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from django.utils.translation import ugettext as _
from corehq.apps.groups.models import Group
from corehq.apps.reports.standard.cases.basic import CaseListReport
from corehq.apps.api.es import CaseES
from corehq.apps.reports.standard import CustomProjectReport
from corehq.apps.reports.datatables import DataTablesHead... | qedsoftware/commcare-hq | custom/bihar/reports/mch_reports.py | Python | bsd-3-clause | 21,109 | [
"VisIt"
] | 41c315dfdf8c1328ead563a32cae61f04369ac8c00f2f0e74ebcf392722d544e |
import matplotlib.pyplot as plt
from camera_position_tools import RectangleObject, CircleObject
#Everything in relation to HR camera coordinate system
#Positive x and y is in the top right quadrant, negative x and positive y is in the right quadrant
#There are two different objects: CircleObject and RectangleObject
#... | magnunor/camera_aperture_position | plot_camera_position.py | Python | gpl-3.0 | 2,143 | [
"ADF"
] | 3f5bab0e11ac052e791a1932d77b62e19cc508ce08503bb8b0878650ee3abe8e |
import unittest
import os
import sys
import io
import contextlib
import blast
TMP_FILE = '__test_tempfile'
def setUpModule():
blast.Platform.open = lambda _: None
blast.Platform.copy_to_clipboard = lambda _: None
def cleanup():
try:
os.remove(TMP_FILE)
except OSError:
pass
class Te... | swarmer/blast | tests.py | Python | mit | 10,868 | [
"BLAST"
] | 552c9a50446e39036677b01f5399b99a2498801ef7a8a32bc5c73867a69c4d1c |
import unittest,types
from DIRAC.WorkloadManagementSystem.DB.JobDB import JobDB
class JobDBTestCase(unittest.TestCase):
""" Base class for the JobDB test cases
"""
def setUp(self):
print
self.jobDB = JobDB('Test',20)
def createJob(self):
result = self.jobDB.getJobID()
jobID = result['Va... | avedaee/DIRAC | WorkloadManagementSystem/DB/test/TestJobDB.py | Python | gpl-3.0 | 6,868 | [
"DIRAC"
] | 472d5b11671ded4f286a611c60542a86b93825ca4c622f89484301be9c83ef5e |
# $Id$
#
# Copyright (C) 2009 Greg Landrum
# All Rights Reserved
#
import pickle
from rdkit import Chem, DataStructs
similarityMethods = {
'RDK': DataStructs.ExplicitBitVect,
'AtomPairs': DataStructs.IntSparseIntVect,
'TopologicalTorsions': DataStructs.LongSparseIntVect,
'Pharm2D': DataStructs.SparseBitVect... | bp-kelley/rdkit | rdkit/Chem/MolDb/FingerprintUtils.py | Python | bsd-3-clause | 3,612 | [
"RDKit"
] | 15402e780cf8db432ed785da8678b36d105a4adcc0a2fbfe2fe9ea5905f6f6d8 |
# -*- coding: utf-8 -*-
"""
Display information about your smartphone with KDEConnector.
Configuration parameters:
cache_timeout: how often we refresh this module in seconds (default 30)
device: the device name, you need this if you have more than one device
connected to your PC (default None)
devi... | docwalter/py3status | py3status/modules/kdeconnector.py | Python | bsd-3-clause | 7,868 | [
"Galaxy"
] | fe18ae862a6dd97481a15499ffd552381fa9a05243e853d7e74869dbb3069250 |
# mako/parsetree.py
# Copyright (C) 2006-2015 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""defines the parse tree components for Mako templates."""
from mako import exceptions, ast, u... | sunze/py_flask | venv/lib/python3.4/site-packages/mako/parsetree.py | Python | mit | 20,434 | [
"VisIt"
] | ecfa94d70b0edcb5cbced03318ffef8308173df4cc44a4bd78510a7656748630 |
# -*- coding: utf-8 -*-
## @package ivf.core.edge_detection.dom
#
# ivf.core.edge_detection.dom utility package.
# @author tody
# @date 2016/02/15
import cv2
from ivf.cv.image import to8U, to32F
## DoM filter.
# @param img input gray image.
# @param sigma sigma for small Gaussian filter.
# @par... | tody411/ImageViewerFramework | ivf/core/edge_detection/dom.py | Python | mit | 540 | [
"Gaussian"
] | 51866f5dcfa2099aed3a31ba4d37677dc3dae2799e91819e29690363a6ca6d07 |
# clip reads in a BAM file to a specified length
import pysam
import sys
def main(in_bam, target_length, out_bam):
samfile = pysam.Samfile(in_bam, "rb")
outfile = pysam.Samfile(out_bam, "wb", template=samfile)
for read in samfile.fetch():
if len(read.seq) < target_length:
continue
... | roryk/junkdrawer | clip_reads.py | Python | mit | 642 | [
"pysam"
] | 96a94f4bc9732c63a32e79683de8f23de5c72a754d4fce07a37df844f6872057 |
#
# @file TestSBMLDocument.py
# @brief SBMLDocument unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file loca... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestSBMLDocument.py | Python | bsd-3-clause | 6,600 | [
"VisIt"
