text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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from django.core.management.base import BaseCommand, make_option, CommandError
from time import time
import path
from django.db import transaction
import ast
import logging
logger = logging.getLogger(__name__)
class CallCollector(ast.NodeVisitor):
'''
A class for visiting nodes, copied and modified from... | nanchenchen/script-analysis | pyanalysis/apps/enhance/management/commands/extract_function_calls.py | Python | mit | 2,576 | [
"VisIt"
] | 2da75f6102e1642d35e6ff995d283f9861dde725862c115fb1987ca996c7e913 |
"""Compute WFS driving functions.
.. include:: math-definitions.rst
.. plot::
:context: reset
import matplotlib.pyplot as plt
import numpy as np
import sfs
from scipy.signal import unit_impulse
# Plane wave
npw = sfs.util.direction_vector(np.radians(-45))
# Point source
xs = -1.... | sfstoolbox/sfs-python | sfs/td/wfs.py | Python | mit | 12,900 | [
"DIRAC"
] | 9851c1ce2c3bc667c68479f6325c1e2e0b0cd3f56c1b13a879ec8b5fca99b5b2 |
import django
from django.db.models import Q, FieldDoesNotExist
if django.VERSION >= (1, 8):
from django.db.models.expressions import Expression, Col
else:
from django.db.models.expressions import ExpressionNode as Expression
from django.db.models.sql.where import WhereNode, AND, Constraint
from collections imp... | philippeowagner/django-hvad | hvad/query.py | Python | bsd-3-clause | 6,968 | [
"VisIt"
] | 1cf4114b0c1e1c186ba52ad8ceca3a1792afcf62cb91e1c23aae7ae858446c58 |
from email import message_from_string
from email.MIMEMultipart import MIMEMultipart
from email.MIMEBase import MIMEBase
from email.MIMEImage import MIMEImage
from email.MIMEText import MIMEText
from email.Utils import COMMASPACE, formatdate
from email import Encoders
import sys
import unittest
class TestContactBase64E... | detrout/pykolab | tests/unit/test-011-base64_encoded_contact.py | Python | gpl-3.0 | 3,039 | [
"VisIt"
] | ae062ba9feed50c348ffb08282783e3e6a844287fcd19e9d38ab95912e059c08 |
# 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 (t... | apache/allura | Allura/allura/command/create_trove_categories.py | Python | apache-2.0 | 134,605 | [
"CRYSTAL"
] | 3543d7964dda1bb47cceabed5f94de967663cc2e02fd96f2b51b3a0339d315d8 |
"""Support the ElkM1 Gold and ElkM1 EZ8 alarm/integration panels."""
from __future__ import annotations
import asyncio
import logging
import re
from types import MappingProxyType
from typing import Any
import async_timeout
import elkm1_lib as elkm1
import voluptuous as vol
from homeassistant.config_entries import SO... | lukas-hetzenecker/home-assistant | homeassistant/components/elkm1/__init__.py | Python | apache-2.0 | 15,069 | [
"Elk"
] | 02f2844fb743a631ae2acbbabc02f521eb5a9b43eafbf510fc9c71e08af4a996 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005, 2006 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program 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 Soft... | andrebellafronte/stoq | stoqlib/gui/editors/profileeditor.py | Python | gpl-2.0 | 3,880 | [
"VisIt"
] | 6798532a3dd59509a211538f910c53a19cd90f8cfe968c61ab7c0c2e84413b34 |
"""
Create a profile from an ASCII CTD datafile
===========================================
Use the TAMOC ambient module to create profiles in netCDF format for use by
TAMOC from data in text files downloaded from a CTD. This file demonstrates
working with the data from the R/V Brooks McCall at Station BM 54 on May ... | socolofs/tamoc | bin/ambient/np_profile_from_ctd.py | Python | mit | 5,414 | [
"NetCDF"
] | ea595e963c376f9be5584ea82387cc374df6567374aa800bc352a6777b2ec770 |
#!/usr/bin/env python
# NetView P v.0.7 - Linux
# Dependencies: PLINK
# Eike Steinig
# Zenger Lab, JCU
# https://github.com/esteinig/netview
import os
import time
import shutil
import argparse
import subprocess
import numpy as np
import multiprocessing as mp
import scipy.sparse.csgraph as csg
import scipy.spatial.dist... | esteinig/netviewP | program/linux/0.7/netview.py | Python | gpl-2.0 | 28,716 | [
"Biopython"
] | 13575270fe0e16a3038a6ffcef7d313f6d51dc5f8e12319f7841579f60bcc943 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Find regions of first bed file that overlap regions in a second bed file. This
program performs a base-by-base intersection, so only runs of bases that are
covered in both of the inputs will be output.
usage: %prog bed_file_1 bed_file_2
"""
import sys
from warnings import... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/bed_intersect_basewise.py | Python | bsd-3-clause | 1,011 | [
"Galaxy"
] | 9124a8db2787bb7b52cce9a493693994782a24e903f6ef8beb044bf619f75db4 |
import re
import os
from markdown.util import etree
from markdown.util import AtomicString
import logging
log = logging.getLogger(__name__)
import MooseDocs
from markdown.inlinepatterns import Pattern
from MooseCommonExtension import MooseCommonExtension
import utils
class MooseBuildStatus(MooseCommonExtension, Patte... | vityurkiv/Ox | python/MooseDocs/extensions/MooseBuildStatus.py | Python | lgpl-2.1 | 3,133 | [
"MOOSE"
] | 1a67d9a1688e6e914b8a496a57f5dc346cc5cb24a6db6eba1b92182086ca21b4 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The maths module provides higher-level interfaces to some of the operations
that can be performed with the niftysegmaths (seg_maths) command-line program.
