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#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/extras.py | Python | gpl-2.0 | 1,727 | [
"Psi4"
] | 93238e2dfc0b5a2287eb113838da4b68251ab8bd8dc33623afdd84f053bdc600 |
#!/home/e89/e89/zd242/src/anaconda2/bin/python
# Application for mechanical properties calculation and analysis using VASP
# Zeyu Deng 16.03.2017
import os
import sys
import shutil
import subprocess
import numpy as np
import argparse
import sympy
#import matplotlib.pyplot as plt
#######################################... | dengzeyu/Elastic | elasticity.py | Python | mit | 43,961 | [
"CRYSTAL",
"VASP"
] | 38d897452f1c231b3c9d9736f61eca0ae480e1d63e4f9fde9a238f237d4cbd19 |
"""
================================================
Kernel Density Estimate of Species Distributions
================================================
This shows an example of a neighbors-based query (in particular a kernel
density estimate) on geospatial data, using a Ball Tree built upon the
Haversine distance metric... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/neighbors/plot_species_kde.py | Python | mit | 4,061 | [
"Gaussian"
] | c16471670053c97fbf1141106dfdec50f64a25164a7e165fa7f03ca29c3e8d47 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | davidzchen/tensorflow | tensorflow/python/eager/function_test.py | Python | apache-2.0 | 162,845 | [
"Octopus"
] | 1e9dcfe6b1b3d77d87a2aa8819d166250afa81d65526ecfb0832e96e8a97049d |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/mms/test/test_mms.py | Python | lgpl-2.1 | 4,051 | [
"MOOSE"
] | bb2a5ce7e010b4a3a3a11916eaa503ae96438baecc8d2bb77c6f15d00782f219 |
"""Options manager for :class:`~.Poly` and public API functions. """
from __future__ import print_function, division
__all__ = ["Options"]
from sympy.core import S, Basic, sympify
from sympy.core.compatibility import string_types, with_metaclass
from sympy.polys.polyerrors import GeneratorsError, OptionError, FlagEr... | kaushik94/sympy | sympy/polys/polyoptions.py | Python | bsd-3-clause | 21,330 | [
"Gaussian"
] | 4f73b475c7c8f4201173fdd602f74a30ee481e1e5f1772322f0c7f7d02063579 |
#!/usr/bin/python
#
# 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) 2015-2017 Hans Hoogenboom, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any ... | gospodnetic/appleseed | scripts/oslextractmeta.py | Python | mit | 16,387 | [
"VisIt"
] | 4ee4216292c5248e3a4ee927c288f613a5f901999cdaff386bf4eaa19454b809 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# 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 Softwa... | bhdouglass/remindor-common | remindor_common/constants.py | Python | gpl-3.0 | 1,839 | [
"Brian"
] | 47e2aea5ca5e535d170fb4a7ccc820b8f92ea139f1f7ae99db5920c6f0b8e759 |
## This file is part of Invenio.
## Copyright (C) 2012, 2013 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
... | labordoc/labordoc-next | modules/bibworkflow/lib/bibworkflow_unit_tests.py | Python | gpl-2.0 | 8,048 | [
"Galaxy"
] | 0a1eae0acfb503b09609c700beb378eed03a00a6f74d34c406f22928d9b7cf8d |
#!/usr/bin/env python3
# Copyright 2015 The Kubernetes 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 appl... | GoogleCloudPlatform/testgrid | hack/verify_boilerplate.py | Python | apache-2.0 | 7,786 | [
"VisIt"
] | 6d103b4dceb9855ba38f7e9fac53e637392338b5a28c52c27401ba8993e42c23 |
########################################################################
# $HeadURL $
# File: RemoveFile.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/25 07:44:19
########################################################################
""" :mod: RemoveFile
================
.. module: RemoveFile
... | calancha/DIRAC | DataManagementSystem/Agent/RequestOperations/RemoveFile.py | Python | gpl-3.0 | 6,620 | [
"DIRAC"
] | 7c3096b440b3623f503deaa7ddaa6d677a735790de06ece1493cb37fcb882280 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-annotationdbi/package.py | Python | lgpl-2.1 | 2,017 | [
"Bioconductor"
] | fea74a5a838d0a0a4d72e73ab775b77c4682a640daf70a59c91ed1407c4b848b |
#!/usr/bin/env python
from __future__ import print_function
import vtk
import numpy
from icqsol.bem.icqBaseLaplaceSolver import BaseLaplaceSolver
class PoissonSolver(BaseLaplaceSolver):
def __init__(self, pdata, max_edge_length, order=5):
"""
Constructor
@param pdata instance of vtkPolyD... | gregvonkuster/icqsol | bem/icqPoissonSolver.py | Python | mit | 3,963 | [
"VTK"
] | f6441f4cd8f2beb9a2a78ddd6503a77e0611224d4d41aa66c9013d0b4ff69063 |
# -*- coding: utf-8 -*-
"""
.. _disc-stats:
=====================
Statistical inference
=====================
Here we will briefly cover multiple concepts of inferential statistics in an
introductory manner, and demonstrate how to use some MNE statistical functions.