] | 9137d97644ee6869a27ad4b859f6c84753bd1083899535be69ad0d77b6fce0d5 |
#!/usr/bin/env python2.7
#
# Copyright (C) 2014 INRA
#
# 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 later version.
#
# This program ... | frederic-mahe/FROGS | tools/biom_to_stdBiom.py | Python | gpl-3.0 | 4,985 | [
"BLAST"
] | 53d985c6b41bbcead3e3c385389ae2f00bab521208d17d5b4b4b6db84b544cac |
"""Collection of common words"""
COMMON_WORDS_EN = """
I
a
able
about
above
act
add
afraid
after
again
against
age
ago
agree
air
all
allow
also
always
am
among
an
and
anger
animal
answer
any
appear
apple
are
area
arm
arrange
arrive
art
as
ask
at
atom
baby
back
bad
ball
band
bank
bar
base
basic
bat
be
bear
beat
beauty
... | patrickshuff/artofmemory | artofmemory/data/words.py | Python | mit | 5,904 | [
"VisIt"
] | 8c7e7b91a8fa59ca59edb79a20abd2165a64f9ba1c37ecc72cdbce1c084ff0e0 |
from django.shortcuts import render
from rango.models import Category, Page
from rango.forms import CategoryForm, PageForm, UserForm, UserProfileForm
from django.contrib.auth import authenticate, login
from django.http import HttpResponseRedirect, HttpResponse
from django.contrib.auth.decorators import login_required
f... | douglasbgatti/rango-tutorial | tango_with_django_project/rango/views.py | Python | apache-2.0 | 10,270 | [
"VisIt"
] | 3ff61f140dd3bf094db5063b4609cb2ddfb7a3b4436a48314e324742b5f42c36 |
"""Function-like objects creating cubic lattices (SC, FCC, BCC and Diamond).
The following lattice creators are defined:
SimpleCubic
FaceCenteredCubic
BodyCenteredCubic
Diamond
"""
from ase.lattice.bravais import Bravais
import numpy as np
from ase.data import reference_states as _refstate
class Simp... | slabanja/ase | ase/lattice/cubic.py | Python | gpl-2.0 | 4,465 | [
"ASE",
"CRYSTAL"
] | 4b40b704b6406a60bd6be4be5c42310765d0d85c9818299ea2de5db06f2e0460 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os.path
class Jmol(Package):
"""Jmol: an open-source Java viewer for chemical structures ... | iulian787/spack | var/spack/repos/builtin/packages/jmol/package.py | Python | lgpl-2.1 | 1,537 | [
"Jmol"
] | 63dd7e77b072c8383ef2aa98d353691b7e09279be625cb931e5151f91333ee04 |
""" Frontend to MySQL DB AccountingDB
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
import datetime
import time
import threading
import random
from DIRAC.Core.Base.DB import DB
from DIRAC import S_OK, S_ERROR, gConfig
fr... | yujikato/DIRAC | src/DIRAC/AccountingSystem/DB/AccountingDB.py | Python | gpl-3.0 | 66,662 | [
"DIRAC"
] | 430a3fe7b771e57159bebd7a58e3f78bc38300e40fd29fc045d12a4865420059 |
# $HeadURL$
__RCSID__ = "$Id$"
""" This module contains three classes associated to Replicas.
The Replica class contains simply three member elements: SE, PFN and Status and provides access methods for each (inluding type checking).
The CatalogReplica class inherits the Replica class.
The PhysicalReplica... | avedaee/DIRAC | DataManagementSystem/Client/ReplicaContainers.py | Python | gpl-3.0 | 4,513 | [
"DIRAC"
] | 4d5aa630d5ab340cbe5cf37290700f6b2fcba47b4af9566b3855ffb58b7c3780 |
#!/usr/bin/env python
# This program creates a squid axon model along with tables to pull data
import sys
from math import *
# The PYTHONPATH should contain the location of moose.py and _moose.so
# files. Putting ".." with the assumption that moose.py and _moose.so
# has been generated in ${MOOSE_SOURCE_DIRECTORY}/py... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/squid/squidModel.py | Python | lgpl-2.1 | 12,792 | [
"MOOSE"
] | f0bb719af177d06deae216fc899260add547f36df8da700959d64b9cec7c26dd |
from __future__ import division
import numpy as np
from pybasicbayes.abstractions import Model, ModelGibbsSampling, \
ModelEM, ModelMeanField, ModelMeanFieldSVI
from states import LDSStates
# TODO make separate versions for stationary, nonstationary,
# nonstationary-and-distinct-for-each-sequence
# NOTE: dynami... | mackelab/pyLDS_dev | pylds/models.py | Python | bsd-3-clause | 12,575 | [
"Gaussian"
] | f355e93a2bd04bc302607c334237b5e356ef892b8cc3536bf723cac8807f96ba |
import os
import sys
import vtkAll as vtk
import math
import time
import types
import functools
import numpy as np
from ddapp import transformUtils
from ddapp import lcmUtils
from ddapp.timercallback import TimerCallback
from ddapp.asynctaskqueue import AsyncTaskQueue
from ddapp import objectmodel as om
from ddapp imp... | gizatt/director | src/python/ddapp/tasks/taskuserpanel.py | Python | bsd-3-clause | 10,807 | [
"VTK"
] | 5f50ea3da97e78799adeaa1577ccdeaae9c118a6cf4731c352aa5612212486cf |
import numpy as np
from scipy import optimize
def gaussian(x, mu, sig):
return np.exp(-np.power(x - mu, 2.) / (2 * np.power(sig, 2.)))
def createModel(X, mu, sig, scale):
model = np.zeros_like(X)
for i, x in enumerate(X):
model[i] = gaussian(x, mu, sig) * scale
return model
class Peak(object):
"""
A distri... | TGAC/KAT | scripts/kat/peak.py | Python | gpl-3.0 | 5,237 | [
"Gaussian"
] | 29c4ca35c1e41317d98017a357064961c02cbaa4140708edd404383eedf3c833 |
#
# solution_transformers.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your op... | kperun/nestml | pynestml/solver/solution_transformers.py | Python | gpl-2.0 | 9,250 | [
"NEURON"
] | 71e983a106323987ccbe8e9ec37eb3d2d63c82786aa6df334af7b980fe206ed6 |
#PPM from RC transmitters Calibrate Version 2.0
#
#PPMRC - PPM interpreter, calibrator and remapper
#Copyright (C) 2017 Francesco Antonetti Lamorgese Passeri
#https://github.com/antlampas/ppmrc
#
#This program is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License... | antlampas/ppmrc | Example/FlightGear/Windows/ppmrc.py | Python | gpl-3.0 | 10,721 | [
"VisIt"
] | e9acc40fb29c8b2e1993b3df009a410132962bb4d80f740250035b4d3d4f27f8 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy,... | alexholcombe/dot-jump | dataRaw/test_dot-jump10Feb2017_09-55.py | Python | gpl-3.0 | 28,959 | [
"Gaussian"
] | b0dd9f6a3d9575591581748f7c8be65c4f961e9d3c476dd5f72d1e6dce36710e |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""This module defines a ``KPoint`` class and the derived ``GlobalKPoint``."""