"""
import os
import numpy as np
from ... | fprados/nipype | nipype/interfaces/niftyseg/maths.py | Python | bsd-3-clause | 7,605 | [
"Gaussian"
] | d7f9d10da899c69a2dc0b094c6056c385a090bf0874fbc0842f499b287c16e1f |
"""
Generalized Linear Models with Exponential Dispersion Family
"""
# Author: Christian Lorentzen <lorentzen.ch@googlemail.com>
# some parts and tricks stolen from other sklearn files.
# License: BSD 3 clause
import numbers
import numpy as np
import scipy.optimize
from ...base import BaseEstimator, RegressorMixin
... | kevin-intel/scikit-learn | sklearn/linear_model/_glm/glm.py | Python | bsd-3-clause | 25,371 | [
"Gaussian"
] | 4bad13d64101645c66d675edc6803a3be9b3e1953b3be60c6cd75431430927f8 |
from itertools import count
import logging
import networkx
import ailment
from claripy.utils.orderedset import OrderedSet
from ...utils.graph import dfs_back_edges, subgraph_between_nodes, dominates, shallow_reverse
from .. import Analysis, register_analysis
from .utils import replace_last_statement
from .structurer... | angr/angr | angr/analyses/decompiler/region_identifier.py | Python | bsd-2-clause | 30,800 | [
"VisIt"
] | 0a0f4e387d48d7e86ccf48f7bd82668a2084f41db17d8d8798903860f86a993c |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/core/test_atomselections.py | Python | gpl-2.0 | 49,876 | [
"MDAnalysis",
"RDKit"
] | c9960877709b579b7f37f03f445e553100c20860ed2e7257c8b979c10c30d480 |
"""
<Author>
Justin Cappos
<Start Date>
March 14th, 2013
<Description>
A basic library that demonstrates PolyHash when applied to passwords (see
https://polypasswordhasher.poly.edu/ for details). This includes thresholdless
password support via AES 256.
<Usage>
import polypasswordhasher
# require kn... | PolyPasswordHasher/PolyPasswordHasher-Python | polypasswordhasher/__init__.py | Python | mit | 2,451 | [
"MOE"
] | 7ef2f66955b6a1469f3bec8019e0b070efa501576990fd64f03bd59bfa75c4fc |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_mixins import simpleVTKClassModuleBase
import vtk
class extractEdges(simpleVTKClassModuleBase):
def __init__(self, module_manager):
simpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkExtractEdges()... | nagyistoce/devide | modules/user/extractEdges.py | Python | bsd-3-clause | 474 | [
"VTK"
] | 0b659b2a034e9a8f300a81f6ab929f1c926c57e3b9ff853fa8ddfe294b914598 |
#!/usr/bin/python3
# encoding=utf-8
#
# Copyright © 2015 Alexandre Detiste <alexandre@detiste.be>
#
# 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... | a-detiste/game-data-packager | game_data_packager/gog.py | Python | gpl-2.0 | 6,641 | [
"VisIt"
] | fd89fc696aae71a5805e4f61909c4745c51983e66ef41a126d732c4527d5b829 |
# -*- coding: utf-8 -*-
"""
Statistical measures of spike trains (e.g., Fano factor) and functions to
estimate firing rates.
Tutorial
--------
:doc:`View tutorial <../tutorials/statistics>`
Run tutorial interactively:
.. image:: https://mybinder.org/badge.svg
:target: https://mybinder.org/v2/gh/NeuralEnsemble/el... | alperyeg/elephant | elephant/statistics.py | Python | bsd-3-clause | 44,651 | [
"Gaussian",
"NEURON"
] | be8175a726b6d6b6a4f973514894626780a381149b4adaa715022a31fab16bd3 |
##############################################################################
# Copyright (c) 2013-2017, 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... | wscullin/spack | var/spack/repos/builtin/packages/r-mclust/package.py | Python | lgpl-2.1 | 1,611 | [
"Gaussian"
] | 3ce3f5c8e2ad47fce8409691f90d6a6cbe6ce8f13c4f421c3e20832a7cd07778 |
import param
import numpy as np
import imagen as ig
from topo.base.arrayutil import DivideWithConstant, MultiplyWithConstant
from topo.base.projection import SheetMask, CircularMask
from topo import optimized, projection, sheet
from topo.sparse.sparsecf import SparseConnectionField, CFPLF_Hebbian_Sparse,\
... | ioam/topographica | topo/submodel/scal.py | Python | bsd-3-clause | 13,601 | [
"Gaussian"
] | 613c4d2a14cc93a07c5f42b668e64df3a775d0c66f638fe34e9d1d0d8d64e92b |
"""Provide analysis of input files by chromosomal regions.
