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'''Hidden module to abstract the cclib interface and convert it to chemlab
'''
# CJS changed relative paths to cclib ones
from chemlab.io.handlers.base import FormatNotSupported, IOHandler
from chemlab.core import Molecule
from chemlab.db import ChemlabDB
import numpy as np
import logging
from cclib.parser import ... | chrisjsewell/PyGauss | pygauss/chemlab_patch/io/handlers/_cclib.py | Python | gpl-3.0 | 2,554 | [
"ADF",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 905ddb0cf37c3510c74a6bcd363f768ec3337a96b6340cb8ab986756f1045f9f |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import random
import pytz
import io
import json
import os
import random
import requests
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
f... | nttks/jenkins-test | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 171,056 | [
"VisIt"
] | 977f5bb8ccaa11661431736e6e54e44e5e9914dec18e0a025ec2183d8f2834b8 |
from __future__ import unicode_literals
from django.test import TestCase
from django.utils import six
from .models import (Building, Child, Device, Port, Item, Country, Connection,
ClientStatus, State, Client, SpecialClient, TUser, Person, Student,
Organizer, Class, Enrollment, Hen, Chick, A, B, C)
class Se... | diegoguimaraes/django | tests/select_related_regress/tests.py | Python | bsd-3-clause | 9,403 | [
"Brian"
] | 40fed1cc01ce5b8f9afad63c823f3e2b311992cce7f17e35d10f3634f205f33d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes for the Piezoelectric tensor
"""
from pymatgen.core.tensors import Tensor
import numpy as np
import warnings
__author__ = "Shyam Dwaraknath"
__copyright__ = "Copyright 2016, T... | montoyjh/pymatgen | pymatgen/analysis/piezo.py | Python | mit | 1,381 | [
"pymatgen"
] | f884f28fd0175735c02d1d918498da5acade1d5c89557d1888169ae0472e3939 |
import matplotlib
matplotlib.use('Agg')
import numpy as np
import scipy.stats
import matplotlib.pylab as plt
import os
import sys
from .context import vfe
from .context import config
import pdb
np.random.seed(42)
# We first define several utility functions
def kink_true(x):
fx = np.zeros(x.shape)
for t in ran... | thangbui/geepee | examples/gpssm_vfe_examples.py | Python | mit | 4,276 | [
"Gaussian"
] | 0fe0304b3b4f628bddfb4eab41e722667a592799ef54b685874c69f9e3e21533 |
# Dual annealing unit tests implementation.
# Copyright (c) 2018 Sylvain Gubian <sylvain.gubian@pmi.com>,
# Yang Xiang <yang.xiang@pmi.com>
# Author: Sylvain Gubian, PMP S.A.
"""
Unit tests for the dual annealing global optimizer
"""
from scipy.optimize import dual_annealing, Bounds
from scipy.optimize._dual_annealing... | scipy/scipy | scipy/optimize/tests/test__dual_annealing.py | Python | bsd-3-clause | 14,709 | [
"VisIt"
] | c35f5bfef53233146b6883cd36357e45f71ba4c04d76929dff62d26aec64dde8 |
from __future__ import division
import os
import glob
import pyaml
import sys
import errno
import operator
from pipes import quote
from lacli.log import getLogger
from lacli.upload import Upload, UploadState
from lacli.capsule import archive_capsule
from lacli.archive import restore_archive
from lacore.adf.util import... | longaccess/longaccess-client | lacli/command.py | Python | apache-2.0 | 30,479 | [
"ADF"
] | 8f51ecf75c6be626c7f614d3dd439208540be8858359958b071644573f9560e1 |
import re
import os
import json
from scrapy.spider import BaseSpider
from scrapy.selector import HtmlXPathSelector
from scrapy.http import Request, FormRequest, HtmlResponse, TextResponse
from scrapy.utils.response import get_base_url
from scrapy.utils.url import urljoin_rfc
from urllib import urlencode
import hashlib... | 0--key/lib | portfolio/Python/scrapy/orange/mobilezone.py | Python | apache-2.0 | 2,457 | [
"Galaxy"
] | b98669665a1886b6e00fbd958dec4a17606b4b1733789c0811bb0670a135a21b |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/sequence/tests/test_grammared_sequence.py | Python | bsd-3-clause | 26,277 | [
"scikit-bio"
] | 4bb2ca0f8d79a46effa68992f9238bd05c1674696d4d8f2c438f2c901142b539 |
#!/usr/bin/env python
#%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%#
#%!% ---------------------------------- OPTIMIZE-analyze.py ---------------------------------- %!%#
#%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%... | klion93/Exciting-Scripts-Tools | OPTIMIZE-Data_analyze.py | Python | apache-2.0 | 18,066 | [
"CRYSTAL"
] | e0238e146219268e5ca091ead842c893be58e19d62faf2e4cfbfdfd2c0e1520d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This module provides utility classes for io operations.
"""
__author__ = "Shyue Ping Ong, Rickard Armiento, Anubhav Jain, G Matteo, Ioannis Petousis"
__copyright__ ... | sonium0/pymatgen | pymatgen/util/io_utils.py | Python | mit | 2,820 | [
"pymatgen"
] | 5d75322351c9d0d48d0ac94c81d5e6843231ab3154d04702af78f392436a763c |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | yipenggao/moose | python/MooseDocs/tests/common/import/test_import.py | Python | lgpl-2.1 | 8,754 | [
"MOOSE"
] | fbe5f0fe2c345f8db5e070973544e5f58f86aeeb4d5f013d110fff2e03b69b8b |
#!/usr/bin/env python
#Dan Blankenberg
"""
Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended.
"""
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.intervals.io
from bx.bitset import BitSet
from galaxy.tools.util import ma... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/tools/maf/maf_stats.py | Python | gpl-3.0 | 5,080 | [
"Galaxy"
] | 6cd5ae164b3e9368491eb50c0f9535b4b8d4d02b66c712998ec8196a5c5a3113 |
"""
Item atlas.
All items and relevant objects/functions will be defined here.
All item data is copied/mirrored from the FoE source.
