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'''
Broken (piecewise continuous) random field generation using
rft1d.random.Generator1D
Note:
When FWHM gets large (2FWHM>nNodes), the data should be padded
using the *pad* keyword.
'''
import numpy as np
from matplotlib import pyplot
import rft1d
#(0) Set parameters:
np.random.seed(12345)
nResponses = 5
nNode... | 0todd0000/rft1d | rft1d/examples/random_fields_broken_2.py | Python | gpl-3.0 | 1,064 | [
"Gaussian"
] | 1b8f819d6efe969a7bb8b4ec781f9df3e2ceb825b54de2922f990b6a1ede1aae |
#!/usr/bin/python2
debug = False
# This is a neural network based on PyBrain,
# taking as input an X and Y and any tree complexity parameters, and
# returning a classifier that can then be analyzed with the classifier.
# See the example in the main method for that and error-checking.
import sys, os
from imputation im... | bravelittlescientist/kdd-particle-physics-ml-fall13 | src/neural_network.py | Python | gpl-2.0 | 7,950 | [
"NEURON"
] | 40f002232a8305a376a5cb37045f3fd32b5d9ccef57b627ab2e984339eaa7c3d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# The MIT License (MIT)
# Copyright (c) 2017 Juan Cabral
# 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 withou... | carpyncho/feets | feets/extractors/ext_stetson.py | Python | mit | 10,889 | [
"Gaussian"
] | f9223860059cf8059bc39c50cae8a74ae37557f77d15d5abc3c8d9a9b11a62cc |
import tempfile
import numpy as np
from pele.systems import AtomicCluster
from pele.potentials import Morse
from pele.utils.xyz import write_xyz
__all__ = ["MorseCluster"]
class MorseCluster(AtomicCluster):
"""
define the System class for a Morse cluster cluster
Parameters
----------
natoms... | cjforman/pele | pele/systems/morse_cluster.py | Python | gpl-3.0 | 4,977 | [
"PyMOL"
] | 438e55cc93bbc38472f923944359e44798a6c0a3d64cc2574980d99fce4ed485 |
# coding: utf-8
"""A tornado based Jupyter notebook server."""
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
from __future__ import absolute_import, print_function
import notebook
import asyncio
import binascii
import datetime
import errno
import gettext
import ... | sserrot/champion_relationships | venv/Lib/site-packages/notebook/notebookapp.py | Python | mit | 90,547 | [
"VisIt"
] | badac7e2156cac9e12f6f4dd13aac59fc49c8128540df7990a4934d9fa9c5c08 |
# -*- coding: utf-8 -*-
#
# tsodyks_depressing.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 Lice... | terhorstd/nest-simulator | pynest/examples/tsodyks_depressing.py | Python | gpl-2.0 | 5,700 | [
"NEURON"
] | fe3aeae3948b68a9eb813c8421e1263d78cc360308ec0e251be9707650b7cd7d |
from django import forms
from django.db import transaction
from . import models, tasks
class RegisterForm(forms.Form):
email = forms.EmailField()
#class LoginForm(forms.Form):
# username = forms.EmailField()
# password = forms.PasswordField()
class PayrollForm(forms.Form):
date_begin = forms.DateField... | koebbe/homeworks | visit/forms.py | Python | mit | 11,137 | [
"VisIt"
] | ad9e6a3eac5a839761a6f7e8f744e35d06209ca3645201f337bd833cf62fae5a |
# 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)
import ast
import spack.directives
import spack.error
import spack.package
import spack.repo
import spack.spec
import spa... | LLNL/spack | lib/spack/spack/util/package_hash.py | Python | lgpl-2.1 | 13,692 | [
"VisIt"
] | 0e80b04e1d7dc7ae3a345ffea68d45b5c11eafeef224d9ce5d18b6ef6fe58ecd |
from copy import deepcopy
from typing import Tuple
import GPy
import numpy as np
from emukit.model_wrappers.gpy_model_wrappers import GPyModelWrapper
class FabolasKernel(GPy.kern.Kern):
def __init__(self, input_dim, basis_func, a=1.0, b=1.0, active_dims=None):
super(FabolasKernel, self).__init__(input_... | EmuKit/emukit | emukit/examples/fabolas/fabolas_model.py | Python | apache-2.0 | 7,115 | [
"Gaussian"
] | f46d50c439b5b089b5faf1c0679225ad95f3f1714fb0a404c6b091c65bf074d0 |
"""
Holds information about what the user asked for (which program, version constraints, etc).