Handle splitting and analysis of files from chromosomal subsets separated by
no-read regions.
"""
import collections
import os
import toolz as tz
from bcbio.distributed.split import parallel_split_combine
def get_max_counts(samples):
"""Retrieve the max... | SciLifeLab/bcbio-nextgen | bcbio/pipeline/region.py | Python | mit | 5,873 | [
"Galaxy"
] | a5c020a32de8c067dd547a0593b23f9ff50f58aa33481519b2b7f316d2082082 |
##########################################################################################
# ______ ______ ___ #
# | ___ \ | _ \ / _ \ #
# | |_/ / | | | ... | jomoeller/bda | ovitos_bcc-defect-analysis.py | Python | gpl-3.0 | 27,806 | [
"OVITO",
"VisIt"
] | c810769cb3945bf5da31a8da91086800883851221d999d585c92874b35af28df |
# Copyright 2016 Intel Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | brainiak/brainiak | tests/utils/test_fmrisim.py | Python | apache-2.0 | 37,943 | [
"Gaussian"
] | 500b57332ade0a9956720261ef4e89c54d5ad953fff56befc75d8903cf359dec |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
from __future__ import unicode_literals
from nose.plugins.attrib import attr
from base_studio_test import StudioCourseTest
from bok_choy.promise import EmptyPromise
from ...fixtures.course import XBlockFixtureDesc
from ..helpers import create_user_par... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 19,760 | [
"VisIt"
] | f3b135576f4cddaf057bce4af200634663ae8a6375918116998ac5a8650b34de |
#!/usr/bin/env python3
"""
sa.py
Parse and possibly sanity-check a .sa file output by bowtie2-build in --sa
mode. These files have a very simple format: first is a uint32_t containing
the length of the suffix array, the rest is an array of that many uint32_ts
containing the suffix array.
"""
import sys
import struc... | BenLangmead/bowtie2 | scripts/sa.py | Python | gpl-3.0 | 2,150 | [
"Bowtie"
] | 13224ef9930156a11607005fd5be8f567b8171ddac9e949282d7ea994b0ba179 |
#!/usr/bin/python
# Copyright: Ansible Project
# 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',
'status': ['preview'],
... | valentin-krasontovitsch/ansible | lib/ansible/modules/cloud/amazon/elb_classic_lb.py | Python | gpl-3.0 | 53,523 | [
"Dalton"
] | b593dbc15bb0009ed067a422bafd04dffc57e4357220d4372df943108ffbd12b |
from django.db.models import Q
from django.utils.timezone import utc
import datetime
from django.contrib.sites.models import get_current_site
import string
import random
from django.conf.urls import url
from django.contrib.auth.models import Group, User, Permission
from django.contrib.auth import authenticate, login, l... | SYNHAK/spiff | spiff/membership/v1_api.py | Python | agpl-3.0 | 16,362 | [
"VisIt"
] | 05ce69e0c4343810e80c90aa6084fcca8a85277be7c9fbf0a7fc0c1b760ab8c3 |
#########################################################################################
# $HeadURL$
# Condor.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" Condor.py is a DIRAC independent class representing Condor batch system.
Condor... | Sbalbp/DIRAC | Resources/Computing/BatchSystems/Condor.py | Python | gpl-3.0 | 6,780 | [
"DIRAC"
] | 8db4d5b4d980c9c120949c760313dee3b03eb73bfc6db1fb07346c8ddb2087e4 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jairideout/scikit-bio | skbio/tree/_nj.py | Python | bsd-3-clause | 11,039 | [
"scikit-bio"
] | 802ca8c3b05ed0799c761101eaf25723dd64f61a1c846b38e5c9d903f0add958 |
""" General Message Queue Interface to create Consumers and Producers
"""
from DIRAC import gLogger, S_OK
from DIRAC.Resources.MessageQueue.MQProducer import MQProducer
from DIRAC.Resources.MessageQueue.MQConsumer import MQConsumer
from DIRAC.Resources.MessageQueue.MQConnectionManager import MQConnectionManager
from D... | andresailer/DIRAC | Resources/MessageQueue/MQCommunication.py | Python | gpl-3.0 | 2,859 | [
"DIRAC"
] | b832e54ed87029295339f537b2b4712b2e606c56304df357756fa5af4efe6ebc |
# Copyright (C) 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 versio... | espressomd/espresso | testsuite/scripts/tutorials/test_lennard_jones.py | Python | gpl-3.0 | 1,432 | [
"ESPResSo"
] | 5da3493eca91595d034276d923b09e9aaea4b2cd724f788e6271499be1b4b1cc |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import pytest
import ansible.con... | maxamillion/ansible | test/units/galaxy/test_token.py | Python | gpl-3.0 | 1,694 | [
"Galaxy"
] | 721f166ebf662bc7f13699ee408e44ffb8a1e4f3a23dfacb1f14cff094150acf |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
TODO:
-Still assumes individual elements have their own chempots
in a molecular adsorbate instead of considering a single
