text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | kmike/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 51,913 | [
"Brian"
] | c17336d8cf2bd4d201c4119b1c7bd162130c0766172099c7bfed21f55526d156 |
# GromacsWrapper: formats.py
# Copyright (c) 2009-2011 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Gromacs topology file (ITP) parser
==================================
.. versionadded:: 0.2.5
Basic reading, manipulat... | jandom/GromacsWrapper | gromacs/fileformats/itp.py | Python | gpl-3.0 | 32,562 | [
"Gromacs"
] | 7936baa6f05f8d94f36ba7d56be65f512e3041178423ff0647fcf8a54f760ebc |
import sys
import os
import psycopg2
import xml.etree.ElementTree as ET
from lxml import etree
import math
from collections import Counter
from operator import itemgetter
import datetime
import collections
#Intended for use with CWar
def block(ch):
'''
Return the Unicode block name for ch, or None if ch has ... | grantdelozier/TopoCluster | experimental/TestResolver_CWar.py | Python | apache-2.0 | 33,965 | [
"FEFF"
] | 323a1b9d83882fb621a4471a80b4942dc82b7ab7f54ecd5611e214f0da37a8b9 |
"""Mayavi/traits GUI for converting data from KIT systems"""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
import numpy as np
from scipy.linalg import inv
from threading import Thread
from ..externals.six.moves import queue
from ..io.meas_info import _read_dig_points... | dimkal/mne-python | mne/gui/_kit2fiff_gui.py | Python | bsd-3-clause | 18,716 | [
"Mayavi"
] | 7b4b0c3cbebba8c24af9ee4bc4aa712f5e8d65c1d9d0ed39fa4d07a0201f26f6 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010 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 Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/gui/search/stockdecreasesearch.py | Python | gpl-2.0 | 3,979 | [
"VisIt"
] | b207217090c76e1b327d88ca7440bc405e31db6efebe49a1bd1328c58b022a88 |
from module_mixins import simpleVTKClassModuleBase
import vtk
import vtkdevide
class imageBorderMask(simpleVTKClassModuleBase):
def __init__(self, module_manager):
simpleVTKClassModuleBase.__init__(
self, module_manager,
vtkdevide.vtkImageBorderMask(), 'Creating border mask.',
... | chrisidefix/devide | modules/user/experimental/imageBorderMask.py | Python | bsd-3-clause | 427 | [
"VTK"
] | ad394caa6579b8f676c761235158bf8ca0d4167645297ce621530a76f6ffac2a |
from graphql.language import ast
from ..query import QueryVisitor, Field
def _name(value):
return ast.NameNode(value=value) if value is not None else None
def _encode(value):
if value is None:
return ast.NullValueNode()
elif isinstance(value, bool):
return ast.BooleanValueNode(value=val... | vmagamedov/hiku | hiku/export/graphql.py | Python | bsd-3-clause | 2,124 | [
"VisIt"
] | 4a426180de28daa4adc6f6d4c8cb146502d803098388354baf8b974372e8054d |
#
# Copyright (C) 2017-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | mkuron/espresso | testsuite/python/coulomb_tuning.py | Python | gpl-3.0 | 3,267 | [
"ESPResSo"
] | 21b491954a22bf9a918e75166b4bd011b72b877d020ad742fde86ea64b124e61 |
"""Get random pairs of same-molecule conformers.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
from __future__ import division
import os
import glob
import logging
import argparse
import numpy as np
import rdkit.Chem
from python_utilities.io_tools import smart_open
from e3fp.conformer.util import mol_from_sdf
fro... | keiserlab/e3fp-paper | project/fingerprint_comparison/random_conformer_pairs/get_random_pairs.py | Python | lgpl-3.0 | 4,032 | [
"RDKit"
] | 6a5ec38d13b72d825a8c68997db5309dac0b9b27531168653d4b17fc17a6607c |
'''==================================================
whitelist - Identify the likely true cell barcodes
==================================================
*Extract cell barcodes and identify the most likely true cell barcodes*
Usage:
------
For single ended reads, the following reads from stdin and outputs to stdou... | CGATOxford/UMI-tools | umi_tools/whitelist.py | Python | mit | 20,963 | [
"Gaussian"
] | 51359ac806f19fa738fa565e322b0430a2dec5046437b2cfe9c3f0f5a6e46c0c |
# TODO: to improve extendability, move this file into separate subfolder
from abc import ABCMeta, abstractmethod
from numbers import Number
import warnings
import numpy as np
import scipy.linalg
from .constants import GAUSSIAN_SD_FWHM
from .operator_tools import (transition_operator, operator_extend, unit_vec,
... | shoyer/qspectra | qspectra/hamiltonian.py | Python | bsd-2-clause | 32,656 | [
"Gaussian"
] | 0302ce10b63deefceb9b0a344e89c67410a14e92d667804e5721844251b67ffa |
## Copyright (c) 2001-2009, Scott D. Peckham
## January 2009 (converted from IDL)
## August 2009
## October 2009 (routines to allow more output file formats)
#-------------------------------------------------------------------
# Functions:
#
# write_profile()
# Number_of_Samples()
# save_step()
# ... | csdms-contrib/erode | model_output.py | Python | apache-2.0 | 32,920 | [
"NetCDF"
] | 6a9ea86ed1346f819162a803d49cefe0958e675e7d980e7aa1cd2bcb24318b01 |
import sympy
import pytest
import numpy as np
from devito import Grid, Function, solve, TimeFunction, Eq, Operator
from devito.ir import Expression, FindNodes
from devito.symbolics import retrieve_functions, retrieve_indexed
def test_float_indices():
"""
Test that indices only contain Integers.
