text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
from rdkit import Chem
from rdkit.Chem import rdConformerParser
from rdkit import RDConfig
import unittest
import os
from rdkit.RDLogger import logger
logger = logger()
class TestCase(unittest.TestCase):
def setUp(self):
pass
def testReadAmberTraj(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', ... | bp-kelley/rdkit | Contrib/ConformerParser/Wrap/testConformerParser.py | Python | bsd-3-clause | 1,253 | [
"RDKit"
] | c40a36a6f4fef3e8eddf3dd50be962b525d67e8c6e1bb9f67761822dc241b09e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/share/psi4/databases/CORE.py | Python | lgpl-3.0 | 23,803 | [
"Psi4"
] | 7e494d245ae960f5881d2a42efe681828c49063dfbbc79e26e0f4e49974edd33 |
"""
CBMPy: CBWx module
===================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2009-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public Lic... | SystemsBioinformatics/cbmpy | cbmpy/CBWx.py | Python | gpl-3.0 | 89,141 | [
"PySCeS"
] | bd12b897be4c94f48144ab23b7bc2047a34890a032857f1c170c1da08bb663b6 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008,2010 Gary Burton
# Copyright (C) 2008 Craig J. Anderson
# Copyright (C) 2009 Nick Hall
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Adam Stein <adam@csh.rit.edu>
# Cop... | pmghalvorsen/gramps_branch | gramps/gui/plug/_guioptions.py | Python | gpl-2.0 | 74,244 | [
"Brian"
] | 047f5876027862fbc0998268503901ca739ddca9eba53123d2b77e11a1d8faad |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree_check.py
The original template file format supports any... | jag1g13/lammps | tools/moltemplate/src/lttree_check.py | Python | gpl-2.0 | 134,306 | [
"LAMMPS"
] | 1db311443dd2e47ae2bae0b2a1167d665e4451f48f2c4cc506ee6b5754a37b10 |
# coding=utf-8
#
# script to create new visits in the patient database
#
# Command line format:
#
# create-patients.py <num-days> <num-patients_per_day> <ip of API>
#
# <num-days> = clinic days to simulate, default = 45
# <num-patients_per_day> how many visits to create per day, default = 100
# <ip of API> ... | MercerU-TCO/CTS | tools/create-admits.py | Python | gpl-3.0 | 9,240 | [
"VisIt"
] | ae2264accb232d914d4c5cddcf7c03aff33ba649d0ffb44f5b5961354f8dc26f |
"""This demo solves the Stokes equations, using linear elements
enriched with a bubble for the velocity and linear elements for the
pressure (Mini elements). The sub domains for the different boundary
conditions used in this simulation are computed by the demo program in
src/demo/mesh/subdomains."""
# Copyright (C) 20... | MiroK/DolfinSurface | demo/undocumented/stokes-mini/python/demo_stokes-mini.py | Python | gpl-3.0 | 2,644 | [
"VTK"
] | 7a7eafd18a4d853aae8c8bdcb63a7ca2297d44aaa7f117d28f6212bfdeefbd71 |
#!/usr/bin/env python
'''
Fly Copter in SITL
AP_FLAKE8_CLEAN
'''
from __future__ import print_function
import copy
import math
import os
import shutil
import time
import numpy
from pymavlink import mavutil
from pymavlink import mavextra
from pymavlink import rotmat
from pysim import util
from pysim import vehiclei... | meee1/ardupilot | Tools/autotest/arducopter.py | Python | gpl-3.0 | 313,742 | [
"Gaussian"
] | 486407450b60a2ad9de085ea8c0956098d52041d2a14c98b62a4c8165466f387 |
#!/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/e2-openwbif | plugin/controllers/views/web/epgmulti.py | Python | gpl-2.0 | 7,477 | [
"VisIt"
] | 960fa0ff7fd417a04c2d8211d88b0428b60f0bf6783659b1569293e38d948bdb |
from .lpi_filter import inverse, wiener, LPIFilter2D
from ._gaussian import gaussian
from .edges import (sobel, hsobel, vsobel, sobel_h, sobel_v,
scharr, hscharr, vscharr, scharr_h, scharr_v,
prewitt, hprewitt, vprewitt, prewitt_h, prewitt_v,
roberts, roberts_... | bgris/ODL_bgris | lib/python3.5/site-packages/skimage/filters/__init__.py | Python | gpl-3.0 | 2,256 | [
"Gaussian"
] | 84d4fbdc669e382100e4a22cbb7ce5bee7a4ff9614ff4cd1c080fe2c88d78e04 |
import unittest, types
from mock import Mock
from DIRAC.RequestManagementSystem.Client.Request import Request
from DIRAC.TransformationSystem.Client.TaskManager import TaskBase, WorkflowTasks, RequestTasks
from DIRAC.TransformationSystem.Client.TransformationClient import TransformationClient
... | Sbalbp/DIRAC | TransformationSystem/Client/test/test_Client.py | Python | gpl-3.0 | 13,260 | [
"DIRAC"
] | 12f8d90c0378c576c7c44527785b25bfe01f881bad1f1fd26e0eec5a6a3c1dbe |
import enum
import inspect
import pydoc
import unittest
from collections import OrderedDict
from enum import Enum, IntEnum, EnumMeta, unique
from io import StringIO
from pickle import dumps, loads, PicklingError, HIGHEST_PROTOCOL
# for pickle tests
try:
class Stooges(Enum):
LARRY = 1
C... | Orav/kbengine | kbe/src/lib/python/Lib/test/test_enum.py | Python | lgpl-3.0 | 58,305 | [
"MOE"
] | 4c93d2ba80fc0913c0255ee9582fb598217d8ec53a5d8e110d5f550a3af78407 |
#!/usr/bin/env python
"""[License: GNU General Public License v3 (GPLv3)]
This file is part of FuMa.