"""
# Authors: Eric Larson <larson.eric.d@gmail.co... | rkmaddox/mne-python | tutorials/stats-sensor-space/10_background_stats.py | Python | bsd-3-clause | 29,158 | [
"Gaussian"
] | d42014faffd82480cd92afd087024e5b41cfc97cc27b97455bfcec5d4a22c604 |
#!/usr/bin/env python3
# Copyright (C) 2012-2015 ASTRON (Netherlands Institute for Radio Astronomy)
# P.O. Box 2, 7990 AA Dwingeloo, The Netherlands
#
# This file is part of the LOFAR software suite.
# The LOFAR software suite is free software: you can redistribute it and/or
# modify it under the terms of the GNU G... | kernsuite-debian/lofar | LTA/ltastorageoverview/lib/scraper.py | Python | gpl-3.0 | 26,376 | [
"VisIt"
] | af73c1c6284c3a809f406f3de8a7cc4f230256a6482cdbde00887606572c3162 |
#!/usr/bin/env python
# Dan Blankenberg
import sys
import bx.align.maf
from galaxy.tools.util import maf_utilities
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
output_name = sys.argv.pop(1)
input_name = sys.argv.pop(1)
species = sys.argv.pop(1)
out = open(output_name, 'w')
count = 0
... | icaoberg/cellorganizer-galaxy-tools | datatypes/converters/maf_to_interval_converter.py | Python | gpl-3.0 | 1,052 | [
"Galaxy"
] | c85a2c3830f673ed20393d14224dd6c7155ece636a958d5835d1f5c847cfd0d7 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | theochem/horton | horton/io/vasp.py | Python | gpl-3.0 | 7,128 | [
"VASP"
] | edabaf2510db29cabae42160455e101f5f011912c8439ff52f63c52a4bc6eea3 |
import networkx as nx
import random
import time
import sys
import tqdm
import os
__author__ = "Giulio Rossetti"
__contact__ = "giulio.rossetti@isti.cnr.it"
__license__ = "BSD 2 Clause"
def timeit(method):
"""
Decorator: Compute the execution time of a function
:param method: the function
:return: the... | GiulioRossetti/DEMON | demon/alg/Demon.py | Python | bsd-2-clause | 8,828 | [
"VisIt"
] | 1c10aa7d1f03adf44184e6d3ebcf29fbb7ee6d3feb42805f42df11a0aec7ba24 |
#!/usr/bin/env python
#JSON {"lot": "RHF/cc-pvtz",
#JSON "scf": "PlainSCFSolver",
#JSON "linalg": "DenseLinalgFactory",
#JSON "difficulty": 1,
#JSON "description": "Basic RHF example with dense matrices, includes export of Hamiltonian"}
from horton import *
import numpy as np
# Hartree-Fock calculation
# -------... | crisely09/horton | data/examples/hf_dft/rhf_n2_dense.py | Python | gpl-3.0 | 3,100 | [
"Gaussian"
] | e04976c3a52f76893cebfaf4a12742f2ed364a0fba932753001ac8f21f20bc5a |
#!/usr/bin/env python
########################################################################
# File : dirac-dms-get-file
# Author : Stuart Paterson
########################################################################
"""
Retrieve a single file or list of files from Grid storage to the current directory.
Exam... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_dms_get_file.py | Python | gpl-3.0 | 1,368 | [
"DIRAC"
] | 97320b323ac47e1796aea79e9d1b6fefecbd55b1f1ef4d2c4c63d9cd5931ff91 |
# -*- coding: utf-8 -*
"""
This file contains the Qudi logic class for optimizing scanner position.
Qudi 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 la... | childresslab/MicrocavityExp1 | logic/optimizer_logic.py | Python | gpl-3.0 | 27,933 | [
"Gaussian"
] | c3ba11e51dceff89a30a18b16a3fdc0a0d38d0c95ed7c53a8e75ec205ffc8f70 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | racemidev/WMI_cmd | pysamba/rpc/oxidresolver.py | Python | gpl-2.0 | 1,376 | [
"VisIt"
] | adedf0b048491e6f203ad2b56a393eb73fe7d3464a664c82d0075feeb678b158 |
# -*- coding: utf-8 -*-
"""
Project: Parallel.Archive
Date: 3/3/17 11:27 AM
Author: Demian D. Gomez
"""
from os.path import getmtime
from pprint import pprint
import traceback
import warnings
import sys
import os
from time import time
from io import BytesIO
import base64
import logging
from logging import INFO, ERROR,... | demiangomez/Parallel.GAMIT | classes/pyETM.py | Python | gpl-3.0 | 110,316 | [
"Gaussian"
] | b18c67febea5e0fc4e1dedf7b920ab9547e6d22686a8d6ab89822a1d2127af10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# pofix - perform string fixups on incoming .po files.
#
# The purpose of this script is to save translators from having to
# apply various string fixes needed before stable release by hand. It is
# intended to be run on each incoming .po file as the Lord of
# Translation... | asimonov-im/wesnoth | utils/pofix.py | Python | gpl-2.0 | 268,282 | [
"BLAST",
"GULP",
"VisIt"
] | e28ffc1be0337643c90e0216e5b5e5a40c2560119220da35d8faf44cdfc8ceef |
from fabric.api import task
from fabric.api import run, sudo
from fabric.api import cd, settings, prefix
# build parameters
MAKEJOBS = '--jobs=4 ' # specify how many make commands to run simultaneously
SRCDIR = '~/src'
PROJ_VER = '4.7.0'
PROJ_SRC = SRCDIR +'/proj/' + PROJ_VER
PROJ_DIR = '/usr/local/proj/' + PROJ_VER... | netcon-source/OpenClimateGIS | fabfile/tasks_system.py | Python | bsd-3-clause | 7,759 | [
"NetCDF"
] | 49dfc3b35cd780d5c3d448d643043bbadb8a86ec9821668fdf9bce80b6e3adf6 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/exodus_tab/test_ExodusViewer2.py | Python | lgpl-2.1 | 2,007 | [
"MOOSE"
] | 1f887165ae1fde3c5ad9ed0e7a3cc4682273f2a0f27ba34250b13753d801ba98 |
# -*- coding: utf-8 -*-
"""
forms.py
~~~~~~~~
Flask-WTForms
"""
from flask_wtf import FlaskForm
from wtforms import TextField, TextAreaField, SelectField
from wtforms.fields.html5 import EmailField
from wtforms.validators import InputRequired, Email
pitchPlaceholder = 'You have 300 characters to sell you... | boulder-python/boulderpython.org | application/forms.py | Python | mit | 2,150 | [
"exciting"
] | 478114d2a785819800cac6879278c1f4d26e0ec6ff4cd123fac7dd8270836ee6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Factory functions producing ABINIT Works.