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
class Requirements(object):
"""
Holds information about what the user asked for (which p... | pombredanne/zero-install | zeroinstall/injector/requirements.py | Python | lgpl-2.1 | 1,734 | [
"VisIt"
] | b72d265db1390b3b837a47a62ade1a76889c81d48defaaf39ae5095b4c77b4f4 |
#!/usr/bin/env python
import sys
import os
from bioblend import galaxy
admin_email = os.environ.get('GALAXY_DEFAULT_ADMIN_USER', 'admin@galaxy.org')
admin_pass = os.environ.get('GALAXY_DEFAULT_ADMIN_PASSWORD', 'admin')
url = "http://localhost:8080"
skip = True
gi = galaxy.GalaxyInstance(url=url, email=admin_email, pas... | morinlab/tools-morinlab | docker/import_workflows.py | Python | gpl-3.0 | 549 | [
"Galaxy"
] | de2af8277490e456a5c3cf3e40f1eb80d716cdf280842acf2f21690d07cb859e |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/autots/model/auto_seq2seq.py | Python | apache-2.0 | 5,299 | [
"ORCA"
] | 3d54e79baf94fa34306d94f26b1b789f4580829221cf48aad131f84e2aafa3a2 |
# coding: utf-8
from __future__ import division, unicode_literals, print_function
import math
import os
import subprocess
import tempfile
import logging
import numpy as np
from monty.dev import requires
from monty.json import jsanitize
from monty.os import cd
from monty.os.path import which
from scipy.constants impo... | xhqu1981/pymatgen | pymatgen/electronic_structure/boltztrap.py | Python | mit | 96,325 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | d673c034b2b3c609ba55546d711050cedebc1a9e52e5a0f6be2cefd940bab613 |
#!/usr/bin/env python
import os
import re
try:
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext as _build_ext
except ImportError:
from distutils.core import setup, Extension
from distutils.command.build_ext import build_ext as _build_ext
def find_eigen(hint=... | andres-jordan/george | setup.py | Python | mit | 6,039 | [
"Gaussian"
] | 38f5afe6499e5886f0f0e375182156796870dd44868dff148a6d57a3286f97c7 |
import logging
import numpy as np
import os
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdmolops
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
class MoleculeLoadException(Exception):
def __init__(self, *args, **kwargs):
Exception.__init__... | Agent007/deepchem | deepchem/utils/rdkit_util.py | Python | mit | 11,878 | [
"OpenMM",
"RDKit"
] | d2b9de4edd629181b22d593edeeeff56cf611aa86b6e2e307f2107a8919374d3 |
#!/usr/bin/env python
'''
calls peaks using MACS v2
use --config to specify file with matched sample/controls
Any additional --flags will be passed to MACS v2 (macs2 callpeak --flag)
'''
from ConfigParser import ConfigParser
import sys
from errno import ENOENT, EACCES
from logging import WARN, ERROR
from os import acc... | benjschiller/seriesoftubes | scripts/call_peaks.py | Python | artistic-2.0 | 7,129 | [
"pysam"
] | cb8f964aa9cbf2bdc3715d6f18965f6acd66922a8c596ed2aeff988795d744b4 |
#Copyright (C) 2013 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the h... | cdcapano/pycbc | pycbc/strain/strain.py | Python | gpl-3.0 | 81,818 | [
"Gaussian"
] | dad0a3cb5ddd98ee23e2d11b0f0f21ab8827127ea1f878cf294c0a1278927f4b |
#!/usr/bin/python
'''
The MIT License (MIT)
Copyright (c) 2016 SLU Global Bioinformatics Centre, SLU
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 ... | fikipollo/iRODS-in-Galaxy | irods_push/iRODSManager.py | Python | mit | 12,901 | [
"Galaxy"
] | 039179487faeb61e2116789417459b480c7aa64c78c2f09bb1e3d9a5aacce48a |
import logging
from django.db.models import get_model
from django.core.exceptions import FieldError
from django.db.models import get_models, get_app
from lis.base.model.models import BaseLabListModel, BaseLabListUuidModel
from edc.subject.visit_tracking.classes import VisitModelHelper
from edc.subject.lab_tracker.model... | botswana-harvard/edc-dispatch | edc_dispatch/classes/dispatch_controller.py | Python | gpl-2.0 | 17,125 | [
"VisIt"
] | beaa44aff0f34d2f24dc3725be03d426f44afdd243912761f7f701488e46207b |
#!/usr/bin/env python
# ----------------------------------------------------------------------------------------
# Created by: Lee Bergstrand
# Description: A simple program that takes a FASTA file protein list and makes a csv of fake BLAST results.
#
# Requirements: - This script requires the Biopython module: http:... | LeeBergstrand/BackBLAST_Reciprocal_BLAST | Visualization/CreateBlankResults.py | Python | mit | 3,174 | [
"BLAST",
"Biopython"
] | def407f24c37eaee1da3c2d6d45f612f9d9ebbb3279ffeaaf77683faeaf568f5 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
# NACCESS interface adapted from Bio/PDB/DSSP.py
from __future__ import print_function
i... | ajing/SIFTS.py | PDBInfo/NACCESS.py | Python | mit | 7,026 | [
"Biopython"
] | 680dedd77d064cb289df5677cb4c31a9537fc3e90ae380c5dc67c2aa89261011 |
#!/usr/bin/env python
from __future__ import print_function
import pysam
import argparse
import sys
import re
chroms = {'1':1, '2':2, '3':3, '4':4, '5':5, '6':6, '7':7,
'8':8, '9':9, '10':10, '11':11, '12':12, '13':13,
'14':14, '15':15, '16':16, '17':17, '18':18, '19':19,
'20':20, '2... | DonFreed/tigger-sv | Scripts/validate_svs.py | Python | mit | 8,645 | [
"pysam"
] | da543ef4c3247c5bd02552846cc22a88ee8679db9042165e93c41911869a7428 |
import sys
sys.path.insert(1, "../../../")
import h2o
def distribution_behaviorGBM(ip,port):
#Log.info("==============================")
#Log.info("Default Behavior - Gaussian")
#Log.info("==============================")
eco = h2o.import_file(path=h2o.locate("smalldata/gbm_test/ecology_model.csv"))
#... | PawarPawan/h2o-v3 | h2o-py/tests/testdir_algos/gbm/pyunit_loss_behaviorGBM.py | Python | apache-2.0 | 2,965 | [
"Gaussian"
] | 2896132480ef7f9700768c1f71825f5f995acbf8a0c714b3dca43c4147606298 |
#!/usr/bin/env python
# $Id$
# -*- coding: utf-8
'''
test libcint
'''
__author__ = "Qiming Sun <osirpt.sun@gmail.com>"
import sys
import os
import ctypes
import numpy
_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../../build')))
PTR_LIGHT_SPEED = 0
PTR_COMMON_ORIG =... | sunqm/libcint | testsuite/test_3c2e.py | Python | bsd-2-clause | 9,977 | [
"PySCF"
] | e41304baeee1e4938bfcd1e702231797b853ef0cb911909be07dd85cccfe8be4 |
import cv2
import numpy as np
import sys
from collections import OrderedDict
import matplotlib.pyplot as plt
from gaussian_pyramid import *
def laplacian(img, levels = 4,save = False):
gau_pyr = gaussian(img,levels)
lap_pyr = [gau_pyr[levels-1]]
for i in range(levels-1, 0, -1):
G1 = cv2.pyrUp(gau... | rohithredd94/Computer-Vision-using-OpenCV | Gaussian-Laplacian-Pyramids/laplacian_pyramid.py | Python | mit | 1,303 | [
"Gaussian"
] | 05a127f26fdee19a452af16b00b2b168ae68d9c5e08b820256645e0aeb39f12f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | Forage/Gramps | gramps/plugins/docgen/svgdrawdoc.py | Python | gpl-2.0 | 11,381 | [
"Brian"
] | fcda8c76174cb1423915fc4dd4f1b911df8effd726f492aaa3a64d2d2d9c0dda |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.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 Foundation, either version 3 of the License, or
# (at your option) an... | grimmjow8/ansible | lib/ansible/playbook/conditional.py | Python | gpl-3.0 | 10,147 | [
"VisIt"
] | 36ec53bbdecfc65d089e64c8076a6f051e5bfaeed027ef635b2baa8fa0bbeb32 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
dump2data.py
Extract dynamical degrees of freedom from a lammps DUMP file (from the stdin)
and construct a new DATA file (to the stdout).