FuMa 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 opti... | yhoogstrate/fuma | fuma/GeneAnnotation.py | Python | gpl-3.0 | 2,648 | [
"HTSeq"
] | 96b43c138947d325b59e5cbb7276d6da4f3c5d8424e129859547a33a11ae358b |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/io/tests/test_fasta.py | Python | bsd-3-clause | 42,435 | [
"scikit-bio"
] | 18906792dc7065c01fbd5febcedc9d898d8b13e533eddf4c674fcbe442687a7c |
# 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.
"""Command-line wrapper for the tree inference program PhyML."""
__docformat__ = "restructuredte... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Phylo/Applications/_Phyml.py | Python | gpl-2.0 | 9,856 | [
"Biopython"
] | 80bf05dd1f770af2c64133a26b1460cce10b55e68bfbd7cf91fd362366b8f18f |
#!/usr/bin/python
#
# Copyright 2012 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required b... | donspaulding/adspygoogle | examples/adspygoogle/adwords/v201302/basic_operations/add_text_ads.py | Python | apache-2.0 | 3,173 | [
"VisIt"
] | 5d0212d2140c61a39e5df37932a3a43cb424893426a0e430231f0b02a571fc53 |
#! python
"""
Slice a NetCDF file along the time dimension.
"""
# TODO: Generalize to slice along any combination of dimensions.
# Change args to source dest dim_name:index_range*
# Don't specify variables, slice em all.
from argparse import ArgumentParser
from netCDF4 import Dataset
def nc_copy(source_fp, dest_fp... | pacificclimate/modelmeta | scripts/nc-copy-modify.py | Python | gpl-3.0 | 4,104 | [
"NetCDF"
] | 296f87034a46be95bfe351c98110b1af15cc078fea832a2ced3311d8ef2fbe4a |
import shutil
import os
import time
import sys
import multiprocessing
import numpy as np
# deepTools packages
import deeptools.utilities
from deeptools import bamHandler
from deeptools import mapReduce
from deeptoolsintervals import GTF
import pyBigWig
debug = 0
old_settings = np.seterr(all='ignore')
def countReads... | fidelram/deepTools | deeptools/countReadsPerBin.py | Python | gpl-3.0 | 42,163 | [
"pysam"
] | e2327c96aece2d0b21d5d20417d155db8bfaa8c29ca57f47de734cc63d5614dc |
'''
This modules contains OpenMP-related stuff.
* OMPDirective is used to represent OpenMP annotations in the AST
* GatherOMPData turns OpenMP-like string annotations into metadata
'''
from pythran.passmanager import Transformation
import pythran.metadata as metadata
from pythran.spec import parse_pytypes
from... | serge-sans-paille/pythran | pythran/openmp.py | Python | bsd-3-clause | 7,977 | [
"VisIt"
] | e7ade9a6692827edd98aed57e0bb689b1f60013843416d3fe9b0d2808f627490 |
"""
Methods related to importing data.
"""
import copy
import csv
import os
import shutil
import re
import subprocess
from tempfile import mkdtemp
from tempfile import mkstemp
from tempfile import NamedTemporaryFile
from BCBio import GFF
from Bio import Entrez
from Bio import SeqIO
from celery import task
from django... | churchlab/millstone | genome_designer/utils/import_util.py | Python | mit | 47,017 | [
"BWA",
"Biopython"
] | 0e072ec80f4e8dc4bf366924ecaf4b3f142d41aeba8460d84196d039ef471851 |
import logging
from warnings import warn
import math
import numpy as np
import shlex
import parmed.unit as units
from intermol.atom import Atom
from intermol.forces import *
import intermol.forces.forcefunctions as ff
from intermol.exceptions import (UnimplementedFunctional, UnsupportedFunctional,
... | mrshirts/InterMol | intermol/desmond/desmond_parser.py | Python | mit | 85,216 | [
"Desmond",
"Gromacs",
"MacroModel"
] | 17e17ca4838f10822f789bdfa801cf41f69543a0f632f6ab98ee8242b752532e |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""
Python wrapper functions for the ``C`` package:
Basic Linear Algebra Subroutines (BLAS)
See also:
http://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms
and
http://www.netlib.org/lapack/lug/node145.html
"""
impo... | robwarm/gpaw-symm | gpaw/utilities/blas.py | Python | gpl-3.0 | 11,661 | [
"GPAW"
] | 42be37c58728d994244516f1ebb5553bef80fa5c3bfef05e84bc37496a241541 |
# these commands get executed in the current scope
# of each new shell (but not for canned commands)
from Autodesk.Revit.DB import *
from Autodesk.Revit.DB.Architecture import *
from Autodesk.Revit.DB.Analysis import *
uidoc = __revit__.ActiveUIDocument
doc = __revit__.ActiveUIDocument.Document
from Autodesk.Revit.U... | architecture-building-systems/revitpythonshell | RevitPythonShell/DefaultConfig/init.py | Python | mit | 3,563 | [
"VisIt"
] | 6733fb262431b6ee1bb2fde43d9b71a09300e869eeeb359f675ee3bff630c5ad |
# -*- coding: utf-8 -*-
"""
This file is part of pyCMBS.