Works are packed together in a flow. A flow can be ran using abirun (abipy)
Entry points for client code (high-level interface)
"""
from __future__ import unicode_li... | migueldiascosta/pymatgen | pymatgen/io/abinit/calculations.py | Python | mit | 17,847 | [
"ABINIT",
"pymatgen"
] | 2f17b7d050ec51ad56b3bcdd8a4cc4a174cb73da708ede5e3db21042d3d81423 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This module is also sponsored by E.T.A.I. (www.etai.fr)
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version... | orgito/ansible | lib/ansible/modules/cloud/vmware/vmware_guest.py | Python | gpl-3.0 | 128,055 | [
"VisIt"
] | a9914fefcece181e166ed005c6744bb253cc24b7945d10ada538717c304fe89b |
#!/usr/bin/env python
"""
Do the initial installation and configuration of a DIRAC service based on tornado
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import exit as DIRACexit
from DIRAC import gConfig, gLogger, S_OK
... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_install_tornado_service.py | Python | gpl-3.0 | 3,388 | [
"DIRAC"
] | cb385e1f1516c399b30af94da3eda7798ba54afb0e4ff9e366a0252733e65c88 |
from compose.config.errors import DependencyError
def get_service_name_from_network_mode(network_mode):
return get_source_name_from_network_mode(network_mode, 'service')
def get_container_name_from_network_mode(network_mode):
return get_source_name_from_network_mode(network_mode, 'container')
def get_sour... | thaJeztah/compose | compose/config/sort_services.py | Python | apache-2.0 | 2,487 | [
"VisIt"
] | 68df8b6c7c23a7b39e73e32c0d5e98c33c96e6f4583cde9610e729a1b4f7df70 |
# -*- coding: utf-8 -*-
# creates: ener.png distance.png angle.png
import os
from ase import *
import matplotlib
matplotlib.use('Agg')
import pylab as plt
e_s = [0.01,0.1,0.2,0.3,0.4,0.5]
E = [-463.2160, -462.9633, -462.4891, -462.0551,
-461.5426, -461.1714]
d = [1.1131, 1.1046, 1.0960, 1.0901,
1.0857, 1.0... | freephys/python_ase | doc/exercises/siesta1/answer1.py | Python | gpl-3.0 | 1,215 | [
"ASE"
] | 3b46e723ada2d015e362ad940f5a5d0694c82dbf6dc2d0ef77c577a837950602 |
#
# Yasara.py
# Python_Xcode
#
# Created by Jens on 31/05/2010.
# Copyright (c) 2010 University College Dublin. All rights reserved.
#
class yasara_handler:
def __init__(self,yasaradir='/local/nielsen/bin/yasara/',console=True):
#
# Default on amylase, mac below
#
import os
... | dmnfarrell/peat | Protool/Yasara_handler.py | Python | mit | 2,097 | [
"YASARA"
] | a860cfb07a66715e4ec75019eae6c9c3d29413cfc24129b75998665c3e244576 |
# Copyright (c) 2021, TU Wien, Department of Geodesy and Geoinformation
# All rights reserved.
# 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 notice,... | TUW-GEO/ascat | src/ascat/eumetsat/level2.py | Python | mit | 12,334 | [
"NetCDF"
] | eb4344c8f43ab4b10dacdd7939e9b9484a7fbaf3e628c3c8e9f78263ae41e6dd |
import ast
import re
from collections import defaultdict, namedtuple
from itertools import count
from ..core.ast_helper import get_call_names_as_string
from .right_hand_side_visitor import RHSVisitor
class CallVisitorResults(
namedtuple(
"CallVisitorResults",
("args", "kwargs", "unknown_args", "u... | python-security/pyt | pyt/helper_visitors/call_visitor.py | Python | gpl-2.0 | 2,319 | [
"VisIt"
] | e653b32165b1d1bd5a7e01c2b84d7dbc2b43b15348b94398c871fb8278359d38 |
#!/usr/bin/env python
import argparse
import logging
import sys
from BCBio import GFF
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqFeature import (
FeatureLocation,
SeqFeature
)
from Bio.SeqRecord import SeqRecord
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)
# Patch... | jj-umn/tools-iuc | tools/progressivemauve/xmfa2gff3.py | Python | mit | 6,214 | [
"Biopython"
] | e3791b47ac1c29cce164b127cc2c739a39267ef87b8bbd85430c2237534eccd1 |
"""Excitation lists base classes
"""
from math import sqrt
import numpy as np
import gpaw.mpi as mpi
from gpaw.output import initialize_text_stream
from ase.units import A, m, s, Bohr, _aut, C
class ExcitationList(list):
"""General Excitation List class.
"""
def __init__(self, calculator=None, txt=None... | robwarm/gpaw-symm | gpaw/lrtddft/excitation.py | Python | gpl-3.0 | 4,616 | [
"ASE",
"GPAW",
"TURBOMOLE"
] | fc9094a3addfb8c41994538275fe2b377fd2e04f146b31139278694bc2f6842d |
import sys, os
import vtkCommonCorePython
def vtkLoadPythonTkWidgets(interp):
"""vtkLoadPythonTkWidgets(interp) -- load vtk-tk widget extensions
This is a mess of mixed python and tcl code that searches for the
shared object file that contains the python-vtk-tk widgets. Both
the python path a... | hlzz/dotfiles | graphics/VTK-7.0.0/Wrapping/Python/vtk/tk/vtkLoadPythonTkWidgets.py | Python | bsd-3-clause | 3,047 | [
"VTK"
