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#!/usr/bin/env python
"""
ldif - generate and parse LDIF data (see RFC 2849)
written by Michael Stroeder <michael@stroeder.com>
See http://python-ldap.sourceforge.net for details.
$Id: ldif.py,v 1.3 2008/02/11 16:35:43 dwelch Exp $
Python compability note:
Tested with Python 2.0+, but should work with Python 1.5.2+.... | matrumz/RPi_Custom_Files | Printing/hplip-3.15.2/base/ldif.py | Python | gpl-2.0 | 16,741 | [
"VisIt"
] | 6afe2324d91e7c7c7c644e843cb4454e2801325cad2ee70e6d01971bc25322a0 |
"""Header value parser implementing various email-related RFC parsing rules.
The parsing methods defined in this module implement various email related
parsing rules. Principal among them is RFC 5322, which is the followon
to RFC 2822 and primarily a clarification of the former. It also implements
RFC 2047 encoded w... | bgris/ODL_bgris | lib/python3.5/email/_header_value_parser.py | Python | gpl-3.0 | 105,210 | [
"CRYSTAL"
] | ca3c64b4e18f2da178624619b9ec5ff44259dc2b45455016c1a67d36d32f5768 |
#!/usr/bin/python
#
# Copyright (C) 2010, Nokia <ivan.frade@nokia.com>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.... | Pelagicore/tracker-ivi | tests/functional-tests/09-concurrent-query.py | Python | gpl-2.0 | 3,760 | [
"MOE"
] | b6833edf05272ae2509607e4c151a898bbd3d99116f7c22b65dc4c94e8646caa |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | civisanalytics/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 30,715 | [
"Galaxy"
] | c359250655546a3bbbde930549fa74e2aa309f451c4a28e2d281229dea79f219 |
# (c) 2015, Brian Coca <briancoca+dev@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) any later v... | wkeeling/ansible | lib/ansible/plugins/action/patch.py | Python | gpl-3.0 | 2,658 | [
"Brian"
] | a592275d76d0098aa1d784881efd639ced52e2f17dd5da4faef9750b47d9f9c3 |
# vim:tw=50
"""Generators
It's head-exploding time!
We recently wrote a function that, given lines
with dates and measurements, splits them up,
makes sure they only move forward, and prints them
out.
Printing is nice, but not impressively useful or
exciting. We want to _transform_ this data
(eventually into a chart... | shiblon/pytour | tutorials/generators.py | Python | apache-2.0 | 2,450 | [
"exciting"
] | 1043a52a53b33c994fd55c98679dfe9d8a4f1d9748115e24e27d229dec4d4c00 |
#!/usr/bin/env python
######################################################
## GUI to vizualize ROMS input/output files
## Nov 2014
## rsoutelino@gmail.com
######################################################
import os
import wx
import datetime as dt
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg a... | rsoutelino/pyromsgui | pyromsgui.py | Python | mit | 21,923 | [
"NetCDF"
] | 85485c286d29d7926ea510c5b5b0295beff03a1f34d0a53ddc2ccfbcb7f44b56 |
#
# Copyright 2019-2020 Johannes Hoermann (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 Softw... | libAtoms/matscipy | examples/electrochemistry/samples_pb_c2d.py | Python | lgpl-2.1 | 63,818 | [
"ASE",
"Avogadro",
"LAMMPS",
"Matscipy"
] | cc796fc7f507165118c13e8b748246008a32b62abd3bdda8ed85ecfe3b9ea7bc |
"""
Algorithms for processing line segments
segments_generator
Yield segments in order of their start/end.
[(1, 4), (2, 3)] => [(1, (1, 4)), (2, (2, 3)), (3, (2, 3)), (4, (1, 4))]
histogram_segments
Number of line segments present in each given range
[(1, 4), (2, 3)] => [((1, 2), 1), ((2, 3), 2), ... | davidastephens/pdftables | pdftables/line_segments.py | Python | bsd-2-clause | 11,444 | [
"VisIt"
] | db9d22ce8e814b0fd3a668ba28a98f3ba29e8f76cf480f22e54a1889acaffe4b |
#!/usr/bin/env python
#======================================================================
# Place holders. These may or may not be required
# Python 2/3 compatibility
#from __future__ import print_function
import sys
sys.settrace
#from glob import glob
#import itertools as it
import os
from operato... | CosmaP/DalekBot | DalekV2MainV2.py | Python | gpl-3.0 | 44,369 | [
"Gaussian"
] | aa2901d88a9a6b4cdb95505e405da7bbd6fa54671c5786d8d252fa9954c8b920 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyWhatshap(PythonPackage):
"""WhatsHap is a software for phasing genomic variants using DN... | iulian787/spack | var/spack/repos/builtin/packages/py-whatshap/package.py | Python | lgpl-2.1 | 1,210 | [
"pysam"
] | df66475c361c408666efa17cdfebeec4b783f09697982a6bc376491f6df241c6 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004 Martin Hawlisch
# Copyright (C) 2005-2008 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Michiel D. Nauta
#
# This program is free software; you can redistribut... | arunkgupta/gramps | gramps/plugins/export/exportvcard.py | Python | gpl-2.0 | 12,420 | [
"Brian"
] | 6ccc9de7d867427b7e39e3eae6d33825678d0e704bb241ed66c38101984af812 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | jrossyra/adaptivemd | adaptivemd/brain.py | Python | lgpl-2.1 | 2,101 | [
"MDTraj"
] | cebc88df217765983ae574e1089c859ac0b5ff21e98265ddf8b0b7215a884c76 |
# Copyright 2008-2014 Nokia Solutions and Networks
#
# 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 l... | userzimmermann/robotframework-python3 | src/robot/result/visitor.py | Python | apache-2.0 | 4,345 | [
"VisIt"