chempot for a single molecular adsorbate. E.g. for an OH
... | dongsenfo/pymatgen | pymatgen/analysis/surface_analysis.py | Python | mit | 82,680 | [
"VASP",
"pymatgen"
] | 57296a7c16ed0af27f9911e4569fdd23b693bed563648d81855d96d147a22c40 |
#
# @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/frac.py | Python | lgpl-3.0 | 26,954 | [
"Psi4"
] | c556f01ac7e566edea75fc6024d0a7470873165846f49759ab29ed08db9d103f |
import sqlite3
import urllib
import re
from urllib.request import urlopen
from bs4 import BeautifulSoup, NavigableString
from phyllo.phyllo_logger import logger
import nltk
from itertools import cycle
nltk.download('punkt')
from nltk import sent_tokenize
sen=''
def parseRes2(soup, title, url, cur, author, date, col... | oudalab/phyllo | phyllo/extractors/columbusDB.py | Python | apache-2.0 | 2,494 | [
"COLUMBUS"
] | 4c5a9de7c5e06eaefdf22c26be2056383863aec208dda04d26dfc72e96364cee |
#!/usr/bin/env python
"""
A program to solve the 2D Klein Gordon equation using a
second order semi-explicit method
More information on visualization can be found on the Mayavi
website, in particular:
http://github.enthought.com/mayavi/mayavi/mlab.html
which was last checked on 6 April 2012
"""
import math
import n... | openmichigan/PSNM | PythonPrograms/Programs/PythonCode/KleinGordonImp2Db.py | Python | bsd-2-clause | 4,679 | [
"Mayavi"
] | 62cf6ecc1727d2b6de818ca10da3a744abbd261d45f4c7335c04895fa4b9e1a1 |
# -*- 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 import defaults as default_views
from .router import urlpatterns as api_urlpatterns
... | javipalanca/ojoalplato | config/urls.py | Python | mit | 3,494 | [
"VisIt"
] | ec22fbee1e05be434fd000819b920d9602c0e1efe47fced0bf0838535322ae85 |
"""
This file is part of gempy.
Created on 07.08.2019
@author: Jan von Harten
"""
import warnings
try:
from scipy.spatial.distance import cdist
except ImportError:
warnings.warn('scipy.spatial package is not installed.')
import numpy as np
import pandas as pd
from gempy.plot import _visualization_2d, _plot,... | cgre-aachen/gempy | gempy/assets/kriging.py | Python | lgpl-3.0 | 24,097 | [
"Gaussian"
] | ca02e185b10a3d711052cf29337a5f9b5d76eaab173043ce5557166bd76ba489 |
#!/usr/bin/env python
#
# Modified based on MINDO/3 implementation in PyQuante-1.6
#
'''
MINDO/3
Ref:
[1] R. C. Bingham, M. J. Dewar, D. H. Lo, J. Am. Chem. Soc., 97, 1285 (1975)
[2] D. F. Lewis, Chem. Rev. 86, 1111 (1986).
'''
import copy
import numpy
from pyscf import lib
from pyscf.lib import logger
from pyscf im... | gkc1000/pyscf | pyscf/semiempirical/mindo3.py | Python | apache-2.0 | 12,861 | [
"PySCF"
] | eea6fc910000a2e1af531155f7750d880f8c373089b6a09e2232a88548ee059b |
# Copyright 2017 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | tensorflow/transform | tensorflow_transform/mappers.py | Python | apache-2.0 | 95,662 | [
"Gaussian"
] | 5a203913fb83ed9e09006b55a430801bab85ce7f4523713ec943d2fc2d3711fc |
"""
Tests a variety of potentially problematic disulfides. Disulfides between
two same resids on different chains, disulfides on the same chain, and
unrelated disulfides on different chains.
Also tests how chains are handled when Maestro puts a capping group
with resid -1 on them
"""
import os
from vmd import molecul... | drorlab/dabble | test/relaxin/test_relaxin.py | Python | gpl-2.0 | 2,483 | [
"Amber",
"CHARMM",
"VMD"
] | 7b581669e97c51b2ca6239b04a37289fd344e0f5425e882ad3ead5443bdfc8f5 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_exc.py | Python | apache-2.0 | 1,305 | [
"PySCF"
] | 1d422dec9f7954eb7b97869c2df9220a4cd4c9c57496a52e23a5b0d16c48c67d |
from django_select2.forms import HeavySelect2Widget
from django import forms
from django.conf import settings # NOQA
from django.contrib.admin.widgets import SELECT2_TRANSLATIONS
from django.utils.translation import get_language
from django.templatetags.static import static
class Select2(HeavySelect2Widget):
"""... | wetneb/dissemin | autocomplete/widgets.py | Python | agpl-3.0 | 1,257 | [
"VisIt"
] | f497ca42afdf9c9ab1096d04da22f34ab0ce85661280417342b219886eeea848 |
from __future__ import print_function
from gpaw import *
from ase import *
import numpy as np
atom = Atoms(symbols='KTaO3',
pbc=np.array([ True, True, True], dtype=bool),
cell=np.array(
[[ 4., 0., 0.],
[ 0., 4., 0.],
... | robwarm/gpaw-symm | doc/tutorials/band_gap/gllbsc_band_gap.py | Python | gpl-3.0 | 1,263 | [
"ASE",
"GPAW"
] | b1db095a1e34c2ad187142e02d6c43e35d492ad3debf4ceb6f5ac83c18df0036 |
'''
Created on 29/03/2010
@author: jose
'''
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of project.