] | c3ca7eeeb0bbd7326df9accfd4143b3d94012c2b6385f80b1dfc661b7dddaf40 |
#!/usr/bin/env python
# generate peak set complete files, binding region files, and report files!
import sys
import time
import optparse
import general
import numpy
import hyper
import pickle
import pdb
import metrn
import modencode
import os
from scipy import stats
print "Command:", " ".join(sys.argv)
print "Times... | claraya/meTRN | python/mapHybrid.py | Python | mit | 29,002 | [
"BWA",
"Bowtie"
] | cbc81f32465f5d40f63a2723d727e5706246a5790dc3e81291129e564619c849 |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | imsut/commons | src/python/twitter/common/lang/__init__.py | Python | apache-2.0 | 4,283 | [
"Brian"
] | 030dcf2f342c87784c74a0d5e6722fb63a85f1d4197e45b49ad4aac9b961f73a |
# License: BSD 3 clause
import pickle
import itertools
import numpy as np
import pytest
from sklearn.metrics import DistanceMetric
from sklearn.neighbors._ball_tree import (
BallTree,
kernel_norm,
DTYPE,
ITYPE,
NeighborsHeap as NeighborsHeapBT,
simultaneous_sort as simultaneous_sort_bt,
n... | manhhomienbienthuy/scikit-learn | sklearn/neighbors/tests/test_neighbors_tree.py | Python | bsd-3-clause | 9,221 | [
"Gaussian"
] | 22fe40daa1f82d00699cdf02758c84d972e2cac531e7eb42b11397731fbf5248 |
# -*- coding: utf-8 -*-
# Copyright (c) 2017 The Pycroft Authors. See the AUTHORS file.
# This file is part of the Pycroft project and licensed under the terms of
# the Apache License, Version 2.0. See the LICENSE file for details.
import datetime
from io import BytesIO
from os.path import dirname, join
from reportlab... | lukasjuhrich/pycroft | pycroft/helpers/printing/__init__.py | Python | apache-2.0 | 19,274 | [
"VisIt"
] | 2385467d4ae95ad3e69449c3bf78847d358b930e01618e1ac6124ff7c6f647db |
#
# @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/p4util/solvers.py | Python | lgpl-3.0 | 37,711 | [
"Psi4"
] | f766c530342223a1add7ce17ab92c8456a2455a89cb3073ed3a14e1e87fd102a |
import random
import numpy as np
"""
Various useful functions for use within TPG, and for using TPG, like metrics,
etc.
"""
"""
Coin flips, at varying levels of success based on prob.
"""
def flip(prob):
return random.uniform(0.0,1.0) < prob
"""
Returns the teams that this team references, either immediate or
re... | Ryan-Amaral/PyTPG | tpg/utils.py | Python | mit | 7,985 | [
"VisIt"
] | e16d7c8d693c217833ba6fe3b25d982908fec251da4bea88e8d519cda58f2e38 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is used to estimate the cost of various compounds. Costs are taken
from the a CostDB instance, for example a CSV file via CostDBCSV.
For compounds with no cost listed, a Phase Diagram style conv... | migueldiascosta/pymatgen | pymatgen/analysis/cost/cost.py | Python | mit | 6,120 | [
"pymatgen"
] | cab762e80f40a15453f477a47c21794bb3f8bc1b013a1e171463e4757aa93c56 |
# Orca
# Copyright (C) 2016 UrbanSim Inc.
# See full license in LICENSE.
import pandas as pd
import pytest
from .. import orca
from ..utils.testing import assert_frames_equal
def setup_function(func):
orca.clear_all()
def teardown_function(func):
orca.clear_all()
@pytest.fixture
def dfa():
return or... | UDST/orca | orca/tests/test_mergetables.py | Python | bsd-3-clause | 7,756 | [
"ORCA"
] | fef5a125b0150c6a7fae10c63c3a51decc7cac38cf5664a1932ead2a15f8b8f0 |
#!/usr/bin/python2
try:
import gi
gi.require_version('NumCosmo', '1.0')
gi.require_version('NumCosmoMath', '1.0')
except:
pass
import matplotlib as mpl
import matplotlib.pyplot as plot
from scipy.stats import norm
from scipy.stats import beta
import numpy as np
import math
from gi.repository import NumCosmo a... | NumCosmo/NumCosmo.github.io | examples/example_epdf1d.py | Python | apache-2.0 | 4,394 | [
"Gaussian"
] | 3460fc39e6c20bd443a12ffa76a78f0522b5a3bf06f433bc46afd388dd0c73cf |
# Copyright 2007-2012 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | pburdet/hyperspy | hyperspy/tests/model/test_fit_component.py | Python | gpl-3.0 | 4,321 | [
"Gaussian"
] | 4b336d804ff596a05fc727d27456893f76a835ba8ad3d8bb5451171e22014565 |
"""
*******************************************************************
Copyright (c) 2013, 2014 IBM Corp.
All rights reserved. This program and the accompanying materials
are made available under the terms of the Eclipse Public License v1.0
and Eclipse Distribution License v1.0 which accompany this distribut... | eclipse/paho.mqtt.embedded-c | test/MQTTV3112.py | Python | epl-1.0 | 31,004 | [
"FEFF"
] | 52d7262dc11bea958baa6324f5a894b3ac919e0eb1e9de78fb84b0d4d414551d |
#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
"""
test_energy_hf_psi4
~~~~~~~~~~~~~~
Test Psi4 implementations for Hartree-Fock energy jobs.