Body related things are NOT defined here! They are in body.py
"""
class Item: # Base Item object
def __init__(self, name_, fxStr_="", desc_="", type_=None):
sel... | PythonicMoron/FoEditor | FoEditor/atlas.py | Python | gpl-3.0 | 10,301 | [
"Amber"
] | f94ca9dec2f738c46d21822f28eaf43bc577b2d9f092347ab76610c76698b417 |
import json
from django.http import HttpResponse
from catmaid.models import Class, ClassInstance, Relation, UserRole
from catmaid.control.authentication import requires_user_role
from catmaid.control.common import get_class_to_id_map, get_relation_to_id_map
# All classes needed by the tracing system alongside their... | htem/CATMAID | django/applications/catmaid/control/tracing.py | Python | agpl-3.0 | 4,974 | [
"NEURON"
] | 61980fcb112f9ce0110b5cf65f7583f09d8b6de440a29fbf6cfdfa7465499aae |
""" Process functions for raw data from position sensitive detectors.
"""
from dateutil.parser import parse
import numpy as np
from scipy.signal import find_peaks, savgol_filter
from scipy.interpolate import interp1d
from scipy.optimize import curve_fit
from nPDyn.dataParsers.xml_detector_grouping import IN16B_XML... | kpounot/nPDyn | nPDyn/dataParsers/process_functions.py | Python | gpl-3.0 | 19,486 | [
"Gaussian"
] | 2bcc490322b92c7be8fca791d2dca54f843f78000eb6a1507d4fa5db2dd67da5 |
import os
import sys
try:
import vistrails
except:
#try to append vistrails source dir relative to examples/scripting
this_dir = os.path.split(__file__)[0]
sys.path.append(os.path.join(this_dir, '../..'))
import vistrails
import vistrails.core.application
import vistrails.core.db.action
import vis... | Nikea/VisTrails | examples/scripting/vtk_book_3rd_p189_script.py | Python | bsd-3-clause | 4,662 | [
"VTK"
] | 58c5046aca16a6ef8603c82c0aa3ca9b2a480a7d5b36085d3a8f0a6014ae4b44 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTreeWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | nagyistoce/devide | modules/vtk_basic/vtkTreeWriter.py | Python | bsd-3-clause | 468 | [
"VTK"
] | 7d4a236582aa714e1798617e4e0b76cf8bc67cc5a426101161a748e3512743e8 |
'''
This is the first Python program I've written completely from scratch.
It is a basic script that will output the U.S. Supreme Court makeup based on user input of a year.
I'm making it to practice objects, syntax, proper PEP 8 conventions, and source code management.
It will be updated with more functionality as I g... | burankar/Supreme-Court-script | SCScript.py | Python | mit | 3,801 | [
"Brian"
] | 9bed3fa726252b2b61d6b3041c35a95b19190494590b1464dc18d9a415165784 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-pilot-summary
# Author : Stuart Paterson
########################################################################
"""
Usage:
dirac-admin-pilot-summary [options] ...
Example:
$ dirac-admin-pilot-s... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_pilot_summary.py | Python | gpl-3.0 | 1,695 | [
"DIRAC"
] | 82e729d7c00753487e1f2cfafda2d0ffdf6a73bf4257a50d1471fb2236f4f845 |
"""
This library allows you to quickly and easily use the SendGrid Web API v3 via
Python.
For more information on this library, see the README on Github.
http://github.com/sendgrid/sendgrid-python
For more information on the SendGrid v3 API, see the v3 docs:
http://sendgrid.com/docs/API_Reference/api_v3.html
F... | blackpioter/sendgrid-python | sendgrid/__init__.py | Python | mit | 665 | [
"VisIt"
] | c8159a95b7811123e682c5f98ba08afc79be03a99b3afcdfbd2b7d62a28747c4 |
import Avogadro
import unittest
from PyQt4.Qt import *
import sys
class TestPluginManager(unittest.TestCase):
def setUp(self):
self.pm = Avogadro.PluginManager.instance
self.pm.loadFactories()
#def test_factories(self):
# factories = self.pm.factories(Avogadro.PluginType.EngineType)
# self.assertN... | rcplane/periodicdisplay | reference/avogadro/libavogadro/src/python/unittest/pluginmanager.py | Python | gpl-2.0 | 2,555 | [
"Avogadro"
] | ea19e62c6641c46e95aa255f580ac1ca2d07ce6df1cb6ecedeb0c9bff10d3145 |
#!/usr/bin/env python
# Corey Brune - Feb 2017
#Description:
# Update Environment
#
#Requirements
#pip install docopt delphixpy
#The below doc follows the POSIX compliant standards and allows us to use
#this doc to also define our arguments for the script.
"""Description
Usage:
dx_update_env.py (--pw <name> --env_na... | mcbrune/delphixpy-automation | v1_8_0/dx_update_env.py | Python | mit | 11,167 | [
"ASE"
] | 87ae2c63724e2b64bca392398607390db020b10ce6865483a709e2bbb4072a74 |
# $HeadURL: $
""" InfoGetter
Module used to match the decision parameters with the CS. In general terms, the
decision parameters dictionary looks like ( but does not need to contain all
key-value pairs ):
{
'element' : str | None | list( str ),
'name' : ..same..
'elementType' : ..same... | Sbalbp/DIRAC | ResourceStatusSystem/Utilities/InfoGetter.py | Python | gpl-3.0 | 7,947 | [
"DIRAC"
] | 9ef3e24d907b61082c9dad9ae4adc36a589129a0cf8c8d0f496f382ed1a532a0 |
infty=1000000
def cheapestPath(states,transitionCost):
#states is of the form [[0,0,0],[0,0],[0,0,0],[(0,0),(0,0)]] with (0,0)'s in the last column
for n in range(1,len(states)):
for s in range(len(states[len(states)-n-1])):
cost=infty+1
for t in range(len(states[len(states... | craigfreilly/masters-project-submission | src/KnotTheory/HFK-Zurich/simplify/pairing.py | Python | mit | 2,696 | [
"VisIt"
] | 98b055f0956211d9ad28fc71387a2d50d30744b8fcd08c0ae20f71ddad9158d4 |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | bkendzior/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 100,060 | [
"Gaussian"
] | 915a79cbba89716d5b440a56b3d57c5d9436bbc8e822e6812fc182cc661756eb |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/export/desktop_service.py | Python | gpl-2.0 | 1,495 | [
"VisIt"
] | 3f90b39a6eb6fb298a4ed4d9d4c75ca8eba4b1e4b6ec42d449ae04df7cca2596 |
# Copyright (c) 2014 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
This script is intended for use as a GYP_GENERATOR. It takes as input (by way of
the generator flag config_path) the path of a json file that dictates th... | greggman/hft-exe | node/win/node_modules/npm/node_modules/node-gyp/gyp/pylib/gyp/generator/analyzer.py | Python | bsd-3-clause | 22,005 | [
"VisIt"