# franklin is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software... | JoseBlanca/franklin | test/backbone/mapping_test.py | Python | agpl-3.0 | 19,660 | [
"BLAST"
] | 2717b3177fe0accde9258b9ff9efee0c1b98a4b0c8c3a3f8811de3ea4d5fdc6d |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | Jozhogg/iris | lib/iris/tests/test_grib_load.py | Python | lgpl-3.0 | 28,575 | [
"Gaussian"
] | 8b1152ed72fa818d892e71521b505dd8a43c4b61c6b4a41fecd2ccd2b40c361d |
import sys, os
class printio():
"""Functions to print comments"""
def __init__(self):
pass
# self.prompt = 0
# self.message = m.Message_Dialog()
# self.message.quit_btn.clicked.connect(self.message_quit_signal)
# self.message.continue_btn.clicked.connect(self.message_con... | emptyewer/DEEPN | functions/printio_gui.py | Python | mit | 3,631 | [
"BLAST"
] | 8be1c863d502a6cc323c4ca9c7f58149bc42baa1a85ff8e884334b7b6edc8077 |
# Copyright 2001 by Gavin E. Crooks. 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.
""" Handle the SCOP HIErarchy files, which describe the SCOP hierarchy in
terms of SCOP uni... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/SCOP/Hie.py | Python | mit | 2,742 | [
"Biopython"
] | 205e32538f142473b2fe7fbd5e2be45d488a13bd550d4d89ef9c202f9769b480 |
# -*- coding: utf-8 -*-
#
# 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
#... | owlabs/incubator-airflow | tests/plugins/test_plugin.py | Python | apache-2.0 | 4,249 | [
"Galaxy"
] | edeb6c14e3b2eb4de8916cb92c49ec8e3d072fd2cf101bde44f4ee93f8f8e7ca |
r"""*File I/O helpers for* ``sphobjinv``.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
5 Nov 2017
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
https://github.com/bskinn/sphob... | bskinn/sphobjinv | src/sphobjinv/fileops.py | Python | mit | 3,152 | [
"Brian"
] | 1a438e52225ec2c0883bf7aefd0760e6f51ddc0560bcdd37899233aa5fe849d5 |
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# 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
# ... | rdkit/rdkit | Contrib/mmpa/search_mmp_db.py | Python | bsd-3-clause | 16,265 | [
"RDKit"
] | 43852bade8e83cf99793c26b80e0a070e8d43f2ff9cb60100cff68ecd9d4d469 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009-2010 Benny Malengier <benny.malengier@gramps-project.org>
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2010 Tim Lyons
# Copyright (C) 2011 ... | sam-m888/gprime | gprime/plugins/docgen/htmldoc.py | Python | gpl-2.0 | 22,518 | [
"Brian"
] | 6cd3f21eecf6270b7a615390c2b82e13aaed5b426d5ee42ab851e5d93a1a2e0d |
""" Oriented graph aka ERD painter """
import types
import os
import sys
# local file subprocess24 is imported only for <2.4
if sys.version_info[:3] < (2, 4, 2):
import subprocess24 as subprocess
else:
import subprocess
class Dot:
"""Oriented graph aka ERD painter.
This class requires GraphViz instal... | sawdog/OraclePyDoc | oraclepydoc/dot.py | Python | gpl-2.0 | 7,213 | [
"VisIt"
] | e73467218e972cac352d92006b2e10a8acc9e279ce987ec1ca21ebbbadfa4edc |
# -*- Mode: Python; test-case-name: flumotion.test.test_common_componentui -*-
# vi:si:et:sw=4:sts=4:ts=4
#
# Flumotion - a streaming media server
# Copyright (C) 2008 Fluendo, S.L. (www.fluendo.com).
# All rights reserved.
# This file may be distributed and/or modified under the terms of
# the GNU General Public Lice... | ylatuya/Flumotion | flumotion/test/test_common_xmlwriter.py | Python | gpl-2.0 | 4,958 | [
"DIRAC"
