text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# proxy module
from __future__ import absolute_import
from mayavi.tools.server import *
| enthought/etsproxy | enthought/mayavi/tools/server.py | Python | bsd-3-clause | 88 | [
"Mayavi"
] | df62320f38346eafcee413b3482b2f0a69a27e2cb19ffae3f230388e8ddd75f6 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/scancode/test_ignore_files.py | Python | apache-2.0 | 4,127 | [
"VisIt"
] | d83e1a794ef6fcac98c48cd97e0608c400cfc6d57651b76db9e26b7567793341 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkStripper(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkSt... | nagyistoce/devide | modules/vtk_basic/vtkStripper.py | Python | bsd-3-clause | 477 | [
"VTK"
] | 1fc9962225c5426517b25ffe356e17fd3b8862508bf230ca14095a7e8412e3f3 |
import sys
import os
import os.path
import hashlib
import re
import fnmatch
import time
import shutil
import errno
import tempfile
import codecs
import cPickle as pickle
import stat
from stat import ST_MTIME
# We import only jumpscale as the j.system.fs is used before jumpscale is initialized. Thus the q cannot be im... | Jumpscale/jumpscale6_core | lib/JumpScale/core/system/fs.py | Python | bsd-2-clause | 79,683 | [
"VisIt"
] | 8671614de14574cee7ea25bf26e39a981347e9318b9f9dfa8018e05fc32fd430 |
"""This package contains the spectral shape item."""
import numpy as np
from glotaran.model import model_attribute, model_attribute_typed
from glotaran.parameter import Parameter
@model_attribute(properties={
'amplitude': Parameter,
'location': Parameter,
'width': Parameter,
}, has_type=True)
class Spect... | glotaran/glotaran | glotaran/builtin/models/kinetic_spectrum/spectral_shape.py | Python | gpl-3.0 | 1,929 | [
"Gaussian"
] | d99fa270a4730356e7f69e21719762db635e86494441fcd9061324c127b9f568 |
#!/usr/bin/env python
import numpy as np
from math import floor
from numpy import linalg as la
from numpy import matlib as matlib
import matplotlib.pyplot as plt
import argparse
import os
import pdb
from scipy import spatial
import time
import operator
import random
import warnings
FISHER = 0
RANDOM_CLASSIFIER = 0
def... | lukefrasera/cs775Homework | tim_midterm/scripts/decisionTree.py | Python | lgpl-3.0 | 13,150 | [
"Gaussian"
] | c73cc0b6123636eee61093b95038201e595325c6885668374a7b80ee35e3b628 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkPostScriptWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
v... | chrisidefix/devide | modules/vtk_basic/vtkPostScriptWriter.py | Python | bsd-3-clause | 492 | [
"VTK"
] | 93ae8c2264bac6c16414d89685158424db7b63916a6f24c95888c332156bd49d |
#
# QAPI event generator
#
# Copyright (c) 2014 Wenchao Xia
# Copyright (c) 2015 Red Hat Inc.
#
# Authors:
# Wenchao Xia <wenchaoqemu@gmail.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from qapi im... | coloft/qemu | scripts/qapi-event.py | Python | gpl-2.0 | 4,247 | [
"VisIt"
] | 99af5fbc5cda5e47ee16a32504d5d66fe9026b260c7a580e58e142aab56d2650 |
# Copyright 2018 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Unit tests for translation_helper.py."""
import unittest
import os
import sys
import translation_helper
here = os.path.realpath(__file__)
testdata_path =... | scheib/chromium | tools/translation/helper/translation_helper_unittest.py | Python | bsd-3-clause | 4,529 | [
"xTB"
] | 269e2ab663d382282831fb207c6cf8758d4b9ee811bf314bd11c183bb58ad484 |
from argparse import ArgumentParser
import os
import shutil
import sys
import yaml
import MDAnalysis
from data import Data
from plots import Plots
from molecule import Molecule
from draw import Draw
from figure import Figure
from analysis.hbonds import HBonds
from analysis.residence_time import Residence_time
from anal... | ldomic/lintools | lintools/lintools.py | Python | gpl-3.0 | 14,779 | [
"MDAnalysis",
"RDKit"
] | a750f1408044759d4c3fc5578d1bfbaf136801f7fac8bb9da18a7bc354967c49 |
import math
import numpy as np
import matplotlib.pyplot as plt
from neuron import Neuron
def gabor1D(phi, m):
sigmaX = 1
scalar = 1.0/(2*math.pi*sigmaX)
k = 2
width = 10
g = np.zeros(m)
for i in range(m):
x = (i - m/2.0) / m * width
g[i] = scalar * math.exp(-x*x/(2*sigmaX*sigma... | nspotrepka/neuron-inference | network.py | Python | mit | 2,308 | [
"NEURON"
] | 3393c54924b30953e420c60959fcc2ff10d711193bb828b1e12d409d45506c16 |
"""Adds a few finishing touches to the IPHAS DR2 binary FITS catalogues.
It will add TDISP keywords, sanitise TUNIT keywords, add checksums,
and add origin information.
"""
import numpy as np
from astropy.io import fits
from astropy import log
def augment(filename_origin, filename_target):
log.info('Opening {0}'... | barentsen/iphas-dr2 | scripts/release-preparation/augment-catalogue.py | Python | mit | 4,349 | [
"VisIt"
] | c088eb5398b2db804d4ec31214cdece92c22da6b7e0f91fce02d1c331d9bcf00 |
# -*- coding: UTF-8 -*-
"""
``RSEM``
-----------------------
:Authors: Liron Levin
:Affiliation: Bioinformatics core facility
:Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.
Short Description
~~~~~~~~~~~~~~~~~~~~
A module for running RSEM
Requires
~~~~~~~~~~~~~~~~~~~~~~~... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/Liron/RSEM_module/RSEM.py | Python | gpl-3.0 | 21,867 | [
"Bowtie"
] | 2242f5006a20a7c2515d7de4389df5bca4ba019d52f620d91602c7556a168d51 |
"""Simple molecular dynamics.
