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# Copyright 2015 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... | girving/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 108,098 | [
"Gaussian"
] | 2fc703c03effbfb9f035b916d871a0fb5ce03b539a2e1622fd0152af9d2ae4a5 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | samples/drude_bmimpf6.py | Python | gpl-3.0 | 14,562 | [
"ESPResSo"
] | e3362f3f3d6f7b8f23a103970423907a1f4507ea0bf412a4dbe8b394aad21785 |
from readtagger.bwa import SimpleAligner
SEQ = 'ATGCATGCATCATGCATCGAGGGGATCATGCATGCATCATGCATCGAGGGGATCATGCATGCATCATGCATCGAGGGGATC'
def test_simplealigner(tmpdir): # noqa: D103
tmp = tmpdir.strpath
with SimpleAligner(reference_sequences=SEQ, tmp_dir=tmp) as aligner:
aligner.align(SEQ)
| bardin-lab/readtagger | tests/test_bwa.py | Python | mit | 306 | [
"BWA"
] | 40763cfca94273c62df1d6eb1119a7eaf35a4150d6893f99224a56e42e0f4248 |
from __future__ import division, absolute_import, print_function
from numpy.testing import TestCase, run_module_suite, assert_,\
assert_raises
from numpy import random
from numpy.compat import asbytes
import numpy as np
class TestBinomial(TestCase):
def test_n_zero(self):
# Tests the corner case ... | megies/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 25,565 | [
"Gaussian"
] | 5088718df8f38d87e62b37844fafdbb9d3620013688bfe9ab157d925a7566c66 |
"""
Container page in Studio
"""
from bok_choy.page_object import PageObject
from bok_choy.promise import Promise, EmptyPromise
from . import BASE_URL
from .utils import click_css, confirm_prompt, type_in_codemirror
class ContainerPage(PageObject):
"""
Container page in Studio
"""
NAME_SELECTOR = '.... | jazkarta/edx-platform-for-isc | common/test/acceptance/pages/studio/container.py | Python | agpl-3.0 | 18,763 | [
"VisIt"
] | 2a18cc8752a3b1e1ec5f549e4dee02c7d40218ec82f286948845e3d4bf5132c3 |
# Copyright 2014-2018 The PySCF Developers. 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 appl... | gkc1000/pyscf | pyscf/gw/__init__.py | Python | apache-2.0 | 639 | [
"PySCF"
] | ef4a8a729e02275bab627b27abc7c6e9cb9e98ed13d8a3d41c4f5db5a2386312 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains some script utils that are used in the chemenv package.
"""
import re
from collections import OrderedDict
import numpy as np
from pymatgen.ext.matproj import MPRester
from pymatgen.io.cif import Ci... | vorwerkc/pymatgen | pymatgen/analysis/chemenv/utils/scripts_utils.py | Python | mit | 17,252 | [
"pymatgen"
] | 32f31ebd9fbcca8631a76b5dea8cbbc60c4bc5e75ac6ff82c38f534b2c07555e |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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
#
# Unle... | rhuss/gofabric8 | vendor/k8s.io/kubernetes/hack/verify-flags-underscore.py | Python | apache-2.0 | 8,826 | [
"VisIt"
] | 915f352aa7609031a284635b3a34a174ef4dbe552fe4e6148f4ea7e8b5712be7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
with open('README.rst') as readme_file:
readme = readme_file.read()
with open('HISTORY.rst') as history_file:
history = history_file.read().replace('.. :changelog:', ... | bnara/hello | setup.py | Python | bsd-3-clause | 1,546 | [
"Brian"
] | 354b848c303f3e79a55be524877a36c9a02e583de0c71119aebb92dd803df331 |
# Copyright 2021 Google LLC
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# version 3 as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without ev... | google-research/heatnet | data/processing.py | Python | gpl-3.0 | 22,620 | [
"NetCDF"
] | a38e10106c1d0e05dfd897c9724f2c837d2f84f094bbdba85961de52a0c5d4d5 |
import mixtape.featurizer, mixtape.tica, mixtape.cluster, mixtape.markovstatemodel, mixtape.ghmm
import numpy as np
import mdtraj as md
from parameters import load_trajectories, build_full_featurizer
import sklearn.pipeline, sklearn.externals.joblib
import mixtape.utils
n_choose = 50
n_components = 2
t = md.load("./s... | kyleabeauchamp/PMTStuff | code/fix_featurizer_mdtraj.py | Python | gpl-2.0 | 900 | [
"MDTraj"
] | f575dd0abed5aabcbcc99a87674f4afd3f2da9e3e15172f68863ed9236c770b0 |
# -*- coding: utf-8 -*-
"""
PyOpenWorm
==========
OpenWorm Unified Data Abstract Layer.
An introduction to PyOpenWorm can be found in the README on our `Github page <https://github.com/openworm/PyOpenWorm/tree/alpha0.5#readme>`_.
Most statements correspond to some action on the database.
