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from galaxy.model import Tag
import re
from sqlalchemy.sql.expression import func, and_
from sqlalchemy.sql import select
from galaxy.model import History, HistoryTagAssociation, Dataset, DatasetTagAssociation, \
HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation, Page, PageTagAssociation
class Tag... | volpino/Yeps-EURAC | lib/galaxy/tags/tag_handler.py | Python | mit | 11,248 | [
"Galaxy"
] | 3b799a80dcc6706394629808e089eff31ef13ab0e690aa97ebc4189300ea8841 |
"""
Adapted from Enis Afgan's mi-deployment code:
https://bitbucket.org/afgane/mi-deployment
"""
import os
import contextlib
from fabric.api import sudo, cd, settings, hide
from fabric.colors import red
from cloudbio.custom.shared import (_write_to_file, _setup_conf_file,
_setup_s... | heuermh/cloudbiolinux | cloudbio/galaxy/__init__.py | Python | mit | 25,453 | [
"Galaxy"
] | ec272518fd87d67b007e90d47994c75f550d3fe193b3b7cb4e8cca754ba9bcf1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A Metropolis-Hastings and Gibbs samplers for a state-ful model.
"""
import numpy as np
from emcee import autocorr
from emcee.sampler import Sampler
import logging
import h5py
from Starfish import constants as C
class StateSampler(Sampler):
"""
The most basic ... | BrownDwarf/Starfish | Starfish/samplers.py | Python | bsd-3-clause | 33,782 | [
"Gaussian"
] | 815d51e45bbb1e7124250ba4a65dfb978d0843cbe5c1e34ff0b33086cb936b97 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | CDSherrill/psi4 | psi4/share/psi4/databases/HBC6.py | Python | lgpl-3.0 | 161,641 | [
"Psi4"
] | 71992ff5194c4f68e31a67668fa39f9ede6fe71987bbb8071a384aaa767e5a57 |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 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 y... | jat255/hyperspy | hyperspy/tests/model/test_model.py | Python | gpl-3.0 | 30,294 | [
"Gaussian"
] | 53c96c702c085c4c14abc1b5d7f360307f396a087e7461f598fe283a5fe280d6 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# this script tests vtkImageResliceToColors with various axes permutations,
# in order to cover a nasty set of "if" statements that check
# the intersections of the raster lin... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/ResliceToColors.py | Python | bsd-3-clause | 5,945 | [
"VTK"
] | d4f6b2ee90e44199c2378c5d9b15a0edcb30a4677290ba20cb95500000728160 |
#!/usr/bin/env python
"""
tide.py
Methods for working tidal forcing files in ROMS
Written by Brian Powell on 04/05/16
Copyright (c)2017 University of Hawaii under the BSD-License.
"""
import numpy as np
import netCDF4
import seapy
import datetime
from warnings import warn
def create_forcing(filename, tide... | dalepartridge/seapy | roms/tide.py | Python | mit | 5,936 | [
"Brian",
"NetCDF"
] | 702d9e7994acb723143df297b1525d319f1ccf676398d815874ed31620aa7bcc |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/mcscf/__init__.py | Python | apache-2.0 | 11,792 | [
"PySCF"
] | 062976834216838863589757d72e9fda13757115321e19d87543f8723cb07c4e |
# Copyright 2014 Roberto Brian Sarrionandia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | sarrionandia/tournatrack | trackurls.py | Python | apache-2.0 | 1,594 | [
"Brian"
] | 71745a4ead9a09507a45ffc6cd68f9e78ae7b27c3257568c4adcaa065481e146 |
#
# Dalton Burke, CU Denver
#
#from utils import ensure_dir, symlink_unless_exists
from __future__ import absolute_import
from __future__ import print_function
from .downloader import download_url, DownloadError, get_dList
from datetime import datetime, timedelta
import os
import os.path as osp
import sys
import log... | openwfm/wrfxpy | src/ingest/retrieve_firms.py | Python | mit | 2,001 | [
"Dalton"
] | b5c6ba71f6f58d9dfdd0dd3cfde223b1e0493cefd22633a865bce305d37b5fd9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from monty.serialization import loadfn, dumpfn
from pymatgen.io.qchem.outputs import QCOutput
from pymatgen.util.testing import PymatgenTest
try:
import openbabel
have_babe... | fraricci/pymatgen | pymatgen/io/qchem/tests/test_outputs.py | Python | mit | 8,699 | [
"pymatgen"
] | 5273d47912b228f3fda7bd0cb7dac47f40e63ad133f3c68e037de13e6e0ce9df |
#!/usr/bin/env python
##############################################################################
#
# This PPXF_POPULATION_GAS_EXAMPLE_SDSS routine shows how to study stellar
# population with the procedure PPXF, which implements the Penalized Pixel-Fitting
# (pPXF) method by Cappellari M., & Emsellem E., 2004, PASP... | zpace/SparsePak-SFH | ppxf_population_gas_example_sdss.py | Python | mit | 12,267 | [
"Galaxy",
"Gaussian"
] | 9114ba401ad4269e5526ebcc1d770426b89bd1e40221c48d4242398b71d8ebc8 |
#!/usr/bin/env python
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--saved_arguments', default='saved_arguments.py',
help='File containing default values of parameters' + \
'(can be overwritten by flags)')
parser.add_argument('--include_ligand', nargs='+', default=None, \
help='O... | gkumar7/AlGDock | Pipeline/run_AlGDock.py | Python | mit | 27,840 | [
"Amber",
"CRYSTAL",
"NAMD"