A block of 27 cubic unit cells of Cu is set up, a single atom is given
a significant momentum, and constant energy molecular dynamics is
performed.
"""
from numpy import *
from asap3 import Atoms, EMT, units, PickleTrajectory
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md... | auag92/n2dm | Asap-3.8.4/Examples/TrajectoryMD.py | Python | mit | 1,070 | [
"ASE",
"NetCDF"
] | 5ac65b7b131d0adff016770c1c844244ddc14059b95b248e43cb1749847c7c41 |
# 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... | espressomd/espresso | testsuite/python/random_pairs.py | Python | gpl-3.0 | 3,429 | [
"ESPResSo"
] | 251d3e23f13f979acd29095cdad6ba9fa6e4349007e98c5db1f660505d47fcc2 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
from pyscf import gto, scf, mcscf
'''
Symmetry is not immutable
CASSCF solver can have different symmetry to the symmetry used by the
reference Hartree-Fock calculation.
'''
mol = gto.Mole()
mol.build(
atom = 'Cr 0 0 0',
basis = 'cc-p... | gkc1000/pyscf | examples/mcscf/20-change_symmetry.py | Python | apache-2.0 | 595 | [
"PySCF"
] | 9c44fe2cdec38ffceb8b5ecf80401f903f2560a576ac80c73de70edcbdc33717 |
"""\
fermi_dirac.py: Utilities for finite temperature Fermi-Dirac occupations.
This program is part of the PyQuante quantum chemistry program suite.
Copyright (c) 2004, Richard P. Muller. All Rights Reserved.
PyQuante version 1.2 and later is covered by the modified BSD
license. Please see the file LICENSE tha... | certik/pyquante | PyQuante/fermi_dirac.py | Python | bsd-3-clause | 3,668 | [
"DIRAC"
] | 869c930689734fb0cd11f6a804ecaa5983b212d7e5c4db2ecce63dd63a9019aa |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and
from frappe import _
from frappe.model.mapper impor... | Tejal011089/trufil-erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 15,380 | [
"VisIt"
] | 0ae3c34894dcac442f8eca005441e70ee1c772ae0298e7e88c0b14489135f55e |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'resources/qosm_settings_dialog.ui'
#
# Created by: PyQt4 UI code generator 4.11.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
... | paleolimbot/qosm | qosmpy/ui_qosm_settings_dialog.py | Python | gpl-2.0 | 11,680 | [
"VisIt"
] | 1c8fa2ccce0838ee8b1e8600670e6e957d5fd2a86cf62e999abea0db511d709c |
from __future__ import absolute_import
from builtins import map
from builtins import str
from . import luqum
from .luqum.parser import parser
from .luqum.utils import LuceneTreeTransformer
from .NED import get_ned_data
from .SIMBAD import get_simbad_data
from .client import client
from astropy import units as u
from as... | adsabs/object_service | object_service/utils.py | Python | mit | 10,867 | [
"VisIt"
] | e6e4876103ddb8ad48b31ade55bda14b2e3116483c701fb9359b8a5925a88bcb |
BOARD_SIZE = 3
MIN_WORD_LENGTH = 3
test_board_size4 = [('b', 'a', 'r', 'i'),
('e', 'c', 'n', 'u'),
('l', 'a', 'o', 'm'),
('i', 'v', 'p', 's')]
test_board_size3 = [('c', 'a', 't'),
('o', 'p', 'c'),
('r', 'e', 'h')]
de... | alexakarpov/boggler | boggler.py | Python | mit | 8,535 | [
"VisIt"
] | 2ae69f7d659106afb118a1d76230cbea58d468d79537b7bf9e26a4e1e74d8b8d |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008 Daniel Moisset, Ricardo Quesada, Rayentray Tappa, Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the follow... | eevee/cocos2d-mirror | cocos/scenes/transitions.py | Python | bsd-3-clause | 22,202 | [
"VisIt"
] | 4f7d8a75ed247589e20972e7cb761d459393f203acf27dc51e5d210d49a20ee9 |
#Copyright 2015 Daniel Gusenleitner, Stefano Monti
#Licensed under the Apache License, Version 2.0 (the "License");
#you may not use this file except in compliance with the License.
#You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
#Unless required by applicable law or agreed t... | montilab/Hydra | scripts/run_bamqc.py | Python | apache-2.0 | 16,391 | [
"pysam"
] | 17688c40de16d31b59850d91bb5e01b722d7fa834f9e58bfeeb37a2251e3b1cd |
"""
A set of basic transformers for python asts
"""
import os
import sys
import ast
from ctypes import c_long, c_int, c_byte, c_short, c_char_p, c_void_p, c_float
import ctypes
from collections import deque
import ctree
from ctree.c.nodes import Constant, String, SymbolRef, BinaryOp, TernaryOp, \
Return, While, Mu... | ucb-sejits/ctree | ctree/transformations.py | Python | bsd-2-clause | 15,638 | [
"VisIt"
] | 01ded3990ace144a8b1d468abda1ab3c191c65d17281e9cd6c9e1ffa79176ed2 |
#!/usr/bin/env python
""" Which - locate a command
* adapted from Brian Curtin's http://bugs.python.org/file15381/shutil_which.patch
* see http://bugs.python.org/issue444582
* uses ``PATHEXT`` on Windows
* searches current directory before ``PATH`` on Windows,
but not before an explicitly passed ... | diogocs1/comps | web/openerp/tools/which.py | Python | apache-2.0 | 6,884 | [
"Brian"
] | 779ce8c96c16e884e8985ce8a3f95622cee9f817110d766489b716c7fa749769 |
import sys
import numpy as np
from ovito import *
from ovito.data import *
from ovito.modifiers import *
from ase.lattice import bulk
from ase.io import read, write
from ase.calculators.singlepoint import SinglePointCalculator
atoms = bulk('Si', cubic=True)
atoms *= (5, 5, 5)
# add some comuted properties
atoms.ne... | srinath-chakravarthy/ovito | examples/scripts/ase-interface.py | Python | gpl-3.0 | 1,114 | [
"ASE",
"OVITO"
] | 61f34d3a0d96c75fb9f9b7bfec2c65ca40888148b5accbbc02130982bbef4acd |
import os
from generic import obj
from project_base import Pobj,modes
from project_manager import ProjectManager
