text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""
A simple VTK widget for wxPython. Note that wxPython comes
with its own wxVTKRenderWindow in wxPython.lib.vtk. Try both
and see which one works better for you.
Find wxPython info at http://wxPython.org
Created by David Gobbi, December 2001
Based on vtkTkRenderWindget.py
"""
"""
Please see the example at the e... | sgh/vtk | Wrapping/Python/vtk/wx/wxVTKRenderWindow.py | Python | bsd-3-clause | 21,609 | [
"VTK"
] | 773da7814b0a9ebf5a280b330e4689e83ea1bca74d3c11b681c1387176b4683f |
from ast import parse, walk, iter_fields, dump, NodeVisitor, get_docstring
import sys
def interpret_async(is_async):
return "an async" if is_async else "a"
class PrettyReader(NodeVisitor):
def visit_list(self, xs):
if len(xs) <= 1:
return ", ".join([self.visit(i) for i in xs ])
... | MaxwellBo/neoreader | rplugin/python3/neoreader/py_ast.py | Python | gpl-3.0 | 16,655 | [
"VisIt"
] | 875094e945d453c62a9c2fb1ff9f06f90aa8887abf650c285e05b5cb1018eb7d |
# -*- coding: utf-8 -*-
"""
:copyright: (c) 2014 by the mediaTUM authors
:license: GPL3, see COPYING for details
Web API node iteration functions.
"""
import logging
from itertools import islice, tee
from utils.compat import iteritems
logg = logging.getLogger(__name__)
global all_node_ids_cached
all_node_i... | mediatum/mediatum | web/services/test/nodeiteration.py | Python | gpl-3.0 | 2,712 | [
"VisIt"
] | 5621c8f1b435e6d1368bfc036bcf1320a13ac45152a7a417845372fbada04545 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | debugger87/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 49,218 | [
"Gaussian"
] | 1ab5671be7f667aac0344857778befe50735b8273d44a2da909206fb0b11a438 |
# sybase/base.py
# Copyright (C) 2010-2020 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is par... | cloudera/hue | desktop/core/ext-py/SQLAlchemy-1.3.17/lib/sqlalchemy/dialects/sybase/base.py | Python | apache-2.0 | 31,953 | [
"ASE"
] | 3751b9b5428eb418de39779172264fea2ba2d4cf02616156f4a72103ea838bfb |
"""GraphQL Language
The :mod:`graphql.language` package is responsible for parsing and operating on the
GraphQL language.
"""
from .source import Source
from .location import get_location, SourceLocation, FormattedSourceLocation
from .print_location import print_location, print_source_location
from .token_kind imp... | graphql-python/graphql-core | src/graphql/language/__init__.py | Python | mit | 4,790 | [
"VisIt"
] | f6da8edec57b32e433ec76eab68641c5c247af7a2fe44038ee919741b2eec862 |
#
# co_co_user_defined_function_correctly_defined.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the L... | kperun/nestml | pynestml/cocos/co_co_user_defined_function_correctly_defined.py | Python | gpl-2.0 | 9,804 | [
"NEURON"
] | 4dd5756c2edd117af717fa5709e294459cb16ead77cd61d7b0b516331c2dee55 |
# encoding: utf-8
"""
Job and task components for writing .xml files that the Windows HPC Server
2008 can use to start jobs.
Authors:
* Brian Granger
* MinRK
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed u... | fzheng/codejam | lib/python2.7/site-packages/ipyparallel/apps/winhpcjob.py | Python | mit | 11,737 | [
"Brian"
] | fb1e0af15565e01fdf56019cb34da42c26e9b44906959dfdfd6f643b63e8b78a |
model = """# Generated by PySCeS 0.7.2 (2010-08-10 13:12)
# Keywords
Description: Birth-death model (001), variant 02
Modelname: BirthDeath02
Output_In_Conc: True
Species_In_Conc: False
# GlobalUnitDefinitions
UnitVolume: litre, 1.0, 0, 1
UnitLength: metre, 1.0, 0, 1
UnitSubstance: item, 1.0, 0, 1
UnitArea: metre,... | SystemsBioinformatics/stochpy | stochpy/pscmodels/dsmts_001_01.py | Python | gpl-3.0 | 2,339 | [
"PySCeS"
] | ddc0c23391a71cbac4d4f287a3b73833fb99f074326f8e202f5553aa5e65afc0 |
#!/usr/bin/env python
# encoding: UTF-8
import asyncio
import datetime
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
import logging
import smtplib
import sqlite3
import sys
import textwrap
from cloudhands.common.connectors import initialise
from cloudhands.common.connectors impor... | cedadev/cloudhands-web | cloudhands/identity/emailer.py | Python | bsd-3-clause | 3,027 | [
"VisIt"
] | dfd8d8b59f28171ce276dc39013e1f631f28e77b68558070cc0e09610502c9c0 |
# coding: utf-8
from django.conf.urls import url, include
from rest_framework import routers
from .views import FeedViewSet, EntryViewSet
from .views import AggrRssFeed, AggrAtomFeed
from .views import EntryRedirectView
router = routers.DefaultRouter()
router.register(r'feeds', FeedViewSet)
router.register(r'entries'... | uraxy/imozzle | api/urls.py | Python | mit | 608 | [
"VisIt"
] | b1bc3f71dc00aad720da1e33e2a773c4f57bc96d91b4ab8a4ff668e83ce6a514 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'Device'
db.create_table(u'djanalytics_device', (
... | analytehealth/django-analytics | djanalytics/migrations/0007_auto__add_device__add_webproperty__add_pagevisit__add_visitor__add_pag.py | Python | bsd-2-clause | 22,449 | [
"VisIt"
] | f13338cbee80ee18c3437c4a5b104ead8de6f08181ca8e92345f31f07ced7a20 |
""" The SGE TimeLeft utility interrogates the SGE batch system for the
current CPU consumed, as well as its limit.
