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 |
|---|---|---|---|---|---|---|---|
"""SCons.Util
Various utility functions go here.
"""
#
# Copyright (c) 2001 - 2015 The SCons Foundation
#
# 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
# wit... | stefanklug/mapnik | scons/scons-local-2.3.6/SCons/Util.py | Python | lgpl-2.1 | 49,031 | [
"VisIt"
] | 536667433b2b6efdc20e38abea100214cee90535c890e953da689c19842bcdb3 |
import unittest
import numpy as np
import cpnest.model
from numpy import log
class AckleyModel(cpnest.model.Model):
"""
Ackley problem from https://en.wikipedia.org/wiki/Test_functions_for_optimization
"""
names=['x','y']
bounds=[[-5,5],[-5,5]]
data = None
@staticmethod
def log_likeliho... | johnveitch/cpnest | examples/ackley.py | Python | mit | 1,070 | [
"Gaussian"
] | 29732d80517902ae40afa0a78ffff16e7fb036bd53f71f964a66552eec117498 |
#
# scope.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later ... | kperun/nestml | pynestml/symbol_table/scope.py | Python | gpl-2.0 | 13,937 | [
"NEURON"
] | 36529207a9c461923c5f0e9b9d93a255861daf800a5e8a486b51458a970c879e |
import tensorflow as tf # neural network for function approximation
import gym # environment
import numpy as np # matrix operation and math functions
from gym import wrappers
import gym_morph # customized environment for cart-pole
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import time
star... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/t39_rlvps01.py | Python | mit | 7,664 | [
"NEURON"
] | b0f126d18161272e75cbb81489561f7f91c8a0a341a31b7c16772059718340c7 |
'''
Overlaying three random-normal distributions on top
of eachother, using the color cycle defined through
`matplotlib.rc`.
The sum of the histograms is plotted using the errorbar
style. This histogram is then smoothed using a Gaussian
filter and plotted as a line.
'''
from cycler import cycler
import numpy as np
fr... | theodoregoetz/histogram | examples/plot_1d_advanced.py | Python | gpl-3.0 | 1,653 | [
"Gaussian"
] | 5a55653694d474bf29535a199a5d95a2e9be57c62dda3c769d534194823238cb |
#!/usr/bin/env python3
import itertools
from collections import defaultdict
import logging
from operator import mul
import networkx as nx
import numpy as np
import pandas as pd
from pgmpy.base import DirectedGraph
from pgmpy.factors.discrete import TabularCPD, JointProbabilityDistribution, DiscreteFactor
from pgmpy.... | kris-singh/pgmpy | pgmpy/models/BayesianModel.py | Python | mit | 33,677 | [
"VisIt"
] | 3ab77497fd651862f64a6ee5833d189be0092dcecd8dd601e1c5c3551f4978d0 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songs/lib/oooimport.py | Python | gpl-2.0 | 9,845 | [
"Brian"
] | 9857ec53f022eba673530690fbca9259eac002c9fa1aa9be7756a528c8206620 |
#!/usr/bin/env python
"""
Important Notice:
--references has been removed, please use --reference (multiple uses are ok)
align FASTQ, SAM, or BAM file (gzip and bzip2 supported)
with bowtie, produces BAM files (sorted and indexed)
output will be in ./align
In align, there will be a folder for each reference genome
... | benjschiller/seriesoftubes | scripts/align.py | Python | artistic-2.0 | 23,102 | [
"Bowtie"
] | e0f40de6966fa18d9d4269d381817a70bd283a95d294c8c1c2e41f7b44040bce |
import matplotlib.pyplot as plt
import os
from astropy.table import Table
import numpy as np
# setup information sources
degas = Table.read(os.path.join(os.environ['SCRIPTDIR'],'degas_base.fits'))
stack = Table.read('/lustre/cv/users/akepley/degas/stack_test/stack_IR6p0_mom1.fits')
plotDir = os.path.join(os.environ['... | low-sky/degas | scripts/plot_SFEdense_vs_mstar_combined_nolim.py | Python | gpl-3.0 | 2,160 | [
"Galaxy"
] | 13e44089e0f9e2d32c59135e2ebad7b372f556ce0fcbb7b5655e47a59f7c7ca0 |
##########################################################################
#
# Copyright (c) 2016, Image Engine Design Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistrib... | boberfly/gaffer | python/GafferArnoldTest/IECoreArnoldPreviewTest/RendererTest.py | Python | bsd-3-clause | 98,013 | [
"Gaussian"
] | 7688e330dd0cecd8a560fc49a9095d98b815f0de61475e0df8ebf7da656b760c |
import json
from collections import namedtuple
from pgmagick import Blob, Image
from django.conf import settings
from django.db import connection
from django.http import Http404, HttpResponse, StreamingHttpResponse
from django.shortcuts import get_object_or_404
from django.templatetags.static import static
from catma... | catsop/CATMAID | django/applications/djsopnet/control/slice.py | Python | gpl-3.0 | 18,511 | [
"NEURON"
] | ccf6959b20bf7548a6540d4109f2ee79d306074adcb105183e6c9eb223fdca44 |
#!/usr/bin/env python
import os
import sys
import numpy as np
import getopt
import subprocess as sub
import lcg
from lxml import etree
from numpy.random import uniform as rnd
def usage():
print('\nUsage: %s mode [option <value>]' % os.path.basename(sys.argv[0]))
print('Simulates a network of neurons randomly ... | danielelinaro/dynclamp | python/lcg/izhikevich_network.py | Python | gpl-3.0 | 14,529 | [
"NEURON"
] | 86a93f52cb39e334ca7e2fef812627bdf47ac2a2279b074db6faf29984417d16 |
from numpy import *
from numpy.random import *
from plotting.plot_images import *
from plotting.myplot import *
from plotting.covariance_ellipse import *
from spikes.spikes import *
import matplotlib.image as img
import matplotlib.cm as cm
import matplotlib.gridspec as gridspec
def new_g_pairs(make):
# make: make i... | zsomko/visualcortex | python/spikes/poster_saved.py | Python | gpl-2.0 | 25,775 | [
"Gaussian",
"NEURON"
] | 90db44e59463929a35a0c0b0482456eb41ab1550bff200c27a62d698b3c54803 |
import os
import signal
from django.core.exceptions import MiddlewareNotUsed
class ColumbusMiddleware(object):
def __init__(self):
current_pid = os.getpid()
print "Checking for an already running supervisor"
if os.path.exists('columbus-supervisor.pid'):
with open('columbus-supe... | jkachika/columbus | pyedf/middleware.py | Python | mit | 1,183 | [
"COLUMBUS"
] | 6dcb34b1d66c1a837b1f6fba92d06b85f2f7721cb515e27ffec90d4127590468 |
#!/usr/bin/env python
'''
V2015-05-03
'''
import os
import csv
from itertools import ifilter