from machines import Job,Machine,Supercomputer,get_machine
from structure import Structure,generate_structure,generate_cell
from physical_system import PhysicalSystem,generate_physical_system
from pseudo... | habanero-rice/hcpp | test/performance-regression/full-apps/qmcpack/nexus/library/project.py | Python | bsd-3-clause | 9,752 | [
"GAMESS",
"QMCPACK",
"VASP"
] | 55a3001b5c70e7ea960edcdb97f960d0cac67ad11caa80ab22ad170a2387adcc |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_lineardensity.py | Python | gpl-2.0 | 1,633 | [
"MDAnalysis"
] | 488f2b868c30351a32acdff5510ca0056442961693bc98a5e6b5fa2c0afe36a3 |
import sys
import subprocess
from clint.textui import puts, indent, colored
from .base import DeweyCommand
from dewey.util import suppress_stdout_stderr
class Command(DeweyCommand):
def pre_default(self, *args, **kwargs):
pass
def run_command(self, *args, **kwargs):
try:
ps = s... | buddyup/dewey | dewey/commands/up.py | Python | mit | 1,768 | [
"GULP"
] | b450549d2256ff64dbde27ce791fa1f6d939bcfcac1256ae853ea73ab91a48ab |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/editors/coloredfloateditor.py | Python | gpl-2.0 | 7,294 | [
"VisIt"
] | 320b11284ad0264772bc9ad4fdd739ca2eb6633e4656c37110bbf17ef9db98a8 |
#!/usr/bin/env @PYTHON_EXECUTABLE@
"""
Description: Viewer for Siconos mechanics-IO HDF5 files based on VTK.
"""
from siconos.io.vview import VView, VViewConfig, VViewOptions
from siconos.io.mechanics_hdf5 import MechanicsHdf5
if __name__=='__main__':
## Persistent configuration
config = VViewConfig()
# ... | siconos/siconos | io/swig/io/siconos_vview.py | Python | apache-2.0 | 762 | [
"VTK"
] | 125409c2518f8f99210d2d96bc4d867117b6594aa123d3264c79d61af85ed208 |
# $Id$
#
# Copyright (C) 2007 by Greg Landrum
# All rights reserved
#
from rdkit import Chem,Geometry
from rdkit.Chem import AllChem
from rdkit.Chem.Subshape import SubshapeObjects
from rdkit.Chem.Subshape import BuilderUtils
from rdkit.six.moves import cPickle
import time
#------------------------------------------... | soerendip42/rdkit | rdkit/Chem/Subshape/SubshapeBuilder.py | Python | bsd-3-clause | 4,317 | [
"PyMOL",
"RDKit"
] | 248c77e7343978e52a07f17c0eb4d21cbc9df54c0c300b22c5a3c834e696befe |
import json
import random
import string
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.db import transaction
from django.http import HttpResponse
from django.http import HttpResponseRedirect
from django.http import JsonResponse
from django.shortcuts import render... | TranDinhKhang/funkychat | chat/views.py | Python | bsd-3-clause | 1,898 | [
"VisIt"
] | f2f72e65b14798144d28a6068f5f6623d581d9230c2f49238d10c0bc3d2a049f |
"""Pipeline functionality shared amongst multiple analysis types.
"""
import os
from contextlib import closing, contextmanager
import fileinput
import functools
import tempfile
import pybedtools
import pysam
import toolz as tz
from bcbio import bam, broad, utils
from bcbio.bam import ref
from bcbio.pipeline import da... | mjafin/bcbio-nextgen | bcbio/pipeline/shared.py | Python | mit | 12,312 | [
"BWA",
"pysam"
] | c4c44ff5e41ffc9f87ff0cf379e8b5dbba01ff4c67d885522e445e51d79adbb5 |
#!/usr/bin/python
import sys, os, argparse, subprocess, shlex, glob
from datetime import datetime
from multiprocessing import cpu_count
from multiprocessing.dummy import Pool as ThreadPool
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
################... | tatumdmortimer/popgen-stats | ancestralReconstruction.py | Python | mit | 9,433 | [
"Biopython"
] | 548b8564f9ffd04120d0fd0d67648c511c0e40abd5c85f7a39eba4b946ba46bd |
'''
Path: magpy.lib.magpy_formats
Part of package: stream (read/write)
Type: Input tester, call to read library
PURPOSE:
Tests which format a file has using the read library.
CONTAINS:
isFormat: (Func) Runs through datatypes in library to find fitting t... | geomagpy/magpy | magpy/lib/magpy_formats.py | Python | bsd-3-clause | 19,144 | [
"NetCDF"
] | 1257ccaf3d7900208a6e9aab21cbaa5ad5b08bbe0dbf64b2765bf247269691a7 |
from .utils import PyKEArgumentHelpFormatter
import numpy as np
from astropy.io import fits as pyfits
from matplotlib import pyplot as plt
from tqdm import tqdm
from . import kepio, kepmsg, kepkey, kepplot, kepstat, kepfunc
__all__ = ['keppixseries']
def keppixseries(infile, outfile=None, plotfile=None, plottype='g... | gully/PyKE | pyke/keppixseries.py | Python | mit | 24,628 | [
"Gaussian"
] | 947c31d8d9d2dc06acd08933e10014234518b8ae1ba623fd8c2eb31af030f5b1 |
import collect_array as ca
import collect_id as ci
import collect_loop as cl
import collect_device as cd
class GenReverseIdx(object):
def __init__(self):
self.ReverseIdx = dict()
self.ReverseIdx[0] = 1
self.ReverseIdx[1] = 0
def get_reverse_idx(ast):
gen_reverse_idx = GenReverseIdx()... | dikujepsen/OpenTran | v2.0/framework/Matmul/collect_gen.py | Python | mit | 5,879 | [
"VisIt"
] | 8eb651e4d7733e8f8867c47017883f1910b5a0343704162a0537a30700d3ed50 |
#!/usr/bin/env python
# (C) Copyright 2018 ECMWF.
#
# This software is licensed under the terms of the Apache Licence Version 2.0
# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
# In applying this licence, ECMWF does not waive the privileges and immunities
# granted to it by virtue of its status... | ecmwf/cdsapi | examples/example-era5-update.py | Python | apache-2.0 | 1,550 | [
"NetCDF"
] | db1fd69705d143bc484e66d06c15053a8e47f43c64652a54e858c63d167b9caa |
r"""
This module is a ParaViewWeb server application.
