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# -*- coding: utf-8 -*-
'''
Module for gathering and managing information about MooseFS
'''
from __future__ import absolute_import
# Import salt libs
import salt.utils
def __virtual__():
'''
Only load if the mfs commands are installed
'''
if salt.utils.which('mfsgetgoal'):
return 'moosefs'
... | smallyear/linuxLearn | salt/salt/modules/moosefs.py | Python | apache-2.0 | 3,939 | [
"MOOSE"
] | 1a57138fba9573cd4fceeb816743cff3517ad78c8d20b8bc6c1f2892fbd5b843 |
"""Implement special border conditions for molecular dynamics."""
#import weakref
# ase.parallel imported in __init__
class Freeze:
"""Class for freezing atoms close to computation cell
in molecular dynamics simulations.
Parameters:
atoms: The atoms.
margin: define freezine region ... | lavakyan/ase-bimetall | borders.py | Python | gpl-2.0 | 2,791 | [
"ASE"
] | 8ef52211a8660b8b9ffd80d1c7203ea632e01bd8163d87b016b01d5ae315588f |
#!/usr/bin/env python2.5
#
# Copyright 2009 the Melange 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 applic... | SRabbelier/Melange | app/soc/views/models/survey.py | Python | apache-2.0 | 37,086 | [
"VisIt"
] | 1928867b88707e2d05ae960663c7d52d34cb7b2eb2c3673344abab7583472c4a |
import pymol
from pymol import cmd
import sys,os
def nat(pdbid,chainid):
cmd.view('v', 'store');
object = cmd.get_names()[0]
cmd.fetch(pdbid)
cmd.select("design_nat","%s and chain %s"%(object,"B"))
cmd.select("native_nat","%s and chain %s"%(pdbid,chainid))
cmd.select("other_nat","%s and not chain %s"%... | weitzner/Dotfiles | pymol_scripts/Native-network.py | Python | mit | 1,095 | [
"PyMOL"
] | 9492880e0289eef1596856df137dad1734c6b29d5f79aea22d0521e2d0868d15 |
from six import ensure_text
from .node import NodeVisitor, ValueNode, ListNode, BinaryExpressionNode
from .parser import atoms, precedence
atom_names = {v: "@%s" % k for (k,v) in atoms.items()}
named_escapes = {"\a", "\b", "\f", "\n", "\r", "\t", "\v"}
def escape(string, extras=""):
# Assumes input bytes are ei... | scheib/chromium | third_party/wpt_tools/wpt/tools/wptrunner/wptrunner/wptmanifest/serializer.py | Python | bsd-3-clause | 4,482 | [
"VisIt"
] | e15a6730ea986c2468a362381b3fd24fa6b29a61adff4a8cb1d3e96c494815d1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# freezefunctions - freeze archive helper functions
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General P... | heromod/migrid | mig/shared/freezefunctions.py | Python | gpl-2.0 | 13,964 | [
"Brian"
] | 0434a6e2363e0b08809076671abf69c712d8a5f870d9bb3db9ee879ffd951bcc |
"""
The ``segment`` module has components to make an image processing workflow.
===============================================================================
Overview
===============================================================================
The ``segment`` (or **segment**\ ation) module contains algorithms use... | DudLab/nanshe | nanshe/imp/segment.py | Python | bsd-3-clause | 160,912 | [
"Gaussian",
"NEURON"
] | ba9bccae3362393c4cae46722e6c01b6e945cca9702f5cea217fbab1f1ab0027 |
import math
import numpy as np
from astropy.io import fits
from pyraf import iraf
import os
# From Henry G. 10/2014
# mkobjects_iraf(): This is the original iraf task to plop down fake galaxies
# onto a real image.
def mkobjects_iraf(inimage, outimage, objfile, radius, magzero):
from pyraf import iraf
iraf... | boada/planckClusters | snippets/mkobjects.py | Python | mit | 4,945 | [
"Galaxy"
] | 040f63644957fd070f918051c7d64d0d4fa9067c0a5d62fa7afdf4254d3385f6 |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Canal para gaypornshare.com
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import urlparse,urllib2,urllib,re
import os,sys
from c... | mariianna/kodi | pelisalacarta/channels/gaypornshare.py | Python | gpl-3.0 | 7,480 | [
"ADF"
] | ec55e5ad10cac9cf64fcf93b5ce196893b0b748984cb8b52baaadfe465ecbfb8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements more advanced transformations.
"""
import logging
import math
import warnings
from fractions import Fraction
from itertools import groupby, product
from math import gcd
from string im... | gmatteo/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 88,529 | [
"ASE",
"CRYSTAL",
"pymatgen"
] | fa03cfa97b0cbef290b46681a53e2dadfa12ae3318b2eea791205ff877eabe52 |
import fftoolbox as fftb
import numpy as np
from scipy.optimize import curve_fit
import matplotlib.pyplot as plt
import seaborn
import logging, sys
#logger = logging.getLogger(__name__)
#lf = '%(levelname)s: %(funcName)s at %(filename)s +%(lineno)s\n%(message)s\n'
#logging.basicConfig(level=logging.DEBUG, format=lf... | maxivanoff/fftoolbox | run-examples/load-complex.py | Python | gpl-2.0 | 3,297 | [
"Gaussian"
] | a1b459e3234ed3c191095ae3cc500c097a91f1b5a9303ac7ceff1c50e93d47fa |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "Screw this"
exit(1)
class Engine(object):
def __init__(self, scene_map)
self.scene_map = scene_map
def play(self):
cur... | ashdude1120/Private | game.py | Python | mit | 2,389 | [
"BLAST"
] | 5e11dee81bf38d27f8cb32b7c8da2723ae2b5956b32559dfdb27ab3ebaf213ed |
from ase import *
atom = Atoms('N', calculator=EMT())
e_atom = atom.get_potential_energy()
d = 1.1
molecule = Atoms('2N', [(0., 0., 0.), (0., 0., d)])
molecule.set_calculator(EMT())
e_molecule = molecule.get_potential_energy()
e_atomization = e_molecule - 2 * e_atom
print 'Nitrogen atom energy: %5.2f eV' %e_atom
pr... | freephys/python_ase | doc/tutorials/N2.py | Python | gpl-3.0 | 426 | [
"ASE"
] | 4d9ecef51c269f6363e78dd6d0e075af28c54b84b7f0c122c27397751698b3bd |
"""Tests for the ImagePlaneWidget module.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from io import BytesIO