import sys
"""
COMMON FUNCTIONS
"""
def output_header_file_old(infile,skip,output_handle,sup_list=[],eliminate=0):
##Version1.0
##write header into files
reader=csv.reader(open(in... | bioliyezhang/c3_utils | c3_utils/general_class.py | Python | mit | 37,965 | [
"BWA"
] | 96bf8f0b75176338ac655fc2f2a8b09488dfca5e1a1c8a1d8c8be326f028c808 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from deepy import *
from attention_reader import AttentionReader
from attention_writer import AttentionWriter
from qsampler import Qsampler
ENCODER_HIDDEN_DIM = 256 # 256
DECODER_HIDDEN_DIM = 256 # 256
LATENT_VARIABLE_DIM = 100 # 100
READING_GLIMPSE_SIZE = 2
WRITING_GLIMP... | dlacombejr/deepy | experiments/draw/core/draw_layer.py | Python | mit | 5,540 | [
"Gaussian"
] | f419ade60f389ceba7ba2a9966f2ea2e0d9d417bffc24798bcfffbb4d497914c |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
import itertools
from django.core.urlresolvers import reverse, NoReverseMatch
from django.template import (TemplateSyntaxError,
Context, Template, loader)
i... | wfxiang08/django178 | tests/test_client_regress/tests.py | Python | bsd-3-clause | 63,999 | [
"VisIt"
] | 92020c500ffb58ddc748587cd1db0f7f9bfb73e70b32094710c459774773e2c0 |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
def grid_wineGBM():
wine = h2o.import_file(path=tests.locate("smalldata/gbm_test/wine.data"))
#wine.summary()
x_cols = range(2,14) + [0]
wine_grid = h2o.gbm(y=wine[1],
x=wine[x_cols],
... | kyoren/https-github.com-h2oai-h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_NOFEATURE_grid_wineGBM.py | Python | apache-2.0 | 569 | [
"Gaussian"
] | 379262c3b0032cfb0064d521c8392d9b3c681c1221026f4d83e9617d31ea43a9 |
#!/usr/bin/env python
#
# Copyright 2008,2009,2011,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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, or (a... | gnychis/grforwarder | gr-uhd/apps/uhd_siggen.py | Python | gpl-3.0 | 15,685 | [
"Gaussian"
] | c9adecf367218d84d5870ed2da47d00b424ea311dcec729c196c6e6287a9769d |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015-2017 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#... | mas-dse-greina/neon | luna16/old_code/LUNA16_VGG.py | Python | apache-2.0 | 8,032 | [
"Gaussian"
] | 6e5ee5721b65f092c49b2d696ae8d9e6c958f944060451e515ac9bbc249eb5fe |
## -*- coding: utf-8 -*-
## Copyright (c) 2015-2022, Exa Analytics Development Team
## Distributed under the terms of the Apache License 2.0
#"""
#ADF Dirac Parser
##########################
#Parser for the output of the DIRAC program (part of the ADF suite).
#"""
#from exatomic.exa import Parser, Matches
#
#
#class DI... | exa-analytics/exatomic | exatomic/adf/dirac/dirac.py | Python | apache-2.0 | 695 | [
"ADF",
"DIRAC"
] | 7fd7c5f3e321fd8eddf8708286422b72d27b131f7c72b42522ad71c8fcb5af4a |
# -*- coding: utf-8 -*-
# PyKnot: A PyMOL plugin for discovery and analysis of knots in protein structures
# Script/plugin by Rhonald Lua (rhonald.lua@gmail.com)
#
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
# NO EVEN... | rlua/PyKnot | PyKnot3.py | Python | mit | 172,710 | [
"PyMOL"
] | e8619fe1eeb8ac3f1f91dd18eb1ce99101f3aebae28d231586234cbe31145b9c |
# -*- coding: utf-8 -*-
import datetime
import uuid
from time import sleep
from unittest import TestCase
import mock
from flask_mauth.cacher.security_token_cacher import SecurityTokenCacher
from flask_mauth.exceptions import InauthenticError, UnableToAuthenticateError
from tests.common import load_key
class TestSe... | mdsol/flask-mauth | tests/test_security_token_cacher.py | Python | mit | 5,333 | [
"GULP"
] | 7ba0345e3e6763a41fa5963ea9c2614ae7a791d2ef9b94b5401371f3ffb9d0d3 |
#!/usr/bin/env python
# Modified to always use the installation path to store and read the client_secrets.json and pyu-oauth2.json file
import httplib
import httplib2
import os
import random
import sys
import time
from apiclient.discovery import build
from apiclient.errors import HttpError
from apiclient.http import ... | rodrigopolo/cheatsheets | upload_video.py | Python | mit | 7,001 | [
"VisIt"
] | 77c27f4b24a1fa15bdc743c92b21ef3775ba0ab14d4693c0fe89874ee4f604ff |
########################################################################
# File: StorageElementHandler.py
########################################################################
"""
:mod: StorageElementHandler
.. module: StorageElementHandler
:synopsis: StorageElementHandler is the implementation of a simple Storag... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Service/StorageElementHandler.py | Python | gpl-3.0 | 17,602 | [
"DIRAC"
] | 5f00de988969bcf8588aba136115131d9ee7d829d81846af6440fcc5172fae9d |
from ddapp import applogic
from ddapp import vtkAll as vtk
from ddapp import callbacks
from ddapp.fieldcontainer import FieldContainer
from ddapp import ik
from ddapp import ikplanner
from ddapp import irisdriver
from ddapp import raycastdriver
from ddapp import objectmodel as om
from ddapp import perception
from ddapp... | edowson/director | src/python/ddapp/robotsystem.py | Python | bsd-3-clause | 8,161 | [
"VTK"
] | 95abe986dccbb96fbc083ba99494558330e6ffdffc3987ab4afef9ae7d127a91 |
"""
========================================
Ammonia inversion transition TKIN fitter
========================================
Ammonia inversion transition TKIN fitter translated from Erik Rosolowsky's
http://svn.ok.ubc.ca/svn/signals/nh3fit/
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
Module API
^^^... | mikelum/pyspeckit | pyspeckit/spectrum/models/ammonia.py | Python | mit | 40,916 | [
"Gaussian"
] | 4595c228aa3e07eee36a703467bdd9e7fb7a8fa84d2dc530e93b88264ffe9c79 |
import os
import sys
# FREEZING REQUIREMENTS
if getattr(sys, 'frozen', False):
sys.path.append(os.path.join(os.path.dirname(sys.executable), 'bin'))
sys.path.append(os.path.join(os.path.dirname(sys.executable), 'bin\\library.zip'))
absDir = os.path.join(os.getcwd(), os.path.dirname(sys.executable))
else:
... | chondonihailka/PyVGDemo | PyVGDemo.py | Python | mit | 852 | [
"VisIt"
] | 6affe8f7e9832a71174b4812d5fe0849bf8518e42085a07f2fecc9ed8b96a654 |
"""
Merge the annotations from singlem to contigs.