The following command line illustrates how to use it::
$ pvpython .../pv_web_data_prober.py --data-dir /.../path-to-your-data-directory
--data-dir
Path used to list that directory on the server and let the client choose a
... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Web/Applications/DataProber/server/pv_web_data_prober.py | Python | gpl-3.0 | 13,167 | [
"ParaView",
"VTK"
] | 8bdfb69a99c21164fa58fa20a38999f07e08be632d7637a6b3c978e7d9dc4110 |
from __future__ import division
from __future__ import print_function
#This module contains several functions which calculate
#observational quantities affected by cosmology
from builtins import range
from builtins import object
from past.utils import old_div
import bpz_tools
import useful
import numpy
import glob
imp... | boada/planckClusters | MOSAICpipe/pipe_utils/cosmology.py | Python | mit | 13,917 | [
"Galaxy"
] | b07bbc3a5ea97ce197e39fe9899a5bf380430de76a28dbee436eef79a92688e6 |
""" This is a test of the ProxyDB
It supposes that the DB is present and installed in DIRAC
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=invalid-name,wrong-import-position,protected-access
import os
import re
import sys
import st... | ic-hep/DIRAC | tests/Integration/Framework/Test_ProxyDB.py | Python | gpl-3.0 | 29,906 | [
"DIRAC"
] | 7de2b8ac1855b14fc448783c4d609292b523a4c35e73fd82b6f2a26a67a468b5 |
from setuptools import setup, find_packages
import imp
version = imp.load_source('librosa.version', 'librosa/version.py')
setup(
name='librosa',
version=version.version,
description='Python module for audio and music processing',
author='Brian McFee',
author_email='brian.mcfee@nyu.edu',
url='... | yunque/librosa | setup.py | Python | isc | 1,429 | [
"Brian"
] | ee009285fa814cbe7a200dbe838812799eeaa98f05689144527d1744649a1682 |
def VtkDefineIdFilter(nmbIdFilter):
# vtkIdFilter genera escalares a partir del identificador
nmbIdFilter= vtk.vtkIdFilter()
nmbIdFilter.SetInput(ugrid)
nmbIdFilter.CellIdsOff()
nmbIdFilter.PointIdsOff()
| lcpt/xc | python_modules/postprocess/xcVtk/vtk_define_id_filter.py | Python | gpl-3.0 | 215 | [
"VTK"
] | ca021d22977d8a8941b896327d1f7913a8e9ce800b92f306780410ff4f25e6bc |
# coding: utf-8
#
# Copyright 2015 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | flavioamieiro/pypln.backend | pypln/backend/celery_app.py | Python | gpl-3.0 | 1,245 | [
"NAMD"
] | 42bfbe3ec41b0656cbdbec890d9dd2d657155ec08081e69c7f69e47998a689e8 |
from __future__ import print_function
from confirmation.models import Confirmation
from django.conf import settings
from django.core.mail import EmailMultiAlternatives
from django.template import loader
from zerver.decorator import statsd_increment, uses_mandrill
from zerver.models import Recipient, ScheduledJob, UserM... | atomic-labs/zulip | zerver/lib/notifications.py | Python | apache-2.0 | 24,261 | [
"VisIt"
] | bca66e01b045ef355f103223627ce94c7cf2c16f4500c5def8e2b2949d4a88be |
#!/usr/local/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Run YANK self tests after installation.
"""
# ===========================... | andrrizzi/yank | Yank/commands/selftest.py | Python | mit | 6,775 | [
"OpenMM"
] | 6311194f12dd3dd1c5b7f74d2ff3403b35755313a11eb71e857a9313e0f1e2e6 |
"""
Canned Views using PySAL and Matplotlib
"""
__author__ = "Marynia Kolak <marynia.kolak@gmail.com>"
import pandas as pd
import numpy as np
import pysal as ps
import matplotlib.pyplot as plt
__all__ = ['mplot']
def mplot(m, xlabel='', ylabel='', title='', custom=(7,7)):
"""
Produce basic Moran Plot
... | ljwolf/pysal | pysal/contrib/viz/plot.py | Python | bsd-3-clause | 1,683 | [
"COLUMBUS"
] | c3a7a1c407ffab8e5fb8207fb201b8c1c4d2f9aaf9681a8ea87bf2e65c04ed7b |
'''
Created on Aug 27, 2014
@author: David Zwicker <dzwicker@seas.harvard.edu>
Provides a dictionary with default parameters for the mouse tracking.
This can also be seen as some kind of documentation of the available
parameters.