] | fbe5015a8fd91d6f0bc80b5ceddfad3dfefe36b9560ca321d673dee4e31cd758 |
#!/usr/bin/env python
# This example demonstrates the use of vtkCubeAxesActor2D to indicate
# the position in space that the camera is currently viewing. The
# vtkCubeAxesActor2D draws axes on the bounding box of the data set
# and labels the axes with x-y-z coordinates.
import vtk
from vtk.util.misc import vtkGetDa... | CMUSV-VisTrails/WorkflowRecommendation | examples/vtk_examples/Annotation/cubeAxes.py | Python | bsd-3-clause | 3,797 | [
"VTK"
] | b4f61121c005b6ced6f83e578d9aa153bafe78e27af3909f095bc0087f141a37 |
import numpy as np
from scipy import sqrt, pi, arctan2, cos, sin, exp
from scipy.ndimage import gaussian_filter
import skimage.color
from skimage import img_as_float, draw
def daisy(img, step=4, radius=15, rings=3, histograms=8, orientations=8,
normalization='l1', sigmas=None, ring_radii=None, visualize=Fal... | chintak/scikit-image | skimage/feature/_daisy.py | Python | bsd-3-clause | 9,846 | [
"Gaussian"
] | 4b38de0ff018406b6b2d6544b77b6441e328ce3d3b05c8b365165892f7fe2af6 |
__author__ = 'marleyjaffe'
import sqlite3 as lite
import argparse
import os
import time
import glob
import platform
# Sets Global variables for verbosity and outFile
verbosity = 3
outFile = False
def ParseCommandLine():
"""
Name: ParseCommandLine
Description: Process and Validate the comma... | marleyjaffe/ChromeSyncParser | ChromeParser.py | Python | mit | 31,480 | [
"VisIt"
] | 7f8f8d7f4c29c9bd66f1645da47d2a449381896f48c3629a8c71e79e8b705384 |
# -*- coding: utf-8 -*-
"""
Spyder Editor
This temporary script file is located here:
/Users/htelg/.spyder2/.temp.py
"""
#ToDo
#- ich denke nicht, dass wir neutral nehen muessen .. unserer laser is polarisiert ...
#- indes of refraction at 405 nm for psl
#- results plotten
# Check using http://omlc.ogi.edu/calc/mie_... | hagne/atm-py | atmPy/aerosols/instruments/POPS/mie.py | Python | mit | 51,963 | [
"Gaussian"
] | b72c39c820626a33d89306bf97cee3bf99260c140729456fb21c46f7aca46c97 |
from math import sqrt, pi
import numpy as np
from gpaw.xc.functional import XCFunctional
from gpaw.sphere.lebedev import Y_nL, weight_n
class LDA(XCFunctional):
def __init__(self, kernel):
self.kernel = kernel
XCFunctional.__init__(self, kernel.name)
self.type = kernel.type
def calc... | robwarm/gpaw-symm | gpaw/xc/lda.py | Python | gpl-3.0 | 7,209 | [
"GPAW"
] | 7368e425e72303e689e3d6ef085320455707f1a644d4cc6d7460840d2a82c04c |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | waveFrontSet/box_management | config/urls.py | Python | mit | 1,516 | [
"VisIt"
] | a60b479f5b1a1f009d43d2da8dccb3ab9a1e9ffcb4589efe44eb4a853bec24a7 |
from datetime import datetime
import logging
import shutil
from subprocess import Popen, PIPE
import os
import pandas as pd
import numpy as np
from pandas.errors import EmptyDataError
import re
BLAST_TABLE_COLS = '''
qseqid
stitle
pident
length
mismatch
gapopen
qstart
qend
sstart
send
evalue
bitscore
qlen
slen
sseq
... | peterk87/sistr_cmd | sistr/src/blast_wrapper/__init__.py | Python | apache-2.0 | 11,454 | [
"BLAST"
] | 3035869f1ce577820997bd4d33dbc3699da364191458c5f4c409109477a7539a |
# -*- coding: utf-8 -*-
# This test shows how to properly use metaclass to avoid
# > TypeError: metaclass conflict: the metaclass of a derived class must be
# > a (non-strict) subclass of the metaclasses of all its bases
# error.
import moose
try:
import six
except ImportError:
print("[INFO ] Requires `six`... | BhallaLab/moose-core | tests/core/test_metaclass.py | Python | gpl-3.0 | 1,013 | [
"MOOSE"
] | 053616bee1d0cefa29efe86fa8be02a1c22f03d39c6ef10403cdbcc93f0dba22 |
from setuptools import setup
setup(
name="gerrit",
version="0.0.2",
author="Brian Waldon",
author_email="bcwaldon@gmail.com",
url="https://github.com/bcwaldon/python-gerrit",
description="Client library for interacting with the Gerrit JSONRPC API",
install_requires=['httplib2', 'SQLAlchemy... | bcwaldon/python-gerrit | setup.py | Python | apache-2.0 | 351 | [
"Brian"
] | 6450385da51f0eb8895c6524f17a6d784452ca73bcf3bfc98d2726c594ef38ee |
# -*- coding: utf-8 -*-
#
# test_refractory.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... | tobikausk/nest-simulator | pynest/nest/tests/test_refractory.py | Python | gpl-2.0 | 8,119 | [
"NEURON"
] | 4788d25c6088cc76d86d58ae4bd498a834191e90ef2b777068dbf8a867a774fb |
from __future__ import print_function
import h5py
import sympy
from sympy.utilities.lambdify import lambdastr
import numpy as np
import math
# Read and evaluate orbitals output from Quantum Espresso using pw2qmcpack.x
class PWOrbitalFile(object):
def __init__(self):
self.e, self.de, self.dde = create_ev... | markdewing/qmc_algorithms | Wavefunctions/read_pw.py | Python | mit | 7,918 | [
"Quantum ESPRESSO"
] | 7b1c8ff64952d624b2b4d8e9354e930603985917acde8ae70a96c8e7f1ef6585 |
# -*- coding: utf-8 -*-
import base64
import datetime
import json
import time
import mock
from nose.tools import eq_, ok_
from nose.plugins.attrib import attr
from pyquery import PyQuery as pq
from urlparse import urlparse
from django.conf import settings
from django.contrib.sites.models import Site
from django.core... | whip112/Whip112 | kuma/wiki/tests/test_views.py | Python | mpl-2.0 | 165,771 | [
"VisIt"
] | 401fb1ffcc1bf3b48d8e31649f26763f1e4c068d9644237975ecf0b8d02f25af |
# $Id$
#
# Copyright (C) 2015 Novartis Institute of BioMedical Research
# All Rights Reserved
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above co... | ptosco/rdkit | Code/GraphMol/FilterCatalog/Wrap/rough_test.py | Python | bsd-3-clause | 22,523 | [
"RDKit"
] | 955ddde356db6453641d135b76aac9dddd0d6e3766e57cda5f01ae79fd75df29 |
from django.db import models
class PortalSubject(models.Model):
'''
Base Model. The eHB Subject
'''
ehb_id = models.CharField(max_length=255, primary_key=True)
research_id = models.CharField(max_length=255)
class Meta:
db_table = u'portal_subject'
verbose_name = 'Portal Subjec... | chop-dbhi/brptoolkit-demo-harvest | brp_demo/models.py | Python | bsd-2-clause | 2,460 | [
"VisIt"
] | 1f99362e4622a6c58b2b2c8011f3683f36d215d177eb0033257782fc233687c2 |
from fiber_properties import (scrambling_gain, image_list,
plot_scrambling_gain_input_output,
plot_scrambling_gain, save_plot, show_plots,
load_image_object, FiberImage)
if __name__ == '__main__':
NEW_DATA = False
... | rpetersburg/FiberProperties | scripts/scrambling_gain.py | Python | mit | 2,704 | [
"Gaussian"
] | 463615a82a1900e4d454bab5bd641c96536be7fe8f0c1943d9cb8924a65376ca |
import os
import time
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
import mdtraj.reporters
import sys
platform_name = "CUDA"
timestep = 2.0 * u.femtoseconds
cutoff = 0.95 * u.nanometers
output_frequency = 25000
n_steps = 500000000
temperature = 293.
