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# -*- coding: utf-8 -*-
#
# Copyright (C) Pootle contributors.
#
# This file is a part of the Pootle project. It is distributed under the GPL3
# or later license. See the LICENSE file for a copy of the license and the
# AUTHORS file for copyright and authorship information.
import logging
from django.contrib.auth imp... | ta2-1/pootle | pootle/core/initdb.py | Python | gpl-3.0 | 10,056 | [
"VisIt"
] | 86dded589ca351f277c320c34be9e8e762f4c89339012af99e68a8ee0403ce54 |
# ERPNext - web based ERP (http://erpnext.com)
# Copyright (C) 2012 Web Notes Technologies Pvt Ltd
#
# 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 yo... | gangadhar-kadam/mtn-erpnext | support/doctype/customer_issue/customer_issue.py | Python | agpl-3.0 | 2,335 | [
"VisIt"
] | 3a7cbf534fb6f10b1abab778a389bc1e41b799a1ea357af1551f7fb596cd0ed3 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/toolkits/Gecko/structural_navigation.py | Python | gpl-3.0 | 11,259 | [
"ORCA"
] | 10a9a66753f71fec363bc575e9b05043ee5e1bf3218fb8fe009a8683105f1924 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#
# GrimoireLib projects support
#
# Copyright (C) 2015 Bitergia
#
# 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
... | sanacl/GrimoireELK | grimoire/elk/projects.py | Python | gpl-3.0 | 1,972 | [
"Elk"
] | 90d8b2aeb850381d613d258c60e6aa32006ab89e9a6bea77ba6d8fe2af531edb |
import operator
from ..node import NodeVisitor, DataNode, ConditionalNode, KeyValueNode, ListNode, ValueNode
from ..parser import parse
class ConditionalValue(object):
def __init__(self, node, condition_func):
self.node = node
self.condition_func = condition_func
if isinstance(node, Condi... | danlrobertson/servo | tests/wpt/web-platform-tests/tools/wptrunner/wptrunner/wptmanifest/backends/conditional.py | Python | mpl-2.0 | 11,566 | [
"VisIt"
] | 81f77d1657f11e0861578d04ad02a6c3e3151c2abb4f51c8339423c3c5542013 |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='geoclaw'):
#------------------------------
"""
Def... | ForestClaw/forestclaw | applications/geoclaw/bowl_slosh/setrun.py | Python | bsd-2-clause | 12,281 | [
"NetCDF"
] | 185a966d51b2bcadc466120e309b05508737d9ea62d9be8cff2416220432e42c |
#!/usr/bin/python
# Copyright 2015 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.
# 'top'-like memory/network polling for Android apps.
import argparse
import curses
import os
import re
import sys
import time
from opera... | ltilve/ChromiumGStreamerBackend | tools/android/appstats.py | Python | bsd-3-clause | 37,223 | [
"Galaxy"
] | af363ae8ee7a75889bf8abb2bf14e8ddb9a89794012f995f4cfd87fa338308b2 |
# pysam versioning information
__version__ = "0.18.0"
__samtools_version__ = "1.14"
__bcftools_version__ = "1.14"
__htslib_version__ = "1.14"
| pysam-developers/pysam | pysam/version.py | Python | mit | 143 | [
"pysam"
] | 69ded8fdf71b0f4fe81d99bd80a12148421b2e9648e066d8f0d0c89bee56afa1 |
import sys
import numpy as np
import data_reader
import time
filename = '/home/kelvin/Desktop/Theano test/HSF_N4x4x4_L200_U9_Mu0_UniformTGrid/N4x4x4_L200_U9_Mu0_T_shuffled_%.2d.HSF.stream'
filename_weight_bias = "./wb.ckpt"
filename_measure = "./HSF_measure.dat"
filenumber = np.arange(1,41,1)
HSF = data_reader.insert_... | kchng/Quantum_machine_learning | TF_HSF_CNN.py | Python | apache-2.0 | 9,381 | [
"NEURON"
] | a6e829a67ad8b384a0a0cebd097bf7aa4d7914a230b43a743cbe37b6c2149c4c |
import unittest
import os
import numpy as np
from phonopy.interface.vasp import read_vasp
from upho.structure.unfolder_symmetry import UnfolderSymmetry
POSCAR_DIR = os.path.join(os.path.dirname(__file__), 'poscars')
class TestUnfolderSymmetry(unittest.TestCase):
def setUp(self):
atoms = read_vasp(os.path... | yuzie007/upho | tests/test_unfolder_symmetry.py | Python | mit | 2,516 | [
"VASP",
"phonopy"
] | 5ddb28b7d4c65334317541ce56ce754f194b6ee474d437d91d60ae49589be9b0 |
# $Id$
#
# Copyright (C) 2006-2008 Greg Landrum
#
# @@ All Rights Reserved @@
#
import os, sys
import io
import unittest
import pickle
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit.Geometry import rdGeometry as geom
def feq(v1, v2, tol2=1e-4):
return abs(v1 -... | ptosco/rdkit | Code/ChemicalFeatures/Wrap/testFeatures.py | Python | bsd-3-clause | 4,214 | [
"RDKit"
] | 84116d9ffc4852e0fa0dab514a599ac2404a15c4d2f2ad76b3552ae432e09369 |
import numpy as np
from george.kernels import ExpSquaredKernel #For Gaussian Processes
from george.kernels import ExpSine2Kernel #For Gaussian Processes
import george
import sys
sys.path.append('/home/arthur/temp/PolyChord') # Put correct path here.