] | 291af1573cee3bfe53fa7f069938b855ab802f25eb77d96a41a2859eaba846de |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/cc/ccsd_t_lambda_slow.py | Python | apache-2.0 | 4,435 | [
"PySCF"
] | 48f727ecf312d9c7fea206b246f8405330dc585677b675835c13b7d9f0b62b74 |
'''
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
from spm1d import rft1d
#(0) Set parameters:
np.random.seed(12345)
nResponses ... | 0todd0000/spm1d | spm1d/rft1d/examples/random_fields_broken_2.py | Python | gpl-3.0 | 1,075 | [
"Gaussian"
] | dd59aeafe80a05497fabe621d96c0adbe1584cd4dd08a2fdb603ae2d391bafc4 |
import numpy as np
from ase import Atoms
from ase.io.trajectory import Trajectory
from ase.calculators.emt import EMT
a = 4.0 # approximate lattice constant
b = a / 2
ag = Atoms('Ag',
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=1,
calculator=EMT()) # use EMT potential
cell = ag.get_... | misdoro/python-ase | doc/tutorials/eos/eos1.py | Python | gpl-2.0 | 491 | [
"ASE"
] | 00e7b15680d9e0a9c879993e6851e1d4fe35595f56d3d09e30ff96455f8522f8 |
from FAdo.fa import *
import math
class MiniTasksAutomaton(object):
_separator_string = " "
_negation_string = "not"
_anything_string = "anything"
_and_string = "and"
_or_string = "or"
_sigma = []
for i in range(26):
_sigma.append(chr(ord('A') + i))
def __init__(self, descrip... | general-ai-challenge/Round1 | src/fsa/__init__.py | Python | bsd-3-clause | 23,932 | [
"VisIt"
] | 61c28caa6bc8e9bdd3fe98d27a0ab20305aa414975b0011bb6c662ede9a225cc |
import numpy as np
from ..numerics.utilities import log_det, chol_inv
class PriorKL0(object):
"""
Prior (Gaussian) moments at t=0 - KL0.
"""
__slots__ = ("mu0", "tau0", "single_dim")
def __init__(self, mu0, tau0, single_dim=True):
"""
Default constructor.
:param mu0: pri... | vrettasm/VGPA | code/src/prior_kl0.py | Python | gpl-3.0 | 4,912 | [
"Gaussian"
] | fb397a16a82a5ced1f0fc2da58713eb7250fc4aff68696b6cd4405c903c1a377 |
# Copyright (C) 2012 Brian Parma
#
# 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 1, or (at your option)
# any later version.
#
# This program is distributed in the hope that it ... | virtuald/exaile | plugins/ipconsole/ipconsoleprefs.py | Python | gpl-2.0 | 1,656 | [
"Brian"
] | 3cafb1900ea3919cb775f4f025469251c975219ed1e4ea518edc29a04216a523 |
arenaRankName = {
"01": "Novice",
"02": "Contender",
"03": "Duelist",
"04": "Berserker",
"05": "Sage",
"06": "Guardian",
"07": "Titan",
"08": "General",
"09": "Master",
"10": "Archfiend",
"11": "Ascended",
"12": "Celestial",
"13": "Apollo",
"14": "Phanes",
"15... | Blackrobe/blackrobe.github.io | BFStoryArchive/storyutil.py | Python | gpl-2.0 | 26,421 | [
"CRYSTAL"
] | 54d81fb47f12c1ae27f694c598578b94179a24553bb4f78f63b00713ae515b12 |
#!/usr/bin/env python3
import sys
from setuptools import setup, find_packages
__version__ = "0.1"
if sys.version_info < (3,5):
print("python version must be at least 3.5")
sys.exit(1)
def readme():
with open('README.md') as f:
return f.read()
setup(name='pybioutils',
version='0.... | T-B-F/pyBioUtils | setup.py | Python | mit | 1,047 | [
"Biopython"
] | 52d92c99df660dcfe38039474a2a50784a4f9893e7f434a918c88a6e0c1bca66 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
# REF [site] >> https://gist.github.com/karpathy
"""
A bare bones examples of optimizing a black-box function (f) using
Natural Evolution Strategies (NES), where the parameter distribution is a
gaussian of fixed standard deviation.
"""
import numpy as np
np.random.seed(... | sangwook236/SWDT | sw_dev/python/rnd/test/artificial_intelligence/evolutionary_computation/nes.py | Python | gpl-3.0 | 1,873 | [
"Gaussian"
] | 5a315a7222291b375fb59f6aa04d55bc7ddc8e66270da3406e92150c4b945d32 |
"""===================================================
pipeline_windows - Window based genomic analysis
===================================================
This pipeline takes mapped reads from ChIP-Seq experiments
such has chromatin marks, MeDIP and performs analyses
of the genomic read distribution. This contrasts w... | CGATOxford/CGATPipelines | CGATPipelines/pipeline_windows.py | Python | mit | 82,564 | [
"BWA",
"Bioconductor"
] | 8da68c8e51f67a91cd6725572f4c3691c5cccafddbd1ee954919aff29793ba32 |
import base64
import json
from django.contrib.auth import get_user_model
from django.http import HttpRequest
from django.core.exceptions import ImproperlyConfigured
from django.conf import settings
from django.test import TestCase
from django.core.urlresolvers import reverse
from django.test.utils import override_sett... | state-hiu/geonode | geonode/geoserver/tests.py | Python | gpl-3.0 | 15,764 | [
"VisIt"
] | 7f5e7f1ed4af7cceed8d83fa1901077114a93207dabec8e8942c994819dd2b8a |
tests = [
("python", "UnitTestTreeUtils.py", {}),
("python", "UnitTestTree.py", {}),
("python", "UnitTestXVal.py", {}),
("python", "UnitTestID3.py", {}),
("python", "UnitTestPrune.py", {}),
("python", "UnitTestQuantTree.py", {}),
("python", "UnitTestSigTree.py", {}),
]
longTests = []
if __name__ == '__ma... | ptosco/rdkit | rdkit/ML/DecTree/test_list.py | Python | bsd-3-clause | 456 | [
"RDKit"