pressure = 1.0 * u.atmospheres... | hainm/open-forcefield-group | nmr/code/multi_T4.py | Python | gpl-2.0 | 1,722 | [
"MDTraj",
"OpenMM"
] | 069505ed264f007ead9e5dfa7c35e2b13d54fb5da658d16e2d9cbde8b7aabb8d |
# 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/area_codes/resolution/hmm_crossvalidation_area_96.py | Python | mit | 16,227 | [
"Gaussian",
"Mayavi"
] | da537ff0360c11ea43c054439fb766c3eb84236e998668e2e0e1401844111bfc |
import os
from setuptools import setup, find_packages, Extension
ext = Extension('utils', ['umis/utils.pyx'])
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name='umis',
version='1.0.7',
description='Package for estimating UMI counts in Transcri... | vals/umis | setup.py | Python | mit | 861 | [
"pysam"
] | 2bb652f37da23dbf6c4d2f0c8ed8c8011da4e415a76c2e821608642b6168211d |
"""
It is used to load classes from a specific system.
"""
from DIRAC.Core.Utilities.ObjectLoader import loadObjects
| DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/Plotting/ObjectLoader.py | Python | gpl-3.0 | 117 | [
"DIRAC"
] | bf615e807d6d1474c70fd2077b6732bb9597d13ad65c4a2f3d3cd92959cfcab8 |
# Copyright 2003 by Bartek Wilczynski. 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.
"""
Classes for pparsing AlignAce and CompareACE files
"""
from Bio.ParserSupport import *... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/AlignAce/Parser.py | Python | apache-2.0 | 3,148 | [
"Biopython"
] | ed45860e6e4dd1869ac40fcb7fe57bb04b38ca0c0621fa3c4c189f4661689b4f |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/bc/OrthorhombicBC.py | Python | gpl-3.0 | 2,539 | [
"ESPResSo"
] | c4a544fb10b3b2d229aa16c3664a72d00cf15e086194efad2c1bd71e7d1e1f67 |
import numpy as np
from audiolab import play
# output one second of stereo gaussian white noise at 48000 hz
play(0.05 * np.random.randn(2, 48000))
| cournape/audiolab | docs/src/examples/over_play.py | Python | lgpl-2.1 | 148 | [
"Gaussian"
] | 48e005d01f9400c0f973414bd3da7abeafc90788e49515d7449cbb9bcb9d5911 |
# -*- coding: utf-8 -*-
import os
import sys
from attributes import check_cclib
if __name__ == "__main__":
# Import cclib and check we are using the version from a subdirectory.
import cclib
check_cclib(cclib)
# Change directory to where tests are and add it to the path. Because there are
# se... | hainm/cclib.github.io | sphinx/coverage.py | Python | lgpl-2.1 | 5,482 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 24b38dbe60a2e7b1d598d6450f668a87194c1a685cb60bc4f67a3975a4f73179 |
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
"{{first_name}} {{last_name}}",
"{{first_name}} {{last_name}}",
"{{first_name}} {{last_name}}",
"{{first_name}} {{last_name}}",
"{{first_name}} {{last_name}}",
"{{first_name}} {{la... | joke2k/faker | faker/providers/person/no_NO/__init__.py | Python | mit | 7,074 | [
"MOE"
] | 3cd3de62db90db3690f40c39cf4ad2d39fb3de42e303eb9f511dcee9435d4414 |
# -*- coding: utf-8 -*-
#
# This file is part of the FMN project.
# Copyright (C) 2017 Red Hat, Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License,... | fedora-infra/fmn | fmn/tests/test_tasks.py | Python | lgpl-2.1 | 21,584 | [
"VisIt"
] | b02d1c568ca1a9208a805f864e7bb59706fd4671a8d7ad9cf8a726aba6e83996 |
import contextlib
import functools
import logging
from typing import (
TYPE_CHECKING,
Dict,
FrozenSet,
Iterable,
Iterator,
List,
Mapping,
NamedTuple,
Optional,
Sequence,
Set,
Tuple,
TypeVar,
cast,
)
from pip._vendor.packaging.requirements import InvalidRequiremen... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py | Python | apache-2.0 | 26,859 | [
"VisIt"
] | 37db5e94d0756ab155fb84ea746761f4a30bf337c059d31ba9448d8a9e877847 |
#!/usr/bin/env python
import numpy
import scipy
import pysam
import logging
# Makes a simple list of windows, where each window is a list [WindowStart, ReadsInWindow].
# Chromosomes are separated by [-1,-1] window
# Sequences of ineligible windows longer than GAP+1 are not stored
def make_windows_list(bam_path, chr... | BroadPeaksBioinf/BroadPeaks | BroadPeaks1/islands.py | Python | gpl-2.0 | 15,862 | [
"pysam"
] | e2979ef9aab94a893b6a285bcf817430d46b9b27b41ae3e8edc95c82f51202da |
"""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.