import PyPolyChord.PyPolyChord as PolyChord
#First data
data = np.loa... | isphus1973/StarPlanets | PC.py | Python | gpl-3.0 | 3,989 | [
"Gaussian"
] | d8ffd33d61070cba5a690a66eabd622f3eb8d82e9d86982e9c203e19cd06d17a |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki,Danelle Cline'
__copyright__ = '2017'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all CANON off season activities in 2017
Mike McCann, Duane Edgington, Danelle Cline
MBARI 4 January 2017
@va... | stoqs/stoqs | stoqs/loaders/CANON/loadCANON_os2017.py | Python | gpl-3.0 | 10,766 | [
"NetCDF"
] | f67416c958bc4dbdb1ac6027daef87cf7cbf7ca9f687fafdaf62e0e194532ee3 |
from imboclient.url import accesstoken
from imboclient.url import url
class UrlImage (url.Url):
def __init__(self, base_url, public_key, private_key, image_identifier, user=None, **kwargs):
url.Url.__init__(self, base_url, public_key, private_key, user=user, **kwargs)
self._image_identifier = im... | imbo/imboclient-python | imboclient/url/image.py | Python | mit | 3,332 | [
"Gaussian"
] | 1625633f6c8904db4a805d84b73b6b9e895d8126cf70b3912c7f839a1a365601 |
# -*- coding: UTF-8 -*-
"""
I/O methods. All the submodules of the WDmodel package use this module for
almost all I/O operations.
"""
from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals
import sys
import os
from emcee.utils import MPIPool
import argparse... | gnarayan/WDmodel | WDmodel/io.py | Python | gpl-3.0 | 56,413 | [
"Gaussian"
] | d95d77f4aee7519557e0cde8435a6a030cadd43b0ce55483c4fc6e042b19b568 |
# -*- coding: utf-8 -*-
#
# Copyright (c), 2015-2016, Quantum Espresso Foundation and SISSA (Scuola
# Internazionale Superiore di Studi Avanzati). All rights reserved.
# This file is distributed under the terms of the MIT License. See the
# file 'LICENSE' in the root directory of the present distribution, or
# http://o... | afonari/q-e_schrodinger | bin/qexsd/qespresso/xsdtypes/xsdtypes.py | Python | gpl-2.0 | 36,280 | [
"Quantum ESPRESSO"
] | 530718ba5c81f76132a389f518b51b43404966679e7f0bd962601a87c0fdf28a |
# Probability Utility Functions
import numpy
#import fun
from itertools import *
from numpy.linalg.linalg import det
from numpy.linalg.linalg import inv
from StringIO import StringIO
def cov(m):
"""
Returns an estimate of the covariance matrix associated with the data m.
m is a dxn matrix where d is the numb... | Atom-machinerule/OpenQbo | qbo_stereo_anaglyph/hrl_lib/src/hrl_lib/prob.py | Python | lgpl-2.1 | 5,184 | [
"Gaussian"
] | dccb1052915f2a67b00a6eb91dbaca9a1d4922412a8a967bf8ce69e57198ea3d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import math
import re
import os
import textwrap
import warnings
from collections import OrderedDict, deque
import six
from six.moves import zi... | xhqu1981/pymatgen | pymatgen/io/cif.py | Python | mit | 51,567 | [
"Avogadro",
"CRYSTAL",
"pymatgen"
] | 5362b2b1d918c8049d096daeb1c02db652b775298827d141013e2f33199be242 |
"""Entry point for client creation.
``build_client_manager`` in particular is the abstraction that should be used
to create a ``ClientManager``, that in return can create Pulsar clients for
specific actions.
"""
import functools
import threading
from typing import Any, Dict, Type
from logging import getLogger
from o... | natefoo/pulsar | pulsar/client/manager.py | Python | apache-2.0 | 12,563 | [
"Galaxy"
] | 05b306e981672ef5902817df0570ab74d5ecd90d6a4bb6ec9cd3cf8262805319 |
# ----------------------------------------------------------------------------
# Copyright 2014 Nervana Systems Inc.
# 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.o... | ypkang/neon | neon/backends/cpu.py | Python | apache-2.0 | 74,595 | [
"Gaussian"
] | d770a0c746c7a035aaf6aecafa967a4d0c0da667ee5d69e393a69d1e8c4b9c29 |
from rdkit import RDConfig
import os, sys, math
import unittest
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem import rdMolTransforms as rdmt
def feq(v1, v2, tol=1.0e-4):
return abs(v1 - v2) < tol
def ptEq(pt, tpt, tol=0.0001):
pt -= tpt
retu... | rvianello/rdkit | Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py | Python | bsd-3-clause | 4,318 | [
"RDKit"
] | d7c1b66e26494ac89420689fc26a792fd0d0fd8c873e7519115d4fddd10b3408 |
__all__ = ['GaussianKernel']
import numpy as np
import sympy as sym
from functools import wraps
from gp.ext import gaussian_c
from . import Kernel
DTYPE = np.float64
EPS = np.finfo(DTYPE).eps
class GaussianKernel(Kernel):
r"""
Gaussian kernel function.