"""
__RCSID__ = "$Id$"
import os
import re
import time
import socket
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.TimeLeft.TimeLeft import runCommand
class SGETimeLeft( objec... | andresailer/DIRAC | Core/Utilities/TimeLeft/SGETimeLeft.py | Python | gpl-3.0 | 6,664 | [
"DIRAC"
] | 49c475d21cfe42980e1728b6834eaec7576bd2378bc4c837b359e4dc9df4f707 |
# Tests for basic Tkinter widgets.
import tkinter
import Test
Test.initialise()
testData = ()
if tkinter.TkVersion >= 8.0:
button_num = 31
frame_num = 16
menu_num = 20
menubutton_num = 32
else:
button_num = 30
frame_num = 15
menu_num = 19
menubutton_num = 31
c = tk... | wolf29f/iCook | iCook/Pmw/Pmw_2_0_0/tests/Tkinter_test.py | Python | gpl-2.0 | 12,225 | [
"Brian"
] | ad125878b63d06e8f69624aabb54eda9555c8538c648526fa9fc21f2c4ce5d8d |
# (c) 2005 Ian Bicking and contributors; written for Paste (http://pythonpaste.org)
# Licensed under the MIT license: http://www.opensource.org/licenses/mit-license.php
# Mostly taken from PasteDeploy and stripped down for Galaxy
import inspect
import os
import re
import sys
from typing import Callable, Dict, List, O... | galaxyproject/pulsar | pulsar/util/pastescript/loadwsgi.py | Python | apache-2.0 | 26,321 | [
"Galaxy"
] | abfd0ec2a8ef93308a0d50975db7f09336a237601902bfa4d14b679f7022636d |
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
import csv
import geometry
import glob
import os
import math
from module_base import ModuleBase
from module_mixins import IntrospectModuleMixin,\
FileOpenDialogModuleMixin
import module_utils
import vtk
import vtkgdcm... | nagyistoce/devide | modules/viewers/LarynxMeasurement.py | Python | bsd-3-clause | 24,986 | [
"VTK"
] | a54c38b5c8e496d7b1c0fda3e94598171c6a542a858e52fa4e7fec151dff87a7 |
# Copyright 2007-2012 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 your option) any later ve... | pburdet/hyperspy | test_model.py | Python | gpl-3.0 | 3,745 | [
"Gaussian"
] | 2de7a1a6b7a605ca2aa31fe89853281fff05960feeffa009008c26f9f1dfb853 |
__doc__ = """Code by Benjamin S. Murphy
bscott.murphy@gmail.com
Dependencies:
numpy
scipy (scipy.optimize.minimize())
Functions:
adjust_for_anisotropy(x, y, xcenter, ycenter, scaling, angle):
Returns X and Y arrays of adjusted data coordinates. Angle is CCW.
adjust_for_anisotropy_3d(x, y, z, x... | yejingxin/PyKrige | pykrige/core.py | Python | bsd-3-clause | 17,003 | [
"Gaussian"
] | 5eb17c583a94a679084a52a46c72ef8259d26db41fcc25596e892e039cdef6a4 |
#!/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... | hkariti/ansible | lib/ansible/modules/network/avi/avi_sslprofile.py | Python | gpl-3.0 | 8,116 | [
"VisIt"
] | 0e8001e166fe49cb4cec4e63bb493e4d2e2a56ec2c174f8178d32938d3e10ceb |
# gapjunction.py ---
#
# Filename: gapjunction.py
# Description:
# Author:Subhasis Ray
# Maintainer:
# Created: Tue Jul 2 14:28:35 2013 (+0530)
# Version:
# Last-Updated: Tue Jul 23 21:28:45 2013 (+0530)
# By: subha
# Update #: 57
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change l... | BhallaLab/moose-examples | snippets/gapjunction.py | Python | gpl-2.0 | 3,075 | [
"MOOSE"
] | 39c9772179ee2dc23702ae8a7450633660227bae62cbb97cbf9db3e915ac1fba |
#!/usr/bin/env python3
import numpy as np
from . import crystal
import scipy
import scipy.constants as constants
import scipy.ndimage
import collections
import json
import argparse
import IPython
def local_maxima(data, size = 5, threshold = 0.05):
data_max = scipy.ndimage.filters.maximum_filter(data, size = siz... | chanjr/rheedsim | src/rheedsim/rheedsim.py | Python | mit | 8,732 | [
"CRYSTAL"
] | 0d9bfb50a1271ff78f618a1804f6a350e1a782b545035deed70c5c4cc997c712 |
"""
A number of functions that enhance IDLE on Mac OSX.
"""
import sys
import tkinter
from os import path
import warnings
def runningAsOSXApp():
warnings.warn("runningAsOSXApp() is deprecated, use isAquaTk()",
DeprecationWarning, stacklevel=2)
return isAquaTk()
def isCarbonAquaTk(root)... | ms-iot/python | cpython/Lib/idlelib/macosxSupport.py | Python | bsd-3-clause | 8,419 | [
"VisIt"
] | 6421e36a368b091c36d28adc726fd2c890047b33bc617aaf6644d87279eeb374 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# this script tests vtkImageReslice with different interpolation modes,
# with the wrap-pad feature turned on and with a rotation
# Image pipeline
reader = vtk.vtkImageReader()
reader... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/ResliceMirrorOblique.py | Python | gpl-3.0 | 3,396 | [
"VTK"
] | 56e3a50f944fa27d83dbc41c7d34ead441c55a71601ba47cb223c6c05b58fb24 |
import pytest
import re
from six import StringIO
from woodpecker.sequences.basesequence import BaseSequence
@pytest.fixture
def stopwatch_sequence():
class stopwatchSequence(BaseSequence):
def steps(self):
self.start_stopwatch('stopwatch_test')
self.end_stopwatch('stopwatch_test'... | steromano87/Woodpecker | tests/sequences/test_basesequence.py | Python | agpl-3.0 | 2,557 | [
"Gaussian"
] | bc055b22e8cf374315647fb8feed1239b38bdf0010d37eb14b102a71b16947d0 |
#!/usr/bin/env python
"""A simple example of how you can use Mayavi without using Envisage
or the Mayavi Envisage application and do off screen rendering.
On Linux/Mac, with VTK < 5.2, you should see a small black window popup
and disappear, see the section :ref:`offscreen_rendering` to avoid this.