(c) 2012- Alexander Loew
For COPYING and LICENSE details, please refer to the LICENSE file
"""
from pycmbs.data import Data
import os
from pycmbs.netcdf import *
import numpy as np
class Icon(Data):
"""
Main class for ICON data handling
"""
d... | pygeo/pycmbs | pycmbs/icon.py | Python | mit | 3,243 | [
"NetCDF"
] | 2a22844c489aa71abf2dbea11534558857916b35e78eee2bea02e2abff201012 |
# -*- coding: utf-8 -*-
#
# if_curve.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# ... | sdiazpier/nest-simulator | pynest/examples/if_curve.py | Python | gpl-2.0 | 5,046 | [
"NEURON"
] | 678709d8105a6d1963cff2190be471ecbf941c01e85c0775450129ee8538660d |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# See license.txt
from __future__ import unicode_literals
import frappe
import unittest
# test_records = frappe.get_test_records('Maintenance Visit')
class TestMaintenanceVisit(unittest.TestCase):
pass
| indictranstech/osmosis-erpnext | erpnext/support/doctype/maintenance_visit/test_maintenance_visit.py | Python | agpl-3.0 | 299 | [
"VisIt"
] | 6db29d789403f234bc740802aa48c1e8e90278a61dbeddf37a91e49e7d6b65e4 |
__author__ = 'sibirrer'
#this file contains a class to make a moffat profile
class Moffat(object):
"""
this class contains functions to evaluate a Gaussian function and calculates its derivative and hessian matrix
"""
def function(self, x, y, amp, alpha, beta, center_x, center_y):
"""
... | sibirrer/astrofunc | astrofunc/LightProfiles/moffat.py | Python | mit | 486 | [
"Gaussian"
] | be7036277a7cf8a1b5ac550c5ab008e31b74371557f30b5d47304445ae93fd88 |
"""
Implements non-blocking search operation(s) in a separate non-modal window
that tracks progress while searches are running. For each search that finishes,
the main thread updates the progress bar to provide the user with an
indication of overall progress.
"""
from tkinter import *
from tkinter import ttk
import th... | chris-klinger/Goat | gui/searches/threaded_search.py | Python | gpl-3.0 | 3,582 | [
"BLAST"
] | d42937928c6c51c7989791ab2ae3517919d3a2f69f770f6b59cd0a5027088bdb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2015, Adrián Gómez Pueyo and Alberto Castro
# This file is part of maxdft.
# maxdft 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... | albertocbarrigon/maxdft | src/read.py | Python | gpl-3.0 | 2,984 | [
"Octopus"
] | 1f14c0c68adea62c99e6bc7a9f291dc9938669b2bc718fcd291fce8baf717071 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "' 취소 ' 자산 로그 항목을 표시합니다 발생하지 않았습니다．",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for the area.": "위치 이... | devinbalkind/eden | languages/ko.py | Python | mit | 244,291 | [
"VisIt"
] | 34d1299e8b201c9ed4126d3d472cbb168f36cc1bfd4ce505d6818fa49331c273 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | smarr/GraalJVMCI8 | mx.jvmci/mx_jvmci.py | Python | gpl-2.0 | 76,362 | [
"VisIt"
] | 62a8f28c0aecceba748062aee466afb87b9210a442894e60cd3daa90e29bb60a |
# 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 | src/config/defines.py | Python | gpl-3.0 | 2,100 | [
"ESPResSo"
] | c73c432566e8ca8b481cf83ae22576c068b934a31553f3e6ecb99748ba20459c |
"""
Script for testing brian on NSG portal.
Still trying to figure out how it all works.
"""
from brian import (Network, NeuronGroup, StateMonitor, SpikeMonitor,
PoissonInput,
mV, ms, second, Hz)
import numpy as np
network = Network()
tau = 20*ms
eqs = "dV/dt = -V/tau : volt"
li... | achilleas-k/brian-scripts | nsgtest.py | Python | apache-2.0 | 968 | [
"Brian"
] | 552983fecc98d1e34e9ab115448a7a829281d83f0f51b1cdd26f9f3e2c9902d4 |
#==========================================================================
#
# Copyright Insight Software Consortium
#
# 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... | 151706061/ITK | Wrapping/ExternalProjects/ItkVtkGlue/Wrapping/Python/Tests/CannyEdgeDetectionImageFilter.py | Python | apache-2.0 | 2,540 | [
"VTK"
] | 883327a64052cb04a3f053828531cd9322f968a4ac6c7c26097f484e91bdf5cf |
from gpaw import GPAW
from ase import Atoms
from gpaw.lrtddft import LrTDDFT
molecule = Atoms('Na2', positions=((0.0, 0.0, 0.0), (3.12, 0.0, 0.0)))
molecule.center(vacuum=6.0)
calc = GPAW(xc='PBE')
molecule.set_calculator(calc)
molecule.get_potential_energy()
lr = LrTDDFT(calc, xc='LDA', istart=0, jend=10, nspins... | robwarm/gpaw-symm | doc/exercises/lrtddft/Na2TDDFT.py | Python | gpl-3.0 | 349 | [
"ASE",
"GPAW"
] | 684cd14a4b250892b036a20c424559ed07e84123523ef1839107f2e146834d50 |
##############################################################################
# The Combustion Flame Engine - pyflam3ng
# http://combustion.sourceforge.net
# http://github.com/bobbyrward/pyflam3ng/tree/master
#
# Copyright (C) 2007-2008 by Bobby R. Ward <bobbyrward@gmail.com>
#
# The Combustion Flame Engine is fr... | bobbyrward/pyflam3ng | pyflam3ng/__init__.py | Python | gpl-3.0 | 37,943 | [
"Gaussian"
] | 7fdaf99d86dcd24e2c12c5bbd720fe25c3d560f496dc6871ed750d5d5f7b9e11 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/bowtie2/package.py | Python | lgpl-2.1 | 3,638 | [
"Bowtie"
] | 72e79672ecd1a60f27776492b28116373f31515438accbd3e54d68c4fc8747c1 |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, or ntpath
- os.name is 'posix', 'nt', 'os2', 'ce' or 'riscos'
- os.curdir is a string representing the current di... | MicroTrustRepos/microkernel | src/l4/pkg/python/contrib/Lib/os.py | Python | gpl-2.0 | 26,337 | [
"VisIt"
] | d49d3b0d4a54fd83062bb8737184d545dcbc9e4ac5bd82af4bd057b5f9890b1d |
"""
A script to prepare/execute/analyse FHI-aims polarisation calculations
@author Tomas Lazauskas, 2016
@web www.lazauskas.net
@email tomas.lazauskas[a]gmail.com
"""
import os
from optparse import OptionParser
import source.IO as IO
import source.Messages as Messages
from source.Messages import log
# a directory w... | tomaslaz/KLMC_Analysis | DM_FHIaims_Spin_Analysis.py | Python | gpl-3.0 | 6,238 | [
"FHI-aims"
] | 3f3432b428f6568e7e91a143515704096eaca9bfb5130300fbd802c35c0b590e |
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# context: context needed to annotate a file
from __future__ import absolute_import
import collections
import contextlib
import hashlib
import os
f... | facebookexperimental/eden | eden/scm/edenscm/hgext/fastannotate/context.py | Python | gpl-2.0 | 31,541 | [
"VisIt"
] | 96232788d50f7b9a15c54eb6722e543aad6f5c59e5603f012f576f2caa532cf8 |
"""
.. module:: Pfn
:synopsis: ProcessPool and related classes
ProcessPool
ProcessPool creates a pool of worker subprocesses to handle a queue of tasks
much like the producers/consumers paradigm. Users just need to fill the queue
with tasks to be executed and worker tasks will execute them.