#---------... | pombredanne/bokeh | setup.py | Python | bsd-3-clause | 21,010 | [
"GULP"
] | cf068c1e5ecb102583049fde656679c54e0dd083fc8f6d8f25ad841e2f0372ad |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/geometric/cylinder_source/cylinder_source.py | Python | lgpl-2.1 | 973 | [
"MOOSE"
] | c64f331844a4a9f52ab082723cf8dc163515feaade169071dc1c2ed241572575 |
import os
import sys
ASCII = 'ascii'
BINARY = 'binary'
PLY_FORMAT = 'ply'
VTK_FORMAT = 'vtk'
POLYDATA = 'POLYDATA'
STRUCTURED_GRID = 'STRUCTURED_GRID'
UNSTRUCTURED_GRID = 'UNSTRUCTURED_GRID'
VTK_DATASET_TYPES = [POLYDATA, STRUCTURED_GRID, UNSTRUCTURED_GRID]
def getFileFormat(file_name):
"""
Return a file fo... | gregvonkuster/icqsol | util/__init__.py | Python | mit | 1,229 | [
"VTK"
] | 68ad562ada640d01046fa5bac44ffe81d365569d9bb8681088c46f8a8e25c01f |
#!/usr/bin/env python
"""
Parses output from vep_parse.py to produce epitopes.
"""
# standard libs
import argparse
import gzip
import re
import sys
# third party libs
from Bio import SeqIO
import Bio.Data.CodonTable
__author__ = 'dkdeconti'
__copyright__ = "Copyright 2017"
__credits__ = ["Derrick DeConti"]
__licens... | dkdeconti/HLA_epitope_prediction_from_WES | epitope_slice.py | Python | mit | 4,954 | [
"Biopython"
] | b7a18158cb543def56a58f2c740291e8ed0a4237ca2920ba85180031cd622537 |
import time
from animation import *
from asteroidField import *
from background import *
from loader import *
from physics import *
from player import *
from powerup import *
import pygame
from pygame.locals import *
from rotatingMenu_img import *
from spacemenu import *
from starField import *
# teclas dos jogadore... | borgaster/SpaceWarsEvolved | main (Joao Costa's conflicted copy 2011-07-29).py | Python | mit | 16,812 | [
"Galaxy"
] | 4881d60b4b24e6555ccf985954bdf20f80ff88b8e822eef27d514ae90d3bd25f |
import pandas as pd
# The Dataset comes from:
# https://archive.ics.uci.edu/ml/datasets/Optical+Recognition+of+Handwritten+Digits
# At face value, this looks like an easy lab;
# But it has many parts to it, so prepare yourself before starting...
def load(path_test, path_train):
# Load up the data.
# You probab... | mr3bn/DAT210x | Module6/assignment2.py | Python | mit | 6,134 | [
"TINKER"
] | 1044164787f605212abca0d9fbe3e26614df28bbe5b89c5b7b25195bf6314ff9 |
# The code in this module is from the publication "Python Cookbook (TM)",
# edited by Alex Martelli and David Ascher, published by O'Reilly Media, Inc. 2002
#
# This code can be found in section 4.18 "Walking Directory Trees" of the above
# listed publication. Credit: Robin Parmar, and Alex Martelli
#
# The following i... | Esri/ops-server-config | SupportFiles/walkingDirTrees.py | Python | apache-2.0 | 3,309 | [
"VisIt"
] | 12a5307548b42a4af5760eac0b5a2a50dfff66ed4882315408e2c89eec508997 |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor 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... | vthorsteinsson/tensor2tensor | tensor2tensor/models/research/transformer_moe.py | Python | apache-2.0 | 14,170 | [
"MOE"
] | 8ecaa4f28a8c73adb624601dfc3ce03fe0f35a69fa1aa30690342e580f160f30 |
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 23 16:31:33 2015
@author: Rick Berg, University of Washington, School of Oceanography
Script for modeling reaction rates in marine sediments.
Starts with existing sediment column, sediment column building upward is
modeled as a downward flow of porewater.
Bottom bound... | rickdberg/mgmodel | centraldiffreal.py | Python | mit | 23,028 | [
"Gaussian"
] | 01b9e4e6d331378c8f0c6b4a77a2cca4cba05a0a27e0d143703a7092514d7be6 |
import urllib
import re
import contextlib
import os
import numpy as np
import cPickle
from datetime import datetime as dt
import logging
logger = logging.getLogger(__file__)
class SpikeParser:
def __init__(self, crop_region=None, resolution=None, simulation_time=None,
timestep_unit='us', scale_... | gdikov/hybrid-stereo-matching | stereovis/utils/spikes_io.py | Python | mit | 15,338 | [
"NEURON"
] | 47892aecf079f75aababb32d45e506cf71d2bd2a43fb8cb9d525e1dc411dd4fe |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import subprocess
import warnings
import numpy as np
import glob
import itertools
import matplotlib.pyplot as plt
from scipy.spatial import KDTree
... | Bismarrck/pymatgen | pymatgen/command_line/critic2_caller.py | Python | mit | 22,763 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | 50fba16212b8fa3d7d32cae0da71179892ea444c9bde872fd0777fede5be750c |
from math import log
import numpy as np
import functools
import tree
from ray.rllib.models.action_dist import ActionDistribution
from ray.rllib.models.modelv2 import ModelV2
from ray.rllib.utils import MIN_LOG_NN_OUTPUT, MAX_LOG_NN_OUTPUT, \
SMALL_NUMBER
from ray.rllib.utils.annotations import override, DeveloperA... | robertnishihara/ray | rllib/models/tf/tf_action_dist.py | Python | apache-2.0 | 19,920 | [
"Gaussian"
] | 0a4efb24b9392ef04c391d1f00835f1ba48513a94def61cab82c93075e9ae60d |
"""
This module is the geometrical part of the ToFu general package
It includes all functions and object classes necessary for tomography on Tokamaks
"""
# Built-in
import sys
import os
import warnings
import copy
# Common
import numpy as np
import scipy.interpolate as scpinterp
import scipy.stats as scpstats
impor... | ToFuProject/tofu | tofu/geom/_core_optics.py | Python | mit | 130,907 | [
"CRYSTAL",
"Gaussian"
] | 84519c3ea4639fbca565c84724690affbbd9f17bc95dddfc421d1e2bad760671 |
"""
Tests for ABINIT DFT calculations.