] | 1d43ff60af0149f92b62d8494966733e2b3d3854acb85f2fcc8637cad1cedd6f |
# Copyright (c) 2014-2016, NVIDIA CORPORATION. All rights reserved.
from __future__ import absolute_import
import wtforms
from wtforms import validators
from ..forms import ModelForm
from digits import utils
class ImageModelForm(ModelForm):
"""
Defines the form used to create a new ImageModelJob
"""
... | dongjoon-hyun/DIGITS | digits/model/images/forms.py | Python | bsd-3-clause | 4,075 | [
"Gaussian"
] | dab7d467decf24a7fe1de33e4b0db48dffd62a2dedca19d7d8651757df32a9b5 |
# 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 | pie/profiles/helpers.py | Python | gpl-3.0 | 2,326 | [
"Brian"
] | a536a9d4fea8cf5d7501000509304178464f6532d0fd67a925d37e0bdbea645d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Stephane Charette <stephanecharette@gmail.com>
# Contribution 2009 by Bob Ham <rah@bash.sh>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2013-2014 Paul Franklin
# Copyright (C) 2015 ... | dermoth/gramps | gramps/plugins/graph/gvhourglass.py | Python | gpl-2.0 | 16,068 | [
"Brian"
] | 57d03e685f3fc85a16d51d0b5f6577bc72039da44a59d81b0ef72b52efe0b3d0 |
import netCDF4
from netCDF4 import Dataset
# Load the file:
ncfile = Dataset('../Spoutnik-I files/PREVIMER_WW3-FINIS-200M_20140123T13Z.nc','r')
####### Exploring the file's attributes #######
ncfile.netcdf_version
ncfile.format_version
# First look at it:
ncfile.variables
ncfile.dimensions
ncfile.dimensions.keys(... | mteule/Spoutnik-I | doc/first_draft.py | Python | gpl-3.0 | 6,269 | [
"NetCDF"
] | 000f346bd3aff0741d6ce8171bbc06ee1dd6135663e07bb424e52d7bfe742d61 |
########################################################################
# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015.
# It is licenced under the GPL 2.1 or higher.
# There is no warranty of any kind. You are welcome to make copies under
# the provisions of the GPL.
# This programme illustrates buildi... | dilawar/moose-full | moose-examples/tutorials/Rdesigneur/currentStep.py | Python | gpl-2.0 | 11,887 | [
"MOOSE",
"NEURON"
] | 19fae012e78022ba1caaa92d9cf4d7cd270a3a8c04854158736774c9f4e3b224 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import math
import warnings
from collections import namedtuple, defaultdict
import ruamel.yaml as yaml
import os
import json
from copy import deepcopy
from monty.dev import deprecated
from pymatgen.analysis... | blondegeek/pymatgen | pymatgen/analysis/local_env.py | Python | mit | 156,741 | [
"Gaussian",
"Jmol",
"Pybel",
"VASP",
"pymatgen"
] | f37ec50b523a15d517772dafe1f96de29ce90b00c3d97820448de359cc20cd11 |
#!/usr/bin/env python
#coding:utf-8
import os
from distutils.core import setup
from geopytool.ImportDependence import *
from geopytool.CustomClass import *
here = os.path.abspath(os.path.dirname(__file__))
try:
README = open(os.path.join(here, 'README.md')).read()
except:
README = 'https://github.com/GeoPyT... | cycleuser/GeoPython | setup.py | Python | gpl-3.0 | 1,631 | [
"VisIt"
] | 62f0b381873788d600f1a9267fb0e5e33fff5396fc74e8ccdd3edafbfbf39a7b |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_state_network_size_request.py | Python | apache-2.0 | 10,097 | [
"VisIt"
] | 77cd82781e4073c3f63ac1638bd25e33699465896b95d442cbc6b083332119b4 |
#!/usr/bin/env python3
"""
1.0-preprocess.py
This script preprocesses raw sequencing data in preparation for VDJ analysis. Paired end fastq
files will be filtered and merged using vsearch, or single read fastq or fasta files can be
specified. For fastq input, an optional QC analysis can be printed (from vsear... | scharch/SONAR | annotate/1.0-preprocess.py | Python | gpl-3.0 | 35,368 | [
"Biopython"
] | f4fe56d7a04f9683ba5b3e3dd38a4dfd4ca36066d175f12187626aeba4685943 |
"""
Filename: __init__.py
Author: Brian Soe
Description: Activates Flask application and send to server.py.
"""
from flask import Flask
from flask.ext.sqlalchemy import SQLAlchemy
from flask.ext.mail import Mail
import sys
import random
import subprocess
# secret key selection characters
selection = '0123456789abcdef... | bsoe003/MWCH_Website | dev/__init__.py | Python | mit | 930 | [
"Brian"
] | f863a2566796abbef39255b615d348f931a412481f81de13c04c9263fdfa8eb2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Andrew Jewett
# License: MIT License (See LICENSE.md)
# Copyright (c) 2014
"""
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).... | smsaladi/moltemplate | moltemplate/dump2data.py | Python | bsd-3-clause | 71,220 | [
"LAMMPS"
