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# -*- coding: utf-8 -*-
"""
Reading and writing from KlustaKwik-format files.
Ref: http://klusters.sourceforge.net/UserManual/data-files.html
Supported : Read, Write
Author : Chris Rodgers
TODO:
* When reading, put the Unit into the RCG, RC hierarchy
* When writing, figure out how to get group and cluster if those a... | rgerkin/python-neo | neo/io/klustakwikio.py | Python | bsd-3-clause | 17,296 | [
"NEURON"
] | 1e1cf3e21c76dddc68f1c2b53a92add35c73e8659c9f622358c5cf60d56b49ed |
#!/usr/bin/python
#
# Open SoundControl for Python
# Copyright (C) 2002 Daniel Holth, Clinton McChesney
#
# 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 Licen... | pepsipepsi/nodebox_opengl_python3 | nodebox/sound/osc.py | Python | bsd-3-clause | 14,673 | [
"VisIt"
] | 3fed9894c386168c45ae51878a4959a348755a417e2a554adfcc7aa6dcce5bdd |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from matplotlib.externals import six
import os, sys, warnings
def fn_name(): return sys._getframe(1).f_code.co_name
if six.PY3:
warnings.warn(
"The gtk* backends have not been tested with Python 3... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py | Python | mit | 37,329 | [
"FLEUR"
] | 942ec8074fe32b6865a5184bc54cf1e9f54fd28c52e07185e7bcd30b81537bd7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#===========================================================================
# interpolate_compare.py
#
# Interactive Jitter modulation of audio files and generated waveforms
#
# See http://stackoverflow.com/questions/6783194/background-thread-with-qthread-in-pyqt
#
# Gener... | chipmuenk/A2SRC | A2SRC/a2src.py | Python | apache-2.0 | 26,027 | [
"Gaussian"
] | 7b22af97c8d92a6850c3539bdc82b48a91f56cbede23ef55d8e0473f8e80f461 |
#!/usr/bin/env python
import os, sys, time, socket, getopt, getpass
import Pyro.core
from Pyro.EventService.Clients import Subscriber
from Bio.Align.Applications import ClustalwCommandline
import Bio
#from Bio.Clustalw import MultipleAlignCL
#from Bio import Clustalw
import logger
import pp
from db_conf import db_conf... | byuphamerator/phamerator-dev | phamerator/phamClientOmega.py | Python | gpl-2.0 | 9,633 | [
"Biopython"
] | 293c7b6b27e6b873e677c861ef8123293c491f93ecac409af9ee11f6f95f8371 |
import os,sys,site
import argparse
import cPickle
base_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
base_path="%s/src"%base_path
for directory_name in os.listdir(base_path):
site.addsitedir(os.path.join(base_path, directory_name))
import cdhit
import violinplot
def removeDuplicates(items):
... | idoerg/BOA | scripts/plot_violinplot.py | Python | gpl-3.0 | 2,941 | [
"BLAST"
] | 710eed12936a6266e8f82dc89489d3e91c591c8163b90c6834b63c74f642843f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoq/gui/test/test_till.py | Python | gpl-2.0 | 8,078 | [
"VisIt"
] | 84fdda8a528754d247c5d0c73796fef1d560dd584f3b5581d429f5f72c636ff9 |
# Copyright (c) 2006 John Gilman
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# ... | go-bears/Final-Project | weblogo-3.4_rd/corebio/ssearch_io/blastxml.py | Python | mit | 9,432 | [
"BLAST",
"BioJava"
] | ffa7eca4a9783a5dfac60c5ee169bb72719898a762d80f49a2f23b3df26caf5c |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from collections import OrderedDict
from datetime import datetime
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import setti... | B-MOOC/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 59,685 | [
"VisIt"
] | 503ef208c60a091af56525e7979214ed8a34ae40f03af39e729b3b59c2715d0f |
import sys
import argparse, os, tempfile
from collections import defaultdict
import matplotlib.pyplot as plt
import numpy as np
from scipy.misc import imresize, imsave, imread
from scipy.ndimage.filters import gaussian_filter
import os
os.environ['GLOG_minloglevel'] = '2' # suprress Caffe verbose prints
import sett... | anguyen8/cnn-vis | cnn_vis.py | Python | mit | 24,397 | [
"NEURON"
] | 7d2ceb3a0e54ac6df448e32f9e7c29b59892fdf5d3a37a956c9f7688438571da |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
StrahlerMetric()
| jeromevelut/Peavip | Testing/StrahlerMetric.py | Python | gpl-3.0 | 127 | [
"ParaView"
] | dcd862155098077958d12541c1b45ac6c97905c0fdf5a643153a80e58cbc2bbe |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Run parser unit tests for cclib."""
import sys
import unittest
sys.path.insert(1, 'parser')
from .parser.testdata im... | cclib/cclib | test/test_parser.py | Python | bsd-3-clause | 490 | [
"cclib"
] | 9aa36f791e9ca23647186899bc5d05b911bdcb940e5d4d5ef041a2edafef4368 |
#!/usr/bin/env python
"""SfePy: Simple finite elements in Python
SfePy (simple finite elements in Python) is a software, distributed
under the BSD license, for solving systems of coupled partial
differential equations by the finite element method. The code is based
on NumPy and SciPy packages.