A reference DATA file is needed (argument).
basic usage
./dump2data.py orig_file.data < dump.lammpstrj > new_file.data
(Thi... | SGenheden/lammps | tools/moltemplate/src/dump2data.py | Python | gpl-2.0 | 60,735 | [
"LAMMPS"
] | feaebb6f66eb2799cc22eec7df1197512629ea6f99679f467a4499e84c14946c |
# -*- coding: ISO-8859-15 -*-
# =============================================================================
# Copyright (c) 2004, 2006 Sean C. Gillies
# Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#
# Authors :
# Dominic Lowe <d.lowe@rl.ac.uk>
#
# Contact email: d.lowe@rl.ac.uk
# =======================... | wonder-sk/QGIS | python/ext-libs/owslib/coverage/wcs110.py | Python | gpl-2.0 | 18,251 | [
"NetCDF"
] | c76974a3fa6a2aaf216d6d4d7098d44d581544cfe377249d60ed4d4cf2b5775f |
#!/usr/bin/env python
"""
Install.py tool to download, compile, and setup the kim-api library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, os, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers... | jeremiahyan/lammps | lib/kim/Install.py | Python | gpl-2.0 | 7,038 | [
"LAMMPS",
"OpenKIM"
] | a262b6bf24a024ea30f96ae5287fe58d31d61eaf77d999a00852de6793b8a2a5 |
import datetime
import errno
import json
from sqlalchemy import orm
from DIRAC.DataManagementSystem.Client.FTS3Job import FTS3Job
from DIRAC.DataManagementSystem.private import FTS3Utilities
from DIRAC.DataManagementSystem.Utilities.DMSHelpers import DMSHelpers
from DIRAC.DataManagementSystem.Client.DataManager impor... | andresailer/DIRAC | DataManagementSystem/Client/FTS3Operation.py | Python | gpl-3.0 | 18,730 | [
"DIRAC"
] | 1c40068942c7d6e877e0b1dfc35048c089fd18ab1e590618d47a4af46b53add8 |
#!/usr/bin/env python
# This example shows how to manually construct unstructured grids
# using Python. Unstructured grids require explicit point and cell
# representations, so every point and cell must be created, and then
# added to the vtkUnstructuredGrid instance.
import vtk
# Create several unstructur... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/DataManipulation/Python/BuildUGrid.py | Python | bsd-3-clause | 14,316 | [
"VTK"
] | 5a21e71c8ce16a2b15b1150d2adeae50bf687e24779cbcdc68fa7721be960709 |
# cmdutil.py - help for command processing in mercurial
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from node import hex, nullid, nullrev, short
from i18n import _
import ... | vmg/hg-stable | mercurial/cmdutil.py | Python | gpl-2.0 | 77,707 | [
"VisIt"
] | 358d3e46f8ce5937692d87ee68f4026f64127adb1fcdcab72e1602bfbb39d6d3 |
from splinter import Browser
import urllib.request
import codecs
import time
import json
import wget
import uuid
import hashlib
##########
# Bandcamp Bulk Album Downloader
#
# This script will download free albums from BandCamp without user-interaction.
# Note: This script does NOT rip audio from BandCamp pages, it j... | marekceglowski/Bandcamp-Download-Automation | DownloadZips.py | Python | mit | 5,222 | [
"VisIt"
] | f889d31be3064d7ca87892a587f8f2addf83496bcad58e720d6c4702ca4b1827 |
from datetime import datetime
from tastypie.resources import ModelResource, ALL, ALL_WITH_RELATIONS
from tastypie import fields
import neuroelectro.models as m
from django.conf.urls import url
from helpful_functions.dict_pop_multiple import dict_pop_multiple
class CustomModelResource(ModelResource):
class Meta:
... | lessc0de/neuroelectro_org | neuroelectro/api.py | Python | gpl-2.0 | 11,819 | [
"NEURON"
] | 248a6a407f96e7e4a3727a974c999393cb3299d8456f03222c13e09f2b99e2d8 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.moltemplate.org