import copy
import numpy
# Enthought library imports.
from traits.api import T... | dmsurti/mayavi | integrationtests/mayavi/test_image_plane_widget.py | Python | bsd-3-clause | 4,716 | [
"Mayavi"
] | 847da542e77f325e84be8fc624221c023d693b9bda45db5b4b25ba3499fac5a4 |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empir... | RomainBrault/scikit-learn | sklearn/covariance/robust_covariance.py | Python | bsd-3-clause | 30,178 | [
"Gaussian"
] | 77d4ed9707ee97fdf0dffad095648b96bf1ecc9aef2f3d2de8286a9a6f56fb04 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
OTBUtils.py
---------------------
Date : 11-12-13
Copyright : (C) 2013 by CS Systemes d'information (CS SI)
Email : otb at c-s dot fr (CS SI)
Contrib... | carolinux/QGIS | python/plugins/processing/algs/otb/maintenance/OTBSpecific_XMLcreation.py | Python | gpl-2.0 | 29,105 | [
"Gaussian"
] | e6f03480481bdc5bf32f8eb1005b28ffc047323b6635545ae9c75f16339bae7b |
# multi1.py ---
# Upi Bhalla, NCBS Bangalore 2014.
#
# Commentary:
#
# This loads in a low-detail model incorporating
# reac-diff and elec signaling in neurons. The reac-diff model
# has just Ca and CaM in it, and there are no-cross-compartment
# reactions though Ca diffuses everywhere. The elec model controls the
... | dilawar/moose-full | moose-examples/snippets/MULTI/multi1.py | Python | gpl-2.0 | 13,980 | [
"MOOSE"
] | b29077441a8d5fbdfd0b92d3934345e5db66c3ba43c08e180d26c9c3c5251bb0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import scipy.optimize as SO
import scipy.integrate as SI
'This module contains various fitting procedures'
class Fit():
'''
A class for fitting
'''
# a number of points needed to fit
np = {0: 1, # 1-peak Gaussian
1: 2, # 2... | ansobolev/shs | shs/gui/fit.py | Python | mit | 3,165 | [
"Gaussian"
] | b205e874e0e2c3f78091117246ec2909905a8f3a661b4ce81a4b6cc64caba760 |
# -*- coding: utf-8 -*-
##
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 CERN.
##
## CDS Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either versio... | lbjay/cds-invenio | modules/bibupload/lib/batchuploader_webinterface.py | Python | gpl-2.0 | 15,328 | [
"VisIt"
] | 4379365b7329ffdffda09427e440d6c9676ff145483c045bf20d462ca3034041 |
#
# Convert raw output of the Caffe 'time' command
# to the CK timing format.
#
# Developers:
# - Grigori Fursin, cTuning foundation / dividiti, 2016
# - Anton Lokhmotov, dividiti, 2016-2017
#
import json
import os
import re
import sys
import sys
import os.path
import glob
import argparse
### copy linux director... | ctuning/ck-math | program/clblast-tune/ck_preprocess.py | Python | bsd-3-clause | 9,305 | [
"ADF"
] | 9ab6429ae6788b644fa97f0572a0e7e551efeff12c0731f626e728a9d41d9c03 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Setup.py for pymatgen."""
import sys
import platform
from setuptools import setup, find_namespace_packages, Extension
from setuptools.command.build_ext import build_ext as _build_ext
class build_ext(_bui... | gmatteo/pymatgen | setup.py | Python | mit | 8,910 | [
"ABINIT",
"ASE",
"CP2K",
"CRYSTAL",
"FEFF",
"Gaussian",
"LAMMPS",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | 1b0c706f6e11c22df35bb1dc003741f82cb147b6681706a0198938a414962441 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.zenoss.OpenStackSwift | ZenPacks/zenoss/OpenStackSwift/tests/testCommandPlugins.py | Python | gpl-2.0 | 3,002 | [
"VisIt"
] | f3f41d8d918959013e00fcd154ab533d4d3c3e4f38ae8302e701f502c1476e4b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides input and output from the CSSR file format.
"""
import re
from monty.io import zopen
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
__author... | gVallverdu/pymatgen | pymatgen/io/cssr.py | Python | mit | 3,006 | [
"pymatgen"
] | 76a30975a768a9951ec09535a85c435fa1297e48b0052fad3dea7bd494f639e1 |
#
# Author: Henrique Pereira Coutada Miranda
# Run a BSE calculation using yambo
# one job per q-point for the dielectric function
#
from __future__ import print_function
from builtins import map
from builtins import range
from yambopy import *
from qepy import *
import multiprocessing
import argparse
import sys
yambo... | henriquemiranda/yambo-py | tutorial/bn/bse_par_bn.py | Python | bsd-3-clause | 4,482 | [
"Yambo"
] | 4d5f6061b9bfd982843a96bb49f1646ad9ad51194389c4567e5e057b3591d278 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import warnings
import numpy as np
from numpy.core.multiarray import normalize_axis_index
from astropy.units import Quantity
from astropy.utils import isiterable
from astropy.utils.exceptions import AstropyUserWarning
from astropy.stats._fast_sigma_clip... | pllim/astropy | astropy/stats/sigma_clipping.py | Python | bsd-3-clause | 39,050 | [
"Gaussian"
] | dfc13bac93535762aa3d6012610dcf92120ad2d6ce7bf1a42700d457bad21447 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | willdecker/adspygoogle | adspygoogle/SOAPpy/Errors.py | Python | mit | 3,127 | [
"Brian"
] | 5147c804ebed07d1bac434ec98177e06cf02150c3bfe2175048f83d2c940c9ad |
import hashlib
import pickle
import sys
import warnings
import numpy as np
import pytest
from numpy.testing import (
assert_, assert_raises, assert_equal, assert_warns,
assert_no_warnings, assert_array_equal, assert_array_almost_equal,
suppress_warnings
)
from numpy.random import MT199... | abalkin/numpy | numpy/random/tests/test_randomstate.py | Python | bsd-3-clause | 79,448 | [
"Gaussian"
] | bcaab61a417f6e4b5870552599b804b856d878c1064bc6f56f0afa42222cfd41 |
"""
DataFrame
---------
An efficient 2D container for potentially mixed-type time series or other
labeled data series.