Given:
- singlem output
- bam file with reads mapped to contigs
Return
- a percentage annotation of each contig
- perhaps also a definitive annotation
"""
import os
import sys
import argparse
import pysam
__author__ = 'Rob Edwards'
def read_kraken... | linsalrob/EdwardsLab | annotations/singlem_reads_to_contigs.py | Python | mit | 6,776 | [
"pysam"
] | 4ca3734323a0ea487aa1b27fe9478b4fda6c9df243bd4159dd7681e206077ecd |
# $Id$
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Dihedrals plugin
================
Analyze one or more dihedral angles.
Plugin class
------------
.. autoclass:: Dihedrals
:members: worker_c... | pslacerda/GromacsWrapper | gromacs/analysis/plugins/dihedrals.py | Python | gpl-3.0 | 10,795 | [
"Gromacs"
] | 4db0d5db8c391b78c17ae0bb3987683b29257a0e0da7b5c83c9c6f680d37cf88 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
#
# 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 Fr... | arunkgupta/gramps | gramps/plugins/rel/rel_pl.py | Python | gpl-2.0 | 33,677 | [
"Brian"
] | 37edec5f5fa9d2b366854023ae8e54b6f87005c8a4cefdd16d03124fdb016c2e |
# 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 | rapid_categorization/cross-validation check/hmm_force_motion_variable_length.py | Python | mit | 15,948 | [
"Gaussian",
"Mayavi"
] | 4a54c71698be0481f75c19a64e552c1968f45a9f8dccebb285a03538d409e861 |
import logging
import lib.const as C
import lib.visit as v
from ...meta.template import Template
from ...meta.clazz import Clazz
from ...meta.method import Method
from ...meta.field import Field
from ...meta.statement import Statement, to_statements
from ...meta.expression import Expression, to_expression
class View... | plum-umd/pasket | pasket/rewrite/android/view.py | Python | mit | 6,397 | [
"VisIt"
] | 937629b8d468ec1db2ff205720e10c2e19efc3c28a2a2a7d93edae48a9417497 |
#!/usr/bin/env python
import os
import time
import argparse
import subprocess
import logging as log
from bioblend import galaxy
from subprocess import CalledProcessError
def main( args, shed_tools_root = '/shed_tools' ):
"""
Load files into a Galaxy data library.
By default all test-data tools from all i... | bgruening/galaxy-rna-workbench-extra | setup_data_libraries.py | Python | mit | 3,108 | [
"Galaxy"
] | b3f7b538e3a1496df65b6a2703ddf216cbedc11ad385ea96fe2a434bc5661753 |
"""
Kernel Density Estimation
-------------------------
"""
# Author: Jake Vanderplas <jakevdp@cs.washington.edu>
import numpy as np
from scipy.special import gammainc
from ..base import BaseEstimator
from ..utils import check_array, check_random_state
from ..utils.validation import _check_sample_weight, check_is_fitt... | bnaul/scikit-learn | sklearn/neighbors/_kde.py | Python | bsd-3-clause | 10,833 | [
"Gaussian"
] | d047dc3a9cafe0ce411ee05287dff09651393dfc53023780235204ca65ae48e9 |
"""
tests the pysat utils area
"""
import pysat
import pandas as pds
from nose.tools import assert_raises, raises
import nose.tools
import pysat.instruments.pysat_testing
import numpy as np
import os
import tempfile
import sys
if sys.version_info[0] >= 3:
if sys.version_info[1] < 4:
import imp
re_l... | aburrell/pysat | pysat/tests/test_utils.py | Python | bsd-3-clause | 7,345 | [
"NetCDF"
] | 1787591ebe02c98f56c6e06a11197ba21ea6018191c017dd28b029b89a00acee |
"""
It is used to load classes from a specific system.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Core.Utilities.ObjectLoader import loadObjects
| ic-hep/DIRAC | src/DIRAC/Core/Utilities/Plotting/ObjectLoader.py | Python | gpl-3.0 | 227 | [
"DIRAC"
] | 3f3c155f22956e22c6101e6e0004ebca24d54b8ac4f99b75381df8fc98ea1dfb |
from appfd.models import Place
from django.core.mail import send_mail
from selenium import webdriver
from time import sleep
import socket
#@then(u'The number of places should be greater than 10 million')
#def check_number_of_places(context):
# assert(Place.objects.count() > 10000000)
@when("we visit the website")
d... | FirstDraftGIS/firstdraft | projfd/features/steps/general.py | Python | apache-2.0 | 3,748 | [
"VisIt"
] | 92d23bbe13c740e7f4a2b27d7420a413f6319fc04d867ee4af0f70fd28c2ef3e |
# coding: utf-8
# # Intro to satellite data I
#
# In this notebook we take a quick look at a 5 minutes of satellite data acquired from the MODIS instrument on the Aqua polar orbiting satellite. The granule covers the period from 20:15 to 20:20 UCT on May 15, 2016 (Julian day 136) while Aqua flew over Ft. McMurray... | a301-teaching/a301_code | notebooks/python/satelliteI.py | Python | mit | 6,461 | [
"Bowtie"
] | 8ed0f5e95c0f0cde2e075754154d6658bd4a7ab81d63e33581b39bae9c086510 |
#!/usr/bin/python2.7
'''
This test is for naive trainer to traine a full imagenet model
'''
from fastnet import data, trainer, net, parser
import pprint
from collections import deque
import os
test_id = 'imagenet_layerwised-2'
data_dir = '/ssd/nn-data/imagenet/'
checkpoint_dir = '/home/justin/fastnet/fastnet/checkpo... | rjpower/fastnet | experiments/run_imagenet_layerwised.py | Python | gpl-3.0 | 6,084 | [
"NEURON"
] | b5cdd421d39aa3848531b4e6a909661b2a872268fc752853709b103991d9ccf0 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
#... | dictoon/blenderseed | ui/objects.py | Python | mit | 7,091 | [
"VisIt"
