text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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from ase import io, visualize
t = io.read('mytrajectory.traj')
for i, s in enumerate(t):
# rotate to the desired direction
s.rotate('z', 'x', rotate_cell=True)
# repeat with keeping old cell
cell = s.get_cell()
s = s.repeat((1,3,3))
s.set_cell(cell)
ofname = str(i) + '.png'
print 'wr... | grhawk/ASE | tools/doc/development/writepngs.py | Python | gpl-2.0 | 479 | [
"ASE"
] | d95eef9b2f4656bb8456b1a33d7ebd97073c15f9cbfb91addcc21989f7ba11b1 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Peter G. LAndgren
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | Forage/Gramps | gramps/plugins/rel/rel_sv.py | Python | gpl-2.0 | 22,804 | [
"Brian"
] | a7532c45548bb006a04dea8ce68d2bb6d13d21c8d95f57283d3b7327f3f1c929 |
"""
Histogram-related functions
"""
from __future__ import division, absolute_import, print_function
import contextlib
import functools
import operator
import warnings
import numpy as np
from numpy.compat.py3k import basestring
from numpy.core import overrides
__all__ = ['histogram', 'histogramdd', 'histogram_bin_ed... | MSeifert04/numpy | numpy/lib/histograms.py | Python | bsd-3-clause | 39,639 | [
"Gaussian"
] | 8e2e0d97da4a9b9ca4f1bbe230b06fc05a1d24df8a47cae905eeb628082fd85b |
"""
pyexcel_server.py
:copyright: (c) 2014-2017 by Onni Software Ltd.
:license: New BSD License, see LICENSE for more details
This shows how to use pyexcel to handle excel file upload. In order
to evaluate it, please install Flask::
pip install Flask
python pyexcel_server.py
Then visit http://localhost:5000/... | chfw/pyexcel | examples/memoryfile/pyexcel_server.py | Python | bsd-3-clause | 2,082 | [
"VisIt"
] | d5c878c600d921b48d05c9cfa494af7615ad5de418d342402b31b35dfd87a3e0 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright (C) 2005-2007 Carabos Coop. V. All rights reserved
# Copyright (C) 2008-2019 Vicent Mas. 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... | uvemas/ViTables | vitables/docbrowser/browsergui.py | Python | gpl-3.0 | 14,862 | [
"VisIt"
] | 58a9a965d40e77ab03b5549c9ee02238d7181378c8f539cab4be3f6e045ab761 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
import ast
import os.path
import re
import shlex
import subprocess
import sys
import traceback
from collections import Order... | wiltonlazary/arangodb | 3rdParty/V8/gyp/input.py | Python | apache-2.0 | 104,932 | [
"VisIt"
] | 0bfa0262546787cd951cf01999cb9a1f466043f45b4437ecff44b86f73a5ab06 |
# -*- coding: utf-8 -*-
"""
=============================================================================
Crystal lattice classes (:mod:`sknano.core.crystallography._xtal_lattices`)
=============================================================================
.. currentmodule:: sknano.core.crystallography._xtal_lattic... | scikit-nano/scikit-nano | sknano/core/crystallography/_xtal_lattices.py | Python | bsd-2-clause | 41,085 | [
"CRYSTAL"
] | 47445e8333ac68900dc5783862be8b6de0b90e1e1d6d5861ed9f18e6078f8198 |
########################################################################
# $Id$
########################################################################
""" DIRAC FileCatalog Database """
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.... | coberger/DIRAC | DataManagementSystem/DB/FileCatalogDB.py | Python | gpl-3.0 | 36,388 | [
"DIRAC"
] | 0a84c1e4a1331e7e15c159d7573b8a0640be5d4c09a2e18719f9ff0b903210fc |
#import unittest
#import sys
#
#from DIRAC.Core.Base import Script
#Script.parseCommandLine()
#
#import DIRAC.ResourceStatusSystem.test.fake_AgentModule
#import DIRAC.ResourceStatusSystem.test.fake_rsDB
#import DIRAC.ResourceStatusSystem.test.fake_rmDB
#import DIRAC.ResourceStatusSystem.test.fake_Logger
#
#class Agents... | Sbalbp/DIRAC | ResourceStatusSystem/Agent/Oldtest/Test_Agents.py | Python | gpl-3.0 | 5,382 | [
"DIRAC"
] | 2ca1b2877c38704e15e29e4909927e4f764cf8ec94350e4b921a7043204249a1 |
import threading
import glob
import gzip
try:
from StringIO import StringIO # Python 2.7
except:
from io import StringIO # Python 3.3+
import uuid
import re
import os
import sys
from collections import defaultdict
import pandas as pd
import pybars
from .column import Column, ColumnSet
from .table import Tab... | yhat/db.py | db/db.py | Python | bsd-2-clause | 45,832 | [
"Brian"
] | d99c07c28662fc8001f2d9a82b4da6a51d093d7d6dec78885a21b0a71ae1419e |
# -*- coding: utf-8 -*-
"""Various Statistical Tests
Author: josef-pktd
License: BSD-3
Notes
-----
Almost fully verified against R or Gretl, not all options are the same.