Some of these actions may b... | travs/PyOpenWorm | PyOpenWorm/__init__.py | Python | mit | 7,576 | [
"NEURON"
] | cf56e89cc423a19094b195ef1ca558299a8f5271ced57b65eceeecc2f534076e |
# Authors: Christian Lorentzen <lorentzen.ch@gmail.com>
#
# License: BSD 3 clause
import numpy as np
from numpy.testing import assert_allclose
import pytest
import warnings
from sklearn.datasets import make_regression
from sklearn.linear_model._glm import GeneralizedLinearRegressor
from sklearn.linear_model import (
... | xuewei4d/scikit-learn | sklearn/linear_model/_glm/tests/test_glm.py | Python | bsd-3-clause | 15,578 | [
"Gaussian"
] | ae350dd24eb8c8af11620a78e8832fc036d5131c3f75a79ffffb7d8c51d22161 |
# import numpy as np
# import matplotlib.pyplot as plt
# import sys
from cv2 import *
from pylab import *
from skimage.color import rgb2gray
from skimage.util import *
from scipy import misc
sys.path.append( '../../core' )
# from imgutils import *
class xor(object):
"""
Class that creates a xor dataset. Note ... | WenboTien/Machine_Learning_prac | project2/dataset.py | Python | mit | 10,206 | [
"Gaussian"
] | 5191dbc2d1f9f30e0015d30187c70326971a1b41d2785ebe279f11e643ea75c6 |
"""
Graphical model (GM)-based optimization algorithm using Theano
"""
__authors__ = "James Bergstra"
__license__ = "3-clause BSD License"
__contact__ = "github.com/jaberg/hyperopt"
import logging
import time
import numpy as np
from scipy.special import erf
import pyll
from pyll import scope
from pyll.stochastic imp... | w1kke/hyperopt | hyperopt/tpe.py | Python | bsd-3-clause | 30,381 | [
"Gaussian"
] | b73375db11a6fba5295c7871946052441cb7435619019e41b6e1382b100020a7 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | fedepad/espressopp | src/analysis/Velocities.py | Python | gpl-3.0 | 2,197 | [
"ESPResSo"
] | 5d03326ae574edb0a5c94746aa27586d9bc87cd08bb00fb9be4845cd2d922464 |
"""
Module extracts metadata from NetCDF file to complete the required MyHPOM NetCDF
Science Metadata
References
reprojection
http://gis.stackexchange.com/questions/78838/how-to-convert-projected-coordinates-to-
lat-lon-using-python
datatype
http://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html
... | ResearchSoftwareInstitute/MyHPOM | hs_file_types/nc_functions/nc_meta.py | Python | bsd-3-clause | 17,016 | [
"NetCDF"
] | c71e83560de3787afbb7ee9ac4e3445603a00a0a6f9183561ec63a030569bf31 |
# coding=utf-8
# --------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# -----------------------------------------------------... | yugangw-msft/azure-cli | src/azure-cli/azure/cli/command_modules/iot/_help.py | Python | mit | 45,068 | [
"VisIt"
] | 30119af7610ab0bd814b54bedb4bd3764f5a183500c87b314160bcfbaf6bda05 |
"""
Module to set up run time parameters for Clawpack -- classic code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='amrclaw'):
#--------------------------... | maojrs/Interface_Euler_AMR | code_mapped/setrun.py | Python | bsd-2-clause | 16,135 | [
"NetCDF"
] | 84ce8d786c562ade5bba4fc31cec9cdd0846b76ccbbb73609c4c2a4d6d18812d |
# -*- coding: utf-8 -*-
"""
Wingrid Insect Wing Color Analysis Package
"""
# Author: William R. Kuhn
# License: GNU GPL License v3
import cv2 # MUST BE version 3.0 or higher
import numpy as np
################################################################################
# HELPER FUNCTIONS
def downscaleIf(image,... | willkuhn/wingrid | wingrid/helpers.py | Python | gpl-3.0 | 4,951 | [
"Gaussian"
] | 0119a83fcf803a0d290761532d0d5f93ecd79683f9033760be356ce9e19ce5dd |
#!/usr/bin/env python
"""Writing for HTML pages."""
import os
import os.path
import shutil
import sys
import xml.sax.saxutils
import jinja2
import proc_doc
import raw_doc
def escapeForXml(s):
"""Return escaped XML of s."""
return xml.sax.saxutils.escape(s)
def escapeName(name):
"""Escape a name such t... | bkahlert/seqan-research | raw/workshop13/workshop2013-data-20130926/trunk/util/py_lib/seqan/dox/write_html.py | Python | mit | 19,063 | [
"VisIt"
] | caf76f1b2602a5449f3deded39bafaa35530933a201f83bd6de2b8d7bcd09aaf |
# Dependencies
from selenium import webdriver
from splinter import Browser
import requests
from selenium import webdriver
import getpass
from lxml import html #Parser
import logging
from table import *
global browser
browser = Browser('chrome', headless=True)
def login():
browser.visit('https://portals.veracross... | sapblatt11/veraScrape | framework.py | Python | apache-2.0 | 2,632 | [
"VisIt"
] | 69c8bfd17adfdbf977102dc6f266292480bac9f1562b8036ec1ec20907ad618c |
"""
Keeps the routing/wiring algorithm
"""
import heapq
import sys
from field import Field, FieldException, FieldNode
class RoutingException(FieldException):
def __init__(self, msg):
FieldException.__init__(self)
self.message += msg
class Routing:
dirs = list(((0, -1), (0, 1), (-1, 0), (... | daringer/schemmaker | src/routing.py | Python | apache-2.0 | 14,924 | [
"VisIt"
] | 69cc2a8794f503ed7b642d4bffef9c3769533e305045cf6221be60656662d063 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | pdxwebdev/yadapy | yada/lib/python2.7/site-packages/setuptools/command/easy_install.py | Python | gpl-3.0 | 85,720 | [
"VisIt"
] | 02599ab05b942f15175e04dc52101195ef3b6bbe2bc12b54e674909fd39a923c |
#!/usr/bin/env python
#
# zip up the titanium mobile SDKs into suitable distribution formats
#
import os, types, glob, shutil, sys, platform, codecs
import zipfile, datetime, subprocess, tempfile, time
sys.path.append(os.path.join(os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename)),'..','support','co... | pinnamur/titanium_mobile | site_scons/package.py | Python | apache-2.0 | 20,788 | [
"VisIt"
] | 1cd19227ec96f07282ac9123efe53c61f07cb42aca4d3b72334803f0d04b10ec |
"""This module contains a widget to create new plots with psyplot
The main class is the :class:`PlotCreator` which is used to handle the
different plotting methods of the :class:`psyplot.project.ProjectPlotter`
class"""
from __future__ import division
import os
import logging
import re
import types
import xarray
from ... | Chilipp/psyplot_gui | psyplot_gui/plot_creator.py | Python | gpl-2.0 | 85,421 | [
"NetCDF"
] | a910cbcf52b08e3ffb68297292e7d62263599ea3f4268515994cb6d2717a9f40 |
if not type(Query.target) is Class:
raise Exception('Needs to be executed on a class')
visitorName = Query.target.name
def addArgument(argType, argName, toMethod):
argument = Node.createNewNode('FormalArgument', None)
argument.typeExpression = AstModification.buildExpression(argType)
argument.name = a... | Vaishal-shah/Envision | InformationScripting/scripts/evaluation/visitorPattern.py | Python | bsd-3-clause | 1,748 | [
"VisIt"
] | 804315f838380a2743f9b22dd7647e8738535fe829bfeed52761f7ffae3338ab |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Defines SymmetryGroup parent class and PointGroup and SpaceGroup classes.
