text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
from __future__ import division, absolute_import, print_function
import numpy as np
import matplotlib
import pytest
from numpy.testing import assert_almost_equal, assert_equal
import gromacs.fileformats.xvg
from gromacs.formats import XVG
@pytest.fixture(scope="module")
def data():
data = np.random.normal(loc=2... | Becksteinlab/GromacsWrapper | tests/fileformats/test_xvg.py | Python | gpl-3.0 | 3,377 | [
"Gromacs"
] | 1c2cd6255cc1494ddf504da84ed8e91ee347becb871e9b4c44a1962d59ed75af |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D., Hirsh Nanda, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any... | madscatt/zazzie_1.5 | trunk/sassie/calculate/sld_mol/sld_mol.py | Python | gpl-3.0 | 26,896 | [
"Gaussian"
] | 2da5a6c4d700c0b7ba85e9d4d3de6278a85ed11b38f4b5d58c4a946fbd71368e |
""" This contains unit tests to make sure that the migration between PyGSI and M2Crypto is as smooth as possible
The test covers only the method exposed by the PyGSI version for the time being.
We are not testing:
* generateProxyRequest -> boils down to testing X509Request
* setCertificate -> not used... | fstagni/DIRAC | Core/Security/test/Test_X509Certificate.py | Python | gpl-3.0 | 11,160 | [
"DIRAC"
] | 6d94ace5c6923326337616c4e0a8433a98f602fd504910e2276144a55b305e8f |
#!/usr/bin/python
import HTSeq
import sys
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
from Bio.Blast import NCBIXML
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast.Applications import NcbiblastpCommandline
from Counter import Counter # --- Counter.py from python3 is needed to ... | mickaelsilva/pythonscripts | AlleleCalling/cluster_versions/callAlleles_protein2.py | Python | gpl-2.0 | 20,863 | [
"BLAST",
"HTSeq"
] | 69a9505025a91ea1e39b93d4208e24e4ea9b0d818eac96fbe243a5cb069463f4 |
import random
import math
from math import degrees as deg, radians as rad
import os
import sys
import pickle
from datetime import datetime as dt
from decimal import *
import numpy as np
import quaternion
import cv2
from visnav.algo.centroid import CentroidAlgo
from visnav.algo.image import ImageProc
from visnav.algo... | oknuutti/visnav-py | visnav/testloop.py | Python | mit | 47,921 | [
"Gaussian"
] | a48e015b49058b89c866e5b7ef11c9fb37aa97c54bc325562a1f09c652ea7f9f |
r"""
===============
Decoding (MVPA)
===============
.. contents:: Contents
:local:
:depth: 3
.. include:: ../../links.inc
Design philosophy
=================
Decoding (a.k.a. MVPA) in MNE largely follows the machine
learning API of the scikit-learn package.
Each estimator implements ``fit``, ``transform``, ``... | adykstra/mne-python | tutorials/machine-learning/plot_sensors_decoding.py | Python | bsd-3-clause | 18,079 | [
"VisIt"
] | ec559b7cd8830a992497ddde1fc1be96c8ba417d745750419269e42ebced2ac5 |
from decimal import Decimal
from app.readers import openms as openmsreader
DB_STORE_CHUNK = 500000
FEATURE_ALIGN_WINDOW_AMOUNT = 1000
PROTON_MASS = 1.0072
def create_isobaric_quant_lookup(quantdb, specfn_consensus_els, channelmap):
"""Creates an sqlite lookup table of scannrs with quant data.
spectra - an i... | glormph/msstitch | src/app/actions/lookups/quant.py | Python | mit | 6,097 | [
"OpenMS"
] | 653875b96521f6a0f3938d1fc81a7dbbc401a9796b5dc0d28828c2725f6f0901 |
#!/usr/bin/env python
# HLstatsX Community Edition - Real-time player and clan rankings and statistics
# Copyleft (L) 2008-20XX Nicholas Hastings (nshastings@gmail.com)
# http://www.hlxcommunity.com
# HLstatsX Community Edition is a continuation of
# ELstatsNEO - Real-time player and clan rankings and statistics
# Co... | jstnmthw/hlstatsx-ce | scripts/GeoLiteCity/geoip.py | Python | gpl-2.0 | 6,312 | [
"VisIt"
] | 848a3b7dc7cc46d2d24b3cdb7ccbc8e25c392051b535b65663126801d80361ff |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2007 Donald N. Allingham
# Copyright (C) 2008-2010 Brian G. Matherly
# Copyright (C) 2007-2010 Jerome Rapinat
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Gener... | beernarrd/gramps | gramps/plugins/rel/rel_ca.py | Python | gpl-2.0 | 31,225 | [
"Brian"
] | c2de217d447c5260129389e17834b074c96936b91fee04508198d1fe586b0af7 |
#
# Copyright (C) 2004-2008 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.
#
import numpy
from rdkit impor... | bp-kelley/rdkit | rdkit/Chem/Pharm3D/Pharmacophore.py | Python | bsd-3-clause | 5,899 | [
"RDKit"
] | 6e1a550fb9ab8ca305085ac5e125f4b18ca44172d91d7077ec8bcbf464e23dcd |
import os
from os.path import join
import numpy as n
def writeScript(rootName, plate):
f=open(rootName+".sh",'w')
f.write("#!/bin/bash \n")
f.write("#PBS -l walltime=260:00:00 \n")
f.write("#PBS -o "+plate+".o.$PBS_JOBID \n")
f.write("#PBS -e "+plate+".e$PBS_JOBID \n")
f.write("#PBS -M comparat@mpe.mpg.de \n")
f... | JohanComparat/pySU | spm/bin/write_run_scripts_dr14_salpeter_nd.py | Python | cc0-1.0 | 984 | [
"Galaxy"