On Win32 you will n... | dmsurti/mayavi | examples/mayavi/advanced_visualization/offscreen.py | Python | bsd-3-clause | 1,670 | [
"Mayavi",
"VTK"
] | 4e74a13385ab87dab89d234a00b4c5bdde3f7581a1f819cb359cb091ed972d26 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Example analyses and calculations based on data parsed by cclib."""
from cclib.method.bader import Bader
from cclib.me... | berquist/cclib | cclib/method/__init__.py | Python | bsd-3-clause | 988 | [
"cclib"
] | d224dd1d7a6cd485f39cbf9f23baa08b5eb183b1cdc1c6ad44111137406b8026 |
#
# ENVISIoN
#
# Copyright (c) 2020-2021 Alexander Vevstad, Gabriel Anderberg, Didrik Axén,
# Adam Engman, Kristoffer Gubberud Maras, Joakim Stenborg
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions a... | rartino/ENVISIoN | envisionpy/hdf5parser/vasp/fermi_parser.py | Python | bsd-2-clause | 12,074 | [
"VASP"
] | a4c364f62f1e7c88b6510b34bb0349ab14ba379d958f91e4dd9d6a7417041a92 |
"""
DIRAC.StorageManagementSystem.Client package
"""
| DIRACGrid/DIRAC | src/DIRAC/StorageManagementSystem/Client/__init__.py | Python | gpl-3.0 | 56 | [
"DIRAC"
] | 6ee3a70640bc0a259c1a77055338e07436226dd327393f5dda2c1d92efecda73 |
# Copyright (C) 2010-2014 CEA/DEN, EDF R&D
#
# 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 library ... | FedoraScientific/salome-paravis | src/PV_SWIG/paravisSM.py | Python | lgpl-2.1 | 112,492 | [
"ParaView",
"VTK",
"VisIt"
] | 0ff5fdc6e963882c7b6fcec6c4d964d7dcdbcce0c8ae6145b6180be94eff9421 |
import tensorflow as tf
import numpy as np
import time
import os
import logging
import models
import inferences
import nomen
import util
import stats
def train(config):
"""Train a Variational Autoencoder or deep latent gaussian model on MNIST."""
cfg = config
logger = logging.getLogger()
t0 = time.time()
... | altosaar/proximity_vi | deep_latent_gaussian_model_train.py | Python | mit | 4,221 | [
"Gaussian"
] | b1c04aafbef2f84ef857cd294b9462d96d78a38710a9aa32c45105cfc743655c |
from ase import *
from ase.lattice.surface import fcc100, add_adsorbate
# 2x2-Al(001) surface with 3 layers and an
# Au atom adsorbed in a hollow site:
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1.7, 'hollow')
slab.center(axis=2, vacuum=4.0)
# Make sure the structure is correct:
#view(slab)
# Fix ... | freephys/python_ase | doc/tutorials/neb/diffusion1.py | Python | gpl-3.0 | 694 | [
"ASE"
] | 47d3cc99622640822c002fa9db7604cb2e0ef28628a79aee41467d2f72c5b0a5 |
import os
from os import path, sys
from shutil import rmtree
import subprocess
import numpy as np
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
TRAFIC_LIB_DIR = path.join(path.dirname(path.dirname(path.abspath(__file__))), "TraficLib")
sys.path.append(TRAFIC_LIB_DIR)
print pat... | PrinceNgattaiLam/Trafic | TraficBi/TrafficBi.py | Python | apache-2.0 | 39,506 | [
"VTK"
] | 577ff142a9106927d75f034fdf12316990a13596e2a446eb890276b630203f7c |
# ******************************************************************************
# Copyright 2014-2018 Intel Corporation
#
# 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.apa... | NervanaSystems/neon | examples/video-c3d/network.py | Python | apache-2.0 | 2,289 | [
"Gaussian"
] | e95a76d3de88dadbcf326866ad1a11160d2a166a166f7f8bdea8524409a0d547 |
"""Polynomial factorization routines in characteristic zero. """
from __future__ import print_function, division
from sympy.polys.galoistools import (
gf_from_int_poly, gf_to_int_poly,
gf_lshift, gf_add_mul, gf_mul,
gf_div, gf_rem,
gf_gcdex,
gf_sqf_p,
gf_factor_sqf, gf_factor)
from sympy.poly... | kmacinnis/sympy | sympy/polys/factortools.py | Python | bsd-3-clause | 33,837 | [
"Gaussian"
] | e6b38eba3f5cc6cd3d1a9544905511cf32d780203e9cee4504e21c6d8fabdc9d |
# -*- coding: utf-8 -*-
import datetime
from lettuce import *
from django.utils.datastructures import SortedDict
from rapidsms.contrib.locations.models import *
from survey.features.page_objects.aggregates import AggregateStatusPage, DownloadExcelPage, InvestigatorReportPage
from survey.features.page_objects.survey_co... | unicefuganda/uSurvey | survey/features/aggregates-steps.py | Python | bsd-3-clause | 13,171 | [
"VisIt"
] | 864f3a5e4e008e6c630146e67581c71203fcf315551347f9efd13fbacdc085ba |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTreeFieldAggregator(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkTreeFieldAggregator.py | Python | bsd-3-clause | 491 | [
"VTK"
] | 8a241fe8fa0dbbb03f67a6f3d9752fbbc1b315375a6effe92ff200691684302a |
"""
Sequence classes
"""
import gzip
import json
import logging
import os
import re
import string
from cgi import escape
from galaxy import util
from galaxy.datatypes import metadata
from galaxy.util.checkers import is_gzip
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.sniff import get_h... | icaoberg/cellorganizer-galaxy-tools | datatypes/sequence.py | Python | gpl-3.0 | 47,418 | [
"BLAST",
"BioPerl",
"Galaxy"
] | 890a7a3a62b74f7e66de904dcab60be7d32bc4f3f65accc9e6ae9b12c2bddea7 |
"""
Module StringFormat
The StringFormat module allows for character-by-character formatting of
strings. It imitates the SPING string drawing and string metrics
interface. The string formatting is done with specialized XML syntax
within the string. Therefore, the interface for the StringFormat module
consists of wrappe... | bp-kelley/rdkit | rdkit/sping/stringformat.py | Python | bsd-3-clause | 17,971 | [
"RDKit"
] | 69590c8d7d6258396f1709ed64621054af5ac042aa9dfcafa1779e608b0110f9 |
#!/usr/bin/env python
"""This module implements radical-bac-fecalc --benchmark.