] | 1af1a39ff536c1edbf7e78b4e16f768aab7a98505886890b88db90ddb99173f0 |
#
# Created by davbzh on 2013-08-14.
#
from Bio import SeqIO
from Bio.Blast import NCBIXML
from collections import defaultdict
import numpy as np
import csv
import os
Part = 3
class BlastParser(object):
'''An iterator blast parser that yields the blast results in a multiblast file'''
def __init__(self, fh... | NIASC/VirusMeta | blast_module/alignment_search_result.py | Python | gpl-3.0 | 15,064 | [
"BLAST",
"Biopython"
] | bb7948326702dfb4dae7540a377d213a36eb720470379beca636d33492a5d4cf |
from __future__ import division
from __future__ import print_function
#created by Brian Trethewey
#
#neGrapher is primary interface for graphing data
#neStats is primary interface for creating statistics output file for a dataset
from future import standard_library
standard_library.install_aliases()
from builtins imp... | popgengui/negui | agestrucne/asnviz/LineRegress.py | Python | agpl-3.0 | 35,999 | [
"Brian"
] | 036132539d8d6eadfc79fb8b270557daf8ebb2ab92db2f3b0ef19d4459068b76 |
""" DISET request handler base class for the TransformationDB.
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.TransformationSystem.DB.TransformationDB import Tr... | marcelovilaca/DIRAC | TransformationSystem/Service/TransformationManagerHandler.py | Python | gpl-3.0 | 31,894 | [
"DIRAC"
] | 5d91a6b20d676ff0a3b76c5585f01c40812424d3dc5cab9937d8e859afe28106 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | juanchopanza/NeuroM | neurom/apps/annotate.py | Python | bsd-3-clause | 3,170 | [
"NEURON"
] | 7e5c158029523182bb0038c1748f759f20b578193ae84e09b983136656accc23 |
__author__ = 'pavel'
import argparse
import sys
from itertools import permutations
from multiprocessing import Pool, cpu_count
from rdkit import Chem
from .mol_context import get_std_context_core_permutations
def process_line(line):
# returns env_smi, core_smi, heavy_atoms_num, core_smarts
output = []
... | DrrDom/crem | crem/frag_to_env_mp.py | Python | bsd-3-clause | 6,389 | [
"RDKit"
] | 46b145e28bce0bd0c41b1d9edea44fd0f8e601db77254ca9a5df81f340f566d9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to specify a translatable setting:
# ! (a) BLOG_TITLE = "My Blog"
# ! (b) BLOG_TITLE = {"en": "My ... | devpool-works/devpool.works | src/conf.py | Python | apache-2.0 | 52,288 | [
"VisIt"
] | 3fdec1126455d38eb4466a4f8ee30c5b988d04776dbe30ed44a33568013518bc |
#!/usr/bin/env python
#
# Gaussian quadrature.
#
# This algorithm was posted to the ActiveState public code repository
# by Alex Pletzer, in March of 2001.
#
# http://code.activestate.com/recipes/52292-gaussian-quadrature-with-or-without-log-singularit/?in=user-98107
#
# python imports
import math
import sys
sys.path... | radiasoft/radtrack | radtrack/quadrature/RbGaussianQuadrature.py | Python | apache-2.0 | 6,316 | [
"Gaussian"
] | 9e5d3a3b2711e3398ee69ce9d53756670e28ed4d41d6cc767df0ae2c4e81f411 |
"""
Provides the class PatternCoordinator and a family of
FeatureCoordinator classes.
PatternCoordinator creates a set of pattern generators whose
parameters are related in some way, as controlled by a subclass of
FeatureCoordinator.
"""
import os
import math
import json
import glob
import collections
import copy
im... | ioam/imagen | imagen/patterncoordinator.py | Python | bsd-3-clause | 18,669 | [
"Gaussian"
] | f13d453c01e396f367b32ff443f9e3b67de6d958a1145a866715d548a921c16e |
"""
Module for Approximate Bayesian Computation
"""
from abc import ABCMeta, abstractmethod
import multiprocessing as mp
import numpy as np
from scipy import stats
from numpy.lib.recfunctions import stack_arrays
from numpy.testing import assert_almost_equal
import time
class ABCProcess(mp.Process):
'''
'''
... | rcmorehead/simpleabc | simple_abc.py | Python | mit | 20,167 | [
"Gaussian"
] | ba730df47048056ee614e693a1e8e6627613dc4650afe563af6d657286a6c394 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | clustering_normalized_cuts/setup.py | Python | apache-2.0 | 3,974 | [
"Gaussian"
] | 1a1203b1a1915f0428bae3050890f639b0f48d5fa9ef4675aa9466e4b85b735e |
'''Dukedom, a more complex game of resource management than Hammurabi, with elements of empire building.
Credits
-------
Original concept by Vince Talbot in 1976, my implementation is based on the BASIC version that appears
in Big Computer Games (1984).
Instructions
------------
- Each peasant requires 13 hectolitres... | fruitnuke/retro | dukedom/dukedom.py | Python | gpl-3.0 | 32,936 | [
"Gaussian"
] | 4fcb9040118ab7c06e823a97aacfb42ab8d72816c63c39de4f4f43471a29e317 |
#!/usr/bin/env python
from __future__ import print_function, division
import bayesloop as bl
import numpy as np
class TestFileIO:
def test_save_load(self):
S = bl.HyperStudy()
S.loadData(np.array([1, 2, 3, 4, 5]))
S.setOM(bl.om.Gaussian('mean', bl.cint(0, 6, 20), 'sigma', bl.oint(0, 2, 20... | christophmark/bayesloop | tests/test_fileio.py | Python | mit | 463 | [
"Gaussian"
] | a6a537b623ebc8af84bfb8db7a6eca3704403aa34ee00577aae991bafe4edbe3 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from datetime import datetime
import os
from unittest import TestCase
from django.utils import html
from django.utils._os import upath
from django.utils.encoding import force_text
class TestUtilsHtml(TestCase):
def check_output(self, function, val... | denisenkom/django | tests/utils_tests/test_html.py | Python | bsd-3-clause | 8,266 | [
"ADF"
] | 976f33ee0ac80b9abc63a6e0dee1d4c24350654b78bbabb0573a65e4bf894890 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# showstats - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of... | heromod/migrid | mig/cgi-bin/showstats.py | Python | gpl-2.0 | 1,106 | [
"Brian"
] | 34b31f37d97ccfbe2a0d7afc15ab24cb6d460961a518b5f085321f6e661bb382 |
#!/usr/bin/env python
########################################################################
# File : dirac-configuration-dump-local-cache
# Author : Adria Casajus
########################################################################
"""
Dump DIRAC Configuration data
"""
from __future__ import print_function
fro... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/scripts/dirac_configuration_dump_local_cache.py | Python | gpl-3.0 | 1,288 | [
"DIRAC"