To construct ProcessPool... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/ProcessPool.py | Python | gpl-3.0 | 35,860 | [
"DIRAC"
] | 180ecafa21ab8ba11ef9aefda06557fec3ddcf00555674dcc0e294c5063eed97 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "' Cancel ' будет указывать актива запись протокола не выполнено",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a b... | flavour/eden | languages/ru.py | Python | mit | 351,319 | [
"VisIt"
] | b1e1eb25ab1d6fc0a6b781066e79ae51e59c49be7794903624c3ce2c87301550 |
########################################################################
# $HeadURL $
# File: PhysicalRemoval.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/02 11:56:10
########################################################################
""" :mod: PhysicalRemoval
=====================
.. modul... | avedaee/DIRAC | DataManagementSystem/Agent/RequestOperations/PhysicalRemoval.py | Python | gpl-3.0 | 6,634 | [
"DIRAC"
] | 8856b308751a705fe655a3b563a8766fef86f6311603042df984833eba5bbb79 |
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.py | Python | cc0-1.0 | 974 | [
"Galaxy"
] | d8a194e9afb8c3852d54817cd76b2af19e158bfe41bfe3456171e1b5dd377a75 |
import plac
from os import path
import numpy as np
from scipy import sparse
from scipy.io import savemat
from cmmlib.inout import load_mesh, save_coff
from cmmlib import cmm
@plac.annotations(
K=('number of CMHBs', 'positional', None, int),
mu=('sparsity parameter mu', 'positional', None, float),
visuali... | tneumann/cmm | compute_cmm.py | Python | gpl-2.0 | 4,422 | [
"Mayavi"
] | 6dfea2166c315fba3b055083f7c07138d4331d558b608d7dd786f4555427c439 |
"""
implements FilenameParsers for scripter
"""
from bowtie import BowtieFilenameParser
#from bwa import bwaFilenameParser
from illumina import BarcodeFilenameParser
from aligned import BAMFilenameParser
from peaks import PeaksFilenameParser
__all__ = [
'BowtieFilenameParser',
# 'bwaFilenameParser',
'Barcod... | benjschiller/seriesoftubes | seriesoftubes/fnparsers/__init__.py | Python | artistic-2.0 | 391 | [
"BWA",
"Bowtie"
] | 28afe94f06a97c0e2718bab4243a3bf86f29daed2c30d0b4df45886b47651a61 |
import os.path
import os
import numpy as np
from PyQt5.QtWidgets import QPushButton, QWidget
from PyQt5.QtWidgets import QComboBox, QLabel, QLineEdit
from PyQt5.QtWidgets import QProgressBar, QApplication
from PyQt5.QtWidgets import QVBoxLayout, QHBoxLayout, QFormLayout
from PyQt5.QtWidgets import QSpinBox,QD... | JohnKendrick/PDielec | PDielec/GUI/PlottingTab.py | Python | mit | 31,711 | [
"CRYSTAL"
] | 2d1e65aa5073157537df718314cec1cd8f36e22c66390fce38a2b48d7d8ca8e4 |
from __future__ import absolute_import
from sfepy.base.testing import TestCommon
import numpy as nm
from sfepy import data_dir
from sfepy.mesh.splinebox import SplineBox, SplineRegion2D
from sfepy.mesh.bspline import BSpline
from sfepy.discrete.fem import Mesh
from six.moves import range
def tetravolume(cells, vertice... | vlukes/sfepy | tests/test_splinebox.py | Python | bsd-3-clause | 6,186 | [
"VTK"
] | e479faaa10672ea814f4d9a3af680b9b2ffbbc540b07eb6f1d4b625833304bc9 |
""" Load and parse configuration file."""