"""
__author__ = "Ole Weidner"
__email__ = "ole.weidner@rutgers.edu"
__copyright__ = "Copyright 2013-2014, The RADICAL Project at Rutgers"
__license__ = "MIT"
import imp
import os, sys, uuid
import urllib
import optparse
import ... | radical-cybertools/HT-BAC | src/radical/ensemblemd/htbac/simchain/workload.py | Python | mit | 4,229 | [
"NAMD"
] | 633386403df052b10a0cabbf7c1f13711d64deeb4130e6055159a319304f301a |
import datetime
import unittest
from unittest.mock import patch
import numpy as np
import pytz
from data.nemo import Nemo
from data.netcdf_data import NetCDFData
from data.variable import Variable
from data.variable_list import VariableList
from utils.errors import APIError
class TestNemo(unittest.TestCase):
de... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | tests/test_nemo.py | Python | gpl-3.0 | 8,292 | [
"Gaussian"
] | 1180a69ab9065ad380ec8567da033a367cdf3780d95ea32c6298c1b0a86b2e4a |
import types
import unittest
import math
import copy
import Numeric
import MLab
import pygsl.testing.rng as rngmodule
import sys
sys.stdout = sys.stderr
rng_types = rngmodule.types_setup()
class _rng_type:
_type = None
for i in rng_types:
tmp = "class %s(_rng_type): _type = rngmodule.%s" % ((i,) * 2)
exe... | juhnowski/FishingRod | production/pygsl-0.9.5/testing/tests/rng_test.py | Python | mit | 9,957 | [
"Gaussian"
] | 88d3d0bad6ec903c0cef9be602252487dfea53e70e620bc1ae72401a149e2af4 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
This... | gadsbyfly/PyBioMed | PyBioMed/PyMolecule/ghosecrippen.py | Python | bsd-3-clause | 3,220 | [
"RDKit"
] | e4e3aeb416eeb1623863eb7af359e5449c9590d42725dec561792154dfef3674 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | dongjoon-hyun/tensorflow | tensorflow/python/autograph/pyct/static_analysis/type_info.py | Python | apache-2.0 | 7,393 | [
"VisIt"
] | 5c6660bd2b66fcf71a7d975e95caeda9f1a45e1ec3661a63e9d378493618f13e |
"""
INFO
-------------------------------------------------------------------------------------------
Ingest model script uploads the respective model of each estimation method.
INPUT:
-i, --input : Absolute path of model_template zip
-m, --method : Estimation method (e.g shallow_ae_km2)
-ht, --ht... | iaklampanos/bde-pilot-2 | data_ingest/ingest_model.py | Python | apache-2.0 | 2,793 | [
"NetCDF"
] | 0bfe5529ca5a20f4620e81729ac17e4f72104072fcd8e73fc0a689b3ad574578 |
import numpy as np
from .shared import StaticContainerStore, StaticContainer
import mdtraj
from openpathsampling.netcdfplus import WeakLRUCache
variables = ['statics']
lazy = ['statics']
storables = ['statics']
dimensions = ['n_atoms', 'n_spatial']
def netcdfplus_init(store):
static_store = StaticContainerStor... | jhprinz/openpathsampling | openpathsampling/engines/features/statics.py | Python | lgpl-2.1 | 2,708 | [
"MDTraj"
] | 6700509fecee92372273f537a0132c34d6db38681d29c21fc7fa204613898305 |
from ase.atoms import Atoms
from multiasecalc.lammps.reaxff import ReaxFF
from multiasecalc.lammps.compass import COMPASS
from multiasecalc.lammps.dynamics import LAMMPSOptimizer, LAMMPS_NVT
from multiasecalc.utils import get_datafile
from ase.data import s22
from ase import units
import numpy as np
import ase.io
from ... | csmm/multiase | tests/lammps/test_dynamics.py | Python | gpl-2.0 | 940 | [
"ASE",
"LAMMPS"
] | 0b5f7f8ee488af7605a1040205dcd6a4ed575460b883179cfbb9036effd62219 |
'''
Created on Apr 2, 2014
Utilities and methods to control rapsbery's GPIO pins
@author: theoklitos
'''
import sys
import time
using_real_pi = True
try:
import RPi.GPIO as GPIO # @UnusedImport
except (RuntimeError, ImportError) as e:
print 'Dependency error: ' + str(e)
print 'Cannot access ... | Theoklitos/chestfreezer | chestfreezer-backend/hardware/chestfreezer_gpio.py | Python | mit | 2,608 | [
"VisIt"
] | 439ed1a77bd6e28409b31962efded729c100ea35ab3d31282e01cd1755ac9645 |
#!/usr/bin/env python
# coding=utf-8
from __future__ import division
from __future__ import print_function
from past.builtins import cmp
from builtins import map
from builtins import str
from builtins import range
from past.utils import old_div
import argparse
from prettytable import PrettyTable
import os
from mako.te... | SandStormHoldings/ScratchDocs | docs.py | Python | mit | 67,531 | [
"VisIt"
] | e7ce62ed96bb934d98772a535b451839a87e24eb11bc26f58d30b8039d9bade2 |
#!/usr/bin/env python
import cStringIO
from itertools import ifilter
from functools import partial
import logging
import operator as op
import os
import sys
from lib.typecheck import *
import lib.const as C
import lib.visit as v
from .. import add_artifacts
from .. import util
from ..anno import parse_anno
from . i... | plum-umd/pasket | pasket/meta/template.py | Python | mit | 14,075 | [
"VisIt"
] | a5391e4e49d9ee4da47e96214bbda90046b3a9c9df2123f18dbc5211e88d8cf3 |
#! /usr/bin/env python
from __future__ import print_function
from openturns import *
import math
TESTPREAMBLE()
RandomGenerator.SetSeed(0)
try:
# for fft, the best implementation is given for N = 2^p
size = 16
# collection for test
collection = NumericalComplexCollection(size)
# Fill the data ... | aurelieladier/openturns | python/test/t_KissFFT_std.py | Python | lgpl-3.0 | 2,094 | [
"Gaussian"
] | 86212575f9e0f189801742005af96fa310845601b883b1e553130bcb0b4f68ae |
'''
Usage:
pipeline.py <r1> <r2> --config <config> [-o <outdir>] [--log <log>]
Options:
-c <config>, --config <config>
--log <log>
'''
import sh
from itertools import imap, izip, tee, chain, groupby, ifilter, starmap
from toolz.dicttoolz import keymap,valfilter,keyfilter,merge
from toolz.itertoolz import m... | averagehat/Pathogen.hs | pipeline.py | Python | gpl-2.0 | 13,378 | [
"BLAST",
"Bowtie"
] | c46a01fb1afa51dcc813710e769a391b62c42573ef8e800205f11960e79fd75d |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['VFM', 'VFM_HFM', 'HFM', 'HFM_Watchpoint', 'Watchpoint', 'Watchpoint_Mask', ... | mkeilman/sirepo | tests/template/srw_generate_data/mask-example.py | Python | apache-2.0 | 25,057 | [
"Gaussian"
] | 661f428ee68da258dcca73107d1edba26d9b1da6297879583b239246b23b66e5 |
#!/usr/bin/env python3
# This file contains examples of usage of scipy.optimize module
from __future__ import division
import numpy as np
from numpy.testing import assert_allclose
from scipy import optimize
# -- root --
# `root` is a function that solves a vector equation f(x) = 0. It providing
# interface to var... | hombit/scientific_python | scientific_python/d_scipy/optimize.py | Python | mit | 3,894 | [
"Gaussian"
] | 65d3c944078fc6495e5b709ccb6dabd40406499445d0df3143b08ca8203406d0 |
""" The CS! (Configuration Service)
The following options can be set for the Configuration Service.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN Server
:end-before: ##END
:dedent: 2
:caption: Service options
"""
from __future__ import absolute_import
from __future__ import division
from _... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/Service/ConfigurationHandler.py | Python | gpl-3.0 | 3,844 | [
"DIRAC"
] | 55b5d169ff4531205afd35fef57f7fc746541f9b00bc1acf8eabdfc6a4383335 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Software License Agreement (Lesser GPL)
#
# Copyright (C) 2009-2012 Rosen Diankov <rosen.diankov@gmail.com>
#
# ikfast 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... | vitan/openrave | python/ikfast.py | Python | lgpl-3.0 | 450,836 | [
"Gaussian"
] | d55cd880c1e5a082b7d6836be7947fcc01490604cb5fd2f6456aa28d1c29ef67 |
'''
Individual stages of the pipeline implemented as functions from
input files to output files.
The run_stage function knows everything about submitting jobs and, given
the state parameter, has full access to the state of the pipeline, such
as config, options, DRMAA and the logger.
'''
from utils import safe_make_di... | khalidm/thepipelinex | src/stages.py | Python | bsd-3-clause | 20,415 | [
"BWA"
] | 40cc44081a2754a4c15405f1bbfc8ff711cd19fcf37fc11059b9b5c089e7f42f |
# PD is a free, modular C++ library for biomolecular simulation with a
# flexible and scriptable Python interface.
# Copyright (C) 2003-2013 Mike Tyka and Jon Rea
#
# 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... | mtyka/pd | examples/rotamer/rotamer_application/run.py | Python | gpl-3.0 | 2,091 | [
"CHARMM"
] | ac5f20e84e0a063cb4871573c76a530b744160a6f3d8b1300d67caf7552e7959 |
# SYSTEM LIBS
from matplotlib.colors import LogNorm
import matplotlib.pyplot as plt; plt.ion();
import matplotlib
import numpy as np
import pandas as pd
# from root_pandas import read_root
import sys
from itertools import islice
from scipy import signal # To find peaks, for edge-detecting the crystal
from scipy.optimiz... | f-forcher/crystal-channeling-analysis | torsion_correction.py | Python | gpl-3.0 | 18,175 | [
"CRYSTAL",
"Gaussian"
] | 5d9e1a53021869517c719fb53db5a7c6b04e4e11e282fd73452ebc5a4d988e3f |
# -*- coding: utf-8 -*-
# Generated by Django 1.10.4 on 2017-01-21 03:24
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
def create_card_set_seed_data(apps, schema_editor):
CardSet = apps.get_model("cards", "CardSet")
CardSet.objects.using... | DaveHynek/LegendaryOnline | cards/migrations/0001_initial.py | Python | mit | 31,608 | [
"BLAST"
] | 5d5e1a167676e6d3c8192619b3d2f6720542af4b20054f75f9e00e5ca179b879 |
import json
import logging
import os
import urllib2
from galaxy import util
from galaxy.util.odict import odict
from galaxy.web import url_for
from tool_shed.util import encoding_util
from tool_shed.util import xml_util
log = logging.getLogger( __name__ )
REPOSITORY_OWNER = 'devteam'
def accumulate_tool_dependencies... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/util/common_util.py | Python | gpl-3.0 | 19,969 | [
"Galaxy"
] | 11cba42edec28968ddf27ecca9d3e4b0c8277a05dcb495f83b6e97e7f05e90d7 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Apr 28, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Apr 28, 2012"
import unittest
impo... | Dioptas/pymatgen | pymatgen/io/tests/test_babelio.py | Python | mit | 2,171 | [
"Pybel",
"pymatgen"
] | 248f2977cae3ac5a215a0a68bbe6b61f75be92a5196b29f04b80c5ab11048e55 |
#!/usr/bin/env python
r"""
This example shows the use of the `dw_tl_he_genyeoh` hyperelastic term, whose
contribution to the deformation energy density per unit reference volume is
given by
.. math::
W = K \, \left( \overline I_1 - 3 \right)^{p}
where :math:`\overline I_1` is the first main invariant of the devia... | BubuLK/sfepy | examples/large_deformation/gen_yeoh_tl_up_interactive.py | Python | bsd-3-clause | 14,158 | [
"VTK"
] | 8926909706a110631dfe73fa7f2266652cda518c5cf929256ed3f7e555f61901 |
import os