Parameters
----------
h : float
O... | jhamrick/gaussian_processes | gp/kernels/gaussian.py | Python | mit | 3,867 | [
"Gaussian"
] | 59eff6a5fb27f636b1fc8851bbc8ec9bfaebe23d35d30ff88f14a06fcd58a322 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, Ve... | sparkslabs/kamaelia_ | Sketches/MPS/BugReports/FixTests/Kamaelia/Kamaelia/Util/RateFilter.py | Python | apache-2.0 | 21,749 | [
"DIRAC"
] | ee2f0cf298016353728209d681d2089f670b59eec65d1c0aa6d4865252f4689b |
# A simple test for a vtkTkRenderWidget. Run it like so:
# python TestTkRenderWidget.py -B $VTK_DATA_ROOT/Baseline/Rendering
import os
import vtk
from vtk.test import Testing
import Tkinter
from vtk.tk.vtkTkRenderWidget import vtkTkRenderWidget
class TestTkRenderWidget(Testing.vtkTest):
# Stick your VTK pipe... | cjh1/VTK | Rendering/Tk/Testing/Python/TestTkRenderWidget.py | Python | bsd-3-clause | 1,869 | [
"VTK"
] | 5cd54357704e32d3f2ca30ce0d9fd98c587503f155dfb9fc8cbd2bbba7e839ed |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'Indicator.formula'
db.delete_column('profiles_indicator', 'formula')
# Deleting... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0015_auto__del_field_indicator_formula__del_field_indicator_data_source.py | Python | mit | 10,237 | [
"MOE"
] | 5958f8b9220d4c25d83ce9ffdf34e26cf1c5ce5706ba0da5b8315cd1d622dcec |
#!/usr/bin/env python3
#* 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/lgp... | harterj/moose | python/pyhit/tests/test_tokenize.py | Python | lgpl-2.1 | 3,997 | [
"MOOSE"
] | 99ffb9f5948416e2a3b656753bf00ce741f1c1cd170c57760a9cbf03ee0d27d0 |
#!/usr/bin/python
# Kullback-Leibler Divergence Program, Copyright 2011 Christopher McClendon
# Released under Lesser GNU Public License
from dihedral_mutent import *
from input_output import *
from optparse import OptionParser
from utils import arr2str2, fmt_floats
from Bio.PDB import PDBIO
from Bio.PDB.PDBParser imp... | chris-lee-mc/MutInf | kl_diverge.py | Python | gpl-3.0 | 150,686 | [
"Biopython",
"Gromacs",
"PyMOL"
] | a50387fdc3076287ba5c30b8048aa2687a6562275139c7ce67910f89d1fd8062 |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
print(session)
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
... | jiobert/python | Velez_Felipe/assignments/flaskolympics/olympics6/server.py | Python | mit | 776 | [
"CASINO"
] | d2aef904fb941bf08df22ec40b0a25cca60a243a4145c75bc6990233397f8759 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0044_auto_20150808_2151'),
]
operations = [
migrations.RemoveField(
model_name='visit',
nam... | koebbe/homeworks | visit/migrations/0045_auto_20150808_2231.py | Python | mit | 952 | [
"VisIt"
] | 121ba51f8e074706a8342ca0633ccaa97dbd161ed69fc12f43a134a94031a96d |
import random
import itertools
import string
import os
import tempfile
import logging
from pkg_resources import resource_filename
import contextlib
import shutil
import mdtraj as md
from mdtraj.utils import enter_temp_directory
from mdtraj.utils.delay_import import import_
import openmoltools.acpype as acpype
try:
... | juliebehr/gaff2xml | openmoltools/utils.py | Python | gpl-2.0 | 19,414 | [
"Amber",
"Gromacs",
"MDTraj",
"OpenMM",
"RDKit"
] | bc2a5bf828055b65c8d1a8dce7f057d5564b962edb25875b96cd47a6d8ba0dc5 |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
########################################
import numpy as np
import math
import pylab as pl
import Scientific.IO.NetCDF as sion
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.ticker as mtick
from mpl_to... | CopyChat/Plotting | Python/globalmap_netrad.py | Python | gpl-3.0 | 4,135 | [
"NetCDF"
] | 5e4581ebf7fac00ea46433e1f5b9203594bedcc7a4ca2cdac782eada253ef86d |
# Prepares a complex for AlGDock
try:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('ligand_mol2', default=None,
help='Input mol2 of the ligand with sybyl atom types')
parser.add_argument('receptor_pdb', default=None,
help='Input PDB of the receptor with AMBER atom types')
pa... | luizcieslak/AlGDock | Pipeline/prep_complex_for_AlGDock.py | Python | mit | 3,731 | [
"Amber"
] | b356560e22b5b7529112cd22873e4a7b29cc3c7af2849134a0a7521dc0b477b5 |
# Author: Artem Pulkin
"""
This and other `_slow` modules implement the time-dependent Hartree-Fock procedure. The primary performance drawback is
that, unlike other 'fast' routines with an implicit construction of the eigenvalue problem, these modules construct
TDHF matrices explicitly via an AO-MO transformation, i.... | gkc1000/pyscf | pyscf/tdscf/rhf_slow.py | Python | apache-2.0 | 7,112 | [
"PySCF"
] | ab1705fe648e2a3c82067978975b961dd0bd7226c12df826a11e5f40b27d4823 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
pass
# Deleting field 'NeuronArticleMap.added_by'
#db.delete_column('neuroelectro_neuronarticlemap', 'ad... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0038_auto__del_field_neuronarticlemap_added_by.py | Python | gpl-2.0 | 25,620 | [
"NEURON"
] | 3930f91f1b8a72f6c570228d8f9fded2b721527c2e5700c99ffa0367ecbe9bac |
import time
from Cookie import SimpleCookie
from unittest import TestCase
import cherrypy
from gearshift import config, controllers, expose, startup, testutil, visit
def cookie_header(response):
"""Returns a dict containing cookie information to pass to a server."""
return dict(Cookie=response.headers['Set... | dbrattli/python-gearshift | gearshift/identity/tests/test_visit.py | Python | mit | 6,181 | [
"VisIt"
] | 6c237c3994a057e618d5d8c58f38fa163a80750f55aaa4f14fc4d7cd9a01ef44 |
# Buzzing Cat <https://github.com/xiaogaozi/buzzingcat>
# Copyright (C) 2010 xiaogaozi <gaochangjian@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the Licens... | xiaogaozi/buzzingcat | bc/handler/xmpp.py | Python | gpl-3.0 | 5,279 | [
"VisIt"
] | 1e9039e6b75d5e50887b9003299e4a2ce4f5ee88b340f2059279a362a5dcd552 |
# coding: utf-8
"""
PyKrige
=======
Code by Benjamin S. Murphy and the PyKrige Developers
bscott.murphy@gmail.com
Summary
-------
Function definitions for variogram models. In each function, m is a list of
defining parameters and d is an array of the distance values at which to
calculate the variogram mod... | bsmurphy/PyKrige | pykrige/variogram_models.py | Python | bsd-3-clause | 2,181 | [
"Gaussian"
] | e38c08d463ba0e1be98697e23e10af5d853b35d6de71da4c449ada6601fe24b6 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
class Migration(DataMigration):
def forwards(self, orm):
"Write your forwards methods here."