Similar to its R counterpart, data.frame, except providing automatic data
alignment and a host of useful data manipulation methods having to do with the
labeling information
"""
from __future__ import... | dsm054/pandas | pandas/core/frame.py | Python | bsd-3-clause | 372,452 | [
"Elk"
] | b3e55985df1b69918a0cd52a79edd7c9febfc2b9c790416e9526126d618bc7e7 |
from django.contrib import admin
from .models import Quote
from crm.admin import UpdatedByAdmin
from django.utils.safestring import mark_safe
from django.core.urlresolvers import reverse
from django.conf.urls import patterns, url
from django.contrib.admin.util import unquote
from django.shortcuts import get_object_or_4... | CMU-Robotics-Club/roboticsclub.org | quotetron/admin.py | Python | mit | 3,959 | [
"VisIt"
] | ef402ec4f7985d1755f16d88ac45951c124fb4ad4f0f1059f9d77e5b589cae35 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
"""
This demo demonstrates how to embed a matplotlib (mpl) plot
into a PyQt4 GUI application, including:
* Using the navigation toolbar
* Adding data to the plot
* Dynamically modifying the plot's properties
* Processing mpl events
* Saving the plot to a file from a menu
... | jcerezochem/fcc_tools | python/fcc_analyzer_PyQt5.py | Python | gpl-2.0 | 98,203 | [
"Gaussian"
] | c24dae705433bd02f3b20199b06d551ceb6dee4ec7db66c32d5190db2158a119 |
# -*- coding: utf-8 -*-
#
# Copyright © Spyder Project Contributors
# Licensed under the terms of the MIT License
# (see spyder/__init__.py for details)
"""
Spyder, the Scientific PYthon Development EnviRonment
=====================================================
Developped and maintained by the Spyder Project
Contr... | kirichoi/tellurium | spyder_mod/Spyder 3.3.0/spyder/app/mainwindow.py | Python | apache-2.0 | 133,996 | [
"CRYSTAL",
"VisIt"
] | 079bb3da3376730c51972bbfea70486e3152bb7e6702b0864f6b500debe7767d |
import numpy as np
from numpy.fft import fft, ifft, fftfreq, rfftfreq
from astropy.io import ascii,fits
from scipy.interpolate import InterpolatedUnivariateSpline, interp1d
from scipy.integrate import trapz
from scipy.special import j1
import multiprocessing as mp
import sys
import gc
import os
import bz2
import h5py
... | BrownDwarf/Starfish | Starfish/grid_tools.py | Python | bsd-3-clause | 53,519 | [
"Gaussian"
] | 34607472fd798153382aa3b0c7badae293eba691a68b7de2de1d74c41f7a9c53 |
#!/usr/bin/env python
"""
``tutorial_full.py`` is a tutorial that trains a multimodal pipeline
from some test data. It shows how to set up a complex training
scenario with multiple data sources.
"""
import argparse
import logging
import os
from gensim.models import TfidfModel
import numpy
import safire
from safire.dat... | hajicj/safire | examples/tutorial_full.py | Python | gpl-3.0 | 33,911 | [
"NEURON"
] | 7953c63bf6880e66dc62a797f617c851149ac02ef561583d009dfa0e64d8a1bd |
#!/usr/bin/env python
# File created on 2 Jul 2014
from __future__ import division
#of credits
__author__ = "Jesse Zaneveld"
__copyright__ = "Vega Thurber Lab Copyright 2014"
__credits__ = ["Jesse Zaneveld","Stephanie Rosales","RyanMcMinds"]
__license__ = "GPL"
__version__ = "0.1-dev"
__maintainer__ = ""
__email__ =... | zaneveld/viroscape | scripts/RAP_to_biom.py | Python | bsd-2-clause | 19,025 | [
"BLAST"
] | 1039c2ffb374074e6e36a4e8cbd273d4ed7586e785e00485849ebb050d81ece5 |
from datetime import datetime
import logging
log = logging.getLogger(__name__)
import numpy
from box import BoundingBox, Vector
from mclevelbase import exhaust
import materials
from entity import Entity, TileEntity
def convertBlocks(destLevel, sourceLevel, blocks, blockData):
return materials.convertBlocks(destL... | tinkerinestudio/Tinkerine-Suite | TinkerineSuite/Cura/util/pymclevel/block_copy.py | Python | agpl-3.0 | 5,598 | [
"VisIt"
] | 21cc107a85c0439a1cf0abb80f8d16e20f2d347d373f2d62f24acb03460d1e73 |
###########################################################
# SPEpy - simplified parquet equation solver for SIAM #
# Copyright (C) 2019 Vladislav Pokorny; pokornyv@fzu.cz #
# homepage: github.com/pokornyv/SPEpy #
# params_siam.py - reading parameter file #
####################... | pokornyv/SPEpy | config_siam.py | Python | gpl-3.0 | 6,095 | [
"DIRAC"
] | ad0d861d8fda36025e4ae550ca4adb8eca16930fd18ddfd4909180579a496d63 |
"""
Copyright (c) 2004-Present Pivotal Software, Inc.