] | c9e217eec111fdbe97da5f18ad8d97b459083c2cd564b02406f5e6d39719cbba |
#!/usr/bin/env python
#=========================================================================
#
# Program: Visualization Toolkit
# Module: TestProbeFilterImageInput.py
#
# Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
# All rights reserved.
# See Copyright.txt or http:#www.kitware.com/Copyrigh... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/TestProbeFilterImageInput.py | Python | bsd-3-clause | 3,405 | [
"VTK"
] | 8101b658e32be9c256d64da7a1038fa72b0445290c2b2fb20e70fff3b09b2e71 |
########################################################################
# $HeadURL$
# File : GridPilotDirector.py
# Author : Ricardo Graciani
########################################################################
"""
Base Grid PilotDirector class to be inherited MW specific PilotDirectors gLite/LCG.
It include... | avedaee/DIRAC | WorkloadManagementSystem/private/GridPilotDirector.py | Python | gpl-3.0 | 18,170 | [
"DIRAC"
] | 43f88f40dc2b3bbe5dfc84a428e020fb4dd4fd3149aff3deeeb78c8fef13c3f4 |
# Generated by Django 2.0.13 on 2019-03-05 10:16
import autoslug.fields
from django.db import migrations
def regenerate_slug(apps, schema_editor):
visits = apps.get_model('advisornotes', 'AdvisorVisit')
for visit in visits.objects.all():
if not visit.slug:
visit.save()
class Migration(m... | sfu-fas/coursys | advisornotes/migrations/0008_fix_slugs.py | Python | gpl-3.0 | 797 | [
"VisIt"
] | 7507edc4e823933329ee0453313d85e6f5e237cf1d1c00f748470c6ed242d75d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""A reader for chemical JSON (CJSON) files."""
import json
from cclib.io import filereader
from cclib.parser.data impor... | cclib/cclib | cclib/io/cjsonreader.py | Python | bsd-3-clause | 1,890 | [
"cclib"
] | 25779b4be0915025f04098186ee2f39e9e9c2b888b22dfe6873b563a355c62f0 |
"""
Replace variable that can be lazy evaluated and used only once by their full
computation code.
"""
from pythran.analyses import LazynessAnalysis, UseDefChain, Literals
from pythran.passmanager import Transformation
import ast
class _LazyRemover(Transformation):
"""
Helper removing D node and replaci... | artas360/pythran | pythran/optimizations/forward_substitution.py | Python | bsd-3-clause | 3,501 | [
"VisIt"
] | baf6674ee221e9bebac5e6e9635a7552e8b777cc9975111d6ab3be6ad8355444 |
# -*- coding: utf-8 -*-
"""Functions for adding highlighting tags to nodes and edges in BEL graphs."""
from typing import Iterable, Optional
from pybel import BELGraph
from pybel.dsl import BaseEntity
from pybel.struct.filters.typing import EdgeIterator
from pybel.struct.pipeline import in_place_transformation, uni_... | pybel/pybel-tools | src/pybel_tools/mutation/highlight.py | Python | mit | 3,982 | [
"Pybel"
] | 5f6573645ba878d68202f2ab1ab02551544e3053503b626c3b129e4b1210d2ac |
"""An Image file reader object.
"""
# Author: KK Rai (kk.rai [at] iitb.ac.in)
# R. Ambareesha (ambareesha [at] iitb.ac.in)
# Chandrashekhar Kaushik
# Suyog Dutt Jain <suyog.jain [at] aero.iitb.ac.in>
# Prabhu Ramachandran <prabhu [at] aero.iitb.ac.in>
# Copyright (c) 2007-2015, Ent... | dmsurti/mayavi | mayavi/sources/image_reader.py | Python | bsd-3-clause | 4,929 | [
"Mayavi",
"VTK"
] | a7c43930aad5b4b3acf8534b2cdeffcb26a58ceba62a7cfab911f12e74559348 |
#!/usr/bin/env python
#########################################################################################
#
# Spinal Cord Automatic Detection
#
# ---------------------------------------------------------------------------------------
# Copyright (c) 2015 Polytechnique Montreal <www.neuro.polymtl.ca>
# Authors: Be... | benjamindeleener/scad | scripts/scad.py | Python | mit | 16,838 | [
"Gaussian"
] | d48985385cfa490622a489418c9962e7af80f0985cf33f472369758ecdffd1b0 |
"""
Parse a blast file and create a blast result object
"""
import os
import sys
import argparse
import gzip
class BlastResult():
def __init__(self, query, db, percent_id, alignment_length, gaps, mismatches, query_start, query_end, db_start, db_end,
evalue, bitscore, query_length=None, subject_le... | linsalrob/EdwardsLab | roblib/blast.py | Python | mit | 1,877 | [
"BLAST"
] | c338be3a137aee82f500fe78a6a6284e6c214c564a7ed1d0f4777727aecbeb23 |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014-2017 CERN.