Shyue Ping Ong thanks Marc De Graef for his generous sharing of his
SpaceGroup da... | migueldiascosta/pymatgen | pymatgen/symmetry/groups.py | Python | mit | 15,273 | [
"pymatgen"
] | 51da211176759c632646312e037524b8a0ce80efebad0fd90e780844e076cd13 |
# Copyright 2012 Brian Waldon
#
# 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,... | neumerance/deploy | .venv/lib/python2.7/site-packages/warlock/model.py | Python | apache-2.0 | 3,874 | [
"Brian"
] | b716f0092ac816384ca695d94ca2cba91ab8def48fe4e0b112358299bde6f92b |
"""
Dump a CSV file of the MADIS data, kind of sad that I do this, but alas
"""
import os
import sys
import time
import subprocess
import warnings
import datetime
from netCDF4 import chartostring # @UnresolvedImport
import numpy.ma
import pytz
from pyiem.util import ncopen, convert_value
warnings.filterwarnings("ig... | akrherz/iem | scripts/outgoing/madis2csv.py | Python | mit | 6,124 | [
"NetCDF"
] | a14a63cea515105d747786352ff1853dc2a6c971c4c28790945db3e2e3c19097 |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 30 23:26:00 2016
@author: noel
"""
import sys
import os
import pandas as pd
import Bio.PDB as struct
#import em.describe.utilities as utilities
import string
import em.manipulate.Molecular_Rigid_Manipulations as MRM
from em.charmm.gen import *
from em.charmm import run
imp... | noelcjr/EntropyMaxima | em/charmm/gen/inputs.py | Python | gpl-3.0 | 13,718 | [
"CHARMM"
] | 51934c699d21c434df78b07ec886583e557904290ebdb1b41a894c756b737643 |
from .BlockDevice import BlockDevice
import ctypes
import gzip
import io
class ADFBlockDevice(BlockDevice):
def __init__(self, adf_file, read_only=False, fobj=None):
self.adf_file = adf_file
self.read_only = read_only
self.fobj = fobj
self.dirty = False
lo = adf_file.lower()
self.gzipped =... | FrodeSolheim/fs-uae-launcher | amitools/fs/blkdev/ADFBlockDevice.py | Python | gpl-2.0 | 3,405 | [
"ADF"
] | ea3b7e6f5def6cef374d299763a266efd22cf4298ee8b134642d39b3a33e33dd |
# coding: utf-8
from __future__ import division, unicode_literals
import unittest
import pickle
import collections
from pymatgen.core.periodic_table import Element, Specie, DummySpecie, \
PeriodicTable, get_el_sp
from pymatgen.core.composition import Composition
from copy import deepcopy
class ElementTestCase(... | rousseab/pymatgen | pymatgen/core/tests/test_periodic_table.py | Python | mit | 12,557 | [
"pymatgen"
] | f6695d3de32563d7f21257325eb70f5609dc1ac95bdd65f7d0755ce8fdb85f90 |
from pylab import figure,scatter,contour,show,legend,connect
from numpy import array, append, arange, reshape, empty, exp
from shogun.Distribution import Gaussian, GMM
from shogun.Features import RealFeatures
import util
util.set_title('EM for 2d GMM example')
#set the parameters
min_cov=1e-9
max_iter=1000
min_change... | ratschlab/ASP | examples/undocumented/python_modular/graphical/em_2d_gmm.py | Python | gpl-2.0 | 2,441 | [
"Gaussian"
] | 724314367b94d1061ad978a2a6305fbfabb2f403a21ef8488d25302e16bb9a33 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=attribute-defined-outside-init
# pylint: disable=no-self-use
import json
import os
import ... | neilswainston/PathwayGenie | parts_genie/test/test_parts.py | Python | mit | 2,650 | [
"VisIt"
] | 542c7cba8284e71c304896d9827f8cfb8d34cba71a119f21cf51c03aebbf2c45 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
from django.conf import settings
import multiselectfield.db.fields
class Migration(migrations.Migration):
dependencies = [
('branch', '0031_merge'),
]
operations = [
migrations.Alter... | MaximeBiset/care4care | branch/migrations/0032_auto_20141203_1653.py | Python | agpl-3.0 | 9,027 | [
"VisIt"
] | ad6dfdce2c60a7180f22ad902131a0b3a6ec7f8e69ab582a685fa727bdd4c37e |
#!/usr/bin/env python
import sys
from ansible import __version__
try:
from setuptools import setup, find_packages
except ImportError:
print("Ansible now needs setuptools in order to build. Install it using"
" your package manager (usually python-setuptools) or via pip (pip"
" install s... | bootswithdefer/ansible | v2/setup.py | Python | gpl-3.0 | 1,105 | [
"Galaxy"
] | 69b88be4fcc6a73ee7f4057b01983e1709fec8ec18250fba982c9f8255749d3f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# ChemPy - A chemistry toolkit for Python
#
# Copyright (c) 2010 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy o... | jwallen/ChemPy | chempy/exception.py | Python | mit | 3,054 | [
"ChemPy"
] | f406c2d89d9495eac440c53d096d5801aa8615121b44dbff5cb9e246f574384c |
'''
Module to create a METADATA file in a vasp directory
The aim of this module is to record information about the user, jobs,
system, etc... this is useful for archiving purposes
this file will store a uuid that can be used as a key in a database.
