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'''
count reads or records in usearch-formatted fastq and tab files
'''
__author__ = "Sonia Timberlake"
import os
import sys
import argparse
from os.path import basename, dirname, join
from Bio import SeqIO
from collections import OrderedDict
# Globals ?
default_delimiter={'fields': ';','key-value':'='}
# Function... | sonia-t/utils | count_reads.py | Python | mit | 4,451 | [
"ASE"
] | fc02c5ac2ef5944d8ecd8c4d95a5716ae163828181a4daa18c0bae8c6a7629a4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
from skimage.transform import rotate
from skimage.util import random_noise
def random_flips(X):
'''
Take random x-y flips of images.
Input:
- X: (N, C, H, W) array of image data.
Output:
- An array of the same shape as X, con... | dnlcrl/PyDatSet | pydatset/data_augmentation.py | Python | mit | 11,052 | [
"Gaussian"
] | 54b5587449c2f67981aa68aca1f0d7fad0766159979bf6a3d4beaf7c4311b8de |
import sys
import cv2
import math
from skimage import draw
import numpy as np
from typing import List
from pathlib import Path
import logging
import argparse
def alpha_blur(img, alpha_mask, kernel_size=10):
"""
Blur image proportional to the given mask
:param img:
:param alpha_mask:
:param kernel_... | 5agado/data-science-learning | graphics/learn_to_paint/image_utils.py | Python | apache-2.0 | 8,095 | [
"Gaussian"
] | 6c869365219d16dfe27852478b450e7e0f6847fd813bb07b779cb7f320ef0c47 |
'''
ModelGenie (c) University of Manchester 2015
ModelGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
import re
def parse_equation(equation, separator):
'''Parses a chemical equation, returning the participants
... | neilswainston/development-py | synbiochemdev/modelgenie/chem_utils.py | Python | mit | 1,183 | [
"VisIt"
] | c23d306ee6418460b221d07b2f054a11bef21e9809bb7cdbe497322a7adbcc12 |
from scipy.optimize import minimize
from scipy.optimize import basinhopping
import matplotlib.pyplot as plt
from sklearn.gaussian_process.kernels import WhiteKernel, DotProduct
from sklearn.metrics import mean_absolute_error
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn import preprocessing... | jboes/CatKit | catkit/learn.py | Python | gpl-3.0 | 3,685 | [
"Gaussian"
] | f7dc6486c442011f41273053bd028c3adc2582e68fd6abee8a252a9013921127 |
"""
Test basic performance report functionality
NOTE: To run these tests, browsermob-proxy-2.0-beta-9 must be installed
These aren't real unittests, just some sample scenarios.
"""
from bok_choy.web_app_test import WebAppTest, with_cache
from bok_choy.performance import MethodNotEnabledInCurrentMode
from .pages impor... | drptbl/bok-choy | tests/test_performance.py | Python | apache-2.0 | 5,710 | [
"VisIt"
] | 756c12bfa7c041aa0043d0b10b2217aeed6c7ad9f4595573554036ac1301f7a3 |
import numpy as np
import matplotlib.pyplot as plt
import dolfin_navier_scipy.stokes_navier_utils as snu
import dolfin_navier_scipy.problem_setups as dnsps
def conv_plot(abscissa, datalist, fit=None,
markerl=None, xlabel=None, ylabel=None,
fititem=0, fitfac=1.,
leglist=None,... | highlando/dolfin_navier_scipy | tests/tdp_convcheck.py | Python | gpl-3.0 | 6,349 | [
"ParaView"
] | 9130bafc3019d89e9525e09d75c571a5af3e5ac709809f5ab3eb33dd44ba7f8d |
#
# Copyright (c) 2007, Novartis Institutes for BioMedical Research 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:
#
# * Redistributions of source code must retain the above copyrigh... | rdkit/rdkit | rdkit/Chem/Recap.py | Python | bsd-3-clause | 24,160 | [
"RDKit"
] | 3a9c03e6c2c00efe556c937d04f439ab78f56146fdd95a53de41b7df546c385d |
import typing as t
from . import nodes
from .visitor import NodeVisitor
VAR_LOAD_PARAMETER = "param"
VAR_LOAD_RESOLVE = "resolve"
VAR_LOAD_ALIAS = "alias"
VAR_LOAD_UNDEFINED = "undefined"
def find_symbols(
nodes: t.Iterable[nodes.Node], parent_symbols: t.Optional["Symbols"] = None
) -> "Symbols":
sym = Symb... | pallets/jinja | src/jinja2/idtracking.py | Python | bsd-3-clause | 10,704 | [
"VisIt"
] | 19f36669d8abe280c02d5c739f70cbf582278490ebebd79b5de036ca07ee0860 |
import os
import unittest
import ansigenome.constants as c
import ansigenome.test_helpers as th
import ansigenome.utils as utils
class TestTemplates(unittest.TestCase):
"""
Integration tests for the templates.
"""
def setUp(self):
self.test_path = os.getenv("ANSIGENOME_TEST_PATH", c.TEST_PATH... | AlbanAndrieu/ansigenome | test/integration/test_templates.py | Python | gpl-3.0 | 2,387 | [
"Galaxy"
] | fc3290f4af9453b8fae45f235ee739634faef2b602b4afe99a74ef1fa7578178 |
# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2009 by Peter Cock.
# 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.
#
# Contact: Leighton Pritchard,... | zjuchenyuan/BioWeb | Lib/Bio/Graphics/GenomeDiagram/_Graph.py | Python | mit | 8,910 | [
"Biopython"
] | 8b5e705b264feffafe26a2bdc86d99760e924cd9916b3b465c8e616fba724043 |
# Zeobuilder is an extensible GUI-toolkit for molecular model construction.
# Copyright (C) 2007 - 2009 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of Zeobuilder.
#
# Zeobuilde... | woutersmet/Zeo_thesis | share/plugins/molecular/geometry.py | Python | gpl-3.0 | 9,350 | [
"MOPAC"
] | 973d0f1b6468307c8e3644de6f5c57a01311d6796d1b71be215e6ec3be6001da |
########################################################################
# $Id$
# File : TorqueComputingElement.py
# Author : Stuart Paterson, Paul Szczypka
########################################################################
""" The simplest Computing Element instance that submits jobs locally.