from __future__ import print_function
import logging
import os
import datetime
import random
import subprocess
from dateutil.relativedelta import relativedelta
from taca.utils.config import CONFIG
from taca.utils import config as conf
from taca.utils import filesystem as fs
f... | SciLifeLab/TACA | taca/testing/create_uppmax_like_env.py | Python | mit | 20,945 | [
"BWA",
"VisIt"
] | 9188b554b393a74c038d2c99334e8cee23dc84e46e5f93a06683401f9f7483b3 |
from __future__ import print_function
import time
import numpy as np
import sympy as sy
from bokeh.objects import Plot, DataRange1d, LinearAxis, ColumnDataSource, Glyph, Grid, Legend
from bokeh.widgetobjects import Slider, TextInput, HBox, VBox, Dialog
from bokeh.glyphs import Patch, Line, Text
from bokeh.document i... | sahat/bokeh | examples/glyphs/taylor_server.py | Python | bsd-3-clause | 3,473 | [
"VisIt"
] | 03ee25590c48c974efcdf5fb4a862438df1267adbc2eb9be93700a1853eb15e6 |
# =====================================================================
# HPClusterJobConfigurator
# Copyright (C) 2014 by Gabriel Nützi <gnuetzi (at) gmail (dot) com>
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# fil... | gabyx/HPCJobConfigurator | HPCJobConfigurator/jobGenerators/jobGeneratorMPI/generatorToolPipeline/scripts/prepareToolPipeline.py | Python | mpl-2.0 | 19,785 | [
"VisIt"
] | 2cb97cb392a52be2208565cef42de4fc691a560f8a00d2755f1fc68fd98a23cc |
"""
Implementation of Harwell-Boeing read/write.
At the moment not the full Harwell-Boeing format is supported. Supported
features are:
- assembled, non-symmetric, real matrices
- integer for pointer/indices
- exponential format for float values, and int format
"""
from __future__ import division, print_... | Universal-Model-Converter/UMC3.0a | data/Python/x86/Lib/site-packages/scipy/io/harwell_boeing/hb.py | Python | mit | 18,497 | [
"exciting"
] | 1b06b122ca1c8ae9c81e9bcffd7cd11b0bae4f95a36f6e624afbf519df3ff13d |
# -*- coding: utf-8 -*-
"""
Client for connecting to Canvas.
"""
import json
import logging
from http import HTTPStatus
import requests
from dateutil.parser import parse
from six.moves.urllib.parse import quote_plus, urljoin
from django.apps import apps
from integrated_channels.canvas.utils import CanvasUtil
from in... | edx/edx-enterprise | integrated_channels/canvas/client.py | Python | agpl-3.0 | 36,426 | [
"VisIt"
] | 22166d21b5efe27af7d00d03358a9f42274029c8a9e41be011609e4f5689e796 |
from django.conf import settings
from django.conf.urls import include, url
from django.urls import reverse_lazy
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic.base import RedirectView
from django.views import defaults as default_views
from rest_framework.routers i... | Hawk94/dust | config/urls.py | Python | mit | 2,306 | [
"VisIt"
] | 804194648ca9afd76e8f277cd6fc1a31aa97ec29ea4e33325c93d2c218abfa40 |
#!/usr/bin/env python
import sys, os, shutil
from socket import gethostname
from datetime import datetime
# if it doesn't import this is probably icestorm and we won't use it anyway
try:
from sqlite3 import dbapi2 as sqlite
except:
pass
############################################################################... | gleicher27/Tardigrade | moose/framework/scripts/timingHTML/timing_utils.py | Python | lgpl-2.1 | 5,329 | [
"MOOSE"
] | 96019e869263782044a6776fb8c58e9ece71ddd80a6c2a66c95697639e428c7d |
#!/usr/bin/env python
import vtk
def main():
fileName = get_program_parameters()
colors = vtk.vtkNamedColors()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Create the pipelin... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/CarotidFlowGlyphs.py | Python | apache-2.0 | 3,480 | [
"VTK"
] | 2aea7ccdea3cccbb31f9fe4f0b755a20879be5719f14d97693af8b5175c80a31 |
import linear_env
import sim_env
from actor import Actor
from critic import Critic
from replay_buffer import ReplayBuffer
import numpy as np
import tensorflow as tf
import keras.backend as kbck
import json
import time
import argparse
import matplotlib.pylab as plt
import os.path
def ou(x, mu, theta, sigma):
return ... | deot95/Tesis | Proyecto de Grado Ingeniería Electrónica/Workspace/Comparison/Full SWMM/ddpg.py | Python | mit | 16,394 | [
"Gaussian"
] | a4a83ba5d7d0b6de1278a947d4fef33f0543bc91ea61a7d4e9b320884043b20a |
# organization/views.py
# Brought to you by We Vote. Be good.
# -*- coding: UTF-8 -*-
from django.http import HttpResponseRedirect, JsonResponse
from django.core.urlresolvers import reverse
from django.contrib import messages
from django.contrib.messages import get_messages
from django.shortcuts import redirect, rende... | wevoteeducation/WeVoteBase | organization/views.py | Python | mit | 20,794 | [
"VisIt"
] | 7ff45d3468545310d62db05ec2c4855e0e26b17d0e754ee41c4a1a8e19debcc6 |
"""
Shared code for builders.
For developers implementing a new builder,
you should inherit from :class:`Builder`.
"""
__author__ = 'Dan Gunter <dkgunter@lbl.gov>'
__date__ = '5/29/13'
## Imports
# system
from abc import ABCMeta, abstractmethod
import copy
import logging
import multiprocessing
import Queue
import tr... | migueldiascosta/pymatgen-db | matgendb/builders/core.py | Python | mit | 17,406 | [
"pymatgen"
] | c16b82b5abcb82391514553b93f3b73b231122792c679c8cb6b77fbba301443e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# listhandling - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms... | heromod/migrid | mig/shared/listhandling.py | Python | gpl-2.0 | 3,240 | [
"Brian"
] | 18a07468237e5fd78afb9baac51a8be2d5d426b3481f166761bb38d6d60110ad |
"""Module containing image transformation functions.
This module contains the function decorator
:func:`jicimagelib.transform.transformation` that can be used
to turn functions into image transformations.
Below is an example of how to create a transformation that inverts an image.