import numpy as np
from gpaw.fd_operators import Gradient
from gpaw.utilities.blas import axpy
from gpaw import extra_parameters
class KPoint... | qsnake/gpaw | gpaw/kpoint.py | Python | gpl-3.0 | 4,987 | [
"GPAW"
] | 6dae73e679be67a9a8d8e922e25ab3e4871488297025bf535f56cc8f1accc9bb |
#!/usr/bin/env python
import sys
import os
import math
# ensure that the kicad-footprint-generator directory is available
#sys.path.append(os.environ.get('KIFOOTPRINTGENERATOR')) # enable package import from parent directory
#sys.path.append("D:\hardware\KiCAD\kicad-footprint-generator") # enable package im... | SchrodingersGat/kicad-footprint-generator | scripts/Crystals_Resonators_THT/make_crystal.py | Python | gpl-3.0 | 30,096 | [
"CRYSTAL"
] | 9e8c68508f69b77207062e6c9d4f225f5e674185c0833947b7817da8d9d606ba |
# examples/api/06_casscf-dft-guess.py
"""Example of a CASSCF computation on singlet methylene starting from triplet UB3LYP orbitals (from psi4)"""
import psi4
import forte
psi4.geometry("""
0 3
C
H 1 1.085
H 1 1.085 2 135.5
""")
psi4.set_options({'basis': 'DZ', 'scf_type': 'pk', 'e_convergence': 12, 'reference': 'uk... | evangelistalab/forte | examples/api/06_casscf-dft-guess.py | Python | lgpl-3.0 | 865 | [
"Psi4"
] | 971bd85bacddd43e1c973e6490d7d7e37c088a83b27b492cef29710697990700 |
# Copyright (c) 2016 Universidade Federal Fluminense (UFF)
# Copyright (c) 2016 Polytechnic Institute of New York University.
# This file is part of noWorkflow.
# Please, consult the license terms in the LICENSE file.
"""Definition provenance collector. Handle multiple files/visitors"""
from __future__ import (absolute... | gems-uff/noworkflow | capture/noworkflow/now/collection/prov_definition/definition.py | Python | mit | 4,602 | [
"VisIt"
] | 4b5872b0925d825dd0a8d0c19636cf654a98afb5a5c18dd983a6c15113a6e54d |
# Copyright (c) 2015-2018, 2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2016 Derek Gustafson <degustaf@gmail.com>
# Copyright (c) 2019-2021 Pierre Sassoulas <pierre.sassoulas@gmail.com>
# Copyright (c) 2019 Ashley Whetter <ashley@awhetter.co.uk>
# Copyright (c) 2020 hippo91 <guillaume.peillex@gmail.com>
# ... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/pylint/tests/unittest_pyreverse_inspector.py | Python | mit | 4,082 | [
"VisIt"
] | 9f29f6b8f881041d43235c498a171886b105bc4e84f9ef5168d7f0b58f7b6158 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | swails/mdtraj | mdtraj/formats/openmmxml.py | Python | lgpl-2.1 | 2,832 | [
"MDTraj",
"OpenMM"
] | d4e219d1251e8168875f49db7dd0172e78ecfa92a53548b411f136fad4eafae9 |
#!/usr/bin/env python
import os.path
import sys
import urllib2
from optparse import OptionParser
# check if the pymol module is installed
try :
import pymol
except :
sys.exit( "error : This script needs 'pymol' module. Please install PyMOL before running." )
# import other modules
import pym
import pyca
de... | nishn/pymol-script | pypdb.py | Python | mit | 1,987 | [
"PyMOL"
] | cdb2a4f67062f21b8634894e0d38c260c700a3e17eb2ffa8074d5556417fc821 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | decause/decauseblog | conf.py | Python | agpl-3.0 | 37,820 | [
"VisIt"
] | ac218edcd526bf92b3dab5840e0d0998dbe68e467557c2c6e82fc1dc085e8385 |
import os,shutil
import plmd.defaultConfig
class PLMD_module:
# Shows the user some text and prompts him to accept it to continue script
def confirmProgress(self):
# Let user review results
var = raw_input("Please review above and confirm with any key press. Press 'n' to disco... | MathiasGruber/plmd | src/plmd/__init__.py | Python | gpl-2.0 | 5,959 | [
"ADF",
"Amber"
] | caafdcf55c4e36b3adcc52bebcdbdaff48374f846d22f55ef21e70936d62cca7 |
#!/usr/bin/env python3
# @file: emotrans.py
# @auth: Sprax Lines
# @date: 2017-06-14 02:20:56 Wed 14 Jun
# -*- coding: utf-8 -*-
#
# # # coding: iso-8859-15
'''
TODO: Add the set of all synonyms to emo_words
TODO: Divide EmoTrans parent class TransEmo which holds a TxtEmo(En) and an
EmoTxt(En).