# http://www.chem.ucsb.edu/~sheagroup
# License: MIT License (See LICENSE.md)
# Copyright (c) 2013, Regents of the University of California
# All rights reserved.
"""
ttree.py is a simple program f... | jewettaij/moltemplate | moltemplate/ttree.py | Python | mit | 247,736 | [
"LAMMPS",
"VisIt"
] | ecf6bc37100c363eb7dce37abec03def469d6dabe1456c20647e23b43b3db977 |
import aenum
import doctest
import sys
import unittest
from aenum import Enum, IntEnum, AutoNumberEnum, OrderedEnum, UniqueEnum, unique, skip, extend_enum
from aenum import EnumMeta, NamedTuple, TupleSize, NamedConstant, constant, NoAlias, AutoNumber, Unique, AutoNumber
from collections import OrderedDict
from datetime... | harshita-gupta/Harvard-FRSEM-Catalog-2016-17 | flask/lib/python2.7/site-packages/aenum/test.py | Python | mit | 89,139 | [
"MOE"
] | 207b63690b2e60f1477b093600b3c0cc1b0f9905d80c3a556ea76c408848896e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# 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 Fr... | arunkgupta/gramps | gramps/gen/plug/report/_bibliography.py | Python | gpl-2.0 | 10,009 | [
"Brian"
] | 6f9caafc6059da4e59d61e4963c2b9610c325de181369048c54174f25cb79ac4 |
import spynnaker.pyNN as Frontend
import spynnaker_external_devices_plugin.pyNN as ExternalDevices
import pylab
Frontend.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
# 64x64 4096
# 32x32 1024
nNeurons = 50
run_time = 1000
cell_params_lif = {'cm' : 0.25, # nF
'i_offset' : 0.0,
... | svadams/SpinnIOTest | examples/send_recv_test.py | Python | gpl-3.0 | 2,696 | [
"NEURON"
] | 07d739e32c3b5d4deb7c8d91696e730fa45abe0bb9952c1d59b1c491acb60c1e |
__source__ = 'https://leetcode.com/problems/graph-valid-tree/description/'
# https://github.com/kamyu104/LeetCode/blob/master/Python/graph-valid-tree.py
# Time: O(|V| + |E|)
# Space: O(|V| + |E|)
#
# Description: Leetcode # 261. Graph Valid Tree
#
# Given n nodes labeled from 0 to n - 1 and a list of undirected edges
... | JulyKikuAkita/PythonPrac | cs15211/GraphValidTree.py | Python | apache-2.0 | 8,446 | [
"VisIt"
] | 27647b0f6dd2218d2eb68a412b3b505a61849e9937233dde47fa9634ff6c8a2e |
# coding: utf-8
# #Statistical Inference for Everyone: Technical Supplement
#
#
#
# This document is the technical supplement, for instructors, for [Statistical Inference for Everyone], the introductory statistical inference textbook from the perspective of "probability theory as logic".
#
# <img src="http://web... | bblais/Tech-SIE | Estimating_Mean_and_Deviation/Estimating_Mean_and_Deviation.py | Python | mit | 8,053 | [
"Gaussian"
] | 2bfe7d990d08a15fbc6762c0b9643ac9bb066f81afc5a4c6e236f26d0a164ab0 |
# Copyright (C) 2016 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# noti... | atztogo/phono3py | phono3py/interface/alm.py | Python | bsd-3-clause | 3,172 | [
"phonopy"
] | 05dd71247492cdd5054fb66aeccd65c11b51da9e4e794c7920393f346d3faa23 |
import numpy as np
from msmbuilder.example_datasets import DoubleWell
from msmbuilder.decomposition import tICA, SparseTICA
from msmbuilder.decomposition.speigh import imported_cvxpy
from numpy.testing.decorators import skipif
def build_dataset():
slow = DoubleWell(random_state=0).get()['trajectories']
data =... | dotsdl/msmbuilder | msmbuilder/tests/test_sparsetica.py | Python | lgpl-2.1 | 933 | [
"Gaussian"
] | 7cacf1d2e536dc554cb3c168140d27f8d4ceaf9dedb404f6d65de635c45cd60d |
from octopus.core import initialise
from service import models, workflow
import sys, time
if __name__ == "__main__":
initialise()
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-t", "--type", help="type of identifier to run")
parser.add_argument("-i", "--identifier", help=... | CottageLabs/oacwellcome | service/scripts/processid.py | Python | apache-2.0 | 1,594 | [
"Octopus"
] | 74399047f5faba194a44023db8d2a601a19187e0c1673e18704e24f53049e6d4 |
'''
Some ingredients that did not clean the exact way we wanted,
so they have been manually reduced here.
'''
synonymdict = {
"black pepper": "pepper",
"onions": "onion",
"vanilla extract": "vanilla",
"sea salt": "salt",
"heavy cream": "cream",
"chicken breasts": "chicken",
"chocolate chips... | cvcassady/RecipeBot | synonymdict.py | Python | mit | 18,215 | [
"ESPResSo",
"FLEUR"
] | 72553bb7fdb170b2429d2dc660f8c6e9228f7c15675f80f19b9374e3170deb3a |
"""
Gromacs TOP - BLOCKS boiled-plate code
======================================
Classes
-------
.. autoclass:: System
:members:
.. autoclass:: Molecule
:members:
.. autoclass:: Atom
:members:
.. autoclass:: Param
:members:
.. autoclass:: AtomType
:members:
.. autoclass:: BondType
:membe... | pslacerda/GromacsWrapper | gromacs/fileformats/blocks.py | Python | gpl-3.0 | 19,526 | [
"CHARMM",
"Gromacs"
] | fc68e5d8826b8ad4434ad856d36b31649b16d9cf9be13699c44c995302b27283 |
#!/usr/bin/env python
import sys, os, re
import time
import datetime
import logging
from watchdog.observers.polling import PollingObserver as Observer
from watchdog.events import FileSystemEventHandler
import threading, thread
import h5py
from Bio import SeqIO
from StringIO import StringIO
import MySQLdb
import subproc... | minoTour/minoTour | mT_web/minoTour/minup/minup.v0.6.py | Python | gpl-3.0 | 124,725 | [
"BWA"
] | 2aa7269570e8aadc3a8300ead12f8a82a904c6ca9f5ba9658e93b5d64312589b |
# proxy module
from __future__ import absolute_import
from mayavi.tools.preferences_mirror import *
| enthought/etsproxy | enthought/mayavi/tools/preferences_mirror.py | Python | bsd-3-clause | 100 | [
"Mayavi"
] | 2ca029450b359d64776ebdbb25283b017dc54260963c418b744a44b330e24b17 |
"""
"""
__author__ = 'donal'
__project__ = 'ribcage'
from datetime import datetime
from functools import wraps
from urlparse import urlparse, urljoin
from flask import render_template, redirect, url_for, flash, \
current_app, request, abort, jsonify
from flask.ext.login import login_user, logout_user, login_requi... | carverdo/homer | app/log_auth/views.py | Python | mit | 10,644 | [
"VisIt"
] | 61703213ebcdcd0db15e3a21e2ee316c55d0c17a29e9b1135313ff82b92a1638 |
#!/usr/bin/env python
"""
This script is a python version of TimingAccuracy. We use some numpy functions
to simplify the creation of random coefficients.