The format of the metadata file is json. You can store the standard
p... | prtkm/jasp | jasp/metadata.py | Python | gpl-2.0 | 3,982 | [
"ASE",
"VASP"
] | 1640062fac686d6cc6c5b3ecfe3101dffd4615f16a92afa3e06ecdb555253a1a |
"""
Tests for adding and removing variants from variant_sets.
"""
import os
import random
from django.conf import settings
from django.test import TestCase
import pyinter
from main.models import AlignmentGroup
from main.models import Chromosome
from main.models import Dataset
from main.models import ExperimentSample... | woodymit/millstone | genome_designer/variants/tests/test_variant_sets.py | Python | mit | 17,547 | [
"BWA"
] | 6310857ab5c14efa002e2eea6fccf85a6f9827582a8d50ce53642bdcecf941b0 |
#! /usr/bin/env python
# linearizedGP -- Implementation of extended and unscented Gaussian processes.
# Copyright (C) 2014 National ICT Australia (NICTA)
#
# This file is part of linearizedGP.
#
# linearizedGP is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public... | NICTA/linearizedGP | tests/test_gps.py | Python | gpl-3.0 | 5,726 | [
"Gaussian"
] | 8415012b6a734faed547952d37c76d0de814a33558ac18ae9426c16e0b6bbda3 |
# Copyright (c) 2015 the GPy Austhors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .. import kern
from .bayesian_gplvm import BayesianGPLVM
from ..core.parameterization.variational import NormalPosterior, NormalPrior
class DPBayesianGPLVM(BayesianGPLVM):
""... | ptonner/GPy | GPy/models/dpgplvm.py | Python | bsd-3-clause | 1,162 | [
"Gaussian"
] | d85c0de738f9adfb555a8321f0bd04ee17c2e5d17e989eb8d828b62e6a501564 |
import os
import numpy as np
from ase import Atoms, Atom
ase = """\
H HH HHH
H H H H
HHH H HH
H H H H
H H HH HHH"""
d = 1.2
logo = Atoms()
for i, line in enumerate(ase.split('\n')):
for j, c in enumerate(line):
if c == 'H':
logo.append(Atom('H', [d * j, d * i, 0]))
logo.set_cell((1... | misdoro/python-ase | doc/logo.py | Python | gpl-2.0 | 1,058 | [
"ASE",
"GPAW"
] | 48b08b671362fff90f7f8d9eaa59131df75fdda76736b6d8fb20b152f886b0a8 |
class Module:
def __init__(self, mainMenu, params=[]):
# metadata info about the module, not modified during runtime
self.info = {
# name for the module that will appear in module menus
'Name': 'PillageUser',
# list of one or more authors for the module
... | Hackplayers/Empire-mod-Hpys-tests | lib/modules/python/collection/osx/pillage_user.py | Python | bsd-3-clause | 5,301 | [
"BLAST"
] | 5fe024cdb60da770e7a67bc7009c37b87d544451891fa4b5b7fae35393adb700 |
'''This is the KIDs Analysis Module, KAM'''
import urllib2
import scipy.io #for loading .mat file
import os
import numpy as np
import tables
import matplotlib as mpl
#mpl.use("pgf")
pgf_with_pdflatex = {
"pgf.texsystem": "pdflatex",
"pgf.preamble": [
r"\usepackage[utf8x]{inputenc}",
r"\use... | mdaal/KAM | KAM.py | Python | mit | 170,489 | [
"Gaussian"
] | 86262c7facffd11c02d9f44cf845b28bbe76fdb7a722d21383e6ec0bceafd7a3 |
__author__ = "Brian O'Neill"
__version__ = '0.3.0'
from log_calls import record_history
import doctest
#-----------------------------------------------------------------------------
# main__record_history_class_deco
#-----------------------------------------------------------------------------
def main__record_histo... | Twangist/log_calls | tests/test_record_history__class_deco.py | Python | mit | 5,829 | [
"Brian"
] | 57e1449ba3da3b87da8b773dc351e90824c9e1f114d4e3ace17810a5e7aa121f |
# Copyright (c) 2014 Universidade Federal Fluminense (UFF)
# Copyright (c) 2014 Polytechnic Institute of New York University.
# This file is part of noWorkflow.
# Please, consult the license terms in the LICENSE file.
from __future__ import (absolute_import, print_function,
division, unicode_li... | paopao74cn/noworkflow | capture/noworkflow/now/prov_definition/__init__.py | Python | mit | 2,142 | [
"VisIt"
] | 3018b671355fa5c12ea747ba397021c6d08346a747e218ba3f9087330e4611ab |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Jason Swails
# Contributors:
#
# This code for reading Amber r... | kyleabeauchamp/mdtraj | mdtraj/formats/amberrst.py | Python | lgpl-2.1 | 31,824 | [
"Amber",
"MDTraj",
"NetCDF"