In many cases of Lagrange multiplier tests both the LM test and the F test is
returned. In some but not all cases, R has the option to choose the ... | pprett/statsmodels | statsmodels/sandbox/stats/diagnostic.py | Python | bsd-3-clause | 52,521 | [
"ADF"
] | 6562324fa36cb5f3c915538f78963707c755be90fdbfa035915ea9ac25e3e63a |
# from tkinter import *
# from tkFileDialog import askopenfilename
# import Tkconstants
# class Interface:
# def __init__(self, master):
# self.master = master
# master.title("SeqPyPlot v0.2 GUI")
# master.geometry('680x500')
# self.button_opt = {'fill': Tkconstants.BOTH, 'padx': ... | paulgradie/SeqPyPlot | dev/SeqPyPlot_GUI.py | Python | gpl-3.0 | 4,216 | [
"HTSeq"
] | bada116d935ac50e390c378b5aedb8c34d37402625de7c70ea092d4fe8283b53 |
import os
import numpy
import logging
import warnings
from contextlib import contextmanager
from scipy.interpolate import InterpolatedUnivariateSpline as spline
from nbodykit.extern import six
from nbodykit.core import DataSource, Painter, Algorithm
from nbodykit.distributedarray import GatherArray
logger = logging.g... | mschmittfull/nbodykit | nbodykit/fkp.py | Python | gpl-3.0 | 29,203 | [
"Galaxy"
] | af497caf163f21b5ebc7a2139068a6a51ab12648ea9ff805fbf4f842ac58b5aa |
from collections import OrderedDict
from edc_constants.constants import REQUIRED, NOT_REQUIRED, ADDITIONAL, NOT_ADDITIONAL
from edc_visit_schedule.classes import (
VisitScheduleConfiguration, site_visit_schedules,
CrfTuple, MembershipFormTuple, ScheduleTuple, RequisitionPanelTuple)
from tshilo_dikotla.constan... | botswana-harvard/tshilo-dikotla | td_infant/visit_schedule/infant_birth_visit_schedule_v3.py | Python | gpl-2.0 | 17,200 | [
"VisIt"
] | 1b42dcacedd7a61e7617b599257eb8044ff153d71257056b39b926b0d1e96258 |
# Install setuptools if not installed.
try:
import setuptools
except ImportError:
from ez_setup import use_setuptools
use_setuptools()
from setuptools import setup, find_packages
# read README as the long description
with open('README.rst', 'r') as f:
long_description = f.read()
setup(
name='urb... | apdjustino/urbansim | setup.py | Python | bsd-3-clause | 1,399 | [
"ORCA"
] | 73d94c11f2cef2411b744d07e2e7f8e9db8625de47dd18226e2306bc733296c8 |
import Avogadro
import unittest
from PyQt4.QtGui import *
from numpy import *
from util import *
class TestMesh(unittest.TestCase):
def setUp(self):
self.molecule = Avogadro.molecules.addMolecule()
self.mesh = self.molecule.addMesh()
def test_name(self):
self.mesh.name = "testing"
self.assertEqual... | rcplane/periodicdisplay | reference/avogadro/libavogadro/src/python/unittest/mesh.py | Python | gpl-2.0 | 2,500 | [
"Avogadro"
] | 15d1014bb8fc61444be814b7571c71a3121ed7d97dc8652e1399b6f009f0e6fc |
#
# Copyright (c) 2019, 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 it
# under the terms of the GNU General Public License version 3 only, as
# published by the Free Software Foun... | graalvm/fastr | com.oracle.truffle.r.test.packages/pkgtest/util.py | Python | gpl-2.0 | 9,588 | [
"VisIt"
] | 4e8cfd514f0e4e6625792b368d70abf15bf0080e1a815a9bd5c80dbf5951b92a |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of seq_crumbs.
# seq_crumbs 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, ... | JoseBlanca/seq_crumbs | crumbs/seq/transcript_orientations.py | Python | gpl-3.0 | 7,260 | [
"BLAST"
] | 448b9a801053968ffd8899553b3ec2607533994987cbbc64fbdfdcf7f0ae02cc |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | Jorge-Rodriguez/ansible | lib/ansible/modules/network/avi/avi_poolgroup.py | Python | gpl-3.0 | 5,725 | [
"VisIt"
] | c5af1250566bf285c01738ffecae1bc136ecba63b35ea58f14370d76377ad161 |
#* 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
#* https://www.gnu.org/licenses/lgpl-2.1.html
import sys
... | nuclear-wizard/moose | python/peacock/ExodusViewer/plugins/ClipPlugin.py | Python | lgpl-2.1 | 5,670 | [
"MOOSE"
] | 06e434c2edebc7a086d26419a824dda14431d3778cb7d97309623f614e416872 |
"""
Mathematical transforms.
"""
# Copyright (C) 2009-2011 University of Edinburgh
#
# This file is part of IMUSim.
#
# IMUSim 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, o... | martinling/imusim | imusim/maths/transforms.py | Python | gpl-3.0 | 7,219 | [
"Gaussian"
] | 048e529c98d75b1d614d585b3fbc85fca593772b14e37390f36406b57872501c |
import sys
import pysam
from collections import Counter
if len(sys.argv) < 2:
sys.exit("usage: alnstat.py in.bam")
fname = sys.argv[1]
mode = "rb" if fname.endswith(".bam") else "r"
bamfile = pysam.AlignmentFile(fname, mode)
stats = Counter()
for read in bamfile:
stats["total"] += 1
stats['qcfail'] += in... | jpgerke/bds-files | chapter-11-alignment/alnstat/alnstat.py | Python | mit | 1,169 | [
"pysam"