"""
from __future__ import absolute_import, division, print_function
import os
import sys
import time
import numpy as np
sys.path.append(os.path.join(os.path.dirnam... | MMesch/SHTOOLS | examples/python/TimingAccuracy/TimingAccuracyDH.py | Python | bsd-3-clause | 2,541 | [
"Gaussian"
] | cce379922ae27a0635d9facda579832fbd49f9a239ebd339fa454d23c8618527 |
# -*- coding: UTF-8 -*-
#This file is part of pyAlienFX.
#
# pyAlienFX 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.
#
#... | notnola/pyalienfx | AlienFX/AlienFXProperties.py | Python | gpl-3.0 | 2,606 | [
"VisIt"
] | 6f6c1328f749deb18aa1a848b7cf77f81d14833a932dd3b6d416f9231ccdda8c |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" periodic table data... | jandom/rdkit | rdkit/Chem/PeriodicTable.py | Python | bsd-3-clause | 5,870 | [
"RDKit"
] | bc49889605d07c9ce2e7619f1c804397752b66e253acd48e986e20b61069a991 |
from ..bpch2netCDF import *
import logging
import pytest
import os
#import urllib.parse, urllib.error
# temporality restore urllib2 as urllib not installed
try:
import urllib2
from urllib import urlopen
# except ModuleNotFoundError:
except ImportError:
import urllib.request
import urllib.error
impor... | tsherwen/AC_tools | AC_tools/Tests/test_bpch2netCDF.py | Python | mit | 2,505 | [
"NetCDF"
] | d43ccddb5b7b789bcac9cc1e4a63e08a93abaa43bd3b67102c6dee0c52ff6812 |
#!/usr/bin/env python3
"""
Purpose:
Download ECWMF ERA5 data fixed/monthly via Copernicus CDS (Copernicus Climate Data Store)
Contact: copernicus-support@ecmwf.int; ERA5 hourly data on single levels from 2000 to present
Usage:
python3 download_era5_from_cds.py arg1 arg2 arg3 arg4
e.g.
case 1:... | OzFlux/PyFluxPro | external/get_era5_from_cds.py | Python | gpl-3.0 | 5,666 | [
"NetCDF"
] | 9a3d27955ac6f99740e6ea7fc1f36a27fbc26daea6af5da6542f5e1111f3de72 |
#!/usr/bin/env python
import cgi
import json
import sqlite3
import random
#
# recreate SQLite database from JSON file
#
def recreateDatabase():
allRecipes = []
with open("../recipe-parser/recipes.json") as jsonFile:
for line in jsonFile:
allRecipes.append(json.loads(line))
try:
# open database and get curso... | kbrohkahn/kevinbrohkahn.com | projects/view-recipes.py | Python | apache-2.0 | 42,428 | [
"MOOSE"
] | 6b2a8aa7e34e2041cfa1fff43bbb5f515abba192e6c5366081189e0eb7248b83 |
#!/usr/bin/env python
import json
import logging
import os
import string
import subprocess
import sys
import time
import uuid
from random import choice
from twisted.internet import reactor, defer
from twisted.internet.task import deferLater
from twisted.internet.defer import CancelledError
from twisted.python import... | johnkit/vtk-dev | Web/Python/vtk/web/launcher.py | Python | bsd-3-clause | 23,746 | [
"ParaView",
"VTK"
] | cd2df33856f74d98db8be3ecfbe593350f35e973c20a5f2afb37c1503f738fbf |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# .. _poisson-topology-example:
#
# .. py:currentmodule:: dolfin_adjoint
#
# Topology optimisation of heat conduction problems governed by the Poisson equation
# ==================================================================================
#
# .. sectionauthor:: Patri... | ellipsis14/dolfin-adjoint | examples/poisson-topology/poisson-topology-optizelle.py | Python | lgpl-3.0 | 12,364 | [
"ParaView",
"VTK"
] | c4fe64cf1933912f1a01b614cf02d7a0c439bc8fb13cf8a6e8db171b6e5cc961 |
from __future__ import print_function
from contextlib import contextmanager
from distutils.util import convert_path
import os
from shutil import copyfile
import sys
import textwrap
from setuptools import setup, Command
from setuptools.command.develop import develop as develop_cmd
from setuptools.command.build_py impo... | duncanwp/iris | setup.py | Python | lgpl-3.0 | 8,908 | [
"NetCDF"
] | 2a38123649d75388958dbb7f8d47cb57025536f084b0e6252e8da1c6a5d2adc4 |
tests=[
("python","Node.py",{}),
("python","Filter.py",{}),
("python","Output.py",{}),
("python","Supply.py",{}),
("python","Transform.py",{}),
("python","test_list.py",{'dir':'NodeLib'}),
]
longTests=[
]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRun... | adalke/rdkit | rdkit/VLib/test_list.py | Python | bsd-3-clause | 383 | [
"RDKit"
] | 3d3c0ffe820cef51782619dd44af52dcc1f381cd02fd66245ca45430dc5791fd |
#!/usr/bin/env py27
from ecmwfapi import ECMWFDataServer
import numpy as np
import datetime as dt
#import calendar
server = ECMWFDataServer()
dir = "/automount/agh/Projects/skiefer/"
#date_first_start = dt.date(1958, 1, 1)
#date_first_end = dt.date(1958, 1, 31)
#date_last_end = dt.date(1978, 12, 1)
#date_last_end ... | sebaki/clim-jet-stream | 01-code/01-ecmwf-py/a-get-era-40-daily-by-year.py | Python | mit | 1,233 | [
"NetCDF"
] | bd01c6549db4ca481384c3224cb3d194f09308bce81796df83856a9f0d4029c1 |
"""
Test the Studio help links.