] | dee398f036d699520dcfec58f47539cfb8c3221d5ef3fd6a1c3b21ba640126bf |
__author__ = 'Matteo'
__doc__='''Comparison of two genomes. One whole, the other in contigs.
As I am currently working on a windows, the two blast commands were done manually'''
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast import NCBIXML
from Bio import SeqIO
import csv
#cmd=NcbiblastnComma... | matteoferla/Geobacillus | geo_genomic_mismatch.py | Python | gpl-2.0 | 4,346 | [
"BLAST"
] | 6ae4997b0be55079a77c845463dd92f4a1caac8d791c4c6674c4c92c601c5352 |
#!/usr/bin/env python3
import os
from pathlib import Path
import pytest
from pysisyphus.helpers import geom_from_xyz_file
from pysisyphus.optimizers.BFGS import BFGS
from pysisyphus.calculators.OpenMolcas import OpenMolcas
from pysisyphus.init_logging import init_logging
@pytest.mark.skip
def test_molcas_s1_opt():
... | eljost/pysisyphus | tests_staging/test_molcas_s1_opt/test_molcas_s1_opt.py | Python | gpl-3.0 | 1,648 | [
"OpenMolcas"
] | 45a667674190225cf8b1c966880f74663b69eb7659a2fa36348cae8e156a844b |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | jlcarmic/producthunt_simulator | venv/lib/python2.7/site-packages/scipy/special/add_newdocs.py | Python | mit | 73,935 | [
"Gaussian"
] | cb72c1a221fa8eba4082b025f17e041cf63400c5586d6c2dda62241804570863 |
# Authors: Nicolas Goix <nicolas.goix@telecom-paristech.fr>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# License: BSD 3 clause
import numbers
import numpy as np
from scipy.sparse import issparse
from warnings import warn
from ..tree import ExtraTreeRegressor
from ..utils import (
chec... | kevin-intel/scikit-learn | sklearn/ensemble/_iforest.py | Python | bsd-3-clause | 18,971 | [
"Gaussian"
] | f31fb7bfc59df87b2326a6598d014414656da04ad2d65fdbc95a9ec78a5765ec |
from termcolor import cprint, colored
import os
import logging
import subprocess
os.system("clear")
import botogram
cprint("First libraries loaded...", "blue")
from serverside import Latte
cprint("Latte loaded...", "yellow")
from serverside import Mocha
cprint("Mocha loaded...", "yellow")
from serverside import Cappuci... | egeemirozkan/Cardinal | cardinal.py | Python | mit | 4,230 | [
"ESPResSo"
] | f3b2e2160fb6fd6cbfa54f17824bf16e10509d6574ecb79632aabe3915795e2a |
# Copyright 2014 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.
from telemetry.page.page_set import PageSet
from telemetry.page.page import Page
class Alexa1To10000Page(Page):
def __init__(self, url, page_set):
su... | mxOBS/deb-pkg_trusty_chromium-browser | tools/perf/page_sets/alexa1-10000.py | Python | bsd-3-clause | 666,176 | [
"ADF",
"CASINO",
"MOE"
] | 47eda75daf1e805baba9c830315f235c55fde2882d9addcd7df63c1c39710f49 |
#******************
# MODULE DOCSTRING
#******************
"""
LOMAP: Graph generation
=====
Alchemical free energy calculations hold increasing promise as an aid to drug
discovery efforts. However, applications of these techniques in discovery
projects have been relatively few, partly because of the difficulty of... | nividic/Lomap | lomap/graphgen.py | Python | lgpl-2.1 | 39,722 | [
"RDKit"
] | 6a92ceb36466d0eba82e576b65f8c8f8706142b76055ab7efd5136772d966d50 |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
renderer = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(renderer)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
vol = vtk.vtkStructuredPoints()
vol.SetDimensions(2... | lorensen/VTKExamples | src/Python/StructuredPoints/Vol.py | Python | apache-2.0 | 1,607 | [
"VTK"
] | c8e863bd0a1af33db7ac26a73f2d38446970b7be417693401685b650c55112b6 |
""" Transition methods to allow to move from DEncode to JEncode
"""
import os
from DIRAC.Core.Utilities import DEncode, JEncode
def encode(inData):
"""Encode the input data
:param inData: data to be encoded
:return: an encoded string
"""
if os.getenv("DIRAC_USE_JSON_ENCODE", "NO").lower() in ("... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/MixedEncode.py | Python | gpl-3.0 | 1,129 | [
"DIRAC"
] | 78d2cc5e746330c1cef18d9763ccd06396382d6234e09f64ca3b312dd9b1f799 |
########################################################################
# $HeadURL $
# File: CleanReqDBAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/17 08:31:26
########################################################################
""" :mod: CleanReqDBAgent
=====================
.. modul... | sposs/DIRAC | RequestManagementSystem/Agent/CleanReqDBAgent.py | Python | gpl-3.0 | 5,684 | [
"DIRAC"
] | aa74678539fadeb1a4248522fe5439d5b7f2fd3fb6a1f6cd9fc3b3b39f122d28 |
import math
import random
import numpy
from numpy import *
# dt = 0.001 # simulation time step
# t_rc = 0.02 # membrane RC time constant
# t_ref = 0.002 # refractory period
# t_pstc = 0.1 # post-synaptic time constant
# N_A = 50 # number of neurons in first population
# N_B = 40 # nu... | harshkothari410/snn-image-segmentation | snn.py | Python | mit | 3,629 | [
"NEURON"