] | 76708ed46e76d8a96c4c794ff46eabed422ec27de984091895bfa621e360aa9b |
# Copyright (c) 2015, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree. An additional grant
# of patent rights can be found in the PATENTS file in the same directory.
from casing import camel, title
... | dosten/graphql-parser-php | deps/libgraphqlparser/ast/cxx_visitor.py | Python | mit | 1,334 | [
"VisIt"
] | e619677e9a8175032875025085d8c52d77f844591904510125049d9f2d71927a |
# -*- coding: utf-8 -*-
"""
Created 2/19/19
@author: cdeline
Using pytest to create unit tests for GroundObj
to run unit tests, run pytest from the command line in the bifacial_radiance directory
"""
import bifacial_radiance
import os, pytest
import numpy as np
# try navigating to tests directory so tests run fro... | NREL/bifacial_radiance | tests/test_groundobj.py | Python | bsd-3-clause | 2,474 | [
"EPW"
] | 95145fc416d9f8580013157fa7fe3513293ee5090a7d8812f4589f0b49706d23 |
# ImageNet 2012 id's to class names
id2label = {
0: "tench, Tinca tinca",
1: "goldfish, Carassius auratus",
2: "great white shark, white shark, man-eater, man-eating shark, Carcharodon carcharias",
3: "tiger shark, Galeocerdo cuvieri",
4: "hammerhead, hammerhead shark",
5: "electric ray, crampfi... | huggingface/pytorch-transformers | src/transformers/utils/imagenet_classes.py | Python | apache-2.0 | 33,616 | [
"Bowtie",
"ESPResSo",
"Jaguar",
"ORCA"
] | 547aff98b1ac5d9e8b5b10bc37c75f7f45a445b1e8436356cf70ed0e6e76b928 |
import json
from django.core.exceptions import ValidationError
from django.core.urlresolvers import reverse
from django.utils.translation import ugettext_lazy as _
from django.utils.translation import ungettext_lazy
from keystoneclient.exceptions import Conflict
from horizon import exceptions
from horizon import form... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/policies/access_control/tables.py | Python | gpl-3.0 | 3,510 | [
"CRYSTAL"
] | 718358ab49889d6346c2e3ef45154b502eab0fb794dc2948c667cd647365a45f |
# -*- coding: utf-8 -*-
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
from __future__ import unicode_literals
import copy
import os
import re
import shutil
import tempfile
import threading
import time
import unittest
import warnings
from django.conf import settings
... | indevgr/django | tests/cache/tests.py | Python | bsd-3-clause | 86,798 | [
"Brian"
] | 0ddc8388bdb7ca15c0be6dd675e2f6e4d376ff4cfbc2ce367e4ccb98dd34b394 |
"""Golem actions"""
import code
import importlib
import os
import pdb
import random as rand
import string
import sys
import time
import uuid
import types
import logging
from contextlib import contextmanager
import requests
from golem import browser, execution, helpers
from golem.core import utils
from golem.test_runn... | lucianopuccio/golem | golem/actions.py | Python | mit | 90,780 | [
"VisIt"
] | 32121f932796c3cbfff5c1ee00075c55c5b8397ddb0c6ab66fcca683fd2a04b1 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | fedepad/espressopp | src/integrator/CapForce.py | Python | gpl-3.0 | 2,706 | [
"ESPResSo"
] | 94d8e48e74bda972011d877b14cada6a146af018873a5bae966e8543e274fa5d |
import re
import os
import setuptools
def match(x):
# ignore comments
if re.search(r'(^\s*#)', x):
return False
return True
def replace(x):
match_replace = re.search(r'egg=(.*)', x)
if match_replace:
return match_replace.group(1)
return x
def find_templates(path, parent=None... | badcure/rackspace_cloud_information | setup.py | Python | apache-2.0 | 1,910 | [
"Brian"
] | f93f005722f0483dba7d615c26bf31e33a13a7158793b86846e43443fe5a555a |
from __future__ import print_function
__author__ = 'Thomas Rueckstiess, ruecksti@in.tum.de; Christian Osendorfer, osendorf@in.tum.de'
from scipy import r_, exp, zeros, eye, array, asarray, random, ravel, diag, sqrt, sin, cos, sort, mgrid, dot, floor
from scipy import c_ #@UnusedImport
from scipy.linalg import solve,... | arabenjamin/pybrain | pybrain/auxiliary/gaussprocess.py | Python | bsd-3-clause | 9,240 | [
"Gaussian"
] | c241f8edae01bb5b566df6f4bb5dd176b1f45ea99b546b5afa492b87ff3b31e5 |
#!/usr/bin/python
#
# March, 2016
#
# @author Soumya Ghosh
#
# @Usage
#
# runlambda.py arg1 arg2 arg3 arg4 arg5
#
# where
# arg1 = name of the 1st equilibrium inputfile without .inp extension
# arg2 = name of the 2nd equilibrium inputfile without .inp extension
# arg3 = name of the 1st non-equilibrium inputfile w... | gms-bbg/test-validation | solvent/reorg/runlambda.py | Python | gpl-3.0 | 21,810 | [
"GAMESS"
] | bc391787252f688b07bc95abaa814c349241a3cda700992bc1ad0db9b1966d05 |
#!/bin/python
from collections import OrderedDict
import inspect
import numpy as np
import pandas as pd
import NotebookTools as NT
import matplotlib
import matplotlib.pyplot as plt
from matplotlib import cm
from scipy import constants
import os
import peakutils
from scipy import fftpack
from scipy import signal
from s... | laserkelvin/IPython-Notebook-Tools | SpectralAnalysis.py | Python | gpl-3.0 | 52,938 | [
"Gaussian"
] | 01ed78ad25fb63c0d0f2a2e5bc8e3a71e3ad14b37d6e44812f20387530f2fee4 |
"""
Author: Justin Cappos
Module: A shell for Seattle called seash (pronounced see-SHH). It's not meant
to be the perfect shell, but it should be good enough for v0.1
Start date: September 18th, 2008
This is an example experiment manager for Seattle. It allows a user to
locate vessels they control and ... | sburnett/seattle | production_nat_new/src/nmpatch/seash.py | Python | mit | 93,814 | [
"VisIt"
] | 012b3d961b3c92d420be8a294dc12a7e5a290bd48de82a9af9f9682965999c3b |
# -*- coding: utf-8 -*-
"""
objc_codegen
~~~~~~~~~~~~
AST to Objective-C code generator.
Based on "codegen", a tool for converting an ast to python, by Armin Ronacher.
:copyright: Copyright 2008 by Armin Ronacher.
:copyright: Copyright 2011 by Anders Hovmöller.