"""
from nose.plugins.attrib import attr
from unittest import skip
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest, ContainerBase
from common.test.acceptance.pages.studio.index import... | pabloborrego93/edx-platform | common/test/acceptance/tests/studio/test_studio_help.py | Python | agpl-3.0 | 49,986 | [
"VisIt"
] | fa74c3f05a5172d58cc633a982631c02d1bf0b07ae4224b8c4fbc6d1cca240a8 |
# -*- coding: utf-8 -*-
#
# Instant Press. Instant sites. CMS developed in Web2py Framework
# Site: http://www.instant2press.com
#
# Copyright (c) 2010 Mulone, Pablo Martín
#
# License Code: GPL, General Public License v. 2.0
# License Content: Creative Commons Attribution 3.0
#
# Also visit: www.web2py.com
# ... | danisuke0781/instant-press | modules/widgets.py | Python | gpl-2.0 | 28,658 | [
"VisIt"
] | fdd5948ab31ad15789e0f14648310c90a0c3b27f1de1295e18cd8005beec354f |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/presentations/lib/__init__.py | Python | gpl-2.0 | 2,297 | [
"Brian"
] | 351653889b5b9091edf3d680abd8a61b406a47566dec3fc1466cc81d7d69a8cf |
import cmath
from math import pi, ceil
import numpy as np
from numpy import sin, cos
from scipy.interpolate import interp1d
"""
References:
[Majkrzak2003] C. F. Majkrzak, N. F. Berk: Physica B 336 (2003) 27-38
Phase sensitive reflectometry and the unambiguous determination
of scattering leng... | reflectometry/direfl | direfl/api/sld_profile.py | Python | mit | 8,500 | [
"Gaussian"
] | 9707211d2f3147923ffd731b58aed5dc382354093aee285d74c12adc194b1a4a |
#!/usr/bin/env python
"""
Kukkaisvoima a lightweight weblog system.
Copyright (C) 2006-2012 Petteri Klemola
Kukkaisvoima is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License version 3
as published by the Free Software Foundation.
Kukkaisvoima is distrib... | clreinki/GalaxyHarvester | blog.py | Python | agpl-3.0 | 55,578 | [
"Galaxy"
] | 5db1f059d29350f3cc1b8d726a9ce1b572d821fd34937949d3a593c58337b6dc |
"""Classes and functions for computing and manipulating accessible
surface areas (ASA)."""
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
from cogent.maths.geometry import coords_to_symmetry, \
coords_to_crystal
from _contact import cnt_loop
... | sauloal/cnidaria | scripts/venv/lib/python2.7/site-packages/cogent/struct/contact.py | Python | mit | 7,278 | [
"CRYSTAL"
] | 04cfe726ef3659a86df2ef7b5fc7378eb549b4228ad41c2137858ec9873c2a43 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | kashif/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 40,423 | [
"Brian"
] | ecc3fc9e7905cbba278ae3b0a1dfeb0a9f5a2e3a6faf1409c9e0bcfed10df7d6 |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 Lice... | OuterDeepSpace/OuterDeepSpace | generators/osgen2.py | Python | gpl-2.0 | 27,347 | [
"Galaxy"
] | 5363449073219af0a83d710c7ba2c5fbe1cb7045441a9d48f0ee41b06d9b2e4c |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py | Python | gpl-2.0 | 7,872 | [
"MDAnalysis"
] | 336ea9ae3194c0ad97b909a3aa5fd1ba0123c65fed4ee7d3198865339cf9b765 |
# coding: utf-8
from sqlalchemy import Column, Integer, ForeignKey, Float, Boolean, String
from sqlalchemy.orm import mapper, relationship
from sqlalchemy.ext.declarative import declarative_base
import random
import pandas as pd
Base = declarative_base()
wf = [0.0625, 0.125, 0.25, 0.5, 1]
wfi = [1, 0.5, 0.25, 0.125... | sostenibilidad-unam/abm2 | empirical_py/model.py | Python | gpl-3.0 | 30,005 | [
"exciting"
] | 69c4c3ac5c62699b09016d8b7dd980e778432dc7902c14e4c7140844bfc1e5d2 |
import numpy as np
from . import RegionType, KernelType
class Get:
def __init__(self, parent=None):
self.parent = parent
def kernel_type(self):
if self.parent.session_dict['reduction']['type'] == KernelType.box:
return KernelType.box
else:
return KernelType.g... | ornlneutronimaging/iBeatles | src/iBeatles/step2/get.py | Python | mit | 2,502 | [
"Gaussian"
] | 7d8a312b8fe775ab39e13ab3abf2044e040fd3eaeaab8c7afb9a28b57f742cc2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2009 Zuza Software Foundation
#
# This file is part of Pootle.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of t... | lehmannro/pootle | local_apps/pootle_language/models.py | Python | gpl-2.0 | 4,030 | [
"VisIt"
] | 267240b59b1d33150c58468be9e98a2283866123aec6c71403d8782a99bd0299 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | sam-m888/gramps | gramps/plugins/webreport/layout.py | Python | gpl-2.0 | 2,438 | [
"Brian"
] | aee780a1c6ed06af228871896ae7d92586806e4d499c4453faeaccaa06ec0cee |
# -*- coding: utf-8 -*-
from django.shortcuts import render, redirect
from django.core.cache import cache
from inviMarket.models import Website, Offer, Request
def index(request):
"""
Display the main page.