This program and the accompanying materials are made available under
the terms of the 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.... | edespino/gpdb | src/test/tinc/tincrepo/mpp/models/regress/sql_related/regress_sql_perf/regress_sql_perf.py | Python | apache-2.0 | 3,942 | [
"ORCA"
] | e4a6b7e74c04bfc57e077a7827b2a3dd7ee9285dd4cfe4535b1d156d89298dd4 |
#!/usr/bin/env python2.7
#
# DNSChef is a highly configurable DNS Proxy for Penetration Testers
# and Malware Analysts. Please visit http://thesprawl.org/projects/dnschef/
# for the latest version and documentation. Please forward all issues and
# concerns to iphelix [at] thesprawl.org.
# Copyright (C) 2015 Peter Kac... | 0x27/MITMf | core/servers/dns/DNSchef.py | Python | gpl-3.0 | 22,123 | [
"VisIt"
] | 91604dc3ca22fcaff84ad7eb5541c3fd56e2115aeaa26a3350e56ed10da3bb7a |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
import re
import sys
import logging
def _activation_summary(x):
"""Helper to create summaries for activations.
Creates a summary that provides a histogram of activations.
... | TensorVision/MediSeg | model/VGG8.py | Python | mit | 8,790 | [
"Gaussian"
] | f96a297ef328f497f07a974d4d7f9df3f0d154f4bb7e1ed081adee0b6897e62f |
#!/usr/bin/env python
import os
import sys
import time
import logging
import numpy as np
import pandas as pd
from datetime import datetime
import xgboost as xgb
from sklearn.model_selection import RandomizedSearchCV
from sklearn.preprocessing import MinMaxScaler
from moloi.config_processing import read_model_config
fr... | DentonJC/virtual_screening | moloi/bin/xgb.py | Python | gpl-3.0 | 4,270 | [
"RDKit"
] | 075a3b554de345121f40108287ee0c6ee245766cb9c2ecf69002a59a9a349be4 |
import sys, time
import numpy as np
#####################################################################################
def twoD_Gaussian2((x, y), amplitude, xo, yo, sigma_x, sigma_y, theta):
# Function for a 2-D Gaussian
# Returns a flattened 1-D array for the Gaussian
xo = float(xo)
yo = float(yo)
... | ctheissen/unwisest | utilities.py | Python | mit | 2,243 | [
"Gaussian"
] | bca3c9bb4a852e002afb1c472b5f76b1bb8c4efba8deef0dc455557cb39479ce |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHOULD H... | mkalewski/sim2net | sim2net/mobility/__init__.py | Python | mit | 2,159 | [
"VisIt"
] | 0092ee3d2d97b49827b27176513bf9c01038450a13101b1a3aa23b98622aae46 |
#pylint: disable=C0111
from lettuce import world, step
from xmodule.modulestore import Location
from contentstore.utils import get_modulestore
from selenium.webdriver.common.keys import Keys
VIDEO_BUTTONS = {
'CC': '.hide-subtitles',
'volume': '.volume',
'play': '.video_control.play',
'pause': '.video... | pelikanchik/edx-platform | cms/djangoapps/contentstore/features/video.py | Python | agpl-3.0 | 6,408 | [
"VisIt"
] | c382c2c5443d6047998cee072837cf89122ca4a2034b68f0bf6629468bd01a95 |
import math
from chainer.functions.connection import linear
from chainer import initializers
from chainer import link
class Linear(link.Link):
"""Linear layer (a.k.a. fully-connected layer).
This is a link that wraps the :func:`~chainer.functions.linear` function,
and holds a weight matrix ``W`` and op... | benob/chainer | chainer/links/connection/linear.py | Python | mit | 2,609 | [
"Gaussian"
] | 1e66bbc5e59f0f98b7f87c50875d87bd9fefcde57a2a1038816c0d1890e2c42a |
import numpy as np
from deepchem.utils.typing import PymatgenComposition
from deepchem.feat import MaterialCompositionFeaturizer
from typing import Any
class ElementPropertyFingerprint(MaterialCompositionFeaturizer):
"""
Fingerprint of elemental properties from composition.
Based on the data source chosen, re... | deepchem/deepchem | deepchem/feat/material_featurizers/element_property_fingerprint.py | Python | mit | 3,189 | [
"CRYSTAL",
"matminer",
"pymatgen"
] | df099c601d7687e073e909fc0e3b81c2af341777875800d19c8e3d8c9abbf0cf |
# Fire.py
# Aaron Taylor
# Moose Abumeeiz
#
# This is the class for the fires in each room.
# They can have a diffrent base hurt isaac.
#
from pygame import *
from random import randint
from const import *
from Animation import *
class Fire:
def __init__(self, variant, xy, sounds, textures):
self.variant = varia... | ExPHAT/binding-of-isaac | Fire.py | Python | mit | 1,977 | [
"MOOSE"
] | 5a57de92d436be199abb95f6e2ab2930c1d14c182be43c5a03e34dcc683981cc |
#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
"""
test_psi4
~~~~~~~~~~~~~~
Test Psi4 specific functionality that is not handled elsewhere.