Keep TxtEmo as... | sprax/python | emo/emotrans.py | Python | lgpl-3.0 | 53,944 | [
"Octopus"
] | cb2e8e366185f2ee145f39bcdefa2d49bb0242a1680da0418c96e44fc157a6fb |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import os
... | adykstra/mne-python | mne/channels/channels.py | Python | bsd-3-clause | 52,814 | [
"Mayavi"
] | 2d443d089241c8572bb01571fb128fa0bfffb8547af4f1708b41ff16ac7456d9 |
from django.utils import timezone
from misago.sessions import CrawlerSession, HumanSession
class SessionMiddleware(object):
def process_request(self, request):
try:
if request.user.is_crawler():
# Crawler Session
request.session = CrawlerSession(request)
... | Maronato/aosalunos | misago/middleware/session.py | Python | gpl-2.0 | 1,115 | [
"VisIt"
] | e0ac1f93387828b8daffaf2edf7b91cbed8f814f1f5783308f6a6a152902e26d |
"""Python script to manage OI imaging input files."""
import argparse
import sys
import os.path
from astropy.io import fits
from imageoi import __version__
from imageoi.imagingfile import ImagingFile, INIT_IMG_NAME, PRIOR_IMG_NAME
from imageoi.initimage import GreyImg
def create(args):
"""Create image reconstr... | jsy1001/OI-Interface-Tools | imageoi/tool/__main__.py | Python | gpl-2.0 | 7,611 | [
"DIRAC",
"Gaussian"
] | e85b8d51cb191d150ebd6b529125b0bbf15dbbb3a67a181b70fb77c3c0f15966 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Rowland circle geometry
==========================
Units here:
angular [deg]
spatial [mm]
energy [eV]
Table of variables and conventions
| description | here | XRT | RT4XES | SHADOW3 |
|------------------------+---------+--------+---------+-----... | maurov/xraysloth | sloth/inst/rowland.py | Python | bsd-3-clause | 31,784 | [
"CRYSTAL"
] | e5313d5e3b449d65758d104c3c91a8d2830d70633e789a39a8bc4367a8325973 |
# -*- coding: utf-8 -*-
# Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., Universit... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_CCompartment.py | Python | artistic-2.0 | 2,096 | [
"COPASI"
] | 1490aa3f99090a8f5cbf4adddfddbfbba777af8b71ae4d5b428c367a3c2ae143 |
#!/usr/bin/env python
"""
Get rid of lines containing duplicate copies of the same atom in the "Atoms"
section of a LAMMPS data file. Duplicate lines which occur later are
preserved and the earlier lines are erased.
The file is read from sys.stdin. This program does not parse the entire
data file. T... | SGenheden/lammps | tools/moltemplate/src/remove_duplicate_atoms.py | Python | gpl-2.0 | 1,277 | [
"LAMMPS"
] | b283feb3cb548e731a9549851178ffba6c11b33caef4d075eb8f6bf2552512dd |
from io import BytesIO
from threading import Lock
import contextlib
import itertools
import os.path
import pickle
import shutil
import tempfile
import unittest
import sys
import numpy as np
import pandas as pd
import xray
from xray import Dataset, open_dataset, open_mfdataset, backends, save_mfdataset
from xray.backe... | hetland/xray | xray/test/test_backends.py | Python | apache-2.0 | 34,197 | [
"NetCDF"
] | 18d22c1be2a51a7e7facdcbca9c7ac96edd53d8403f3b7c5a764e15ad278bd71 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Mathematical models."""
import numpy as np
from astropy import units as u
from astropy.units import Quantity, UnitsError
from astropy.utils.decorators import deprecated
from .core import (Fittable1DModel, Fittable2DModel,
ModelDefi... | MSeifert04/astropy | astropy/modeling/functional_models.py | Python | bsd-3-clause | 79,385 | [
"DIRAC",
"Gaussian"
] | 954a527255fe5643822fa717d8cb1f2f16b5d6199fc1fff2938b2838220e0f5b |
import urllib.request, urllib.parse, urllib.error
import re
from bs4 import BeautifulSoup
import requests
import click
from tvoverlord.config import Config
class Provider (object):
provider_urls = [
'http://thepiratebay.se',
'http://thepiratebay.org',
]
name = 'The Pirate Bay'
shor... | 8cylinder/tv-overlord | tvoverlord/search_providers/thepiratebay_sx.py | Python | gpl-3.0 | 4,050 | [
"ADF"
] | c34a6b6c431b7734e1b7f8424b57fffcbd86ab6774cd493ce44c5cee3d5b2622 |
#!/usr/bin/env python
# readgeom reads bed elevation and ice thickness from BEDMAP2 files
# and either shows as figures or writes into NetCDF file
# edit these:
BM2PATH = '/home/ed/Desktop/bedmap2_bin/'
showgeom = False
import numpy as np
import numpy.ma as ma
import matplotlib.pyplot as plt
import sys... | talbrecht/pism_pik06 | examples/bedmap2/readgeom.py | Python | gpl-3.0 | 2,609 | [
"NetCDF"
] | 9a9fa7285ef05dbb9455f65b44fba03c0c73208b31635a1f66d5360d48e21c4d |
"""
Author: Remi Lafage <remi.lafage@onera.fr>
This package is distributed under New BSD license.