"""
g... | opesci/devito | tests/test_symbolics.py | Python | mit | 2,909 | [
"VisIt"
] | b4d53a56bcf08fd63433471dfb83c974adfd692513badfb963fea59d5a847148 |
import os
import urllib
from ConfigParser import ConfigParser
BASE_DIR = os.path.abspath(os.path.dirname(__file__))
cf = ConfigParser()
cf.read(os.path.join(
BASE_DIR, 'static', 'config.ini'
))
_filename = 'papsim_wfdei.cru_hist_{}_{}_{}_{}_annual_1979_2012.nc4'.format(
cf.get('nc4', 'harms'), cf.get('nc4',... | RDCEP/atlas-viewer | atlas/constants.py | Python | apache-2.0 | 703 | [
"NetCDF"
] | 87df39e1867be5fb5fb57cb8217025c994024dadc8ac4d72ae9caf455d574de4 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Lic... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/updater.py | Python | gpl-2.0 | 10,778 | [
"VisIt"
] | 333c5fc2edff2e3061a65998774627ca6baf97e7c9a913bbbde54e1ad31e8178 |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# _generate_pyx.py to generate the docstrings for the ufuncs in
# scipy.special at the C level... | lhilt/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 190,012 | [
"Gaussian"
] | 8bed3fea4bfc8f9b293a52aa2e7604cbc8edfa278117397ee643f325a19120dc |
# -*- coding: utf-8 -*-
import numpy as np
from shapely.geometry.polygon import Polygon
import datetime
import netCDF4 as nc
import itertools
import geojson
from shapely.ops import cascaded_union
#from openclimategis.util.helpers import get_temp_path
#from openclimategis.util.toshp import OpenClimateShp
from shapely.ge... | OpenSource-/OpenClimateGIS | src/openclimategis/util/ncconv/experimental/OLD_experimental/in_memory_oo_multi.py | Python | bsd-3-clause | 23,081 | [
"NetCDF"
] | 63a126f295eadd11f299b7d90c392322101ca2d028b0acd8a57d2ecb176ed923 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import django.utils.timezone
import geoposition.fields
import ruhvz.game.models
import mptt.fields
import django.db.models.deletion
from django.conf import settings
import ruhvz.overwrite_fs
class Migration(migra... | EternalDeiwos/ruhvz | ruhvz/game/migrations/0001_initial.py | Python | mit | 11,870 | [
"Desmond"
] | cd2e0f7e31bad4860acdfdd9a8cc049630d0d53c50713db86ab9d2bad6309119 |
# $Id$
#
# 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.
#
""" tools for interacti... | rdkit/rdkit-orig | rdkit/utils/chemdraw.py | Python | bsd-3-clause | 11,604 | [
"RDKit"
] | 8cea1c645a60168aca6928325d60391348f1a012fee08ec073f06ed4cd0a450a |
#!/usr/bin/env python
# Part of BP discovery pipeline
# For each line in the bam file, count the number of matches (not mismatches, since the CIGAR M flag may represent match or mismatch)
# Output each seqname and the corresponding # matches
# Note that the input sam/bam file is generated using bowtie2 local mode, so ... | yfu/tools | parse_bam/report_n_matches.py | Python | gpl-3.0 | 2,368 | [
"pysam"
] | ddb160d3590b5f05eef9a4f7a39865ba3d3d589e43db6e6e7b7b77d307269346 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#Copyright (C) 2007 Adam Spencer - Free Veterinary Management Suite
#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 ... | cyncyncyn/evette | languagefiles/language_norwegian_1.3.2.py | Python | gpl-2.0 | 68,083 | [
"VisIt"
] | f892ac715f9f20be5806f9c0b0267aadb6380c5b81acc581f65d81275fb61275 |
import binascii
import bisect
from datetime import date, timedelta
from collections import defaultdict
import math
import time
import unittest
import uuid
import redis
def to_bytes(x):
return x.encode('latin-1') if isinstance(x, str) else x
def to_str(x):
return x.decode('latin-1') if isinstance(x, bytes) ... | josiahcarlson/redis-in-action | python/ch09_listing_source.py | Python | mit | 25,549 | [
"BWA",
"VisIt"
] | 42b591d964418bca093880165c098ec85408b17671bf7dba8e114bd79bb814ef |
##
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Copyright:: Copyright 2012-2019 Uni.Lu/LCSB, NTUA
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Kenneth Hoste
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>
# License:: MIT/GPL
#... | hpcugent/easybuild-easyblocks | easybuild/easyblocks/b/bwa.py | Python | gpl-2.0 | 3,099 | [
"BWA"
] | 78760c14f13deb02b9a6ab508f61999704fe69791a50649c659af8210e89b7c3 |
from __future__ import print_function, absolute_import, division
from mdtraj.utils.six import PY2
import logging
logger = logging.getLogger(__name__)
import numpy as np
from mdtraj.geometry import dihedral as _dihedralcalc
from .baseclasses import Vectorized, AbstractDistanceMetric
class Dihedral(Vectorized, Abstra... | mpharrigan/msmbuilder | MSMBuilder/metrics/dihedral.py | Python | gpl-2.0 | 5,761 | [
"MDTraj"
] | dc8cd3ae1e789ca843c40bc46691cfe20c7f59823a96cc7515c805668f50d472 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/lb_stokes_sphere.py | Python | gpl-3.0 | 4,268 | [
"ESPResSo"
] | 13817570f0195eec96e01a3ba70bc4b9007b504e3dbeafdf85766f67204ef9ee |
# Copyright 2013 Pau Haro Negre
# based on C++ code by Carl Staelin Copyright 2009-2011
#
# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with... | pauh/neuron | test/test_run_experiment.py | Python | apache-2.0 | 3,331 | [
"NEURON"
] | 118b66134a6a98a84d32603cd0a81abbed1acf14b6b783e9674fab90bbbd2ac6 |
from multiasecalc.lammps.compass import COMPASS
from multiasecalc.lammps.charmm import CHARMM
from multiasecalc.lammps.reaxff import ReaxFF
from multiasecalc.lammps.oplsaa import OPLSAA
from multiasecalc.lammps.bonds import Bonds
| csmm/multiase | multiasecalc/lammps/__init__.py | Python | gpl-2.0 | 234 | [
"CHARMM",
"LAMMPS"
] | 33771794f16df3942ffa5fdbd5a39bf4e9ce9c7a7d6b275495b900c8e99b9bfc |
import os
import sys
from fnmatch import fnmatchcase
from distutils.util import convert_path
from setuptools import setup, find_packages
VERSION = __import__("pinax").__version__