"""
import sys
import unittest
import geoprep
from adapters import psi4
from tests import adapter
... | mattbernst/polyhartree | tests/test_psi4.py | Python | gpl-3.0 | 5,017 | [
"Psi4"
] | b15c83938cce5739b1c9e9db5ae7e13100610c17af5e553149e60ea6c02e3551 |
#!/usr/bin/env python
# Copyright (c) 2012 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.
"""Moves C++ files to a new location, updating any include paths that point
to them, and re-ordering headers as needed. If multipl... | endlessm/chromium-browser | tools/git/move_source_file.py | Python | bsd-3-clause | 9,670 | [
"VisIt"
] | 4b8a53bcdca354ec552e7c8559c68749e509138af5e66e5ecbc10f43d3ed452e |
import logging
import re
import os
import signal
from avocado.utils import path
from avocado.utils import process
from avocado.utils import linux_modules
from .versionable_class import VersionableClass, Manager, factory
from . import utils_misc
# Register to class manager.
man = Manager(__name__)
class ServiceMana... | spcui/avocado-vt | virttest/openvswitch.py | Python | gpl-2.0 | 16,818 | [
"ASE"
] | 2f48d37e7c9a9af0fd90b761f440947ef36ea65f3d03723028ed08e921d2ea4e |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyPymol(PythonPackage):
"""PyMOL is a Python-enhanced molecular graphics tool. It excels a... | iulian787/spack | var/spack/repos/builtin/packages/py-pymol/package.py | Python | lgpl-2.1 | 1,857 | [
"PyMOL"
] | cc08ad26c727ceacabb1077ce3e5f0abc4deb5768e5a4c43b478a970fd16cfe5 |
# IM - Infrastructure Manager
# Copyright (C) 2011 - GRyCAP - Universitat Politecnica de Valencia
#
# 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... | indigo-dc/im | IM/ConfManager.py | Python | gpl-3.0 | 71,025 | [
"Galaxy"
] | c500841f75dd7ba381bf382943f7c40afba56f10f13976a3c4c687576f218086 |
from __future__ import print_function
"""
Copyright (C) 2015-2016 Jakub Krajniak <jkrajniak@gmail.com>
This file is distributed under free software licence:
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 ... | MrTheodor/bakery | src/tools_sim.py | Python | gpl-3.0 | 20,437 | [
"Gromacs"
] | e46ddf718a043c6fe19481730ca6562320ee6f36ea8bfe4d42bb366fb6287b68 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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) any later ver... | spring01/libPSI | lib/python/molutil.py | Python | gpl-2.0 | 16,164 | [
"Psi4"
] | 4406d099b375765e707a8b7ed0cb3e4077fda427079ac6fd3fdd4103db9efd8f |
"""
Feature calculations.
"""
import types
import numpy as np
from rdkit import Chem
from rdkit.Chem import rdGeometry, rdMolTransforms
from deepchem.utils.save import log
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "BSD 3-clause"
class ComplexFeaturizer(object):
... | Agent007/deepchem | deepchem/feat/base_classes.py | Python | mit | 2,802 | [
"RDKit"
] | 23e9e2c31b155ee7dbea4ba1bcb47d59829e97b90c060c574f0c4201b54e63d4 |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import directives
from sphinx import __version__ as sphinx_ver, addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.util.compat import Directive
from sphinx.util... | 52ai/django-ccsds | docs/_ext/djangodocs.py | Python | bsd-3-clause | 12,198 | [
"VisIt"
] | 525277c229f3e4c28768e0f73b94eee1f1fb369628f1729949379af9d26f6bd2 |
#!/usr/bin/python
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it wi... | alej0varas/spqr | scripts/spqr_events.py | Python | gpl-3.0 | 19,452 | [
"VisIt"
] | 32a2ce44e2a820a6d2db2ed080c418abeceabef4813dd0b3a2a6ed370e93e00c |
"""
=====================================
Blind source separation using FastICA
=====================================
An example of estimating sources from noisy data.
:ref:`ICA` is used to estimate sources given noisy measurements.
Imagine 3 instruments playing simultaneously and 3 microphones
recording the mixed si... | lesteve/scikit-learn | examples/decomposition/plot_ica_blind_source_separation.py | Python | bsd-3-clause | 2,191 | [
"Gaussian"
] | 4b5c10c63970f23690e375da8cd51d43ac27b40946e9173309710b025c2e8621 |
#!/usr/bin/env python
import numpy as np
import RNA
import sys
import random
import subprocess
import re
import decimal
import math
import os
import shutil
import time
import types
import uuid
import argparse
from argparse import RawTextHelpFormatter
import networkx as nx
from scipy.interpolate import *
##############... | RobertKleinkauf/antaRNA | antarna/antarna.py | Python | mit | 127,551 | [
"VisIt"
] | 1bd5681aeaba56007c3a55675b5fc01710e187eccd2bf8e8639cc5cbd6daa036 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest2 as unittest
import os
import numpy as np
from pymatgen import Element
from pymatgen.phasediagram.entries import PDEntryIO, PDEntry
from pymatgen.phased... | aykol/pymatgen | pymatgen/phasediagram/tests/test_plotter.py | Python | mit | 3,991 | [
"pymatgen"
] | 996603d1431241224defc1440fb0d6d189096b51ee3fffd24abde4aaffb688b3 |
#! /bin/python3
# $Id
# -----------------------------------------------------------------------------
# CppAD: C++ Algorithmic Differentiation: Copyright (C) 2003-15 Bradley M. Bell
#
# CppAD is distributed under multiple licenses. This distribution is under
# the terms of the
# Eclipse Public Licen... | kaskr/CppAD | bin/proj_desc.py | Python | epl-1.0 | 6,719 | [
"VisIt"
] | 0179a4ca6cc99c64a1671494c75fa023c8e0b804aca708171029ba566a0241c3 |
# ============================================================================
#
# 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/admin/list_action/__init__.py | Python | gpl-2.0 | 8,575 | [
"VisIt"
] | db995cc3b16d7b4ec0ce25dce809fa95add6fb335425a970bb4f4e25d7a5ab49 |
#! /usr/bin/env python
from __future__ import print_function
from pymol import cmd
from numpy import *
def zero_residues(sel1,offset=0,chains=0):
offset = int(offset)
# variable to store the offset
stored.first = None
# get the names of the proteins in the selection
names ... | weitzner/Dotfiles | pymol_scripts/roeAsBfact.py | Python | mit | 2,936 | [
"PyMOL"
] | 9008237b1f5cf4905a3505a450d1e0df7dae3e5dfa342f0bfec10178e0f54f75 |
"""Emojione autogen.