"""
DOCLINES = __doc__.... | RexFuzzle/sfepy | setup.py | Python | bsd-3-clause | 7,713 | [
"Mayavi"
] | 41ef18db103a26b0900da5729cd8b492cb83bc0024347ad9e1bfd8d282619848 |
from couchdbkit.exceptions import ResourceNotFound
from datetime import timedelta
from django.utils.translation import ugettext as _, ugettext_noop
from corehq.apps.users.models import CouchUser
from custom.succeed.reports import *
from custom.succeed.reports.patient_details import PatientDetailsReport
from dimagi.util... | SEL-Columbia/commcare-hq | custom/succeed/reports/patient_interactions.py | Python | bsd-3-clause | 4,668 | [
"VisIt"
] | 0f8187fb53c59efed89a9164a2f9820ebfc49a3efad77fef2559fbe0f05260b8 |
#!/usr/bin/env python
"""
Tensors
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
$Revisi... | chunshen1987/iSS | utilities/for_paraview/lib/Tensors.py | Python | mit | 1,790 | [
"VTK"
] | 0366671e8926457c26dc7f80142eeed6ac5a92948c000c60607bc5df25b74f5a |
"""
Test the about xblock
"""
import datetime
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.core.urlresolvers import reverse
from django.test.utils import override_settings
from milestones.tests.utils import MilestonesTestCaseMixin
from mock import patch
from nose.plu... | hastexo/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 25,620 | [
"VisIt"
] | 33e03c1f3a599eaafeca58dad0077cdb4edf3a94d9b478fa51575908f17b4919 |
from __future__ import print_function
import unittest as ut
import tests_common
import espressomd
import espressomd.lb
import os
import numpy as np
try:
import vtk
except ImportError:
print("Module \"vtk\" not available, skipping test!")
exit()
@ut.skipIf(not espressomd.has_features(["ENGINE", "LB"]),
... | KonradBreitsprecher/espresso | testsuite/engine_lb.py | Python | gpl-3.0 | 3,089 | [
"VTK"
] | 605ae735d1ca8bfc6d42e8070069b50a7276c31330930c3d48e536186eaf2856 |
"""
This file demonstrates the creation of a directed graph using the
Python interface to VTK.
"""
from vtk import *
xdim = 600
ydim = 600
#------------------------------------------------------------------------------
# Script Entry Point
#----------------------------------------------------------------------------... | jeffbaumes/jeffbaumes-vtk | Examples/Infovis/Python/merge_graphs.py | Python | bsd-3-clause | 3,482 | [
"VTK"
] | 6e86f30a4b9801ddee894cecd4236718cebebece6a05e02e45d5d196c3989c08 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Corinne Maufrais
# Institut Pasteur, Centre d'informatique pour les biologistes
# corinne.maufrais@pasteur.fr
#
# version 2.1
import os
import sys
import argparse
class RankOptimizerError:
def __init__(self, err):
self.err = err
def __repr__(self):
... | C3BI-pasteur-fr/taxo_pack | src/rankoptimizer.py | Python | gpl-3.0 | 24,532 | [
"BLAST"
] | bb050cbd6f72d8c9573b1872dcc8c3bc383ad65d2410aac90e0659ce4007764d |
#!/usr/bin/python
# -- Content-Encoding: UTF-8 --
"""
Python modules repository
:author: Thomas Calmant
:license: Apache Software License 2.0
..
Copyright 2014 isandlaTech
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
... | isandlaTech/cohorte-demos | led/dump/led-demo-raspberry/cohorte/dist/cohorte-1.0.0-1.0.0-20141201.234602-19-python-distribution/repo/bundles/cohorte/repositories/python/modules.py | Python | apache-2.0 | 20,244 | [
"VisIt"
] | 9aeb4984e3cf01c239c7ef0b3ea61372ddb2b89036de5b8236a3b8e518c7e136 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
... | barbagroup/pygbe | versioneer.py | Python | bsd-3-clause | 68,903 | [
"Brian"
] | b6ad854ad5605e7269bab9a9773e4e78f91f6beed88933698ca7ae8102423da0 |
from django.test import TestCase
from django.core.exceptions import ValidationError
from mozdns.soa.models import SOA
from mozdns.domain.models import Domain
class SOATests(TestCase):
def setUp(self):
Domain.objects.all().delete()
def do_generic_add(self, primary, contact, retry, refresh, descriptio... | rtucker-mozilla/inventory | mozdns/soa/tests/model_tests.py | Python | bsd-3-clause | 5,782 | [
"ADF"
] | 43f10db8854387e6a95a05f027152dcaf3cc98fe37d90a2dce4714c646943058 |
"""A component that provides a selection of poly data source widgets
to be used by various modules.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Event, Instance, List, Trait, Bool, TraitPrefixL... | dmsurti/mayavi | mayavi/components/source_widget.py | Python | bsd-3-clause | 11,887 | [
"Mayavi",
"VTK"
] | 4bf2e2a564548a4437ff2e77a1bea725588018cfeff3385c79f539fd77bc0edb |
# 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... | nburn42/tensorflow | tensorflow/contrib/autograph/converters/name_scopes.py | Python | apache-2.0 | 2,485 | [
"VisIt"
] | c2b60eb422d63c7f5afbe143ce2f96213e4c77110a66b6b7e571db5c3e4ae830 |
"""
The paramselect module handles automated parameter selection for linear models.
Automated Parameter Selection
End-members
Note: All magnetic parameters from literature for now.
Note: No fitting below 298 K (so neglect third law issues for now).
Note: Should use calculate(..., mode='numpy') for this step for perf... | richardotis/pycalphad-fitting | paramselect.py | Python | mit | 69,413 | [
"pycalphad"
] | 1e0c7818f238ae271a399ef7b949408f2303d273c17559da1fefb897a360b4ea |
#!/usr/bin/python2
# pymeg.py
#
# Copyright 2010 dan collins <danc@badbytes.net>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License,... | badbytes/pymeg | gui/gtk/pymeg.py | Python | gpl-3.0 | 59,177 | [
"VTK"
] | e0013c3a43c9eb02a3ca061f8ad73356064fcc37011b69d70271772921eaacd1 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/stats/ordination/_ordination_results.py | Python | bsd-3-clause | 16,917 | [
"scikit-bio"
] | f9c538752159b3960fc04c70514aa02ec144aaabfe8df729a874fd8008c89832 |
#
# Copyright 2016, 2021 Lars Pastewka (U. Freiburg)
# 2016 Adrien Gola (KIT)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License ... | libAtoms/matscipy | matscipy/tool/plot.py | Python | lgpl-2.1 | 6,316 | [
"LAMMPS",
"Matscipy"