] | 250d3724d9b3870927d237ad55cb112463952e9a69294ba014e9d336cf03f0e5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from fractions import Fraction
import numpy as np
import re
from pymatgen.core import Lattice
from pymatgen.util.string import transformation_to_string
from py... | czhengsci/pymatgen | pymatgen/symmetry/settings.py | Python | mit | 7,044 | [
"pymatgen"
] | 1e4ba4d315c0722dbb7729ffc7e7d06e29108dc804454ceb58134cc4b3db2500 |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, PurePoly, poly,
parallel_poly_from_expr,
degree, degree_list,
total_degree,
LC, LM, LT,
pdiv, prem, pquo, pexquo,
div, rem, quo, exquo,
half_gcdex, gcdex, invert,
subre... | wxgeo/geophar | wxgeometrie/sympy/polys/tests/test_polytools.py | Python | gpl-2.0 | 111,970 | [
"Gaussian"
] | dba601b6d0b133c23020094d91af15a1d04ed029bdfa2fef1c3f0ce296900fd4 |
import schwalbe_couplings
import mdtraj as md
import msmbuilder.decomposition, msmbuilder.featurizer, msmbuilder.msm
import pymbar
import pandas as pd
lag_time = 25
#filename0 = "./data/mixed_alanineexplicit_LangevinIntegrator_2.000_0.%s"
#filename0 = "./data/mixed_alanineexplicit_XCHMCRESPAIntegrator_2.000_0.%s"
#fi... | kyleabeauchamp/HMCNotes | code/obsolete/analyze_inefficiency.py | Python | gpl-2.0 | 3,285 | [
"MDTraj"
] | 295c3e54933ef57b62376d923390ca24d80a571c3f8c0748a43f2698677461a5 |
#! /usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Module: netcdf_to_shape.py
Created on Sun Jul 28 15:51:04 2013
@author: gcoombes
Dexcription: Create a shapefile of contours or probability regions from teh netcdf data
"""
### IMPORTS ###
from __future__ import print_function
import sys, os
import time
from itertoo... | gjcoombes/banks | banks/shape/profile_shape.py | Python | mit | 8,378 | [
"NetCDF"
] | c8e5c8a599f50ff242edaa044c70adabd892f7335cdf30b9760f0605be27c610 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Brian Meeker
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at http://trac.edgewall.org/wiki/TracLicense.
#
# This software consists of vol... | nextview/medicticket | txomon/ticket/batch.py | Python | bsd-3-clause | 9,285 | [
"Brian"
] | 530aba9ac43b7bc6e0e2fc98f653edc559a2e05411479db95e8585e754d1d311 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# lccs.py - Waqas Bhatti (wbhatti@astro.princeton.edu) - Aug 2018
# License: MIT - see LICENSE for the full text.
'''This contains functions to search for objects and get light curves from a
Light Curve Collection server (https://github.com/waqasbhatti/lcc-server) using
i... | lgbouma/astrobase | astrobase/services/lccs.py | Python | mit | 72,693 | [
"VisIt"
] | ae1ca7e01dc3bb9b7e3c2a8980ce28d591038bb23e8c8c4d44344e201f5e5daa |
WORDS = (
'Aaron',
'Abdul',
'Abe',
'Abel',
'Abraham',
'Abram',
'Adalberto',
'Adam',
'Adan',
'Adolfo',
'Adolph',
'Adrian',
'Agustin',
'Ahmad',
'Ahmed',
'Al',
'Alan',
'Albert',
'Alberto',
'Alden',
'Aldo',
'Alec',
'Alejandro',
'Alex',
'Alexander',
'Alexis',
'Alfonso',
'Alfonzo',
'Alfred',
'Al... | geradcoles/random-name | randomname/lists/names_male.py | Python | apache-2.0 | 28,040 | [
"Brian",
"COLUMBUS",
"Dalton",
"Desmond",
"MOE"
] | 72ea5c85db62c8dc6447a0e9f08d428bf02e8f59cd4dc762bdb29fcce481d04d |
#!/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.
"""Generates .h and .rc files for installer strings. Run "python
create_string_rc.py" for usage details.
This script generates an ... | patrickm/chromium.src | chrome/installer/util/prebuild/create_string_rc.py | Python | bsd-3-clause | 15,550 | [
"xTB"
] | 40cbd128ba31bd45f1d6619afed56bc3ad2e39bc6adb7369b84e71bb0582747e |
########################################################################
# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015.
# It is licenced under the GPL 2.1 or higher.
# There is no warranty of any kind. You are welcome to make copies under
# the provisions of the GPL.
# This program builds a multiscale ... | dilawar/moose-full | moose-examples/paper-2015/Fig4_ReacDiff/Fig4GHIJ.py | Python | gpl-2.0 | 9,902 | [
"MOOSE"
] | 1452eb5d7c5ea8fe8fe1fcaea5cecab863891c794219b95a7f92e4c901df2ff4 |
# -*- coding: utf-8 -*-
"""Models for the flooding_lib app."""
import datetime
import logging
import operator
import os
from shutil import copyfile
from treebeard.al_tree import AL_Node # Adjacent list implementation
from django.conf import settings
from django.contrib.auth.models import User, Group
from django.con... | lizardsystem/flooding-lib | flooding_lib/models.py | Python | gpl-3.0 | 75,687 | [
"NetCDF"
] | dbb2b78b0d7116f48d2765a4aa7c5b0c7f93eab8e0adc33608b831053da676ab |
import unittest
from test import support
import sys
import random
import math
import array
# SHIFT should match the value in longintrepr.h for best testing.
SHIFT = sys.int_info.bits_per_digit
BASE = 2 ** SHIFT
MASK = BASE - 1
KARATSUBA_CUTOFF = 70 # from longobject.c
# Max number of base BASE digits to use in te... | technologiescollege/Blockly-rduino-communication | scripts_XP/Lib/test/test_long.py | Python | gpl-3.0 | 49,171 | [
"Brian"