] | a3d9cd380864c9bd8cb66d5c81e628f1b5609a4479c12fdfc1fff957be75e775 |
from __future__ import division
# -----------------------------------------------------------------------------
# Copyright (c) 2014--, 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.
# ---------------... | RNAer/qiita | qiita_ware/util.py | Python | bsd-3-clause | 5,985 | [
"scikit-bio"
] | 4762af4b203db89bb947956c471b79d2ad835307fb11cdb53870c25c49eab466 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | do/magic/get_ukidss.py | Python | agpl-3.0 | 1,219 | [
"Galaxy"
] | 29d8f8373ed28eb48394c01566a5977720284d945635e7e59196b4dd86ab8a62 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_16000/brian2_benchmark_COBAHH_clocksyn_hidens_16000.py | Python | gpl-3.0 | 3,781 | [
"Brian"
] | 8fdc1b7e55e15a6866a1a36de1b6b3fab3852133ca0245b38ffc3685cd1f8e4a |
import tempfile
from pygmin.landscape import DoubleEndedConnect, DoubleEndedConnectPar
from pygmin import basinhopping
from pygmin.storage import Database
from pygmin.takestep import RandomDisplacement, AdaptiveStepsizeTemperature
from pygmin.utils.xyz import write_xyz
from pygmin.optimize import mylbfgs
from pygmin.t... | js850/PyGMIN | pygmin/systems/basesystem.py | Python | gpl-3.0 | 16,801 | [
"PyMOL"
] | 27f36effa280b874a13183842890d1f9a0755e9ae735fccd405d51ed63d9001e |
## -*- coding: utf-8 -*-
import re
from collections import namedtuple, OrderedDict
from datetime import time
from itertools import zip_longest
import logging
log = logging.getLogger(__name__)
SSA_NEWLINE = '\\N'
SSA_NEXT_COLOR = '{\\c&HFFFFFF&}'
SSA_HEIGHT_TO_FONT_SIZE_RATIO = 14
SRT_FORMAT = '''\
{index}
{start} ... | calaldees/KaraKara | processmedia2/processmedia_libs/subtitle_processor.py | Python | gpl-3.0 | 14,849 | [
"ASE"
] | e4f41477219e0bea9406bcd97117e9ca63c07e068b987b803384dfc15e2e40ff |
airports = {}
airports['AGGH'] = 'HONIARA INTL'
airports['AGGL'] = 'Santa Cruz'
airports['AGGM'] = 'MUNDA'
airports['AGGN'] = 'Gizo/Nusatope'
airports['ANYN'] = 'Nauru International'
airports['AREN'] = 'Arendal Gullknapp'
airports['AYBK'] = 'Buka'
airports['AYCH'] = 'Chimbu'
airports['AYDU'] = 'Daru'
airports['AYGA'] =... | freeflightsim/fg-flying-club | flying-club.appspot.com/data/airports.py | Python | gpl-2.0 | 321,149 | [
"CASINO",
"COLUMBUS",
"CRYSTAL",
"Dalton",
"Elk",
"FEFF",
"MOOSE",
"TINKER"
] | 5938af4cdc2259f0b896335426cad9e13050ab046be6e98279b77cc04e6ff488 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-webrisk | tests/unit/gapic/webrisk_v1/test_web_risk_service.py | Python | apache-2.0 | 75,685 | [
"Octopus"
] | 9b2edbfd922ed001c951c361aafb206ac6aacc1c486824372daaf0ac64622d33 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import copy
import sys
from math import acos, sin, cos, sqrt, pi, exp, log, floor
from abc import ABCMeta, abstractmethod
from inspect import signature
import warnings
import numpy as np
from . import scalar_inv_efuncs
from astropy import constants as ... | aleksandr-bakanov/astropy | astropy/cosmology/core.py | Python | bsd-3-clause | 118,127 | [
"Galaxy"
] | ef3e364b4f742ebd6fd1c78ff8297e759034814d7ee1321628d00bc6f1baa20b |
# Name: Maud Ottenheijm
# Student nr: 10641785
# This file contains code for writing csv to json format. Takes input from InternetUsersPer100.csv, outputs in
# data.json. Part of D3 Datamaps assignment week 5, Data Processing.
country_codes = [
["af", "AFG", "Afghanistan"],
["ax", "ALA", "Aland Islands"],
... | MaudOtten/programmeerproject | WomenInScience/data/trial_data_files/csvreader_2.py | Python | unlicense | 16,678 | [
"BWA"
] | a244a697983d6da6db1de5656d2e8b7bca5003dc81176ea8ea433e8ceed9a051 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | JWDebelius/scikit-bio | skbio/stats/distance/tests/test_base.py | Python | bsd-3-clause | 31,879 | [
"scikit-bio"
] | bd92ac46dbaf17256487da1283651e694486e748f20f2935b331ec2622ee789c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# 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 prog... | magic-trip/split_fasta | ExtractNCBIDB2.py | Python | gpl-2.0 | 9,277 | [
"BLAST"
] | ddd52cd1054dd14276f102daf68f08c4c904c993cbe4d9d00c09a80f06f2aee1 |
"""FHIaims calculator interface."""