#
# INSPIRE 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 ... | zzacharo/inspire-next | inspirehep/modules/authors/views.py | Python | gpl-3.0 | 13,511 | [
"VisIt"
] | 3e1b6c79b70b80a8c7eb15b6e09a7e8a076c2a29a4adb681145bbdbf0c042947 |
#!/usr/bin/env python
# File: plot_icd_vs_mass.py
# Created on: Mon 12 Mar 2012 11:50:09 AM CDT
# Last Change: Thu Oct 4 15:47:52 2012
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import pylab as pyl
from mk_galaxy_struc import mk_galaxy_struc
def plot_icd_vs_mass():
galaxies = mk_galaxy_struc()
#... | boada/ICD | sandbox/legacy_plot_code/plot_icd_vs_mass_vs_z.py | Python | mit | 4,352 | [
"Galaxy"
] | 6e51a524d981a2f13afdc979f2889029ccbac9c086ad42b3f97e8eed1eccf005 |
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
import DIRAC
__RCSID__ = "$Id$"
class DataOperation(BaseAccountingType):
def __init__(self):
BaseAccountingType.__init__(self)
self.definitionKeyFields = [('OperationType', "VARCHAR(32)"),
... | andresailer/DIRAC | AccountingSystem/Client/Types/DataOperation.py | Python | gpl-3.0 | 1,590 | [
"DIRAC"
] | 20348724b3f43e48503c510179417e6004e12a1375c88d4df5853f2e6666558f |
from random import random
from ase.io import write
import time
from ase.ga.data import DataConnection
from ase.ga.population import Population
from ase.ga.standard_comparators import InteratomicDistanceComparator
from ase.ga.cutandsplicepairing import CutAndSplicePairing
from ase.ga.offspring_creator import OperationSe... | askhl/ase | doc/tutorials/ga/ga_basic_parallel_main.py | Python | gpl-2.0 | 3,308 | [
"ASE"
] | 2593b214d356390894e6fd4cbf5df1ef68e98d7db144250e6f6c3a55723d1590 |
# store.py - repository store handling for Mercurial
#
# Copyright 2008 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from i18n import _
import scmutil, util, parsers
import os, stat, errno
_sha =... | vmg/hg-stable | mercurial/store.py | Python | gpl-2.0 | 16,921 | [
"VisIt"
] | a24c7332a0d41d9a7afd5661655e5a0e6eeb538f714bdcdfb119bbcccbf4d481 |
#!/usr/bin/env python2
#
# Copyright (C) 2020(H)
# Institute Jozef Stefan
# Max Planck Institute for Polymer Research
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
... | govarguz/espressopp | testsuite/FixedLocalTuple/TestFixedLocalTupleList.py | Python | gpl-3.0 | 4,703 | [
"ESPResSo"
] | 50973e48911ab73bc188c10100782b25bf0a46edc0b7bcb23ea35712e1373b39 |
#!/usr/bin/env python
from __future__ import print_function, division
import os
import scipy as sp
import scipy.linalg as LA
import scipy.spatial.distance as sp_dist
from ase.atoms import Atoms
from ase import units
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
import ase.io
import theano
import... | marcocaccin/LearningMetaDynamics | mlsampling.py | Python | gpl-2.0 | 17,377 | [
"ASE",
"CP2K",
"Gaussian",
"LAMMPS"
] | 691c4db6388869f5d74769efe19aeddc9adddc417d781dd2a6dc4f2d84cde152 |
#!/usr/bin/env python
# nicechart.py
#
# Copyright 2011
#
# Christoph Sterz
# Florian Weber
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
#... | Florianjw/NiceCharts | nicechart.py | Python | gpl-3.0 | 22,515 | [
"Gaussian"
] | df19fa4df2d715ac039ae916dd237e6404d9e234e0fb1431f66d3ef8aed098da |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os, sys
from optparse import OptionParser
from zeroinstall import _
from zeroinstall.injector import requirements
from zeroinstall.injector.policy import Policy
from zer... | dabrahams/zeroinstall | zeroinstall/0launch-gui/main.py | Python | lgpl-2.1 | 5,187 | [
"VisIt"
] | 0fc89ec046f81a1713b3222c4e1822df13a540541839fc517219c0917d5a62bc |
import operator as op
import logging
import lib.const as C
import lib.visit as v
from .. import util
from ..meta import class_lookup
from ..meta.template import Template
from ..meta.clazz import Clazz, find_mtds_by_sig
from ..meta.method import Method, sig_match
from ..meta.field import Field
from ..meta.statement im... | plum-umd/pasket | pasket/rewrite/accessor_adhoc.py | Python | mit | 5,944 | [
"VisIt"
] | b0f3e5931410a28f483d9416ebdad3236938651e57f0b7c2f2e3617478d96f0c |
from __future__ import division, print_function
from random import random as _random, expovariate as _exp, gauss as _gauss
from random import uniform as _uniform, seed as _seed
from math import sqrt as _sqrt, log as _log
try:
import pypdt
except ImportError:
print('You will not be able to use the massPDG() func... | ajo2eq/DecaySim | distributions.py | Python | mit | 1,442 | [
"Gaussian"
] | 5d89c7c46878ae56204211fcb1967ffa240450d2d4802815fc1a0065fcf048e5 |
#!/usr/bin/env python
#
# __COPYRIGHT__
#
# 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, merge, publish,
... | timj/scons | test/Parallel/duplicate-target.py | Python | mit | 3,301 | [
"VisIt"
] | 5a41a620ba2a088e74d94504881dad1e22168a898a36c274401467a64b8d0a27 |
"""\
MP.py: Moller Plesset Perturbation Theory
MP2 has been tested for H2. Should work for all closed shell systems.
This program is part of the PyQuante quantum chemistry program suite.
Copyright (c) 2004, Richard P. Muller. All Rights Reserved.