def read(*path):
return open(os.path.join(os.path.abspath(os.path.dirname(__file__)), *path)).read()
# Provided as an attribute, ... | jhaus/pinax | setup.py | Python | mit | 4,842 | [
"Brian"
] | 1a328f8621fef59af4ec4e25a02e4c8933fa9f3f1f3c561b37083538b42bf1c8 |
import warnings
# Show warnings for our package
warnings.filterwarnings('always', module='msmbuilder.*')
# Show warnings for packages where we want to be conscious of warnings
warnings.filterwarnings('always', module='mdtraj.*')
warnings.filterwarnings('always', module='scipy.*')
warnings.filterwarnings('always', mod... | stephenliu1989/msmbuilder | msmbuilder/tests/__init__.py | Python | lgpl-2.1 | 337 | [
"MDTraj"
] | 3aa9f892530561e83fb38896df446908db53960d36d1149c30fcbcaa1f210443 |
#!/usr/bin/env python3
import argparse
import numpy as np
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter, description='Calculates an appropriate RBF shape parameter for Gaussian basisfunctions')
# parser.add_argument('basisfunction', choices=["Gaussian"], default="Gaussian", ... | precice/precice | extras/rbfShape/rbfShape.py | Python | lgpl-3.0 | 871 | [
"Gaussian"
] | 46ac47cc7d39f7478f87fd5aecf558e037b28af12b5a01eaa84843bcefc9ca29 |
# 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... | tensorflow/tensorflow | tensorflow/python/data/kernel_tests/rejection_resample_test.py | Python | apache-2.0 | 6,317 | [
"DIRAC"
] | 7ec9ea3a628a659e3d5e61a177f57c712f8712b8f7192e5a5629350326322177 |
from __future__ import unicode_literals
from django.contrib.auth.models import User
from django.utils import six
from djblets.webapi.decorators import (webapi_login_required,
webapi_response_errors,
webapi_request_fields)
from djblets.webapi... | davidt/reviewboard | reviewboard/webapi/resources/base_archived_object.py | Python | mit | 3,435 | [
"VisIt"
] | 866e962ba7787ef2fe4e6afede42d278668ffb02a00dd57ddbc30055b5faa274 |
# -*- coding: utf-8 -*-
"""
Deal with DER encoding and decoding.
Adapted from python-ecdsa at https://github.com/warner/python-ecdsa
Copyright (c) 2010 Brian Warner
Portions written in 2005 by Peter Pearson and placed in the public domain.
The MIT License (MIT)
Copyright (c) 2013 by Richard Kiss
Permission is here... | devrandom/pycoin | pycoin/tx/script/der.py | Python | mit | 4,582 | [
"Brian"
] | 4ef841ac6141f65e947722ddaaa64b6e0c6c9738dd5b586ee3c2289e6136ddb5 |
# -*- coding: utf-8 -*-
from pyqtgraph.Qt import QtCore, QtGui
from ..Node import Node
from scipy.signal import detrend
from scipy.ndimage import median_filter, gaussian_filter
#from pyqtgraph.SignalProxy import SignalProxy
from . import functions
from .common import *
import numpy as np
import pyqtgraph.metaarray as ... | ibressler/pyqtgraph | pyqtgraph/flowchart/library/Filters.py | Python | mit | 10,018 | [
"Gaussian"
] | b1e91e276a8f7d7d34705565a1c123aa0a94bca1cf31951b96d7346f5a5cad66 |
#!/usr/bin/env python
# Copyright 2014-2018 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... | sunqm/pyscf | pyscf/pbc/grad/test/test_kuks.py | Python | apache-2.0 | 3,104 | [
"PySCF"
] | 0e670f72be3a52dd6fbaf9168152f45940f4fe4d276612055f834842a3e5ab57 |
# -*- coding: utf-8 -*-
"""
.. module:: skrf.network
========================================
network (:mod:`skrf.network`)
========================================
Provides a n-port network class and associated functions.
Much of the functionality in this module is provided as methods and
properties of the :class:`... | temmeand/scikit-rf | skrf/network.py | Python | bsd-3-clause | 215,992 | [
"Gaussian"
] | ccfc20ed7c2311060f0b454b92cd025d00ed7569a3e5551e42a593dc63643430 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Provides an interface to communicate with the device via the adb command.
Assumes adb binary is currently on system path.
"""
import collections
imp... | pozdnyakov/chromium-crosswalk | build/android/pylib/android_commands.py | Python | bsd-3-clause | 50,916 | [
"Galaxy"
] | 75538446674edc01c3db32f8801e980ead30cddf1e336b9c584e83ccb246f1c0 |
from __future__ import (absolute_import, division,
print_function, unicode_literals)
from builtins import *
import logging
import re
import sys
import tempfile
from datetime import datetime
import pytz
import psycopg2
import numpy
import xarray
from windb2.insert import Insert
from windb2 impor... | sailorsenergy/windb2 | windb2/model/gfs/insert.py | Python | gpl-3.0 | 7,479 | [
"NetCDF"
] | 656166bc7102bec1130099ecf33d8ef3a4ef56c16eb7ae2a7a4550679c31f4c8 |
'''
We base the WNN-GIP implementation on the one from PyDTI project, https://github.com/stephenliu0423/PyDTI, changes were made to the evaluation procedure
[1] van Laarhoven, Twan, Sander B. Nabuurs, and Elena Marchiori. "Gaussian interaction profile kernels for predicting drug-target interaction." Bioinformatics 27... | lpeska/BRDTI | wnngip.py | Python | gpl-2.0 | 4,491 | [
"Gaussian"
] | 0a64ce94b02c343b8cfa6dc186401a03408983fb64449c23e9163089b376c26c |
# written by: Ioannis Paraskevakos
# tested by: Ioannis Paraskevakos
# debugged by: Ioannis Paraskevakos
hashtable=[{'name':'New York, NY','lat':40.71,'long':-73.99},
{'name':'Los Angeles, CA','lat':34,'long':-118.25},
{'name':'Chicago, IL','lat':41.83,'long':-87.68},
{'name':'Houston, TX','lat':29.76,'long':-95.38},
{... | mohjaba/Health-Activity-Monitoring | 1_code/data_filtering/hashtable.py | Python | gpl-2.0 | 400,597 | [
"COLUMBUS",
"CRYSTAL",
"Dalton",
"Elk"
] | 110adc887aada6d22fc2d63bc6b616c0312355337b6f7d3c723134155c573642 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# preferences_dialog.py