"""
import matplotlib
matplotlib.use("Agg")
import unittest
import numpy as np
from sys import argv
from smt.applications import MOE, MOESurrogateModel
from smt.utils.sm_test_case import SMTestCase
from smt.problems i... | relf/smt | smt/applications/tests/test_moe.py | Python | bsd-3-clause | 15,061 | [
"MOE"
] | 400f948fc858a0c06990ac4e842c72478e9fa22219f84ad37c5978ba9c8ce591 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Li... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/version.py | Python | gpl-2.0 | 8,910 | [
"VisIt"
] | bcbc8de9fddec8a0017ad44e1cb3fd9bd6e0825321890bff89409f192956c0de |
from __future__ import print_function, division
import textwrap
import numpy as np
from ..utils import listify, angstrom_to_bohr, header_line
from ..core.writable import Writable
from .sorting import input_variable_blocks
from .variable import InputVariable
from .structures import structure_to_abivars
__all__ = ['Abi... | trangel/OPTpy | OPTpy/io/abinitinput.py | Python | gpl-3.0 | 8,587 | [
"ABINIT",
"pymatgen"
] | e2826fbaebc335b1b98d407bfb39ab7e51cd5ad2041a783a03b5be8e5bf72247 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | davidzchen/tensorflow | tensorflow/python/autograph/pyct/ast_util.py | Python | apache-2.0 | 10,374 | [
"VisIt"
] | f3a81fb50a14015af7384ed1f3ea23f63271c6bac220cf97f4cf2cceeece0572 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_trafficcloneprofile.py | Python | bsd-3-clause | 4,001 | [
"VisIt"
] | ca057b053ef65408dbc89030eaa1b33bdac286aa60e3c1dd1aa8a35764ecd744 |
# -*- coding: utf-8 -*-
"""
============================================
4D Neuroimaging/BTi phantom dataset tutorial
============================================
Here we read 4DBTi epochs data obtained with a spherical phantom
using four different dipole locations. For each condition we
compute evoked data and comput... | adykstra/mne-python | tutorials/sample-datasets/plot_phantom_4DBTi.py | Python | bsd-3-clause | 2,537 | [
"Mayavi"
] | d543d3ee5cd65870a727d67461f31e6610869cb5fff81bb275f53b9275b7ff62 |
from __future__ import print_function, division
from sympy.core import S, sympify, Dummy, Mod
from sympy.core.function import Function, ArgumentIndexError
from sympy.core.logic import fuzzy_and
from sympy.core.numbers import Integer, pi
from sympy.core.relational import Eq
from sympy.ntheory import sieve
from math i... | oliverlee/sympy | sympy/functions/combinatorial/factorials.py | Python | bsd-3-clause | 27,507 | [
"VisIt"
] | b6fae16c3aee4c49c25fa6f5c2cd2ba18bb8511c1191d8d64baaf1395561ffef |
# Lint as: python3
# 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 ... | tensorflow/docs | tools/tensorflow_docs/api_generator/traverse.py | Python | apache-2.0 | 6,806 | [
"VisIt"
] | c5404345b3c5424ba7d1e376989fd90b8158347e29b50bcd58c57db4c91f9637 |
# Copyright (c) 2015, James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ...util.linalg import pdinv
from .posterior import Posterior
from . import LatentFunctionInference
log_2_pi = np.log(2*np.pi)
class VarGauss(LatentFunctionInference):
"""
The Variational Gaus... | ptonner/GPy | GPy/inference/latent_function_inference/var_gauss.py | Python | bsd-3-clause | 2,641 | [
"Gaussian"
] | 3e9c1eed1d28865bb32ff548e0692edb3b122a0d9c1272f012af9c3a9b9ddc52 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# HiPart is a program to analyze the electronic structure of molecules with
# fuzzy-atom partitioning methods.
# Copyright (C) 2007 - 2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>
#
# This file is part of HiPart.
#
# HiPart is free software; you can redistribute it and/... | molmod/hipart | hipart/atomdb.py | Python | gpl-3.0 | 14,589 | [
"Gaussian"
] | f3d8d1f6d7be55389c20d7b45229149c85a00f7e61ae10c2caa3f850221a19b4 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/test_log.py | Python | gpl-2.0 | 7,911 | [
"MDAnalysis"
] | a63f722da3def27ae8c760169b2d949d5f67ec70a34d6af16055ee77a085c90b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from distutils.core import setup
from distutils.command.install_egg_info import install_egg_info
from distutils.versionpredicate import VersionPredicate
from distutils.command.build import build
import sys
class nohup_egg_info(install_egg_info):
def run(self):
... | C3BI-pasteur-fr/taxo_pack | setup.py | Python | gpl-3.0 | 2,603 | [
"BLAST"
] | a46f10f9eed03a42bfab962c102adbf061347a093f3cf608d94aff26f61ae69d |
from numpy.testing import *
from numpy import random
import numpy as np
class TestRegression(TestCase):
def test_VonMises_range(self):
"""Make sure generated random variables are in [-pi, pi].
Regression test for ticket #986.
"""
for mu in np.linspace(-7., 7., 5):
r = ... | teoliphant/numpy-refactor | numpy/random/tests/test_random.py | Python | bsd-3-clause | 6,174 | [
"Gaussian"
] | 6c40a3980755f437729f885dc78335d3c5231c2ad8f780c96774df8d665e45a7 |
"""An NNTP client class based on RFC 977: Network News Transfer Protocol.
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print 'Group', name, 'has', count, 'articles, range', first, 'to', last
Group comp.lang.python has 51 articl... | deanhiller/databus | webapp/play1.3.x/python/Lib/nntplib.py | Python | mpl-2.0 | 21,824 | [
"Brian"
] | b028b2098928f453bf9356b3fcd49ebdf96ce6969ee5c5d71a724c96405b90e3 |
#
# A file that opens the neuroConstruct project LarkumEtAl2009 and run multiple simulations stimulating random terminal branches with variable number od synapses and variable rate/delay in order to determine the P(NMDAs)
#
# Author: Matteo Farinella
from sys import *
from java.io import File
from java.lang... | pgleeson/TestArea | models/LarkumEtAl2009/pythonScripts/PNMDAs_randombranches5ms.py | Python | gpl-2.0 | 22,616 | [
"NEURON"
] | d05402ea5315dfb1d0d34a8f2578395a05e853c7b10787fe1bde322247e69498 |
"""Test the Elk-M1 Control config flow."""
from unittest.mock import MagicMock, patch
from homeassistant import config_entries
from homeassistant.components.elkm1.const import DOMAIN
def mock_elk(invalid_auth=None, sync_complete=None):
"""Mock m1lib Elk."""