PyQuante version 1.2 and later is covered by the modified BSD
... | berquist/PyQuante | PyQuante/MP.py | Python | bsd-3-clause | 4,439 | [
"Jaguar"
] | 7e3438a748c0ba24e89a8f1f90c5e9fd36fb1542a791df06de40488bbfa5d70e |
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar, Evan Feinberg, and Karl Leswing"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import os
import shutil
import time
import tempfile
import hashlib
i... | joegomes/deepchem | deepchem/feat/rdkit_grid_featurizer.py | Python | mit | 43,687 | [
"RDKit"
] | 4258fef2a353bd0e4fccd53da22f720acfb94208839172e2eff497b5d71e491f |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | ambv/yapf | yapf/yapflib/subtype_assigner.py | Python | apache-2.0 | 13,797 | [
"VisIt"
] | 2cc729198b846dec0038ede986bb6c53eb95dd3d210ec55f487d5c6b337a74c0 |
#!/usr/bin/env python
import math, numpy as np
#from enthought.mayavi import mlab
import matplotlib.pyplot as pp
import matplotlib.cm as cm
import pylab as p
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 as h... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/Image_Video/plotdata_video_foliage.py | Python | mit | 2,747 | [
"Mayavi"
] | f91e6214ffd44bc52464f869532dc4383c010c15ea99a924f6893b233217bcf9 |
from setuptools import setup
setup(name='gp_emu_uqsa',
version='1.1',
description='Gaussian Process emulation for Uncertainty Quantification and Sensitivity Analysis',
url='http://github.com/samcoveney/GP_emu_UQSA',
author='Sam Coveney',
author_email='coveney.sam@gmail.com',
license... | samcoveney/GP_emu_UQSA | setup.py | Python | gpl-3.0 | 613 | [
"Gaussian"
] | 307cede92fd015a0ff5f02b9f495a65ec3f84148649ad323a3b144c8860c3d81 |
# deploying Gaussian Naive Bayes algorithn to predict the values of unknown parameters
# based on a training set included in the code.
import numpy as pin
#the following is the feature training set
X=pin.array([[-1,-1],[-2,-1],[-3,-2],[1,1],[2,1],[3,2]])
#the following is the label training set
Y=pin.array([-1,-1,-1,1... | pinakinathc/python_code | smart_py_codes/predict.py | Python | gpl-3.0 | 582 | [
"Gaussian"
] | 3d62edf3c6013b48f7448dc445f12577eb06ddfa30424269acec3c4db13f41b0 |
# ============================================================================
#
# 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/action_steps/change_object.py | Python | gpl-2.0 | 18,043 | [
"VisIt"
] | 42d9c12b18aec8798068248b4e493bb70004bcfc0fb46323927d87988c4b8701 |
#!/usr/bin/env python
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
$Revision: 1.1 $
$Date:... | chunshen1987/iSS | utilities/for_paraview/lib152/Field.py | Python | mit | 1,700 | [
"VTK"
] | 23c131fabff450252eb315408c5bc3e55b275441d3d8d33b1080db5fc7276d5a |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/build/representations/generator.py | Python | agpl-3.0 | 7,835 | [
"Galaxy"
] | ca14e9c8783e4b574c2bb2e5ed40f8622bef9fe8df9b257ca2ab458ed623bbf1 |
'''
Only image the region directly around the OH detection
'''
import os
import sys
import socket
from tasks import rmtables, impbcor, exportfits, tclean
# orig_dir = os.getcwd()
myspw = int(sys.argv[-4])
assert myspw in [3, 5, 6, 7]
use_contsub = True if sys.argv[-3] == "True" else False
myweighting = str(sys.... | e-koch/VLA_Lband | 17B-162/OH/OH_imaging.py | Python | mit | 6,662 | [
"Galaxy"
] | d653e004417541a2dab3f0510911c48a1cc8323fa7a40d479351f70812d391b7 |
from django.utils.translation import ugettext as _
from custom.succeed.utils import CONFIG
from dimagi.utils.parsing import ISO_DATE_FORMAT
PM1 = 'http://openrosa.org/formdesigner/111B09EB-DFFA-4613-9A16-A19BA6ED7D04'
PM2 = 'http://openrosa.org/formdesigner/4B52ADB2-AA79-4056-A13E-BB34871876A1'
PM_PM2 = 'http://openro... | puttarajubr/commcare-hq | custom/succeed/reports/__init__.py | Python | bsd-3-clause | 11,081 | [
"VisIt"
] | a7668ea98b9f5766fca1f43fcf92b697bcaab2d99e43fec3cbf81cef6b0fccda |
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name_male}} {{last_name_male}}',
'{{first_name_male}} {{last_name_male}}',
'{{first_name_male}} {{last_name_male}}',
'{{first_name_male}} {{last_name_male}}',
'{{first_name_male}}... | danhuss/faker | faker/providers/person/tw_GH/__init__.py | Python | mit | 11,369 | [
"Amber"
] | abc508fb90ec077f22c05b1069e398394970b3545bdffa524bef87a425e504d8 |
"""Affinity matrix refinemnet operations."""
import abc
import enum
import numpy as np
from scipy.ndimage import gaussian_filter
class RefinementName(enum.Enum):
"""The names of the refinement operations."""