"""
# pylint: disable=redefined-outer-name
import os
import shutil
import tempfile
import pytest
import z2pack
@pytest.fixture
def abinit_system(sample):
"""
Create ABINIT system.
"""
def inner(build_dir):
sample_dir = sample('abinit')
input_fi... | Z2PackDev/Z2Pack | tests/fp/test_abinit.py | Python | gpl-3.0 | 1,468 | [
"ABINIT",
"Wannier90"
] | 592004d31170792853eb97cbf3216496a054994afb2d40b9c674afcf52b32595 |
# Copyright 2017-2019 Tom Eulenfeld, MIT license
"""Reading and writing correlations and stretching results"""
import h5py
import obspyh5
import yam
import os.path
import obspy
from yam.util import _analyze_key, _get_fname
INDEX = ('{key}/{network1}.{station1}-{network2}.{station2}/'
'{location1}.{channel... | trichter/yam | yam/io.py | Python | mit | 4,972 | [
"VisIt"
] | 833e3679cac85dc4f4ca54563514ef38e48a6b3915675c46bdd958c42af16fed |
"""
=========================
Bayesian Ridge Regression
=========================
Computes a Bayesian Ridge Regression on a synthetic dataset.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary least squares) estimator, the coefficient
weights are slightly shift... | manhhomienbienthuy/scikit-learn | examples/linear_model/plot_bayesian_ridge.py | Python | bsd-3-clause | 3,860 | [
"Gaussian"
] | d94f32f485857241797acc74e85ed6619901ca5ac33ef64a92caa30655e61b63 |
import argparse
import base64
from datetime import datetime
import os
import shutil
import numpy as np
import socketio
import eventlet
import eventlet.wsgi
from PIL import Image
from flask import Flask
from io import BytesIO
from keras.models import load_model
import h5py
from keras import __version__ as keras_versio... | camigord/Self-Driving-Car-Nanodegree | P3-Behavioral-Cloning/drive.py | Python | mit | 4,281 | [
"Gaussian"
] | 7bb677c7bad34ea4091afff865d35fc49fe5a6c1458fdc0fc0ba3f213348c5b2 |
'''
This module performs the return type inference, according to symbolic types,
It then reorders function declarations according to the return type deps.
* type_all generates a node -> type binding
'''
from pythran.analyses import LazynessAnalysis, StrictAliases, YieldPoints
from pythran.analyses import LocalN... | serge-sans-paille/pythran | pythran/types/types.py | Python | bsd-3-clause | 25,503 | [
"VisIt"
] | 920bff7d316bed7e549ea2a7b4adef440ead31e9deb6137e1434679a2dae8036 |
# menu.py
# Aaron Taylor
# Moose Abumeeiz
#
# The main menu for the game, it is reposnible for changing
# key bindings, character selection, and seed.
#
from pygame import *
from math import *
from random import *
from func import *
def menu(screen, jController, sounds, nextSong, changeSong):
#Establishes all the ... | ExPHAT/binding-of-isaac | menu.py | Python | mit | 17,551 | [
"MOOSE"
] | 02d1b0317e2b230296feff58cea166e4a5ebf03d678f579e8153dfa44e3d0558 |
"""MCMC sampling methods."""
import logging
import numpy as np
logger = logging.getLogger(__name__)
# TODO: combine ESS and Rhat?, consider transforming parameters to allowed
# region to increase acceptance ratio
def eff_sample_size(chains):
"""Calculate the effective sample size for 1 or more chains.
Se... | elfi-dev/elfi | elfi/methods/mcmc.py | Python | bsd-3-clause | 16,681 | [
"Gaussian"
] | c64bd31550f75d9ebc71fa81fa65a50b67aab96a3b0c6525075d674a847c5a81 |
# -*- coding: utf-8 -*-
# Copyright 2014 Matt Austin
# 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 ... | mattaustin/gaussian | gaussian/__init__.py | Python | apache-2.0 | 4,688 | [
"Gaussian"
] | e49cf96991ba796bd9e2862e88b16b8609d397bd13046d7c23249dc353ce766e |
import copy
import warnings
from collections.abc import Iterable, Iterator, Generator
import numpy as np
import scipy
import scipy.optimize
import scipy.stats
from astropy import log
import matplotlib.pyplot as plt
from stingray.exceptions import StingrayError
from stingray.gti import bin_intervals_from_gtis, check_g... | StingraySoftware/stingray | stingray/crossspectrum.py | Python | mit | 96,951 | [
"Gaussian"
] | 53d50d825ef70e65567a02ed9155c13bdbd3f28668e7aac2d732377cc97d8aeb |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | Forage/Gramps | gramps/gen/plug/menu/_boolean.py | Python | gpl-2.0 | 1,783 | [
"Brian"
] | 2e2662caff4cb082086e1d085891b3e8a59b7fbd4e1796f4a6d4eac1bab0ab71 |
#!/usr/bin/env python
# install.py tool to download, compile, and setup the kim-api library
# used to automate the steps described in the README file in this dir
from __future__ import print_function
import sys,os,re,subprocess
# help message
help = """
Syntax from src dir: make lib-kim args="-b -v version -a kim-... | jag1g13/lammps | lib/kim/Install.py | Python | gpl-2.0 | 10,607 | [
"LAMMPS",
"OpenKIM"
] | 968835d7c01604e748c1439ddb223415148b2edf1a0917280cfd4824555c966e |
import tempfile
import re
import os
import logging
import sys
from math import floor, ceil, log10
from edl.util import open_input_file
def checkTmpDir(tmpDir, jobName):
"""
Make sure tmp dir is empty.