"""
__RCSID__ =... | sposs/DIRAC | Resources/Computing/TorqueComputingElement.py | Python | gpl-3.0 | 11,637 | [
"DIRAC"
] | 654867c2b658c9fa276d26c2d9f432c9938b6b9436b65d7db135b499b0a69f34 |
#!/usr/bin/env python
# boards.txt python builder for esp8266/Arduino
# Copyright (C) 2017 community
# Permission is hereby granted, free of charge, to any person who buy it,
# use it, break it, fix it, trash it, change it, mail - upgrade it, charge
# it, point it, zoom it, press it, snap it, work it, quick - erase it... | Lan-Hekary/Arduino | tools/boards.txt.py | Python | lgpl-2.1 | 69,429 | [
"CRYSTAL",
"ESPResSo"
] | 87f34de12e9d6b0e5e532cfce5da797716e3a4a3fe5c9d0684451db3cb68f7a8 |
import itertools
import math
import re
import time
from collections import defaultdict as ddict, deque
from lib.tree import Tree
from common import log
from common.hgraph.hgraph import Hgraph
from common.cfg import Chart
from vo_item import CfgItem, HergItem, SynchronousItem
from vo_rule import VoRule
import pprint
c... | GullyAPCBurns/bolinas | parser/parser.py | Python | mit | 23,547 | [
"VisIt"
] | 610b431a7f826439789a9cf41a129dba7824cc3e44d43712e8236f8aa8b5c0e0 |
# 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... | nburn42/tensorflow | tensorflow/contrib/autograph/converters/continue_statements.py | Python | apache-2.0 | 4,655 | [
"VisIt"
] | 2ade4cd519e102c6cc30b22ecb6bd7a8913f06efa8fdbd7ee70c29ce4f77620b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# ace2fasta.py
# From ACE format to FASTA format
# Eric Normandeau
# 2010 04 15
# Create an output_file.fasta containing contig sequences alignements from
# an input_file.ace
# Clean each contig by removing insertions '*' in the contig consensus and
# all the sequences i... | wkh124/wkh124 | ace2fasta.py | Python | gpl-3.0 | 4,772 | [
"Biopython"
] | 997e2b55484077a0af77695b174006a236c5ffc914525836b757f1edb89436d3 |
'''
===========================================
Using the Kalman Filter and Kalman Smoother
===========================================
This simple example shows how one may apply the Kalman Filter and Kalman
Smoother to some randomly generated data.
The Kalman Filter and Kalman Smoother are two algorithms for predic... | PierrotLC/pykalman | examples/standard/plot_filter.py | Python | bsd-3-clause | 2,121 | [
"Gaussian"
] | 23f3158391c7663e98e54d291c26424212382dabd47cf532984548e9a9bd9aa5 |
# -*- coding: UTF-8 -*-
import gethtml
"""
weblogin
by Anarchintosh @ xbmcforums
Copyleft (GNU GPL v3) 2011 onwards
this example is configured for Fantasti.cc login
See for the full guide please visit:
http://forum.xbmc.org/showthread.php?p=772597#post772597
USAGE:
in your default.py put:
import weblogin
... | jlongman/xbmc-hockeystreams-plugin | weblogin.py | Python | gpl-3.0 | 4,283 | [
"VisIt"
] | 63ba12abaaec2b75af97768eaaf9698f98d3ae6fa4cbff46f8f334eb30ecfd6e |
#!/usr/bin/env python
""" ir.py - parse c declarations
(c) 2002, 2003, 2004, 2005 Simon Burton <simon@arrowtheory.com>
Released under GNU LGPL license.
version 0.xx
"""
import sys
#import cPickle as pickle
import pickle
#from lexer import Lexer
from parse_core import Symbols #, Parser
import node as node_module
im... | jpflori/mpir | yasm/tools/python-yasm/pyxelator/ir.py | Python | gpl-3.0 | 35,563 | [
"VisIt"
] | 8aab32227dc40876799ebfc4b7261128b3dca2a5d5239f10c2bb74fcc7ac6f16 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2010 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 Free Software Foundation; either version 2 of the License, or
# (at your optio... | gramps-project/gramps | gramps/gen/user.py | Python | gpl-2.0 | 6,849 | [
"Brian"
] | 831f2c16a22262904030cc982a8bb396ceaf5db27f34da54485c6ffd9c0ea357 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | googlecodelabs/migrate-python2-appengine | mod0-baseline/main.py | Python | apache-2.0 | 1,599 | [
"VisIt"
] | fce9d1eac95bf25f1814953ec357cbe26aafb43f67eeaeea80c15cba15fc3a97 |
# -*- coding: utf-8 -*-
"""Unit tests for IOs
"""
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
... | tomkralidis/pywps | tests/test_inout.py | Python | mit | 19,534 | [
"NetCDF"
] | accff82708850719b8ad05258d27d8a65a1519cf600b2d922127e6fbac2ab75e |
import numpy as np
import scipy as sci
from scipy.io import loadmat
from itertools import chain,izip_longest
from numpy.random import rand
from scipy.stats import scoreatpercentile
from matplotlib.pyplot import *
import matplotlib
from collections import defaultdict
from zlib import compress
matplotlib.rcParams['xtic... | mac389/brainpy | lib/neuroTools.py | Python | gpl-3.0 | 8,658 | [
"NEURON"
] | 3f3916240b9ab044fdd337705aeb54e610f064f5bfdf4e4c3cb1782cb126ef3b |
import numpy as np
import pytest
from numpy import linalg
import numpy.testing as npt
import itertools
from utils import get_rstate, get_printing
import dynesty # noqa
from dynesty import utils as dyfunc # noqa
"""
Run a series of basic tests to check whether anything huge is broken.