#
# This file is part of PushBullet-Indicator
#
# Copyright (C) 2014
# Lorenzo Carbonell Cerezo <lorenzo.carbonell.cerezo@gmail.com>
# Copyright (C) 2017 Alp Erbil
# beratalp@gmail.com
#
# This program is free software: you can redistribute it and... | beratalp/indicator-pushbullet | src/answer_dialog.py | Python | gpl-3.0 | 4,479 | [
"ORCA"
] | d7603391d8d6469acb3d95e2bb0c62fbf0abc8226c49dea0e255bba1158f2aeb |
# coding=utf-8
#
# BSD 3-Clause License
#
# Copyright (c) 2016-21, University of Liverpool
# 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 abov... | rigdenlab/conkit | conkit/core/contactmap.py | Python | bsd-3-clause | 42,722 | [
"Gaussian"
] | ec91f7488309a026289b43145bc8ef33ac133d788b025e40af63d9abfd17bc6a |
#!/usr/bin/python3
import deep_feedback_learning
import numpy as np
import matplotlib.pyplot as plt
print("testBackpropWithFilters")
with open('test_bp_filt_py.csv', 'wb') as csvfile:
csvfile.close()
with open('test_bp_filt_py.csv', 'ab') as csvfile:
# two input neurons, two hidden ones and one output ne... | nlholdem/icodoom | tmp/test_bp_learning_with_filters.py | Python | gpl-3.0 | 1,610 | [
"NEURON"
] | ca04615f12fd883dda75ecc3eba9aa18ac7637b0e78f9c5e8cb6efef2e523657 |
"""Next-gen alignments with TopHat a spliced read mapper for RNA-seq experiments.
http://tophat.cbcb.umd.edu
"""
import os
import shutil
import sys
import glob
import subprocess
import numpy
import pysam
try:
import sh
except ImportError:
sh = None
from bcbio.pipeline import config_utils
from bcbio.ngsalign... | brainstorm/bcbio-nextgen | bcbio/ngsalign/tophat.py | Python | mit | 14,302 | [
"Bowtie",
"pysam"
] | 4272b894e4c2be213ddf3683c67007cc9cfc6718b667dca357ac32d924606de9 |
# -*- coding: utf-8 -*-
import os
import sys
import array
import numpy as np
import scipy.ndimage
import scipy.interpolate
from scipy.interpolate import UnivariateSpline
from matplotlib.pyplot import *
from matplotlib.mlab import *
####### Check for h5py to Read AMR data ######
try:
import h5py as h5
hasH5 = T... | DeovratPrasad/Galaxy-Cluster-PLUTO | Tools/pyPLUTO/pyPLUTO/pyPLUTO.py | Python | gpl-2.0 | 63,860 | [
"VTK"
] | 402ca11bdac5573b5c089cef9918c4403579716f3008e35b011149331212d064 |
#!/usr/bin/env python3
import numpy as np
import pytest
from pysisyphus.helpers import geom_from_library
from pysisyphus.calculators.PyXTB import PyXTB
from pysisyphus.calculators.XTB import XTB
# module load intel/2018.0.33
# module load xtb/6.2
@pytest.mark.skip
def test_pyxtb():
geom = geom_from_library("be... | eljost/pysisyphus | tests_staging/test_pyxtb/test_pyxtb.py | Python | gpl-3.0 | 1,324 | [
"Psi4",
"xTB"
] | b32aca51f75f6eb139728e3e63d6970a5810ed753e5dba571ad62fcbae9c4d8f |
# $Id$
#
# Copyright (C) 2006 Greg Landrum
#
import unittest,os,sys
from rdkit import RDConfig
from rdkit import Chem
from rdkit import DataStructs
import cPickle
from rdkit.Chem import MolCatalog
class TestCase(unittest.TestCase):
def test1(self):
cat = MolCatalog.CreateMolCatalog()
es = []
for smi in... | rdkit/rdkit-orig | Code/GraphMol/MolCatalog/Wrap/rough_test.py | Python | bsd-3-clause | 1,264 | [
"RDKit"
] | 13a6e7926c57140fbb04a9bc980c0f5077ea754f68dcd7713f791445ef83b2ea |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 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 requi... | googleapis/python-automl | scripts/fixup_automl_v1_keywords.py | Python | apache-2.0 | 7,032 | [
"VisIt"
] | c1f4c956373cf1b5ed47fc76af122316bf6aa5ebf0a372c0e8921cc2e7a70d50 |
#!/usr/bin/env python
import pyemma
import numpy as np
import mdtraj
import time
import os
# Source directory
source_directory = '/cbio/jclab/projects/fah/fah-data/munged3/no-solvent/11400' # Abl ensembler
################################################################################
# Load reference topology
####... | jchodera/MSMs | jchodera/abl-11400/pyemma/cluster.py | Python | gpl-2.0 | 3,309 | [
"MDTraj"
] | 7eca973c105ed74acb5002f4fd365baaeaf83b6c1552b169652cfecc42b275f2 |
"""
Module for 2D depth averaged solver
"""
from __future__ import absolute_import
from .utility import *
from . import shallowwater_eq
from . import timeintegrator
from . import rungekutta
from . import implicitexplicit
from . import coupled_timeintegrator_2d
from . import tracer_eq_2d
from . import conservative_trace... | tkarna/cofs | thetis/solver2d.py | Python | mit | 29,868 | [
"VTK"
] | adf1b6238203f36a65a08c89ad554855eea6b49d93dc8481fc6d1b58181a5584 |
class OWLClassExpressionVisitor(object):
"""Marker class"""
def visit(self, ce):
"""
:param ce: an object of one of the following classes:
- owlapy.model.OWLClass
- owlapy.model.OWLObjectIntersectionOf
- owlapy.model.OWLObjectUnionOf
- owlapy.mode... | patrickwestphal/owlapy | owlapy/model/owlclassexpressionvisitor.py | Python | gpl-3.0 | 2,126 | [
"VisIt"
] | caf65ffee344b3c0dea0c0143fc91d0ebe859a91208abb2ade288eec12b63b54 |
import doctest
import unittest
import os
from rdkit import Chem
from rdkit.Chem.SaltRemover import SaltRemover, InputFormat
def load_tests(loader, tests, ignore):
""" Add the Doctests from the module """
tests.addTests(doctest.DocTestSuite(Chem.SaltRemover, optionflags=doctest.ELLIPSIS))
return tests
class ... | bp-kelley/rdkit | rdkit/Chem/UnitTestSaltRemover.py | Python | bsd-3-clause | 3,172 | [
"CDK",
"RDKit"
] | cbd0179b741487d336645f1075b5206b1a545a9915293091f196aa7408221229 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | modules/geochemistry/python/tests/test_gwbreader.py | Python | lgpl-2.1 | 10,487 | [
"MOOSE"
] | 64ad2ef80a67a7c4b9fc822c792c13f2574dcb105dd33bbfc8b79e2771d8ea28 |
import ast
from unittest import TestCase
from .utils import reindent
from darglint.analysis.analysis_visitor import AnalysisVisitor
class AnalysisVisitorTests(TestCase):
def assertFound(self, program, attribute, args, transform=None):
"""Assert that the given attribute values were found.