:copyright: Copyright 2012 b... | boxed/Misc | codegen_objc.py | Python | mit | 25,032 | [
"VisIt"
] | b557dd300b3b060a0008b085c0afb7c1dfaed337dd25f5d5684f96b5071dc0bc |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | value_dice/twin_sac.py | Python | apache-2.0 | 13,437 | [
"Gaussian"
] | 1096427afda21515221f9a010c6e9a3e41c35dd5128cfe92691137a9b373f1fc |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-zlibbioc/package.py | Python | lgpl-2.1 | 1,945 | [
"Bioconductor"
] | efd7ab7e14e30275a3d42f58f6bbfe965a08570cf4536444ae3687ec6b87fc5d |
from __future__ import print_function
import warnings
from math import pi
import numpy as np
from pyfisher import TheorySpectra
from scipy.interpolate import interp1d
from scipy.integrate import quad
import itertools
try:
import cPickle as pickle
except:
import pickle
import time, re, os
from scipy.integrate i... | msyriac/orphics | orphics/cosmology.py | Python | bsd-2-clause | 61,842 | [
"Galaxy",
"Gaussian"
] | 3105f33551c7632832979c6d9781e1e1dc2c073bea9072677e19976c49b7df18 |
#!/usr/bin/env python
########################################################################
# :file: dirac-dms-directory-sync
# :author: Marko Petric
########################################################################
"""
Provides basic rsync functionality for DIRAC
Syncs the source destination folder recu... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_directory_sync.py | Python | gpl-3.0 | 18,178 | [
"DIRAC"
] | 556c8a8be3c99281b418cc1f722e5a41404d439550186c96630bd508cfda5bf1 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | wangmiao1981/spark | python/pyspark/pandas/generic.py | Python | apache-2.0 | 104,770 | [
"Elk"
] | a999ffb4dff489939d37474d8fbbfce387ef776838f76c676f889764a808d3d1 |
import numpy as np
from mdtraj import compute_dihedrals, compute_phi
from mdtraj.testing import eq
from scipy.stats import vonmises as vm
from msmbuilder.example_datasets import AlanineDipeptide, MinimalFsPeptide
from msmbuilder.featurizer import get_atompair_indices, FunctionFeaturizer, \
DihedralFeaturizer, Atom... | dr-nate/msmbuilder | msmbuilder/tests/test_featurizer.py | Python | lgpl-2.1 | 4,624 | [
"MDTraj"
] | b334e11835ce6de3a366d201c7723ed24f43feebe127546dd721c716074450fd |
'''
Pmt
===
module with the photomultiplier response function
'''
import numpy as np
from scipy import stats, constants
def apply_pmt(pulse,t,ndynodes=10,delta=4,sigma=5.,transittime=100.):
'''Adds the pmt response to a signal.
The pmt response is modeled as a gaussian with amplitude depending on the
n... | FedericoBinda/dacsim | src/pmt.py | Python | lgpl-3.0 | 1,592 | [
"Gaussian"
] | 820c55e94412a7eee1a66a81d92ff27db484e9cbf1805b75fe4320dc8fb4eb69 |
from ase.lattice import bulk
from gpaw import GPAW, FermiDirac
from gpaw.wavefunctions.pw import PW
a = 5.431
atoms = bulk('Si', 'diamond', a=a)
calc = GPAW(
mode=PW(200), # energy cutoff for plane wave basis (in eV)
kpts=(3,3,3),
xc='LDA',
eigensolver=... | robwarm/gpaw-symm | doc/tutorials/gw_tutorial/Si_groundstate.py | Python | gpl-3.0 | 609 | [
"ASE",
"GPAW"
] | 64b8402bc10720db18eafe583dd3be063c91ba860db1206f86422faf96c019ca |
import sys
from datetime import datetime
import pkg_resources
pkg_resources.require("SQLObject>=0.10.1")
from sqlobject import *
from turbogears.database import AutoConnectHub, PackageHub
from sqlobject import SQLObject, SQLObjectNotFound, RelatedJoin
from sqlobject.inheritance import InheritableSQLObject
# import s... | yCanta/yCanta | webapp/model.py | Python | unlicense | 8,205 | [
"VisIt"
] | d190b989173dd276dd23623b753a8c59816c3283fc8112ef5d141de4eccc72fb |
config ={
"name" : "Ijwu's MazeWorld Generator", #plugin name
"type" : "generator", #plugin type
"description" : ["Generates a maze world."] #description
}
import omnitool.colorlib as clib
import omnitool.database as db
from pgu import gui
import pygame
from random import randint, choice, random
i... | Berserker66/omnitool | plugins/mazeGen.py | Python | mit | 27,378 | [
"CRYSTAL"
] | 798a9ab72d3691e5e5a2ef5bd5baefe703c7d4a43f29f90e48446677d322ab70 |
#!/usr/bin/env python
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Af... | bgoli/pysces | setup.py | Python | bsd-3-clause | 11,657 | [
"PySCeS"
] | 1e5eb11e290b6a719ccd5538fa2f1e3735951a08747d478416594c70afb32954 |
import csv
from datetime import datetime, timedelta
import dateutil.parser
from dateutil.parser import parse as parsedate
class TestVisits:
VISIT_INTERVAL_SECONDS = 600
def test_no_tag(self, helper):
admin = helper.admin_user()
cosmo = helper.given_new_user(self, "cosmo")
cosmo_group ... | TheCacophonyProject/Full_Noise | test/test_visits.py | Python | agpl-3.0 | 15,461 | [
"VisIt"
] | b3d9abf4419e72918313c01772f3ada45631b8886bb9a467c6576a9a3e8ab1f6 |
"""Integration with Python standard library module urllib2: OpenerDirector
class.
Copyright 2004-2006 John J Lee <jjl@pobox.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file
COPYING.txt included with the distribution).