# Note: Don't use "from appname.models imp... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0022_hospital_materials.py | Python | bsd-2-clause | 15,027 | [
"VisIt"
] | bb20473388e485a1a90053f25a0242aee07362074b856ef1736ba34a1008bc35 |
#-------------------------------------------------------------------------------
# Name: grad
# Purpose: Encapsulation of parsing/handling of data from gradient files.
#
# Author: Brian Skinn
# bskinn@alum.mit.edu
#
# Created: 28 Oct 2014
# Copyright: (c) Brian Skinn 2016
# License:... | bskinn/opan | opan/grad.py | Python | mit | 20,808 | [
"Brian",
"ORCA"
] | 829b9b5c2ceb12b5f562618cfd496f7b355bf3b3377f52bb9afad2214efeb3ee |
"""
Test extracting of reflection intensities for export.
Two main use cases supported:
- exporting after scaling, should export only the 'scale' intensities and
variances with the inverse scale correction applied.
dials.scale should choose the best intensities, filter outliers and apply all
corrections except ... | dials/dials | tests/util/test_filter_reflections_export.py | Python | bsd-3-clause | 31,485 | [
"CRYSTAL"
] | 3e4e861c560fd63aac4714af28adac1b05b7a306f5b316127831a63a8ec9fbdf |
from __future__ import absolute_import
from zasim import cagen
from zasim.features import *
from .testutil import *
from random import randrange
from itertools import product
import numpy as np
import pytest
MIN_SIZE, MAX_SIZE = 5, 25
class TestCAGen:
@pytest.mark.skipif("not HAVE_WEAVE")
def test_gen_wea... | timo/zasim | test/test_cagen.py | Python | bsd-3-clause | 21,289 | [
"VisIt"
] | 186e884b1addd0b2381ed6a102db941caa3922f0ab7c554f85dd9d18b20e96fd |
#invariant object recognition
import nest as n
import nest.raster_plot as rp
import nest.topology as tp
import pylab as pl
import numpy as np
n.ResetKernel()
C_E = 0.5
C_I = 0.2
g_E = 25.
g_I = 20.
V_th = -50.
V_reset = -55.
tau_AMPA = 2.4
tau_NMDA = 100.
tau_GABA = 7.
tau_m_E = C_E/g_E
tau_m_I = C_I/g_I
tau_pre = 20... | shiina/invariant-object-recognition | obj_invariance.py | Python | lgpl-3.0 | 6,063 | [
"Gaussian",
"NEURON"
] | adc88e63ec48e9b7d198ae6485792e67b8606a853af225ae4395ba01ce34a5b9 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
renderer = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(renderer)
iren = vtk.vtkRenderWindowInteractor()
i... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/General/Testing/Python/TestDeformPointSet.py | Python | gpl-3.0 | 2,749 | [
"VTK"
] | e367d95d5f87b1b8a62f742b2ddcd3b2d2deb3a391f920060137258895eee9d6 |
"""Convenience functions for running common Picard utilities.
"""
import os
import collections
from contextlib import closing
import pysam
from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
def picard_rnaseq_metrics(picard, align_bam, ref, ribo="null", out_file... | elkingtonmcb/bcbio-nextgen | bcbio/broad/picardrun.py | Python | mit | 13,582 | [
"pysam"
] | 8b4cdaa87880085a8fdee6903da1a6e76d5cb924752c9a2b934ac2983b058c21 |
########################################################################
# $HeadURL $
# File: StorageElementProxyHandler.py
########################################################################
"""
:mod: StorageElementProxyHandler
.. module: StorageElementProxyHandler
:synopsis: This is a service which represe... | calancha/DIRAC | DataManagementSystem/Service/StorageElementProxyHandler.py | Python | gpl-3.0 | 11,977 | [
"DIRAC"
] | d14088c372f13303c988d77f0317c567932d2021c498e6c89c98a63248531d7c |
import numpy as np
from gpaw.mpi import world, MASTER
from gpaw.blacs import BlacsGrid
from gpaw.blacs import Redistributor
def parallel_eigh(matrixfile, blacsgrid=(4, 2), blocksize=64):
"""Diagonalize matrix in parallel"""
assert np.prod(blacsgrid) == world.size
grid = BlacsGrid(world, *blacsgrid)
i... | qsnake/gpaw | doc/tutorials/blacs/parallel_eigh.py | Python | gpl-3.0 | 2,410 | [
"GPAW"
] | 8a8d10d1b0b7ca1db104dc8cf5de3306d62dcfd048f76737e1e0d444d686cf29 |
# Copyright 2013 Colm Ryan colm@colmryan.org
# License GPL v3 (http://www.gnu.org/licenses/gpl.txt)
'''
Script to go from fasta files to hopcounts and aggregate hop counts for TnSeq experiments.
Usage: python fasta2hopcount.py FastaFile IndexName AnnotationFile OutputFile
Author: Colm Ryan
'''
# import sys
impor... | caryan/PyBio | TnSeq/HopCounts.py | Python | gpl-3.0 | 7,021 | [
"Bowtie",
"Galaxy"
] | 37ee51760ab26d92a3564bd0190f518bef6e5fa116fa3219a2ed45d141bf2780 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | samples/visualization_cellsystem.py | Python | gpl-3.0 | 2,111 | [
"ESPResSo"
] | 329658d7d612e5a1c0fa138bd7981cd71bd27f7b252029e87c2e61310add3bc5 |
# Portions Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# context.py - changeset and file context objects for mercurial
#
# Copyright 2006, 2007 Matt Mackall <mpm@selenic.com>
#
# This software may... | facebookexperimental/eden | eden/scm/edenscm/mercurial/context.py | Python | gpl-2.0 | 103,510 | [
"VisIt"
] | 227d9cb5b08911e37691da143c0f8b1c155d57f27d20050d84cb9e7ab1598952 |
# -*- coding:utf-8 -*-
#
# Copyright 2012 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 vers... | rsouza/pypln.web | pypln/web/core/models.py | Python | gpl-3.0 | 2,869 | [
"NAMD"
] | 062e00de2d9720e8e1f29ea2f0d1f6e54f8342d9fd8eed33c259056ebe53c741 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008,2010 Gary Burton
# Copyright (C) 2008 Craig J. Anderson
# Copyright (C) 2009 Nick Hall
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Adam Stein <adam@csh.rit.edu>
# Cop... | prculley/gramps | gramps/gui/plug/_guioptions.py | Python | gpl-2.0 | 76,274 | [
"Brian"
] | c8eb808e764e3ff1d4e5f6d8ca5186fffbf4dc9d94dca7b17c33a71284e594ac |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | dnjohnstone/hyperspy | hyperspy/tests/model/test_set_parameter_state.py | Python | gpl-3.0 | 4,051 | [
"Gaussian"
] | a3fbe20fb643214c67505f5f754950df354b8118e7c23af1111eb14357ad2d47 |
# sql/visitors.py
# Copyright (C) 2005-2013 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Visitor/traversal interface and library functions.