] | cf9cbac67a7c1622ebdcd6a5c220a0a3562f2654a460ecbc45e4c9a61a052885 |
# (c) Nelen & Schuurmans. GPL licensed, see LICENSE.rst.
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from __future__ import print_function
from django.contrib.gis.gdal import DataSource as GDALDataSource
from django.db import models
from django.utils.translation import ugettext_lazy as _
from dpn... | nens/dpnetcdf | dpnetcdf/models.py | Python | gpl-3.0 | 8,148 | [
"NetCDF"
] | b459e52a29f8aed1c829f84be3e5938d2c0754a01c0bdca25b3371b49fb2920e |
# Copyright 2017 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... | jiaphuan/models | research/gan/mnist/networks.py | Python | apache-2.0 | 9,112 | [
"Gaussian"
] | 4bc200fdd184a40ebad7bac755cee79d53b5a74a9b4a11ac86ec2c390788ab91 |
#!/usr/bin/python
import os, subprocess, argparse, sys, re
from random import randint
from shutil import rmtree, copytree
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--bowtie_index',nargs=1,help='path to bowtie index',required=True)
parser.add_argument('--genome',nargs=1,help='path refere... | jason-weirather/py-seq-tools | seqtools/cli/legacy/splicemap_wrapper.py | Python | apache-2.0 | 3,515 | [
"Bowtie"
] | 3903bd02cf5267b7636382e0f28beefed413133a8f09263828da14a9da33c8f1 |
# coding: utf-8
from __future__ import unicode_literals, division
import math
# New QChem job module
import os
import shutil
import copy
import subprocess
import numpy as np
from pymatgen.core import Molecule
from pymatgen.io.qchem.inputs import QCInput
from pymatgen.io.qchem.outputs import QCOutput
from pymatgen.a... | specter119/custodian | custodian/qchem/jobs.py | Python | mit | 12,713 | [
"pymatgen"
] | 4b859a979ea531386ab4ade8381065806d0daedbee1c914ca423ffe4d4541c74 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk, gobject, pango
from zeroinstall import _, translation
from zeroinstall.support import tasks, pretty_size
from zeroinstall.injector import model, reader
import properties
from zeroinstall.gtkui.icon import... | dabrahams/zeroinstall | zeroinstall/0launch-gui/iface_browser.py | Python | lgpl-2.1 | 17,972 | [
"VisIt"
] | f9e3d714f9c113ddce6b5261eea8aad8fc52957a95e35328f5d9a245920fa19c |
import numpy as np
from ase import Atom, Atoms
from ase.structure import bulk
from ase.units import Hartree, Bohr
from gpaw import GPAW, FermiDirac
from gpaw.response.bse import BSE
GS = 1
bse = 1
df = 1
check_spectrum = 1
if GS:
a = 6.75 * Bohr
atoms = bulk('C', 'diamond', a=a)
calc = GPAW(h=0.2,
... | ajylee/gpaw-rtxs | gpaw/test/bse_diamond.py | Python | gpl-3.0 | 1,675 | [
"ASE",
"GPAW"
] | 7f105828c623695416191fc24c1d386c59e4af28b81ac1fa37beebae275d7f9a |
#!/usr/bin/env python
from sys import stdout
class Disc:
def __init__(self, size):
self.size = size
def __str__(self):
return '(' + '//' * self.size + ')'
def __repr__(self):
return str(self.size)
def __cmp__(self, other):
return self.size - o... | foop/LeToco | ToOfHanoi.py | Python | gpl-3.0 | 5,993 | [
"VisIt"
] | ec4770a9fdfcab68830c992ecc2c479bcbfc395356fa72ec0ec064f2c0b7d9aa |
#! PsiAPI scanning a potential energy curve
import psi4
import numpy as np
psi4.set_output_file("output.dat", False)
mol_string = """
He
He 1 **R**
"""
mols = [(d, mol_string.replace("**R**", "%5.3f" % d)) for d in np.linspace(2, 5, 4)]
psi4.set_options({"SCF_TYPE": "DF",
"BASIS": "6-31G"})
out... | ashutoshvt/psi4 | tests/python/curve/input.py | Python | lgpl-3.0 | 710 | [
"Psi4"
] | 7e55c1ab411b76826b245be7d0faf4c84e2394c78a5df450952f05f16cc39aaf |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | civisanalytics/ansible | lib/ansible/modules/network/avi/avi_sslkeyandcertificate.py | Python | gpl-3.0 | 5,610 | [
"VisIt"
] | 11745b62d8dac047b30cf7f60fd915ad2d5346ba57a91295355c83d93f3e046c |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Description
-----------
ADVI implementation of "nerual network for posterior" with accurate entropy of
q-distribution.
TF version
----------
Tested on TF 1.4.0.
"""
import numpy as np
import tensorflow as tf
from tensorflow.contrib.distributions import Categorical,... | shuiruge/nn4post | nn4post/nn4post_advi.py | Python | gpl-3.0 | 11,626 | [
"Gaussian"
] | 22f3d1e6057061f07f3af3eb212325b536e70d2094f8ed480ef13e41dc845c29 |
# -*- coding: utf-8 -*-
"""Various text used throughout the website, e.g. status messages, errors, etc.
"""
# Status Messages
#################
# NOTE: in status messages, newlines are not preserved, so triple-quotes strings
# are ok
# Status message shown at settings page on first login
# (upon clicking primary e... | njantrania/osf.io | website/language.py | Python | apache-2.0 | 7,784 | [
"VisIt"
] | 6bb62a48379c6e37274cd231a4d73cc89879cc4f1bfa1ad41bd770cc6c2a6bde |
"""Export a rendering window to a VTKjs file.
This module holds a set of tools for exporting a VTK rendering window
to a VTKjs file that can be viewed in a web browser.
PVGeo has a webveiwer_ set up to load these files.
.. _webviewer: http://viewer.pyvista.org
Much of this export script was adopted from the
`VTKjs... | akaszynski/vtkInterface | pyvista/plotting/export_vtkjs.py | Python | mit | 25,312 | [
"ParaView",
"VTK"
] | 638db2b2c54d2f232376cac3c412ddaa6ccd21525a09977584388b1f77c9e352 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Spunky Bot - An automated game server bot
http://www.spunkybot.de
Author: Alexander Kress
This program is released under the MIT License. See LICENSE for more details.