] | 4554075d5ba5b976f7dfdbd09debb4005221bd585f2defe55cb483d2a6356a7e |
# pb_status.py TEST PROGRAM for Pyboard MQTT link
# Demonstrates the interception of status messages.
# Author: Peter Hinch.
# Copyright Peter Hinch 2017-2018 Released under the MIT license.
# From PC issue (for example)
# mosquitto_pub -h 192.168.0.9 -t green -m on
# mosquitto_sub -h 192.168.0.9 -t result
import py... | peterhinch/micropython-mqtt | pb_link/pb_status.py | Python | mit | 3,279 | [
"Amber"
] | b4585974acf47e34ddaf9891cb1260efc09c11d82664cdd95e252de241f1f475 |
# -*- coding: utf-8 -*-
"""
Runs a series of tests to check that PyNoddy is functioning correctly.
Created on Sun Aug 09 12:33:35 2015
@author: Sam Thiele
"""
import sys,os
##############
#check imports
##############
err = False
#pynoddy
try:
import pynoddy
except ImportError:
sys.stderr.write("Error: no... | flohorovicic/pynoddy | pynoddy/check_pynoddy.py | Python | gpl-2.0 | 7,768 | [
"VTK"
] | c0ad1dbc2426a621f8ce8b123d54cad430b452fe865ce108cba6a77aebb86d8d |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2013, 2014 CERN.
##
## Invenio 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 opt... | egabancho/invenio | invenio/modules/workflows/testsuite/test_workflows.py | Python | gpl-2.0 | 31,952 | [
"Galaxy"
] | 575f1520f55d9aba026e227aae5f9901948e5bc2003a0f3a6440ea5c92560ce6 |
# 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/analysis/NeighborFluctuation.py | Python | gpl-3.0 | 1,852 | [
"ESPResSo"
] | 8a6f8e9d58d77c15fda9061040a4c1f966a0205db5784344b5fa01a509c547d7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from PIL import Image
from PIL import ImageFilter
from itertools import product
from random import random
import os, re
def changeToRGBMode(im):
if im.mode != "RGB":
im = im.convert("RGB")
return im
def rotatePic(inputPath, outputPath, deg=90):
im = Image.open(... | nutszebra/ddp | noise.py | Python | mit | 1,868 | [
"Gaussian"
] | c94d56f547bdd388ee22c89a89b52e3b53e116cf170d863cb530ac546f470552 |
"""
"""
import os, sys, posixpath
import fnmatch
import py
# Moved from local.py.
iswin32 = sys.platform == "win32" or (getattr(os, '_name', False) == 'nt')
try:
from os import fspath
except ImportError:
def fspath(path):
"""
Return the string representation of the path.
If str or byte... | marcuskelly/recover | Lib/site-packages/py/_path/common.py | Python | bsd-2-clause | 14,239 | [
"VisIt"
] | 727818561983e6648eb9a4eb9da1a8f330f9cc2bdfec2a3c0dd15f6ee5ab4e0e |
#!/usr/bin/env python
from CPT_GFFParser import gffParse, gffWrite
from Bio.SeqFeature import FeatureLocation
from Bio import SeqIO
from Bio.Seq import Seq
import csv
import argparse
def table_annotations(gff3In, tabularIn, fastaIn, out_gff3, out_changelog):
# CSV parse tabular
header = csv.DictReader(tabul... | TAMU-CPT/galaxy-tools | tools/gff3/gff3_table_annotations.py | Python | gpl-3.0 | 9,690 | [
"Biopython"
] | cc4963607f8b4412361e23f2873508406206756baa35788ac4e9e91441458504 |
#!/usr/bin/env python
"""
refguide_check.py [OPTIONS] [-- ARGS]
Check for a Scipy submodule whether the objects in its __all__ dict
correspond to the objects included in the reference guide.
Example of usage::
$ python refguide_check.py optimize
Note that this is a helper script to be able to check if things ar... | grlee77/scipy | tools/refguide_check.py | Python | bsd-3-clause | 32,985 | [
"Gaussian"
] | 5802a3eb77d3eba11047b3f411b8ce16d1f0dc0471243d7c85f8deb49923427d |
#!/usr/env python
#
# Calculate the cross correlation of two time series
# Estimates the uncertainties using Monte Carlo Simulation
import matplotlib.pyplot as plt # plot library
import numpy as np # array manipulation
from astropy import table # handle data tables
from scipy import signal, stats # signal processi... | evandromr/python_crosscorr | pycrosscorr.py | Python | mit | 16,660 | [
"Gaussian"
] | e952fe4c2fe61d20e7fc253b208845d2a88ca40c80f0bae7fd9c164fdc820347 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGenericContourFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkGenericContourFilter.py | Python | bsd-3-clause | 507 | [
"VTK"
] | 0bcbf9a9084ce43d56fccda45e645f9d15cef247e5cf9ebf8916662beda2bd5c |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/sequence/tests/test_nucleotide_sequence.py | Python | bsd-3-clause | 8,425 | [
"scikit-bio"
] | 831aed61b50f5d1d0124d65a3f6b0a68b8c6c216bba95849affac04f8a80bb99 |
import glob
import sys
import os
from setuptools import setup, find_packages, Extension
from cy_build import CyExtension as Extension, cy_build_ext as build_ext
import pysam
test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1]
test_module_name = "PysamTestModule_{}".format(test_module_su... | kyleabeauchamp/pysam | linker_tests/link_pre_489/setup.py | Python | mit | 778 | [
"pysam"
] | 773d26b0541f634d98415cfcf4a516a6bb1552bfa9ef1dcd1308cb584326c068 |
# UPDATE THIS SECRET INFORMATION ! #
# UNCOMMENT THIS FILE IN .gitignore BEFORE YOU COMMIT! #
# SuperUser Default Password
SUPER_USER_PASSWORD = 'CHANGEME'