"""
nlive = 500
printing = get... | joshspeagle/dynesty | tests/test_gau.py | Python | mit | 10,528 | [
"Gaussian"
] | cd49e5c2a2b65ba7c7acc9164756ef4db63314fb1ffaaec82089f7b10d169ff8 |
def gaussianQuadrature(function, a, b):
"""
Perform a Gaussian quadrature approximation of the integral of a function
from a to b.
"""
# Coefficient values can be found at pomax.github.io/bezierinfo/legendre-gauss.html
A = (b - a)/2
B = (b + a)/2
return A * (
0.2955242247147529*function(-A*0.1488743389816312 ... | FCDM/py-dml | dml/maths/gquad.py | Python | mit | 877 | [
"Gaussian"
] | e704acdc1369cf4335fae0e34706f4b4eed62073dc1aa5c4f79e7242a0f54c07 |
from test import test_support
import unittest
import codecs
import StringIO
class Queue(object):
"""
queue: write bytes at one end, read bytes from the other end
"""
def __init__(self):
self._buffer = ""
def write(self, chars):
self._buffer += chars
def read(self, size=-1):
... | mancoast/CPythonPyc_test | cpython/241_test_codecs.py | Python | gpl-3.0 | 21,080 | [
"FEFF"
] | 2bd6267132b52b4fb554c83c318b4dce45b1f64b5a338fcde7d60641ac702503 |
# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# 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 ... | google-research/adapter-bert | modeling.py | Python | apache-2.0 | 40,966 | [
"Gaussian"
] | 2e80e9b6f8e05e369bbf68e0fc035722c3bd3b0735b608afd1122ddad5da17aa |
#!/usr/bin/python
import numpy as np
import scipy.stats as stats
#Variable explanation
#I believe maleSamples and femaleSamples are meant to be lists of the required samples to use for processing
#numBins is likely archaic to my system but included in case compatability is needed
def checkXcounts(male... | suzannerohrback/somaticCNVpipeline | bin/simulations/copynumbernoise.py | Python | mit | 3,193 | [
"Bowtie"
] | 1209f4ef60a82ec66d364c0395d87fa69404da760ed480cfd8b4e746e0afea95 |
import theano
import theano.tensor as T
from theano.sandbox.rng_mrg import MRG_RandomStreams
from theano.tensor.nnet.conv import conv2d
from theano.tensor.signal.downsample import max_pool_2d
from theano.tensor.shared_randomstreams import RandomStreams
import numpy as np
import scipy.io
import time
import sys
import l... | tigerneil/Theano-Lights | models/vae1.py | Python | mit | 3,725 | [
"Gaussian"
] | c7c8b3f9326b1a544990a834e69e933da423b6d50c18bda836afe19b834a37b2 |
import os
from collections import defaultdict
from os.path import join as pjoin
import numpy.testing as npt
from dipy.data import read_viz_icons, fetch_viz_icons
from dipy.viz import ui
from dipy.viz import window
from dipy.data import DATA_DIR
from dipy.testing.decorators import xvfb_it
# Conditional import machi... | villalonreina/dipy | dipy/viz/tests/test_ui.py | Python | bsd-3-clause | 5,390 | [
"VTK"
] | dc7e930928190bda7da986180fc5381ebc733bb9a86fda92d0bccf4ae76b7fef |
#!/usr/bin/python
import pylab
import sys
import argparse
import numpy as np
import matplotlib.pyplot as plt
import readpng as rpng
import tikhonov as tik
import scipy.sparse.linalg
import time
import random_light as rl
import sklearn.linear_model as lm
if __name__ == "__main__":
parser = argparse.ArgumentParser(d... | HajimeKawahara/pinvprob | pinvprob/random_light_fast.py | Python | gpl-2.0 | 4,980 | [
"Gaussian"
] | f7f1cd62cec87d33ce70ba6535f0772d4a3a1f174f11830e13533d17f0f6913a |
# TODO: Add tests based on taxonomy, once we know how to mock mysql.
import six
import platform
from six.moves import builtins
from copy import deepcopy
from json import dumps
from unittest import TestCase, skip
try:
from unittest.mock import patch, mock_open
except ImportError:
from mock import patch
from .... | terrycojones/dark-matter | test/diamond/test_alignments.py | Python | mit | 90,520 | [
"Biopython"
] | 4e862168c2ed92dddca792fb2e27e9bacd5554c3d0b3eeedc2707740ce0e4b3b |
#######################################################################
#
# Filelistmod for VU+ by markusw and schomi (c) 2013
# www.vuplus-support.org
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported License.
# To view a copy of this license, visit http://creat... | popazerty/e2-gui | lib/python/Plugins/Extensions/FilebrowserVTi/FileListmod.py | Python | gpl-2.0 | 17,967 | [
"VisIt"
] | 4f318b255e36bcebc4b14754d160a0e2d838b632d67c60aa4db1dc588917b4ac |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_0001/brian2_benchmark_COBAHH_clocksyn_lodens_0001.py | Python | gpl-3.0 | 3,795 | [
"Brian"
] | 78c70a8c85c78f58c3f960f41a581dae5630fb471db8a66475bb41e3bae44707 |
# vim: set expandtab:
# vim: set tabstop=4:
import MDAnalysis as mda
import numpy as np
import pytim
from pytim.datafiles import *
from pytim import observables
##########################
sampling_frequency = 50 # change this to 1 to sample each frame
##########################
u = mda.Universe(WATER_GRO, WATER_XTC... | balazsfabian/pytim | pytim/examples/example_rdf.py | Python | gpl-3.0 | 1,012 | [
"MDAnalysis"
] | 5ba32f99fa81a6d5f5c9c4f75f4ec79da97c88c40489a186fea360198536c606 |
r"""Plot figure: Different outcomes of a Gaussian kernel approximation."""