] | 4f0272cda630690e5b2b250408a174304bdbbafb4cffd7841b03ac747b6a6f1e |
# Definition for singly-linked list with a random pointer.
# class RandomListNode(object):
# def __init__(self, x):
# self.label = x
# self.next = None
# self.random = None
class Solution(object):
def copyRandomList(self, head):
# use DFS to visit the graph
# DFS info mu... | luosch/leetcode | python/Copy List with Random Pointer.py | Python | mit | 736 | [
"VisIt"
] | e322bc028f282cfd1058104127754ce0d3dd554967c0ce8153f77f81e0d04fab |
# 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, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the Li... | gkc1000/pyscf | pyscf/prop/esr/uhf.py | Python | apache-2.0 | 8,648 | [
"PySCF"
] | 7188a821c67bcd43a0c5b94929730208d6ac28311e0f87216663678aa0c1a8c8 |
__author__ = "Andre Merzky, Ole Weidner, Mark Santcroos"
__copyright__ = "Copyright 2012-2015, The SAGA Project"
__license__ = "MIT"
""" PBSPro job adaptor implementation
"""
import threading
import saga.url as surl
import saga.utils.pty_shell as sups
import saga.adaptors.base
import saga.adaptors.... | telamonian/saga-python | src/saga/adaptors/pbspro/pbsprojob.py | Python | mit | 48,804 | [
"Jaguar"
] | 1caa3a329628841c070c03e37e45792d37ae95b80502c4c9adc345a6c1ee5cc8 |
# -*- coding: utf-8 -*-
#
# pyNastran documentation build configuration file, created by
# sphinx-quickstart2 on Thr Nov 18 13:26:34 2016.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# ... | saullocastro/pyNastran | docs/html_docs/conf.py | Python | lgpl-3.0 | 13,660 | [
"VTK"
] | 561d81658ad1d7bef830d97c6067b1f78b1b008e15994603445c1308d9709f72 |
""" ProxyManager is the implementation of the ProxyManagement service
in the DISET framework
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Core.Security import Properties
from DIRAC.Core.Utilities.ThreadScheduler import gThrea... | arrabito/DIRAC | FrameworkSystem/Service/ProxyManagerHandler.py | Python | gpl-3.0 | 16,014 | [
"DIRAC"
] | 052c7c8bd6fab1cf83d01d98b93335998752c5fac4f6e0c71bfba609adea7e8a |
'''
Primary Collaborative Filtering Code used for method recommendation
Written by Mark Fuge and Bud Peters
Heavily based on the 'Scalable Collaborative Filtering' code written by Mark Fuge at:
https://github.com/markfuge/scalable-collaborative-filtering
For more information on the project visi... | IDEALLab/design_method_recommendation_JMD_2014 | collaborative_filter.py | Python | apache-2.0 | 9,139 | [
"VisIt"
] | ded6ff018724d20d8b3192b9b5858798701a7e2e9369bfdcf99f42f29f6a498f |
# coding: utf-8
"""
Acceptance tests for licensing of the Video module
"""
from __future__ import absolute_import, unicode_literals
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.lms.courseware import CoursewarePage
from common.test.acceptance.pages.studio.overvi... | ESOedX/edx-platform | common/test/acceptance/tests/video/test_video_license.py | Python | agpl-3.0 | 4,975 | [
"VisIt"
] | 7973893617c0ad6d7bd53bc20f3558c240da7db25c8d950a64d69abc2b0cfc57 |
# -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""
Utilities for the Dictionary Editor Widget and Dialog based on Qt
"""
import re
#----Numpy arrays support
class FakeObject(object):
"""Fake class used in replace... | openfisca/openfisca-qt | openfisca_qt/gui/spyder_widgets/dicteditorutils.py | Python | agpl-3.0 | 8,223 | [
"NetCDF"
] | 210d887d31ae16220443b324ed951cdd44f56b8d1e787aac73bdcec4ee8b5d27 |
"""
TODO: Change the module doc.
"""
__author__ = "shyuepingong"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__status__ = "Beta"
__date__ = "6/18/13"
import glob
import os
import shutil
import unittest
from custodian.nwchem.handlers import NwchemErrorHandler
test_dir = os.... | materialsproject/custodian | custodian/nwchem/tests/test_handlers.py | Python | mit | 1,047 | [
"NWChem"
] | 52126fba4e26b8ee7b68e102a482e5658445554f98b2ac5faa8a453f1c1eecbf |
# -*- coding: utf-8 -*-
"""
Read SMC Ca2+ values from a line of cells in temporal series and produce a 2D plot
"""
import re
import os
import vtk
import numpy
import matplotlib.pyplot as plt
print 'Importing ', __file__
def tryInt(s):
try:
return int(s)
except:
return s
def alphaNumKey(s):
... | BlueFern/DBiharMesher | util/PlotColumn2D.py | Python | gpl-2.0 | 2,787 | [
"VTK"
] | 9834f35b241afd62bd5c08da3e9a36065069e6f789fb5be0cc0afd76ff107e34 |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_HTTPError,
compat_http_client,
compat_urllib_error,
co... | Nikoli/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 47,013 | [
"VisIt"
] | df78dc18b37d4fbd3d56b9545ff76689fd0e56bd65fd517dec8961dc3f7d3087 |
"""This module includes all account related stuff"""
# Django imports
from django.conf import settings
from django.db import models
class Account(models.Model):
"""Represents an OGame Account
An Account object is the root for all data. An Account is associated with
a Django User (``owner``).
Th... | Mischback/django-oweb | oweb/models/account.py | Python | mit | 1,791 | [
"CRYSTAL"
] | 1fb27f53f05a2d397dd2b0454983cc44fdff229b804b2f1f9280ded52d531249 |
"""
==================
Two-class AdaBoost
==================
This example fits an AdaBoosted decision stump on a non-linearly separable
classification dataset composed of two "Gaussian quantiles" clusters
(see :func:`sklearn.datasets.make_gaussian_quantiles`) and plots the decision
boundary and decision scores. The di... | treycausey/scikit-learn | examples/ensemble/plot_adaboost_twoclass.py | Python | bsd-3-clause | 3,123 | [
"Gaussian"
] | 72dedf29259d13618ad4b45f47de4cf82637ababb9913103dd50147c339f17ee |
from Q50_config import *
from ArgParser import *
import sys, os
from GPSReader import *
from GPSTransforms import *
from VideoReader import *
from LidarTransforms import *
from VtkRenderer import *
from transformations import euler_matrix
import numpy as np
from ColorMap import *
import vtk
import copy
import cv2
impor... | sameeptandon/sail-car-log | process/LidarHandCalibration.py | Python | bsd-2-clause | 12,096 | [
"VTK"
] | dfa1a2caae90257ddf7163ac6dc6cb794ea37afe7c96441ec71dae06626ffb65 |
# -*- coding: utf-8 -*-
from octopus.app import create_app
from octopus.settings import ProdConfig, DevConfig
def test_production_config():
app = create_app(ProdConfig)
assert app.config['ENV'] == 'prod'
assert app.config['DEBUG'] is False
assert app.config['DEBUG_TB_ENABLED'] is False
assert app.config['AS... | quaintm/octopus | tests/test_config.py | Python | bsd-3-clause | 514 | [
"Octopus"
] | daf56447b62beb261b8dd1d0e3b750134444f07d1e7c929e3823b315aa515f28 |
"""
PureMVC Python Demo - wxPython Employee Admin
By Toby de Havilland <toby.de.havilland@puremvc.org>
Copyright(c) 2007-08 Toby de Havilland, Some rights reserved.