# Log into your Loggly account, visit: https://<Username>.loggly.com/tokens and copy the token here
LOGGLY_TOKEN = 'CHANGEME'
# Generate a very secure Django Sec... | Chaffleson/blupy | settings_local.py | Python | gpl-2.0 | 1,195 | [
"VisIt"
] | f71a2037f463b7f0305d672a1cf2cd5ad3e2cf8d39f79c661450eec4ba0caad6 |
#! /usr/bin/python
from setuptools import setup
from setuptools import find_packages
setup(name='setgame',
version='0.1',
description='Set game simulation and rules',
author='Brian Kinney',
author_email='briankanokinney@gmail.com',
url='https://github.com/briankinney/setgame',
pack... | briankinney/setgame | setup.py | Python | apache-2.0 | 376 | [
"Brian"
] | a125e37db1fb5e8187e83ae0a7a4bf9a0b9feef760e33cc34b603bd0ba8abf83 |
# -*- coding: utf-8 -*-
import datetime
import pygame.sprite
import engine
import ennemies
class BasePlatform(pygame.sprite.Sprite):
def __init__(self, x, y, image_filename):
super(BasePlatform, self).__init__()
self.image = pygame.image.load(engine.image_path(image_filename)).convert_alpha()
... | sblondon/jumpjump | src/platforms.py | Python | gpl-3.0 | 1,194 | [
"Octopus"
] | e4141248d2bc23d43d63a1e6c945591773414ef28d8bc10ac8302b5afb731083 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/interfaces/android_adb/adb_helper.py | Python | gpl-3.0 | 6,030 | [
"ORCA"
] | 80e1777014c38722c0f23c2cc448913b90edd488e3b58c61329ec61a571d43b4 |
#!/usr/bin/env python
import sys
import os
import re
import glob
import xmltodict
import json
import yaml
import copy
import logging
from argparse import ArgumentParser
from argparse import RawDescriptionHelpFormatter
from elasticsearch import Elasticsearch
from collections import OrderedDict
import datetime
import d... | ICGC-TCGA-PanCancer/pcawg-central-index | pcawg_metadata_parser/generate_oxog_whitelist_json.py | Python | gpl-2.0 | 25,936 | [
"BWA"
] | a689e4a4515124a33fcb9c5b978ab7e3a47c1737418944d7afadd5068d82a382 |
# this module defines classes that can be used to massage the content of an
# article, mostly to remove gunk like ads
from __future__ import print_function
import sys, re, requests, sqlite3
from . import param, util, dbop
class Filter:
"""Virtual class with the interface for all degunking filters"""
def apply(self... | fazalmajid/temboz | tembozapp/degunk.py | Python | mit | 5,095 | [
"VisIt"
] | 608afdf43f4500a2f95c40060ccca0487294cad2d19a8d66f4a2af08fc5df868 |
"""
This is our testing framework.
Goals:
* it should be compatible with py.test and operate very similarly
(or identically)
* doesn't require any external dependencies
* preferably all the functionality should be in this file only
* no magic, just import the test file and execute the test functions, that's it
* po... | maniteja123/sympy | sympy/utilities/runtests.py | Python | bsd-3-clause | 81,153 | [
"VisIt"
] | ab1f0ffc747285e184807c48e037c2713e1784dcb2b9d987629fddf9d00592ac |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2018, 2021, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | smarr/Truffle | compiler/mx.compiler/mx_graal_benchmark.py | Python | gpl-2.0 | 23,334 | [
"VisIt"
] | 9addf80009b34eeef0d4342d57cce50232b491cb442d24a389da9ec259ad9f14 |
""" Client to interact with the S3Gateway """
from DIRAC.Core.Base.Client import Client, createClient
@createClient("DataManagement/S3Gateway")
class S3GatewayClient(Client):
"""Client code to the S3Gateway"""
def __init__(self, url=None, **kwargs):
"""Constructor function."""
super(S3Gatewa... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Client/S3GatewayClient.py | Python | gpl-3.0 | 1,172 | [
"DIRAC"
] | 0916a5305356446619a7a5919f22c3408ec7284a7e00347e577e67e0e9ee8293 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/dds-and-bh-gpu.py | Python | gpl-3.0 | 5,996 | [
"ESPResSo"
] | 7af73ad9b001a1c6bdb1bf0de5f6ca7027cad44ea799f6e3608b0a8e125dcc85 |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------... | Kleptobismol/scikit-bio | skbio/parse/sequences/tests/test_fasta.py | Python | bsd-3-clause | 6,698 | [
"scikit-bio"
] | 05cc3891a9edbb25aabe6340ee519c37e1cd7ee53638a779433233ea355d52b4 |
from sympy.core.add import Add
from sympy.core.basic import Basic, C
from sympy.core.function import count_ops
from sympy.core.power import Pow
from sympy.core.symbol import Symbol, Dummy
from sympy.core.numbers import Integer, ilcm, Rational, Float
from sympy.core.singleton import S
from sympy.core.sympify import symp... | ichuang/sympy | sympy/matrices/matrices.py | Python | bsd-3-clause | 137,689 | [
"DIRAC",
"Gaussian"
] | cb59ec27b931010077ff4f66134c4db90bcf02aab67a2001aabdd6e36bb62aec |
__author__ = "Just van den Broecke"
__date__ = "Dec 21, 2011 3:46:27 PM$"
"""
Naam: BAGObject.py
Omschrijving: Classes voor BAG-objecten
Per BAG-objecttype (woonplaats, openbareruimte, nummeraanduiding,
ligplaats, standplaats, verblijfsobject, pand) is er een aparte class.