"""
import o... | cloudfflies/qldt2 | src/controllers/gaemechanize2/_opener.py | Python | gpl-3.0 | 14,926 | [
"VisIt"
] | 7bb76d72f5c93c457aca3bbc8bfd9b596ed016bdefacd2562757e9d7180f4f58 |
import logging
logger = logging.getLogger(__name__)
from os import path , mkdir, listdir
import ocgis
def get_equation(culture_type='fallow', climate_type=2):
"""
returns the equation as basis to calculate the segetal flora
:param culture_type: Type of culture. possible values are
'fallo... | sradanov/flyingpigeon | flyingpigeon/segetalflora.py | Python | apache-2.0 | 12,347 | [
"NetCDF"
] | a7ddfde4a4cb01e7a308903472baa79559d44b2ac85b47e491abe6384893ce46 |
# Copyright 2004-2015 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, m... | joxer/Baka-No-Voltron | tmp/android.dist/private/renpy/display/image.py | Python | gpl-2.0 | 12,312 | [
"VisIt"
] | d1c15db1c81181a727f582153ffbb98f5e158db83b27aa3d233c80a29cd0e4a6 |
'''
Working from Miguel Rocha's script: genSunriseInput.py. This script
generates the cameras to use in Sunrise and makes some projection plots for
a few of the cameras.
'''
import numpy as np
from numpy import *
import os, sys, argparse
from collections import OrderedDict
import time
#from blist import blist
import ... | gsnyder206/vela-yt-sunrise | genSunriseInput.py | Python | gpl-3.0 | 16,955 | [
"Galaxy"
] | 5d51daaf45c90d8a5d2fa3f479ab68aabac2643ba9c205b7788a1a9eaa16505a |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import warnings
import threading
from . import sigtools
from scipy.lib.six import callable
from scipy.lib._version import NumpyVersion
from scipy import linalg
from scipy.fftpack import (fft, ifft, ifftshift, ff... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/scipy/signal/signaltools.py | Python | apache-2.0 | 66,141 | [
"Gaussian"
] | 43798977d6da78e52b9ad0b260b3120130ed4ce863835479aa64b653501d7274 |
import sys
from ma import MA
from readwrite import *
def main(args, with_visual_appeal=True):
datadict = read_shp(args.infile, densify_n_times=args.densify, roll=args.roll)
if args.noise != 0:
add_noise(datadict, args.noise, args.recompute_normals)
# creating shrinking ball object
ma = M... | Ylannl/masb2d | main.py | Python | gpl-3.0 | 2,130 | [
"Gaussian"
] | b95fc3dd5c2da6db1f81776749fe493f2fa5feacd7d94f1c6bec3203518efebe |
#pylint: disable=no-init,invalid-name,too-many-locals,too-many-lines, redefined-builtin
from __future__ import (absolute_import, division, print_function)
from six.moves import range
import numpy as np
import re
import os.path
import math
from collections import OrderedDict
from mantid.kernel import *
from mantid.api... | dymkowsk/mantid | Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SimulatedDensityOfStates.py | Python | gpl-3.0 | 34,538 | [
"CASTEP",
"Gaussian"
] | 5685d644d897f7f981f1764a1412b2fdfd72632a00bd0cad1e3a87b9da988cff |
# -*- coding: utf-8 -*-
"""
End-to-end tests for LibraryContent block in LMS
"""
import ddt
import textwrap
from nose.plugins.attrib import attr
from unittest import skip
from ..helpers import UniqueCourseTest, TestWithSearchIndexMixin
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview im... | nttks/edx-platform | common/test/acceptance/tests/lms/test_library.py | Python | agpl-3.0 | 13,897 | [
"VisIt"
] | 661db76f60fbc4460c50db0571a7b2c471a7629a6ae98fa0d752e264c73ef670 |
"""SM group theory and fields classes and functions."""
from sympy import Rational
global GUTU1
GUTU1 = True # Is U(1) coupling normalized for GUT unification?
def CA(N):
"""Quadratic Casimir in adjoint rep C2(A)."""
if N == 1:
return 0 # no self-interaction in U(1)
else:
return N
... | openhep/ackp16 | smgroup.py | Python | gpl-3.0 | 2,641 | [
"DIRAC"
] | 1956eafb6cd349d8a10abdb84eaccb8abc2337e641835a055be50303c7bf22de |
#-------------------------------------------------------------------------------
# Cloud-COPASI
# Copyright (c) 2013 Edward Kent.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available... | edkent/cloud-copasi | cloud_copasi/web_interface/aws/vpc_tools.py | Python | gpl-3.0 | 5,673 | [
"COPASI"
] | f91a63756e5937dd448e5cc9e3ca58b8e98cd3403fb3440447530fa7138f73fd |
# Copyright (C) 2017 Alex Nitz
#
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in t... | tdent/pycbc | pycbc/noise/reproduceable.py | Python | gpl-3.0 | 8,187 | [
"Gaussian"
] | 5e36ce2ab77eeb07f110302dc7fb7fe499ef62185544825471d74d870fa5d355 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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
# ... | halberom/ansible | lib/ansible/modules/network/lenovo/cnos_backup.py | Python | gpl-3.0 | 11,184 | [
"VisIt"
] | c28cf10fb045cc5a2231307db40a7e3acb47d665bfaa20418d043198630c5831 |
"""
Module for evolutionary parameter optimization
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from builtins import zip
from builtins import range
from builtins import open
from builtins import str
from futu... | Neurosim-lab/netpyne | netpyne/batch/evol.py | Python | mit | 19,543 | [
"NEURON"
] | 82dc54bacc359df7a2154c226101059cc8e6691011b3a47c7d2bad0e808257b8 |
#
# Copyright (C) 2003-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" functionality for finding ... | bp-kelley/rdkit | rdkit/Chem/Pharm2D/Matcher.py | Python | bsd-3-clause | 4,027 | [
"RDKit"
] | 8069211c542b25042d2c39a353fa1a1c9c8add3efc11bd04e52748f9f2f66b13 |
"""
This model solves the time dependent advection-diffusion equation using FEM
SUPG is used in terms of numerical stability issues
Copyright 2017 Anna Wirbel and Alexander H. Jarosch
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Pu... | awirbel/debadvect | 2D_btest/advect_gl.py | Python | gpl-3.0 | 6,764 | [
"VTK"
] | 4f6edd15047a04bc727a30c3ca67018673b34ebc18bde718b557f1bc03218162 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Original source: github.com/okfn/bibserver
# License: AGPLv3
'''
BibTex parser.