def handler_callbacks(type_, callback):
n... | jawilson/home-assistant | tests/components/elkm1/test_config_flow.py | Python | apache-2.0 | 11,319 | [
"Elk"
] | 60dce0812649eb2218fa0f47a98cd5e6adcc295d5466ea1725c7df6be4bb509d |
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.adsorption import *
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen import Structure, Lattice, Molecule
from pymatgen.util.coord import in_coord_list
test_dir = os.path.join(os.path.dirname(__file__), "..", "... | gVallverdu/pymatgen | pymatgen/analysis/tests/test_adsorption.py | Python | mit | 9,079 | [
"pymatgen"
] | dc394b6892357a37798deb4c382c3c5bfa98475a6779321cffc4d3d4cb4f9a68 |
# Author: Brian M. Clapper, G Varoquaux
# License: BSD
import numpy as np
# XXX we should be testing the public API here
from sklearn.utils.linear_assignment_ import _hungarian
def test_hungarian():
matrices = [
# Square
([[400, 150, 400],
[400, 450, 600],
[300, 225, 300]],
... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/utils/tests/test_linear_assignment.py | Python | mit | 1,349 | [
"Brian"
] | f0e585b8726388e35318a2088ff5bb33549f9ae74edb616b3943599e0011cfff |
'''
Nacker is a tool to circumvent 802.1x Network Access Control (NAC) on
a wired LAN.
Copyright (C) 2013 Carsten Maartmann-Moe
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 t... | mehulsbhatt/nacker | caravan/chassis.py | Python | gpl-2.0 | 2,998 | [
"MOE"
] | 35b43fbee7d053881b53cacf3db5e900547b104879c9bbadcde2378216c88576 |
# Copyright (c) 2015-2016 Cisco Systems
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publ... | rjfellman/molecule | molecule/ansible_playbook.py | Python | mit | 5,530 | [
"Galaxy"
] | 7641cb424ac1b49f8879123d409073c96393b45be13a70d21bbc5c28a894814e |
# -*- coding: utf-8 -*-
#
# brunel_alpha_numpy.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 Lice... | kristoforcarlson/nest-simulator-fork | pynest/examples/brunel_alpha_numpy.py | Python | gpl-2.0 | 11,564 | [
"NEURON"
] | 147330de8bba23f95ba51ffcae9483fdcb44abd2a8e92c1da8932f0d9e21c95c |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
from types import ListType
from PDBExceptions import PDBException
__doc__="Selection of ... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PDB/Selection.py | Python | apache-2.0 | 2,413 | [
"Biopython"
] | 59dbbe9205aa964ca2de5c91cc233ee1b4f982eb01ee0bbe661054cbdf0683aa |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# ePuck.py
#
# Copyright 2010 Manuel Martín Ortiz <mmartinortiz@gmail.com>
#
# 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; eit... | verlab-ros-pkg/epuck_driver | src/epuck/ePuck.py | Python | gpl-2.0 | 30,177 | [
"VisIt"
] | fcfcfaea366a994027d3226551ac9a93f3991f1adfab70ca26fb1c39b01e3128 |
#!/usr/bin/env python
import socket
from json import dumps
import string
from random import choice
from ssl import wrap_socket
from sys import exit, exc_info
from random import random
import logging
import time
import threading
import traceback
import struct
import os
import ctypes
import datetime
version = "0.9"
de... | bwall/ircsnapshot | ircsnapshot/ircsnapshot.py | Python | mit | 24,100 | [
"Brian"
] | b08d9efe1af7e18e1410b9dfa807791828981f386b7fa7b2fc039bdeec584bf8 |
# -*- coding: utf-8 -*-
# vim: tabstop=4 shiftwidth=4 softtabstop=4
#
# Copyright (C) 2012-2017 GEM Foundation
#
# OpenQuake 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, either version 3 of the Licen... | gem/oq-hazardlib | openquake/hazardlib/gsim/chiou_youngs_2008.py | Python | agpl-3.0 | 14,611 | [
"Brian"
] | 94025e20a1139ef212c3e7e86fdddc93c3c5abf57d8e4a62cae8e92656812471 |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | dnjohnstone/hyperspy | hyperspy/io_plugins/__init__.py | Python | gpl-3.0 | 2,141 | [
"NetCDF"
] | 11ca24cde0db180d70c2486d3998e7413b4078d58745d73549e520c61e88b6a8 |
import gen_utils
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
class imageGreyErode(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_mana... | nagyistoce/devide | modules/filters/imageGreyErode.py | Python | bsd-3-clause | 2,191 | [
"VTK"
] | 8ab765e34202ba0a393faf341ff76153418528743c7f64b05cdfb4c5dab7a05e |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-deploy-scripts
# Author : Adria Casajus
########################################################################
"""
Deploy all scripts and extensions
"""
__RCSID__ = "$Id$"
import os
import shut... | Sbalbp/DIRAC | Core/scripts/dirac-deploy-scripts.py | Python | gpl-3.0 | 6,009 | [
"DIRAC"
] | ab966454ef2756e3ee4852a3a8130cd8af06bfd0ec88c554df4744a4e5d6ac95 |
import types
import select
import time
import socket
try:
import multiprocessing
except:
multiprocessing = False
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.private.Service import Service
from DIRAC.Core.DISET.private.GatewayService import GatewayService
from DIRAC.Core.DISET.RequestHandler im... | avedaee/DIRAC | Core/DISET/ServiceReactor.py | Python | gpl-3.0 | 7,469 | [
"DIRAC"
] | b62c03c1756bb11ae38d4f9f8d88409af12a7f150653fc62c89da11c79cc218b |
#!/usr/bin/env python3
# ver 0.1 - copy from rdf_itf.py (v0.1) and modify codes on 3/28/2018
import argparse
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='calculation center of mass of polymers you select')
## args
parser.add_argument('-i', '--input',... | jht0664/Utility_python_gromacs | python/com_pol.py | Python | mit | 5,469 | [
"Gromacs",
"MDAnalysis"
] | 3cf9aba4df22e936ce09a335983c92ff826974fa92d19f136f18655431aa7b3a |
##############################################################################
# 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-delayedarray/package.py | Python | lgpl-2.1 | 3,231 | [
"Bioconductor"
] | b842603598c24e036712a933519ebbc5b2d8f296365e0bb78bdefea769711dd5 |
from Cython.Compiler.Visitor import VisitorTransform, CythonTransform
from Cython.Compiler.ModuleNode import ModuleNode
from Cython.Compiler.Nodes import *
from Cython.Compiler.ExprNodes import *
class ExtractPxdCode(VisitorTransform):
"""
Finds nodes in a pxd file that should generate code, and
returns th... | hpfem/cython | Cython/Compiler/CodeGeneration.py | Python | apache-2.0 | 1,193 | [
"VisIt"
] | 81377fd7e62cd66d3e60898579dafee3a3e83691421cfc42d6effe851033cde4 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for LibraryContent block in LMS
"""
import textwrap
import ddt
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.fixtures.library import LibraryFixture
from common.test.acceptance.pages.common.auto_auth import A... | ahmedaljazzar/edx-platform | common/test/acceptance/tests/lms/test_library.py | Python | agpl-3.0 | 13,856 | [
"VisIt"
] | 2a93815edb51de6e3989a07545f4e04b1ac0760ca24190f155f30a0b1686f621 |
"""Setup script for Bokeh."""