De BAGObject classes zijn pure ... | micfort/2IV05 | PreProcess/bag/src/bagobject.py | Python | gpl-3.0 | 27,141 | [
"Elk"
] | 22a5dc1a3abfe8b563ce48632fbf80c63baf19ce219e6555e38262c4dd4a8def |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# 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... | steckdenis/rlglue-py3 | rlglue/agent/AgentLoader.py | Python | apache-2.0 | 2,156 | [
"Brian"
] | d34d237e35499f9dd559ac39f6a6826f3400113f40f1485a7b6ba3e229b5092b |
import numpy as np
import pickle
from math import pi, sqrt
from time import time, ctime
from datetime import timedelta
from ase.parallel import paropen
from ase.units import Hartree, Bohr
from gpaw import GPAW
from gpaw.mpi import world, rank, size, serial_comm
from gpaw.utilities.blas import gemmdot
from gpaw.utilitie... | ajylee/gpaw-rtxs | gpaw/response/gw.py | Python | gpl-3.0 | 18,760 | [
"ASE",
"GPAW"
] | 52f8a65c6454a6278ab5f081a3ef5e9e531155e18a9c5da57fb1ceb1912d542e |
#!/usr/bin/python
# this script creates a baseline submission using Gaussian Process Regression
# it will be properly commented later
import pandas as pd
import numpy as np
import datetime as dt
import os
pd.set_option('display.mpl_style', 'default')
pd.set_option('display.width', 10000)
pd.set_option('display.max_... | yanyuchka/bikesharing | baseline2.py | Python | mit | 4,575 | [
"Gaussian"
] | edd7c500a463c31a1a420e88e51f5804bb2c2582fb45368ae22d6b96d2c7d086 |
"""calc - Calculation functions"""
import glob
import itertools
import os
from os.path import join
import subprocess
import tempfile
from typing import (Sequence, List, Tuple, Dict, Union, Optional, Mapping)
import h5py
import numpy as np
import pandas as pd
import scipy.stats
from .io import read_nmr, read_rdc
from... | tlhr/plumology | plumology/calc.py | Python | mit | 18,567 | [
"Gromacs"
] | e01998f9b2441c6dae512ef89383118f2169f04efdcefe8692eb607956b9c474 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | odejesush/tensorflow | tensorflow/contrib/linalg/python/ops/linear_operator_test_util.py | Python | apache-2.0 | 22,884 | [
"Gaussian"
] | 8fa781a781d8831792614ebf7586565b80cd967468da2805705cc1772e126745 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
cc_plugin_ncei/ncei_timeseries.py
'''
from compliance_checker.base import BaseCheck
from cc_plugin_ncei.ncei_base import TestCtx, NCEI1_1Check, NCEI2_0Check
from cc_plugin_ncei import util
from isodate import parse_duration
class NCEITimeSeriesOrthogonalBase(BaseChec... | ioos/cc-plugin-ncei | cc_plugin_ncei/ncei_timeseries.py | Python | apache-2.0 | 15,849 | [
"NetCDF"
] | 6f7797364c6329a3f2f5273095d31adc01fcb6c4b4364a2c0d681a33f69df495 |
# -*- coding utf-8 -*-
from __future__ import print_function
# This script gathers the routines to extract kilosort/phy (kwikteam) generated units features,
# stored in an instance of DataManager():
# - Sampling rate (30Khz)
# - Spike times in sample units
# - Spikes times in seconds
# - Spikes units, unit correspondi... | MS047/XtraDataManager | XtraDataManager/FeaturesExtraction.py | Python | gpl-3.0 | 57,057 | [
"Gaussian"
] | d694c801c201dfcfa3c8c92c9e2f940bae3b2ba4a710cc9db6c0217b42899646 |
#!/usr/bin/env python
#
# Copyright (C) 2009-2014 ABINIT Group (Damien Caliste)
#
# This file is part of the ABINIT software package. For license information,
# please see the COPYING file in the top-level directory of the ABINIT source
# distribution.
#
# The purpose of this file is to check the documentation consiste... | SamKChang/abinit-7.10.5_multipole | special/scripts/check-input-vars.py | Python | gpl-3.0 | 7,641 | [
"ABINIT"
] | 9b2ad8d04ed17c20d89fd2f9102c0fc7b72ac953f77d685fc29548785c7522ac |
'''
These are utilites used by the VisTrails
wrappers of the SAHM command line applications
@author: talbertc
test
'''
import os, sys, shutil
import traceback
import csv
import time
import tempfile
import subprocess
from PyQt4 import QtCore, QtGui
from core.modules.basic_modules import File, Path, Directory, new_c... | VisTrails/vistrails-contrib-legacy | sahm/utils.py | Python | bsd-3-clause | 14,984 | [
"ADF"
] | d7a3323b67a22980a57d95e21ceaaced0e292a39a1b5efc1d3d5c5a21a516a8a |
#!/usr/bin/env python
import re
import sys
import os
import itertools
import termcolor
from cirosantilli import files
from cirosantilli import argparse_extras
if __name__ == '__main__':
parser = argparse_extras.ArgumentParser(
description="find recursivelly paths whose basenames match all given regexes... | cirosantilli/python-utils | bin/find_basename_res.py | Python | mit | 5,355 | [
"ADF"
] | bc1a7b8a5128ea5b6bb268e8494dd00a5c143c12d0ee8e5df625d7d3909cc90b |
#!/usr/bin/env python
"""
A linting tool to check for xss vulnerabilities.