Create it if necessary.
If name is None, create dir name based on job name
"""
if tmpDir is N... | jmeppley/py-metagenomics | edl/batch.py | Python | mit | 18,380 | [
"Biopython"
] | fabc97e42acba3bfd2a7892628cef9bb5d11202bcd0b6e9d1c63c68b7fa0c7bd |
import pytest
@pytest.fixture
def analysis_step_run_with_no_status(analysis_step_version, lab, award):
return {
'analysis_step_version': analysis_step_version['@id'],
'award': award['@id'],
'lab': lab['@id']
}
@pytest.fixture
def analysis_step_run(testapp, analysis_step_version):
... | ENCODE-DCC/encoded | src/encoded/tests/fixtures/schemas/analysis_step_run.py | Python | mit | 6,771 | [
"BWA"
] | 7ce28a818bdad789905959404ceb45a63a9ffafb00e57907b1c5e04876f2bb5e |
#!/usr/bin/env python
"""
Plots total energies vs volume for directory given as a command-line argument
"""
__author__ = "Andrey Sobolev"
__year__ = "2015"
import os
import sys
import numpy as np
import matplotlib.pyplot as plt
from calc_delta import BM, read_ref_data, calcDelta
def read_energy(element, alat):
... | ansobolev/PseudoGenerator | pseudogen/get_energies.py | Python | mit | 2,236 | [
"WIEN2k"
] | ea546885c73b2bc6735ad02fca309d50a22abaeb2444c70a2268ed8b0dcbb933 |
"""
This module defines a classs for a generic Workflow Parameter. It also defines
a ParameterCollection class as a list of parameters as well as an AttributeCollection
class which is the base class for the main Workflow classes.
"""
from __future__ import print_function
from DIRAC.Core.Workflow.Utility imp... | chaen/DIRAC | Core/Workflow/Parameter.py | Python | gpl-3.0 | 24,462 | [
"DIRAC"
] | 001cb1ff3704f175b1071139a55c0719b96deac5ddef6c222fb093ea95dadaa4 |
#!/usr/bin/env python
# =========================================================================
#
# Copyright NumFOCUS
#
# 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:/... | richardbeare/SimpleITK | Examples/FilterProgressReporting/FilterProgressReporting.py | Python | apache-2.0 | 2,030 | [
"Gaussian"
] | ee30124b38e847b9b0149bd92bc4636f4eb3997f146721d51f317ae0ded5d62f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgeexamples/exset2_singlecell_simulations/singlecell_simulation020.py | Python | bsd-2-clause | 4,482 | [
"NEURON"
] | 3b222f2d3b31f22e9fcda41bb6e1ea3c473fd9b188da91bf745edddc7c73abc6 |
#! /usr/bin/env python
# -*- encoding: utf-8 -*-
from flask import Flask, render_template, jsonify, request, flash, redirect, url_for, session,send_file, Response
import logging
import os
import re
from os import path
import tsf
from sse import Publisher
from datetime import datetime
from pyinotify import WatchManager,... | bumblebeefr/tsf-manager | web_controller.py | Python | gpl-3.0 | 4,620 | [
"VisIt"
] | bf382b3dd54478d30a3bfe19f0106b8aed4261443fb9dbe889df69eb3fabb536 |
# -*- coding: utf-8 -*-
"""
Created on nov. 28, 2018, 14:39
Copyright François Durand 2018
fradurand@gmail.com
This file is part of SVVAMP.
SVVAMP 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, eith... | francois-durand/svvamp | svvamp/preferences/generator_profile_gaussian_well.py | Python | gpl-3.0 | 3,473 | [
"Gaussian"
] | cccc11f672bc800579f07c529f08c809e7d02e1729074a19cd33000dffd7165b |
#!/usr/bin/env python
from __future__ import print_function,division
from astropy.io import fits
import matplotlib.pyplot as plt
import numpy as np
import matplotlib
from pint.templates import lctemplate,lcprimitives,lcfitters
from pint.eventstats import z2m,sf_z2m, hm, sf_hm, sig2sigma
import sys
from astropy import ... | paulray/NICERsoft | scripts/fitharms.py | Python | mit | 11,515 | [
"Gaussian"