'''
import sys
import string
import io
import json
import unicodedata
import re
class BibTexParser(object):
def __init__(self, fileobj):
data = fileobj.read()
... | sciunto/ZimBibliographer | ZimBibliographer/bibtexparser.py | Python | gpl-3.0 | 95,336 | [
"Bowtie"
] | ebdd6456c9cc9d5896dc7c52689bf3ffa667e4d041bbf641d31c27cb5011ec38 |
from __future__ import print_function, division
import multiprocessing, time
import numpy as np
import scipy.sparse, h5py
import fabio
from ImageD11 import cImageD11
#from .
import sparse_peak_searching
import sys, os, glob
# Estimate a noise level and determine a threshold
def sigma_cut( img, nsigma=3. ):
"""
... | jonwright/ImageD11 | sandbox/collect_peak_pixels.py | Python | gpl-2.0 | 4,240 | [
"Gaussian"
] | 7c34c980315e79dc6e49c99786d07b93354d1a522e8ca2eb608334e2ad68bd1c |
# An example of embedding CEF browser in wxPython on Mac.
# Tested with wxPython3.0-osx-3.0.2.0-cocoa-py2.7.dmg which
# was downloaded from the wxpython.org website.
# IMPORTANT - importing CEF Python
# --------------------------------------------------------------
# The cefpython library must be the very first librar... | gf0842wf/cefjs | refer_to.py | Python | mit | 34,697 | [
"VisIt"
] | 5d4c2e84dbb3f4c7a54b0196141a8c5e941c2d79fd152aa91e13f11cef1265c7 |
from google.appengine.ext import db
import datetime
import markdown
from libs import PyRSS2Gen
import logging
import md5
import layer_cache
from google.appengine.api import memcache
class BaseModel(db.Model):
pass
class Tag(BaseModel):
tag = db.StringProperty()
class NewsItem(BaseModel):#Which in ... | bbondy/brianbondy.gae | blog/models.py | Python | mit | 9,067 | [
"Brian"
] | 12d81a160296bb5788dae936d862ad03916bcbd9120edd331a3df691af75b297 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/thole.py | Python | gpl-3.0 | 3,181 | [
"ESPResSo"
] | fbb4a3a44532d1e37631e0c3fa18686f0f763081959f7c126bef164ff1f31592 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import re
import csv
import collections
import itertools
from io import open
import math
from six.moves import zip
import warnings
from monty.json import MSON... | setten/pymatgen | pymatgen/analysis/phase_diagram.py | Python | mit | 76,238 | [
"pymatgen"
] | 08b6b45746f4a123152c1c7f7dca413f5554123196cdc2657dd79c40dce8e2d8 |
from yargy.visitor import Visitor
from yargy.dot import (
style,
DotTransformator,
BLUE,
ORANGE,
RED,
PURPLE,
GREEN,
DARKGRAY
)
from yargy.predicates import is_predicate
from .constructors import (
is_rule,
Production,
EmptyProduction,
Rule,
OrRule,
OptionalRule... | bureaucratic-labs/yargy | yargy/rule/transformators.py | Python | mit | 14,871 | [
"VisIt"
] | 1deae8f469478b4385be44717168c8f042b1c066deb4c12e239e9be8ed0f40ab |
# -*- coding: ISO-8859-15 -*-
# =============================================================================
# Copyright (c) 2004, 2006 Sean C. Gillies
# Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#
# Authors :
# Oliver Clements <olcl@pml.ac.uk>
#
# Contact email: olcl@pml.ac.uk
# =======================... | ocefpaf/OWSLib | owslib/coverage/wcs201.py | Python | bsd-3-clause | 20,092 | [
"NetCDF"
] | 8d38376c043b9032b2f7149672679289e13b01b2ac74638ff0d95a221b8d9e9e |
#!/usr/bin/env python
# coding: utf-8
"""
This script replaces strings in the source files. See replace_string function.
"""
import sys
import os
TOPDIR = os.path.dirname(os.path.realpath(__file__))
def source_paths_from_abinit_src(top=None):
"""
Return list with absolute paths of source files extracted from... | abinit/abinit | change_source.py | Python | gpl-3.0 | 4,570 | [
"ABINIT"
] | 9ee3c1071294b7522cb6f8489d60300a4311b834c2f862e5bd0041bbfdf0a3ae |
# Copyright 2013 Lenna X. Peterson. 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.
"""Unit test for Bio.PDB.DSSP which need the binary tool.
See also test_PDB.py for dependenc... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_DSSP_tool.py | Python | gpl-2.0 | 1,392 | [
"Biopython"
] | 2e0bd0b779673e13a6844c44e3c98ef2bdb45d0e6bf1234e34080bfe26e7f990 |
from web.template import CompiledTemplate, ForLoop, TemplateResult
import admin
# coding: utf-8
def about():
__lineoffset__ = -5
loop = ForLoop()
self = TemplateResult(); extend_ = self.extend
extend_([u'<div>\n'])
extend_([u' <p>\n'])
extend_([u' ', escape_(safemarkdown(settings.ABOUT), Fal... | systempuntoout/buckethandle | app/views/__init__.py | Python | bsd-3-clause | 63,534 | [
"VisIt"
] | aaa8f45d2acc0754ecd878857bc7a2cbe8d00e44d687a5e3214902303e3a19fb |
import os, logging, time
from pytopol.parsers.psf import PSFSystem
from pytopol.parsers.par import ParType
import blocks
module_logger = logging.getLogger('mainapp.charmmpar')
'''
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html
'''
class CharmmPar(object):
""" A class for re... | resal81/PyTopol | pytopol/parsers/charmmpar.py | Python | gpl-3.0 | 18,888 | [
"CHARMM",
"NAMD"
] | 314e1517bc4b907c1663a228642cfe9416772011dcfe19f277029d0f186bceb4 |
#numpy.set_printoptions(threshold=numpy.nan) # Makes arrays print fully when they are large.