] | 61080591074cc7d73b07e3460ab896f3d2c0c490c50eec1384bf5c056b8f21ba |
#!/usr/bin/env python2
#
# This is a PyMol extension script to load all PyMol extensions in the same
# directory.
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in... | joy13975/elfin | pymol_scripts/extensions/load_all_extensions.py | Python | mit | 870 | [
"PyMOL"
] | d4188ab1f71184be45a4b24cae11db74b1020f4e374a90e3a165931dcdcb31d2 |
import os
import sys
import numpy as np
import matplotlib.pyplot as plt
import fitelp.constants as constants
from fitelp.make_latex_tables import average_velocities_table_to_latex, halpha_regions_table_to_latex
from fitelp.bpt_plotting import bpt_plot
from fitelp.kinematics_calculations import RegionCalculations
from f... | daniel-muthukrishna/GiantStarFormingRegions | run_analysis.py | Python | mit | 7,619 | [
"Gaussian"
] | afae2284e2a756fe228f21e1ab577c150813d27fc9d68c522c55baf59c4f8f72 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os.path
import collections
from tempfile import mkdtemp
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinit import *... | matk86/pymatgen | pymatgen/io/abinit/tests/test_works.py | Python | mit | 1,425 | [
"ABINIT",
"pymatgen"
] | 3abfdc368c53fc40525eb47aad9dd82f5460d98161de9ce6fd559eb5ee11dab2 |
#!/usr/bin/env python
from rdkit import RDConfig
import os, sys
from rdkit import Chem
from rdkit.Chem import Draw, AllChem
suppl = Chem.SDMolSupplier()
if sys.argv[1].endswith('.sdf'):
suppl = Chem.SDMolSupplier(sys.argv[1])
elif sys.argv[1].endswith('.smi'):
suppl = Chem.SmilesMolSupplier(sys.argv[1])
else:
... | jandom/rdkit | Code/GraphMol/MolDraw2D/test_dir/test_rdkit_draw.py | Python | bsd-3-clause | 515 | [
"RDKit"
] | 9ac2b837676b36e59e5714e804d67d36eb51ed3ba6cc59c0b689dae03cfbd41c |
#!/usr/bin/python
#####################################################
##### An example featuring a closed box made up #####
##### from six planes ("membranes"), involving: #####
##### #####
##### - 3D diffusion inside the box #####
##### - 2D diffusion on the p... | gfrd/egfrd | samples/1D+2D+3D_example/1D+2D+3D_example.py | Python | gpl-2.0 | 18,853 | [
"VTK"
] | bc272f27e261413d9edd494ab9b8be8e82b99f1748a6d1d8e3f7d9a9dcd7764e |
#!/usr/bin/env python
"""
=======
textext
=======
:Author: Pauli Virtanen <pav@iki.fi>
:Date: 2008-04-26
:License: BSD
Textext is an extension for Inkscape_ that allows adding
LaTeX-generated text objects to your SVG drawing. What's more, you can
also *edit* these text objects after creating them.
This brings some o... | AidanDelaney/textext | textext.py | Python | bsd-3-clause | 45,866 | [
"Brian"
] | 47265937ba4799b25577cdf1989c359541740b7e0dbe422eb476eae660037a38 |
from __future__ import with_statement
__license__ = 'GPL v3'
__copyright__ = '2008, Kovid Goyal <kovid at kovidgoyal.net>'
'''
Defines various abstract base classes that can be subclassed to create powerful news fetching recipes.
'''
__docformat__ = "restructuredtext en"
import os, time, traceback, re, urlparse, sy... | ashang/calibre | src/calibre/web/feeds/news.py | Python | gpl-3.0 | 77,621 | [
"VisIt"
] | 06ec106bb6ed4e2609f6368bcf043583bb4235462a9f4872e398d8a18b6f4f3b |
#coding=utf-8
#author='Shichao-Dong'
import unittest
import os,sys
reload(sys)
sys.path.append('D:\Ptest\Appium\Testcase')
import time
import HTMLTestRunner
from public import public
from visit import visit_temp
from xlsb import test_xlsb
suite=unittest.TestSuite()
#suite.addTest(unittest.makeSuite(test_xlsb.xlsb))
... | NJ-zero/Android | Appium/Testcase/runtest/runtest.py | Python | mit | 592 | [
"VisIt"
] | 1b1bc3ef054a87197e8ef68e739511a97f47b396f223dc5938488597e8aaa986 |
"""Contains the Config class with utility configuration methods"""
# config.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import os
impor... | spierepf/mpf | mpf/system/config.py | Python | mit | 18,136 | [
"Brian"
] | 2832a5371448c926f5f804f2d6f125b90a648ab32ef78352196d2aac339df972 |
#
# 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... | chuckchen/spark | python/pyspark/pandas/tests/test_series.py | Python | apache-2.0 | 122,394 | [
"Elk"
] | 83adb2f3945ba4f931a27cbfcc576a3ee12566139c11a56301c82c0931debca7 |
#
# Copyright 2015 LinkedIn Corp. 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 applicable law or ... | hangzhang925/WhereHows | wherehows-etl/src/main/resources/jython/ElasticSearchIndex.py | Python | apache-2.0 | 16,183 | [
"ESPResSo"
] | fa729874c63829cf1267843ea67d737ed0ebbb1727ad75f1fa41b4f30b5ab391 |
#main source for this is : http://inventwithpython.com/makinggames.pdf
#credit also to http://nebelprog.wordpress.com/2013/08/14/create-a-simple-game-menu-with-pygame-pt-1-writing-the-menu-options-to-the-screen/
#for menu stuffz.