] | 919ec2769cbdff12394b58b14615c605a10cd5221a3cced12c99f86881ea4849 |
# -*- coding: utf-8 -*-
# Copyright 2020 The Chromium OS Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""DeDeDe configs."""
from __future__ import print_function
BUILD_WORKON_PACKAGES = (
'chromeos-ec',
'coreboot',
'de... | endlessm/chromium-browser | third_party/chromite/lib/firmware/ap_firmware_config/dedede.py | Python | bsd-3-clause | 1,957 | [
"Octopus"
] | 8d2ac0e3a6652627cfb48b877c6292a8ef22035f6083c649522596139a005553 |
import os
import json
import numpy as np
from ..abinit import AbinitJob
from ...tasks import Task
from ...relaxator import Relaxator
from pychemia.crystal import KPoints
from pychemia import pcm_log
__author__ = 'Guillermo Avendano-Franco'
class IonRelaxation(Relaxator, Task):
def __init__(self, structure, workd... | MaterialsDiscovery/PyChemia | pychemia/code/abinit/task/relax.py | Python | mit | 5,092 | [
"ABINIT",
"CRYSTAL"
] | ebd9ecb2b8c08bba626a3a1a0ff90c568ef27142de1bcbb2cebc7a6d932ffe34 |
import ocl
import pyocl
import camvtk
import time
import datetime
import vtk
def main(filename="frame/f.png"):
print(ocl.revision())
myscreen = camvtk.VTKScreen()
myscreen.camera.SetPosition(-15, -8, 15)
myscreen.camera.SetFocalPoint(5,5, 0)
# axis arrows
camvtk.drawArrows(... | aewallin/opencamlib | src/attic/ocode/cutsim_test_2.py | Python | lgpl-2.1 | 7,600 | [
"VTK"
] | 0c4b2cdd4edf708c8420db14f22632d5ee12b66f1599d8066a71abd21df13f31 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/scf/_response_functions.py | Python | apache-2.0 | 7,913 | [
"PySCF"
] | 1d0c0707d59178a90257830571ccf5aa8168c33b5f9cdc1bda1f57ec09559296 |
import abc
import os
import matplotlib
import numpy
from mpl_toolkits.mplot3d import Axes3D
from Paths import Paths
import datasets
import matplotlib.pyplot as plt
from infos.InfoElement import PrintableInfoElement, SimpleDescription
from infos.InfoGroup import InfoGroup
from infos.InfoList import InfoList
from infos... | GiulioGx/RNNs | sources/datasets/LupusFilter.py | Python | lgpl-3.0 | 7,350 | [
"VisIt"
] | db5903c1d618b2518cc4ca6c3c03b275f339e3f78264e4acfe7139730bcf6b78 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | sysadmin75/ansible-modules-core | cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,526 | [
"Dalton"
] | cfb7a866066da8b3bdf94f41187daaac5b5c7358dbb6b1c2d7416dabdb4b24be |
#!/usr/bin/env python
# pylint: disable=I0011,C0111
import sys
from parsimonious.exceptions import ParseError
from structures import jbovlaste_types
from camxes import configure_platform
from parsers.camxes_ilmen import Parser
from transformers.vlatai import Visitor
VLATAI_RULE = "vlatai"
def run(text):
parse... | teleological/camxes-py | vlatai.py | Python | mit | 831 | [
"VisIt"
] | 360b8468c14840b5cc716e18e134e336ab8e5c41d30b60db5fd0faca788c2d13 |
import re
from functools import wraps
from bottle import response, request, template, redirect, static_file
from short import app, config, backend
from short.link import Link
from short.errors import *
urlre = re.compile(config["regex-url"])
namere = re.compile(config["regex-name"])
def set_cookie(name, value):
... | JuhaniImberg/short-piesome | short/views.py | Python | mit | 3,452 | [
"VisIt"
] | 98578111d6341569596687ad08dcedf8dae9ad50efe44b93f26a9f70df448f05 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | jasperfurniss/schooled | config/urls.py | Python | bsd-3-clause | 1,431 | [
"VisIt"
] | 35f50074f1d4825d54e8704a2225ec3c6137e94f77cfde69e209b41890c2d6f2 |
from allensdk.model.biophys_sim.config import Config
from utils import Utils
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import numpy as np
config = Config().load('config.json')
# configure NEURON
utils = Utils(config)
h = utils.h
# configure model
manifest = config.manifest
utils.gener... | wvangeit/AllenSDK | doc_template/examples/multicell/multi.py | Python | gpl-3.0 | 1,070 | [
"NEURON"
] | 9d801524f920832529909e3831e92fa9d025fcb696e6fa8c1f796230b1ceb4e2 |
#!/usr/bin/env python
"""Prepare GFF transcript files for use as input to RNA-seq pipelines
Usage, from within the main genome directory of your organism:
prepare_tx_gff.py <organism> <org_build>
requires these python and external packages which come pre-installed
with bcbio using bioconda:
mysql-python
gffutils
r... | chapmanb/cloudbiolinux | utils/prepare_tx_gff.py | Python | mit | 33,487 | [
"Bioconda",
"HTSeq"
] | 05218b96eecd834799ab1af110a2f1271d4c321fa584ecf7cf82412ad895343b |
9#!/usr/bin/env python
import argparse
import sys
import os
import subprocess as sp
DEFAULT_SUB_FILE = '''#!/bin/csh
#$ -M {}@nd.edu
#$ -m ae
#$ -N {}
#$ -q {}
#$ -r n
{}
module load schrodinger/2015u3
module load gaussian/09D01
module load tinker
setenv SCHRODINGER_TEMP_PROJECT "~/.schrodtmp"
setenv SCHRODINGER_TMP... | Q2MM/q2mm | tools/submit.py | Python | mit | 3,435 | [
"Gaussian",
"TINKER"
] | 63cf2a54f3d489b65ac9c5379302436bc30d81e2ea068a3441a9b3c5fd044b43 |
from electrum_ltc.util import print_error
import httplib, urllib
import socket
import hashlib
import json
from urlparse import urlparse, parse_qs
try:
import PyQt4
except Exception:
sys.exit("Error: Could not import PyQt4 on Linux systems, you may try 'sudo apt-get install python-qt4'")
from PyQt4.QtGui impor... | amaivsimau/electrum-ltc | plugins/labels.py | Python | gpl-3.0 | 8,706 | [
"VisIt"
] | 3849f03b992e8a59c2b0738fc60baeab136691afa3ca1d47b54ec86e497c9e63 |
"""
Copyright 2016 Brian Quach
Licensed under MIT (https://github.com/brianquach/udacity-nano-fullstack-catalog/blob/master/LICENSE) # noqa
"""
import json
from catalog import db
from catalog.models import Catagory
from catalog.models import CatagoryItem
# Create database schema
db.create_all()
# Create and add de... | brianquach/udacity-nano-fullstack-catalog | vagrant/catalog/create_db.py | Python | mit | 910 | [
"Brian"
] | 3d441fb23e1dbe6c7197ca4a04d72d6a7e033b6a20f84c97116fa68efae1f4be |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | decvalts/iris | lib/iris/fileformats/__init__.py | Python | gpl-3.0 | 6,991 | [
"NetCDF"
] | b2984a91d92d898b66712a998f5f8a3bdc7e7635499313598fe55aabb180067d |
"""
Continuous GCAL - A continuous version of vanilla GCAL
"""
import math, copy
from collections import OrderedDict
import param
from param import ParamOverrides
import topo
from topo.submodel import Model, ArraySpec, select
from topo.submodel.gcal import ModelGCAL
import numbergen
from imagen.transferfn import Ide... | ioam/topographica | topo/submodel/cgcal.py | Python | bsd-3-clause | 14,150 | [
"Gaussian"
] | 166707912019885b1a7f51eef80dba8b1628ee3fe4194d17a8cb45d9958fed91 |
# written by Aidan Bharath
# Fabry-Perot Etalon Absorption Features
import numpy as np
from matplotlib import pyplot as plt
# Variable Definitions
dg = 1 # HWHM of the incident light source
dh = 1 # HWHM of flatness defect Gaussian
df =8 # Free spectral range of the Etalon
dt = 4 # HWHM... | Aidan-Bharath/Absorption_Feature | absorption_feature.py | Python | mit | 6,223 | [
"Gaussian"
] | 61dc71965790437527f4649072d2d17281029bd6717c21610c758713baf28528 |
"""Teem package for VisTrails.