] | 048975420491a6b21d307a0134b97b5e1abf93ea02ede8f15345901e0009ed80 |
# A simple image denoising example
# The example 1D image is one of the examples from
# C. R. Vogel, Computational Methods for Inverse Problems,
# Frontiers in Applied Mathematics Series #23, SIAM, Philadelphia, 2002.
try:
from scipy.linalg import toeplitz
except:
raise ImportError, 'SciPy is required for th... | dpo/nlpy | examples/demo_image.py | Python | gpl-3.0 | 4,920 | [
"Gaussian"
] | 97a1cfec2caa3e84eea67d6023d763928de3fdb268a4398905ae08b68cbfabb7 |
import sys, config
import galaxy.model
from galaxy.web import security
class UniverseApplication( object ):
"""Encapsulates the state of a Universe application"""
def __init__( self, **kwargs ):
print >> sys.stderr, "python path is: " + ", ".join( sys.path )
# Read config file and check for err... | volpino/Yeps-EURAC | lib/galaxy/webapps/reports/app.py | Python | mit | 1,162 | [
"Galaxy"
] | 19c40704b5c9eee362df97132cf02e1f7bcd82aac4593f773de98475258613bd |
#!/usr/bin/env python2.7
"""
smartSam2Fastq.py: turn sorted-by-names SAM input into a properly deduplicated
FASTQ. Also work around the bug in bwa mem where some even-length alignments to
reverse strands of alts will have incorrect bases for one of the middle two
bases.
accounts for both secondary and supplementary al... | adamnovak/hgvm-graph-bakeoff-evaluations | scripts/smartSam2Fastq.py | Python | mit | 16,296 | [
"BWA",
"pysam"
] | 516b5cb4f43c3581e55642a1dfe473cd5ad37d701560924d6d6d4f2374e3e6c8 |
#!/usr/bin/env python
import os
import sys
import math
import time
import importlib
import sysconfig
import subprocess
import collections
if sys.version_info <= (3, 0):
print('Much of this script needs py3')
sys.exit()
# good
#import numpy as np
#import psi4
# bad
import psi4
import numpy as np
def test_t... | ashutoshvt/psi4 | psi4/share/psi4/scripts/test_threading.py | Python | lgpl-3.0 | 10,851 | [
"Psi4"
] | f9178336440321a0cf57728cb9b44d3c69f4672f3fda6a570078582216bfd6b6 |
#!/usr/bin/env python
################################################################################
# Copyright (C) 2014, 2015 GenAP, McGill University and Genome Quebec Innovation Centre
#
# This file is part of MUGQIC Pipelines.
#
# MUGQIC Pipelines is free software: you can redistribute it and/or modify
# it und... | ccmbioinfo/mugqic_pipelines | bfx/htseq.py | Python | lgpl-3.0 | 1,636 | [
"HTSeq"
] | c0c071a6fdb28b11da196f13cc506dbede1dc52c4542e302e7cbf48cdc83e17e |
import numpy as np
import pytest
from pandas.errors import UnsupportedFunctionCall
import pandas.util._test_decorators as td
from pandas import (
DataFrame,
Series,
Timedelta,
concat,
date_range,
)
import pandas._testing as tm
from pandas.api.indexers import BaseIndexer
@td.skip_if_no_scipy
def ... | rs2/pandas | pandas/tests/window/test_win_type.py | Python | bsd-3-clause | 4,929 | [
"Gaussian"
] | 139498c32d211383a875f0c77f4285aad2c99e75cf5ce4e6986a6846ab2cf22c |
import numpy as np
from .linear_regression import gaussian_basis
from sklearn.metrics import pairwise_kernels
class NadarayaWatson(object):
"""Nadaraya-Watson Kernel Regression
This is basically a gaussian-weighted moving average of points
Parameters
----------
kernel : string
kernel is ... | nhuntwalker/astroML | astroML/linear_model/kernel_regression.py | Python | bsd-2-clause | 1,568 | [
"Gaussian"
] | 7525bc2f8b4ed962e3a7c553a3a511efba91a5d4111e0668c4b923f1812de6bd |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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 ... | andysim/psi4 | psi4/driver/procrouting/interface_cfour.py | Python | gpl-2.0 | 19,001 | [
"CFOUR",
"Psi4"
] | f7216e0e027ae92d642b65d5262c1b375db5f43c0d0b44879732260531592ab6 |
import gzip
from urllib.request import urlretrieve
from pkg_resources import resource_filename
def get_example_model(model):
"""
Fetches the specified model from bnlearn repository and returns a
pgmpy.model instance.
Parameter
---------
model: str
Any model from bnlearn repository (ht... | pgmpy/pgmpy | pgmpy/utils/utils.py | Python | mit | 3,733 | [
"Gaussian"
] | 0ed76aaa3c588d6f0053949d69bedfc487a9bb772224d5a56a4c73f0e3455828 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | yajiedesign/mxnet | tests/python/unittest/test_gluon_probability_v2.py | Python | apache-2.0 | 93,954 | [
"Gaussian"
] | 49dbce18b7837b4b2e8077cc0429c567d5fc2897cb266bfe00a2febb7b0ba8de |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from TestHa... | harterj/moose | python/TestHarness/tests/test_DistributedMesh.py | Python | lgpl-2.1 | 1,104 | [
"MOOSE"
] | 7654133639d19643e97f80cc8d186821f89d6a7e9c149b321c7e29865cb8f10b |
# pylint: disable=bad-continuation
"""
Certificate HTML webview.