"""
import sys
import geoprep
from adapters import psi4
from tests.common_testcode import runSu... | mattbernst/polyhartree | tests/test_energy_hf_psi4.py | Python | gpl-3.0 | 812 | [
"Psi4"
] | c476a0d65250b5c0cc9251df5ea0f1dd4bcc917501c74270b4840660e672bd27 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2018, Chris Houseknecht <@chouseknecht>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | haad/ansible | lib/ansible/modules/clustering/k8s/k8s_raw.py | Python | gpl-3.0 | 4,091 | [
"Galaxy"
] | 55feea5ba0ae91264a8afcecd71b6664464af789ef9c9b49a5e7a505a75ad290 |
'''
Extract virulence genes by genus from the VFDB database at http://www.mgc.ac.cn/VFs/Down/CP_VFs.ffn.gz
'''
import sys, re
from argparse import ArgumentParser
# BioPython modules for reading and writing sequences
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.... | ingled/srst2 | database_clustering/VFDBgenus.py | Python | bsd-3-clause | 1,482 | [
"Biopython"
] | 10289bf37af34a0d1314a7775e83b1e14983fdaad7a2e921c01e8c450d287aa8 |
__author__ = 'jiataogu'
import theano
theano.config.exception_verbosity = 'high'
import logging
import copy
import emolga.basic.objectives as objectives
import emolga.basic.optimizers as optimizers
from emolga.layers.recurrent import *
from emolga.layers.ntm_minibatch import Controller, BernoulliController
from emol... | MingyuanXie/CopyNet | emolga/models/ntm_encdec.py | Python | mit | 53,418 | [
"Gaussian"
] | 105b953f7b4a6ceb51e94b764b13870b1f39fe1ddfe2af510c49dfe4bdf6ffd0 |
#!/usr/bin/python
import numpy as np
import matplotlib.pyplot as plt
import scipy.special as spc
'''
To evaluate Change of Kinetic energy due to orthogonalization (Deltat E_kin ) which is Valence-Bond model for Pauli repulsion
see:
[1] eq.4 in http://aip.scitation.org/doi/10.1063/1.3272671
Jaramillo-Bo... | ProkopHapala/SimpleSimulationEngine | cpp/sketches_SDL/Molecular/python/eFF_KineticAndOverlap.py | Python | mit | 4,811 | [
"Gaussian"
] | 9ffd408fb28f5e79fc962178a091be1302d5c0a530df409f04ee3c0ac0bd2c82 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.zenoss.CloudStack | ZenPacks/zenoss/CloudStack/tests/testModel.py | Python | gpl-2.0 | 9,144 | [
"VisIt"
] | 1812b034ff9960918fae8c550e02a958268ce6150bed8ea107dffa6c43421eb4 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Configuration file for chios documentation."""
import os
import sys
from datetime import datetime
try:
import sphinx_rtd_theme
except ImportError:
sphinx_rtd_theme = None
try:
from sphinxcontrib import spelling
except ImportError as e:
print(e)
sp... | kallimachos/chios | doc/conf.py | Python | gpl-3.0 | 1,267 | [
"Brian"
] | 9f67114667d6fc90ee0297e4a55265282a9f1bd6afc89edb459343a27138e261 |
from __future__ import division, print_function
import numpy as np
from .miscellaneous_utilities import BCTParamError
def adjacency_plot_und(A, coor, tube=False):
'''
This function in matlab is a visualization helper which translates an
adjacency matrix and an Nx3 matrix of spatial coordinates, and plots ... | boomsbloom/dtm-fmri | DTM/for_gensim/lib/python2.7/site-packages/bct/utils/visualization.py | Python | mit | 26,277 | [
"Mayavi"
] | 79bf72f66f0405284501b96d8a3f9c1dbdfac0579b4c184c36cba97fb827f693 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright 2017 Romain Boman
#
# 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
#
#... | rboman/progs | sandbox/versions/versions.py | Python | apache-2.0 | 3,657 | [
"VTK"
] | ee5839e9515db0aaac45aebb4aa3ae6717df2ae826d854bae2fb87d3d4a82619 |
tests=[
("python","testCMIM.py",{}),
]
longTests=[]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| rdkit/rdkit-orig | Code/ML/FeatureSelect/Wrap/test_list.py | Python | bsd-3-clause | 221 | [
"RDKit"
] | 97ca7f0c049680b6d73832fa11760ca739ff8cdf2b3198f58df2b0ac305de538 |
#!/usr/bin/env python
import os
from math import *
nopyfoam=False
try:
from PyFoam.Applications.Runner import Runner
from PyFoam.Applications.PlotRunner import PlotRunner
from PyFoam.Applications.CloneCase import CloneCase
except:
nopyfoam = True
from aerofoilmesher import *
# clone wing_template case... | fruitynoodles/pyaeromesh | test_afmesher.py | Python | gpl-3.0 | 3,629 | [
"ParaView"
] | 596bc3a350249c614af8c95079584275718b49c65748bd8a5b080f515cb40125 |
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2021, 2021, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it... | graalvm/mx | mx_cmake.py | Python | gpl-2.0 | 9,358 | [
"VisIt"
] | 93762966800fc1c73a25664c3dbbeb30b457bdeb3710a841caa18968dafa71cc |
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
import DIRAC
__RCSID__ = "$Id$"
class Job(BaseAccountingType):
def __init__(self):
BaseAccountingType.__init__(self)
self.definitionKeyFields = [('User', 'VARCHAR(32)'),
('UserGroup', 'VAR... | arrabito/DIRAC | AccountingSystem/Client/Types/Job.py | Python | gpl-3.0 | 2,637 | [
"DIRAC"
] | 0d565152ee0be7e397da38237a939828b37331f5178cca64fd53e8936346e09c |
# pylint: disable=R0913,R0914,W0201,W0622,C0302,R0902,R0903,W1001,W0612,W0613
"""Useful functions and objects used more or less everywhere."""