"""
from __future__ import print_function
import argparse
import ast
import os
import re
import sys
import textwrap
from enum import Enum
class StringLines(object):
"""
StringLines provides utility methods to work with a string in te... | proversity-org/edx-platform | scripts/xss_linter.py | Python | agpl-3.0 | 101,648 | [
"VisIt"
] | 96e5d04c9aa0755288048e24f3e28fb7a2002230ba6cedfe906a44127918ae7f |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import (
UniqueCourseTest,
EventsTestMixin,
... | jazztpt/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 46,632 | [
"VisIt"
] | 41c7c3caefc7cc132241f8663d5c6da24ee7e52460c2214be5602d3c7254cfbd |
import os
import sys
import gzip
import json
import tqdm
import ete3
import asyncio
import aiohttp
import warnings
import pandas as pd
from collections import defaultdict
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqRecord import SeqRecord
from tictax import tictax
def ... | bede/tictax | tictax/tictax.py | Python | gpl-3.0 | 11,286 | [
"Biopython"
] | 15a97862f57707f62079c1b55593d903ed1c5396ddc4b7af55c236c63fa7e293 |
import random
# TODO: Clean up printing of empty sets
class TripCalculator(object):
list_of_cities = {'Boston', 'New York', 'Albany', 'Portland', 'Philadelphia'}
city_to_accessible_cities = {
'Boston': {'New York', 'Albany', 'Portland'},
'New York': {'Boston', 'Albany', 'Philadelphia'},
'... | Azenwrath/codeguild-labs | lab_road_trip.py | Python | gpl-3.0 | 2,186 | [
"VisIt"
] | 6fc9821fb420bc118c418ca7c50336cf57c64b96dd16fd243e25ee5d77985ef7 |
# mooseplots.py ---
#
# Filename: mooseplots.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Wed Jul 1 12:58:00 2009 (+0530)
# Version:
# Last-Updated: Fri Jul 24 13:37:46 2009 (+0530)
# By: subhasis ray
# Update #: 317
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#... | BhallaLab/moose-thalamocortical | pymoose/gui/mooseplots.py | Python | lgpl-2.1 | 7,929 | [
"MOOSE"
] | 4700b0c9d305fa7fc662751dddb0805f8fb5404ab2e6fa5367b11783b91fe253 |
import numpy as np
def create_log_kernel(radius, ndims, calibration):
"""Largely inspired from Trackmate Fiji plugin.
https://github.com/fiji/TrackMate/blob/master/src/main/java/fiji/plugin/trackmate/detection/DetectionUtils.java#L53
"""
# Compute sigma
sigma = radius / np.sqrt(ndims)
sigma_... | hadim/spindle_tracker | spindle_tracker/detector/utils.py | Python | bsd-3-clause | 1,762 | [
"Gaussian"
] | 03aafa329d234366aa6dec0fb4f3772b7cea69bc4075548fd446a7b5deee02d8 |
##########################################
# functional style, uses multiprocessing #
# this version threads within processing #
##########################################
import numpy as n
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as p
import applytelcal, applycals2
from scipy import signal
fro... | caseyjlaw/tpipe | leanpipedt.py | Python | apache-2.0 | 51,791 | [
"Gaussian"
] | 53af4b4211694be4e9a6ba63dc60e15619b72db92da11a69bbff30184f534b98 |
import os
import pytest
from espresso.siteconfig import SiteConfig
def test_pbs_exceptions(tmpdir):
'check if an exception is raised when `scratchenv` variable is undefined'
tmpdir.chdir()
pytest.raises(OSError, SiteConfig, 'PBS', scratchenv='MYSCRATCH0000')
def test_slurm_exceptions(tmpdir):
'ch... | lmmentel/ase-espresso | tests/test_siteconfig.py | Python | gpl-3.0 | 1,784 | [
"ESPResSo"
] | 818c92e11a79b3636570661ed1c96435e7017d3d8710a9893ee441d1dd6d8f33 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.core import Lattice
from pymatgen.electronic_structure.core import Orbital, Spin, Magmom
import numpy as np
class SpinTest(unittest.TestCase):
def test_init(self):
... | dongsenfo/pymatgen | pymatgen/electronic_structure/tests/test_core.py | Python | mit | 5,553 | [
"pymatgen"
] | 3cc7d21d5d5bc7185f53075f2b404b6a5b69e88af5eda46cc5ce12d5827c2afa |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | shikhardb/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 33,063 | [
"Brian"
] | fbf1746298cb247dbed0a375ac1cc14e5172be1db795753b4efff4917aff600c |
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 22 10:55:20 2012
@author: Shreejoy
"""
from django.db import models
from django.contrib.auth.models import AbstractUser as auth_user
from django_localflavor_us import us_states
from db_functions import countries
from picklefield.fields import PickledObjectField
... | lessc0de/neuroelectro_org | neuroelectro/models.py | Python | gpl-2.0 | 23,075 | [
"NEURON"
] | fef2cedb0b9012dcc25a1f537cb0a88101557279d947f0da44f070e798c04bbb |
import numpy as np
import os
from collections import namedtuple
import quantumpropagator.graph as gg
import quantumpropagator.Propagator as Pr
import quantumpropagator.EMPulse as pp
import quantumpropagator.GeneralFunctions as gf
import quantumpropagator.GeneralFunctionsSystem as gfs
import quantumpropagator.h5Reader ... | acuzzio/GridQuantumPropagator | src/quantumpropagator/GridIntegrator.py | Python | gpl-3.0 | 9,945 | [
"Gaussian",
"MOLCAS"
] | eee4380be8b8757a1422f8d0e48f464ae11ab6dcdd70f78ad5101e5b8849a297 |
# -*- encoding:ascii -*-
from mako import runtime, filters, cache
UNDEFINED = runtime.UNDEFINED
__M_dict_builtin = dict
__M_locals_builtin = locals
_magic_number = 6
_modified_time = 1417014282.0602
_template_filename='templates/webapps/galaxy/tool_executed.mako'
_template_uri='tool_executed.mako'
_template_cache=cache... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/database/compiled_templates/tool_executed.mako.py | Python | gpl-3.0 | 6,600 | [
"Galaxy"
] | 5fd0670a0bf5a99c4a60e9e020cba87440509d93ff95c0130259e497407718e3 |
"""
Methods to interconvert between json and other (cif, mol, smi, etc.) files
"""
import imolecule.json_formatter as json
from collections import Counter
from fractions import gcd
from functools import reduce
try:
import pybel
ob = pybel.ob
table = ob.OBElementTable()
has_ob = True
except ImportError... | CorySimon/CorySimon.github.io | imolecule/format_converter.py | Python | mit | 7,474 | [
"CRYSTAL",
"Open Babel",
"Pybel"
] | 79e4a12ac153edba4c0135eda71b471f7bcb979fa5cc063a1fc782c54f71a4f7 |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2005-2012 Jinsong Ren
For documentations of the project, please go to:
http://osjren.github.com/PhotoSorter
For bugfixes, updates and support, please go to:
https://github.com/osjren/PhotoSorter/issues
This file is part of PhotoSorter.