#basic gui program, displays a big black blank square.
import pygame, sys#load up pygam... | Antonf26/DesKwanAdv | mainv0-0-0-1.py | Python | gpl-2.0 | 9,807 | [
"Desmond"
] | efe5979350e1185eb5b986ed240d0d8d9a842f9ef813c00feaa4c3dfd1463a95 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | tqchen/tvm | python/tvm/script/parser.py | Python | apache-2.0 | 33,614 | [
"VisIt"
] | 146cef7148cf602f9f83295456f01535edd76f64024ebec6bf33ea81e005e7a9 |
#!/usr/bin/env python
#
# $File: RandomMating.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribu... | BoPeng/simuPOP | docs/RandomMating.py | Python | gpl-2.0 | 1,562 | [
"VisIt"
] | f503abe03a5ff9b548e359698e9bb731f28868965f601f761e6347c7034744ed |
##
# file: predictor.py
# author: Polcz Péter <ppolcz@gmail.com>
#
# Created on Sat Nov 29 15:41:43 CET 2014
#
from intellistock.data.data import int2year, date2year
from intellistock.ui.plotwidget import PlotWidget
from intellistock.predictor.predictor_helper import create_training_set, create_training_set_2, ... | morta-code/IntelliStock | intellistock/predictor/predictor.py | Python | gpl-2.0 | 16,022 | [
"Gaussian"
] | f68755aea8af6c226b1173555d75fc173fd800af267dcf39c09c8849cff4f8b8 |
from GangaCore.Core.exceptions import BackendError, ApplicationConfigurationError
from GangaCore.Core.exceptions import SplitterError
from GangaCore.Utility.logging import getLogger
from GangaCore.Utility.Config import getConfig
from GangaCore.Utility.util import unique
from GangaDirac.Lib.Splitters.SplitterUtils impor... | ganga-devs/ganga | ganga/GangaDirac/Lib/RTHandlers/DiracRTHUtils.py | Python | gpl-3.0 | 9,888 | [
"DIRAC"
] | 08c0c932f7e966a3fe6ce97a30c5bf2e3c81bffcdf38a30109b71ca57de43125 |
"""STIX 2.1 Common Data Types and Properties."""
from collections import OrderedDict
from . import _Extension
from ..custom import _custom_extension_builder, _custom_marking_builder
from ..exceptions import InvalidValueError, PropertyPresenceError
from ..markings import _MarkingsMixin
from ..markings.utils import che... | oasis-open/cti-python-stix2 | stix2/v21/common.py | Python | bsd-3-clause | 12,123 | [
"Amber"
] | 2986cfcb0bfd51d8583b559b0d1a3e502dfcc9ba424d5da6ed24d526760cfe4b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/qcdb/options.py | Python | lgpl-3.0 | 11,046 | [
"CFOUR",
"ORCA",
"Psi4",
"Q-Chem"
] | 046859d02cee9a0a256c6b9aadb0f2fc3c83c94ec8f688701034ce9172827a40 |
from ..libmp.backend import xrange
from .functions import defun, defun_wrapped
def _check_need_perturb(ctx, terms, prec, discard_known_zeros):
perturb = recompute = False
extraprec = 0
discard = []
for term_index, term in enumerate(terms):
w_s, c_s, alpha_s, beta_s, a_s, b_s, z = term
h... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/sympy/mpmath/functions/hypergeometric.py | Python | mit | 51,574 | [
"Gaussian"
] | 92440e82fa2b9d11e480f6fcdaed363d7e2eb046677e700695667e945c6b55bc |
# -*- coding=utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
import unittest
import copy
from chemfiles import UnitCell, CellShape
from chemfiles import ChemfilesError
from _utils import remove_warnings
class TestUnitCell(unittest.TestCase):
def test_repr(self):
self.as... | Luthaf/Chemharp-python | tests/cell.py | Python | mpl-2.0 | 3,340 | [
"Chemfiles"
] | 6f496a08f4106e782121372c747945478498b4db52153f6ea6cdbffd4f6ea8af |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2016, Shoop 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.
from django.conf import settings
from django.core.exceptions import Middlewa... | shawnadelic/shuup | shuup/testing/utils.py | Python | agpl-3.0 | 2,136 | [
"VisIt"
] | fa645f4a7a78bb5a63c351c42532003d19e338d35d393f60fac752d6669af407 |
#
# 20,000 Light Years Into Space
# This game is licensed under GPL v2, and copyright (C) Jack Whitham 2006.
#
import pygame , random , sys , math , time , webbrowser , urllib
from pygame.locals import *
import game , stats , storms , extra , save_menu , resource , menu
import config , startup , sound , alien_inva... | yngfng/LightYears_craft | code/main.py | Python | gpl-2.0 | 10,820 | [
"VisIt"
] | 807c42ade85225e86a0aee8d7a716bca189b86e63d93a73ea80d961b0866d0dc |
"""
mtzutil.py
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
import sys
import os
import struct
import math
import subprocess
##
# MTZ COLUMN TYPES
#H index h,k,l
#J intensity
#F structure amplitude, F
#D anomalous differenc... | keitaroyam/yam_scripts | mtzutil.py | Python | bsd-3-clause | 7,399 | [
"CRYSTAL"
] | b706116aca7e376bb23d95bf240ceeebc15547968986ea5f6c7c4be4cd85f318 |
import datetime
import json
from sqlalchemy import orm
from DIRAC.DataManagementSystem.Client.FTS3Job import FTS3Job
from DIRAC.DataManagementSystem.private import FTS3Utilities
from DIRAC.DataManagementSystem.Client.DataManager import DataManager
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Re... | Andrew-McNab-UK/DIRAC | DataManagementSystem/Client/FTS3Operation.py | Python | gpl-3.0 | 17,697 | [
"DIRAC"
] | b210b002beb53fcae036913eb672f69c9ecbd85cd1668975c4fc29174266875d |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-today OpenERP SA (<http://www.openerp.com>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms o... | inovtec-solutions/OpenERP | openerp/addons/project/project.py | Python | agpl-3.0 | 74,083 | [
"VisIt"
] | 961e4a65f425f867bbab6561efd93151e25cc0fe80f574972559c242d40b0225 |
import inputparser
import utilities
import textwrap
import os
import os.path
from subprocess import call
import readline
import glob
from setup import setup_manual
#===============================================================================
def complete(text, state):
"""For filepath autocompletion."""