Generated from emojione source. Do not edit by hand.
MIT license.
Copyright (c) http://www.emojione.com
"""
from __future__ import unicode_literals
version = "v3.1.2"
name = "emojione"
emoji = {
":100:": {
"category": "symbols",
"name": "hundred points",
"unicode": "1... | brunobergher/dotfiles | sublime/pymdownx/st3/pymdownx/emoji1_db.py | Python | mit | 480,982 | [
"CRYSTAL",
"FLEUR",
"Octopus"
] | eaf42ee45626d04f915c413bfc5d8d13867d97ccbdb3240c1016c7734ad7c6b1 |
"""
The Optimizer base class is an agent that polls for jobs with a specific
status and minor status pair. The checkJob method is overridden for all
optimizer instances and associated actions are performed there.
"""
from DIRAC import S_OK, S_ERROR, exit as dExit
from DIRAC.AccountingSystem.Client.Types.Job im... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/OptimizerModule.py | Python | gpl-3.0 | 13,633 | [
"DIRAC"
] | 2bf255e200a7954fb079587b6d337cf1d27af81aab794013de01c237d7d98da8 |
from django.conf import settings
from django.utils.text import slugify
from django.db import IntegrityError, connection
from protein.models import Protein, ProteinConformation
from residue.models import Residue
from structure.models import Structure
from construct.models import *
from ligand.models import Ligand, Liga... | cmunk/protwis | construct/functions.py | Python | apache-2.0 | 75,086 | [
"CRYSTAL",
"Jmol"
] | c16b61d7f081c5fba7cbb45b6bf1cbe56ac3f6bd02c553e8c0dddca59a5b6497 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from collections import OrderedDict
from io import StringIO
import itertools
import re
import warnings
import numpy as np
import pandas as pd
from monty.json import MSONable
from monty.dev import deprecated
fro... | dongsenfo/pymatgen | pymatgen/io/lammps/data.py | Python | mit | 49,155 | [
"LAMMPS",
"pymatgen"
] | 1d07134efd84dddd52959b3b9d33fb3977bbb1ef790ec6c00feec9c9f901ce70 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | dfelinto/invesalius3 | invesalius/project.py | Python | gpl-2.0 | 12,267 | [
"VTK"
] | 331c60b89892f5c556934ea2622b3856460af07198ee58a707de7c89fc12dd52 |
"""
Random number generators
"""
def probability_transform(shape, inv_cum, cum_min=0., cum_max=1.):
"""
Generic sampler based on the probability transform.
@param shape: shape of the random sample
@param inv_cum: inversion of the cumulative density function from which one seeks to sample
@param cu... | csb-toolbox/CSB | csb/statistics/rand.py | Python | mit | 7,293 | [
"Gaussian"
] | d24b38a885991d008a0c789643f6efc7a77f35812189c2fad13ebb40d3c89902 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Apr 25, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Sh... | matk86/pymatgen | pymatgen/vis/tests/test_structure_vtk.py | Python | mit | 1,209 | [
"pymatgen"
] | dcd04cd1f75bbaf1aa4dcf0e5ed42bcabdbc2a95104af079aeea428268b3a7b6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Automated optimization of simulation of Basket cell
"""
__version__ = 0.1
from neuron import h
import neuron
import numpy as np
from neurotune import optimizers
from neurotune import evaluators
from pyelectro import analysis
import sys
class Simulation(object):
"""
... | vellamike/neurotune | examples/example_2/optimization.py | Python | bsd-3-clause | 14,133 | [
"NEURON"
] | 16c7b4e7e8e5e57c530e144cea7a404f4df44226ce0b001594be0f623e343572 |
""" ConfigurationData module is the base for cfg files management
"""
import os.path
import zlib
import zipfile
import thread
import time
import DIRAC
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.Core.Utilities import List, Time
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.Core.Uti... | andresailer/DIRAC | ConfigurationSystem/private/ConfigurationData.py | Python | gpl-3.0 | 13,092 | [
"DIRAC"
] | 385425f5fcf9e25f6672a7f583435a3ef18bb73691ceeb2eedbeaf677cf5abc2 |
#/*
# *
# * TuneIn Radio for Kodi.
# *
# * Copyright (C) 2015 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... | brianhornsby/plugin.audio.tuneinradio | resources/lib/astralradio.py | Python | gpl-3.0 | 2,025 | [
"Brian"
] | 37777e078018fc571b8d02a764e7111776a235a52d3115a5ef1339eab7efc77d |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
import ast
import textwrap
import numba
from numba import *
from numba import error, closures, function_util
from numba import macros, utils, typesystem
from numba.symtab import Variable
from numba import visitors, nodes, error, f... | shiquanwang/numba | numba/specialize/loops.py | Python | bsd-2-clause | 10,565 | [
"VisIt"
] | 3ea6f2209452ce7dd8621d4269f1f2ae295db2c7b08dc30faff4b93d26b86229 |
import numpy as np
import netCDF4 as netCDF
from datetime import datetime
import pyroms
import pyroms_toolbox
# load 2-dimentional discharge data
print 'Load discharge data'
nc_data = netCDF.Dataset('CI_runoff.nc', 'r')
nc_rivers = netCDF.Dataset('Cook_Inlet_rivers.nc', 'a')
data = nc_data.variables['Runoff'][:]
ti... | dcherian/pyroms | examples/rivers/make_river_clim.py | Python | bsd-3-clause | 1,859 | [
"NetCDF"
] | 50e90725044e5066b1316246a90c16b0fb271c73aaba1cadf5fe4855729b112e |
# -*- coding: utf-8 -*-
#
# test_connect_array_fixed_indegree.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versio... | mdjurfeldt/nest-simulator | pynest/nest/tests/test_connect_array_fixed_indegree.py | Python | gpl-2.0 | 3,309 | [
"NEURON"
] | bcbdf48bf5560b5065cd986cdc48818257864b1a54aae44b1630edb9f131420a |
import pytest
from csirtg_indicator.format.zbindrpz import BindRPZ, get_lines
from csirtg_indicator import Indicator
from pprint import pprint
import re
@pytest.fixture
def indicator():
i = {
'indicator': "example.com",
'provider': "me.com",
'tlp': "amber",
'confidence': "85",
... | csirtgadgets/csirtg-indicator-py | test/format/test_bindrpz.py | Python | mpl-2.0 | 933 | [
"Amber"
] | aa346dd80801263081f708e4dcaf00547e02917443b048df06bc727f89d14010 |
"""Perform realignment of BAM files around indels using the GATK toolkit.