from collections import OrderedDict
# Planck's constant [eV-s]
h = 4.135667517e-15;
#h = 6.626068e-34 ; %SI
# Classical electron radius [m]
r0 = 2.8179403268e-15;
# Speed-o-light m/s
c = 299792458;
# Avogadro's number [mol-1]... | ZGainsforth/MultiLaue | SiHyperlaueFinal_shielded_results/PhysicsBasics.py | Python | epl-1.0 | 4,541 | [
"Avogadro"
] | 32aff7b13d369e9d1866bcdf0f884e378465c698efd6fb0254f7df09cdd4f8ab |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAcde(RPackage):
"""Artificial Components Detection of Differentially Expressed Genes.
... | iulian787/spack | var/spack/repos/builtin/packages/r-acde/package.py | Python | lgpl-2.1 | 1,628 | [
"Bioconductor"
] | ef068338afddb8fbe851f8b78118b276f7d3fc3c74101ca85fcb78fd84283e60 |
# Main basic file to run a simple NEURON-Python file. See manual for detailed instructions.
from __future__ import division
from neuron import h
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
#function to calculate derivatives of voltage and gating variables
def deriv(a,b):
der=[]
if len(a... | mohitganguly/IRBlock_Vanderbilt | 2/main_basic_mHH.py | Python | gpl-3.0 | 3,958 | [
"NEURON"
] | 58ffb01d573cf5d98887c5819a9aaa1d354e4f3570ff4debc489e771808d04b4 |
# Copyright (c) 2018 PaddlePaddle 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 appli... | baidu/Paddle | python/paddle/fluid/layers/nn.py | Python | apache-2.0 | 409,633 | [
"NEURON"
] | f9db0081304e4a683cd92daf9dbebcc813ccdbc707f1f00598dcd242a959e0b1 |
"""
PackageKit integration.
"""
# Copyright (C) 2010, Aleksey Lim
# See the README file for details, or visit http://0install.net.
import os
import locale
import logging
from zeroinstall import _, SafeException
from zeroinstall.support import tasks
from zeroinstall.injector import download, model
_logger_pk = loggi... | timdiels/zeroinstall | zeroinstall/injector/packagekit.py | Python | lgpl-2.1 | 10,105 | [
"VisIt"
] | be7921f9ccbfea3a9fdc59319be304db47fa032e3c0a7e7640610a60b3e64704 |
# coding: utf-8
from __future__ import unicode_literals
import unittest
import os
from numbers import Number
from pymatgen.core.composition import Composition
from pymatgen.core.periodic_table import Element
from pymatgen.phasediagram.pdmaker import PhaseDiagram
from pymatgen.phasediagram.pdanalyzer import PDAnalyz... | yanikou19/pymatgen | pymatgen/phasediagram/tests/test_pdanalyzer.py | Python | mit | 4,651 | [
"pymatgen"
] | e246e2498e3162cec6acc1d38258630d7ca42fe0a2eccd61ede00c7be19ab964 |
# Copyright (c) 2003-2011 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | michalliu/chromium-depot_tools | third_party/pylint/checkers/variables.py | Python | bsd-3-clause | 23,518 | [
"VisIt"
] | 208921a786bb3a58a75d09807c7e6437331b3100e186e5bfd3312cfd8b4347d1 |
#
# Copyright (C) 2013 Stefano Sanfilippo
# Copyright (C) 2013 BITS development team
#
# This file is part of bitsd, which is released under the terms of
# GNU GPLv3. See COPYING at top level for more information.
#
"""
Assorted Tornado UI widgets and mixins.
"""
import tornado.web
from tornado.options import options... | BitsDevelopmentTeam/bits-server | bitsd/server/uimodules.py | Python | gpl-3.0 | 3,392 | [
"Dalton"
] | b51a9882abf07efd00cfa35ec05634cb16317964b9c87a9762efc447c02d99a8 |
# -*- coding: utf8 -*-
from __future__ import absolute_import
"""
"""
__author__ = "Jerome Samson"
__copyright__ = "Copyright 2014, Mikros Image"
import logging
import time
try:
import simplejson as json
except ImportError:
import json
from tornado.web import HTTPError
from octopus.core.communication.http i... | mikrosimage/OpenRenderManagement | src/octopus/dispatcher/webservice/job.py | Python | bsd-3-clause | 3,190 | [
"Octopus"
] | 633d6aae83b7c245b4bceae8f53dfc71a4a1b4b94cbe560e91a17b16dd7393fd |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of hadoop-galaxy, released under the terms of the BSD
# 3-Clause License <http://opensource.org/licenses/BSD-3-Clause>.
#
# END_COPYRIGHT
import os
import urlparse
class Pathset(object):
"""
A collection of paths, with an associated data type.
... | crs4/hadoop-galaxy | hadoop_galaxy/pathset.py | Python | bsd-3-clause | 4,175 | [
"Galaxy"
] | 1661b03b070f4512c95beed4a641254fad5c8eee0f2923c2a349bfec3a729898 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2020 University of Liège
#
# 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
#
# ... | rboman/progs | classes/sph0/louis/tests/waterdrop2.py | Python | apache-2.0 | 2,670 | [
"VTK"
] | b11379c71f5b54ee8d4dd30eda095068d667c654e1124b6e6d6878d98a0f7166 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, 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.