# FHIaims.py - IO routines for phonopy-FHI-aims
# methods compatible with the corresponding ones from ase.io.aims
# only minimal subset of functionality required within phonopy context is implemented
#
# Copyright (C) 2009-2011 Joerg Meyer (jm)
# All rights reserved.
#
# This file is... | atztogo/phonopy | phonopy/interface/aims.py | Python | bsd-3-clause | 7,939 | [
"ASE",
"FHI-aims",
"VASP",
"phonopy"
] | eead80904d386aeebcb1d62d9f1505ab7f116a0723bd73d55edd3f793f0fb67b |
#completely rewritten by Rolarga, original from mr
# Shadow Weapon Coupons contributed by BiTi for the Official L2J Datapack Project
# Visit http://forum.l2jdp.com for more details
import sys
from com.l2scoria.gameserver.model.quest import State
from com.l2scoria.gameserver.model.quest import QuestState
from com.l2sco... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/quests/232_TestOfLord/__init__.py | Python | gpl-3.0 | 13,609 | [
"VisIt"
] | f8277ffafafb297e4b2da7a2dd45bb8a9e74b4bb65960b00a4029f6a1f1835bd |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | emonty/ansible-modules-core | system/systemd.py | Python | gpl-3.0 | 14,929 | [
"Brian"
] | bdc8a7785d5a88f24460120cffc1f3c1aed08778c61712b4608265c308cfbbd5 |
"""
Retrieve input sandbox for a DIRAC job
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import DIRAC
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
import os
import pprint
class Params(object):
def __init__(self):
... | DIRACGrid/COMDIRAC | src/COMDIRAC/Interfaces/scripts/dinput.py | Python | gpl-3.0 | 5,443 | [
"DIRAC"
] | 169e9256a08d73e4bef29e3c0c8cef9cd340cc63efb21b55be1d92107bf5efa9 |
'''
Created on Jul 14, 2011
@author: sean
'''
from __future__ import print_function
from meta.decompiler.simple_instructions import SimpleInstructions
from meta.decompiler.control_flow_instructions import CtrlFlowInstructions
import _ast
from meta.asttools import print_ast
from meta.utils import py3, py3op, py2op
fro... | enthought/Meta | meta/decompiler/instructions.py | Python | bsd-3-clause | 15,084 | [
"VisIt"
] | ffb7bbad5fba7a7b2ea9cafff608ea4c4157322f47fa0b25024a02478156f35a |
# This file is part of the lattice-dmet program. lattice-dmet 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, version 3.
#
# lattice-dmet is distributed in the hope that it will be useful,
# but WITHOUT ANY... | zhengbx/BBQ | lattice_dmet.20121221/meanfield.py | Python | gpl-3.0 | 20,612 | [
"DIRAC"
] | 7123c64644faa7a37174f1207df986cd5293b5c34e0a2de034c1834bd5be06b1 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either versi... | markovmodel/PyEMMA | pyemma/coordinates/util/patches.py | Python | lgpl-3.0 | 14,343 | [
"Amber",
"LAMMPS",
"MDTraj",
"NetCDF"
] | 55cc55aec35dd9fae98df30bfaa0f68f1a48d793792817845e854f22a535c90a |
# ICE Revision: $Id$
"""
Class that implements pyFoamPVSnapshot
"""
from optparse import OptionGroup
from PyFoamApplication import PyFoamApplication
from PrepareCase import PrepareCase
from CommonSelectTimesteps import CommonSelectTimesteps
from PyFoam.RunDictionary.SolutionDirectory import SolutionDirectory
from ... | mortbauer/openfoam-extend-Breeder-other-scripting-PyFoam | PyFoam/Applications/PVSnapshot.py | Python | gpl-2.0 | 34,423 | [
"ParaView",
"VTK"
] | aaeae214ba4def7352c2fd70655269126e19bcd1ee7ee7d3194393c4d4b4f2b5 |
"""Test of BLACS Redistributor.
Requires at least 8 MPI tasks.
"""
import sys
import numpy as np
from gpaw.band_descriptor import BandDescriptor
from gpaw.grid_descriptor import GridDescriptor
from gpaw.mpi import world, distribute_cpus
from gpaw.utilities import compiled_with_sl
from gpaw.utilities.scalapack impor... | qsnake/gpaw | gpaw/test/parallel/realspace_blacs.py | Python | gpl-3.0 | 3,766 | [
"GPAW"
] | a8b5fd22f5f702ef87311dde91c010f4a9ee9dc828ba0adef266c25893ed9f30 |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from decimal import Decimal
import pytz
import logging
import smtplib
import StringIO
import csv
from courseware.courses import get_course_by_id
from boto.exception import BotoServerError ... | dsajkl/reqiop | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 59,531 | [
"VisIt"
] | 6c114eb81a93090cee7da56cee7b966b17cb7d2b62405bc6ea35dd1470ee8ca4 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | AnishShah/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 49,329 | [
"VisIt"
] | ae5d19bfb6d774fb0a70b8315fe160a07e6498cbbb0c3072da4f84795c2754ed |
#####################################################################
# File: ReqManagerHandler.py
########################################################################