"""
import logging
import urllib
from datetime import datetime
from uuid import uuid4
import pytz
from django.conf import settings
from django.contrib.auth.models import User
from django.http import Http404, HttpResponse
from django.template import Reque... | CredoReference/edx-platform | lms/djangoapps/certificates/views/webview.py | Python | agpl-3.0 | 32,051 | [
"VisIt"
] | 5fbf8ea0dd8ba2d5e0820070d731720a0b7d56ab6cabca6c2bda0701ea488e8f |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/main/templatetags/contentblock.py | Python | apache-2.0 | 1,667 | [
"Galaxy"
] | b50f42be6bebc37167a2ee50313ce914494ab3477697c8b156c5985342a376db |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | GoogleCloudPlatform/explainable_ai_sdk | explainable_ai_sdk/common/explain_metadata.py | Python | apache-2.0 | 94,321 | [
"Elk",
"Gaussian"
] | f16fdb3bfe2623101e1d1e70e1b3733c2e66be2e7e5f68e952c220a4dcc9f9c7 |
# coding: utf-8
from __future__ import unicode_literals
import unittest
import os
import json
from pymatgen import Spin, Orbital
from pymatgen.electronic_structure.dos import CompleteDos
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
try:
import scipy... | yanikou19/pymatgen | pymatgen/electronic_structure/tests/test_dos.py | Python | mit | 5,421 | [
"pymatgen"
] | 65fa2bb27298a5a64be10977a4f57d8c7552cb0833c73c3ca66df9fe6be6b3a5 |
########################################################################
# $HeadURL$
########################################################################
""" RemovalAgent takes removal requests from the RequestDB and executes them
:deprecated:
"""
__RCSID__ = "$Id$"
## from DIRAC
from DIRAC.FrameworkSystem.... | sposs/DIRAC | DataManagementSystem/Agent/RemovalAgent.py | Python | gpl-3.0 | 3,322 | [
"DIRAC"
] | 9d20e7b00f02f848cfcde00db6bec11d3edf501834a8ae725fe341608c65c36b |
import scipy.ndimage as ndimage
import numpy as np
import pylab
import gc
import os
from scipy import fftpack
from matplotlib.colors import LinearSegmentedColormap
import pyfits
def matrc1():
MatPlotParams = {'axes.titlesize': 15, 'axes.linewidth' : 2.5, 'axes.labelsize': 16, 'xtick.labelsize': 12, 'ytick.labelsiz... | vvinuv/kappabias | bias/kappa_utils.py | Python | gpl-2.0 | 15,514 | [
"Galaxy"
] | 8820d7354361db9d15ef22e154ebd963b06d3d1564f1b553ef00cfe74b7438de |
"""
# Notes:
- This simulation seeks to emulate the CUBA benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008).
- The time taken to si... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_CUBA_nosyn_0004/brian2_benchmark_CUBA_nosyn_0004.py | Python | gpl-3.0 | 1,997 | [
"Brian"
] | a22e13b97b26a99c89c91db40827881cdbe69488b9fbbc5f13559456ab3f769e |
"""Generic object and catalog classes for redmapper.
This file contains classes to describe numpy wrappers which makes things look
like the old idl code (for good or ill). It also makes some things a bit more
readable.
"""
import fitsio
import esutil as eu
import numpy as np
import itertools
class DataObject(objec... | erykoff/redmapper | redmapper/catalog.py | Python | apache-2.0 | 9,396 | [
"Galaxy"
] | bb763f956d8e2a263f8c6fac00efab9f2a5737b13999e32fc7883b6a573275c9 |
import os,sys
import numpy as np
import scipy.misc
from scipy import ndimage
import matplotlib
import matplotlib.pyplot as plt
from pylab import plot, loadtxt, imshow, show, xlabel, ylabel
'''
first, source 'ManifoldEM' conda environment;
#then run bash script (which will access this one) via: 'sh mrc2denoise.sh'
den... | hstau/covar-cryo | covariance/postProc/mrc2denoise.py | Python | gpl-2.0 | 1,976 | [
"Gaussian"
] | 0fbf4e3f959c07d3830445b8f15d6aa788cb31528a1f53222f341c4c8556ab03 |
# spud - keep track of photos
# Copyright (C) 2008-2013 Brian May
#
# 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.
#
# ... | brianmay/spud | spud/views.py | Python | gpl-3.0 | 11,895 | [
"Brian"
] | 4701b6685db06bf6fd57b785bb030d225482c6220b3da36753fa43b7231f94e7 |
# coding: utf-8
from django.conf import settings
from django.core.checks import Error
from django.db import connections
from django.utils.translation import ugettext as _
from kpi.management.commands.is_database_empty import (
test_table_exists_and_has_any_row,
)
class TwoDatabaseConfigurationChecker:
"""
... | onaio/kpi | kpi/utils/two_database_configuration_checker.py | Python | agpl-3.0 | 6,471 | [
"VisIt"
] | 7392aeaf76468719e2ded19848a70c18a7eb47c8743d1ba170a20f004bf69389 |
'''
Created on Oct 11, 2012
@author: gorgolewski
'''
#import os
#subjects = os.listdir("/scr/namibia1/baird/MPI_Project/Neuroimaging_Data/")
subjects = ['11065.70',
'07070.79',
'13061.30',
'18066.85',
'10576.44',
'11944.79',
'11111.28',
'13536.51',
'14102.d1',
'12522.80',
'06222.f4',
'13649.8d',
'13565.7c',
'14018.65... | NeuroanatomyAndConnectivity/pipelines | src/reading_by_default/variables.py | Python | mit | 7,033 | [
"NEURON"
] | f13af44f1484c7a38f7f8d130bf0cae81933d2c778d094105896d380b79162db |
"""Config flow for Elk-M1 Control integration."""