## About ##
Spunky Bot is a lightweight game server administration bot and RCON tool,
inspired by t... | suchacoder/Urban-Terror-Server-Config-Files | opt/spunkybot/spunky.py | Python | gpl-3.0 | 196,736 | [
"VisIt"
] | 473d423579b1734c3405d3f338b08ec25b8fdb8b158d5695acdbde037a0cac9f |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/core2/PyscesCore2Interfaces.py | Python | bsd-3-clause | 69,756 | [
"PySCeS"
] | 1804ef12ff9816c34c2fb749f319362cd1d3f187236b07fe4ead602717ef4196 |
from datetime import timedelta
from dateutil.relativedelta import relativedelta
from django.utils import timezone
from edc_consent.models import ConsentType
from edc_registration.models import RegisteredSubject
from edc_constants.constants import SCHEDULED, YES, NO, NOT_APPLICABLE, POS
from td_maternal.models import ... | botswana-harvard/tshilo-dikotla | td_maternal/tests/test_maternal_ultrasound_initial.py | Python | gpl-2.0 | 3,185 | [
"VisIt"
] | 3ebeadc507d6b380d5143333cebdcbf30382a843674851f99a970a646064a00b |
#!/usr/bin/env python
from time import sleep
from django.conf import settings
from django.test import TestCase, TransactionTestCase
from django.test.client import Client
from django.utils import simplejson as json
from django.utils.timezone import now
from tastypie.bundle import Bundle
from panda import solr
from pa... | PalmBeachPost/panda | panda/tests/test_api_dataset.py | Python | mit | 26,102 | [
"Brian"
] | c0efdbbbf05311edb10f4b16560665d79ade7c5becbbe100740e2e37415631e6 |
import sys, os, string
def vtkLoadPythonTkWidgets(interp):
"""vtkLoadPythonTkWidgets(interp) -- load vtk-tk widget extensions
This is a mess of mixed python and tcl code that searches for the
shared object file that contains the python-vtk-tk widgets. Both
the python path and the tcl path are searche... | sgh/vtk | Wrapping/Python/vtk/tk/vtkLoadPythonTkWidgets.py | Python | bsd-3-clause | 2,159 | [
"VTK"
] | 0d69bfa2f5ef1f200d36446d1baf7a7a05632408565f1622bc6c656cf3234f9a |
from distutils.core import setup
setup(name="watertruck",
version="1.0",
description="watertruck REST API",
author_email="brian@python.org, annegentle@rackspace.com",
url="http://www.watertruck.io",
keywords="watertruck",
py_modules=["watertruck"],
)
| annegentle/watertruck | setup.py | Python | mit | 294 | [
"Brian"
] | 1e1b0aa50f8701a65388d2bc7d1351d152aee6f53d759afc547f2ccc4bb008a9 |
# 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 +
#pylint: disable=invalid-name,no-init
"""
Sys... | mganeva/mantid | Testing/SystemTests/tests/analysis/Diffraction_Workflow_Test.py | Python | gpl-3.0 | 9,468 | [
"CRYSTAL"
] | ce9d1cfeb679cd1c5b35bbafdaba6340db095e6cfbdb93cd4e264ff70aa562c4 |
__author__ = 'AT'
import math
from GPy.util.linalg import mdot
from numpy.ma import argsort, sort
from scipy.linalg import inv, det
from scipy.misc import logsumexp
from scipy.special import erfinv
from scipy.special._ufuncs import gammaln
import numpy as np
from util import cross_ent_normal
class Likelihood:
... | adezfouli/savigp | GP/likelihood.py | Python | apache-2.0 | 16,432 | [
"Gaussian"
] | 07393402ed03400e08bcc4375de627c6d68ef5e976935d9c22188d1215cc8625 |
"""
Filename: _clean.py
From: Brian Soe
Description: Remove all created databases.
"""
import subprocess
subprocess.call(['rm','-rf','repo'])
subprocess.call(['rm','-rf','table.db']) | bsoe003/MWCH_Website | database/_clean.py | Python | mit | 184 | [
"Brian"
] | 476e03baa5f7ca0219a6a4588b98f696d36e182c24274535b47d2a8881a23995 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test the various population analyses (MPA, LPA, CSPA, Bickelhaupt) in cclib"""
import os
import unittest
import numpy... | langner/cclib | test/method/testbader.py | Python | bsd-3-clause | 3,491 | [
"Psi4",
"cclib"
] | dde2b31dfc250d17e3e49d7d5f1614044337b89d10416aa0ef51939ec7918f5b |
# Copyright 2018 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | sbc100/yapf | yapf/yapflib/identify_container.py | Python | apache-2.0 | 2,279 | [
"VisIt"
] | 20b8761a006b72640cbf3d20f703c1cc842c3891b52a5983fe60144774abb873 |
"""
Module for managing the installation of DIRAC components:
MySQL, DB's, NoSQL DBs, Services, Agents, Executors
It only makes use of defaults in LocalInstallation Section in dirac.cfg
The Following Options are used::
/DIRAC/Setup: Setup to be used for any operation
/LocalInstallation/InstanceName: ... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Client/ComponentInstaller.py | Python | gpl-3.0 | 101,351 | [
"DIRAC"
] | 55c8435ff03f4a759a4fed4e6c249572afa357b983e8c7d68b00093d2b7c076a |
"""
=====================================================================
Reconstruction of the diffusion signal with the kurtosis tensor model
=====================================================================
The diffusion kurtosis model is an expansion of the diffusion tensor model
(see :ref:`example_reconst_dti... | villalonreina/dipy | doc/examples/reconst_dki.py | Python | bsd-3-clause | 11,951 | [
"Gaussian"
] | 5c113cfddcef9c1124d58c4a747dee48d8e4720a910e67144da463cede30eaa6 |
#!/usr/bin/env python
import sys
sys.path.append('/opt/lib/python2.7/site-packages/')
import math
import numpy as np
import pylab
import nest
import nest.raster_plot
import nest.voltage_trace
import nest.topology as tp