"""Implementation of the RequestDB service in the DISET framework
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN ReqManager
:... | yujikato/DIRAC | src/DIRAC/RequestManagementSystem/Service/ReqManagerHandler.py | Python | gpl-3.0 | 13,201 | [
"DIRAC"
] | 7515319d6072f4d544bd5c9fae8eda94319806d244bb540958875eda054a1fba |
#! /usr/bin/env python
import matplotlib
if __name__ == '__main__':
matplotlib.use('Agg')
import numpy as np
import pylab as plt
import os
import sys
import tempfile
import datetime
import gc
from functools import reduce
from scipy.ndimage.morphology import binary_dilation
from scipy.ndimage.measurements import la... | dstndstn/unwise-coadds | unwise_coadd.py | Python | gpl-2.0 | 109,227 | [
"Galaxy"
] | a7f24d98f0f38ebdba7d5416ded2bc8cebfec218b19ad780aaccf42de6a7cf42 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Adapted from Graphviz.py (now deprecated)
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2005-2006 Eero Tamminen
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Cont... | gramps-project/gramps | gramps/plugins/graph/gvrelgraph.py | Python | gpl-2.0 | 45,021 | [
"Brian"
] | ef26567058595040a751c6f66f366efc639d4b1f794e08623613ce4ec64dfc08 |
"""
User policy settings
"""
from askbot.conf.settings_wrapper import settings
from askbot.conf.super_groups import LOGIN_USERS_COMMUNICATION
from askbot.deps import livesettings
from django.conf import settings as django_settings
from askbot.skins import utils as skin_utils
from django.utils.translation import ugettex... | coffenbacher/askbot-devel | askbot/conf/user_settings.py | Python | gpl-3.0 | 4,846 | [
"VisIt"
] | 95a1f56efe6b975539b990401e67311bf220075d85d2c39b9ae3eaedacfe5061 |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns)
from numpy import random
from numpy.compat import asbytes
class TestBinomial(TestCase):
def test_n_zero(s... | immerrr/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 28,174 | [
"Gaussian"
] | 49b4d685c165f048a119d7dbbe3acdac2173facc33d696552a3f91c0f5d588c5 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | src/python/espressomd/highlander.py | Python | gpl-3.0 | 2,412 | [
"ESPResSo"
] | 61698bd1e81809ae3fa6ab37ebd7a24d24f2a6ac68cec7316a971aff6121d69c |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
{% if c... | aeikenberry/cookiecutter-django-rest-babel | {{cookiecutter.project_slug}}/config/urls.py | Python | bsd-3-clause | 1,975 | [
"VisIt"
] | 99c73a5940fcc9f9ecaaf17b5987a719093e2d01f345e3043fea52279f377acd |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Pass through blocks from a maf file until a certain number of columns
have been passed.
usage: %prog -c cols < maf > maf
"""
import sys
from bx.align import maf
from optparse import OptionParser
def __main__():
# Parse command line arguments
parser = OptionPar... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_truncate.py | Python | bsd-3-clause | 786 | [
"Galaxy"
] | 5bcb08ad4cc0d0040f17229cb1d4a475e50ff073d432a9014ce4b956fa36013e |
#!/usr/bin/env python
import os
import argparse
import subprocess
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Python shell to suppress pipe errors in Prophet")
parser.add_argument("--evalue_cutoff", type=str)
parser.add_argument("--window_size", type=str)
parser.add_argu... | TAMU-CPT/galaxy-tools | tools/external/Prophet/runProphet.py | Python | gpl-3.0 | 929 | [
"Galaxy"
] | 77813441eb91a2eabdd32ad1faed1afde60203771d0058c42a90947beb00ed8f |
'''
MFEM example 5
See c++ version in the MFEM library for more detail
'''
import os
import mfem.ser as mfem
from mfem.ser import intArray
from os.path import expanduser, join, dirname
import numpy as np
from numpy import sin, cos, exp
# time.clock deprecated and removed in PY3.8
import time
try:
clock = t... | mfem/PyMFEM | examples/ex5.py | Python | bsd-3-clause | 9,052 | [
"ParaView"
] | 265fc40c0e46a43634b46bd15d65a9214d7a9e56636a326119127dab8746ecbf |
# -*- coding: utf-8 -*-
# Generated by Django 1.11.3 on 2017-07-27 11:23
from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
('stein', '0021_auto_20170707_1744'),
]
operations = [
migrations.AlterModelOptions(
name='classification',
... | GeoMatDigital/django-geomat | geomat/stein/migrations/0024_auto_20170727_1323.py | Python | bsd-3-clause | 612 | [
"CRYSTAL"
] | f4c933bd0b202265f28ee77fdf4511aebf3f97319d4c761b603f49202e5ac7da |
# CREATED:2015-09-16 14:46:47 by Brian McFee <brian.mcfee@nyu.edu>
# -*- encoding: utf-8 -*-
'''Evaluation criteria for hierarchical structure analysis.