Args:... | terrencepreilly/darglint | tests/test_analysis_visitor.py | Python | mit | 3,306 | [
"VisIt"
] | f643fc3dcb36a6acf5ee53fc152abe93f90f73193b61f97fb8b68f68dcaf8402 |
#!/usr/bin/python
import sys
import os
import glob
import re
DriverPath = ''
InsertPath = '/../../../'
if (len(sys.argv) == 2):
DriverPath = sys.argv[1] + '/'
sys.path.insert(0, os.path.abspath(os.getcwd()))
import apply_relpath
IncludePath = apply_relpath.get_topsrcdir_asrelativepathto_objdirsfnxsou... | spring01/libPSI | doc/sphinxman/document_databases.py | Python | gpl-2.0 | 1,026 | [
"Psi4"
] | 10908ed04ad80ce709565739c3430b0f4a5f66e3f5c936648b165d4c105dffbc |
#!/usr/bin/env python
import sys
import os
import re
import json
from collections import OrderedDict
from argparse import ArgumentParser
from argparse import RawDescriptionHelpFormatter
from elasticsearch1 import Elasticsearch
import glob
import shutil
import copy
def get_project_donor_count(es, es_index, dcc_project... | ICGC-TCGA-PanCancer/pcawg-central-index | pcawg_metadata_parser/pc_report-transfer_summary.py | Python | gpl-2.0 | 8,779 | [
"BWA"
] | f17db01e49645c80c6fc63247216b922149f574125c13f38ebf69b316e0d09fc |
##############################################################################
# Copyright (c) 2013-2018, 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... | tmerrick1/spack | var/spack/repos/builtin/packages/qmcpack/package.py | Python | lgpl-2.1 | 12,162 | [
"ESPResSo",
"QMCPACK",
"Quantum ESPRESSO"
] | 29022d086ca403153ac8a09b1a4baa0c82019ab18d6f9dc0535088a9e33f31b3 |
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import cm
import glob
import os
## Convert xml files to cvs
for i in glob.glob('*.xml'):
name = os.path.splitext(i)[0]
#bashcommand = "xmltable2csv --input ./%s.xml --output ./%s.csv --tag Data" %(name)
bashcommand = 'xmltable2csv --input ./%s.x... | zeromon77/EMtools | plot_intensity_V02.py | Python | gpl-2.0 | 1,115 | [
"ADF"
] | ccade83c3362729e81d008746019193b82383f6dcad42b8257342c14ed635887 |
""" A computing element class that attempts to use glexec if available then
defaults to the standard InProcess Computing Element behaviour.
"""
__RCSID__ = "$Id$"
import os
import stat
import tempfile
import pickle
import shutil
import random
import base64
from string import Template
import distutils.spawn
from ... | miloszz/DIRAC | Resources/Computing/glexecComputingElement.py | Python | gpl-3.0 | 19,617 | [
"DIRAC"
] | 0dc7ca7fc111098c2c78f71d48daf14718f22cb4a18b8bec9c6b1719981f5a53 |
# coding: utf-8
from __future__ import unicode_literals
import time
import datetime
import os
from django.contrib.auth.models import Permission
from django.conf import settings
from django.core import mail
from django.core.cache import cache
from django.core.urlresolvers import reverse
from django.core.exceptions impo... | springmerchant/pybbm | pybb/tests.py | Python | bsd-2-clause | 103,366 | [
"VisIt"
] | 82507f0c3bc42abb2b42b5a57822a2ca440deff773faa628cefc3aff46e56568 |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version 0... | scipy/scipy | scipy/optimize/_optimize.py | Python | bsd-3-clause | 136,080 | [
"Gaussian"
] | 3d0ba0ed0939e70c7c79b7b0c8015fcbf2317f48ce6375c53087466ed148a462 |
# Module wordnet.py
#
# Original author: Oliver Steele <steele@osteele.com>
# Project Page: http://sourceforge.net/projects/pywordnet
#
# Copyright (c) 1998-2004 by Oliver Steele. Use is permitted under
# the Artistic License
# <http://www.opensource.org/licenses/artistic-license.html>
"""Utility functions to use wit... | boompieman/iim_project | project_python2/lib/python2.7/site-packages/pattern/text/en/wordnet/pywordnet/wntools.py | Python | gpl-3.0 | 12,214 | [
"Amber"
] | 206ac87997ddd95bae7c383576195573474622aeb0fc8f1d673498b7dc9a2037 |
import argparse
import pdb
from multiprocessing import Pool
import numpy as np
import os
import pylab as pl
import astropy.io.fits as pf
import sys
import warnings
import datetime
import NPK.Fit
import NPK.Bar as Bar
from astropy.table import Table
from scipy.spatial import KDTree
import scipy.signal as SG
from num... | scizen9/kpy | SEDMr/Wavelength.py | Python | gpl-2.0 | 63,038 | [
"Gaussian"
] | 15b1e58bf1ba6ebbf07591b6a23c321cc1f712bd75221834e9d8bb5c6232ce58 |
'''
GenderGenreMod2
Copyright 2016 Brian N. Larson and licensors
GENDER/GENRE PROJECT CODE: Module 2
This code is the second segment used to generate and analyze the data for the article
Gender/Genre: The Lack of Gendered Register in Texts Requiring Genre Knowledge.