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
from sklearn.metrics import pairwise_kernels
def phi(x, w, D):
r"""RFF map."""
Z = np.dot(x, w)
return np.hstack((np.cos(Z), np.sin(Z))) / np.sqrt(D)
def crea... | RomainBrault/JMLR-ORFF | src/not_mercer.py | Python | unlicense | 3,271 | [
"Gaussian"
] | 5f457b893bf84567d9eb939ad0a3e39be8421f35114b05f9ee8d5c6fb3055917 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import math
import unittest
from collections import namedtuple
from gi.repository import GLib
from gi.repository import Hkl
from numpy import (array, cross, dot, empty, hstack, reshape, vstack)
from numpy.linalg import inv, norm
#########
# Types #
#########
D... | picca/hkl | tests/bindings/polarisation.py | Python | gpl-3.0 | 13,010 | [
"CRYSTAL"
] | 02e23791bd2de73a1182c33d19a7d667c8c33428171c25751a8b143dee929792 |
# (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 Software Foundation; either version 2, or (at your option)
# any later version.
#
# This program is distr... | RTS2/rts2 | scripts/u_point/u_point/worker.py | Python | lgpl-3.0 | 4,078 | [
"VisIt"
] | 759d2ffeb0943da108f34bf853a2d564e82128d8b12caae807709a6359b2664c |
# UNICODE CHARACTER DATABASE
# This file was generated with the command:
# ./generate_unicodedb.py --unidata_version=6.0.0 --output=unicodedb_6_0_0 --base=unicodedb_5_2_0
from rpython.rlib.rarithmetic import r_longlong
import unicodedb_5_2_0 as base_mod
version = '6.0.0'
_names = {
128673: 'AERIAL TRAMWAY',
920... | oblique-labs/pyVM | rpython/rlib/unicodedata/unicodedb_6_0_0.py | Python | mit | 306,402 | [
"CRYSTAL",
"Octopus"
] | bdcd08d3b2319d36d581f213b2b517da1a231170d59b2cf8c71fa76660fb8f20 |
# Note this also shows the final datastructure for ontology.json
ntr_assays = {
"NTR:0000612": {
"assay": ['RNA binding'],
"category": [],
"developmental": [],
"name": "Switchgear",
"objectives": [],
"organs": [],
"preferred_name": "",
"slims": [],
... | ENCODE-DCC/encoded | src/encoded/commands/ntr_terms.py | Python | mit | 39,761 | [
"NEURON"
] | 1d67dcdbb4d30616bc7af8ad680536ad42dbc1b3605655677186d3e5c83c5c0f |
"""Read basis in CP2K format."""
from pathlib import Path
import h5py
import pkg_resources
from qmflows.type_hints import PathLike
from nanoqm.workflows.initialization import store_cp2k_basis
def test_read_cp2k_basis(tmp_path: PathLike) -> None:
"""Read Basis set in CP2K format."""
tmp_hdf5 = Path(tmp_path)... | SCM-NV/qmworks-namd | test/test_read_cp2k_basis.py | Python | mit | 881 | [
"CP2K"
] | 786bc759caa5d6c6bef584d7ce9975a5aba97e309dfc66d2c0d217a4be513737 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import logging
import re
import pyparsing as pp
from td.constants import EV2NM, HARTREE2EV, HARTREE2NM
from td.ExcitedState import ExcitedState
def parse_ricc2(text):
num_sym_spin_re = "symmetry, multiplicity:\s*(\d+)\s*([\w\"\']+)\s*(\d+)"
ids_syms_spins = re... | eljost/td | td/parser/turbomole.py | Python | gpl-3.0 | 6,601 | [
"TURBOMOLE"
] | b9d628a79c8824e6f08fee90020f62ad687442d9c0365c43f7932bf56a735501 |
#!/usr/bin/env python
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | goozbach/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 9,665 | [
"Galaxy"
] | 85d86f2aa2f15c61e97a22744cb6c49d4b9ab363ba56a4a73ab99aed44734fa3 |
#!/usr/bin/env python
"""
zonal_stats - Calculates statistics of a raster variable within a region.
Reads array from netCDF file and regions from ashapefile.
Usage: zonal_stats raster_file variable_name region_file results_file
raster_file - filename of netCDF file. If a directory is given all
... | tiagoams/python_tools | zonal_stats.py | Python | gpl-3.0 | 7,383 | [
"NetCDF"
] | 667041301185de8862e8fc19829e7c30aafb966b5c31bd15a63ffa6bcb72d7a3 |
""" JobEfficiencyPolicy
Policy that calculates the efficiency following the formula::
( completed + done ) / ( completed + done + failed )
if the denominator is smaller than 10, it does not take any decision.