Hierarchical structure analysis seeks to annotate a track with a nested
decomposition of the temporal elements of the piece, effectively providing
a kind of "parse tr... | craffel/mir_eval | mir_eval/hierarchy.py | Python | mit | 24,990 | [
"Brian"
] | a78de9a08215069bc02f0e8c859480f4efe4455fff63c8779788f36de0e3c346 |
""" Test class for Job Cleaning Agent
"""
import pytest
from mock import MagicMock
# DIRAC Components
from DIRAC.WorkloadManagementSystem.Agent.JobCleaningAgent import JobCleaningAgent
from DIRAC import gLogger
gLogger.setLevel("DEBUG")
# Mock Objects
mockReply = MagicMock()
mockAM = MagicMock()
mockNone = MagicMock... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/test/Test_Agent_JobCleaningAgent.py | Python | gpl-3.0 | 5,418 | [
"DIRAC"
] | 441574899b1afda463ae1134812e6dd3f47b204f677abd8512daa57c40f14bb0 |
#!/usr/bin/env python2
from subprocess import Popen, PIPE
import multiprocessing as mp
import numpy as np
import os
import re
__DIR_PATH__ = os.path.dirname(os.path.realpath(__file__))
__RUN__ = __DIR_PATH__ + "/run_mopac"
__PWD__ = os.getcwd()
__SCRATCH__ = __PWD__
def shell(cmd, shell=False):
if shell:
... | ppqm/fitting | deprecated/bin/mopac.py | Python | cc0-1.0 | 4,532 | [
"MOPAC"
] | b5b332302dcd9026db96760f176c201c607013ef2be18dec08eaa88429c1acdd |
from __future__ import division
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
import pytest
from sklearn.datasets import load_digits, load_iris
from sklearn.model_selection import train_test_split
from sklearn.model_selection import cross_val_score
from sklearn.externals.six.moves impo... | vortex-ape/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 26,086 | [
"Gaussian"
] | 92d4264655a0219a969e9ee04c0a5f0d380621612256a296e69dd01d9f753b77 |
import numpy as np
import pytest
import rmsd
from context import MOPAC_OPTIONS, RESOURCES
from ppqm import chembridge, mopac, tasks
def _get_options(scr):
mopac_options = {"scr": scr, **MOPAC_OPTIONS}
return mopac_options
def test_optimize_water_and_get_energy(tmpdir):
smi = "O"
# Get molecule
... | ppqm/ppqm | tests/test_mopac.py | Python | mit | 3,853 | [
"MOPAC"
] | 2ab6707c8fbb2158ba2f30f20ec2b1956590d59b3575a1062db77ae3d49b0bf9 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RLumi(RPackage):
"""The lumi package provides an integrated solution for the Illumina
... | rspavel/spack | var/spack/repos/builtin/packages/r-lumi/package.py | Python | lgpl-2.1 | 1,762 | [
"Bioconductor"
] | 7cd3fa4f5ee17ca0639b6c7392e6b700750a1aa53f04357860bbdf4313fba448 |
# Copyright (C) 2008, 2009 Sayamindu Dasgupta <sayamindu@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
... | Boquete/activity-scribble | scribblewidget.py | Python | gpl-2.0 | 9,291 | [
"FLEUR"
] | 64e78bdbf4ed6a9b8b071e391c68fafe37f3c4dc2c8325e9b2a3e06e6f1b073a |
# 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)
from spack import *
class RMergemaid(RPackage):
"""Merge Maid.
The functions in this R extension are intende... | LLNL/spack | var/spack/repos/builtin/packages/r-mergemaid/package.py | Python | lgpl-2.1 | 1,710 | [
"Bioconductor"
] | ba0de0ff77ece349b44e59ff558682cdb1eeb0e01778aef4c39cd2175b6bcba1 |
""":mod:`ShopOfOffers` -- Contains the ShopOfOffers class
.. module:: ShopOfOffers
:synopsis: Contains the ShopOfOffers class
.. moduleauthor:: Joshua Gilman <joshuagilman@gmail.com>
"""
from neolib.daily.Daily import Daily
from neolib.exceptions import dailyAlreadyDone
from neolib.exceptions import parseException... | jmgilman/Neolib | neolib/daily/ShopOfOffers.py | Python | mit | 1,392 | [
"VisIt"
] | bfcfe1eb4f0a785c1768d1fc09bed06c26f29c60fefb2909cf58658bf3c4b356 |
import copy
import re
import urllib
import cv2
import numpy as np
import urllib3
from . import config
from .course import Course, courseTimeParser
import datetime
import threading
from queue import Queue
urllib3.disable_warnings()
def capture_idft_worker(qin):
from . import capture
while True:
img... | a710128/Lesson9 | API/user.py | Python | mit | 6,589 | [
"VisIt"
] | b081fdd884bd8d7659146d8d3e2e6b759e83338d07e6d766348b4ddb10278b84 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
from pymatgen.analysis.structure_prediction.substitution_probability import (
SubstitutionPredictor,
SubstitutionProbability,
)
from pymatgen.core.composition import Composition
... | materialsproject/pymatgen | pymatgen/analysis/structure_prediction/tests/test_substitution_probability.py | Python | mit | 3,655 | [
"pymatgen"
] | dccfc166f5314acc22a98b85ba966b545b899a56ef082dccd9e4f8610aa82545 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 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... | eustislab/horton | horton/io/molpro.py | Python | gpl-3.0 | 5,610 | [
"Molpro"
] | 0e22f36b3f161787180c2ab9aceff8fb69bdbdff22491ca02d77c4200b076bfb |
"""
Protein
=======
"""
import logging
import requests
import shutil
import pandas as pd
import numpy as np
import os.path as op
import json
import seaborn as sns
from slugify import Slugify
from collections import defaultdict
from six.moves.urllib.error import URLError
from Bio.Seq import Seq
from Bio import SeqIO
f... | nmih/ssbio | ssbio/core/protein.py | Python | mit | 196,135 | [
"BLAST",
"Biopython"
] | 95b755a487b123bf6779b6e01e54766c1206534770f7afa9233f6648a1417d60 |
import catmap
from catmap import ReactionModelWrapper
from catmap.model import ReactionModel
from catmap import string2symbols
IdealGasThermo = catmap.IdealGasThermo
HarmonicThermo = catmap.HarmonicThermo
molecule = catmap.molecule
np = catmap.np
copy = catmap.copy
class ThermoCorrections(ReactionModelWrapper):
""... | starry99/catmap | catmap/thermodynamics/enthalpy_entropy.py | Python | gpl-3.0 | 21,455 | [
"ASE"
] | a94891ef32ce5bbeabd00a41a296e7ce733d74f59653fb188e3124cd410a1702 |
from aiida import load_dbenv
load_dbenv()
from aiida.orm import Code, DataFactory
import numpy as np
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
codename = 'lammps_comb@boston'
############################
# Define input parameters #
############################
a = 5.404
ce... | abelcarreras/aiida_extensions | plugins/launcher/launch_lammps_combinate.py | Python | mit | 3,459 | [
"LAMMPS"
] | 04d96fe483d16932abd6f0cd53c0007aca89848b6bcde137b2c553509dfae4d4 |
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