Addapted for pyjamas: Kees Bos
"""
from puremvc.patterns.proxy import Proxy
import vo
import ApplicationConstants
from ApplicationConstants import Command... | spaceone/pyjs | examples/employeeadmin/libemployeeadmin/model.py | Python | apache-2.0 | 4,499 | [
"MOE"
] | 4cd2f998bacb526747d4ada19778c4bf765e9719f6b28de1218a6c85c53040b7 |
# Copyright 2011 by Eric Talevich. All rights reserved.
# 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.
"""Phylogenetics command line tool wrappers."""
__docformat__ = "restructuredtext en"
from ._P... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Phylo/Applications/__init__.py | Python | gpl-2.0 | 595 | [
"Biopython"
] | 7114edbeb7e9f44c46e43871fa54d929ae4d0e3d860c661ff740c725a716855d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a Composition class to represent compositions,
and a ChemicalPotential class to represent potentials.
"""
import collections
import numbers
import string
from itertools import combin... | mbkumar/pymatgen | pymatgen/core/composition.py | Python | mit | 51,218 | [
"pymatgen"
] | e33b38360d22df8cae90464d48007ba077b300e0b55c2642e424195ef8f44964 |
#Copyright 2015 Daniel Gusenleitner, Stefano Monti
#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 t... | montilab/Hydra | hydra_pkg/featureCount.py | Python | apache-2.0 | 10,613 | [
"HTSeq"
] | 36cc6f91ed9e269cea3e258bf99fb16959ecc353e6502daaed496a46caa21aa2 |
# 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,... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Graphics/GenomeDiagram/_LinearDrawer.py | Python | gpl-2.0 | 64,200 | [
"Biopython"
] | 7c8dc124dcd2bb9c2b22c3346cdc941c73f26f2a8f56dad6e3774495c0232833 |
#!/usr/bin/python
# encoding: utf-8
# Berreman4x4 example
# Author: O. Castany, C. Molinaro
# Example of a cholesteric liquid crystal
import numpy, Berreman4x4
from numpy import sin, sqrt, abs
from Berreman4x4 import c, pi, e_y
import matplotlib.pyplot as pyplot
# Materials
glass = Berreman4x4.IsotropicNonDispersiv... | ocastany/Berreman4x4 | examples/cholesteric-example.py | Python | gpl-3.0 | 4,926 | [
"CRYSTAL"
] | 9c6a422223c77a183fff3ad4ac2977c5dd91d304128213173ba2a80c2ea627af |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.common.action_chains import ActionChains
from .course_p... | UXE/local-edx | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 23,238 | [
"VisIt"
] | d761b2bbb5d46f7caba28ec954cc5360c2bcd3022810861692830c675d24f84f |
"""
DiagonalProjection.py
This file is part of ANNarchy.
Copyright (C) 2013-2016 Julien Vitay <julien.vitay@gmail.com>,
Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public Licens... | ANNarchy/ANNarchy | ANNarchy/extensions/diagonal/DiagonalProjection.py | Python | gpl-2.0 | 16,376 | [
"Gaussian",
"NEURON"
] | c1438b202dda52eb7e69c202b6ed57ed5354b9e1a1c68dd3fbc0f423bb9d2ae3 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | junghans/espressopp | src/esutil/collectives.py | Python | gpl-3.0 | 1,801 | [
"ESPResSo"
] | f642abaf4297621650f02e023adc5f07a9262423705c9dda13fcace780781c25 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 230,506 | [
"Gaussian"
] | 0b50793c8e6f319c18412a01e380582a112b11729bc413fb2c95559aeeaaedd9 |
import ovito
from ovito.io import *
import os
import os.path
import_file("../../files/LAMMPS/animation.dump.gz")
if os.path.isfile("scene.ovito"): os.remove("scene.ovito")
ovito.dataset.save("scene.ovito")
assert(os.path.isfile("scene.ovito"))
os.remove("scene.ovito")
| srinath-chakravarthy/ovito | tests/scripts/test_suite/save_scene.py | Python | gpl-3.0 | 273 | [
"LAMMPS",
"OVITO"
] | 603cce880ce077d9100f5914e91144bef4345afef6598f672fbf22c16f0a86d9 |
from __future__ import (
unicode_literals,
print_function,
absolute_import,
division,
)
try:
from itertools import izip as zip
except ImportError:
pass
from time import sleep
from itertools import repeat, cycle, chain
from threading import Lock
from collections import OrderedDict, Counter
... | MrHarcombe/python-gpiozero | gpiozero/boards.py | Python | bsd-3-clause | 58,243 | [
"Amber"
] | 72a5559386dbdf02b0c085d32ac744edc6c643d8d4aaad9636bbb2a8e6ac9843 |
from __future__ import print_function
from __future__ import absolute_import
import os
import numpy as nm
from sfepy.base.base import get_default, Struct, output
from sfepy.base.ioutils import get_print_info
from sfepy.base.timing import Timer
from sfepy.discrete.fem import extend_cell_data, Mesh
from sfepy.homogeniz... | BubuLK/sfepy | sfepy/homogenization/recovery.py | Python | bsd-3-clause | 23,388 | [
"VTK"
] | 0408d7ccfe522c80a7e798d5e75eaca642c8c5bda85c75f4f67c3fb9866d6050 |
import numpy as np
import pytest
from pysisyphus.calculators import XTB
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.helpers import geom_loader
from pysisyphus.helpers_pure import eigval_to_wavenumber
from pysisyphus.modefollow import geom_davidson
from pysisyphus.modefollow.NormalMode import NormalM... | eljost/pysisyphus | tests/test_davidson/test_davidson.py | Python | gpl-3.0 | 2,147 | [
"PySCF",
"xTB"
] | e75c5e0d6a5a9c9e5dc98ad5c7cd005cc6f2c4a204ed9047c08c221e96bd021b |
# coding: utf8
'''
Created on 16 mars 2010
@author: Cyril MORISSE <cmorisse@boxes3.net>
edofx_integration is an example use of edofx parser to parse an OFX
file into a graph of specific classes (Statement and StatementTransaction).