'''
from __future__ import division
from collections import namedtuple, defaultdict
im... | david-zwicker/cv-mouse-burrows | mouse_burrows/algorithm/parameters.py | Python | bsd-3-clause | 39,885 | [
"Gaussian"
] | 147189dba110af9c6a68eb536e393306ce7f10d22ffcf048a02e150fe32437f3 |
# -*- coding: utf-8 -*-
#-------------------------------------------------------------------------------
# Name: misc.py
# Purpose: Miscellaneous utility functions.
# Licence: MIT License
# This file is subject to the terms and conditions of the MIT License.
# For further detail... | indranilsinharoy/PyZDDE | pyzdde/misc.py | Python | mit | 11,707 | [
"Gaussian"
] | 56ad6ea67a418a8bcb1838ffba194c65fe324e44ca69853da25f09d25c96cdcf |
# -*- coding: utf-8 -*-
# Author: Josh Dick <josh@joshdick.net>
# <https://github.com/joshdick/weeprowl>
#
# Requires WeeChat version 0.3.7 or greater
# Released under GNU GPL v2
#
# Based on the 'notify' plugin version 0.0.5 by lavaramano <lavaramano AT gmail DOT com>:
# <http://www.weechat.org/scripts/source/stable/n... | qguv/config | weechat/plugins/python/weeprowl.py | Python | gpl-3.0 | 7,394 | [
"VisIt"
] | dbd163050dbebb7355cd1c7b7a41788babd0d58a8374f054c83873ef03f51202 |
#!/usr/bin/python
import time
from bioblend.galaxy import GalaxyInstance
gi = GalaxyInstance('http://galaxytest', key='admin')
gi.histories.create_history()
#print gi.tools.get_tool_panel()
history = gi.histories.get_most_recently_used_history()
#print dir(history)
history_id = history['id']
#print history_id
tool_out... | chambm/docker-galaxy-stable | test/gridengine/test_outputhostname.py | Python | mit | 831 | [
"Galaxy"
] | 5d08906a705938fce530370155d33122ec0afbbd0ae5e974d7a0960f8ecfb0cf |
'''
example07 -- crystal -- dynamical diffraction (ocelot.optics.bragg)
'''
from ocelot.optics.utils import *
def save_filter(filt, f_name):
f= open(f_name,'w')
for i in xrange( len(filt.ev)):
f.write(str(filt.ev[i]) + '\t' + str(np.abs(filt.tr[i])**2) + '\t' + str(np.abs(filt.ref[i])**2) + '\n')
E_... | iagapov/ocelot | demos/optics/ex7.py | Python | gpl-3.0 | 1,987 | [
"CRYSTAL"
] | 128b75b727c56a05d89db0783274f82ffd0ee03b5f4210d2a6b5ef2f804a6263 |
"""Support for building and spinnaker releases."""
# pylint: disable=wrong-import-position
# These would be required if running from source code
SPINNAKER_RUNNABLE_REPOSITORY_NAMES = [
'clouddriver',
'deck',
'echo', 'fiat', 'front50',
'gate', 'igor', 'kayenta', 'orca', 'rosco']
SPINNAKER_HALYARD_REPO... | skim1420/spinnaker | dev/buildtool/__init__.py | Python | apache-2.0 | 2,095 | [
"ORCA"
] | 3e49b1d3e61660055080cd7114fd2d4c433540c7b6b602233e13002b1e258e83 |
# -*- coding: utf-8 -*-
# Copyright (C) 2016 Google Inc. All Rights Reserved.
#
# Authors:
# Arkadiusz Socała <as277575@mimuw.edu.pl>
# Michael Cohen <scudette@google.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 obt... | dsweet04/rekall | tools/layout_expert/layout_expert/visitors/type_collecting_visitor.py | Python | gpl-2.0 | 2,224 | [
"VisIt"
] | f4a9e754044d3c2c3b67b916fa71055ab6fff200b31dfa75a9a1d4fc2bc91161 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <markdowncell>
# # Testing Glider CMRE access in Python
#
# This is a url from NATO CMRE "grid" format, where glider data are stored as profiles. These follow the GROOM convention, and in contrast the the IOOS Glide DAC 2.0 format, instead of one combined profile ... | rsignell-usgs/notebook | Glider_CMRE_test.py | Python | mit | 2,362 | [
"NetCDF"
] | 35464b81a82dc4414e202821ea7ea20c545d5f1847fb53ca019629d81c941564 |
# -*- coding: utf-8 -*-
{
"'Sounds-like' name search allowing search even the spelling of the name is not known exactly": "'Sounds-like'名稱搜尋或搜尋,即使名稱的拼字不完全",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that ha... | flavour/eden | languages/zh-tw.py | Python | mit | 338,534 | [
"VisIt"
] | 4ffed5cc5216a1b9d187b8579e4393fbf12a331da78fb2e7e3a20e1b2f3131e9 |
#!/bin/env python
""" script to obtain release notes from DIRAC PRs
"""
from __future__ import print_function
from collections import defaultdict
from datetime import datetime, timedelta
import argparse
from pprint import pformat
import logging
import textwrap
import requests
try:
from GitTokens import GITHUBTOKEN
... | petricm/DIRAC | docs/Tools/GetReleaseNotes.py | Python | gpl-3.0 | 9,873 | [
"DIRAC"
] | 7ae3c4b2f111cfe2a5e16a09dd1fbea0c3d5e75b8bd826a7254ad56f124c317e |
# -*- coding: utf-8 -*-
# YAFF is yet another force-field code.
# Copyright (C) 2011 Toon Verstraelen <Toon.Verstraelen@UGent.be>,
# Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>, Center for Molecular Modeling
# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
# stated.
#
# This file is pa... | molmod/yaff | yaff/examples/007_monte_carlo/co2_in_mil53/process.py | Python | gpl-3.0 | 2,053 | [
"RASPA"
] | 947d26fc2c4a17bdf4ff6c4b56a561c045547783cafa19d228a89475dbc580fd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Tests for Vowpal Wabbit LDA wrapper.
Will not be run unless the environment variable 'VOWPAL_WABBIT_PATH' is set
and points to the ... | ziky90/gensim | gensim/test/test_ldavowpalwabbit_wrapper.py | Python | lgpl-2.1 | 8,151 | [
"Jaguar"
] | abcac4d6519b267a903e107bbecbe37d5b45051d7d30babe29e3511ba82cfe84 |
import sys
tests = [("testExecs/testDescriptors.exe", "", {}), ]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| jandom/rdkit | Code/GraphMol/Descriptors/test_list.py | Python | bsd-3-clause | 239 | [
"RDKit"
] | 4fc6ebbca0a5abd2b40c1f178de4cb20d650c029fa52ee8b659ac5a5292d9abf |
#!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test Force classes in forces.py.