CropDiagonal = enum.auto()
GaussianBlur = enum.auto()
RowWiseThreshold = enum.auto()
Symmetrize = e... | wq2012/SpectralCluster | spectralcluster/refinement.py | Python | apache-2.0 | 9,215 | [
"Gaussian"
] | da95b6aebf9e90db41cad5381137589e1d59438a1a70b0ce0d6e869030de43f4 |
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# 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, inc... | melissawen/gcp-vala-backend | backends/js/gcpbackendjs/ast.py | Python | gpl-3.0 | 10,847 | [
"VisIt"
] | 7161e3a6dfe9a0970cfeb98d91d3d16553babad5e7aaf4627fbbc7c67b14c5b6 |
from __future__ import (absolute_import, division, print_function)
import stresstesting
from mantid.simpleapi import Abins, mtd, DeleteWorkspace
from AbinsModules import AbinsConstants, AbinsTestHelpers
class HelperTestingClass(object):
def __init__(self):
self._temperature = 10 # K
self._sample... | ScreamingUdder/mantid | Testing/SystemTests/tests/analysis/AbinsTest.py | Python | gpl-3.0 | 17,651 | [
"CASTEP",
"CRYSTAL",
"DMol3",
"Gaussian"
] | 0daf00f1f1d16806aa64ea58d9f288971336946da36c84821a22f677bc6b0bfb |
# Author: Muneeb Sultan <msultan@stanford.edu>
# Copyright (c) 2016, Stanford University and the Authors
# All rights reserved.
from __future__ import print_function, division, absolute_import
import numpy as np
import itertools
from .featurizer import Featurizer, ContactFeaturizer
import warnings
class CommonContactF... | mpharrigan/mixtape | msmbuilder/featurizer/multiseq_featuizer.py | Python | lgpl-2.1 | 7,337 | [
"MDTraj"
] | 835e9d6cf57de2c7856f29a0b1fcc7f7b12add0cd614c4e03c91358b8d49d946 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | scripts/tests/test_sqa_check.py | Python | lgpl-2.1 | 897 | [
"MOOSE"
] | 84ab1e77084d643037bd65ceb8ffc05784edf320a0acef18ab75a19a1f89f5b1 |
# -*- coding: utf-8 -*-
"""
Created on Wed Jul 20 12:12:04 2016
@author: marian
many elements of this script are taken from
py_28_pRF_finding from Ingo Marquardt
"""
# %%
# *** Import modules
from __future__ import division # so that 1/3=0.333 instead of 1/3=0
import os
import numpy as np
import scipy as sp
from scip... | MSchnei/py_pRF_motion | pyprf_feature/simulation/pRF_simulateTC_xval.py | Python | gpl-3.0 | 19,453 | [
"Gaussian"
] | 099ed6847b8ef2d03992e659931640f179fe2c58b63d5510ad365e766c63bf0b |
def TF_meanSB(dataflag, datanot, aper, band, magname, labs,zrange, outdir):
import matplotlib.pyplot as plt
import numpy as np
import math
import matplotlib.patches as mpatches
pi=math.pi
if not zrange:
zrange='None Specified'
else:
zrange=str(zrange)
nflag=len(dataflag)
numflag=str(nflag) #string versio... | anewmark/galaxy_dark_matter | not currently in use/def2clump.py | Python | mit | 8,355 | [
"Galaxy"
] | d286ce03a01ec77d1f99c34557516520f67acaba3d43c4428330a7c3d78ee5ad |
DEBUG = True
SECRET_KEY = "development"
SQLALCHEMY_DATABASE_URI = "postgresql+psycopg2://poker:1234@localhost:5432/poker"
CASINO_HOST = "localhost"
CASINO_PORT = 5154
SLACK_API_KEY = "not-in-dev"
SLACK_CHANNEL = "#casino"
SLACK_USERNAME = "CasinoLogs"
MATCH_LOGS = "/Users/nathan/sources/casino/logs/matches/"
| gnmerritt/casino | matchmaker/default_settings.py | Python | mit | 310 | [
"CASINO"
] | a9e93501bccbe3febdfb2ca2b5e47602f7f1287f25ea002ff2ec3cc469a84fc2 |
import datetime
import hashlib
import itertools
import logging
import os
import time
from collections import defaultdict
from dataclasses import asdict, dataclass, field
from operator import itemgetter
from typing import (
IO,
AbstractSet,
Any,
Callable,
Collection,
Dict,
Iterable,
List,... | eeshangarg/zulip | zerver/lib/actions.py | Python | apache-2.0 | 315,023 | [
"Octopus"
] | 91120258df8fa2418fb284e602c2fee10ac7109713b9e00c0a7e40d5a56447f3 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/share/psi4/databases/HSG.py | Python | lgpl-3.0 | 46,405 | [
"Psi4"
] | 63089ceb78a2627030880f2b79c2ff0d7749e2de7c2fc10960c53fc2455a0a63 |
#
# Copyright (C) University College London, 2007-2012, all rights reserved.
#
# This file is part of HemeLB and is provided to you under the terms of
# the GNU LGPL. Please see LICENSE in the top level directory for full
# details.
#
import wx
from vtk.wx.wxVTKRenderWindowInteractor import wxVTKRenderWindowIntera... | jenshnielsen/hemelb | Tools/setuptool/HemeLbSetupTool/View/VtkViewPanel.py | Python | lgpl-3.0 | 2,477 | [
"VTK"
] | 3c3e08f3ed437aaa49fc8fc105f547b0425738de08e2b9fceff0b24524dbe192 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create a pipeline: some skinny-ass triangles
sphere = vtk.vtkSphereSource()
sphere.SetThetaResolution(6)
sphere.SetPhiResolution(24)
ids = vtk.vtkIdFilter()
ids.SetInputConnection(... | keithroe/vtkoptix | Filters/Modeling/Testing/Python/TestAdaptiveSubdivisionFilter.py | Python | bsd-3-clause | 1,433 | [
"VTK"
] | 31c1cb00c7d1fb5bf551e5d8c13cf33c8e803fb05b7ded5ef164cd97b170114c |
#!/usr/bin/python
# Log Hygrosens readings to a MySQL database
# Copyright 2005 by Brian C. Lane
# All Rights Reserved
# Licensed under GPL v2, see the COPYRIGHT and COPYING files
"""
Hygrosens MySQL logging
Copyright 2005 by Brian C. Lane <bcl@brianlane.com>
SQL commands are in the hygrosens.sql file
"""
import os... | bcl/hygrosens | examples/log_mysql.py | Python | gpl-2.0 | 2,571 | [
"Brian"
] | 68322ccc9b6a32e1c349b91d08ee222f988cd9075d074147fe4dd7d487cc1618 |
from __future__ import absolute_import
import filecmp
import os
import sys
import llvmbuild.componentinfo as componentinfo
from llvmbuild.util import fatal, note
###
def cmake_quote_string(value):
"""
cmake_quote_string(value) -> str
Return a quoted form of the given value that is suitable for use in C... | llvm-mirror/llvm | utils/llvm-build/llvmbuild/main.py | Python | apache-2.0 | 34,212 | [
"VisIt"
] | 1fad3bd7307937cbb7f6371b58a1309574e065a78b805b959d99db353ae66688 |
#~~~~~~~GLOBAL IMPORTS~~~~~~~#
# Standard library packages import
import gzip
from os import close, remove, path
from multiprocessing import cpu_count
from time import time
from tempfile import mkstemp
# Local library packages
from pyDNA.Utilities import run_command, file_basename, fgunzip
from BlastHit import BlastHi... | a-slide/pyDNA | Blast/BlastnWrapper.py | Python | gpl-2.0 | 4,335 | [
"BLAST",
"BWA"
] | 48137280dffe66b7baf52376a125b3ccebd02b9110944b568c44aedf87e94c93 |
import collections
import copy
import functools
# import pprint
import threading
import tkinter.font as tkfont
from enum import Enum
from tkinter import *
from tkinter import messagebox
from tkinter.ttk import *
import itertools
from lib.CurrencyManager import cm
from lib.FilterManager import FilterManager, fm, lower... | senuido/stash-scanner | ui/FilterEditor.py | Python | gpl-3.0 | 71,075 | [
"CRYSTAL"
] | b755b12bce9212b083fb76b0e03d0c22fc8713828c701f3836c16072e1b09c54 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