'''
from datetime import date
class StatementTransaction(object):
'''
Used ... | cmorisse/inouk.edofx | tests/edofx_integration.py | Python | mit | 6,083 | [
"VisIt"
] | ce2e371a850f387d16395270621ecd16191276596f9c09b7ebd9812addb52c46 |
#!/usr/bin/env python
# encoding: utf-8
"""
quickstart.py
Created by Dan Foreman-Mackey on Jun 03, 2011
"""
import time
import pylab as pl
import numpy as np
np.random.seed()
import markovpy
# dimensions of space
nwalkers = 100
ndim = 20
initial_position = [np.random.rand(ndim)+5.0 for i in xrange(nwalkers)]
... | dfm/MarkovPy | quickstart.py | Python | gpl-2.0 | 1,461 | [
"Gaussian"
] | 4680dc59f7888d66c3019e8d6e20b100e025d316e1fcad8aedaa061e0c1e8ca8 |
"""The xonsh abstract syntax tree node."""
from ast import Module, Num, Expr, Str, Bytes, UnaryOp, UAdd, USub, Invert, \
BinOp, Add, Sub, Mult, Div, FloorDiv, Mod, Pow, Compare, Lt, Gt, \
LtE, GtE, Eq, NotEq, In, NotIn, Is, IsNot, Not, BoolOp, Or, And, Subscript, \
Load, Slice, List, Tuple, Set, Dict, AST, ... | szlin/gitsome | xonsh/ast.py | Python | gpl-3.0 | 8,109 | [
"VisIt"
] | 41ed1d4189719861f6d6a542f9a70d9a0411829887c2c55b58fd43ff01041acf |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/qmcpack/package.py | Python | lgpl-2.1 | 12,146 | [
"ESPResSo",
"QMCPACK",
"Quantum ESPRESSO"
] | eb2188f0149536c2f04f18c80fc4ac0d586635d19b43ecdd98c4eaa429e91024 |
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Ladybug is free software; you can redistribute it and/or modify
# it under the terms of the GNU Gener... | boris-p/ladybug | src/Ladybug_Branch Data.py | Python | gpl-3.0 | 5,994 | [
"EPW"
] | 25822ce5b492cc5f8e241a7db5140ef475d05ba4c71a72859fc4c1153c449991 |
from ..utils import *
# Damage 1
class XXX_001:
play = Hit(TARGET, 1)
# Damage 5
class XXX_002:
play = Hit(TARGET, 5)
# Restore 1
class XXX_003:
play = Heal(TARGET, 1)
# Restore 5
class XXX_004:
play = Heal(TARGET, 5)
# Destroy
class XXX_005:
play = Destroy(TARGET)
# Break Weapon
class XXX_006:
play =... | smallnamespace/fireplace | fireplace/cards/debug/all.py | Python | agpl-3.0 | 4,670 | [
"CRYSTAL"
] | 0beed721b8a1ec3b80e7b9d0e8ec57cbfa51910656ebdac00b739336f871facc |
#!/usr/bin/env python
import argparse
import numpy as np
import matplotlib as mpl
mpl.use('Agg')
mpl.rcParams.update({'font.size': 18})
mpl.rcParams.update({'savefig.dpi': 200})
mpl.rcParams.update({'savefig.bbox': 'tight'})
import matplotlib.pyplot as plt
import scipy.interpolate
import astropy.units as u
import... | dmargala/tpcorr | examples/plot_acceptance_contours.py | Python | mit | 3,423 | [
"Gaussian"
] | c26da5dd7afc2e1a810de29de026d465064d5193bcd2267f0392e1070cc985ee |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world
from .factories import *
from django.conf import settings
from django.http import HttpRequest
from django.contrib.auth.models import User
from django.contrib.auth import authenticate, login
from django.contrib.auth.middleware import Authenticati... | wwj718/edx-video | common/djangoapps/terrain/course_helpers.py | Python | agpl-3.0 | 2,265 | [
"VisIt"
] | 77811ff53781bf0acb95945f3a912be69a5bf896016e0da6bc79e24d9a4315ee |
# 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... | fweik/espresso | testsuite/python/array_properties.py | Python | gpl-3.0 | 8,660 | [
"ESPResSo"
] | 088ebc6b6b942d42743e8fb2b486653d645472417ed08c4f12a33be9cef571d2 |
"""Implements API endpoints under ``/api/link``"""
from datetime import datetime
from typing import Any, Optional, Dict
from flask import Blueprint, jsonify, request
from flask_mailman import Mail
from bson import ObjectId
import bson
from werkzeug.exceptions import abort
from shrunk.client import ShrunkClient
from ... | oss/shrunk | backend/shrunk/api/link.py | Python | mit | 24,812 | [
"VisIt"
] | 073ace7a519cee6767b68e7482ae6bf9473aecd75e9201fdf15c4b5c15f15a89 |
### import ####################################################################
import os
import itertools
import matplotlib.pyplot as plt
import matplotlib.gridspec as grd
import scipy
from scipy.optimize import leastsq
from scipy.interpolate import griddata, interp1d, interp2d, UnivariateSpline
import numpy as n... | wright-group/WrightData | unpublished Thompson - Automated OPA Tuning/figures.py | Python | cc0-1.0 | 7,404 | [
"Gaussian"