import re
from f90nml import Namelist
from jinja2 import Environment, FileSystemLoader
import glob
import sh
import pdb
import tarfile
# from gfdl import create_alert
# import getpass
from isca import GFDL_WORK, GFDL_DATA, GFDL_BASE, _module_directory, get_env_file, EventEmitter
from isca.diagtable import ... | jamesp/Isca | src/extra/python/isca/experiment.py | Python | gpl-3.0 | 14,643 | [
"NetCDF"
] | 76dc7e3d12cffbc433335a31b87862130e28441caa574b02e7038db80bbc5a00 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 2000
n = 4000
k = 3000
testMehrotra = Tru... | birm/Elemental | examples/interface/LPAffine.py | Python | bsd-3-clause | 4,092 | [
"Gaussian"
] | 14a512ab8754fc9b7790e2d61905e33e117ec79735de85a74bc89e480a8e8e8b |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2016, Shoop Commerce Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
import random
import pytest
from django.core.urlresolvers import r... | suutari/shoop | shuup_tests/front/test_checkout_flow.py | Python | agpl-3.0 | 10,136 | [
"VisIt"
] | eecad0da752c5de7b5cf288892f89a85b85b777a7a7f50146e40ae90c837ef8e |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2010-2018 (ita)
"""
Classes and functions enabling the command system
"""
import os, re, imp, sys
from waflib import Utils, Errors, Logs
import waflib.Node
# the following 3 constants are updated on each new release (do not touch)
HEXVERSION=0x2000b00
"""Constan... | blablack/deteriorate-lv2 | waflib/Context.py | Python | gpl-3.0 | 21,029 | [
"VisIt"
] | 7565e96d5acae8a47d81469b5ab2addc0654db1f23d022abeb88b6352a36bc2f |
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2015 Uni.Lu/LCSB, NTUA
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Kenneth Hoste
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>
# License:: MIT/GPL
# $Id... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/b/bwa.py | Python | mit | 2,456 | [
"BWA"
] | bd8a07b568b8493f62dcbcc6f2db910e90f5b3b617058474ba6581eba2b34448 |
#! /usr/bin/env python
from __future__ import print_function
from openturns import *
TESTPREAMBLE()
RandomGenerator.SetSeed(0)
try:
dim = 10
R = CorrelationMatrix(dim)
for i in range(dim):
for j in range(i):
R[i, j] = (i + j + 1.0) / (2.0 * dim)
mean = NumericalPoint(dim, 2.0)
... | dubourg/openturns | python/test/t_HypothesisTest_std.py | Python | gpl-3.0 | 3,238 | [
"Gaussian"
] | a056c0e1ea19db268df31df3e40a5272f7a0d8090de57cbdf9b4202b6b381125 |
from __future__ import print_function, division
from sympy.core import Mul
from sympy.functions import DiracDelta, Heaviside
from sympy.core.compatibility import default_sort_key
from sympy.core.singleton import S
def change_mul(node, x):
"""change_mul(node, x)
Rearranges the operands of a product, bring... | wxgeo/geophar | wxgeometrie/sympy/integrals/deltafunctions.py | Python | gpl-2.0 | 7,416 | [
"DIRAC"
] | 168da773ea018c5d03b29d85c657bf3ff668e4fa7ebb238e2aa7605269cdf95b |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 vers... | markovmodel/PyEMMA | pyemma/util/tests/statistics_test.py | Python | lgpl-3.0 | 1,879 | [
"Gaussian"
] | 1b50302ef981cd83217509e1f5fbf9b92760ecf34863ee77a01ff92acb6c6880 |
"""
Gaussian Mixture Model
"""
import numpy as np
from scipy.stats import multivariate_normal
class GaussianMixture(object):
"""
Gaussian Mixture classification
"""
def __init__(self, c=2):
"""
Attributes:
samples (np.ndarray): Data to determine gaussian mixtures for
... | christopherjenness/ML-lib | ML/gaussianmixture.py | Python | mit | 4,378 | [
"Gaussian"
] | 71a16329ba70da459d9ee4bee2f41e8c5ee910328a6759b9e07b263256e5b700 |
""" This module loads all the classes from the VTK Rendering library into
its namespace. This is an optional module."""
import os
if os.name == 'posix':
from libvtkRenderingPython import *
else:
from vtkRenderingPython import *
| sgh/vtk | Wrapping/Python/vtk/rendering.py | Python | bsd-3-clause | 239 | [
"VTK"
] | 875786b9541e65bca95eaae74a9a34ad1c54a133fd98a07770948c6c5e4c5a5e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Produce word vectors with deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative samp... | markroxor/gensim | gensim/models/word2vec.py | Python | lgpl-2.1 | 87,112 | [
"VisIt"
] | b78d5b9cb42dd3064c4503c7fea06bc9c51b2d0b32406b6488c568097e1d8811 |
from i3pystatus.core.util import internet, require
from i3pystatus.weather import WeatherBackend
from datetime import datetime
from urllib.request import urlopen
GEOLOOKUP_URL = 'http://api.wunderground.com/api/%s/geolookup%s/q/%s.json'
STATION_QUERY_URL = 'http://api.wunderground.com/api/%s/%s/q/%s.json'
class Wun... | teto/i3pystatus | i3pystatus/weather/wunderground.py | Python | mit | 11,898 | [
"VisIt"
] | c1d900eece9b2511fe1daae25ccdca0d0cc6c22d49a7750f83b9028fc26bdc69 |
#! /bin/env python
from landlab.io.vtk.writer import VtkWriter
from landlab.io.vtk.vtktypes import VtkUniformRectilinear
from landlab.io.vtk.vtkxml import (VtkRootElement, VtkGridElement,
VtkPieceElement, VtkCoordinatesElement,
VtkPointDataElement, ... | decvalts/landlab | landlab/io/vtk/vti.py | Python | mit | 1,346 | [
"VTK"
] | 6de2442a4c7b71f3fabd0d198b8f200bd923a461de83b6688073ba1716209f69 |
#!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Classes that represent a portion of the state of an OpenMM context.