SQLAlchemy schema and expressio... | Drvanon/Game | venv/lib/python3.3/site-packages/sqlalchemy/sql/visitors.py | Python | apache-2.0 | 10,003 | [
"VisIt"
] | a8aa6d377bde06caf56c2d3cbf369b37144b99de4f3632774d678bc59996cfeb |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | andrebellafronte/stoq | stoqlib/gui/search/searchcolumns.py | Python | gpl-2.0 | 6,189 | [
"VisIt"
] | e8ca553d9586c048efd44cdb7a9b7e00645b90ba3ca40922472bf185c1213063 |
import sys,os,unittest
from lammps import lammps
has_mpi=False
has_mpi4py=False
has_exceptions=False
try:
from mpi4py import __version__ as mpi4py_version
# tested to work with mpi4py versions 2 and 3
has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
except:
pass
try:
if 'LAMMPS_MACHINE_NAME... | agiliopadua/lammps | unittest/python/python-open.py | Python | gpl-2.0 | 3,337 | [
"LAMMPS"
] | 0a68ca88c2c5cb9fb74446881be9fd99681a5d151bc8a5cfb82d78f433fcf380 |
from iminuit import Minuit
from probfit import BinnedLH, gaussian, Extended
from matplotlib import pyplot as plt
from numpy.random import randn
data = randn(1000)*2 + 1
#Unextended
blh = BinnedLH(gaussian, data)
#if you wonder what it loos like call desceibe(blh)
m = Minuit(blh, mean=0., sigma=0.5)
plt.figure(figsi... | mtresch/probfit | doc/pyplots/costfunc/blh.py | Python | mit | 733 | [
"Gaussian"
] | 7b8c379bf9a823648f3ace1083f6f659b451aa790bd046ddeb8d2a0d8997d1e4 |
"""
menu.py
Class instance used to create menu for ARTview app.
"""
from __future__ import print_function
import numpy as np
import pyart
import os
import sys
import glob
from ..core import (Variable, Component, common, QtWidgets, QtCore,
componentsList, log)
class Menu(Component):
'''Class... | gamaanderson/artview | artview/components/menu.py | Python | bsd-3-clause | 25,416 | [
"NetCDF"
] | eb124070c60198927d2261e2d167e424843931a35c1c8f1770022af9e6694396 |
#!/usr/bin/env python
#
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
# standard modules
import string
import types
# pyutil modules
from config import DEBUG_MODE
fr... | zooko/egtp | common/MojoMessage.py | Python | agpl-3.0 | 16,518 | [
"VisIt"
] | bfe56e2ef491c658eb2b3277f2889775202d50cd11246a5b30d605843db6dda4 |
import os
from AlGDock import path_tools
from AlGDock.BindingPMF import DEBUG
from AlGDock.BindingPMF import HMStime
import time
import numpy as np
import MMTK
import MMTK.Units
from MMTK.ParticleProperties import Configuration
import multiprocessing
from multiprocessing import Process
# In APBS, minimum ratio of ... | CCBatIIT/AlGDock | AlGDock/postprocessing.py | Python | mit | 36,523 | [
"Amber",
"NAMD",
"OpenMM"
] | fcccf5c1265aa17169e42804cec8af0d04e48d468e6cf54b1f5362d93b3dc0ee |
# -*- coding: utf-8 -*-
"""
Created on 24.9.2012
@author: huqa / pikkuhukka@gmail.com
"""
import random
import time
import logging
class Gun:
"""Russian roulette gun"""
def __init__(self):
self.has_bullet = False
self.in_use = False
self.bullet_slot = 0
self.current_slot... | huqa/pyfibot_modules | module_pyssy.py | Python | mit | 4,979 | [
"GULP"
] | 02e7ec66e5ee134725878991b3c558a32098b60d41ea7d5ab51c1fc81dc09d32 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2010 Brian G. Matherly
#
# 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, or
# (at your option... | Forage/Gramps | gramps/gui/widgets/progressdialog.py | Python | gpl-2.0 | 19,992 | [
"Brian"
] | f23271a994a7f9c0f025fd5afc3b2d159eb9bccc757ac4ad9b64daa7417b4c28 |
"""
Pyperclip
A cross-platform clipboard module for Python,
with copy & paste functions for plain text.
By Al Sweigart al@inventwithpython.com
BSD License
Usage:
import pyperclip
pyperclip.copy('The text to be copied to the clipboard.')
spam = pyperclip.paste()
if not pyperclip.is_available():
print("Cop... | dsm054/pandas | pandas/io/clipboard/__init__.py | Python | bsd-3-clause | 21,528 | [
"VisIt"
] | c111ba6dac613bd8bcd223e9046887b36cb8e3444c456a43737e301c81c44cde |
## \file
## \ingroup tutorial_roofit
## \notebook
##
## \brief Likelihood and minimization: demonstration of options of the RooFitResult class
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
from __future__ import print_function
import ROOT
# Create pdf, data
# --... | karies/root | tutorials/roofit/rf607_fitresult.py | Python | lgpl-2.1 | 3,841 | [
"Gaussian"
] | ae96352d96b8c42bb8c6a21767c255dd53f7ebfa8ba1948659e93a1a824b1317 |
"""
========================================================================
Illustration of Gaussian process classification (GPC) on the XOR dataset
========================================================================
This example illustrates GPC on XOR data. Compared are a stationary, isotropic
kernel (RBF) and ... | RPGOne/Skynet | scikit-learn-0.18.1/examples/gaussian_process/plot_gpc_xor.py | Python | bsd-3-clause | 2,132 | [
"Gaussian"
] | 8dc830bbb6704078ac1d07ff88aef6c0634514cae3b33feb04d4400096d2c239 |
""" The POOL XML Slice class provides a simple plugin module to create
an XML file for applications to translate LFNs to TURLs. The input
dictionary has LFNs as keys with all associated metadata as key,
value pairs.