] | d55390aac362a18883dc64dc90eec4fa871c6921758897a7d0df78272f3d25bd |
#!/usr/bin/env python3
# Copyright (C) 2017, Weizhi Song, Kerrin Steensen and Torsten Thomas.
# songwz03@gmail.com and t.thomas@unsw.edu.au
# HgtSIM is free software: you can redistribute it and/or modify it under the terms of the GNU Affero
# General Public License as published by the Free Software Foundation, eithe... | songweizhi/HgtSIM | Test_datasets_Assessment_scripts_and_Commands/Assessment_scripts/Assembler_recovered_transfers_iden100.py | Python | gpl-3.0 | 10,420 | [
"BLAST"
] | e9e301ed8e7a2b5fd0135052eeb41581aeea90afdaf7ec9b28aac6acb77eec63 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 1000
n = 2000
display = True
worldRank = ... | birm/Elemental | examples/interface/BPDense.py | Python | bsd-3-clause | 1,232 | [
"Gaussian"
] | 40e46ced93637531a15a400c6c69ce91a561a4fac4ef978691d30e3ab4580c3f |
#!/usr/bin/env python
##### findSpanin.pl --> findSpanin.py
######### Incooperated from the findSpanin.pl script, but better and more snakey.
import argparse
from cpt import OrfFinder
from Bio import SeqIO
from Bio import Seq
import re
from statistics import median
from spaninFuncs import *
import os
# if __name__ =... | TAMU-CPT/galaxy-tools | tools/spanin/generate-putative-isp.py | Python | gpl-3.0 | 9,676 | [
"Galaxy"
] | 4bade1bc57da7b0cae1b9fcc6cb7b9aecd2a69426f69fd5ab2df770b2ca64935 |
# Refer to the following link for PyQt documentation:
# http://pyqt.sourceforge.net/Docs/PyQt4/classes.html
# Written for AMIS-30543 driver.
'''
At an RPM of 60 and an input of 200 steps in mode 1/1, takes motor 1 second to complete task
At an RPM of 120 and an input of 200 steps in mode 1/2, takes motor 1 second to c... | kemerelab/Elevator | ElevatorGUI/PyQt GUI/ElevatorGUI.py | Python | mit | 32,249 | [
"VisIt"
] | 628511491aa5abf573e441a358417731c467e9586a0fdbc9cfa966b8d0f447f7 |
#!/usr/bin/env python3
# (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.
#
# ... | RTS2/rts2 | scripts/u_point/transform/u_taki_san.py | Python | lgpl-3.0 | 5,152 | [
"VisIt"
] | 53fb0516e10178818eba483387bc84fba8fc43d006687dd6fbfdf41e18ffd933 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 vers... | marscher/PyEMMA | pyemma/coordinates/api.py | Python | lgpl-3.0 | 93,871 | [
"Amber",
"CHARMM",
"Gromacs",
"LAMMPS",
"MDTraj",
"NAMD",
"NetCDF",
"TINKER"
] | 27deeb3b38e91648e3bd2d7686e3650df0257c1fc6887b8003aaff0fed259e68 |
#!/usr/bin/env python
import argparse
import datetime
import os
import sys
import matplotlib
matplotlib.use( "Agg" )
import matplotlib.pyplot as plt
import MySQLdb
import numpy as np
import pandas as pd
DATE_FORMAT = "%Y-%m-%d"
UNIX_EPOCH = datetime.datetime( 1970, 1, 1 )
ylabels = { "mpi4py-import" : "... | rcthomas/nersc-benchmarks | scripts/plot-benchmark.py | Python | bsd-3-clause | 5,321 | [
"VisIt"
] | 5c9f37b6c487268c0c3b470f4522919b5b62f4f0c8b4e23cf2079166d0b700e2 |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | dennisss/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 171,006 | [
"Gaussian"
] | 6a3bda42a2fe1f44c134d2d141270721a7a5e2224d3a95f604972b182699fe3a |
# (C) British Crown Copyright 2014 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | ajdawson/iris | lib/iris/tests/integration/test_netcdf.py | Python | gpl-3.0 | 11,416 | [
"NetCDF"
] | 0dceba68d5b7bb6a787e984a6cc45357c682b259b1eaaf3bff4d40e175df2c8e |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | backmari/moose | python/chigger/base/ChiggerSource2D.py | Python | lgpl-2.1 | 2,342 | [
"MOOSE",
"VTK"
] | 3beff2278e1e2abe02dadfe9904c2e6ac8ee8c87d386f04cd370d63d2d0e4d3a |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Finishing pipeline, starting with a phase1/2 BAC. The pipeline ideally should
include the following components
+ BLAST against the Illumina contigs to fish out additional seqs
+ Use minimus2 to combine the contigs through overlaps
+ Map the mates to the contigs and pe... | sgordon007/jcvi_062915 | assembly/postprocess.py | Python | bsd-2-clause | 10,779 | [
"BLAST"
] | 90f5db998e4f98ffb079a8f041e3cecdcda6dfaf231f6887d1e183e45c7ea3c5 |
############################################################################
##
## Copyright (C) 2006-2010 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software Foundat... | VisTrails/vistrails-contrib-legacy | vtksnl/vtkcell.py | Python | bsd-3-clause | 41,122 | [
"VTK"
] | 88be7f733c050bbf5672ea9c32e8b9c371c280f256eb53d241f475d934ff125c |
#!/usr/bin/python
#====================================================================#
# Script to get the eigenvalues from an abinit _EIG.nc netcdf file #
#====================================================================#
#########
#IMPORTS#
#########
import numpy as N
import matplotlib.pyplot as P
import ne... | jmbeuken/abinit | scripts/post_processing/ab_extended_scissors_guess.py | Python | gpl-3.0 | 101,073 | [
"ABINIT",
"NetCDF"
] | 2fad7e2dda9c3e9401cc02d55156907b85d3271960b76c85468d8bd79134f667 |
#!/usr/bin/env python
import os
import vtk
import math
import numpy
from paraview.simple import *
import paraview.servermanager
paraview.simple._DisableFirstRenderCameraReset()
#
# Load data
#
#RootFolder = '/Volumes/WAILERS/UCI/Collaborators/Marcos/Data/NoFoldExperiment-TimeVaryingData/18C/Control'
#File = 'CA_9_1... | vianamp/Utils | ImaginalDisk/python/makeboxEctopic.py | Python | gpl-3.0 | 1,358 | [
"ParaView",
"VTK"
] | 1ab4cf4b14e45ef1c3d5f5adc5625bedda45cb455e9c70e208a108734ccb8748 |
# -*- coding: utf-8 -*-
'''
author: zhangnq
website: http://www.sijitao.net/
'''
import requests