"""
##############################################################################
# Changes
#
# 20081002: Added UnuSlice
import core.modules
import core.modules.module_registry
import core.modules.basic_modules as basic
from core.modules.vistrails_module import Module, ModuleError, \
... | VisTrails/vistrails-contrib-legacy | edu_utah_sci_cscheid_teem/__init__.py | Python | bsd-3-clause | 33,813 | [
"VTK"
] | 470b5d7579ccffebcff957419bdf5b17a08607880e947a291e45af3faa942bec |
# Create your views here.
from django.template import Context, loader
from django.http import HttpResponse
import os
from jasp import *
JASPRC['mode'] = None # do not run calculations
DATAROOT = '/home/jkitchin/dft-org'
def index(request):
vaspdirs = []
for dirpath, dirnames, fnames in os.walk(DATAROOT):
... | prtkm/jasp | jasp/www/vasp_django/vasp/views.py | Python | gpl-2.0 | 2,647 | [
"VASP"
] | 2bea8db919bd3c2930d6f7cb868f48de7e746caf45cee0d429813700776ce323 |
# coding: utf-8
#
# Copyright 2018 The Oppia 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 requi... | prasanna08/oppia | scripts/linters/pylint_extensions.py | Python | apache-2.0 | 78,064 | [
"VisIt"
] | 17f58cb3864e444c25eb5cdb0fad1fcc476877813977c6ab300218b277150ac4 |
# -*- coding: utf-8 -*-
"""
"""
__author__ = "Konstantin Klementiev"
__date__ = "14 October 2014"
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
Rs = 250
thetaDegs = np.linspace(40, 80, 5)
colors = ['r', 'm', 'b', 'c', 'g']
xtalDx, xtalDy = 25, 12
detDx, detDy = 32, 8
def get_clasical_xt... | kklmn/xrt | examples/withRaycing/06_AnalyzerBent1D/vonHamosPos.py | Python | mit | 5,289 | [
"CRYSTAL"
] | 7a845bff7de3e9c6cd09714344892de3344919b2673f480d8f861a883104ad66 |
from core.modules.simulations_manager.weather.DatabaseWeatherSeries import DatabaseWeatherSeries
from core.modules.simulations_manager.weather.HistoricalSeriesMaker import HistoricalSeriesMaker
from core.modules.simulations_manager.weather.CombinedSeriesMaker import CombinedSeriesMaker
from core.modules.simulations_man... | schmidtfederico/PRinde | test/test_subclass.py | Python | gpl-2.0 | 1,217 | [
"NetCDF"
] | ddeb2a443ec7a4bbca1f9e305821a6c2ab645de12ea9905d169f14256037c8b0 |
# ----------------------------------------
# USAGE:
# python res_res_distances.py config_file
# ----------------------------------------
# PREAMBLE:
import sys
import numpy as np
from numpy.linalg import *
import MDAnalysis
from distance_functions import *
zeros = np.zeros
square = np.square
sqrt = np.sqrt
flush = ... | rbdavid/DENV-NS3h | Res-Res_distances/res_res_distances.py | Python | gpl-3.0 | 3,749 | [
"MDAnalysis"
] | a6c49415fa81b9fbffae122bee49bd63fa8a283e4a1740965395bba5647e57ed |
#!/usr/bin/env python
"""
This is the main function to call for disambiguating between a human and
mouse BAM files that have alignments from the same source of fastq files.
It is part of the explant RNA/DNA-Seq workflow where an informatics
approach is used to distinguish between human and mouse RNA/DNA reads.
For rea... | roryk/disambiguate | disambiguate.py | Python | mit | 15,496 | [
"BWA",
"pysam"
] | c1e47dd0bc1cc3bcaec0293ec412f82bc79e09b1189aa9b24cd40f1a72896a5b |
# coding: utf-8
import astropy
import todsynth
from todsynth.pointing._pointing import getArrayICRSCoords, getArraySourceCenteredCoords, getSourceAltAzCoords
from todsynth.projection.core import projectToMatrices, matricesToMaps
from todsynth.convolution._convolution import deprojectTODWithBeam ... | pafluxa/todsynth | test_convolution.py | Python | gpl-3.0 | 3,097 | [
"Gaussian"
] | 110589f04ab5d88e788e7d6cdd8af4dca571c4b39e882fd3a4043d510f913799 |
__author__ = 'gpratt'
import pybedtools
import pysam
def compute_frip(bam, bed):
bam_tool = pybedtools.BedTool(bam)
peaks = pybedtools.BedTool(bed)
num_reads_peaks = len(bam_tool.intersect(peaks, u=True, s=True))
bamtool = pysam.Samfile(bam)
total_mapped_reads = bamtool.mapped
return... | YeoLab/gscripts | gscripts/clipseq/calculate_frip.py | Python | mit | 1,106 | [
"pysam"
] | 79a2c86277633a40c03eb4b2c546c523328489caa07e6ddc3183b208e8a94b91 |
# Python test set -- part 1, grammar.
# This just tests whether the parser accepts them all.
from test.test_support import run_unittest, check_syntax_error, \
check_py3k_warnings
import unittest
import sys
# testing import *
from sys import *
class TokenTests(unittest.TestCase):
de... | teeple/pns_server | work/install/Python-2.7.4/Lib/test/test_grammar.py | Python | gpl-2.0 | 32,702 | [
"GULP"
] | f6e10e6bf54d3fb5e8cf0b1230dab15bbe499ee362f6b360ec6ba58dd1e77a46 |
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