"""
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBas... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/JobEfficiencyPolicy.py | Python | gpl-3.0 | 2,134 | [
"DIRAC"
] | be785e08a2c6bc7455612d30eb15b5f7fd64c89eec9516c85f3c7166ab7a9623 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | glennq/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 42,704 | [
"Brian"
] | e71958ef86efccec7df61ed8fd577ae6d2cbdd98e76e142bca016931ffa06cd3 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
translate.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
*****************************... | m-kuhn/QGIS | python/plugins/processing/algs/gdal/gdaladdo.py | Python | gpl-2.0 | 5,974 | [
"Gaussian"
] | 23a42f22b0c988b7f0360ddb3c3d8a252882ff237f5ca84b6c11ba0d6169fedb |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import tempfile
import time
import re
import sys
from contextlib import contextmanager
from selenium.common.exceptions import NoSuchEle... | devenbansod/SWD-Query | splinter/driver/webdriver/__init__.py | Python | gpl-2.0 | 16,225 | [
"VisIt"
] | 7658e298de7d6b03bffeee6946e6d8c83fc9c6013c70e4a1751a972104ef7fd1 |
import unittest
import numpy as np
import bayesnet as bn
class TestGaussian(unittest.TestCase):
def test_gaussian(self):
self.assertRaises(ValueError, bn.random.Gaussian, 0, -1)
self.assertRaises(ValueError, bn.random.Gaussian, 0, np.array([1, -1]))
if __name__ == '__main__':
unittest.main(... | ctgk/BayesianNetwork | test/random/test_gaussian.py | Python | mit | 322 | [
"Gaussian"
] | 6a744a2ca26330801d8a5d390a665e382cd5fee50ad5d6b77fdd2292446e9062 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute i... | arunkgupta/gramps | gramps/gen/plug/docgen/basedoc.py | Python | gpl-2.0 | 3,715 | [
"Brian"
] | 7595ed8d32d4b7dca6068a260e00c26ff95ffd70e2d562327a64ab978ebde96a |
########################################################################
# $HeadURL $
# File: ReplicateAndRegister.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/13 18:49:12
########################################################################
""" :mod: ReplicateAndRegister
=========================... | Sbalbp/DIRAC | DataManagementSystem/Agent/RequestOperations/ReplicateAndRegister.py | Python | gpl-3.0 | 19,137 | [
"DIRAC"
] | 6678666899e473e30003142cf6ccff45fe976e230513cff3cb2779a91a67b71e |
# Copyright (c) 2008-2011, Jan Gasthaus
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions... | jgasthaus/gpu_python | plotting.py | Python | bsd-2-clause | 9,120 | [
"Gaussian"
] | 64d66a84bcebed33f385286bb559c9da8bb0562e88fcf4015b39fa9e8999e320 |
#-------------------------------------------------------------------------------
# Name: xlwsf_parse
# Purpose: Parse Microsoft webpage source for Excel functions and page
# addresses
#
# Author: Brian Skinn
# bskinn@alum.mit.edu
#
# Created: 24 May 2016
# Copyright: (... | bskinn/intersphinx-xlwsf | xlwsf_parse.py | Python | mit | 2,136 | [
"Brian"
] | 060dcd9972b6b57d2e8e87b94f96c286a88d7ffd4b9f8fbd9cab5b1f4ad07abd |
# -*- coding: utf-8 -*-
try:
import numpy as np
except ImportError:
np = None
else:
from ..stoich import (
get_coeff_mtx,
decompose_yields,
)
from chempy.units import units_library, allclose, _sum
from ..testing import requires
@requires("numpy")
def test_get_coeff_mtx():
r = [({"... | bjodah/aqchem | chempy/util/tests/test_stoich.py | Python | bsd-2-clause | 2,987 | [
"ChemPy"
] | c0f40e0754ad85b793832bad09dd72e11906343033b481607279117ab56ee715 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/df/__init__.py | Python | apache-2.0 | 1,540 | [
"PySCF"
] | b12f7d8466fafcb118df874fb874267e07dbed93ca4cf5803c3934137b7bb2cd |
from __future__ import division
import math
from random import random, randint
from threading import Lock
from NeuralNetwork.NeuralNetwork import NeuralNetwork
TWO_PI = math.pi * 2
class Food(object):
def __init__(self, world, x, y, size):
self._world = world
self.x = x
self.y = y
... | zshimanchik/iron-unconditioned-reflexes | iron-unconditioned-reflexes/animal.py | Python | mit | 8,376 | [
"NEURON"
] | 90819dcd11ccfb69348760adedcf75e6b40d7021511e753ec19b884cea15ddf7 |
import os
from secomo.convRBM import *
from secomo.sequences import *
from secomo.utils import *
def tutorial(path):
# List of Biopython sequences
onehot = load_sample()
# Obtain a cRBM object
# Epoch = 1 is not sufficient to train meaningful features
# however, it speeds up automatic testing.
... | schulter/crbm | secomo/tutorial.py | Python | gpl-3.0 | 2,161 | [
"Biopython"
] | 010a3832529c82282169cd9a8e7c2f2ca8a82f66404b4f94e030dadbfa745885 |
# Read .Mat Files
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 scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz as ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/paper_related/state_accuracy_variation.py | Python | mit | 5,407 | [
"Mayavi"
] | f73d93c60a479e5acac641857005b986e672576824232bcbebe8918a8a33db41 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | jandom/rdkit | rdkit/Chem/EState/UnitTestFingerprints.py | Python | bsd-3-clause | 1,898 | [
"RDKit"
] | a3670e2fbbcc00fdf93727fc9afb8504bb933bfca78468e26dc12d5944655fcb |
import os
import sys
from bisect import bisect_left
import neuron
import numpy as np
import CurrentGenerator
import cPickle as pickle
def data_records(dictionaryofvalues, path):
import h5py
import time
timestr = time.strftime("%m.%d.%H:%M:%S")
PATH_FLAT = '### FILL IN ###'
EXPERIMENT_PATH = '##... | mjaquier/NestModelSimplification | Simulator.py | Python | mit | 11,090 | [
"NEURON"
] | a71488cbcd97a2434e087517b24c0c9f2abcc97f6461135aded2641f8da86c6f |
"""milkyway URL Configuration
The `urlpatterns` list routes URLs to views. For more information please see:
https://docs.djangoproject.com/en/1.9/topics/http/urls/
Examples:
Function views
1. Add an import: from my_app import views
2. Add a URL to urlpatterns: url(r'^$', views.home, name='home')
Class-ba... | craigderington/SagittariusA | milkyway/milkyway/urls.py | Python | gpl-3.0 | 1,213 | [
"Galaxy"
] | 04670d6125d90c7dcc4388c6ba5d2bfeee6b0fc3e088f29ebd2408d86ffa4c24 |
# coding: utf8
# Copyright 2014-2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as a... | blond-admin/BLonD | unittests/llrf/test_signal_processing.py | Python | gpl-3.0 | 30,820 | [
"Gaussian"
] | 98b422c7c53c3f5b1f1e0b99acecf68fcc269dbb73b5fb73bbd6f08e809068cb |
########################################################################
# $HeadURL$
# File: FileTest.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/08/06 13:48:54
########################################################################
""" :mod: FileTest
=======================
.. module: FileTest
... | sposs/DIRAC | RequestManagementSystem/test/FileTests.py | Python | gpl-3.0 | 6,001 | [
"DIRAC"