ret... | SINGROUP/pycp2k | setup_manual.py | Python | lgpl-3.0 | 8,316 | [
"CP2K"
] | 3da2c5ccfbc5b436e3667cd44902f5e9c0eb2092afcea64b563c08888b33b7ce |
"""
Python Interchangeable Virtual Instrument Library
Copyright (c) 2012-2014 Alex Forencich
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the... | lude-ma/python-ivi | ivi/agilent/agilent3000A.py | Python | mit | 2,721 | [
"Gaussian"
] | fbcd46a7923b5414b068000789bca23c8565f68992464214ff6f474aac1e2a04 |
# -*- coding: utf-8 -*-
# Copyright 2020 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... | googleads/google-ads-python | google/ads/googleads/v9/common/types/matching_function.py | Python | apache-2.0 | 8,722 | [
"VisIt"
] | ef318ae42c27e8c5bb20a70306c34f77067431e57946b1fc53e8fbd6090a83d5 |
#!/usr/bin/env python
""" update local cfg
"""
import os
from DIRAC.Core.Base import Script
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
' %s [option|cfgFile] ... DB ...' % Script.scriptName]))
Script.parseCommandLine()
arg... | andresailer/DIRAC | tests/Jenkins/dirac-cfg-update-server.py | Python | gpl-3.0 | 9,946 | [
"DIRAC"
] | ad8fe3e5d4e17ccfca5cee638ca6d5b729291744f95cf4de10540927146dba0f |
# -*- coding: utf-8 -*-
"""
Gestisce le comunicazioni rpg e off-rpg tra i giocatori.
"""
#= IMPORT ======================================================================
import datetime
import random
import re
from src.color import remove_colors, get_first_color, close_color, color_first_upper
from src.confi... | Onirik79/aaritmud | src/channel.py | Python | gpl-2.0 | 28,417 | [
"CASINO"
] | 97b5d1f5b8c58b9e5bb6eafdeba1314b8a8ecd5d34e6e9b49719276d894b0b75 |
########################################################################
#
# (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 by
# the Free Software ... | filipenf/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 30,820 | [
"Galaxy"
] | 37b3c3c243c748452304a13c7bdb782aa6c8bb5939cd964a66772776f4e27486 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | CZ-NIC/thug | src/Analysis/androguard/decompiler/dad/basic_blocks.py | Python | gpl-2.0 | 11,191 | [
"VisIt"
] | c0734a555e7e218e262f1327c39082531f58c391e733fec5210b40c5cbc332a3 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
class Bowtie(Package):
"""Mock package to test conflicts on compiler ranges"""
homepage = "http://www.example.org"... | LLNL/spack | var/spack/repos/builtin.mock/packages/bowtie/package.py | Python | lgpl-2.1 | 578 | [
"Bowtie"
] | 6645f47db40537221435819f9f0b6f9b177da27044a1d135524a6d5bf710a87c |
# -*- coding: utf-8 -*-
"""Add example Bom."""
import logging as log
from google.appengine.ext import ndb
from boilerplate.lib.basehandler import BaseHandler
from boilerplate.lib.basehandler import user_required
from web.models import Bom, Part, AuthWriterError
# logging system
log.basicConfig(level=log.DEBUG)
# ... | nortd/bomfu | web/bom_example.py | Python | lgpl-3.0 | 35,769 | [
"CRYSTAL"
] | 778b7f5b47ffefedd5255a485b7f1b1c01c8ca68aa1570335af5aca241e19947 |
import pyspeckit
# neet matplotlib so we can make mouse-click events from the script
import matplotlib
import os
# list of annotations so we can clear them
annotations = []
excesslines = []
# get the data from http://cdsarc.u-strasbg.fr/ftp/cats/II/179/sp/hr2421.fit
import urllib2
url = urllib2.urlopen('http://cdsarc... | allisony/pyspeckit | examples/interactive_example_hr2421.py | Python | mit | 11,287 | [
"Gaussian"
] | 059ac104c7a322d26f9d7ad3e6baa0e96050f0949259472e31b0f25749460068 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os
im... | harterj/moose | python/MooseDocs/commands/init.py | Python | lgpl-2.1 | 5,261 | [
"MOOSE"
] | 170c69d0819fd732ca630c86ff34e2576d6159726194a6054b0f2efa240c631b |
#!BPY
"""
Name: 'Sunflow Exporter 1.4.18 (.sc)...'
Blender: 2.45
Group: 'Export'
Tip: 'Export to a Sunflow Scene File'
Version : 1.4.18 (January 2008)
Author : R Lindsay (hayfever) / Christopher Kulla / MADCello /
olivS / Eugene Reilly / Heavily Tessellated / Humfred
Descri... | k-matsuzaki/sunflow | exporters/blender/sunflow_export.py | Python | mit | 114,863 | [
"Gaussian"
] | 674c182ced340a76e1e92528120a591aac2c2561561dadb5570669b7dddf0540 |
# ============================================================================
#
# Copyright (C) 2007-2012 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... | jeroendierckx/Camelot | camelot/view/action_steps/print_preview.py | Python | gpl-2.0 | 9,711 | [
"VisIt"
] | 0e1d2e7383a57824e43bad6ea0cd89c494ebbef9515665d9469859340339af13 |
# -*- coding: utf-8 -*-
'''
This module implements constant folding on the AST. It handles simple cases
such as
* 1 + 2 -> 3
* 2 ** 10 -> 1024
* N=1; N + 1 -> 2 (for N is assigned as global variable or a variable
that's only assigned once)
from __future__ import print_function, division, ab... | shiquanwang/numba | numba/ast_constant_folding.py | Python | bsd-2-clause | 10,738 | [
"VisIt"
] | 28366a6756f963bde411369d1d3d3905a422909d41b67abcb7dcdeabe58fb1e6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Client related data, work codes and their respective hourly rates."""