"""Parser for GAMESS-UK output files"""
import re
import numpy
from cclib.parser import logfileparser
from cclib.parse... | cclib/cclib | cclib/parser/gamessukparser.py | Python | bsd-3-clause | 31,242 | [
"GAMESS",
"Gaussian",
"cclib"
] | 8681a00782cf6f7c55ae0027fe2892acba1e358f583bd839bbb8f0ce0db6be7e |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | alxgu/ansible | lib/ansible/modules/network/avi/avi_scheduler.py | Python | gpl-3.0 | 5,272 | [
"VisIt"
] | ac19610c0532eb4d5a837329d67e70285a1fd2f7394b07a1d8267f7888135d84 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RNlme(RPackage):
"""Fit and compare Gaussian linear and nonlinear mixed-effects models
... | LLNL/spack | var/spack/repos/builtin/packages/r-nlme/package.py | Python | lgpl-2.1 | 1,491 | [
"Gaussian"
] | 79e6a24367126c35436625bbe158c9a437457e22e2c7f4ef7677d1d317535405 |
#!/usr/bin/env python3
from __future__ import with_statement
from setuptools import setup
from io import open
with open('README.txt') as file:
long_description = file.read()
setup(name='ipfix',
version='0.9.8',
description='IPFIX implementation for Python 3.3+',
long_description = long_descript... | britram/python-ipfix | setup.py | Python | lgpl-3.0 | 1,085 | [
"Brian"
] | 883dded2130e81349316881030e40492567470e12115fc33cc1774faaf4f5fc3 |
import time, re, os, argparse,shutil, sys
from tree_refine import tree_refine
from virus_clean import virus_clean
from virus_filter import flu_filter
from date_util import numerical_date
from collections import defaultdict
from process import process, virus_config
from Bio import SeqIO, AlignIO
from Bio.Seq import Seq
... | neherlab/treetool | augur/src/mutation_tree.py | Python | mit | 16,279 | [
"BLAST"
] | 995e305395f4fbc15ad048d1d328d96ecb530b874e42a865b1202a8eba8c863c |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import pytest
import os.path as osp
from sisl.io.siesta.basis import *
pytestmark = [pytest.mark.io, pytest.mark.siest... | zerothi/sisl | sisl/io/siesta/tests/test_basis.py | Python | mpl-2.0 | 1,033 | [
"SIESTA"
] | 749832fb510aede7a8d5424951e0630bdf94e368d7800ee84abf1490c144b918 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/powerstate.py | Python | gpl-2.0 | 5,042 | [
"VisIt"
] | e08087627bb8a3afd987f6d85edd50b6cde2c92d78083deb6532f3d3fec16cb0 |
import sys
import os
import argparse
import multiprocessing
import logging
import collections
import itertools
import traceback
from functools import partial
import json
import base64
import time
import pysam
import pybedtools
from defaults import *
from sv_interval import *
def concatenate_files(files, output):
... | chapmanb/metasv | metasv/generate_sv_intervals.py | Python | bsd-2-clause | 43,857 | [
"pysam"
] | 2d10665581c4eac1cef79dcd3aa64a4a5f2b57ec0e24ff2d1dd73a033ffee3ec |
"""Visualization helpers."""
from contextlib import contextmanager
import copy
import os.path as op
import numpy as np
from scipy import linalg
from mne import read_proj, read_events, pick_types
from mne.utils import verbose
from mne.viz.utils import tight_layout, plt_show
from ._sss import compute_good_coils
from ... | Eric89GXL/mnefun | mnefun/_viz.py | Python | bsd-3-clause | 17,918 | [
"Mayavi"
] | 87e69084da9c0a4ec1b742adabb5e7c583f6697deed2bb156533e7182dfa4e3c |
#
# This source file is part of the EdgeDB open source project.
#
# Copyright 2016-present MagicStack Inc. and the EdgeDB 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... | edgedb/edgedb | edb/graphql/codegen.py | Python | apache-2.0 | 5,528 | [
"VisIt"
] | 03101d18f2664186d5282dd5e0d364645b73d29ed4e830009b25e4a863401e56 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-06-20 16:36:37
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-11-13 15:16:57
from __future__ import print_function, division, absolute_import
from marvin.utils.genera... | albireox/marvin | python/marvin/tests/utils/test_images.py | Python | bsd-3-clause | 11,203 | [
"Brian",
"Galaxy"
] | 7f19b405ad6ec8d83279c5345e2dab1a6c83d1b2031305e6a0a65b7998a5c90d |
#!/usr/bin/env python
"""
PUQ Analysis Tool
Martin Hunt
Purdue University
This file is part of PUQ
Copyright (c) 2013-2016 PUQ Authors
See LICENSE file for terms.
"""
from __future__ import absolute_import, division, print_function
import matplotlib
matplotlib.use('TkAgg', warn=False)
import scipy
import numpy as n... | c-PRIMED/puq | puq/analyzer.py | Python | mit | 56,659 | [
"Gaussian"
] | c345d13370170233f5be5190775a2205ae12ff97e0a2a1c9936a7877c6cc0a90 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import sys
import os
import subprocess
import shutil
import argparse
import json
import datetime
import funannotate.library as lib
from natsort import natsorted
... | nextgenusfs/funannotate | funannotate/predict.py | Python | bsd-2-clause | 106,582 | [
"BLAST"
] | 4d1d6d4093055ac02cc64d4dd12bbfe3e3d4f27f67fe35a51e453a03f2d7950e |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS that utilize the
progress page.
"""
from contextlib import contextmanager
import ddt
from nose.plugins.attrib import attr
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.common.logout import LogoutPage
from ...pages.lms.courseware ... | fintech-circle/edx-platform | common/test/acceptance/tests/lms/test_progress_page.py | Python | agpl-3.0 | 17,036 | [
"VisIt"
] | d86319c2e7789c863abf34ba1f5227b890cd45bbfbb21a301a8abfc51488de7b |
#
# This file is part of the Connection-Set Algebra (CSA).
# Copyright (C) 2010,2011,2012 Mikael Djurfeldt
#
# CSA 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
# (a... | INCF/csa | tests/test_csa.py | Python | gpl-3.0 | 6,860 | [
"Gaussian"
] | 921da7e144aca043c0564b09c148b2f58a2293f5702c6f846ab7ff0652fdcef0 |
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