import cookielib
import re
import random
import time
import datetime
#http代理配置，有用户名和密码。
proxie = {
'http' : 'http://username:password@www.sijitao.net:1080'
}
#配置hostloc论坛的用户名密码
users=[
{'username':'user1','passw... | zhangnq/scripts | python/hostloc/hostloc.py | Python | apache-2.0 | 3,103 | [
"VisIt"
] | dcd2fbcfa3172160e8d5a99a4d0fa425db9b07d3a7ea638f13440a2a01a3461c |
from scipy import stats
import numpy as np
from numpy.testing import (assert_almost_equal, assert_,
assert_array_almost_equal, assert_array_almost_equal_nulp, assert_allclose)
import pytest
from pytest import raises as assert_raises
def test_kde_1d():
#some basic tests comparing to normal distribution
np.... | pizzathief/scipy | scipy/stats/tests/test_kdeoth.py | Python | bsd-3-clause | 15,933 | [
"Gaussian"
] | 1ecf506e82ef0bb7135ece0a67330523865e44f3c490b6a53c6052e80ae95f3c |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse
import sys
import fnmatch
import os
import dma_resolver
import shlex
import pickle
import re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directo... | AndKe/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 73,366 | [
"CRYSTAL"
] | b7a015ee7f527cf636bdc20d866a01736fe12cee9254135467d28f534a58b705 |
#!/usr/bin/env python
#
# Author: Sheng Guo <shengg@princeton.edu>
# Qiming Sun <osirpt.sun@gmail.com>
#
from pyscf import gto
from pyscf import scf
from pyscf import mcscf
from pyscf import dmrgscf
from pyscf import mrpt
'''
DMRG-CASCI then DMRG-NEVPT2 calculation for excited states.
'''
b = 1.4
mol = gto.M... | gkc1000/pyscf | examples/dmrg/11-excited_states.py | Python | apache-2.0 | 1,805 | [
"PySCF"
] | 1c7fe02a4abae166ed752269112ea942f0f6e23a18abf0395e6f04d7173e21b9 |
# -*- coding: utf-8 -*-
#
# MDAnalysis documentation build configuration file, created by
# sphinx-quickstart on Mon Sep 27 09:39:55 2010.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# ... | MDAnalysis/mdanalysis | package/doc/sphinx/source/conf.py | Python | gpl-2.0 | 11,863 | [
"MDAnalysis",
"RDKit"
] | a5489e63bc6aeef9c51cbefebc3c19ea311484fbdd79563705c438c92113db3e |
# -*- coding: UTF-8 -*-
#retriever
from retriever.lib.models import Table, Cleanup, correct_invalid_value
from retriever.lib.templates import Script
from pkg_resources import parse_version
try:
from retriever.lib.defaults import VERSION
except ImportError:
from retriever import VERSION
class main(Script):
... | goelakash/retriever | scripts/pantheria.py | Python | mit | 2,910 | [
"Amber"
] | 06d47221a419e959e7c0765744a68fc075b2927a478ebd098db0832f465e51fd |
#!/usr/bin/env python
"""
This example shows how to automatize the execution
of ABINIT starting with just the input file "t44.in"
The abinit.files is written with the right
locations for the pseudopotentials and the results
are post-process using the output in NetCDF format
"abinit-o_OUT.nc"
"""
import os
import sys
... | MaterialsDiscovery/PyChemia | tests/test_zexample1.py | Python | mit | 3,186 | [
"ABINIT",
"NetCDF"
] | 9ee3152150395122397405d05f876de30b638a290bce52c8b3410d54613c3c55 |
#!/usr/local/epd/bin/python
#------------------------------------------------------------------------------------------------------
#
# Dirac propagator in the phase space x-px
#
#------------------------------------------------------------------------------------------------------
import numpy as np
import scipy.fft... | cabrer7/PyWignerCUDA | GPU_WignerDiracKvN2D_4x4.py | Python | mit | 144,987 | [
"DIRAC",
"Gaussian",
"Psi4"
] | 30c8965ca4d267195d896daee15c535a2868da559261af6af62ab15dbe15089c |
# -*- coding: utf-8 -*-
from Plugins.Extensions.MediaPortal.plugin import _
from Plugins.Extensions.MediaPortal.resources.imports import *
from Plugins.Extensions.MediaPortal.resources.twagenthelper import TwAgentHelper
import base64
spezialagent = "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.11 (KHTML, like Gecko... | n3wb13/OpenNfrGui-5.0-1 | lib/python/Plugins/Extensions/MediaPortal/additions/porn/megaskanks.py | Python | gpl-2.0 | 15,564 | [
"ADF"
] | e582275b9fb0b2a9135a3431b542ed4cff722e1751bce735358bbea9c3df4760 |
# -*- coding: utf-8 -*-
# Python imports
import datetime
from decimal import Decimal
import string
# Django imports
from django.conf import settings
from django.contrib.auth.models import Permission
from django.contrib.contenttypes.models import ContentType
from django.db import connection
from django.db.models.field... | SmartElect/SmartElect | libya_elections/tests/test_utils.py | Python | apache-2.0 | 17,089 | [
"VisIt"
] | 87bfc284277225912b4ad3e773e53dee4ba8ce83755d2771d366d682ba2c6f90 |
"""
Geckopush was built for Python 3.
Author: Patrick Lee (me@patricklee.nyc)
Git Repo: http://www.github.com/patleeman/geckopush
"""
import urllib.request
import json
class Dashboard(object):
"""
Dashboard object. Used to hold the dashboard's API key and a collection
of all the widgets that have been c... | patleeman/geckopush | geckopush/geckopush.py | Python | mit | 28,716 | [
"Amber"
] | 65b84e101f60210ac671c659e09da4f3f258656ac3e2b4b35fcf5797d9dc7f28 |
# creates: Al_phonon.png Al_mode.gif Al_mode.pdf
from ase.lattice import bulk
from ase.calculators.emt import EMT
from ase.dft.kpoints import ibz_points, get_bandpath
from ase.phonons import Phonons
# Setup crystal and EMT calculator
atoms = bulk('Al', a=4.05)
calc = EMT()
# Phonon calculator
N = 6
ph = Phonons(atom... | askhl/ase | doc/ase/phonons.py | Python | gpl-2.0 | 2,289 | [
"ASE",
"CRYSTAL"
] | f67bd6a39de52910a94f0d727e41dc7e1e6910a1b8fd0e13508d45cf44693526 |
"""
Interactive kinetics app with sliders (with units).