>>> import numpy as np
>>> @transfo... | JIC-CSB/jicimagelib | jicimagelib/transform.py | Python | mit | 5,662 | [
"Gaussian"
] | 957150d4d5b93c7baffb887b565c7bfd9ddf1cc367708cea1772e78bf271452d |
class VisitorBase(object):
def visit(self, node):
clsname = node.__class__.__name__
method = "visit_%s" % clsname.lower()
if hasattr(self, method):
return getattr(self, method)(node)
else:
return self.generic_visit(node)
def generic_visit(self, node):
... | lisael/fastidious | fastidious/compiler/astutils.py | Python | gpl-3.0 | 823 | [
"VisIt"
] | 371dec67180d87c211377d08909a2433152c63920243131012a06b9eb1390061 |
"""
DIRAC.WorkloadManagementSystem.PilotAgent package
"""
__RCSID__ = "$Id$" | fstagni/DIRAC | WorkloadManagementSystem/PilotAgent/__init__.py | Python | gpl-3.0 | 80 | [
"DIRAC"
] | 77cfb031279458fc985f0e0a9140f823a6e1e4ed8ee80f6c06710dd61c4a83dc |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | ellonweb/merlin | Hooks/victim/surprisesex.py | Python | gpl-2.0 | 4,771 | [
"Galaxy"
] | 1a6c004f10eafac6979da520a2d9eb1db45a1ec4396ac8571609ed2890d6acf1 |
# Copyright 2003 Iddo Friedberg. 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.
import string
"""A parser for the NCBI blastpgp version 2.2.5 output format. Currently only suppo... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Blast/ParseBlastTable.py | Python | apache-2.0 | 3,467 | [
"Biopython"
] | b5858b3c832152914095119c1fde8a1d1d94315c393cd5b68cf50ee1702da367 |
# 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.
"""
# pylint: disable-all
... | ondra-novak/chromium.src | build/android/pylib/android_commands.py | Python | bsd-3-clause | 72,615 | [
"Galaxy"
] | 378fcb99f9337ca332cd3b9b3e7b3b9418d1f6705a1059a4740cb6d56dd04b8b |
#!/usr/bin/env python
"""
sacfs_flexcode.py - Database of SAGRN FLEX Addresses (for pagers)
Copyright 2010 - 2015 Michael Farrell <http://micolous.id.au/>
This file is automatically generated by a script (urgmsg_export_codes.py).
This program is free software: you can redistribute it and/or modify
it under the terms ... | Shaggs/cfsprinter | src/pagerprinter/misc/sacfs_flexcode.py | Python | gpl-3.0 | 103,474 | [
"CRYSTAL"
] | ba3b4c94f0d83cd774eb7f0c7fc6a3318eee1054d33ce9c70eda4dc5a577e183 |
from sys import version_info
from unittest import TestCase
from nose import SkipTest
from nose.tools import eq_, assert_raises, ok_
from parsimonious.exceptions import UndefinedLabel, ParseError
from parsimonious.expressions import Sequence
from parsimonious.grammar import rule_grammar, RuleVisitor, Grammar, TokenGra... | smurfix/parsimonious | parsimonious/tests/test_grammar.py | Python | mit | 16,132 | [
"VisIt"
] | 2404961055aa3f2a7451809dcb76707cf0367bbc409940ae21cc9b2166d9c6ab |
import __main__
import unittest, copy, shutil, tempfile
from numpy.testing import assert_array_equal
from param import normalize_path,resolve_path
from imagen import Gaussian, Line
import topo
from topo.sheet import GeneratorSheet
from topo.command import save_snapshot,load_snapshot
from topo.base.simulation import S... | ioam/topographica | topo/tests/unit/testsnapshots.py | Python | bsd-3-clause | 2,461 | [
"Gaussian"
] | 7662ebc755a1476b4d16f50e2b7211fea37ee487b59dffed76baebfef117fc57 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of the PyNeurActiv project, which aims at providing tools
# to study and model the activity of neuronal cultures.
# Copyright (C) 2017 SENeC Initiative
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of th... | Silmathoron/PyNeurActiv | lib/aeif.py | Python | gpl-3.0 | 2,426 | [
"NEURON"
] | 4d73b8a73dc59880ff6a7ad3464ce2c47c04a3a46247b0d1754d154909c41b76 |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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 y... | mazaclub/electrum-dash | plugins/trustedcoin.py | Python | gpl-3.0 | 25,605 | [
"VisIt"
] | 67b4a39f2208266de5978233d3ce810745b9ca6f26220f0d030717971537635f |
from .system import System
from .molecule import Molecule, guess_bonds
from .atom import Atom
from .system import (subsystem_from_molecules,
subsystem_from_atoms,
merge_systems)
from .trajectory import Trajectory
from .spacegroup.crystal import crystal
from .random import rand... | chemlab/chemlab | chemlab/core/__init__.py | Python | gpl-3.0 | 347 | [
"CRYSTAL"
] | f0315d77ec124a3a2172af12cae15ec261b91dbe3216f7fdbba7c55cd92d9fc9 |
from builtins import range
import sys, os
sys.path.insert(1, os.path.join("..",".."))