from __future__ import print_function
from builtins import zip
from builtins import str
from builtins import range
from builtins import object
__author__ = 'Lorenzo Bolla'
i... | DavidRimel/EMpy | EMpy/utils.py | Python | mit | 39,651 | [
"CRYSTAL"
] | c9987b89a8b23230e605946ea933f694c27e72fb5b1108a679115b2e4b9459b8 |
import sys
import gzip
from glob import glob
from io import BytesIO
from .. import backends, conventions
from .common import ArrayWriter
from ..core.alignment import auto_combine
from ..core.utils import close_on_error, is_remote_uri
from ..core.pycompat import basestring, OrderedDict, range
def _get_default_engine(... | hetland/xray | xray/backends/api.py | Python | apache-2.0 | 14,163 | [
"NetCDF"
] | 5440a0e13b112644c812013d22c83a601833f79ecdf596d875e652743db769ad |
#!/usr/bin/python
# 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) any later version.
#
# Ansible is distributed... | adityacs/ansible | lib/ansible/modules/cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 53,190 | [
"Dalton"
] | f2084f88f7f1308d994e89dacb4f55644db6d57f1cd09dba5250256f815190b4 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2019 Chris Caron <lead2gold@gmail.com>
# All rights reserved.
#
# This code is licensed under the MIT License.
#
# 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 th... | SickGear/SickGear | lib/apprise/plugins/NotifyGitter.py | Python | gpl-3.0 | 13,774 | [
"VisIt"
] | 41f4ff78a19a7266685cc489f1ae85568211a63ee1603e1e62d4ef8f0208bbc4 |
../../../../share/pyshared/orca/orca_platform.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/orca_platform.py | Python | gpl-3.0 | 48 | [
"ORCA"
] | e5ac06c4513d0fc7c85aba880086262adf9994a37795120694b088ba8be0cd06 |
import numpy as np
import cv2
import sys
from self_driving.optical_flow.python import video
from scipy import misc
def color_seg(img_raw, red_thresh=0, green_thresh=0, blue_thresh=0):
img_color_mask = np.copy(img_raw)
red_mask = img_raw[:,:,0] < red_thresh
green_mask = img_raw[:,:,1] < green_thresh
rg... | mengli/MachineLearning | self_driving/lane_detect/udacity_lane_detect.py | Python | apache-2.0 | 4,363 | [
"Gaussian"
] | 6081a5be8f40e7807d1dba5174cad5dedf1f183d9e1e3bd57b020012c98b57ff |
# Copyright 2015 Planet Labs, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy of
# the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | planetlabs/datalake-common | setup.py | Python | apache-2.0 | 1,698 | [
"Brian"
] | c86dcb6cb777c0fca5b14d7af9f058b78ea7732662c04e04847ac20e51fc8805 |
from datetime import timedelta
from random import randint
from jarr.controllers import ArticleController, FeedController
from jarr.controllers.article_clusterizer import Clusterizer
from jarr.controllers.cluster import ClusterController
from jarr.lib.clustering_af.grouper import get_best_match_and_score
from jarr.lib.... | jaesivsm/pyAggr3g470r | tests/controllers/cluster_test.py | Python | agpl-3.0 | 7,816 | [
"Brian"
] | d010c0425362092089c944dcb9638f62e0b8a8e800ca360417d3aa87d2eaf13e |
from ..core import cmutinf, ncmutinf
from .base import (AlphaAngleBaseMetric, ContactBaseMetric, DihedralBaseMetric,
BaseMetric)
import numpy as np
from itertools import product
from multiprocessing import Pool
from contextlib import closing
__all__ = ['AlphaAngleTransferEntropy', 'ContactTransfe... | msmbuilder/mdentropy | mdentropy/metrics/tent.py | Python | mit | 2,499 | [
"MDTraj"
] | 76c0ab305d99c34ccbb8b84a783bcb15c03af2dff5d8f9621738132f5807b582 |
import numpy as np
__all__ = ['Linear', 'Sine', 'Cosine', 'Square', 'Cube', 'Powerlaw',
'Exponential', 'Lorentzian', 'Gaussian', 'LogNormal']
def Linear(x, a, b):
"""First-order polynomial
Inputs:
-------
``x``: independent variable
``a``: slope
``b``: offset
Form... | awacha/sastool | sastool/fitting/fitfunctions/basic.py | Python | bsd-3-clause | 3,673 | [
"Gaussian"
] | e83e09ecf186bcb45879531865cbfde54f80df3aea36214322fbaa7a217041d5 |
#!/usr/bin/env python
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import time
import json
import glob
import logging
import numpy as np
import pandas as pd
from simtk import ... | MobleyLab/SAMPL6 | host_guest/Analysis/Scripts/analyze_yank.py | Python | mit | 26,710 | [
"Gromacs"
] | 3bdc4a58bb1071aa01a551d4d70541806b3948cfb2d2fc3462a29d1638871aea |
#!/usr/bin/env python
from sklearn.mixture import GaussianMixture
from scipy import stats
import numpy as np
import sys
from math import sqrt, log, exp, pi
"""
https://www.kaggle.com/charel/learn-by-example-expectation-maximization
The way to estimate a single gaussian from the dataset is by taking the mean and sta... | qeedquan/misc_utilities | math/probability/mixtures/estimate-gaussian-mixture.py | Python | mit | 1,634 | [
"Gaussian"
] | 2d46f44771a28be9da330a1a173f9fd5b34249cd6dd7125e4415c7512cd08c75 |
## thermo.py
## I implement symbolic computation in thermodynamics to solve examples and problems
##
############################################################################
## Copyleft 2015, Ernest Yeung <ernestyalumni@gmail.com>
## ... | ernestyalumni/Propulsion | thermo.py | Python | gpl-2.0 | 5,854 | [
"Avogadro"
] | 0c1cdce723f121c0ab9c1197ee71112315f632fad5ddf0eb28e113b6d1fd67db |
# $HeadURL: $
''' Synchronizer
Module that updates the RSS database ( ResourceStatusDB ) with the information
in the Resources section. If there are additions in the CS, those are incorporated
to the DB. If there are deletions, entries in RSS tables for those elements are
deleted ( except the Logs table ).