"""
# ========================================================================... | choderalab/openmmtools | openmmtools/tests/test_forces.py | Python | mit | 16,194 | [
"OpenMM"
] | 8be20f55249b6babc19931067425c3816c008881eaf49f4cf8bcd5ab1fdf7af8 |
#######################################################################################
# Python-code: SAINT pre-processing from Scaffold "Samples Report" output
# Author: Brent Kuenzi
#######################################################################################
# This program reads in a raw Scaffold "Sam... | bornea/APOSTL | SAINT_preprocessing/toolshed_version/SAINT_preprocessing.py | Python | gpl-2.0 | 10,226 | [
"Galaxy"
] | 306fc4d72f4998e057fd023bda6c80bd129cdb6aa72d5ff8b51ad6ae3f156387 |
# 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/.
from ..sile import add_sile
from .sile import SileSiesta, SileCDFSiesta
from sisl._internal import set_module
from sisl... | zerothi/sisl | sisl/io/siesta/basis.py | Python | mpl-2.0 | 12,101 | [
"NetCDF",
"SIESTA"
] | bdb7ecc31ef99787c9594b3d8e6b0cc0181ee9199e01bc199d0c3086530bdbcc |
#!/usr/bin/env python
import json
from colors import bcolors, print_ok, print_ok_pending, print_done
from subprocess import call
from pkg_resources import resource_filename
def drop_git(path):
call(["rm", "-rf", path + "/.git"])
def init(arg_vars, project_root):
app_name = arg_vars['app-name']
ansible_dir = a... | onyx-platform/engraver | src/init_command.py | Python | epl-1.0 | 3,913 | [
"Galaxy"
] | 7b8460e294b183ccfd00ffc7121c83152a73af31a0eba00f6f1071384f176aee |
# Copyright 2016 Brian Innes
#
# 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, ... | brianinnes/vPiP | python/test1.py | Python | apache-2.0 | 1,586 | [
"Brian"
] | 4029a14de01c7aab201fd55cb57b9861f318277ce03e7876c271c6748abdadd8 |
#!/usr/bin/env python3
"""fasta file access with buffer"""
import pysam
class cachedFasta:
"""fasta seq fetcher, use buffer to improve performance
example:
fa = cachedFasta("hg19.fa")
seq = fa['chr1'][2000:3000]
"""
def __init__(self, fa, trans=None, buffer_size = ('-2k', '8k') )... | sein-tao/pyBioUtil | BioUtil/cached_fasta.py | Python | gpl-2.0 | 5,118 | [
"pysam"
] | c7a9d37702ad8fd7fe04f197eb47eee30c1067af92db9c21e49ed47483219fea |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/misc/info.py | Python | agpl-3.0 | 5,110 | [
"Galaxy"
] | a07d6bbc640036f2c48dab0631a9b138aac1e57c63a12dcccd5cdf7030e9b6c1 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2... | PeterLauris/aifh | vol1/python-examples/examples/example_error.py | Python | apache-2.0 | 4,455 | [
"VisIt"
] | 228f15829f140196de423d2c68f0bb7bcbe587c648b5b63ca9fde2e33d3c3164 |
__author__ = 'brian'
from django import forms
from django.contrib.auth.models import User
from rango.models import Page, Category, UserProfile
class CategoryForm(forms.ModelForm):
name = forms.CharField(max_length=128, help_text="please enter the "
"category ... | bjing/tango_with_jango_project | rango/forms.py | Python | gpl-3.0 | 1,658 | [
"Brian"
] | 89f7d5d328685cfdaf7ed2404397244284930007259cc683d79187277b9a9500 |
import codecs
import os
from setuptools import setup, find_packages
here = os.path.abspath(os.path.dirname(__file__))
about = dict(
__version__=0.4,
__title__="pymerra2",
__description__="A tool for downloading and repackaging NASA MERRA-2 Data",
__url__="https://github.com/Ouranosinc/pymerra2",
_... | bstdenis/pymerra2 | setup.py | Python | apache-2.0 | 1,794 | [
"NetCDF"
] | a4c6ba25baa0115bf419ff6b031a55e570c275fffa0198d9e0afc5c515afa8b7 |
import unittest
import pam
import bpy
import numpy
import random
import pickle
import sys
SEED = 42
class TestAddon(unittest.TestCase):
def testAddonEnabled(self):
self.assertNotNone(pam.bl_info)
class TestPamModelCreate(unittest.TestCase):
def setUp(self):
# Seed the rng
random.seed(... | MartinPyka/Parametric-Anatomical-Modeling | tests/model/model.test.py | Python | gpl-2.0 | 4,374 | [
"NEURON"