#-----------------------------------------------------------------------------
# Copyright (c) 2012 - 2014, Continuum Analytics, Inc. All rights reserved.
#
# Powered by the Bokeh Development Team.
#
# The full license is in the file LICENCE.txt, distributed with this software.
#---------... | srinathv/bokeh | setup.py | Python | bsd-3-clause | 19,863 | [
"GULP"
] | debcb4d139fe910b99888f32e0d2f734dc91bb0cfde0e94ed9ce895d25b21301 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkKdTreeSelector(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | nagyistoce/devide | modules/vtk_basic/vtkKdTreeSelector.py | Python | bsd-3-clause | 490 | [
"VTK"
] | 176d8f62803f01da0ebd4bec997c79d5dfec8a87fc63cd19b8023a4a45d275b4 |
from template import Template
from template.document import Document
from template.test import TestCase, main
# Define a dummy object for runtime processing
class DummyContext:
def visit(self, *args):
pass
def leave(self, *args):
pass
class DocumentTest(TestCase):
def testDocument(self):
# Create... | aifeiasdf/Template-tookit | t/document_test.py | Python | artistic-2.0 | 2,779 | [
"VisIt"
] | 25d78e3f7653ab88d18cedb0a093498037aefb55bcb9a85d581acd5d0cf6301f |
"""
@created_at 2014-07-19
@author Exequiel Fuentes <efulet@gmail.com>
@author Brian Keith <briankeithn@gmail.com>
"""
# Se recomienda seguir los siguientes estandares:
# 1. Para codificacion: PEP 8 - Style Guide for Python Code (http://legacy.python.org/dev/peps/pep-0008/)
# 2. Para documentacion: PEP 257 - Docst... | efulet/pca | pca/lib/pca_lda.py | Python | mit | 6,111 | [
"Brian"
] | 8ba0baa5dd8ff6f43983e265bec2bbebae70012a66ef0e8246e7e078fbafc8b2 |
# -*- coding: utf-8 -*-
"""Functions to make 3D plots with M/EEG data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Maina... | adykstra/mne-python | mne/viz/_3d.py | Python | bsd-3-clause | 114,181 | [
"Mayavi"
] | fda264014992da2e1a213a410d8e40a490a0c70daeed231ef92ffedf5b700787 |
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
# create planes
# Create the RenderWindow, Renderer
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer( ren )
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
pl3d = vtk.vtkMulti... | ashray/VTK-EVM | Filters/Core/Testing/Python/streamSurface.py | Python | bsd-3-clause | 2,054 | [
"VTK"
] | 8c4aa35dfc9c6bdf8014e44cbc45146fa9c3e3c06a2af2c33028e194847e09af |
import ast
import codecs
import os
from setuptools import setup, find_packages
class VersionFinder(ast.NodeVisitor):
def __init__(self):
self.version = None
def visit_Assign(self, node):
if getattr(node.targets[0], 'id', None) == '__version__':
self.version = node.value.s
def r... | d0ugal-archive/home | setup.py | Python | bsd-3-clause | 1,896 | [
"VisIt"
] | d64e8f3e6f1f603eab57234f266460ee519718f235a4e0c02c0e400b804d75a0 |
"""unit testing code for 3D stuff
"""
from rdkit import RDConfig
import unittest, os
import sys
import random
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import TorsionFingerprints
class TestCase(unittest.TestCase):
def testConformerRMS(self):
m1 = Chem.MolFromSmiles('CNc(n2)nc(C)cc2... | ptosco/rdkit | rdkit/Chem/UnitTestMol3D.py | Python | bsd-3-clause | 19,733 | [
"RDKit"
] | 288a14c481d95e3ab65246a1bf5792d9ba677e38e465fbfb4715f9ae3872607a |
#==============================================================================
# Copyright (c) 2015, Kitware Inc., Los Alamos National Laboratory
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Wrapping/Python/paraview/cinemaIO/pv_introspect.py | Python | gpl-3.0 | 22,673 | [
"ParaView"
] | d373da73fd7de52919c672302003661513ab5437d3760d43fb858bacf2c89c20 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
#
# Vladimír Slávik 2008
# Python 2.5
#
# for Simutrans
# http://www.simutrans.com
#
# code is public domain
#
# read all dat files in all subfolders
# weed out all except houses
# reformat them and save aside
# WARNING: frontimage is not considered! ONLY backimage!
... | hdomos/pak128 | tools/split-houses-singletile.py | Python | artistic-2.0 | 6,192 | [
"VisIt"
] | 9dd73757a048a5fd795f4de94d515935fa7c51ccbe39cd6eb130628ec3a8a975 |
#!/usr/bin/env python
import pyemma
import numpy as np
import mdtraj
import time
import os
# Source directory
source_directory = '/cbio/jclab/projects/fah/fah-data/munged3/no-solvent/10472' # Abl single
################################################################################
# Load reference topology
#######... | jchodera/MSMs | jchodera/abl-10472/pyemma/cluster.py | Python | gpl-2.0 | 3,306 | [
"MDTraj"
] | d5a1afab5a2d507b2ffdfe4a8d73f7da9f0aa403cc2c892957ef11f578da7992 |
"""Classes and methods for segmenting cells based on cytosolic fluorescence."""