import h2o
from tests import pyunit_utils
from h2o.estimators.deeplearning import H2ODeepLearningEstimator
def weights_and_distributions():
htable = h2o.upload_file(pyunit_utils.locate("smalldata/gbm_test/moppe.csv"))
htable["p... | YzPaul3/h2o-3 | h2o-py/tests/testdir_algos/deeplearning/pyunit_weights_and_distributions_deeplearning.py | Python | apache-2.0 | 1,335 | [
"Gaussian"
] | 5307a307ffd5eef0db0c2d749257f7e7b5099279febce988281a9b93dcb7bb8e |
import opencor as oc
import sys
sys.dont_write_bytecode = True
import utils
if __name__ == '__main__':
# Test the Noble 1962 model using different solvers
utils.run_simulations('noble_model_1962.cellml', 'Noble 1962 model')
| agarny/opencor | src/plugins/support/PythonSupport/tests/data/noble1962tests.py | Python | gpl-3.0 | 236 | [
"OpenCOR"
] | db476bf4a84a2b76dea8f31c83cd4d95f6183129409cf73025e0ab89c8768f46 |
# Copyright 2018 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | google/differentiable-atomistic-potentials | dap/tests/test_ag.py | Python | apache-2.0 | 4,875 | [
"ASE"
] | 6f8e1ec0faefa7bee6f2422d476977cb7f5d749259939561a7c0d7db95fed2bd |
import matplotlib.pyplot as plt
import os
from astropy.table import Table
import numpy as np
# setup information sources
degas = Table.read(os.path.join(os.environ['SCRIPTDIR'],'degas_base.fits'))
stack = Table.read('/lustre/cv/users/akepley/degas/stack_test/stack_IR6p0_mom1.fits')
plotDir = os.path.join(os.environ['... | low-sky/degas | scripts/plot_SFEdense_vs_r25_combined_nolim.py | Python | gpl-3.0 | 2,162 | [
"Galaxy"
] | 3aec4bf7cf1de65c8cc49a3748c6bfa0eff0b1623e506710891db69daeb6c003 |
# -*- coding: utf-8 -*-
from io import StringIO, BufferedReader
import os
import string
import py
import pytest
import hashfs
from hashfs._compat import to_bytes
@pytest.fixture
def testpath(tmpdir):
return tmpdir.mkdir('hashfs')
@pytest.fixture
def testfile(testpath):
return testpath.join('hashfs.txt')
... | bopo/hashfs | tests/test_hashfs.py | Python | mit | 7,615 | [
"VisIt"
] | 817ca3559f114c5be709630ca8789ebc56b969df4f65577e48dded91e0af66f2 |
##############################################################################
# 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/r-absseq/package.py | Python | lgpl-2.1 | 1,928 | [
"Bioconductor"
] | e8354087f4e969a179b58fa09858e442e631f3a7ef5803756f2805364b786596 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/DBAP-algorithm | third_party/rlkit_library/rlkit/torch/pytorch_util.py | Python | apache-2.0 | 9,233 | [
"Gaussian"
] | 5bc30e1d5da29d43a511430e3863f7ece998fcdb7b910e7d2854810f54737717 |
"""
UUTrack.Model.Cameras.Hamamatsu.py
==================================
Model class for controlling Hamamatsu cameras via de DCAM-API. At the time of writing this class,
little documentation on the DCAM-API was available. Hamamatsu has a different time schedule regardin support of
their own API. ... | uetke/experimentor | experimentor/models/Cameras/Hamamatsu.py | Python | mit | 6,645 | [
"ORCA"
] | 1ed13cba7790edd872992d9ffbc1dcb3c2a4456aeb13da37a092f71d7c793506 |
# coding=utf-8
# Copyright 2022 GradMax Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... | google-research/growneuron | growneuron/cifar/vgg.py | Python | apache-2.0 | 5,639 | [
"Firefly"
] | 7eda791c5a53f31594581765eb9336290ad0fc29f57e3f6716dd5622643e33ee |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
try:
CLAW = os.environ['CLAW']
except:
raise Exception("*** Must first set CLAW enviornment variable")
#... | clawpack/geoclaw_tutorial_csdms2016 | chile2010a/setrun_original.py | Python | bsd-2-clause | 13,629 | [
"NetCDF"
] | bcbbc2b0371216da1088438e69eb52e74c00e1e6445e7d8db2ea1afa24931d2b |
#!/usr/bin/env python3
import sys
import os
import argparse
def write_pymol_arrows(base, structs, scale, color, radius, hradius, hlength, threshold):
pymol_file = base + '_arrows.pymol'
lines = []
arrow_objs = set()
t2 = threshold**2
s2 = scale**2
for i, struct in enumerate(structs):
... | gnina/scripts | pymol_arrows.py | Python | bsd-3-clause | 5,070 | [
"PyMOL"
] | b439473ee026ef10aca592772399fce4a2dc3bcd1fcb84d1b04574a40e72faa0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jturney/psi4 | psi4/driver/p4util/python_helpers.py | Python | lgpl-3.0 | 44,073 | [
"Psi4"
] | 975c3e0fc9e52c68fd6caa347d3aa826e7e19545efc2e4297cdf8fff171a7d50 |
##
# Copyright 2009-2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | geimer/easybuild-easyblocks | easybuild/easyblocks/o/openfoam.py | Python | gpl-2.0 | 11,828 | [
"ParaView"
] | 3896277cd144d896090c4b326baf82e66e92b06fc3feb36f09d670751ad6b0fd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals
from __future__ import absolute_import
"""
This module provides a class used to describe the elastic tensor,
including methods used to fit the ... | aykol/pymatgen | pymatgen/analysis/elasticity/elastic.py | Python | mit | 13,916 | [
"VASP",
"pymatgen"
] | 505a6739ccbf123ae789ac87c0d2ba46f68b6d1fad986ec83058e20bdfbca732 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Variable_Stiffness_Variable_Velocity/HMM/with 0.8s/hmm_crossvalidation_force_10_states.py | Python | mit | 27,332 | [
"Mayavi"
] | 4e19a8057eebd53dc96b0b6253590b331da54438b1bc1bdd750873a114c21400 |
from behave import when, given, then
from custom.django import DjangoStep
@given('I am a new user')
def impl(context):
pass
@given('I am an authenticated user')
def impl(context):
pass
@when('I visit the home page')
def impl(context):
context.browser.get(context.server_url)
@then('I will see the tex... | contracode/libreshop | libreshop/bdd_tests/features/steps/storefront.py | Python | gpl-3.0 | 533 | [
"VisIt"
] | 027c47420d5cef2af18e3080c68d2f80b74fd8d684a8675004b95d34822c5a9c |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import functools
import random
import pytz
import io
import json
import shutil
import tempfile
from django.conf import settings
from django.contrib.auth.models import User
from django.core import mail
from django.core.fil... | synergeticsedx/deployment-wipro | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 224,197 | [
"VisIt"
] | 3b2c8b49bba9f8326b586f9fda051f5d7291597c28c557e2c0f1b9157f3e0c35 |
''' A moduled used by maxent.py and phlearn.py to find the ideal weights for a tableau.