] | 4ce20cdb626867045b4618f103bdfe262fb794f5875073b6f5c1fd31af888428 |
from __future__ import unicode_literals
from django.db import models
from django.contrib.auth.models import User
import random, string
# Create your models here.
class Patient(models.Model):
GENDER_CHOICES = (
('M', 'Male'),
('F', 'Female'),
)
identifier = models.CharField(max_length=255)
... | aliakbars/tbdc | patient/models.py | Python | apache-2.0 | 5,381 | [
"VisIt"
] | 9df4f0ede9f657ad40f738698b98557776d952f600516bd0802eba7333371063 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# relevant imports
import sys
import time
import espressopp
import mpi4py.MPI as MPI
import Tetracryst # Preparation of tetrahedral crystal and constuctions of bonds in tetrahedral liquid
from espressopp import Real3D, Int3D
from espressopp.tools import decomp
from espre... | junghans/espressopp | examples/hadress/hadressPlain/hadress.py | Python | gpl-3.0 | 7,455 | [
"CRYSTAL"
] | b33f9adb8bce105c5443b52f1766f121f54c19c4cab90a4d51c1aa24e993d81a |
from django.shortcuts import render
from django.http import HttpResponse
from rango.models import Category,Page
from rango.forms import CategoryForm
from django.contrib.auth.decorators import login_required
from datetime import datetime
def index(request):
category_list = Category.objects.order_by('-likes')[:... | ZheJiuShiMing/tango_with_django_project | tango_with_django_project/rango/views.py | Python | gpl-2.0 | 10,530 | [
"VisIt"
] | 3576436965b3649bf5168bced152aaf8c9bd3d6dbae2b4b759f026f261b3df6f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_costcentereditor.py | Python | gpl-2.0 | 1,441 | [
"VisIt"
] | 13124ed61f53820c8f3a3959fd47f6af10515acb6d093804448fc74bb051ee9c |
#!/usr/bin/env python
import glob
import sys
import numpy as np
from setuptools import setup, find_packages
try:
from Cython.Build import cythonize
have_cython = True
except ImportError:
have_cython = False
# Determine shared library suffix
if sys.platform == 'darwin':
suffix = 'dylib'
else:
suf... | liangjg/openmc | setup.py | Python | mit | 2,715 | [
"VTK"
] | 7d074e9b39927c73e56eb31cb6769ebc343b6b53c6332c1f2f2b00a311c9a272 |
# Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of ... | govarguz/espressopp | src/analysis/Configurations.py | Python | gpl-3.0 | 3,386 | [
"ESPResSo"
] | 2ae051fad35708f8ad660b816428464dd37c88e457277a9e409eccc4f2287a88 |
""" ResourceManagementClient
Client to interact with the ResourceManagementDB.
"""
__RCSID__ = '$Id$'
from DIRAC.Core.DISET.RPCClient import RPCClient
def uppercase_first_letter(key):
""" a method that makes the first letter uppercase only (and leaves the remaining letters unaffected)
"""
return key[0].up... | petricm/DIRAC | ResourceStatusSystem/Client/ResourceManagementClient.py | Python | gpl-3.0 | 26,914 | [
"DIRAC"
] | f16e4c0d4c3e973100c2cfd1d7d8eed8673467220b3d2d6bebfcc5b046827974 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-preprocesscore/package.py | Python | lgpl-2.1 | 1,640 | [
"Bioconductor"
] | e7df437590cacf3bee250fd741fc324a77e350b3cd0a455f950a9e066de4b570 |
# 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... | aselle/tensorflow | tensorflow/contrib/autograph/pyct/templates.py | Python | apache-2.0 | 9,765 | [
"VisIt"
] | 5f6ec6aa64273efb45911069244ebe25b274342c3b29413bd68c6e2724708657 |
"""
This modules defines two functions that can be used in place of the ``RPCClient`` and
``TransferClient`` to transparently switch to ``https``.
Example::
from DIRAC.Core.Tornado.Client.ClientSelector import RPCClientSelector as RPCClient
myService = RPCClient("Framework/MyService")
myService.doSo... | yujikato/DIRAC | src/DIRAC/Core/Tornado/Client/ClientSelector.py | Python | gpl-3.0 | 3,489 | [
"DIRAC"
] | b80d6f65cfb5d1ea5ff92d4a1e79498d19fba8b92bf4a291d91a746065e47a0b |
# Copyright (C) 2001 greg Landrum and Rational Discovery LLC
"""basic unit testing code for query mols
"""
from rdkit import RDConfig
import unittest, os, sys
class TestCase(unittest.TestCase):
def setUp(self):
print('\n%s: ' % self.shortDescription(), end='')
# decipher the name of the executable
i... | ptosco/rdkit | Code/GraphMol/UnitTestQueryMol.py | Python | bsd-3-clause | 703 | [
"RDKit"
] | 7502f1f1ae617fd3d92685b31103cb6c642f3704a0eccb98db32b8ce09d64632 |
##############################
# #
# Instructions #
# #
##############################
# To run, use the following command:
# $ python longest_distance.py <input_file>
# where <input_file> is the filename with the question's input
import sys
import r... | joseph-roque/advent-of-code | day_09/longest_distance.py | Python | mit | 2,625 | [
"VisIt"
] | 675e8df0c818e7ce24bcc8dcadefb2d43751897793401edf912af94321c1cf6a |
# -*- coding: utf-8 -*-
"""
Initial AST validation and normalization.
