
"Biopython"
] | 8055466b647ce927591964d3b77178793c4cd7f7d9febe87c5a407c94c49c9f7 |
import version
version.append ('$Revision: 90095 $')
del version
import ktl
import tkFileDialog
import Tkinter
from Tkinter import N, E, S, W
import traceback
import Box
import Button
import Color
import Event
import Images
import Icon
import Log
import Monitor
import Stage
import Value
class Detail:
def __init_... | alexrudy/Cauldron | Cauldron/bundled/GUI/Popup.py | Python | bsd-3-clause | 46,718 | [
"MOE"
] | 3aa4f9fb23955402ffaf2bf7aa4bf8b1e423842f8eeacda7f48e70fd9e8374df |
#!/usr/bin/env python
"""
PATHMARK.py
Author: Sam Ng
Last Updated: 2014-06-13
"""
import math, os, random, re, sys, types
from copy import deepcopy
import pandas
import networkx
import matplotlib.pyplot as plt
from xml.dom.minidom import Document
from optparse import OptionParser
from jobTree.scriptTree.target impor... | UCSC-MedBook/MedBook_ | tools/old-external-tools/shazam/PATHMARK.py | Python | bsd-3-clause | 52,348 | [
"Cytoscape",
"Galaxy"
] | 10f5e7cd564c5d217000d1d1b6ee761a0d60aa06e9c065d6c1ce8895689b9905 |
r"""
This module is made to provide a set of tools and helper classes for data
exploration for Web deployment.
"""
import math, os, json, datetime, time
from paraview import simple, servermanager
#==============================================================================
# Run management
#========================... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Wrapping/Python/paraview/data_exploration.py | Python | gpl-3.0 | 64,121 | [
"ParaView"
] | 985b84cdf5f8fb6465294d1e42d57ad502fd0e0a115e93aeaae5dbf7e1f6a651 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 ver... | spring01/libPSI | lib/python/frac.py | Python | gpl-2.0 | 21,649 | [
"Psi4"
] | b3551a843f5ae661a4fd3e0e58258e5a5d28eb934c72a5a70617b0754d9c97e2 |
#!/usr/bin/env python
#JSON {"lot": "UKS/6-31G(d)",
#JSON "scf": "CDIISSCFSolver",
#JSON "er": "cholesky",
#JSON "difficulty": 7,
#JSON "description": "Basic UKS DFT example with hybrid MGGA exhange-correlation functional (M05)"}
import numpy as np
from horton import * # pylint: disable=wildcard-import,unused-wil... | QuantumElephant/horton | data/examples/hf_dft/uks_methyl_hybmgga.py | Python | gpl-3.0 | 4,551 | [
"Gaussian"
] | cbdf1f90b2a22731b0f7b6246df97944a6580edf02dbb2df9b7dd014af84f2e9 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/bonds.py | Python | gpl-2.0 | 24,824 | [
"PyMOL"
] | abc96fc2c58b9258ecd8d0ddcab3f8cedf666be9adf85545808c23160abf5c3b |
'''
whitelist_methods.py - Methods for whitelisting cell barcodes
=============================================================
:Author: Tom Smith, Ian Sudbery
:Release: $Id$
:Date: |today|
:Tags: Python UMI
'''
import collections
import re
import random
from functools import partial
import umi_tools.Utilities as U
... | CGATOxford/UMI-tools | umi_tools/sam_methods.py | Python | mit | 24,734 | [
"pysam"
] | d4ce31d59aad7027db51ac9c55874c2c62785ee2c62f7f29b6f18646e45ef703 |
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each input into a vector of dime... | vermouth1992/tf-playground | analysis/cs231n/layers.py | Python | apache-2.0 | 31,030 | [
"NEURON"
] | cb8830d1b2ca2a64b38286f1adbf10cf50d3be3f77727af9776f4ab5aa0b75af |
"""
==================
Physical constants
==================
Values of common physical constants are defined here as instances of
:class:`pgradd.Units.Quantity`.