**Context**
``popular``
An object array containing the five most popular sites.
``... | moiseshiraldo/inviMarket | inviMarket/views/index.py | Python | agpl-3.0 | 2,077 | [
"VisIt"
] | b4476090cea96f48081332c7f570f6b64c11071f1d9e3bb50df84472d6a50f20 |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# ---------------------------... | adamrp/qiita | setup.py | Python | bsd-3-clause | 4,844 | [
"scikit-bio"
] | 03e628a3bc0ec9d304299919fafc2609b996b53e284dd3b1280346dda962b083 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
ettree.py
ettree.py is an extension of the generic ttree.py pr... | quang-ha/lammps | tools/moltemplate/moltemplate/ettree.py | Python | gpl-2.0 | 23,693 | [
"ESPResSo"
] | b985d99678adc99c7a51baa8dad9fda5438a45df0ff6a2c651357e85e6603c61 |
# -*- coding: utf-8 -*-
"""
pysteps.utils.cleansing
=======================
Data cleansing routines for pysteps.
.. autosummary::
:toctree: ../generated/
decluster
detect_outliers
"""
import warnings
import numpy as np
import scipy.spatial
def decluster(coord, input_array, scale, mi... | pySTEPS/pysteps | pysteps/utils/cleansing.py | Python | bsd-3-clause | 8,792 | [
"Gaussian"
] | 2c5aff585b02a87a39a01fb1c9296eaacfcaf61c1ca101da655fd7e118993adc |
# Copyright (C) 2016
# Jakub Krajnika (jkrajniak at gmail.com)
# Copyright (C) 2012,2013,2015
# 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 soft... | espressopp/espressopp | src/FixedPairList.py | Python | gpl-3.0 | 4,055 | [
"ESPResSo"
] | 36701bdadbc709db904dc9cb4365e9090fedb91f268d36937ffaf309cd6fddf9 |
# Copyright (c) 2017, Frappe Technologies Pvt. Ltd. and Contributors
# See license.txt
import unittest
import frappe
from frappe.utils import flt, nowdate
import erpnext
from erpnext.hr.doctype.employee.test_employee import make_employee
from erpnext.hr.doctype.employee_advance.employee_advance import (
EmployeeAdv... | almeidapaulopt/erpnext | erpnext/hr/doctype/employee_advance/test_employee_advance.py | Python | gpl-3.0 | 7,504 | [
"VisIt"
] | 6062997e73872a62bd6e41401ce2b89414c2818b08b19c430202f59345677a27 |
# -*- coding: utf-8 -*-
import logging
import re
from django.apps import apps
from modularodm import Q
from modularodm.exceptions import ValidationValueError
from website import settings
from website.project.metadata.schemas import OSF_META_SCHEMAS
from website.util import sanitize
logger = logging.getLogger(__name... | cwisecarver/osf.io | website/project/model.py | Python | apache-2.0 | 4,224 | [
"VisIt"
] | 2947c1a8543f28d13ac0e6962539d3f0bdfa74bf4f526987db73486fa8bee87e |
import logging
import numpy as np
# https://vtk.org/doc/nightly/html/vtkCellType_8h_source.html
vtk_to_meshio_type = {
0: "empty",
1: "vertex",
# 2: 'poly_vertex',
3: "line",
# 4: 'poly_line',
5: "triangle",
# 6: 'triangle_strip',
7: "polygon",
# 8: 'pixel',
9: "quad",
10: ... | nschloe/meshio | tests/legacy_writer.py | Python | mit | 6,820 | [
"VTK"
] | 1f5cf419d5de97ce78cfb24b7c1c06775f031fdd4cace0bbb5b89cf97ae5af09 |
#! /usr/bin/env python
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
#
# This file is part of ChemLab.
#
# ChemLab 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... | cgchemlab/chemlab | tools/mix_table.py | Python | gpl-3.0 | 4,432 | [
"Gromacs"
] | 17543c21200e4fed5a94b7282ad06c6e6775d86c2aebbb913d775d641479680c |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | mafiya69/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 174,006 | [
"Gaussian"
] | 8426ff6ef7301646ce2fdb3cc8fc447db1185c5002b7b74065dba0376998dbca |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# ... | dictoon/blenderseed | translators/nodetree.py | Python | mit | 7,534 | [
"VisIt"
] | c9d98871289cadd6e346f0daa00bb8a22322bc57b34de1139d6ebe5f9993f817 |
from module_mixins import simpleVTKClassModuleBase
import vtktud
class imageExtentUnionizer(simpleVTKClassModuleBase):
"""This is the minimum you need to wrap a single VTK object. This
__doc__ string will be replaced by the __doc__ string of the encapsulated
VTK object, i.e. vtkStripper in this case.
... | nagyistoce/devide | modules/user/imageExtentUnionizer.py | Python | bsd-3-clause | 836 | [
"VTK"
] | d4432ef0ed68376f0d1f19ace42d0d7157c93d77152957719c2b6c095a501cba |
DISTRO_IDS = ['2x', '4mlinux', '64studio', 'absolute', 'abuledu', 'adamantix',
'adios', 'admelix', 'agilia', 'aleader', 'alinex', 'alinux',
'alixe', 'alpine', 'alt', 'amaroklive', 'amber', 'androidx86',
'ankur', 'annvix', 'annyung', 'anonymos', 'antemium', 'antergos',
... | m4tx/linux-distro-timeline | data_collectors/distro_ids.py | Python | gpl-3.0 | 10,731 | [
"Amber",
"Firefly"
] | b12c2e37f00b83738455f024c6f057a174bbdebbdc8e75884695a2d91da7f738 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__version__ = "1.0.0"
__maintainer__ ... | dilawar/moose-core | python/moose/plot_utils.py | Python | gpl-3.0 | 9,866 | [
"MOOSE"
] | 5aaf21e3b2e460f785da924ca43a7f3cd4ff275481ec94faae743b892368cd8c |
import struct
import os
import unittest
import subprocess
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import numpy
import re
import collections
#
# DEETO
#
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer... | mnarizzano/DEETO | slicer-wrapper/DEETO/DEETO.py | Python | gpl-3.0 | 31,584 | [
"VTK"
] | 468e41481ccc5b57b945c2bdadf61d65f7d4344f8a7b586b2ecba0c1e50aa63a |
# -*- coding: utf-8 -*-
import os
#-- Method only accessible when importing cc.data.