"""
import os
import shutil
from contextlib import closing
import pysam
from bcbio import bam, broad
from bcbio.bam import ref
from bcbio.log import logger
from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_trans... | Cyberbio-Lab/bcbio-nextgen | bcbio/variation/realign.py | Python | mit | 4,077 | [
"pysam"
] | bf17cc24fa1b7fe7e44ae10d7170d35384845487ae09cb2569ba6de67f40c8d4 |
#-----------------------------------------------------------------------------
# Copyright (c) 2010-2012 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distributed as part of this software.
#-----... | ellisonbg/pyzmq | zmq/tests/test_poll.py | Python | lgpl-3.0 | 7,700 | [
"Brian"
] | 141c5e941eaaf544c74e32f3b01a238fc52523d581930a2464614ca5b790ca0e |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | Chuban/moose | python/chigger/utils/Options.py | Python | lgpl-2.1 | 13,870 | [
"MOOSE"
] | 7c4ddb47147264ff51eff7cca0e94e07a33f8e1c1bf8e1928b19995ea04aa05d |
# coding: utf8
{
' Quotas: %(quotas)s x%(quota_amount).2f': ' Quotas: %(quotas)s x%(quota_amount).2f',
' Transaction number: %s': ' Transaction number: %s',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field... | reingart/gestionlibre | languages/hu.py | Python | agpl-3.0 | 15,772 | [
"VisIt"
] | 055075d7fefb8edcd61937b9e329d4e372a207e139616ac57a9748c155f21b91 |
import logging
logging.basicConfig(filename='galaxy_tests.log',level=logging.DEBUG)
logger = logging.getLogger()
logger.info('start of run')
import ResolvedStellarPops as rsp
import os
import sys
import difflib
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.nxutils as nxutils
from mpl_toolkits.ax... | philrosenfield/TPAGB-calib | galaxy_tests.py | Python | bsd-3-clause | 131,692 | [
"Galaxy",
"Gaussian"
] | 126aee632b64327d54a507eb082933b7860337c23c499ac05db1d0f916fa3252 |
# -*- coding: utf-8
# pylint: disable=line-too-long
"""
Classes for pan operations.
anvi-pan-genome is the default client using this module
"""
import os
import json
import math
import copy
import multiprocessing
import pandas as pd
from itertools import chain
import anvio
import anvio.utils as utils
import ... | meren/anvio | anvio/panops.py | Python | gpl-3.0 | 51,088 | [
"BLAST"
] | 732b1bf0ab0ad1d6fe429b746e51e997b7c16e20784132ad405efd060b7af807 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | ehogan/iris | lib/iris/fileformats/netcdf.py | Python | lgpl-3.0 | 80,100 | [
"NetCDF"
] | e6ae2aee3eb3219f7c250b1bb8ae3183d8c75d1b7a91f49d701b9e4fb9e5e773 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google/autocjk | src/evaluate_glyphwiki.py | Python | apache-2.0 | 8,074 | [
"VisIt"
] | a99bfe4e0ecb9138d4bc3e1bd2bd2f6d2520f847af16c6d37a46f336d7957022 |
import random
import unittest
from SDWLE.agents.basic_agents import PredictableAgent, DoNothingAgent
from SDWLE.engine import Game
from testsSDW.agents.testing_agents import OneCardPlayingAgent, CardTestingAgent, PlayAndAttackAgent, SelfSpellTestingAgent
from SDWLE.constants import CHARACTER_CLASS
from testsSDW.testin... | jomyhuang/sdwle | testsSDW__copy/card_tests/priest_tests.py | Python | mit | 37,931 | [
"BLAST"
] | 8b797709fdf1e32e19253a8ee9c75e1341d1effd7112b6a381e7eb372a7dffbb |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# PMDA
# Copyright (c) 2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher ve... | MDAnalysis/pmda | pmda/test/test_version.py | Python | gpl-2.0 | 509 | [
"MDAnalysis"
] | bdc5caf5968bc53c41bf293b4f72cf1dd3b49807b859ad385b0bc88e8ac43f54 |
from setuptools import setup
packages_yambopy = ['yambopy',
'yambopy.io',
'yambopy.dbs',
'yambopy.bse',
'yambopy.rt',
'yambopy.double_grid',
'yambopy.data',
'yambopy.plot',
... | alexmoratalla/yambopy | setup.py | Python | bsd-3-clause | 1,201 | [
"Quantum ESPRESSO",
"Yambo"
] | 16608f3c6ee95b480fdece919455da227a0de46c78986552bd19d6a324e460da |
"""
Test for the laser heater infrastructure using the Gauss-Hermite laser mode
and a planar undulator. The parameters are fixed based on the LCLS laser
heater described by Huang et al., PRST-AB 7, 074401 (2004)
moduleauthor:: Stephen Webb <swebb@radiasoft.net>
Copyright (c) 2014 RadiaBeam Technologies. All rights res... | radiasoft/radtrack | experimental/laserHeater/laserHeater04.py | Python | apache-2.0 | 6,427 | [
"Gaussian"
] | 9f88e6be60ea65b57a8351d1df5cde60e5b9fac9efc6144090a60f097afef19b |
# Ignacio Funke Prieto <igofunke@gmail.com>
# Pablo Gordillo Alguacil <tutugordillo@gmail.com>
# Ignacio Gago Padreny <igago@ucm.es>
## License GPL
"""
This module plots a surface given its parametrization and a geodesic curve in the surface. It is based on the differential equation obtained from the definition in... | huig-/Computational-Geometry | Curves/surface3d.py | Python | gpl-3.0 | 3,644 | [
"Mayavi"
] | e38716837029333a252fe279756d1cb0d15cf428363579eb9bae650937dbc2d8 |
"""A thorough test of polling PUB/SUB sockets."""