_Written Communication_, 33(4), 360–384. https://doi... | rhetoricked/WrittenCommunication2016 | Module2.py | Python | gpl-3.0 | 7,910 | [
"Brian"
] | 8beaf9899f3b79af049b2a416c9c50dc70b07aa7fa4bf47ccca6d5d9fa25d884 |
import unittest
import numpy as np
import pysal
from pysal.spreg.twosls_sp_regimes import GM_Lag_Regimes
from pysal.spreg import utils
from pysal.spreg.twosls_sp import GM_Lag
class TestGMLag_Regimes(unittest.TestCase):
def setUp(self):
self.w = pysal.queen_from_shapefile(pysal.examples.get_path("columbus.... | spreg-git/pysal | pysal/spreg/tests/test_twosls_sp_regimes.py | Python | bsd-3-clause | 16,120 | [
"COLUMBUS"
] | 821c5df4ee6b9555f083fb47f8387ad8b8418ac921e82bb6fe08ead301dfd0e9 |
from django.db import models
from django.core.validators import MinValueValidator, MaxValueValidator
# from edc_base.audit_trail import AuditTrail
from edc_constants.choices import YES_NO
from .infant_crf_model import InfantCrfModel
class InfantFu(InfantCrfModel):
""" A model completed by the user on the infan... | TshepangRas/tshilo-dikotla | td_infant/models/infant_fu.py | Python | gpl-2.0 | 2,085 | [
"VisIt"
] | bb9ef311d2d174a6805fd982e1df197db233611f528793bd19bf047d2dbcdca3 |
""" JobCommand
The JobCommand class is a command class to know about present jobs efficiency
"""
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.ResourceStatusSystem.Command.Command import Command
from DIRA... | Sbalbp/DIRAC | ResourceStatusSystem/Command/JobCommand.py | Python | gpl-3.0 | 9,975 | [
"DIRAC"
] | e612f4a433b1e3f6ecb8e87192bdb4bbbdcf208f9febd3a4c4106d3a0861ab04 |
#
# Copyright (c) 2003-2006 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.
#
""" utility functionality for molecular simila... | rdkit/rdkit | rdkit/Chem/Fingerprints/MolSimilarity.py | Python | bsd-3-clause | 9,579 | [
"RDKit"
] | 8f5efb10af935a3379d15ce8386b13b05cb0b152641b9f472dc20f4565f1fb0b |
#!/usr/bin/python
# Python Imports
from hashlib import sha256
import collections
import datetime, numbers
# Django Imports
from django.conf import settings
from django.db import models
# Local Imports
from contacts.models import PhoneCall, Practitioner, Visit, Connection
from utils import enums
from utils.models impo... | tperrier/mwachx | contacts/models/contact.py | Python | apache-2.0 | 28,017 | [
"VisIt"
] | 33ec2f44e33a0a1174831b9c2fd163746ee80e7451f19693e12546a0f0283672 |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2017, Shoop Commerce Ltd. All rights reserved.
#
# This source code is licensed under the OSL-3.0 license found in the
# LICENSE file in the root directory of this source tree.
import pytest
from shuup import configuration
from shuup.api.admi... | suutari-ai/shoop | shuup_tests/api/test_admin.py | Python | agpl-3.0 | 1,366 | [
"VisIt"
] | 752689b62827ecbd554ac851cf1c7d3c73f3514b5b1f6025300901bfdc459ea3 |
# Copyright (c) 2010 Howard Hughes Medical Institute.
# All rights reserved.
# Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
# http://license.janelia.org/license/jfrc_copyright_1_1.html
import osg, osgGA, osgManipulator, osgUtil, osgViewer
import sys
import os
import display... | JaneliaSciComp/Neuroptikon | Source/display/pick_handler.py | Python | bsd-3-clause | 11,973 | [
"NEURON"
] | 98526fe92cc4ebe9d3b186251d104205c8cf36285b6a23613a4c0850c2706c0a |
# -*- coding: utf-8 -*-
# Copyright 2022 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... | googleapis/python-aiplatform | tests/unit/gapic/aiplatform_v1beta1/test_vizier_service.py | Python | apache-2.0 | 171,570 | [
"Octopus"
] | 1cbe0e1d542a7be5e2e1312912aa82c854c88c580c1db74951cf5949877164ee |
"""@file galaxy_sample.py Catalog handling for the COSMOS galaxy sample in sersic tests.
"""
import numpy as np
def get(filename="cosmos_sersics_sample_N300.asc"):
"""Returns (n_sersic, half_light_radius [arcsec], |g|), a tuple of NumPy arrays.