"""
from DIRAC.Resources.Catalog.PoolXMLCatalog import PoolXMLCatalog
from DIRAC import S_O... | fstagni/DIRAC | WorkloadManagementSystem/Client/PoolXMLSlice.py | Python | gpl-3.0 | 2,674 | [
"DIRAC"
] | ea4d87937f07d208fb237da5066ad749484ab684fdb81a13679074fd09264251 |
../../../../share/pyshared/orca/chat.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/chat.py | Python | gpl-3.0 | 39 | [
"ORCA"
] | 3d95737bd4012e846e1152da37ea5208b48d4a9369b470d672ad0b19684b0abb |
"""
Plots flux distribution as a function of redshift for
IR luminous galaxies. The plot is presented in the
Herschel I paper of Niemi et al.
"""
import matplotlib
matplotlib.use('Agg')
matplotlib.rc('text', usetex=True)
matplotlib.rcParams['font.size'] = 17
matplotlib.rc('xtick', labelsize=13)
matplotlib.rc('ytick', l... | sniemi/SamPy | herschel/plotFluxRedshiftDistribution.py | Python | bsd-2-clause | 7,176 | [
"Galaxy"
] | 77e72fc6e12a371c3c01ef9c833df9f4136d373aae73c30bff2bf541baaf7767 |
from ase.structure import molecule
from gpaw import GPAW
import warnings
# Silence those warnings.
warnings.filterwarnings('ignore', 'Setup for',)
m = molecule('H')
m.center(vacuum=2.0)
calc = GPAW(mode='lcao')
m.set_calculator(calc)
m.get_potential_energy()
calc.write('r.gpw')
calc = GPAW('r.gpw', xc='PBE', idiotpro... | robwarm/gpaw-symm | gpaw/test/fileio/idiotproof_setup.py | Python | gpl-3.0 | 358 | [
"ASE",
"GPAW"
] | 6ff7b5fa341d015824e25dfd2945d1260cc7db62183d572f29b55d379e282bb5 |
# -*- coding: utf-8 -*-
"""
This sample demonstrates a simple skill built with the Amazon Alexa Skills Kit.
The Intent Schema, Custom Slots, and Sample Utterances for this skill, as well
as testing instructions are located at http://amzn.to/1LzFrj6
For additional samples, visit the Alexa Skills Kit Getting Started gui... | Ernestyj/PyStudy | alexa-smarthome/sample_lambda/lambda_function_stand_meeting.py | Python | apache-2.0 | 8,188 | [
"VisIt"
] | 7cfb1bef5906187c5d9bef7cbee4cce46adce58c1f0d5c63ffd1a42be97862d8 |
import re
wires = {}
for i in open('day7.txt'):
set = re.match(r'([a-z0-9]+) -> ([a-z]+)',i)
if set:
wires[set.group(2)] = set.group(1)
op1 = re.match(r'(NOT) ([a-z0-9]+) -> ([a-z]+)',i)
if op1:
wires[op1.group(3)] = [op1.group(1), op1.group(2)]
op2 = re.match(r'([a-z0-9]+) (AND|OR|LSHIFT|RSHIFT) ([a-z0-9]+) ... | jsvennevid/adventofcode | 2015/07/puzzle2.py | Python | mit | 1,071 | [
"VisIt"
] | 249b63a3ce1256fce73a9750514a3ab79cab40fe40d314ed2d20f376fcdbf76d |
#!/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... | thaim/ansible | lib/ansible/modules/network/avi/avi_dnspolicy.py | Python | mit | 3,851 | [
"VisIt"
] | e44c16f9bef4f2713e4d29840c0c6cd780b2a5dd0b33d5d54f3a364239eb286b |
'''
Functions used to manipulate CDS records in the context of the VCF
being processed.