#-----------------------------------------------------------------------------
# Copyright (c) 2010 Brian Granger
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distributed as part of this software.
#---------... | mgadi/naemonbox | sources/psdash/pyzmq-13.1.0/examples/poll/pubsub.py | Python | gpl-2.0 | 1,404 | [
"Brian"
] | 47a5c65e6b31e2ecb53f81dde25407f42bc37a38bea05c1246c9268ebfd59191 |
#Django settings for the basic OpenHatch 'mysite' project
# Imports
import subprocess
import os
import logging
import datetime
import sys
import dj_database_url
LOGGING_CONFIG = None
LOGGING = {
'version': 1,
'formatters': {
'verbose': {
'format': '\n%(levelname)08s %(asctime)25s - %(name)... | waseem18/oh-mainline | mysite/settings.py | Python | agpl-3.0 | 13,248 | [
"VisIt"
] | b687a0601244d605fbd5d88f3db4002dfb6defd0f840f7e530152c9c542cc798 |
#!/usr/bin/env python
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | cmvelo/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 10,176 | [
"Galaxy"
] | 0b0aa289d3c25fffad9f79aad2296b3dd6b1324cba5c1cc23f2a1ad93deb64d2 |
import os
import numpy as np
from ase.units import Bohr, Hartree
from ase.io.elk import read_elk
from ase.calculators.calculator import FileIOCalculator, Parameters, kpts2mp, \
ReadError
elk_parameters = {
'swidth': Hartree,
}
class ELK(FileIOCalculator):
command = 'elk'
implemented_properties =... | alexei-matveev/ase-local | ase/calculators/elk.py | Python | gpl-2.0 | 14,118 | [
"ASE",
"DIRAC",
"Elk",
"Gaussian"
] | bb51a92e57955e26a84c5a2f04e0ba88a092bdc5616089ed4fe96a393145913f |
"""
Acceptance tests for the Import and Export pages
"""
from nose.plugins.attrib import attr
from datetime import datetime
from abc import abstractmethod
from bok_choy.promise import EmptyPromise
from .base_studio_test import StudioLibraryTest, StudioCourseTest
from ...fixtures.course import XBlockFixtureDesc
from .... | simbs/edx-platform | common/test/acceptance/tests/studio/test_import_export.py | Python | agpl-3.0 | 15,669 | [
"VisIt"
] | 215e7fbeea8e4d3612ea10a6cf79e5aa319b2114eab803fbe104e162bc0db1ae |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2014, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | spbguru/repo1 | nupic/algorithms/anomaly_likelihood.py | Python | gpl-3.0 | 22,774 | [
"Gaussian"
] | cf0775173311327e303bfa3beb3a771a330bd8609c47c22681a77b840e2a43e6 |
#!/usr/bin/env python
import click
import os
import shutil
import sys
import tarfile
from itertools import product
from sh import git, curl, ErrorReturnCode, Command as shCommand
from aeriscloud.cli.helpers import Command, info, fatal, warning, success, \
move_shell_to
from aeriscloud.ansible import get_organiza... | AerisCloud/AerisCloud | aeriscloud/cli/cloud/organization.py | Python | mit | 10,201 | [
"Galaxy"
] | b5855f59620340013bbfa5b2832197560643888d7dd963d03165b4f4b19db001 |
#!/usr/bin/env python
'''
'''
import numpy as np
import pandas as pd
import scipy.io
from functions import *
# from pylab import *
import ipyparallel
import os, sys
import neuroseries as nts
import time
from Wavelets import MyMorlet as Morlet
data_directory = '/mnt/DataGuillaume/MergedData/'
datasets = np.loadtxt(dat... | gviejo/ThalamusPhysio | python/main_search_up_down.py | Python | gpl-3.0 | 4,603 | [
"Gaussian"
] | 51f86f22a5837fddf47b8c16b6286cfd8869fabce12aa904ff3c8292ffdcf9b4 |
#! /usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------... | JWDebelius/scikit-bio | skbio/stats/ordination/tests/test_ordination.py | Python | bsd-3-clause | 31,562 | [
"scikit-bio"
] | d78cc15301f1c4c9b09693938914764e8f84b660c2327792370261b29f8eb11f |
from datetime import timedelta
from dateutil.relativedelta import relativedelta
from django.test import TestCase, tag
from edc_base.utils import get_utcnow
from ..schedule import Schedule, AlreadyRegisteredVisit
from ..schedule import ScheduleNameError
from ..simple_model_validator import InvalidModel
from ..visit imp... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/tests/test_schedule.py | Python | gpl-2.0 | 12,163 | [
"VisIt"
] | 5003c6b594d9008978a298b8726b22b9201d250c09bdb2b5be923254a9df97ea |
import astropy.io.fits as pyfits
from astropy.io import ascii
from astropy.table import Table, Column
import astropy.wcs as pywcs
import os
import numpy as np
import montage_wrapper as montage
import shutil
import sys
import glob
import time
from matplotlib.path import Path
from scipy.ndimage import zoom
from pdb impor... | arlewis/galaxy_cutouts | versions/extract_stamp_good.py | Python | mit | 24,946 | [
"Galaxy"
] | 1efe11dbe10207e8d98996a6132c02272067907ed4d313d53bc07e139d8c751b |
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