"""
try:
data = np.loadtxt(filename)
except IOError:
... | mardom/GalSim | devel/external/test_sersic_highn/galaxy_sample.py | Python | gpl-3.0 | 618 | [
"Galaxy"
] | f3b7f49be72d311a43158ebfb9019902b271f6fb15df50c5a36ba92c57c9bc43 |
#!/usr/bin/env python
import matplotlib.pyplot as plt
import numpy as np
import scipy.io.netcdf as netcdf
from scipy.special import erf
plt.ion()
dir1 = '../run/mnc_test_0001/'
file1 = 'state.0000000000.t001.nc'
f1 = netcdf.netcdf_file(dir1 + file1,'r')
z = f1.variables['Z'][:].copy()
time = f1.variables['T'][:].... | bderembl/mitgcm_configs | bl_selfsimilarity/analysis/plot_prof.py | Python | mit | 589 | [
"NetCDF"
] | e32eb2e5e4ad1a853baac1c09d5a0cddffa2b991ffdf26dcc0e8a81fa62e5d0a |
# -*- coding: utf-8 -*-
from __future__ import division
def shape(m):
if not m:
return (0, 0)
return (len(m), len(m[0]))
def null(f):
return abs(f) < 1e-10
def nullrow(r):
return all(map(null, r))
def find_pivot_row(m):
candidates = []
for i, row in enumerate(m):
# Only rows ... | Kingdread/sgl | sgl/solver.py | Python | gpl-3.0 | 4,012 | [
"Gaussian"
] | 3c3497bcc5a0a2a9e99f42bea43ff7438e7c47dd5364b9f635c3f828e21bbda9 |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import unittest
import numpy as np
import GPy
class PriorTests(unittest.TestCase):
def test_studentT(self):
xmin, xmax = 1, 2.5*np.pi
b, C, SNR = 1, 0, 0.1
X = np.linspace(xmin,... | befelix/GPy | GPy/testing/prior_tests.py | Python | bsd-3-clause | 5,630 | [
"Gaussian"
] | e2924b7c6bb4b685d5bea708bf636f6e0025cfa05a8ba6ebbf844cbf60b39bd1 |
from __future__ import absolute_import
from typing import Any, DefaultDict, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import Quer... | aakash-cr7/zulip | zerver/models.py | Python | apache-2.0 | 63,101 | [
"VisIt"
] | 596728342337df8c2ed163b1061292ca5fa9144c3e747c09b49edae46621cfb6 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/movielist.py | Python | gpl-2.0 | 7,515 | [
"VisIt"
] | 2253a78962b0de2f816adfff9b541fdea1bc97e208e8bb1a2efa20f089ea0a29 |
import pandas as pd
import numpy as np
import crystal
np.random.seed(42)
covs = pd.DataFrame({'gender': ['F'] * 10 + ['M'] * 10,
'age': np.random.uniform(10, 25, size=20) })
methylation = np.random.normal(-1, 1, size=(5, covs.shape[0]))
cluster = [crystal.Feature('chr1', i* 10, m) for i, m in ... | brentp/crystal | crystal/tests/test_models.py | Python | mit | 3,828 | [
"CRYSTAL"
] | 3f48c9925d61983e5c2427fd59090fa0546f208320f3828dcdd87745cee5243c |
"""Core visualization operations."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Joan Massich <mailsik@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
import sys
import os
from contextlib im... | kambysese/mne-python | mne/viz/backends/renderer.py | Python | bsd-3-clause | 10,641 | [
"Mayavi"
] | 66173411ac0c3d14168775e90c4e4ff004bca28b8ad0aa3a1aa537926e4d359f |
from Scientific.IO.NetCDF import NetCDFFile
from numpy import *
def createNcDim(ncfile,name,d):
print "creating netcdf dimension:",name,d
ncfile.createDimension(name,d)
#assumes ncfile will be written over (opened with 'w')
def createNcVar(ncfile,vname,data,vtype,dims,desc):
print "creating netcdf variable",vname
... | meierue/RNNLIB | utils/netcdf_helpers.py | Python | gpl-3.0 | 1,105 | [
"NetCDF"
] | 81e41a3b70fc11efdf48089a6eec53bb0217bba50b8e878712f306c4a952c1ae |
"""Compat testing."""
from bowtie._utils import func_name
def hello():
"""A function."""
return func_name()
def test_function_names():
"""Test we get the correct function name."""
assert hello() == 'hello'
| jwkvam/bowtie | bowtie/tests/test_utils.py | Python | mit | 227 | [
"Bowtie"
] | d02f95fb07eda1fe404fde33534a4381326b23e7499482c3a350695e679f41a0 |
'''
This module defines :class:`Unit`, a container of :class:`SpikeTrain` objects
from a unit.
:class:`Unit` derives from :class:`Container`,
from :module:`neo.core.container`.
'''
from neo.core.container import Container
class Unit(Container):
'''
A container of :class:`SpikeTrain` objects from a unit.
... | JuliaSprenger/python-neo | neo/core/unit.py | Python | bsd-3-clause | 2,560 | [
"NEURON"
] | 3c7f70215b4c278feba2f6e2ec1f7410b04be0b2529122cf017eea86ef7c9441 |
from .listener import ListenerType
class PluginAPI(object):
"""Holds the decorator-based plugin PluginAPI.
It gets mixed in to the main Espresso class, which is what plugins call the API off of.
Having a seperate class is _not_ necessary, but it's nicer to hack on.
"""
def hear(self, regex, **op... | ratchetrobotics/espresso | espresso/plugin_api.py | Python | bsd-3-clause | 774 | [
"ESPResSo"
] | b2ae9edcd2943789b89b78c6c76aba19965fbb831715f29e5487277a8f5d6e92 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
... | jensengroup/propka-3.1 | versioneer.py | Python | lgpl-2.1 | 68,607 | [
"Brian"
] | 7849947f8031af37a8c16b9d3f58324245be70ceade9e5bcc5afa8b913186feb |
#!/usr/bin/env python
__author__ = 'Mike McCann, Danelle Cline'
'''
Monitor the dods web site for new realtime hotspot or sbdlog data from LRAUVs and use
DAPloaders.py to load new data into the stoqs database.
Mike McCann
MBARI 12 March 2014
'''
import os
import sys
if 'DJANGO_SETTINGS_MODULE' not in os.environ:
... | stoqs/stoqs | stoqs/loaders/LakeMichigan/monitorLrauv.py | Python | gpl-3.0 | 23,212 | [
"NetCDF"
] | 537845f518ca241a3c3ef8b325814b6ba883028cfbc3814ac893354f72ded7b6 |
"""
jonesy-daemon daemonization library
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jonesy-daemon is a Python daemonization library. To use it, do something
like this:
from jonesy-daemon import daemonize
def main():
...some setup stuff here...