Start by runing:
$ bokeh serve interactive.py
Add --show argument or navigate to:
http://localhost:5006/bokeh_interactive_units
"""
from collections import defaultdict
import sys
from chempy.util.bkh import integration_with_sliders
from chempy.units impor... | bjodah/aqchem | examples/bokeh_interactive_units.py | Python | bsd-2-clause | 1,113 | [
"ChemPy"
] | b64a0f8f5892a2774ce96582178e79fe57fdc9bff512f245fc9ef1787168e1e8 |
#########################################################################
#
# spatial.py - This file is part of the Spectral Python (SPy) package.
#
# Copyright (C) 2012-2014 Thomas Boggs
#
# Spectral Python is free software; you can redistribute it and/
# or modify it under the terms of the GNU General Public ... | ohspite/spectral | spectral/algorithms/spatial.py | Python | gpl-2.0 | 27,407 | [
"Gaussian"
] | ab2a44bac7204b8646abf3cc969adce46acddee89c7ec8b208ac42b0d565a118 |
# ---- define some conversions ---
# ---- use: ----
# from define_my_consts import mb2Pa
import numpy as np
mb2Pa = 100.0 # convert mb to Pa
Pa2mb = 0.01 # and back
cal2J = 4.18400 # convert cal to J
Angstr2m = 1e-10 # Angstrom to m
# ---- define my constants ----
avogadro = 6.022142e23 ... | portyankina/little_helpers | define_my_consts.py | Python | bsd-3-clause | 4,592 | [
"Avogadro"
] | a8248c50d63ee52ffb87edcd85766ec974cd71d528637b270956a2b0cb8a68ff |
#!/usr/local/bin/yade-trunk -x
# -*- encoding=utf-8 -*-
# CWBoon 2015
from yade import pack
import math
import os
import errno
try:
os.mkdir('./vtk/')
except OSError as exc:
if exc.errno != errno.EEXIST:
raise
pass
Gl1_PotentialParticle().store=True
O.engines=[
ForceResetter(),
InsertionSortCollid... | cosurgi/trunk | examples/PotentialParticles/cubePPscaled.py | Python | gpl-2.0 | 18,912 | [
"VTK"
] | a2669111abcd25ca0a10b9224112a35ad3dea1e8727aa5937de3febfc3c3e1d8 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 02 16:24:22 2015
Fit uniform, normal or shuffled distribution of cell DYs
@author: sweel
"""
from tvtk.api import tvtk
from collections import defaultdict
from tubule_het.autoCor.fitDistr import vtkdata, vtkshuf, vtksamp
# pylint: disable=C0103
def fitdrfp(files):
""... | moosekaka/sweepython | tubule_het/rfp_analysis/fitDistRFP.py | Python | mit | 1,876 | [
"VTK"
] | 13e7edc4c50b5ea606de7504a7914a9e4ab7699cfafce91857f18671ee64d343 |
from copy import deepcopy
import numpy as np
import numba
from scipy import stats
from .utils import model_matrix, centers_to_edges, default_alignment_options
def gain_sampler(mu=1, sigma=0.35, dpe_fraction=0.16):
"""Return function mapping n -> n photon gains
:param mu: Mean of 1pe gaussian.
:param sigm... | JelleAalbers/xeshape | xeshape/simulator.py | Python | mit | 5,545 | [
"Gaussian"
] | 3695e5d628523460a42f640fff3376d1cec6a9e605d9e5c47dd91a7bb331c421 |
import re
import mdtraj
from mdtraj.testing.docstrings import docstring_verifiers, import_all_modules
from mdtraj.testing.docstrings import import_all_modules
import pytest
SKIP_MODULES = [
r'mdtraj\.utils\.external',
r'mdtraj\.utils\.six',
r'mdtraj\.utils\.unit\.unit_math',
r'mdtraj\.utils\.unit\.base... | rmcgibbo/mdtraj | tests/test_docstrings.py | Python | lgpl-2.1 | 1,032 | [
"MDTraj"
] | 466bb6a542b1a8a56f384532a919a46064a0b5e1b4efff1c68b49f4dd0abecc0 |
"""
Abstract Domain
===============
Interface of an abstract domain.
Abstract domain elements support lattice operations and program statements.
:Author: Caterina Urban
"""
from abc import ABCMeta, abstractmethod
from collections import defaultdict
from copy import deepcopy
from typing import Set, Optional, List, T... | caterinaurban/Lyra | src/lyra/abstract_domains/state.py | Python | mpl-2.0 | 33,017 | [
"VisIt"
] | 19abd0db1871ae8c261aed4e365f5fe5668b8085310af0ebc9aecaca366a1411 |
# Another code written by Jagger Kyne
# Copyright 2006 - 2013 Jagger Kyne <jagger.kyne@gmail.com>
__author__ = 'Jagger Kyne'
from tkinter import *
tk = Tk()
canvas = Canvas(tk,width=500,height=500)
canvas.pack()
canvas.create_text(150,100, text = 'There once was a man from Toulouse',fill='red')
# canvas.create_text(3... | jaggerkyne/PyKids | Part_01/Chapter_12/displaying_text.py | Python | gpl-2.0 | 752 | [
"MOOSE"
] | 387000d8ed6e58b7d280ce265637cda462737b2d2ecafab7acd9583458b05526 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
from unittest import TestCase
import numpy as np
import pandas as pd
import h5py
from exatomic import Universe
from exatomic.base import resource
from exatomic.molcas.output import O... | exa-analytics/exatomic | exatomic/molcas/tests/test_output.py | Python | apache-2.0 | 8,381 | [
"Gaussian",
"MOLCAS"
] | 351db0a21f87df0c9f9f4700b626578533ec316a03df1051067a561623bdde49 |
#!/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... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/mediaplayerload.py | Python | gpl-2.0 | 5,268 | [
"VisIt"
] | acdfecd65b014b5649fc4dd7803eb97e008e349ab97069fa3f6deaf774908b77 |
"""
Contains an abstract base class that supports chemically aware data splits.