"""
from . Units import eval_qty
#: Planck's constant
PLANCK_CONSTANT = eval_qty('6.626068*10^-34 J s')
#: Boltzman's constant
BOLTZMANN_CONSTANT = eval... | VlachosGroup/VlachosGroupAdditivity | pgradd/Consts.py | Python | mit | 495 | [
"Avogadro"
] | 4bc03857e6fc816b177ff1b3cdddb436fa5f0560f3a7f11f4d8ff8f9ffbdc53c |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kobejean/tensorflow | tensorflow/contrib/layers/python/layers/feature_column_test.py | Python | apache-2.0 | 53,780 | [
"MOOSE",
"Octopus"
] | bcd5f7bdbac6a42f53423b5a6a6b28e59c04323098c6a66994ea0966abb1f9f2 |
""" A module for Geometry stuff
"""
from rdkit import DataStructs
from rdGeometry import *
| rdkit/rdkit-orig | rdkit/Geometry/__init__.py | Python | bsd-3-clause | 94 | [
"RDKit"
] | 335c9fcdac90d192bae631e0f060b42264e8ab610b1d04aa1804547eff7d8318 |
"""
# -*- coding:utf-8 -*-
# based on:
# - txamqp-helpers by Dan Siemon <dan@coverfire.com> (March 2010)
# http://git.coverfire.com/?p=txamqp-twistd.git;a=tree
# - Post by Brian Chandler
# https://groups.google.com/forum/#!topic/pika-python/o_deVmGondk
# - Pika Documentation
# http://pika.readthedocs.org/en... | vrtsystems/pika | examples/twisted_service.py | Python | bsd-3-clause | 7,931 | [
"Brian"
] | c5fd1c8dbda4a9b005910b8993d4c8d94bba59137a3d20b0792778f29090cef7 |
#!/usr/bin/python
import sys
import re
def main(argv):
# Define regex patterns
#httpNewPage = re.compile(r"^http://.*?(\s|\n)")
httpNewPage = re.compile(r"^WARC-Target-URI: (https?://.*?(\s|\n))")
iphoneRe = re.compile(r" iphone.*?(review|critique|look\sat|in\sdepth|analysis|evaluat|assess)", re.IGNORE... | ggodreau/c3t2 | mapper.py | Python | mit | 10,808 | [
"Galaxy"
] | 75403e5e23ef5e839dae0a09be5991f43bd04813c556d207cfd958d8659048dc |
"""
Statistical tools for time series analysis
"""
from statsmodels.compat.python import (iteritems, range, lrange, string_types,
lzip, zip, long)
from statsmodels.compat.scipy import _next_regular
import numpy as np
from numpy.linalg import LinAlgError
from scipy import stats
f... | phobson/statsmodels | statsmodels/tsa/stattools.py | Python | bsd-3-clause | 42,522 | [
"ADF"
] | 52638568248ade4372068bc10e9a08bb723540e99958d0bdb7c623086d3a6c7f |
# copyright 2003-2010 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
# copyright 2003-2010 Sylvain Thenault, all rights reserved.
# contact mailto:thenault@gmail.com
#
# This file is part of logilab-astng.
#
# logilab-astng is free software: you can redi... | karban/field | resources/python/logilab/astng/builder.py | Python | gpl-2.0 | 8,996 | [
"VisIt"
] | f5677ca8e1595276c35e5ba757be842a983659a700e017ded58ce6f28e95d119 |
# 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... | junghans/espressopp | src/integrator/LBInitPopWave.py | Python | gpl-3.0 | 2,743 | [
"ESPResSo"
] | a928957f42719d57aeb8fc8bddc8597a970c37f5ccf255610ab46f889fae0b4d |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Variable_Stiffness_Variable_Velocity/HMM/with 2s/hmm_crossvalidation_force_20_states.py | Python | mit | 29,263 | [
"Mayavi"
] | e4842763f405c76a65486358007dfab907d6712f551cb31ebc3781c48a9486c6 |
import logging
import os
import sys
import traceback
from smif.controller.modelrun import ModelRun
from smif.exception import SmifDataNotFoundError
from smif.model import ScenarioModel, SectorModel, SosModel
def get_model_run_definition(store, modelrun):
"""Builds the model run
Arguments
---------
s... | nismod/smif | src/smif/controller/build.py | Python | mit | 4,517 | [
"CRYSTAL"
] | d51e691a5281a884215886b747b276aed339757b914e06fec681fa6b2303bdb3 |
##
# Copyright 2009-2016 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://vscentrum.be/nl/en),
# Flemish Research Foundation ... | wpoely86/easybuild-easyblocks | easybuild/easyblocks/g/gamess_us.py | Python | gpl-2.0 | 14,041 | [
"GAMESS"
] | 97a1aa5ad2a434bff3fa38b117cefe58922cf642df1fa0eab6f4bf34e37ef26b |
########################################################################
# File: FileCatalogHandler.py
########################################################################
"""
:mod: FileCatalogHandler
.. module: FileCatalogHandler
:synopsis: FileCatalogHandler is a simple Replica and Metadata Catalog service ... | hgiemza/DIRAC | DataManagementSystem/Service/FileCatalogHandler.py | Python | gpl-3.0 | 28,291 | [
"DIRAC"
] | 5b1ebc56dac9d28e948afbbff7bcaf9b382b8bc5589cac23b9947438b0201f65 |
#!/usr/bin/env python3
#
# Author: Heresh Fattahi
#
# Modified from insarApp.py originally written by Giangi Sacco, Eric Gurrola
from __future__ import print_function
import time
import os
import sys
import logging
import logging.config
import isce
import isceobj
import iscesys
from iscesys.Component.Application i... | leiyangleon/FSH | ISCE_processing_scripts/stripmapApp_substitute/stripmapApp.py | Python | gpl-3.0 | 33,124 | [
"Gaussian"
] | 8631371866d143be37a189aa055a8fee1cb00088f4617360a71ac2d78bc806df |
from erukar.system.engine import TieredKey
from erukar.content.modifiers import Crystal
class DiamondKey(TieredKey):
Probability = 1
Tier = 'Diamond'
BasePrice = 3200
def __init__(self):
super().__init__()
Crystal().apply_to(self)
| etkirsch/legends-of-erukar | erukar/content/inventory/consumables/keys/DiamondKey.py | Python | agpl-3.0 | 265 | [
"CRYSTAL"
] | a6cc2df4450a3d5fd23e657b2cbb1245e397006a35b35a15ff5eb21dd4ccf048 |
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