'... | sposs/DIRAC | ResourceStatusSystem/Utilities/Synchronizer.py | Python | gpl-3.0 | 17,289 | [
"DIRAC"
] | 47ee71504fe6a5c9a4f6e14de6ff733cc279a55532b2021eb2c240142863eaee |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | social/questions/tests.py | Python | gpl-3.0 | 3,210 | [
"Brian",
"exciting"
] | 400bdf88ced2f22c685fbd6d331bcfd41c77cbbcd166b5d14161405deb933836 |
import numpy as np
from scipy.interpolate import CubicSpline
from ..numerics.utilities import chol_inv
class VarGP(object):
"""
Variational Gaussian Process Approximation class.
"""
__slots__ = ("model", "fwd_ode", "bwd_ode", "kl0", "likelihood",
"obs_y", "obs_t", "dt", "dim_n", "dim... | vrettasm/VGPA | code/src/variational.py | Python | gpl-3.0 | 12,977 | [
"Gaussian"
] | a66b062030143715bbe5dfa09d012854f9fa69f205f504b8967b84e361721e87 |
#
# 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... | SnappyDataInc/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 59,072 | [
"Gaussian"
] | df8c00d5431945011993ed5ddadc439b2aea71ea7973cd1bfb752d6665a99f0a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (division, print_function, absolute_import,
unicode_literals)
__all__ = ["Sampler", "default_beta_ladder"]
import numpy as np
import multiprocessing as multi
from . import util
def default_beta_ladder(ndim, ntemps=None, Tm... | asteca/ASteCA | packages/best_fit/ptemcee/sampler.py | Python | gpl-3.0 | 26,776 | [
"Gaussian"
] | c8f6cb2215ef15fea499ae6b21736deabc67350edd42ed393f28cabce1781e7a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
COUNTRIES_LIST = [(u'Afghanistan', u'AF', u'AFG', 4, u'ISO 3166-2:AF'),
(u'\xc5land Islands', u'AX', u'ALA', 248, u'ISO 3166-2:AX'),
(u'Albania', u'AL', u'ALB', 8, u'ISO 3166-2:AL'),
(u'Algeria', u'DZ', u'DZA', 12, u'ISO 3166-2:DZ'),
(u'American Samoa', u'AS', u'ASM', ... | yesudeep/mils-secure | app/data/countries.py | Python | mit | 69,183 | [
"BWA"
] | d9975534a4c3b15f8570446fb558d447f30de4f032893cfe3a2e3015716ca348 |
# -*- coding: utf-8 -*-
{
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for the area.": "Uma localização que especifica a área geográfica para esta região. Pode ser uma localização da hierarq... | code-for-india/sahana_shelter_worldbank | languages/pt.py | Python | mit | 207,773 | [
"VisIt"
] | 9025f9c3b8100e81038cbf472bbcc3cf1997160784998200f35004e5538f8f6b |
#!/usr/bin/python2
#~main.py~
import actions
import player
from time import sleep
version = 1.2
#enables the debug menu option in the main menu
DEBUG_MODE = "enabled"
#DEBUG_MODE = "disabled"
if DEBUG_MODE == "enabled":
import debug
cache = None #place to remember last function
def menu(Player):
global ... | brando56894/Dungeon-Quest | main.py | Python | gpl-3.0 | 2,837 | [
"VisIt"
] | b9192d4c97c2e68b0a34928d4defea1389e922a270aa7179c2c71e251653bb91 |
"""
Extended docstrings for functions.py
"""
pi = r"""
`\pi`, roughly equal to 3.141592654, represents the area of the unit
circle, the half-period of trigonometric functions, and many other
things in mathematics.
Mpmath can evaluate `\pi` to arbitrary precision::
>>> from mpmath import *
>>> mp.dps = 50; m... | lidavidm/mathics-heroku | venv/lib/python2.7/site-packages/sympy/mpmath/function_docs.py | Python | gpl-3.0 | 276,842 | [
"Gaussian"
] | 4d229ff6cf4ea85ee09d111a5f549f4c60e14a0f2995534def76865a3e5c2edb |
import numpy as np
from time import time
from os.path import isfile
from ase import Atoms
from gpaw import GPAW, Mixer
from gpaw.lcao.projected_wannier import ProjectedWannierFunctions, get_phs
if not isfile('al8.gpw'):
atoms = Atoms('Al', cell=(2.42, 7, 7), pbc=True)
atoms*=(8, 1, 1)
calc = GPAW(h=0.2, ... | qsnake/gpaw | oldtest/pwftest_Al_gamma.py | Python | gpl-3.0 | 1,276 | [
"ASE",
"GPAW"
] | 5ba275248a014cc129ccd3aeb332bda58f74ec84cd40619e33274553f479e6a6 |
try: paraview.simple
except: from paraview.simple import *
import numpy as np
from mpi4py import MPI
import os
import csv
from scipy import interpolate
import gc
import sys
gc.enable()
comm = MPI.COMM_WORLD
#label = 'm_10_1'
#labelo = 'm_10_1'
tt = int(sys.argv[1]) - 1
labelo = sys.argv[2]
label = sys.argv[2]
bas... | jungla/ICOM-fluidity-toolbox | 2D/U/extract_Velocity_CG_temp.py | Python | gpl-2.0 | 3,678 | [
"ParaView"
] | a467ec2ee9e06587cc491f2c5275046c81f3c4d9afa3fb1567fad226dbfd28db |
# -*- coding: utf-8 -*-
import pytest
import sys
from test_base_class import TestBaseClass
try:
from collections import Counter
except ImportError:
from counter26 import Counter
aerospike = pytest.importorskip("aerospike")
try:
from aerospike.exception import *
except:
print "Please install aerospike ... | trupty/aerospike-client-python | test/test_exists_many.py | Python | apache-2.0 | 6,125 | [
"ASE"
] | 3c7f638317ae191b58dfd3ca004633e898cff3125657e5bd39b948983c62ff5b |
import pysam
import click
import gc
import gzip
from sidr import common
from Bio.SeqUtils import GC # for GC content
from Bio.SeqIO.FastaIO import FastaIterator
def readFasta(fastaFile):
"""
Reads a FASTA file and parses contigs for GC content.