# IMPORT DEPENDENCIES
import os
import sys
import pickle
import time
import pandas as pd
import numpy as np
from skimage import io
from skimage.morphology import watershed
from scipy.ndimage.filters import gaussian_filter, maximum_filter
... | nrweir/pyto_segmenter | CellSegment.py | Python | gpl-3.0 | 26,771 | [
"Gaussian"
] | 9e4900b91bf3ea7d434a14db135b2f7ad69b81885c98ecc231ab2ca9c874e891 |
#!/usr/bin/env python
from __future__ import (absolute_import, division, print_function, unicode_literals)
import os
import sys
DOCS = {
'index.rst':'''.. _v{version}:
===========================
Mantid {version} Release Notes
===========================
.. figure:: ../../images/ImageNotFound.png
:class: scre... | ScreamingUdder/mantid | tools/release_generator/release.py | Python | gpl-3.0 | 9,287 | [
"CRYSTAL"
] | c1b50120f592967831d376f85e0523592472728786fabee157cbab09f21b5e96 |
# 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... | psci2195/espresso-ffans | testsuite/python/observable_cylindrical.py | Python | gpl-3.0 | 9,163 | [
"ESPResSo"
] | b637eccbfee0fbc70b32cd10109f73f3fa45727a768d0137d17d1d0a681a423d |
# Copyright 2020 DeepMind Technologies Limited.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed... | deepmind/ferminet | ferminet/train.py | Python | apache-2.0 | 21,274 | [
"Gaussian",
"PySCF"
] | 0081a94bd67c632e3b1bd4ea06817dc272dc22ab0504cadcb5f4984aee8338f9 |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | testsuite/python/virtual_sites_relative.py | Python | gpl-3.0 | 14,732 | [
"ESPResSo"
] | e7a5b1d5cbdefa49ac23864f0bdfd12078f9d9941c0e8dfe6f3a9982e1d4c115 |
import requests
import h2o
import h2o_test_utils
from h2o_test_utils import ModelSpec
from h2o_test_utils import GridSpec
def build_and_test(a_node, pp, datasets, algos, algo_additional_default_params):
####################################################################################################
# Bui... | YzPaul3/h2o-3 | py/rest_tests/test_models.py | Python | apache-2.0 | 17,071 | [
"Gaussian"
] | cabf3bc5ed4def6942231704d1167739dc97fd250c8f619c08a57ca7fa5e5cac |
import configparser
import hashlib
import os
import platform
import random
import tempfile
from typing import Any, Dict, Optional
# download delegate
__wget__ = ("WGET_PATH",)
__transmission__ = (
"TRANSMISSION_RPC_URL",
"TRANSMISSION_RPC_PORT",
"TRANSMISSION_RPC_USERNAME",
"TRANSMISSION_RPC_PASSWORD",... | BGmi/BGmi | bgmi/config.py | Python | mit | 8,830 | [
"MOE"
] | ae2eeeeb20168b373e9904faa425689218b5ca4d90b8c08d76734b81cb8a3697 |
from __future__ import (absolute_import, division, print_function)
import glob
import io
import os
import sys
from setuptools.dist import Distribution
if sys.version_info < (2, 6):
raise SystemExit("""matplotlib and the basemap toolkit require Python 2.6 or later.""")
# Do not require numpy for just querying the... | guziy/basemap | setup.py | Python | gpl-2.0 | 6,013 | [
"NetCDF"
] | a6315318115dc8aa6837e08f9717c04e60763a505f5404111b04dc00d618982d |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_lammps.py | Python | gpl-2.0 | 23,751 | [
"LAMMPS",
"MDAnalysis"
] | 87e3f68e291e14ccf517eb5f8c2a13ac045c24c66537a125a19bf51151ab7198 |
#!/usr/bin/env python
## category Conversion
## desc Converts to BAM format (unmapped)
'''
Convert FASTQ to BAM. This doesn't perform any mapping, it simply stores the
read sequences in BAM format as unmapped reads. If given two files, the reads
will be correctly flagged as pairs.
'''
import os
import sys
import itert... | ngsutils/ngsutils | ngsutils/fastq/tobam.py | Python | bsd-3-clause | 2,304 | [
"pysam"
] | 16d4bd0a2cbcf702d2e7081afcf6f4eb2d4ab4109b8188f377cb8f863f1c4afe |
import os
import sys
import time
import queue
import shutil
import socket
import struct
import datetime
import threading
import subprocess
import numpy as np
import ujson as json
import multiprocessing as mp
from .util import call_or, maybe_mkdir
TN_MODEL_JSON_NAME = 'model.json'
TN_MODEL_TNBM_NAME = 'model.tnbm'
TN... | vmonaco/pytruenorth | pytruenorth/truenorth.py | Python | bsd-3-clause | 22,893 | [
"NEURON"
] | 0e83aa4c2abf3e635d33eb29abfac70afbea3e9aefca5632fa1cc064abf60cfd |
import logging
from dirac.lib.base import *
import dirac.lib.credentials as credentials
from DIRAC import S_OK, S_ERROR,gLogger
from DIRAC.WorkloadManagementSystem.Client.SandboxStoreClient import SandboxStoreClient
log = logging.getLogger(__name__)
class JobadministratorController(BaseController):
def getSandbox(... | DIRACGrid/DIRACWeb | dirac/controllers/jobs/JobAdministrator.py | Python | gpl-3.0 | 1,404 | [
"DIRAC"
] | cc05d2e777aa032635ca2e7f57a994e0617dc4966106bbb58ac65d757c461430 |
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