'''
from copy import deepcopy
from warnings import warn
from Bio.SeqFeature import FeatureLocation
from .utils import AnnotationWarning
from .constants import SYNM, MISS, FRSH, SPAC, SPDN, STGN, STLS, \
SRLS, IFIS, IFDL, INTV, ... | tfrayner/vcf_walker | vcf_walker/cds.py | Python | gpl-3.0 | 8,301 | [
"Biopython"
] | fecec6bd393ec3b169b6bbf59b26a9cdcf2a922c26e8c66df614f3b1367bbaf2 |
import imp, sys, os
from __main__ import qt, ctk, vtk, slicer
from Workflow import *
class WorkflowStep( ctk.ctkWorkflowWidgetStep ) :
def __init__( self ):
self.Observations = []
def createUserInterface( self ):
# if the user interface has already be created, quit
# \todo: f) have an option to setup... | agirault/VesselView | Modules/Scripted/Workflow/Widgets/WorkflowStep.py | Python | apache-2.0 | 9,259 | [
"VTK"
] | 8955542c906396f2b2cc0bc04a368f8c03855653bd4acc6ba2fe26531d2bb51c |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
import collections
import logging
import threading
import time
FIRST_COMPLETED = 'FIRST_COMPLETED'
FIRST_EXCEPTION = 'FIRST_EXCEPTION'
ALL_COMPLETED = 'A... | prefetchnta/questlab | bin/x64bin/python/37/Lib/concurrent/futures/_base.py | Python | lgpl-2.1 | 22,456 | [
"Brian"
] | d97adb8da29bc898ac0864151e7d29bf6fb45b81a2ae293dd8eaa944d944fc64 |
##############################################################################
# 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-annotationfilter/package.py | Python | lgpl-2.1 | 1,982 | [
"Bioconductor"
] | 42535412500646c834d97fd5f7eca339432e0a8491594bd1dc0d3c6202f649ed |
#!/usr/bin/env python
#coding: utf-8
# Back-end server for Wasabi web application (http://wasabiapp.org). Compatible with Python 2.7 and Python 3+
# Copyright Andres Veidenberg (andres.veidenberg{at}helsinki.fi) and Alan Medlar, University of Helsinki (2015)
# Distributed under AGPL license (http://www.gnu.org/license... | veidenberg/wasabi | wasabi_server.py | Python | agpl-3.0 | 64,022 | [
"VisIt"
] | 11548abfbed5c9a261c750b0c580833000a3565ad17e36fc565e3a6d7641f36e |
import numpy as np
from gpaw import GPAW
from gpaw.dipole_correction import DipoleCorrection
from gpaw.poisson import PoissonSolver
from ase.structure import molecule
from gpaw.mpi import rank
from gpaw.utilities import h2gpts
"""
Test the dipole correction code by comparing this system:
H
z1 O z2
H
(wh... | ajylee/gpaw-rtxs | gpaw/test/dipole.py | Python | gpl-3.0 | 2,687 | [
"ASE",
"GPAW"
] | 09488b9900477ce76a4e51c68190ebd21c20e4dc743f48a927c5dddacbf66a96 |
# -*- coding: utf-8 -*-
"""
Illumination correction toolbox.
The module provides a function to correct illumination/vignetting systematic
variations in intensity.
The intensity image :math:`I(x)` given a flat field :math:`F(x)` and
a background :math:`B(x)` the image is corrected to :math:`C(x)` as:
.. math:
... | ChristophKirst/ClearMap | ClearMap/ImageProcessing/IlluminationCorrection.py | Python | gpl-3.0 | 11,226 | [
"Gaussian"
] | 7e15dbfea842a5cbb8f37887e4c75c0ffff7035a927bd2b00460231fe57a190d |
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is... | stanmoore1/lammps | tools/python/pizza/pdbfile.py | Python | gpl-2.0 | 9,536 | [
"LAMMPS"
] | fab2ce938f550c5b3b4f48a6617307e2012047679e3d10f5490424bcf19185c8 |
# -*- coding: utf-8 -*-
"""
End-to-end tests related to the cohort management on the LMS Instructor Dashboard
"""
from __future__ import absolute_import
import os
import uuid
from datetime import datetime
import unicodecsv
from bok_choy.promise import EmptyPromise
from pytz import UTC, utc
from common.test.acceptan... | ESOedX/edx-platform | common/test/acceptance/tests/discussion/test_cohort_management.py | Python | agpl-3.0 | 42,483 | [
"VisIt"
] | 8588534e112dec1f619e4c7aa4f1acdce1e49dbe4a4b1f9f61422f52bc29ab9e |
"""
Visualization for structures using chemview.
"""
import numpy as np
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.analysis.molecule_structure_comparator import CovalentRadius
from monty.dev import requires
try:
from chemview import MolecularViewer
from chemview.utils import get_a... | gVallverdu/pymatgen | pymatgen/vis/structure_chemview.py | Python | mit | 3,234 | [
"pymatgen"
] | 7acbbc7bfc4d2498668474a4ac624aecf8c240f9ea9f0286ad8f97222d70be0a |
""" This is the guy that you should use when you develop a script that interacts with DIRAC
And don't forget to call parseCommandLine()
"""
import sys
import os.path
import inspect
from DIRAC.ConfigurationSystem.Client.LocalConfiguration import LocalConfiguration
from DIRAC.FrameworkSystem.Client.Logger import gL... | ic-hep/DIRAC | src/DIRAC/Core/Base/Script.py | Python | gpl-3.0 | 5,667 | [
"DIRAC"
] | 6dc9b441e66f8a0e6b18e0129d20ab9699a9dac00dbd8151f0d1f380c8736e02 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Retrieve parameters associated to the given DIRAC job
"""
__RCSID__ = "$I... | Sbalbp/DIRAC | Interfaces/scripts/dirac-wms-job-parameters.py | Python | gpl-3.0 | 1,186 | [
"DIRAC"
] | 80050e61d6e7ad7d867c15767f91dadd827dbf1c9e3aee3fd6e6e4687e536d70 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/bibles/forms/booknamedialog.py | Python | gpl-2.0 | 6,425 | [
"Brian"
] | a854d159a6a49bdea3eb0a2db64a3a7567ec1e1a0e01efa5f0458660fe2090ea |
# * *************************************************************
# *
# * Soft Active Mater on Surfaces (SAMoS)
# *
# * Author: Rastko Sknepnek
# *
# * Division of Physics
# * School of Engineering, Physics and Mathematics
# * University of Dundee
# *
# * (c) 2013, 2014
# *
# * School of Scienc... | sknepneklab/SAMoS | utils/RastkoVisu/particle_tracking.py | Python | gpl-3.0 | 4,289 | [
"VTK"
] | d457f0c3ba1b3ac30115a57f15e5c4268912d59c3643b745a8c46c65a661c7ca |
'''
Created on Dec 17, 2014
@author: sergio
'''
import numpy as np
import ctypes
import numpy.ctypeslib as npct
import matplotlib.pyplot as plt
import psycopg2
import time
import neodb.core
from math import e, pow
from scipy.optimize import leastsq
#cfsfd = ctypes.cdll.LoadLibrary('/home/sergio/iibm/sandbox/t.so')
#... | sergiohr/NeuroDB | test/test8.py | Python | gpl-3.0 | 7,060 | [
"Gaussian"
] | dfdf649a59dc6c9f88ff5e2eda42f2b0967e4043044d7c7c16567ae60df8ba1f |
#!/usr/bin/env python
"""Predict rotamers from low resolution information"""
# Copyright 2010 Kevin Keating
#
# Licensed under the Educational Community 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.os... | jlec/coot | rcrane/pseudoPredictor.py | Python | gpl-3.0 | 8,155 | [
"Gaussian"
] | 9ebbe5286be709d1a4738b1f09f2d8c73d3749ed26079a7373ff27c500249624 |
# vim: ts=4 : sts=4 : sw=4 : et :
import wx
import survey
import sqlite3
import datetime, time
import os.path
import tabulation
def adapt_datetime(ts):
"""For use with sqlite3.register_adapter so that datetime is used correctly."""