PhotoSorter is free softwa... | osjren/PhotoSorter | RenLib.py | Python | gpl-3.0 | 30,612 | [
"VisIt"
] | 38758526784ebda78710ebd1594009f390ead6814bfa804d376bfe617c9d2a42 |
from __future__ import print_function
import string
import sys
from collections import deque
import numpy as np
from sklearn.base import BaseEstimator
from sklearn.utils import check_random_state
from sklearn.utils.extmath import logsumexp
import _hmmc
from utils import normalize
decoder_algorithms = frozenset(("v... | ShenLab/hotspot | base.py | Python | bsd-3-clause | 17,881 | [
"Gaussian"
] | ef22bb67e65ecfbddc3fd630e19336f9be0d7a08e9fc532d90a5dd255deecbe7 |
# Copyright (c) 2017 Zhenwen Dai
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import SparseGP
from .. import likelihoods
from .. import kern
from .. import util
from GPy.core.parameterization.variational import NormalPosterior, NormalPrior
from ..core.parameterization.par... | esiivola/GPYgradients | GPy/models/gp_multiout_regression_md.py | Python | bsd-3-clause | 11,908 | [
"Gaussian"
] | 0b52710d1a179c64372c6f6d2b0470c10c390c993e664b957bf77b6530a91d0f |
#
# curses console
#
# // license
# Copyright 2016, Free Software Foundation.
#
# This file is part of Solent.
#
# Solent 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,... | solent-eng/solent | solent/console/curses/curses_console.py | Python | lgpl-3.0 | 10,230 | [
"Amber"
] | bf26cf98a853ac88c82942308bd20dc2d3820ea2516e8f80a2f23b6df2e53226 |
import pytest
import re
import os
from centinel.primitives import dnslib
class TestDnslib:
@pytest.fixture(scope='class')
def ipregex(self):
return "^((((2(([0-4]\d)|(5[0-5]))\.)|(1\d\d\.))|([1-9]\d\.))|(\d\.)){3}((((2(([0-4]\d)|(5[0-5]))$)|(1\d\d$))|([1-9]\d$))|(\d$))"
@pytest.fixture(scope='cl... | lianke123321/centinel | centinel/unit_test/test_dnslib.py | Python | mit | 5,419 | [
"ADF"
] | e09774caf1fe8783e88691699e71567125cc0007c77be051e2d14825910afbd5 |
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2021, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software you can redistribute it and/or modify
# it under... | mrcslws/nupic.research | projects/dendrites/permutedMNIST/experiments/prototype_ten_segments.py | Python | agpl-3.0 | 5,574 | [
"NEURON"
] | f66fe251ee69a454907ccf1d897251e42fb4e2ca21527ad132cfa835233b06ca |
#from ctx_base import StandardBaseContext
from .libmp.backend import basestring, exec_
from .libmp import (MPZ, MPZ_ZERO, MPZ_ONE, int_types, repr_dps,
round_floor, round_ceiling, dps_to_prec, round_nearest, prec_to_dps,
ComplexResult, to_pickable, from_pickable, normalize,
from_int, from_float, from_str,... | devs1991/test_edx_docmode | venv/lib/python2.7/site-packages/sympy/mpmath/ctx_mp_python.py | Python | agpl-3.0 | 36,688 | [
"Gaussian"
] | 24c9a4dee848e07f898d1ef05db17f1cd8b04023113cb7206e1a8bdf7671d163 |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from unittest import skipUnless
from urllib import urlencode
import json
import mock
import ddt
import markupsafe
from django.conf import settings
from django.core.urlresolvers import reverse
from django.core import mail
from django.contrib im... | Shrhawk/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 18,341 | [
"VisIt"
] | cb92d043f90bb60d998505d57306a168deb129c98627982061737fc3c1594fb0 |
import unittest, random, sys, time
sys.path.extend(['.','..','../..','py'])
import h2o, h2o_cmd, h2o_glm, h2o_import as h2i, h2o_exec as h2e
def define_params():
paramDict = {
'alpha': [0,0.2,0.4],
'beta_epsilon': [None, 0.0001],
'family': [None, 'gaussian', 'binomial', 'poisson'],
... | rowhit/h2o-2 | py/testdir_single_jvm/test_GLM2_params_rand2.py | Python | apache-2.0 | 3,182 | [
"Gaussian"
] | bbddef8772dfc0253fc866f0f7e33dee8b796db9618b79d12d4d4cd1ac2ea0ae |
#!/usr/bin/env pvbatch
from paraview.simple import *
import pviz
import sys
oviz = pviz.viz(sys.argv) # instantiate viz object (and load data)
bulletTimeAnimation(O=[0,0,0],R=10,axis='z',nFrames=20) | ruizanthony/pviz | examples/advanced/restoreState_bulletTime.py | Python | lgpl-3.0 | 200 | [
"ParaView"
] | 7dfb470fa45bc9f20f1249b0020c66987eaa3db76543a7b89a1f8943e44a49b2 |
import random
from kernel_tuner import util
from kernel_tuner.strategies.minimize import _cost_func
def get_neighbors(neighbor_method, values, element, randomize):
""" get the list of neighboring elements of element in values """
# If Hamming neighbors, all values are possible neighbors
if neighbor_metho... | benvanwerkhoven/kernel_tuner | kernel_tuner/strategies/hillclimbers.py | Python | apache-2.0 | 5,245 | [