"""
import inspect
import os
import random
import tempfile
import itertools
import logging
from typing import Any, Dict, List, Iterator, Optional, Sequence, Tuple
import numpy as np
import pandas as pd
import deepchem as dc
from deepchem.... | deepchem/deepchem | deepchem/splits/splitters.py | Python | mit | 53,440 | [
"RDKit"
] | e73840f6192a7b114d6948408e1496b69ca21a1111c826db14f1c21b89feebd5 |
# -*- coding: utf-8 -*-
import time
from threading import Thread
import redis
import redisco
import unittest
from datetime import date
from redisco import models
from redisco.models import managers
from redisco.models.base import Mutex
from dateutil.tz import tzlocal
class Person(models.Model):
first_name = model... | kiddouk/redisco | redisco/models/basetests.py | Python | mit | 35,495 | [
"VisIt"
] | 5ae61d6afff064672a2d999f84c43c315df626213ece93743be0a0c8a4f9ad96 |
import vtk
skinReader = vtk.vtkImageReader()
skinReader.SetFilePrefix("c:/Users/Rinske/Documents/GitHub/scientific-visualization/ass4/WholeFrog/frog.")
skinReader.SetFilePattern('%s%03d.raw')
skinReader.SetDataScalarTypeToUnsignedChar()
skinReader.SetFileDimensionality(2)
skinReader.SetDataSpacing(1,1,1.5)
skinReade... | stablum/scientific-visualization | ass4/frog2.py | Python | gpl-3.0 | 3,869 | [
"VTK"
] | 02dd00032725570575b054e482b8bbda0d0aee0776e353a279b8c82f82a1e5aa |
import pyscf.pbc.tools.make_test_cell as make_test_cell
from pyscf.pbc import gto, scf, ci
from pyscf.pbc.ci import KCIS
import unittest
cell = make_test_cell.test_cell_n3(mesh=[29] * 3)
cell.build()
def tearDownModule():
global cell
del cell
class KnownValues(unittest.TestCase):
def test_n3_cis_high_cos... | sunqm/pyscf | pyscf/pbc/ci/test/test_ci.py | Python | apache-2.0 | 1,804 | [
"PySCF"
] | e6e7092b067600f43f74dccfc0a30f0e9247c4ccc463a69ed2cf1562bf028420 |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# 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 and the following d... | kapteyn-astro/kapteyn | kapteyn/filters.py | Python | bsd-3-clause | 34,205 | [
"Gaussian"
] | aef444b49bc409d471f4db1464e790d7dc3324d5cca14ea8521137e5c6c8d741 |
# Copyright 2007-2010 by Peter Cock. All rights reserved.
# Revisions copyright 2010 by Uri Laserson. All rights reserved.
# 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.
"""Internal code for parsin... | zjuchenyuan/BioWeb | Lib/Bio/GenBank/Scanner.py | Python | mit | 92,059 | [
"Biopython"
] | c81417e79f52898b7cf3da0114cbaf5fdd962271dce505d18df5ee4bde854876 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | yipenggao/moose | python/chigger/tests/geometric/line_source/line_source.py | Python | lgpl-2.1 | 1,241 | [
"MOOSE"
] | bea1c5074eb6285689c4f1b67a09aa50a10b99178b2e20f72d2ad9505940bf94 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2016 Loreto Parisi <loretoparisi@gmail.com>
# Copyright (C) 2016 Silvio Olivastri <silvio.olivastri@gmail.com>
# Copyright (C) 2016 Radim Rehurek <radim@rare-technologies.com>
"""
USAGE: $ python -m gensim.scripts.word2vec2tensor --input <Word2Vec model f... | markroxor/gensim | gensim/scripts/word2vec2tensor.py | Python | lgpl-2.1 | 3,331 | [
"VisIt"
] | 9a1c238ea5735d4d289a450bbae2e9dce41578693c171c23ea5e9d70ec9727f9 |
#!/usr/bin/env python3
# Author: Bede Constantinides - b|at|bede|dot|im
# TODO
# | Decide on BWA vs Bowtie2
# | GZIP support
# | Report % read alignment in mapping to ref and contig
# | Interleaved reads (ONE TRUE FORMAT)
# | add minimum similarity threshold for reference selection
# | report on trimming, %remapped
#... | bede/sparNA | sparna.py | Python | gpl-3.0 | 29,351 | [
"BLAST",
"BWA",
"Biopython"
] | 0922659bc69d96474dede6ba65e0b6e7a53c624ce52afb43b611d7493a308127 |
# Copyright 2016 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... | chenjun0210/tensorflow | tensorflow/contrib/learn/python/learn/estimators/__init__.py | Python | apache-2.0 | 12,228 | [
"Gaussian"
] | d8240d6b158b9b61fb1490aa951ba3a0be133a30c8907facacf7ce1faabffea2 |
"""Test subclassing support in VTK-Python
VTK classes can be subclassed in Python. There are
some caveats, such as:
- protected items are inaccessible to the python class
- virtual method calls from C++ are not propagated to python
To be tested:
- make sure that subclassing works
- make sure that unboun... | timkrentz/SunTracker | IMU/VTK-6.2.0/Common/Core/Testing/Python/TestSubClass.py | Python | mit | 3,448 | [
"VTK"
] | 98b2b91aba1188a02183f335baa1121877ea7c210f2f500f7596479d0adbb29c |
"""
Implementation of a working memory model.
Literature:
Compte, A., Brunel, N., Goldman-Rakic, P. S., & Wang, X. J. (2000). Synaptic mechanisms and
network dynamics underlying spatial working memory in a cortical network model.
Cerebral Cortex, 10(9), 910-923.
Some parts of this implementation are inspired by materi... | EPFL-LCN/neuronaldynamics-exercises | neurodynex3/working_memory_network/wm_model.py | Python | gpl-2.0 | 15,324 | [
"Gaussian",
"NEURON"
] | 416a914b9a358ae4b685d1a7119d14d777f31c70253f88e01b85d7ede993d720 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.