'''
import megatableau
import scipy, scipy.optimize
import math
import numpy as np
### HELPER FUNCTIONS FOR CALCULATING PROBABILITY ###
def maxent_value(weights, tableau, ur, sr):
""" Compute maxent value P* = exp(harmony) fo... | rdaland/PhoMEnt | optimizer.py | Python | bsd-3-clause | 4,662 | [
"Gaussian"
] | f15d37a6dda554a5e224cc1f6a89e7ae51332377434642e2f4e9765b1c3c31c7 |
#===============================================================================
# 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/helpers/mmshelper.py | Python | gpl-2.0 | 3,807 | [
"VisIt"
] | 2c950d7583ae41d0362d82447114e0e0e6274061553f2d536989613cd5a7868e |
#!/usr/bin/python
# python parser module for pipeline for miRNA full profiling with bowtie 20/4/2011
# version 1
# Usage class_mirparser.py <bowtie_out> <bowtie miRNA index> <LABEL> <output1 file> <output2 file>
# still to work. Split count still bugged
import sys, subprocess
from collections import defaultdict
def ge... | JuPeg/tools-artbio | unstable/local_tools/class_mirparser.py | Python | mit | 5,141 | [
"Bowtie",
"Galaxy"
] | 3453a33a38b3e5720b0e099f64ea05e287d2c38011f81f003128389503cf2f45 |
########################################################################
# $HeadURL $
# File: ReTransfer.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/02 14:24:21
########################################################################
""" :mod: ReTransfer
================
.. module: ReTransfer... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/ReTransfer.py | Python | gpl-3.0 | 5,674 | [
"DIRAC"
] | 69e666ac671012e1bd1246aadb04f2ffcdfcd6d07b92d0e85302c4872986d02d |
# Copyright (c) 2012 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functionality ... | Menooker/gem5_pcm | src/python/m5/SimObject.py | Python | bsd-3-clause | 43,257 | [
"VisIt"
] | 9a14781e8b1a59e39c78654cca8197d9a01eefdf858d817f97ad508b5e6423c9 |
import unittest
import client
import utilities
import datetime
class TestSeriesFunctions(unittest.TestCase):
def setUp(self):
self.rs = client.RSSeriesClient()
def test_get_identifier(self):
identifier = self.rs.get_identifier('A1')
self.assertEqual(identifier, 'A1')
def test_ge... | wragge/recordsearch_tools | tests.py | Python | cc0-1.0 | 16,330 | [
"VisIt"
] | f27598ef7b2337f1af463743db065a4c25756b1db267cb32f6c12f0701677ae9 |
import MDAnalysis
try:
from MDAnalysisTests.datafiles import PSF, DCD
except:
pass
try:
from MDAnalysis.analysis import rms
except:
pass
class SimpleRmsBench(object):
"""Benchmarks for MDAnalysis.analysis.rms.rmsd
"""
params = ([100, 500, 2000],
[None, [1.0, 0.5]],
... | MDAnalysis/mdanalysis | benchmarks/benchmarks/analysis/rms.py | Python | gpl-2.0 | 3,079 | [
"MDAnalysis"
] | dcf3c48d7a41ad15aa8e21c7c1692972cfcdb420d25746637c10ebd470ec512f |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkExtractPolyDataGeometry(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkExtractPolyDataGeometry.py | Python | bsd-3-clause | 507 | [
"VTK"
] | 7ad12ce414b4485f2331f019fea414b67a265883fa05bf918f6a092909bd08c3 |
"""
MUSE -- A Multi-algorithm-collaborative Universal Structure-prediction Environment
Copyright (C) 2010-2017 by Zhong-Li Liu
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
version 2 of ... | zhongliliu/muse | muse/Calculators/Run_lammps.py | Python | gpl-2.0 | 2,241 | [
"LAMMPS"
] | 9841f08a4ea126e7078ba1ef0fd58ec19d36f0465a480c833d9dda536a67e3c9 |
import numpy as np
def compute_gat(arr, sigma_sq, alpha=1):
"""
Generalized Anscombe variance-stabilizing transformation
References:
[1] http://www.cs.tut.fi/~foi/invansc/
[2] M. Makitalo and A. Foi, "Optimal inversion of the generalized
Anscombe transformation for Poisson-Gaussian noise", IE... | simonsfoundation/CaImAn | caiman/external/houghvst/gat.py | Python | gpl-2.0 | 2,529 | [
"Gaussian"
] | 8e0696831569cd69645486503faf11477f046bd901c445544e0de4c0b2f0e126 |
from ase import Atoms
from ase.lattice.surface import fcc111, add_adsorbate
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.io import write
# Find the initial and final states for the reaction.
# Set up a (4 x 4) two layer slab of Cu:
slab = fc... | misdoro/python-ase | doc/tutorials/N2Cu-Dissociation1.py | Python | gpl-2.0 | 1,268 | [
"ASE"
] | b2c8e037d5152b24f67f35aa26f91bc7fd06ff4013ddc259bb0a4c040279c64b |
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