] | 1d8b7e4e3ae2afe9f093269f9bbbbe1fdb74dcc26f1a3280e14e056978929b9f |
# This file is part of beets.
# Copyright 2014, Adrian Sampson.
#
# 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, ... | Wen777/beets | beetsplug/discogs.py | Python | mit | 12,882 | [
"VisIt"
] | 6f36ad9957a2a79ea61280e2459b849fdf15a366a5671ba4d0d237f07333fc16 |
from test import test_support
import unittest
import codecs
import locale
import sys, StringIO
try:
import _testcapi
except ImportError:
_testcapi = None
class Queue(object):
"""
queue: write bytes at one end, read bytes from the other end
"""
def __init__(self):
self._buffer = ""
... | bussiere/pypyjs | website/demo/home/rfk/repos/pypy/lib-python/2.7/test/test_codecs.py | Python | mit | 57,686 | [
"FEFF"
] | 6e04c80e8c91b34f842767ab94f307ab1d0f1e3e22f24f8f4735df3c75aeacae |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import os
try:
from setuptools import setup
from setuptools.command.test import test as TestCommand
except ImportError:
from distutils.core import setup
from distutils.core.command.test import test as TestCommand
with open('README.rst') as re... | napsternxg/pyLDAvis | setup.py | Python | bsd-3-clause | 2,649 | [
"scikit-bio"
] | dc11f8623eb3569f7646ecf2bae732fd01747c698e7875790cdcd7701cc70ef8 |
from fabric.api import local, cd, put, env, shell_env, run
from fabric.context_managers import lcd
from fabric.contrib.project import rsync_project
env.use_ssh_config = True
env.hosts = ['root@server.artquest.ninja']
def deploy(what='all'):
with shell_env(GOOS="linux", GOARCH="amd64"):
local('godep go bu... | RollingBalls/rollingballs-server | fabfile.py | Python | mit | 608 | [
"GULP"
] | 8c40dd63b2432cdb8f9a3c04bb4dd602d734ed6f3613f0623e665e6fb0abfb0e |
"""This module contains the "Viz" objects
These objects represent the backend of all the visualizations that
Superset can render.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import copy
import hashlib
import l... | nekia/incubator-superset-dev | superset/viz.py | Python | apache-2.0 | 58,235 | [
"VisIt"
] | 1f93dd14390b4e8402665d88f17ee3207bef40afb735929dab9e947986ea62c7 |
import argparse
from os import path as path
import re
from subprocess import check_output, Popen, PIPE
import json
from os import remove
parser = argparse.ArgumentParser(description="Convert a Seqware decider JSON file for BWA to an ansible host inventory file")
parser.add_argument("--run_generator", help="Enabling th... | SeqWare/seqware-sandbox | ansible_pancancer/host_inventory_form_json.py | Python | gpl-3.0 | 1,811 | [
"BWA"
] | 55e4aee073690b28c5f7f5673e70dd83b8a3a10e72ba4483255ba33100beb42d |
# -*- coding: utf-8 -*-
from collections import OrderedDict
from gluon import current
from gluon.html import *
from gluon.storage import Storage
from gluon.validators import IS_NOT_EMPTY
from s3 import FS, ICON, IS_LOCATION, IS_ONE_OF, S3DateTime, S3LocationSelector, S3Represent, \
S3SQLCustomForm, S3... | flavour/eden | modules/templates/historic/Philippines/config.py | Python | mit | 166,125 | [
"Amber"
] | bcd891357a99ab977467bde428486a1968079e61c6223e0f75994557c3022635 |
import pdb
import six
import numpy as np
from astropy.io import fits
import astropy.units as u
from utils import bin_ndarray as rebin
from utils import gauss_kern
from utils import clean_nans
from utils import clean_args
from utils import map_rms
from astropy import cosmology
from astropy.cosmology import Planck15 as c... | marcoviero/Utils | skymaps.py | Python | mit | 3,302 | [
"Gaussian"
] | 39f71ec235de21fe0d8cb2d74a0c453f58b081edb7dc487f0c78db10d67ba45e |
# """
# :mod: DataLoggingHandler
#
# .. module: DataLoggingHandler
#
# :synopsis: DataLoggingHandler is the implementation of the Data Logging service in the DISET framework.
#
# The following methods are available in the Service interface:
#
# - addFileRecord()
# - addFileRecords()
# - getFileLoggingInfo()
#
# """
#
#... | Sbalbp/DIRAC | DataManagementSystem/Service/DataLoggingHandler.py | Python | gpl-3.0 | 2,542 | [
"DIRAC"
] | 9b2f6019f3e5ee9e1182975c0af7aeb33a593898dc372713f51569ab92eb478e |
import math
import ast
import inspect
import re
import os.path
import sys
import subprocess
from org.nmrfx.processor.math.units import Fraction
from org.nmrfx.processor.math.units import Frequency
from org.nmrfx.processor.math.units import Index
from org.nmrfx.processor.math.units import PPM
from org.nmrfx.processor.ma... | onemoonsci/nmrfxprocessor | src/main/resources/pyproc.py | Python | gpl-3.0 | 119,470 | [
"Gaussian"
] | 19e58f7563be81d84e678b09eab7d1533dad021da601c34dca0505024334f6d8 |
# 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/layout.py | Python | gpl-2.0 | 55,212 | [
"VisIt"
] | c0455997ae265fddfdbe2a195b727d4a98a16e1a99dfa2cfc33c06b51e4f3aeb |
# $Id$
#
# Copyright (C) 2001-2006 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.
#
""" This has all be r... | soerendip42/rdkit | rdkit/DataStructs/BitVect.py | Python | bsd-3-clause | 4,250 | [
"RDKit"
] | 00a37da6799eb40a01e7656ee161c66e1cdb83e22c80c264ba33dd2cdfedc93e |
"""Support the ElkM1 Gold and ElkM1 EZ8 alarm/integration panels."""
import asyncio
import logging
import re
import async_timeout
import elkm1_lib as elkm1
import voluptuous as vol
from homeassistant.config_entries import SOURCE_IMPORT, ConfigEntry
from homeassistant.const import (
CONF_EXCLUDE,
CONF_HOST,
... | sander76/home-assistant | homeassistant/components/elkm1/__init__.py | Python | apache-2.0 | 14,937 | [
"Elk"
] | df10e1c6c789bbce1b7b4baeaedd2730c8d8830fdc357ca6f72c4adc68113ea9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# PySCM -- Python Spike Counter Model
# Copyright (C) 2016 Christoph Jenzen, Andreas Stöckel
#
# 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 Found... | hbp-sanncs/pyscm | run.py | Python | gpl-3.0 | 3,469 | [
"NEURON"
] | de9521acb7eb19d115530c24c72b7e9da4fd5c72cf1d6c818fe10e54e30c203c |
from keys import *
from simulation_params import *
import nest
import numpy.random as random
# Neuron parameters
hh_neuronparams = {'E_L': -70., # Resting membrane potential in mV
'V_T': -63., # Voltage offset that controls dynamics.
# -63mV ... | research-team/NEUCOGAR | NEST/cube/noradrenaline/scripts-2/synapses.py | Python | gpl-2.0 | 3,267 | [
"NEURON"
] | d00e7e349223e5a9f5e19c1e918f1023db7b184610381db1fdff043bed35eeb2 |
from __future__ import annotations
import argparse
import sys
from typing import Iterable
from typing import Sequence
from tokenize_rt import src_to_tokens
from tokenize_rt import Token
from tokenize_rt import tokens_to_src
from add_trailing_comma._ast_helpers import ast_parse
from add_trailing_comma._data import FU... | asottile/add-trailing-comma | add_trailing_comma/_main.py | Python | mit | 3,062 | [
"VisIt"
] | fde25e78fe623625d25936a3d1fc3c2d3be3cd58ee9fb718eb5dae9e7bf43f77 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# Revisions Copyright 2007 by Peter Cock. All rights reserved.