return time.mktime(ts.timetuple())
sqlite3.register_adapter(datetime.datetime,... | pizzasgood/galactiscan | data.py | Python | gpl-3.0 | 16,152 | [
"Galaxy"
] | 2bd6048fd7fc7bff04acbceda113ba7cad48d3e77b6dd2682cc62015ec7ab0d8 |
#!/usr/bin/env python
""" The GUI wrapper for the jaide CLI utility.
This python file is used to spawn the GUI that wraps around jaide,
providing ease of use for those that don't want to use the command line.
This Class is part of the jaidegui project.
It is free software for use in manipulating junos devices. More i... | NetworkAutomation/jaidegui | jaidegui/gui.py | Python | gpl-2.0 | 55,872 | [
"VisIt"
] | a63f53293f84e6a83006dfe110cdf88e49be6d498195ab5e9338711a69ca968d |
# coding=utf-8
# Copyright 2020 The SimCLR Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | google-research/fnc | data_util.py | Python | apache-2.0 | 20,266 | [
"Gaussian"
] | e6e217d9d6d9ddc4768d389fe0bacc17ba89014d759d41dc7bd040f4074ae1da |
#!/usr/bin/env python2
# -*- coding: utf8 -*-
"""Pipeline for Goodman High Troughput Spectrograph spectra Extraction.
This program finds reduced images, i.e. trimmed, bias subtracted, flat fielded,
etc. that match the ``<pattern>`` in the source folder, then classify them in
two groups: Science or Lamps. For science i... | simontorres/goodman | goodman_pipeline/spectroscopy/redspec.py | Python | bsd-3-clause | 24,699 | [
"Gaussian"
] | 2e042b2aced74c7ba13603213600e3de191a7587f880538674de65ba1731e105 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'GeoRecord.notes'
db.add_column('profiles_georecord', 'notes', self.gf('django.db.models.fi... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0037_auto__add_field_georecord_notes.py | Python | mit | 13,840 | [
"MOE"
] | 9919a2afe1be5718f332ffc71b6cb72342f564e43137a02648a25f6e4dc2fdc7 |
# 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 u... | wangsheng1001/incubator-singa | examples/cifar10/caffe/caffe_net.py | Python | apache-2.0 | 1,717 | [
"Gaussian"
] | 405effd3c2bb8b243102d1860cc64ece29c075cb1cb922fb69f557a77ff3f5af |
# -*- coding: utf-8 -*-
## @package gmapcatcher.widgets.widDrawingArea
# DrawingArea widget used to display the map
import mapDrawingArea
import gtk
import pango
import math
import gmapcatcher.mapUtils as mapUtils
from gmapcatcher.mapConst import *
## This widget is where the map is drawn
class DrawingArea(mapDrawin... | mdraeger/gmapcatcher | gmapcatcher/widgets/widDrawingArea.py | Python | gpl-2.0 | 16,118 | [
"FLEUR"
] | 24f957c8dbd033c235475db9036838f1944dfe0dc68ce00025d98fec270c9638 |
#!/usr/bin/env python
# --------------------------------------------------------------------------
# OligoMiner
# probeRC.py
#
# (c) 2017 Molecular Systems Lab
#
# Wyss Institute for Biologically-Inspired Engineering
# Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
#... | brianbeliveau/OligoMiner | probeRC.py | Python | mit | 4,198 | [
"Biopython"
] | 26b5d5d3245aedea34472aec3994c9f498751063d473c2a32886309a64753700 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | sam-m888/gramps | gramps/plugins/gramplet/soundgen.py | Python | gpl-2.0 | 3,691 | [
"Brian"
] | d872aa665adf5cfe2cde1bcfe37a66e6362016c24073e2d6b97038d1a588609e |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Test for the piezo tensor class
"""
__author__ = "Shyam Dwaraknath"
__version__ = "0.1"
__maintainer__ = "Shyam Dwaraknath"
__email__ = "shyamd@lbl.gov"
__status__ = "Development"
__date__ = "4/1/16"
import os
import un... | vorwerkc/pymatgen | pymatgen/analysis/tests/test_piezo.py | Python | mit | 2,238 | [
"pymatgen"
] | 9a59623a41d3b78eab452ca5ff6a9946171849774b65ca3e05c937535d3b6d74 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import six
import ruamel.yaml as yaml
import os
import json
"""
This module provides classes to perform analyses of
the local environments (e.g., finding near... | matk86/pymatgen | pymatgen/analysis/local_env.py | Python | mit | 31,293 | [
"Jmol",
"pymatgen"
] | c7bf1d52606d227a0c5fcf57970909464e651d7776e2597264ecb90b01aa254e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''Ripyl protocol decode library
Statistical operations test suite
'''
# Copyright © 2013 Kevin Thibedeau
# This file is part of Ripyl.
# Ripyl is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public Licen... | kevinpt/ripyl | test/test_stats.py | Python | lgpl-3.0 | 3,176 | [
"Gaussian"
] | 07fccf174a0d3a49a51191887fbc8dcb04a1530e7e8ccefd89f202030f96ac42 |
#/*
# *
# * Overcast for Kodi.
# *
# * Copyright (C) 2017 Brian Hornsby
# *
# * 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 lat... | brianhornsby/plugin.audio.overcast | resources/lib/overcast.py | Python | gpl-3.0 | 4,460 | [
"Brian"
] | 160d3b15e3fd9434908537bf454f0afcd143318fe6497d3d6c4011f622a81bc8 |
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