"""
# ====================================... | choderalab/openmmtools | openmmtools/states.py | Python | mit | 165,224 | [
"OpenMM"
] | 325486bbdd1534d4e113365f95c1c49e225f72437cc1e513b4914ba557ab8e04 |
# -* coding: utf-8 -*-
# Utility functions for moose.
import types
import token
import symbol
import math
from datetime import datetime
from collections import defaultdict
import re
import logging
logger_ = logging.getLogger("moose.utils")
import moose
from moose.moose_constants import *
from moose.print_utils impo... | dilawar/moose-core | python/moose/utils.py | Python | gpl-3.0 | 40,615 | [
"MOOSE",
"NEURON"
] | 1123e3214367b379a319a927a95afd31a98e75d01051238554ecc880fdbedce6 |
#!/usr/bin/env python
from tempfile import TemporaryFile, SpooledTemporaryFile
import os, sys, re, socket, time, pickle, csv, uuid, subprocess, argparse, decimal, select, platform, signal
class Debugger:
"""
The Debugger class is the entry point to our stack tracing capabilities.
It determins which debugger to inhe... | giopastor/moose | scripts/memory_logger.py | Python | lgpl-2.1 | 47,922 | [
"MOOSE"
] | 37a038c5a3e3046adb40f1c3bbe871cbed5e4b5992b7d96ca38074cbf92b0575 |
# Generated from STIXPattern.g4 by ANTLR 4.8
from antlr4 import *
# This class defines a complete generic visitor for a parse tree produced by STIXPatternParser.
class STIXPatternVisitor(ParseTreeVisitor):
# Visit a parse tree produced by STIXPatternParser#pattern.
def visitPattern(self, ctx):
return... | chisholm/cti-pattern-validator | stix2patterns/v20/grammars/STIXPatternVisitor.py | Python | bsd-3-clause | 5,117 | [
"VisIt"
] | 04164adf4bea47729c39af9179772a3f32d8f40cc27ff7163f50fbb8b0e17cdf |
"""pybutton.py - a button for displaying Python code.
This module defines two classes, together they implement a button that
a module can use to display Python.
PyButton
--------
PyButton is a gkt.Button with the label 'Python'. When pressed, it
opens a PyWindow displaying some Python code, or an error message if
... | slabanja/ase | ase/gui/pybutton.py | Python | gpl-2.0 | 2,355 | [
"ASE"
] | b2d4b76ca165e1c41c401922297e22839a1d24951f728cecf31ff34e00812d5b |
# -*- coding: utf-8 -*-
"""
sphinx.pycode
~~~~~~~~~~~~~
Utilities parsing and analyzing Python code.
:copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from __future__ import print_function
import re
import sys
from os import path
from si... | bgris/ODL_bgris | lib/python3.5/site-packages/Sphinx-1.5.1-py3.5.egg/sphinx/pycode/__init__.py | Python | gpl-3.0 | 13,599 | [
"VisIt"
] | 5ead088a6d090561951d8427d7cefde5d66656bf19d0269b7d5208cbbe64de4e |
"""This module defines the Atom object."""
import numpy as np
from ase.data import atomic_numbers, chemical_symbols, atomic_masses
# singular, plural, type, shape
data = {'symbol': ('symbols', str, () ),
'number': ('numbers', int, () ),
'position': ('positions', float, (... | slabanja/ase | ase/atom.py | Python | gpl-2.0 | 9,569 | [
"ASE"
] | 1ba5b17c9b5e3e5f8c874dc5a4050b7e8d324ef4678520dade3fac94711978df |
# Write the benchmarking functions here.
# See "Writing benchmarks" in the asv docs for more information.
import os
import sys
import py_entitymatching as mg
p = mg.get_install_path()
datasets_path = os.sep.join([p, 'datasets', 'example_datasets'])
bb = mg.BlackBoxBlocker()
o... | anhaidgroup/py_entitymatching | benchmarks/benchmark_blackbox_blocker.py | Python | bsd-3-clause | 13,074 | [
"VisIt"
] | 7741198eded2b7d2032c83f95104006db1ddd906c0dae6d3739a3753ad0f123c |
"""
alignReads
"""
from __future__ import print_function
import subprocess
import os
import logging
logger = logging.getLogger('root')
logger.propagate = False
def alignReads(BWA_path, HG19_path, read1, read2, outfile):
sample_name = os.path.basename(outfile).split('.')[0]
output_folder = os.path.dirname(o... | tsailabSJ/circleseq | circleseq/alignReads.py | Python | agpl-3.0 | 2,711 | [
"BWA"
] | 924cfdc58a215d8feab9d401251af4f30d68b33777f6e8fe7b4bd1fcea32d687 |
import numpy
import math
import re
import csv
import os
import sys
import logging
from __main__ import vtk, qt, ctk, slicer
from random import randint
from slicer.ScriptedLoadableModule import *
class MeshStatistics(ScriptedLoadableModule):
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, ... | jbvimort/LongitudinalQuantificationExtension | MeshStatistics/MeshStatistics.py | Python | apache-2.0 | 45,519 | [
"VTK"
] | bd367ddadba88354056e83193a8688bb985e9d1fc5f1c537e7b20ffb2555e235 |
# Copyright 2012 Viewfinder Inc. All Rights Reserved.
"""JSON Schemas for request/response pairs used with Viewfinder ops.
All times are expressed in seconds (possibly subsecond floating-point
precision) since the epoch (January 1st, 1970) in UTC.
Every mutating request may be run synchronously by specifying
'synchr... | 0359xiaodong/viewfinder | backend/www/json_schema.py | Python | apache-2.0 | 81,009 | [
"Galaxy"
] | 3818a65ebef4471b1a643052ea73e0dc830f59ee9b724ff4fc19e96b42532dca |
# Copyright (C) Ivan Kravets <me@ikravets.com>
# See LICENSE for details.
from math import ceil
from os.path import dirname, join, realpath
from sys import exit as sys_exit
from sys import path
path.append("..")
from platformio import util
from platformio.platforms.base import PlatformFactory, get_packages
def is_... | bkudria/platformio | scripts/docspregen.py | Python | mit | 8,124 | [
"VisIt"
] | 537b2b930077b1b7b5b72772afef1a7d7dfe1b50aa523e8bda240ba1f11190e1 |
'''
Created on 2014-07-09
This module contains meta data and access functions for the updated PRISM climatology as distributed by
PCIC (Pacific Climate Impact Consortium).