########################################################################
# Solves problem 36 from projectEuler.net.
# Finds the sum of the numbers below 1 millon which are both palindromic
# in their decimal and binary representation.
# Copyright (C) 2010 Santiag... | sanSS/programming-contests | project-euler/problem036.py | Python | gpl-3.0 | 1,367 | [
"VisIt"
] | 42bfcf822225b8c4625376d163f0eacc2b680590ebb35bd8d97613f52cbe1351 |
##########################################################################
#
# Copyright (c) 2019, Image Engine Design Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistrib... | andrewkaufman/gaffer | python/GafferUI/SpreadsheetUI/_SectionChooser.py | Python | bsd-3-clause | 12,775 | [
"VisIt"
] | 475bc401469c65e2bf4a81be2a101dfa6d8f6a8110229ed474700057cd00cb8a |
# -----------------------------------------------------------------------------
# Milky Way - Turn based strategy game from Milky Way galaxy
#
# URL: https://github.com/FedericoRessi/milkyway/
# License: GPL3
# -----------------------------------------------------------------------------
'''
@author: Federic... | FedericoRessi/milkyway | milkyway/pyside/new_game.py | Python | gpl-3.0 | 2,068 | [
"Galaxy"
] | f8b913dd0a7279b9813f6e7436ca7527bc474151bed3c6ad86bc6f7b08619568 |
#!/usr/bin/env python
##
## @file create_sedml2.py
## @brief cerates a SED-ML document.
## @author Frank T. Bergmann
##
## <!--------------------------------------------------------------------------
## This file is part of libSEDML. Please visit http://sed-ml.org for more
## information about SEDML, and the l... | 0u812/libSEDML | examples/python/create_sedml2.py | Python | bsd-2-clause | 3,098 | [
"VisIt"
] | 65779f6a7ddef4ad266c12a0c7863c98acb0b99d2325e98fc32bfac0d445008d |
#########
# firstConfig.py
# This program is part of the online PS-Drone-API-tutorial on www.playsheep.de/drone.
# It shows how to set and read out configurations of a Parrot AR.Drone 2.0 using the PS-Drone-API. The drone will stay on the ground.
# Dependencies: a POSIX OS, PS-Drone-API 2.0 beta or higher.
# (w) J. Phi... | reixd/ps-drone | tutorials/firstConfig.py | Python | artistic-2.0 | 5,377 | [
"VisIt"
] | 256175fb8fae4f6a17f64198d07ba292baf55b34262bad2bf0a0fa25e2613873 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest2 as unittest
import os
import json
import numpy as np
import warnings
import xml.etree.cElementTree as ET
from pymatgen.electronic_structur... | aykol/pymatgen | pymatgen/io/vasp/tests/test_outputs.py | Python | mit | 36,965 | [
"VASP",
"pymatgen"
] | d238f385c84435d677e141bc2dc2cd27d9622e145b0764a8d3002be444e9796d |
import numpy as np
import psi4
from psi4.driver import p4util
psi4.set_output_file("output.dat", False)
# Generate JSON data
json_data = {}
json_data["molecule"] = """He 0 0 0\n--\nHe 0 0 1"""
json_data["driver"] = "gradient"
json_data["method"] = 'SCF'
json_data["kwargs"] = {}
json_data["options"] = {"BASIS": "STO-3... | rmcgibbo/psi4public | tests/json/gradient/input.py | Python | lgpl-3.0 | 1,377 | [
"Psi4"
] | 9bf0cda2144becc6d143d8a0f43b0097952c1091ffda07a19cb4b5ef74f7635b |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/colorbar/colorbar_horiz.py | Python | lgpl-2.1 | 1,217 | [
"MOOSE"
] | 800c7aa49456242a62a51f180d48c3a9bf15b8470ef72d6a77087aaa9eba8c00 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
""" sextractor.py:
Classes to read SExtractor table format
Built on daophot.py:
:Copyright: Smithsonian Astrophysical Observatory (2011)
:Author: Tom Aldcroft (aldcroft@head.cfa.harvard.edu)
"""
from __future__ import absolute_import, division, print_f... | piotroxp/scibibscan | scib/lib/python3.5/site-packages/astropy/io/ascii/sextractor.py | Python | mit | 4,824 | [
"Galaxy"
] | de2edb50980800ef9be569ea20fe02a0d6eacc2c93fa9c6912da1d3f9c0f85bd |
from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
from builtins import zip
# 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
# rega... | kaiping/incubator-singa | examples/cifar10/caffe/caffe_net.py | Python | apache-2.0 | 1,896 | [
"Gaussian"
] | 533eaccb097be3efce7f996ede44ccb6501a90f47643898d895e6d928aa3b359 |
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