# Should not be called otherwise. Method is here to avoid unnecessary globals
def __readPaths():
'''
Read the relevant paths from the usr/Path.dat file.
Default values typically return an expected location for mo... | IvS-KULeuven/ComboCode | cc/path/__init__.py | Python | gpl-3.0 | 2,249 | [
"MOPAC"
] | 9cc522b4d786375d2eaaa19a6ea6f50d178c996e687f11837a8a0d377bd5e739 |
from collections import defaultdict
from datetime import datetime, timedelta
import logging
from random import getrandbits
from google.appengine.ext import ndb, blobstore
from google.appengine.api.memcache import Client
from google.appengine.api.images import Image, JPEG, get_serving_url, delete_serving_url
import cl... | alecdotico/blablastar | models.py | Python | mit | 6,751 | [
"Galaxy"
] | df2c5d9c6cd76d079792b75e63c9ec4672f18b844bb62b32e3f2a7eba7fac90a |
#
# @file TestUnit.py
# @brief Unit unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
# src/sbm... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestUnit.py | Python | bsd-3-clause | 8,334 | [
"VisIt"
] | 3be33ed1c909f88149f38c9751e86ee6f3f6c98e56d670c76efd8e1497231a17 |
#!/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
# ---------------------------------------------------------------------------##
#
# Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
# Copyright (C) 2003 Mt. Hood Playing Card Co.
# Copyright (C) 2005-2009 Skomoroh
#
# This program is free so... | jimsize/PySolFC | pysollib/help.py | Python | gpl-3.0 | 5,284 | [
"VisIt"
] | bdc7a2bc6400b85ff131d651bdd791e7da0816d8c41fdc81c31bf969f8a40610 |
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#
# This file is part of the E-Cell System
#
# Copyright (C) 1996-2016 Keio University
# Copyright (C) 2008-2016 RIKEN
# Copyright (C) 2005-2009 The Molecular Sciences Institute
#
#:::::::::::::::::::::::::::::::::::::::... | ecell/ecell3 | ecell/frontend/model-editor/ecell/ui/model_editor/ModelStore.py | Python | lgpl-3.0 | 30,894 | [
"Avogadro"
] | 161320dbfbcefd0b9801d4dc6428cb4c227734a4f66f12097988a602fac337df |
# ----------------------------------------------------------------------------
# Copyright 2015-2016 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apa... | Jokeren/neon | tests/test_gradient_bias.py | Python | apache-2.0 | 2,875 | [
"Gaussian"
] | 4875bf0f2779ce7ffd8f5ce9eb50657a9260394b743dd302694d512fce9c8df7 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/mediaplayercurrent.py | Python | gpl-2.0 | 6,147 | [
"VisIt"
] | 198ea5ff1182149b5f0ac573c6827631bcc33eac8b13d4380768b85aeb9f3b52 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/region/tools.py | Python | agpl-3.0 | 11,851 | [
"Galaxy"
] | 369f7cc75441bf9aad5c3b61c17b826ab3a27046ef810a569da7aa95fa0f6977 |
import os
from ddapp import lcmUtils
import ddapp.objectmodel as om
import ddapp.applogic as app
from ddapp import transformUtils
from ddapp.debugVis import DebugData
from ddapp import ioUtils
from ddapp import filterUtils
from ddapp.shallowCopy import shallowCopy
from ddapp import vtkAll as vtk
from ddapp import visu... | rdeits/director | src/python/ddapp/drakevisualizer.py | Python | bsd-3-clause | 14,621 | [
"VTK"
] | fbf0335bde75a1ec02075bed3bcb9c323efed43ca08de3491db8a3c1db444e3b |
"""
Tests for the tkParameterized classes.
"""
## CB: add test for change of po
import __main__
import unittest
from Tkinter import Frame,Toplevel
import param
import paramtk as tk
from topo.base.simulation import Simulation
from topo.base.patterngenerator import PatternGenerator
from topo.base.sheet import Sheet... | Tasignotas/topographica_mirror | topo/tests/unit/testparameterizedobject_tk.py | Python | bsd-3-clause | 12,722 | [
"Gaussian"
] | 043e53dd52f75b24a567b194bb0e33b8e3aab55d8fc2d1320ff7e069800db3d2 |
import numpy as np
class Reduction(object):
"""Callable modal reduction object.
Example usage:
xreduction = Reduction(X), X shape [n_features, n_samples], make sure X is
zero-mean
xmean, ux, at, energy_content = xreduction.PCA(n_components=3)
"""
def __init__(self, X):
self._X = X
... | APC524/tsap | tsap/reduction.py | Python | gpl-3.0 | 5,120 | [
"Gaussian"
] | 482a400c5783517920baf3c132c6deaa3091f58c3be967d6c2f34b14c047de37 |
import os
import re
import external.cclib as cclib
import logging
from subprocess import Popen
from rmgpy.molecule import Molecule
from qmdata import CCLibData
from molecule import QMMolecule
class Mopac:
"""
A base class for all QM calculations that use MOPAC.
Classes such as :class:`MopacMol` will ... | comocheng/RMG-Py | rmgpy/qm/mopac.py | Python | mit | 13,046 | [
"MOPAC",
"cclib"
] | 45143606130cc719f007bcc448dc87427f445b4df5d7631b585ff3dbd8d46289 |
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