@author: Andre R. Erler, GPL v3
'''
# external imports
import numpy as np
import os
# internal imports
from geodata.netcdf import D... | aerler/GeoPy | src/datasets/PCIC.py | Python | gpl-3.0 | 11,430 | [
"NetCDF"
] | d79df48380408651291384c0a30552e911e90503287bcf0af32b65f0bb06f58e |
# qmpy/analysis/thermodynamics/phase.py
import numpy as np
from collections import defaultdict
import os.path
import qmpy
from io import StringIO
import fractions as frac
import logging
from qmpy.utils import *
from django.db.models import F, Q
import operator
from functools import reduce
from functools import total_... | wolverton-research-group/qmpy | qmpy/analysis/thermodynamics/phase.py | Python | mit | 21,375 | [
"VASP"
] | 2aed8ed6e9479eb1093ef80a89b36d810702dceb445f3efb909805bd6dcf7943 |
import serial
import inspect
import time
import itertools
from util import two_byte_iter_to_str, to_two_bytes
# Message command bytes - straight from Firmata.h
DIGITAL_MESSAGE = 0x90 # send data for a digital pin
ANALOG_MESSAGE = 0xE0 # send data for an analog pin (or PWM)
DIGITAL_PULSE = 0x91 # SysE... | dariobottazzi/pyfirmata | pyfirmata/pyfirmata.py | Python | bsd-3-clause | 18,814 | [
"CRYSTAL"
] | aa5bf48b4ddbe19a05d40143d8058027ce1cd2f12fa40cba5499dbe4ab834568 |
#!/usr/bin/python2
# ----------------------------------------------------------------------
# Copyright (2010) Aram Davtyan and Garegin Papoian
# Papoian's Group, University of Maryland at Collage Park
# http://papoian.chem.umd.edu/
# Last Update: 03/04/2011
# -----------------------------------------------... | luwei0917/awsemmd_script | archive/tertiary_create_project_helper.py | Python | mit | 9,765 | [
"LAMMPS"
] | e43469f2c79507fd6189740aa8599a519dd3dd66168c7d2d158f1a56d7f38c6b |
#!/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... | nuclear-wizard/moose | python/peacock/tests/execute_tab/ExecuteTabPlugin/test_ExecuteTabPlugin.py | Python | lgpl-2.1 | 6,150 | [
"MOOSE"
] | 0a5e9415a691690ad5154f4ff6ac5e94696c18678ddd6d314546e9fd6ac72974 |
# Copyright (C) 2015-2018 Hydriz Scholz
#
# 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 distribute... | Hydriz/Balchivist | modules/__init__.py | Python | gpl-3.0 | 981 | [
"VisIt"
] | c63fe70de3efcb832bb8a73fafc7cf66fee35165e7db1b6aec6d6befed983f9a |
#!/usr/bin/python
'''This package will take an input query and generate list of blast hits.
The input query must be a refseq protein gi number.
The default cutoff is a Blast score of 100
This script can be invoked as::
python blast_search.py 6319393
where 6319393 is the gi_number being queried.
The output... | davebridges/biomolecule-scripts | biopython/blast_search.py | Python | cc0-1.0 | 2,368 | [
"BLAST"
] | 0e00b70e1bed895d45741e6c56cd601215c84397b519979fc5ba40b032a4da3e |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
points = vtk.vtkPoints()
points.InsertNextPoint(0,-16,0)
points.InsertNextPoint(0,0,-14)
points.InsertNextPoint(0,0,14)
points.InsertNextPoint(14,0,0)
points.InsertNextPoint(10,20,-10... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Modeling/Testing/Python/KlineBottle.py | Python | gpl-3.0 | 9,138 | [
"VTK"
] | c87dfb8b5fc439b5fd67d5f5f120964915d70d00e010fd7e00661017cc3be943 |
#!/home/bin/python2
import multiprocessing;
import string;
import argparse;
import gzip;
import tempfile;
import subprocess;
import itertools;
import sys;
import time;
from scipy.stats import binom;
import numpy;
import os;
import pysam;
import math;
import copy;
import shutil
import resource
import glob
import collec... | secastel/phaser | phaser/phaser.py | Python | gpl-3.0 | 98,504 | [
"ASE",
"pysam"
] | 99fe6e83a3b56d781e0b21061d3f4c7f285077e913ddbe36bfea7201dfecd62f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Unit tests for data_ingestion.py script."""
from __future__ import unicode_literals
__version__ = '$Id$'
import os
from tests import _data_dir
from tests import _images_dir
from tests.aspects import unittest, TestCase, ScriptMainTestCase
from scripts import data_ingestion... | xZise/pywikibot-core | tests/data_ingestion_tests.py | Python | mit | 3,809 | [
"CRYSTAL"
] | ba9c2c83cbd1e43105c28ce48c9984a7b360d690e4dcb7e656c3b4df1f373501 |
# Copyright 2013 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.Application related tests for command line application wrappers.
This is intended to chec... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Application.py | Python | gpl-2.0 | 4,176 | [
"Biopython"
] | 26482f4e33d1f5c7056c55a753bf54ee889ed37bab980cecf4cb37c579c633a7 |
'''
MAP Client, a program to generate detailed musculoskeletal models for OpenSim.
Copyright (C) 2012 University of Auckland
This file is part of MAP Client. (http://launchpad.net/mapclient)
MAP Client is free software: you can redistribute it and/or modify
it under the terms of the GNU General Publi... | MusculoskeletalAtlasProject/mapclient-tests | test_resources/updater_test/mayaviviewerstep-master/mapclientplugins/mayaviviewerstep/widgets/mayaviviewerwidget.py | Python | apache-2.0 | 8,972 | [
"VTK"
] | afa245459035dc4e27d1d33e977c7783cdad4cd87e0de4fd8beb84cba67bc047 |
#
# Copyright 2019 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/zetasql | zetasql/parser/gen_extra_files.py | Python | apache-2.0 | 6,124 | [
"VisIt"
] | 054158911a8c6221553e09f3fddf44c5b8265831942f4a23f52209eb82db42fb |
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