import ggplot
t_sim = 500
populations = [1, 100]
no_recurrent = True
neuron_model = 'iaf_psc_e... | synergetics/nest_expermiments | sparse_entertainment.py | Python | mit | 2,559 | [
"Gaussian"
] | b85e74042d13e85aa88381479589a6e257099b1704a534e9712861cb1c1bf7d5 |
__author__ = 'jiataogu'
import theano
# theano.config.exception_verbosity = 'high'
import logging
import emolga.basic.objectives as objectives
import emolga.basic.optimizers as optimizers
from emolga.layers.recurrent import *
from emolga.layers.embeddings import *
from emolga.models.encdec import RNNLM, Encoder, Decod... | memray/seq2seq-keyphrase | emolga/models/variational.py | Python | mit | 63,827 | [
"Gaussian"
] | 969586aed3df20b39f6a75f43b9ff0ae8a0eadb56d53bcb95ce3d2a7f6787ae1 |
#
# @file TestModel_newSetters.py
# @brief Model unit tests for new set function API
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by co... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestModel_newSetters.py | Python | bsd-3-clause | 35,461 | [
"VisIt"
] | 9112e69b13f4ed02852c1aae20aacebca51cedfd12ad96e1244d8a906bf83223 |
#!/usr/bin/env python
#===============================================================================
# Copyright 2017 Geoscience Australia
#
# 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... | alex-ip/geophys_utils | geophys_utils/_array_pieces.py | Python | apache-2.0 | 5,360 | [
"NetCDF"
] | 78c875f666cd8f98384417f4a7be6c151b64c950658fc4fe04df799bca7c7e29 |
#!/usr/bin/env python
# coding=utf-8
#Copyright (C) 2013 Ben Dyer
#
#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, m... | sfwa/TRICAL | python/TRICAL/__init__.py | Python | mit | 8,922 | [
"Gaussian"
] | 4ac1d218c9567f33decbfb3d4946b7e2ae654308120af9a81183c44391937c6d |
"""
Implementation of Extended-Connectivity Fingerprints algorithm (David Rogers and Mathew Hahn 2010).
This is based on the MorganFingerprints.cpp code from rdkit:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Fingerprints/MorganFingerprints.cpp
"""
from bitarray import bitarray
import copy
def gen_has... | ubccr/pinky | pinky/fingerprints/ecfp.py | Python | bsd-2-clause | 2,715 | [
"RDKit"
] | 84a09f051a868ba115a765b83067f4434c30a10c9b127a0ca60742232f5a2d2d |
# Author: Giacomo Vianello (giacomov@stanford.edu)
from scipy import interpolate
from sklearn.neighbors import KernelDensity
from astroML.density_estimation import KNeighborsDensity
import numpy
import matplotlib.pyplot as plt
import sys
class DensityEstimation(object):
def __init__(self):
raise NotImplem... | giacomov/XtDac | XtDac/DivideAndConquer/KDE.py | Python | bsd-3-clause | 4,211 | [
"Gaussian"
] | 6f34fad99f88a0110f9e02f0b603a070a3cf1b21f261ae0e8116f3d27442aa8a |
"""
Module containing implementations of some unnormalized probability density
functions.
"""
from __future__ import division
from builtins import range
from past.utils import old_div
from builtins import object
from future.utils import with_metaclass
__author__ = 'wittawat'
from abc import ABCMeta, abstractmethod
i... | wittawatj/kernel-gof | kgof/density.py | Python | mit | 19,525 | [
"Gaussian"
] | 7a25ff47d7b3497a28c604f05c8fdb97c5f7a8e9981f85c3889cf2ef885e4cc3 |
# -*- coding: utf-8 -*-
# Copyright 2009-2012 Jaap Karssenberg <jaap.karssenberg@gmail.com>
from __future__ import with_statement
import gtk
import pango
import logging
import re
import zim.datetimetz as datetime
from zim.utils import natural_sorted
from zim.parsing import parse_date
from zim.plugins import PluginC... | fabricehong/zim-desktop | zim/plugins/tasklist.py | Python | gpl-2.0 | 41,137 | [
"VisIt"
] | 5a4ca11b44d6d252f71808d0923e4a901c66131ca4468acf2cff1f8d2089e541 |
"""
A simple VTK widget for PyQt v4, the Qt v4 bindings for Python.
See http://www.trolltech.com for Qt documentation, and
http://www.riverbankcomputing.co.uk for PyQt.
This class is based on the vtkGenericRenderWindowInteractor and is
therefore fairly powerful. It should also play nicely with the
vtk3DWidget code.
... | spthaolt/VTK | Wrapping/Python/vtk/qt4/QVTKRenderWindowInteractor.py | Python | bsd-3-clause | 14,082 | [
"CRYSTAL",
"VTK"
] | c9be87a42ad9ba1818dbb0daeda8e3a9f05fd39570a5883221291019675e8aff |
# CLEANUP NOTES:
# - remove unused comments
# - add documentation for each method
# - add comments inline explaining each piece
# - add a unit test for each method (at least)
# stdlib
from functools import lru_cache
from typing import Any
from typing import Callable
from typing import Dict as TypeDict
from typing impo... | OpenMined/PySyft | packages/syft/src/syft/core/adp/search.py | Python | apache-2.0 | 14,627 | [
"VisIt"
] | b5a488e3fbc8d9e98c98f8294a02e81e8df989a60a8f177292214b7026acc2da |
#!/usr/bin/env python
import sys
import os
import re
import glob
import xmltodict
import json
import yaml
import copy
import logging
from argparse import ArgumentParser
from argparse import RawDescriptionHelpFormatter
from elasticsearch import Elasticsearch
from collections import OrderedDict
import datetime
import d... | ICGC-TCGA-PanCancer/pancancer-sandbox | pcawg_metadata_parser/generate_pcawg_specimen_alignment_summary.py | Python | gpl-2.0 | 15,813 | [
"BWA"
] | 22c46017721ba3d86c87c4a0add7c564f4a1f67563d9c58044309cb6599d0e3d |
"""CASTEP calculator interface."""