"VisIt"
] | c3d2d4b322ab53100c0310a7bb260053884682d214f360646c4109c40fa51423 |
#!/usr/bin/env python
# Author: Samuel Ponc\'e + Yannick Gillet
# Date: 30/04/2013 -- 11/09/2014 -- 07/08/2015
# Version: 1.4
# This is the executable script
from __future__ import division, print_function
import sys
import os
import copy
try:
from rf_final import system
from rf_final import zpm
except ImportErr... | jmbeuken/abinit | scripts/post_processing/temperature-dependence/temperature_final.py | Python | gpl-3.0 | 19,814 | [
"ABINIT",
"Gaussian"
] | b0303ffa236793bd352e4aef21b2acbfe22cc21cf0cfc09d140222dc6e88e193 |
import numpy as np
import scipy.constants as const
from hagpack import unit_conversion
def h2p(h, T=293., P0=1000., m=28.966, unit_p='mbar'):
"""
Parameters
----------
h: {flaot, array}
altitude from reference higth in meter (if reference hight is not sealevel, you probably want to adjust P0)
... | lo-co/atm-py | build/lib/atmPy/tools/conversion_tools.py | Python | mit | 1,895 | [
"Avogadro"
] | c1ea91b355209b59e8e19684daf5f788064a2b12d8bca7f8d1ac289dcd1dc0f4 |
import os.path, sys
sys.path.append(os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir))
import unittest
from unittest import skipIf
from lomap.dbmol import DBMolecules
from lomap.graphgen import GraphGen
from lomap.mcs import MCS
import argparse
import multiprocessing
import networkx as nx
import net... | nividic/Lomap | test/test_lomap.py | Python | lgpl-2.1 | 9,781 | [
"RDKit"
] | f6ffc5516bb7eb9a0700e9a32eb563e3de3f77c21e3bb0adbcdb13a80b56c793 |
# 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
#
# Unless required by appl... | sunqm/pyscf | examples/local_orb/pmloc.py | Python | apache-2.0 | 8,550 | [
"Jmol",
"PySCF"
] | c43b9b2557420deef64f1419fbb30e7c11fcdfea39a66d59fef1ee1453c5209a |
# Copyright 2021 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/vmoe | vmoe/nn/routing_test.py | Python | apache-2.0 | 4,760 | [
"MOE"
] | 9b042487a78c7448156f7bb08e83f8fc7c3ac1d8a22b630e11c3e96fc7b71707 |
#!/usr/bin/env python
# Copyright 2015 Coursera
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... | coursera/courseraprogramming | courseraprogramming/commands/oauth2.py | Python | apache-2.0 | 17,355 | [
"VisIt"
] | 89a9486b6878f81dc930bf26816701ad53391867089b30eb1e76fc84e1939b8a |
'''
__author__ = 'Brian Chow'
__date__ = '2013-06-26'
__Comments__ 'Modified from code by Paul Duan'
__comments__ = 'Modified from code by Miroslaw Horbal (miroslaw@gmail.com)
Kaggle Amazon Employee Access Challenge Ensemble Logistic Regression Model constructed using an ADABOOST implementation
'''... | bachow/kaggle-amazon-contest | boost.py | Python | mit | 8,825 | [
"Brian"
] | 55439578771c5a9a6500d2139ceb58368e492fbe65c85c26438dc092541db2f9 |
import numpy as np
from ase.atoms import Atom, Atoms
from ase.parallel import paropen
"""Module to read and write atoms in PDB file format"""
def read_pdb(fileobj, index=-1):
"""Read PDB files.
The format is assumed to follow the description given in
http://www.wwpdb.org/documentation/format32/sect9.h... | grhawk/ASE | tools/ase/io/pdb.py | Python | gpl-2.0 | 2,715 | [
"ASE",
"RasMol"
] | 463a4a577ea6c779bc3ef587f4b6c9921da739229dee898cc861054a447909b8 |
# -*- 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... | Silmathoron/nest-simulator | pynest/nest/tests/test_refractory.py | Python | gpl-2.0 | 8,471 | [
"NEURON"
] | cae0fdd0961edddec7ab89e0355128cf53f0d3058a45859e7c2333fdb21e65f9 |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/urls.py | Python | apache-2.0 | 1,783 | [
"Galaxy"
] | 27734f69d35780441db5ac65f457d81e06982edc5a9e35e4e7d07c35b018fa58 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Hybrid LFP scheme example script, applying the methodology with the model of:
Potjans, T. and Diesmann, M. "The Cell-Type Specific Cortical Microcircuit:
Relating Structure and Activity in a Full-Scale Spiking Network Model".
Cereb. Cortex (2014) 24 (3): 785-806.
doi: ... | espenhgn/hybridLFPy | examples/Hagen_et_al_2016_cercor/cellsim16pops_default.py | Python | gpl-3.0 | 6,653 | [
"NEURON"
] | cd1e63a5ef6048b097500615ab7bd0ad5874210de200665e97317d8b10e758a6 |
#!/usr/bin/env python
# Copyright 2015 Ryan Wick
# This file is part of Irsat.
# Irsat 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
# versi... | rrwick/Irsat | Irsat.py | Python | gpl-3.0 | 21,157 | [
"BWA",
"Bowtie"
] | 9c00cde80df25b8468dc02f7f4ff6dc934a32d08141f6e284c8aec28a9eb2112 |
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