HOURLY_RATE = {
1: ['Research', 250.00],
2: ['Type letter', 280.00],
3: ['Phone call', 150.00],
4: ['Type contract', 500.00],
5: ['Court visit', 400.00],
6: ['Client meeting',... | adrianjengel/IS210-FINAL-PROJECT | clientdata.py | Python | mpl-2.0 | 1,306 | [
"VisIt"
] | 445564f4d05fbcae1a988bdb9620ae4fdd69ad4ecb1cb12eaa98d4ef707270da |
# Copyright 2013 Devsim 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, s... | devsim/devsim | testing/dio2_element_2d.py | Python | apache-2.0 | 4,191 | [
"VTK"
] | 4792f9a5d6b812e6fc67681180d700f0947b859c596be56ba1fe6c5f54fbbafa |
"""
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 License, or
(at your option) any later ... | MrTheodor/bakery | src/gromacs.py | Python | gpl-3.0 | 5,032 | [
"Gromacs"
] | c5c0a4ccfad1bb3ec731031df7e65cdb5b2ed68f7624f0d731585bd0190cd958 |
###############################################################################
# volumina: volume slicing and editing library
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# modify it und... | jakirkham/volumina | volumina/view3d/view3d.py | Python | lgpl-3.0 | 22,806 | [
"VTK"
] | 53dc4a92efa5b3325e1057d4779e92a6a6e3e13da42cb3875bfb7b6a606aa706 |
import sys
import io
import re
import logging
import pysam
import xlsxwriter
import os
import json
from collections import OrderedDict, defaultdict
from .ped_file import PedFile, Individual, PedError
from .vcf_reader import VcfReader
from .ensembl_rest_queries import EnsemblRestQueries
from .utils import csv_to_dict
fr... | gantzgraf/vape | vase/vase_reporter.py | Python | gpl-3.0 | 34,357 | [
"pysam"
] | d3967144b424c2b6e0ccf29daf91fddd0c260e787f79835f383b420a8903e41e |
#-------------------------------------------------------------------------------------------------------------------#
#
# IB2d is an Immersed Boundary Code (IB) for solving fully coupled
# fluid-structure interaction models. This version of the code is based off of
# Peskin's Immersed Boundary Method Paper in Acta Num... | nickabattista/IB2d | data_analysis/analysis_in_python/Perform_Analysis_Here/Standard_Data_Analysis_Script.py | Python | gpl-3.0 | 5,208 | [
"VTK"
] | 45ef8d77c10c1c3e05dd9297bc8c16792f5dbd7c8efb02992f10c12519efa20c |
"""
Dummy lammps class, good for debugging purposes. It only logs
everything on a file
"""
class Lammps(object):
"""
Dummy lammps object that just debugs
"""
def __init__(self, args, vals):
"""
Constructor. Can be overriden with lammps real class
Parameters
----------
args : iterable
... | pabloalcain/lammps-python | pylammps/DummyLammps.py | Python | gpl-3.0 | 677 | [
"LAMMPS"
] | b9383b1e3ddb9e4dd75f07ab3623e286ed5a096a159321bd2975e0e684076afb |
import bpy
from bpy.app.handlers import persistent
from .. core.util import getInstallPath, getAddonDir
from ..extensions_framework.util import find_config_value, write_config_value
from .. import export, bl_info
from .. core.util import PlatformInformation, getInstallPath
import os
def find_indigo():
rp = getIn... | glaretechnologies/blendigo | sources/indigo_exporter/properties/render_settings.py | Python | gpl-2.0 | 28,196 | [
"Gaussian"
] | 0fb0e5ef0bcb2b49fdf03e8985c18462289017af4c11c29d3a493d9af264a0a6 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/delegates/many2onedelegate.py | Python | gpl-2.0 | 3,725 | [
"VisIt"
] | 20ebc44d3036a44327751e75112cc274e9ba6e3f1921a6c74a4c5eec2c6a58dc |
try: paraview.simple
except: from paraview.simple import *
from paraview import coprocessing
#--------------------------------------------------------------
# Code generated from cpstate.py to create the CoProcessor.
# ----------------------- CoProcessor definition -----------------------
def CreateCoProcessor()... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Examples/Catalyst/FortranPoissonSolver/SampleScripts/coproc.py | Python | gpl-3.0 | 3,079 | [
"ParaView"
] | b773ee88778151c137c444dbe6adb666e1f879f1cf8df65f5bdb89a091bd5ab6 |
# 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 *
import glob
class PyMixedhtseq(PythonPackage):
"""HTSeq for mixed single and paired end reads"""... | iulian787/spack | var/spack/repos/builtin/packages/py-mixedhtseq/package.py | Python | lgpl-2.1 | 1,355 | [
"HTSeq"
] | f69de98e164f1699e90196e8b818f3d7f2833c5f3a01865b5fc8485c4dc43c41 |
import copy
import datetime
import json
from itertools import groupby
from unittest.mock import Mock, patch
import ddt
from django.conf import settings
from django.core import management
from django.test import override_settings
from django_dynamic_fixture import G
from elasticsearch import Elasticsearch
from rest_fra... | edx/edx-analytics-data-api | analytics_data_api/v0/tests/views/test_learners.py | Python | agpl-3.0 | 40,326 | [
"Brian"
] | 308b2288fcf6840e10f2e2f73dd9f356cf0f6e2f69252344534001d950b2e3a9 |
# TODO: replace ExprInner by passes that replaces the objects by what's needed
# for arybo
import functools
import operator
import six
import collections
from six.moves import range, reduce
from arybo.lib import MBA, simplify_inplace
from pytanque import imm, expand_esf_inplace, simplify_inplace, Vector, esf
class ... | quarkslab/arybo | arybo/lib/mba_exprs.py | Python | bsd-3-clause | 22,502 | [
"VisIt"
] | d04ae2b79d7b836f210424f37dabdd203a4d9a86a4f72917d0148f42334b7595 |
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