"""
from __future__ import print_function, division, absolute_import
import ast
import copy
from numba import error
from numba import nodes
from numba import visitors
from numba import typesystem
class NormalizeAST(visitors.NumbaTransformer):
... | shiquanwang/numba | numba/normalize.py | Python | bsd-2-clause | 5,040 | [
"VisIt"
] | c0f4af9b3ae45a08aae78e2d920c34484cf6addeeb70917db457254b3fb68d67 |
# Copyright (c) 2015-2018, 2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015-2016 Ceridwen <ceridwenv@gmail.com>
# Copyright (c) 2016 Jakub Wilk <jwilk@jwilk.net>
# Copyright (c) 2018 Bryce Guinta <bryce.paul.guinta@gmail.com>
# Copyright (c) 2019 Ashley Whetter <ashley@awhetter.co.uk>
# Copyright (c) 2020... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/astroid/tests/unittest_transforms.py | Python | mit | 8,215 | [
"VisIt"
] | bde535d4094ba78e32b500f182fd83a02bc942b960a7f0bbf38c707a1a6aaeda |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='amrclaw'):
#------------------------------
"""... | clawpack/adjoint | examples/acoustics_2d_radial_timepoint/compare/setrun_pflag.py | Python | bsd-2-clause | 11,189 | [
"NetCDF"
] | 645bee7570f9dad41d8c75b1cba09098d0c0a3d6263b2d02312964418784ed84 |
""" Defines the SX127x class and a few utility functions. """
# -*- coding: utf-8 -*-
# Copyright 2015-2018 Mayer Analytics Ltd.
#
# This file is part of pySX127x.
#
# pySX127x is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public
# License as published by the Free... | mayeranalytics/pySX127x | SX127x/LoRa.py | Python | agpl-3.0 | 37,104 | [
"CRYSTAL"
] | 22bad47a7d0279b7526c7132998e63bd8cf108e86d72be55e6ef10867e481a4b |
# -*- coding: utf-8 -*-
# Copyright 2013-2014 Victor Amin, http://vamin.net/
"""MESS.DB import module
This module contains the import tool class and load function.
"""
from __future__ import print_function
from __future__ import unicode_literals
import codecs
import math
import os
from collections import OrderedDic... | vamin/MESS.DB | mess/tools/import.py | Python | agpl-3.0 | 12,410 | [
"Open Babel",
"Pybel"
] | 6bed2bffb2476cd9b611282e3b6e9170f8d88692161be9fda074cc0c824f2e7a |
#!/usr/bin/env python
from __future__ import print_function
import urllib2
import re
from pymatgen.core.periodic_table import PeriodicTable
#pattern = r'elemParams[%d] = ['%s','%s','%s']'
#'\definecolor{atom-H}{rgb}{1.000000,1.000000,1.000000}'
def atoms_style_jmol():
url = 'http://jmol.sourceforge.net/jscolo... | ldamewood/figures | scripts/tikzlibraryatoms/tikblibraryatoms.style.py | Python | mit | 1,763 | [
"Jmol",
"pymatgen"
] | 723d3042733314f5d09f2635cbcee763141754d3615cfe479d8ce4188a809028 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | iambocai/ansible | lib/ansible/utils/__init__.py | Python | gpl-3.0 | 56,744 | [
"Galaxy",
"VisIt"
] | 0c3a6ce52b54fce273f3f0414ff16d3fdd1399be472276acabb42457b21be6ff |
"""
Module for handling state variables.
"""
from __future__ import absolute_import
import numpy as nm
from sfepy.base.base import Struct
import six
class State(Struct):
"""
Class holding/manipulating the state variables and corresponding DOF
vectors.
Manipulating the state class changes the underlyi... | vlukes/sfepy | sfepy/discrete/state.py | Python | bsd-3-clause | 10,040 | [
"VTK"
] | 8a20d734ea986527166e8edea1638b5cf0e22ab209ce5350091eaf4bdb11ffb3 |
from WebAppDIRAC.Lib.WebHandler import WebHandler, asyncGen
from DIRAC.Resources.Catalog.FileCatalog import FileCatalog
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getVOForGroup
from DIRAC import gConfig, gLogger
from DIRAC.Core.Utilities import Time
from hashlib import md5
class FileCatalogHandler... | zmathe/WebAppDIRAC | WebApp/handler/FileCatalogHandler.py | Python | gpl-3.0 | 12,082 | [
"DIRAC"
] | 1ddcd5a57dbadd264466dc664b5ef6deb883c7b90c089edbf548eca2cf44e380 |
import numpy as np
import numpy.random as ra
from gpaw.test import equal
from gpaw.setup import create_setup
from gpaw.grid_descriptor import GridDescriptor
from gpaw.localized_functions import create_localized_functions
from gpaw.spline import Spline
from gpaw.xc import XC
from gpaw.utilities import pack
from gpaw.mpi... | ajylee/gpaw-rtxs | gpaw/test/gga_atom.py | Python | gpl-3.0 | 2,043 | [
"GPAW"
] | 2470e03e248a7a48ef0332e700e9560955a9b3697fd4a4270670218523fb90b2 |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE... | Pakketeretet2/lammps | python/lammps.py | Python | gpl-2.0 | 38,678 | [
"LAMMPS"
] | 3c28be0c75d71d317e71912efc6bd8ea022861842dfec8ffcc8ad5355e1144a2 |
# coding: utf-8
"""
Works for Abinit:
"""
from __future__ import unicode_literals, division, print_function
import os
import shutil
import time
import abc
import collections
import numpy as np
import six
import copy
from six.moves import filter
from monty.collections import AttrDict
from monty.itertools import chunks... | rousseab/pymatgen | pymatgen/io/abinitio/works.py | Python | mit | 52,370 | [
"ABINIT",
"Gaussian",
"NetCDF",
"pymatgen"
] | a2dc0cbef396c50c3159f61fec5cfd20eb82102af153a2de79f46fef78322e8f |
"""
@name: Modules/House/Security/garage_door.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2019-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on aug 26, 2019
@Summary:
"""
__updated__ = '2019-12-29'
__version_info__ = (19, 10, 2)
__version__ = '.'.join(... | DBrianKimmel/PyHouse | Project/src/Modules/House/Security/Garagedoors/garagedoors.py | Python | mit | 4,586 | [
"Brian"
] | f3595fb1cd19f26c65862d792942803f6548cd70b7fccae155a84373750208a0 |
import math
from ..libmp.backend import xrange
class QuadratureRule(object):
"""
Quadrature rules are implemented using this class, in order to
simplify the code and provide a common infrastructure
for tasks such as error estimation and node caching.