Args:
fastaFile: The path to the FASTA file.
R... | damurdock/SIDR | sidr/default.py | Python | mit | 5,335 | [
"BLAST",
"pysam"
] | 1806ae62c955fd500fe2faffcb15d68800b1085f55c1f46ebc7d93d70c064050 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('upload_file_from_server')
@click.argument("library_id", type=str)
@click.argument("server_dir", type=str)
@click.option(
"--folder_id",
help="id of the folder where to place... | galaxy-iuc/parsec | parsec/commands/libraries/upload_file_from_server.py | Python | apache-2.0 | 1,929 | [
"Galaxy"
] | e4420f4739978b15135687a92321ef6430b7d55b0529da6dc8faafe9d0941576 |
from functools import partial
import re
import logging
from sets import Set
import lib.visit as v
import lib.const as C
from .. import util
from ..meta import methods, classes, class_lookup
from ..meta.template import Template
from ..meta.clazz import Clazz
from ..meta.method import Method, find_formals
from ..meta.f... | plum-umd/pasket | pasket/decode/accessor_uni.py | Python | mit | 8,646 | [
"VisIt"
] | 03c89c0eafe0c656ab7585591dd30486d50ae6a1b8d21e6c2145571fbf29ea6e |
#!/usr/bin/env python
#----------------------------------------------------------------------
# Copyright (c) 2011-2015 Raytheon BBN Technologies
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and/or hardware specification (the "Work") to
# deal in the Work without ... | plantigrade/geni-tools | src/gcf/oscript.py | Python | mit | 66,572 | [
"ORCA"
] | ebac4be7ef9b78b7aa464268079c24dfae012c305d1fdfd90234881d7ea11fe2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import numpy as np
import unittest
import os
from pymatgen.analysis.structure_analyzer import VoronoiCoordFinder, \
solid_angle, contains_peroxide, RelaxationAnalyz... | setten/pymatgen | pymatgen/analysis/tests/test_structure_analyzer.py | Python | mit | 32,291 | [
"VASP",
"pymatgen"
] | f9ec59037fbecebbd88e8a2ab84d36a2dd6e44baf7f607c2646eb48230d76aa7 |
import json
from algorithm.PassFilter import low_filter, high_filter
def loadRouteFromMap(mapName, routeName, direction = 1):
mapData = json.load(open(mapName, 'rb'))
for route in mapData['graphEdge']:
if route['name'] == routeName:
routes = route['fingerdata']
for n in range(le... | icymorn/magnetic-info-process | data/MapLoader.py | Python | mit | 614 | [
"MOE"
] | 9d6552b13a818ac90351a44de5ddf660d9b51adb39bae85bb4ece041e6deb56e |
# Copyright 2007-2009 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os
import unittest
from Bio import SeqIO
from Bio.Alphabet import single_letter_alph... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SeqUtils.py | Python | gpl-2.0 | 7,033 | [
"Biopython"
] | 9ff288fee7d3b026e8de85157e14e2f9b58776e644b355030afae3f13be011c2 |
import numpy as np
#<Localized>
def gaussianType(x,u,v):
"""A gaussian type basis function
This takes parameters:
'mean', the locality of the curve
'variance', the spread of the curve.
Note that this is not a normal distribution, and is thus not normalized.
"""
#x.sh... | azane/for-learnings-sake | bayes/regression/linearparametric/bases.py | Python | mit | 541 | [
"Gaussian"
] | 0099cbf078da213a2843958ac46085d16eaf97de33fe1f46300b397f55fd2e46 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""EMSL Api.
Usage:
EMSL_api.py list_basis [--basis=<basis_name>...]
[--atom=<atom_name>...]
[--db_path=<db_path> |--db_dump_path=<db_dump_path>]
[--average_mo_number]
EMSL_api.py list_atoms --... | TApplencourt/EMSL_Basis_Set_Exchange_Local | EMSL_api.py | Python | mit | 6,539 | [
"GAMESS"
] | 6aa1af4b2e104fc25bff64bf19130896dceff742f039aee1c502cc6da149439b |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Generate a Markdown document listing all supported sites"""
import os
import sys
import collections
import util
from gallery_dl import extractor
CATEGORY_MAP = {
"2chan" : "Futaba Channel",
"35photo" : "35PHOTO",
"adultempire" : "Adul... | mikf/gallery-dl | scripts/supportedsites.py | Python | gpl-2.0 | 13,530 | [
"MOE"
] | d6a7ab4a64f38b2591eda38e815fb8298798145431ff6b068fba6dfa19e5f723 |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ghutchis/cclib | src/cclib/method/__init__.py | Python | lgpl-2.1 | 826 | [
"cclib"
] | 15a5cc92adac53eb691aab2491744e3524b079664ed7232483e778689342a611 |
import random, math
class Connection:
weight = None
deltaWeight = None
def __init__(self, weight = None, deltaWeight = None):
self.weight = random.random() if weight == None else weight
self.deltaWeight = 0.0 if deltaWeight == None else deltaWeight
def toJSON(self):
return {'__class__': 'Connection', '__w... | aaiijmrtt/LEARNING | v2/NN.py | Python | mit | 5,972 | [
"NEURON"
] | 57ae1996fbb66264263e8118a4c567ef70b0900e98bb0da429cd8fd00378f6c0 |
"""
=============================================
Whitening evoked data with a noise covariance
=============================================
Evoked data are loaded and then whitened using a given noise covariance
matrix. It's an excellent quality check to see if baseline signals match
the assumption of Gaussian white... | adykstra/mne-python | examples/visualization/plot_evoked_whitening.py | Python | bsd-3-clause | 3,115 | [
"Gaussian"
] | 5e0d13a1fdde492620d4168d500e5cf9ceb9ba0090ea2611167686a382c8411c |
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