# Copyright (C) 2014 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must r... | atztogo/phonopy | phonopy/interface/castep.py | Python | bsd-3-clause | 9,507 | [
"CASTEP",
"CRYSTAL",
"VASP",
"phonopy"
] | 3ff5015d273b9dc7d0fc4824fcee327532eee677d3128712d8427198df16a102 |
#!/usr/bin/env python3
########################################################################
# Solves problem 15 from projectEuler.net.
# Finds the number of routes in a 20x20 sided square.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redistribute it and/or modify
# ... | sanSS/programming-contests | project-euler/problem015.py | Python | gpl-3.0 | 1,495 | [
"VisIt"
] | bac4798f989d67c46af955b8c8b582749fb03330580ba0ae32815682f2e3bc00 |
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from numpy.polynomial.hermite_e import HermiteE
from scipy.misc import factorial
from scipy.stats import rv_continuous
import scipy.special as special
# TODO:
# * actually solve (31) of Blinnikov & Moessner
# * numeri... | bert9bert/statsmodels | statsmodels/distributions/edgeworth.py | Python | bsd-3-clause | 6,838 | [
"Gaussian"
] | 095c660241f8775f34f0089cebd0abfd4f235f3293f147cd2cb78177e7a5c173 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""Utilities for handling, displaying and exporting Phylo trees.
Third-party libraries ... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Phylo/_utils.py | Python | gpl-2.0 | 20,914 | [
"Biopython"
] | 03c1dc801b1308e9ea2774607ef05af08618a9743cb60a1d5f12de17e2bb3b32 |
# This is an example of firing up PyMOL inside of a subordinate
# process via an "import pymol"
#
# NOTE: for this to work, PyMOL must be installed in a
# Python-dependent fashion (e.g. pymol-0_98-bin-win32-py23) etc.
#
# WARNING: stability issues have been known to occur with this
# approach, so anticipate problems..... | gratefulfrog/lib | python/pymol/pymol_path/examples/devel/importing.py | Python | gpl-2.0 | 1,994 | [
"PyMOL"
] | eb4fc791e2b9e57c9afb9af3ac4304360dc4a1382706c84b7bfa41b064421f6d |
#!/usr/bin/env python
"""
Get information on resources available for the given VO: Computing and Storage.
By default, resources for the VO corresponding to the current user identity are displayed
Usage:
dirac-resource-info [option]...
"""
from __future__ import absolute_import
from __future__ import division
from __... | yujikato/DIRAC | src/DIRAC/Resources/scripts/dirac_resource_info.py | Python | gpl-3.0 | 4,737 | [
"DIRAC"
] | 2b22c5f5ab3f28c707dee1e011e01008db16ac0a2f8543bfd475368942b9f9da |
# -*- mode: python; coding: utf-8 -*-
# Copyright (c) 2018 Radio Astronomy Software Group
# Licensed under the 2-clause BSD License
"""Tests for FHD object.
"""
import pytest
import os
import glob
import numpy as np
from shutil import copyfile
from pyuvdata import UVData
import pyuvdata.utils as uvutils
import pyuvd... | HERA-Team/pyuvdata | pyuvdata/uvdata/tests/test_fhd.py | Python | bsd-2-clause | 18,686 | [
"Gaussian"
] | d064661a24adac5e19da28f3609ab44adcd8934fd5dae534071434ae82254e3e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or ... | hlzz/dotfiles | graphics/VTK-7.0.0/Interaction/Style/Testing/Python/TestStyleJoystickCamera.py | Python | bsd-3-clause | 2,225 | [
"VTK"
] | c5542a5f52289545f90ff7c1a259ef4a89ac161ade21dac9990bd602e5fd2ac3 |
tests = [
("python", "UnitTestFilter.py", {}),
("python", "UnitTestMLData.py", {}),
("python", "UnitTestQuantize.py", {}),
("python", "UnitTestStats.py", {}),
("python", "SplitData.py", {}),
("python", "DataUtils.py", {}),
]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRun... | ptosco/rdkit | rdkit/ML/Data/test_list.py | Python | bsd-3-clause | 409 | [
"RDKit"
] | cabfd36108ecc2ff6b302ab88b4cb288f68a036f5b99865c8141ba8c05204708 |
def savevtk(v, nx, ny, nz, filename) :
""" Save a 3-D scalar array in VTK format. """
f = open(filename, 'w')
out = ""
out += '# vtk DataFile Version 2.0\n'
out += 'Comment goes here\n'
out += 'ASCII\n'
out += '\n'
out += 'DATASET STRUCTURED_POINTS\n'
out += 'DIMENSIONS %i %i %i\n' %... | robertsj/ME701_examples | vis/VTK.py | Python | mit | 959 | [
"VTK"
] | 23e29dc815d142e23e5a308840e8135e29796eab03f02338d749f506fcc5141c |
import re
import traceback
from enum import IntEnum, auto
from contextlib import suppress
from dataclasses import dataclass
from datetime import datetime
from pathlib import Path
from typing import Pattern, Union, Optional, Tuple
from dateutil.parser import parse as parse_date
from dateutil.tz import UTC
import pandas... | panoptes/PIAA | src/panoptes/pipeline/utils/metadata.py | Python | mit | 19,737 | [
"Galaxy"
] | dbe53f7cd728af267f2c46394037b55c6ca64b9a06a9ffa86fdea24811c20cad |
# (C) http://scipy-cookbook.readthedocs.io/items/Matplotlib_Interactive_Plotting.html
# Thanks to scipy
# (C) 2016, Markus Wildi, wildi.markus@bluewin.ch
#
# 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 Softw... | RTS2/rts2 | scripts/u_point/u_point/callback.py | Python | lgpl-3.0 | 5,619 | [
"VisIt"
] | 32e7a580c8284788666e916b75de45cfb829028acd33df530ec2a90c028c8f44 |
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import datetime
from matplotlib.dates import DayLocator, HourLocator, DateFormatter, drange, date2num, num2date
fr... | CopyChat/Plotting | Python/plot_date.py | Python | gpl-3.0 | 2,154 | [
"NetCDF"
] | 0c60a97052ce1a60fb2b72a42477f98d32ea00f899746aeaaddead76baa14799 |
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