if not args.run_in_foreground:
daemonize(user='www-data', pidfi... | bkjones/jonesy-daemon | jonesy_daemon/__init__.py | Python | bsd-3-clause | 785 | [
"Brian"
] | 21f3ab91c7bb94cbd387c0f8e77ac10d882b449f98837c372a013209cd307b96 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, absolute_import
"""
This module implements classes for generating/parsing Lammps data file i.e
the file that defines the system configuration(... | xhqu1981/pymatgen | pymatgen/io/lammps/data.py | Python | mit | 33,053 | [
"LAMMPS",
"pymatgen"
] | 3a2a52dfef79a26fdafbf211b935c507433ae0324f69bde8f54ca01b2345011f |
"""
genomescan module
"""
import os, sys
import time
import fasta, genscan, sequence
from useful import smartopen
from useful import multipart
def genomescan(dna, protein, description='', email='', oFileHandle=None,
proxy='wehiproxy.alpha.wehi.edu.au', proxyPort=3128, debug=False):
"""
@param dna: DN... | PapenfussLab/Mungo | mungo/genomescan.py | Python | artistic-2.0 | 6,090 | [
"BLAST"
] | 874492996c145e902e1068790dd4a37bbe01d4692aee6705ccb97f0bcc3a7adc |
import pytest
from capybara.tests.helpers import extract_results
class TestWithFieldset:
@pytest.fixture(autouse=True)
def setup_session(self, session):
session.visit("/fieldsets")
def test_restricts_scope_to_a_fieldset_given_by_id(self, session):
with session.fieldset("villain_fieldset"... | elliterate/capybara.py | capybara/tests/session/test_with_fieldset.py | Python | mit | 795 | [
"VisIt"
] | 623087edead40afb047c98d2df133e2981f058699eb5e4bfc52016b63611f369 |
#!/usr/bin/env python3
# Copyright 2016-2018 Brian Warner
#
# 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... | OSSHealth/ghdata | workers/facade_worker/facade_worker/facade05repofetch.py | Python | mit | 13,465 | [
"Brian"
] | ff328148c22cd8db5341f631b952193a860004f635a7dcb6281df69461c75531 |
import pytest
import py
import os
from imagesort import imagesort
import filecmp
import sys
def test_available_operations():
ops = set([op for op in imagesort.OPERATIONS])
# Hardlinks for windows came in version 3.2
if sys.platform == 'win32' and sys.hexversion < 0x03020000:
assert ops == set(['c... | leinz/imagesort | imagesort/tests/test_imagesort.py | Python | mit | 4,506 | [
"VisIt"
] | d57d8d9d2b6a95bf707bd25f689d29aab229362303a99ba0dfde6e1e8914e2ab |
import os
import tmd.pwscf.cell as cell
def build_pw2wan(material):
pw2wan = [" &inputpp"]
pw2wan.append(" outdir='./',")
pw2wan.append(" prefix='{}',".format(material["prefix"]))
pw2wan.append(" write_mmn=.true.,")
pw2wan.append(" write_amn=.true.,")
if material["soc"]:
pw2wan... | tflovorn/tmd | tmd/pwscf/build.py | Python | mit | 7,986 | [
"CRYSTAL",
"Wannier90"
] | a31b102c940f7aaf8a4e56f247fce4211fb37401c23a04b60346ee618f015baa |
# THIS SCRIPT WAS PRODUCED VIA THE NCBI HACKATHON IN AUGUST 2015
# WRITTEN (INITIALLY) BY PAUL CANTALUPO, HIROKO OHMIYA, ALLISSA DILLMAN, AND RUSSELL DURRETT
# TO DO - UPDATE TO SUBREAD PACKAGE (for counting) INSTEAD OF HTSEQ (TOO SLOW, SUBREAD SUPER FAST)
# FASTAREF='/resources/ensembl/fasta/Homo_sapiens.GRCh38.... | NCBI-Hackathons/HASSL_Homogeneous_Analysis_of_SRA_rnaSequencing_Libraries | legacy/cobrasnake.py | Python | cc0-1.0 | 4,990 | [
"HTSeq"
] | ccd69567ebaa3864fb99c1a26d49db18f8e913ea6345bdecbaca91e5bbb1603c |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
# Copyright 2010 Joanmarie Diggs
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your op... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/toolkits/J2SE-access-bridge/speech_generator.py | Python | gpl-3.0 | 6,535 | [
"ORCA"
] | 6ceed74b55f456c5fcef84d545440d7172dd0f5be02198a0ea9d69c6a64f1577 |
# (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... | adityacs/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 29,384 | [
"Galaxy",
"MOOSE"
] | 07ff76a14f3158a721520e1ab4effbf5878179e5b7109c9cc9d2f0c9cfb67f89 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The maths module provides higher-level interfaces to some of the operations
that can be performed with the fslmaths command-line program.
"""
import os
import numpy as np
from nipype.interfaces... | mick-d/nipype_source | nipype/interfaces/fsl/maths.py | Python | bsd-3-clause | 11,040 | [
"Gaussian"
] | a09e0608a322332ba64448896875a9b19b9e1b85c82f92ba35fcf257fa0f8bd3 |
from setuptools import setup, find_packages
setup(
name="thermof",
version="0.1.2",
description="Investigating thermal conductivity of MOFs using Lammps",
author="Kutay B. Sezginel",
author_email="kbs37@pitt.edu",
url='https://github.com/kbsezginel/thermof',
include_package_data=True,
... | kbsezginel/tee_mof | setup.py | Python | mit | 699 | [
"ASE",
"LAMMPS"
] | f387118d5ca5df9851ac225d4fc7990d33b1d155ca2ad9747c1c3520d0e76c4d |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
generate random permutation
distributions on the real line:
------------------------------
uniform
normal (Gaussian)
... | ermo/privateer_wcu | modules/vsrandom.py | Python | gpl-2.0 | 21,908 | [
"Gaussian"
] | 3249391541b7bfe76c91acd77dd295abcc77c2ef98c5276800944040b44933e5 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import bitfield.models
import django.db.models.deletion
import django.utils.timezone
from django.conf import settings
import zerver.models
class Migration(migrations.Migration):
dependencies = [
('au... | zachallaun/zulip | zerver/migrations/0001_initial.py | Python | apache-2.0 | 23,610 | [
"VisIt"
] | 09de57143eb467ddb05e5d29e15f0dd6067962fd863615fee4c6a4fbd7c9213d |
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