# Revisions Copyright 2009 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# l... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/ExPASy/Prosite.py | Python | apache-2.0 | 11,153 | [
"Biopython"
] | 9ca026de31634278b42386d4682ef6bce229147c61b664dab5dddc149ad96e67 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/espresso/package.py | Python | lgpl-2.1 | 5,919 | [
"ESPResSo"
] | 31173d3e3983a93ef1b63633bd5087568594b366722ceeee0ac6eee9ec4430a8 |
# uncompyle6 version 2.9.10
# Python bytecode 2.7 (62211)
# Decompiled from: Python 3.6.0b2 (default, Oct 11 2016, 05:27:10)
# [GCC 6.2.0 20161005]
# Embedded file name: pycodegen.py
import imp
import os
import marshal
import struct
import sys
from cStringIO import StringIO
from compiler import ast, parse, walk, synta... | DarthMaulware/EquationGroupLeaks | Leak #5 - Lost In Translation/windows/Resources/Python/Core/Lib/compiler/pycodegen.py | Python | unlicense | 44,909 | [
"VisIt"
] | 6622da9584f02142d739b00281cb52488f44033bf441d14c1d7fe0e44a8a04e7 |
# Copyright (c) 2001, Stanford University
# All rights reserved.
#
# See the file LICENSE.txt for information on redistributing this software.
#
# Authors:
# Brian Paul
"""
Tile layout functions
This is a collection of functions for computing tile layouts for
tilesort configs, specifically image reassembly configs.... | alown/chromium | mothership/server/tilelayout.py | Python | bsd-3-clause | 6,243 | [
"Brian"
] | a5362247dc7f37d42e5c968bf017061d05b4260bbd2ada77389efa483419f932 |
#!/usr/bin/env python
# Copyright (c) 2014 UCLA
#
# This software is distributable under the terms of the GNU General
# Public License (GPL) v2, the text of which can be found at
# http://www.gnu.org/copyleft/gpl.html. Installing, importing or
# otherwise using this module constitutes acceptance of the terms of
# this ... | haodongchen/BSseeker2_FOO | MyBamPostProcess.py | Python | gpl-2.0 | 2,517 | [
"pysam"
] | 14fc0a927321cd23d7146ca7d2168d2eb8d4d45e2a7f8b0647d653fed5a56c84 |
# NOTE: parts of this file were taken from scipy's doc/source/conf.py. See
# scikit-bio/licenses/scipy.txt for scipy's license.
import glob
import sys
import os
# Check that dependencies are installed and the correct version if necessary
sphinx_version = '1.2.2'
import sphinx
if sphinx.__version__ != sphinx_version:
... | jensreeder/scikit-bio | doc/source/conf.py | Python | bsd-3-clause | 15,372 | [
"scikit-bio"
] | 0eb7d0081b92ac0662963c9d1e7b2a9129003b772d527bf0843f6ad068aa7fd7 |
"""
Module responsible for translating read data into GA4GH native
objects.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import datetime
import os
import pysam
import ga4gh.protocol as protocol
import ga4gh.datamodel as datamodel
import ga4gh.excep... | shajoezhu/server | ga4gh/datamodel/reads.py | Python | apache-2.0 | 10,535 | [
"pysam"
] | f85980c0c9d6fd32599e3cd142395a5dc831065bce8a402e44abf392e9ca950f |
import hashlib
import hmac
from twisted import logger
import urllib
from matrix_gitter.gitter_oauth import setup_gitter_oauth
from matrix_gitter.utils import assert_http_200, Errback, JsonProducer, \
read_json_response, http_request
log = logger.Logger()
class GitterAPI(object):
"""Gitter interface.
T... | remram44/matrix-appservice-gitter-twisted | matrix_gitter/gitter.py | Python | bsd-3-clause | 5,961 | [
"VisIt"
] | 03f0cc415b044208bf1426b0fa9fb2f31ea884978f6beb2b3335420728d68557 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/media/vlcplayer.py | Python | gpl-2.0 | 10,978 | [
"Brian"
] | 68cdce8c856c5caa10c6fc9ca86776135a4f95d38738a14bc23d9db15b5d45ec |
'''
Functions and classes for infilling missing observations in an
incomplete station time series using probabilistic principal component analysis (PPCA):
Stacklies W, Redestig H, Scholz M, Walther D, Selbig J. 2007.
pcaMethods-a bioconductor package providing PCA methods for incomplete data.
Bioinformatics 23: 1164-... | jaredwo/topowx | twx/infill/infill_daily.py | Python | gpl-3.0 | 27,924 | [
"Bioconductor"
] | 0ae3ac503b469199242919b86cc825faaa61e2b124f006c2199895d1f056561b |
import os
import tempfile
from ase.io import write
import ase.parallel as parallel
def view(atoms, data=None, viewer='ase-gui', repeat=None, block=False):
# Ignore for parallel calculations:
if parallel.size != 1:
return
vwr = viewer.lower()
if vwr == 'ase-gui':
format = 'traj'
... | suttond/MODOI | ase/visualize/__init__.py | Python | lgpl-3.0 | 1,727 | [
"ASE",
"Avogadro",
"RasMol",
"VMD"
] | c7802f48f43cf026b1b8a45ed738529ad0577ee2a945b72eb783e365571680e1 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2003-2011 Edgewall Software
# Copyright (C) 2003-2007 Jonas Borgström <jonas@edgewall.com>
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at htt... | apache/bloodhound | trac/trac/env.py | Python | apache-2.0 | 39,717 | [
"VisIt"
] | 08414cc08c173dec4391bff800c6ffe9337306a9db26b19c12fcb36a3b53dce7 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.