You can implement a custom quadrature rule by ... | klkuhlm/mpmath | mpmath/calculus/quadrature.py | Python | bsd-3-clause | 38,292 | [
"Gaussian"
] | 444277256b8d0b9ee22b0d05acd1352fdc1626e6448b92839fd554dc42a08bbb |
from go_to_adjacent_systems import *
from go_somewhere_significant import *
import vsrandom
import launch
import faction_ships
import VS
import Briefing
import universe
import unit
import Director
import quest
import gettext
class escort_local (Director.Mission):
def __init__ (self,factionname,numsystemsaway, enemy... | costalfy/Vega-Strike | data/modules/missions/escort_local.py | Python | gpl-2.0 | 10,666 | [
"VisIt"
] | 68ce559e0675c6c7acb12d01d760d21aa1ff929db898a4b2a200a0ffd1be28b3 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | liuwenf/moose | python/MooseDocs/html2latex/MooseExtension.py | Python | lgpl-2.1 | 2,953 | [
"MOOSE"
] | 1b852c4ecc5d5dd6ada0b898bf37098f8083b60901d74b22b5e8fc9c7c99e25f |
#!/usr/bin/env python2
# vim:fileencoding=utf-8
# License: GPLv3 Copyright: 2015, Kovid Goyal <kovid at kovidgoyal.net>
from __future__ import (unicode_literals, division, absolute_import,
print_function)
from collections import OrderedDict
from functools import partial
import textwrap
from P... | timpalpant/calibre | src/calibre/gui2/tag_mapper.py | Python | gpl-3.0 | 18,847 | [
"MOOSE"
] | 18cf58b33e4840d3d7a6e3f4fb8744d92049f830469f94c0940d5c695d4f2a01 |
# FIXME: do we still need this test case, if test_provider_skeleton is working fine?
from unittest import TestCase
from openarticlegauge.plugins.nature import NaturePlugin # TUTORIAL: change this to import *your* plugin
from openarticlegauge import config, models
# TUTORIAL: no need to modify any of this unless you ... | CottageLabs/OpenArticleGauge | openarticlegauge/tests/test_nature.py | Python | bsd-3-clause | 14,097 | [
"VisIt"
] | a61a570d069dac198954319753534c70086487726a40d799673f2e5ec5453f71 |
from __future__ import print_function
from __future__ import absolute_import
import numpy as nm
import sys
from six.moves import range
sys.path.append('.')
from sfepy.base.base import output, assert_
from sfepy.base.ioutils import ensure_path
from sfepy.linalg import cycle
from sfepy.discrete.fem.mesh import Mesh
from... | lokik/sfepy | sfepy/mesh/mesh_generators.py | Python | bsd-3-clause | 27,183 | [
"VTK"
] | cb0bcb77fbb630bf61b2973dd52e57197b3a90194e0432e93a8214f78ea58fe8 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | ashutoshvt/psi4 | psi4/driver/qcdb/psivardefs.py | Python | lgpl-3.0 | 15,690 | [
"Psi4"
] | 0e55901597e7cea5da747bd8c4aba85fddad6c8b06238dbe80755aa61d466959 |
#!/usr/bin/env python
#
# $File: IdTagger.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute i... | BoPeng/simuPOP | docs/IdTagger.py | Python | gpl-2.0 | 1,541 | [
"VisIt"
] | f29f239c21beca38717930fe5d3d79be0ce67a1937d72ceb9c36d745c63b0799 |
import os, copy
from bashlex import yacc, tokenizer, state, ast, subst, flags, errors, heredoc
def _partsspan(parts):
return parts[0].pos[0], parts[-1].pos[1]
tokens = [e.name for e in tokenizer.tokentype]
precedence = (
('left', 'AMPERSAND', 'SEMICOLON', 'NEWLINE', 'EOF'),
('left', 'AND_AND', 'OR_OR'),
... | vikasgorur/bashlex | bashlex/parser.py | Python | gpl-3.0 | 24,684 | [
"VisIt"
] | 4dec7475af35c13a79a18200090d72c376d739e1048b0771f93e952d2a7f4772 |
# Copyright 2017 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... | duftler/spinnaker | dev/validate_bom__deploy.py | Python | apache-2.0 | 62,240 | [
"ORCA"
] | 865f6d021921105f4b8c9221a4fed1f3ebdfb559ae7c2fd4c835586fb123af3e |
"""Read genome build configurations from Galaxy *.loc and bcbio-nextgen resource files.
"""
import ConfigParser
import glob
import os
from xml.etree import ElementTree
import toolz as tz
import yaml
from bcbio import utils
from bcbio.ngsalign import star
from bcbio.pipeline import alignment
from bcbio.provenance impo... | SciLifeLab/bcbio-nextgen | bcbio/pipeline/genome.py | Python | mit | 10,747 | [
"Galaxy"
] | d644cbd8a3b4c2c11bab4bd454b732a9e8c919e611c59373784502432ed6331b |
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