import asyncio
import logging
from urllib.parse import urlparse
import elkm1_lib as elkm1
import voluptuous as vol
from homeassistant import config_entries, exceptions
from homeassistant.const import (
CONF_ADDRESS,
CONF_HOST,
CONF_PASSWORD,
CONF_PREFI... | partofthething/home-assistant | homeassistant/components/elkm1/config_flow.py | Python | apache-2.0 | 4,893 | [
"Elk"
] | 2babb603e644ddf104472390b7cc9b1bc92122e5528b11528da4fc0a2b948c84 |
import warnings
warnings.simplefilter('always', DeprecationWarning)
import os
import functools
import os.path
import re
import urllib
import urllib2
import json
import imp
import random
import tabulate
from connection import H2OConnection
from job import H2OJob
from expr import ExprNode
from frame import H2OFrame, _py_... | mrgloom/h2o-3 | h2o-py/h2o/h2o.py | Python | apache-2.0 | 75,759 | [
"Gaussian"
] | 464b2cf8e47cb51cd685879229cc9742085ac71534cbe6417664d0bc8e7156bb |
# -*- coding: utf8 -*-
# SXRD_Collect - GUI program for collection single crystal X-ray diffraction data
# Copyright (C) 2015 Clemens Prescher (clemens.prescher@gmail.com)
# GSECARS, University of Chicago
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General P... | Luindil/SXRD_Collect | sxrd_collect/views/MainView.py | Python | gpl-3.0 | 12,596 | [
"CRYSTAL"
] | 45828078cb540bad310e0d5332c54057365b25c162c615a3d06b59c0aefc5e96 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of OpenDrift.
#
# OpenDrift 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 2
#
# OpenDrift is distributed in the hope that it will b... | knutfrode/opendrift | tests/integration/test_netcdf.py | Python | gpl-2.0 | 3,122 | [
"NetCDF"
] | ad4ea029b6f36578a10c1421b52bc93be4035708de50730bc28f7b14b0499a90 |
#!/usr/bin/env python
# This file is part of MSMBuilder.
#
# Copyright 2011 Stanford University
#
# MSMBuilder 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 opt... | mpharrigan/msmbuilder | scripts/BuildMSM.py | Python | gpl-2.0 | 5,662 | [
"MDTraj"
] | 9c1ffb15b98b8e90770ceb5d02f09c079dd14ca69c807467cad1b4876712d606 |
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 11 12:52:09 2013
@author: tisimst
"""
import math
import cmath
import copy
from random import randint
from numbers import Number
try:
import numpy
numpy_installed = True
except ImportError:
numpy_installed = False
__version_info__ = (1, 3, ... | terhorst/psmcpp | smcpp/ad/__init__.py | Python | gpl-3.0 | 40,630 | [
"ADF"
] | 54dd568124d1944bdbdc2885b4784f7e7525457de89f8857d7d26e582eb4650e |
# -*- coding: utf-8 -*-
# Copyright (c) Siemens AG, 2015
#
# This file is part of MANTIS. MANTIS 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 late... | siemens/django-mantis-actionables | mantis_actionables/models.py | Python | gpl-2.0 | 33,932 | [
"Amber"
] | 3b50031a881338ec090ff048a781a409067e4b44187c16607a7a39ca597ac214 |
import tensorflow as tf
import numpy as np
import sys
import logging as log
class KernelND(object):
'''Base class for kernels in ND.
ndims : int
the number of dimensions of input
'''
def __init__(self,_hyperparams={},_hyperparams_bounds={},use_initializer=True,**kwargs):
self.use_initia... | Joshuaalbert/IonoTomo | src/ionotomo/bayes/phase_screen_interp.py | Python | apache-2.0 | 42,398 | [
"Gaussian"
] | 6ae2c82ef67e93d5bde0eda0ddfb0133c18b5ffa07f396552bd1ea2a6e852ec6 |
import pandas as pd
import os.path
TRANSCRIPT_GTF_FILE = "TRANSCRIPT_GTF_FILE"
GENOME_FASTA_DIR = "GENOME_FASTA_DIR"
SIMULATED_READS = "SIMULATED_READS"
LEFT_SIMULATED_READS = "LEFT_SIMULATED_READS"
RIGHT_SIMULATED_READS = "RIGHT_SIMULATED_READS"
FASTQ_READS = "FASTQ_READS"
QUANTIFIER_DIRECTORY = "QUANTIFIER_DIRECTORY... | COMBINE-lab/piquant | piquant/quantifiers.py | Python | mit | 16,279 | [
"Bowtie"
] | 7a1062462fd8e5eafbfeeb2ba63942cdb7fcdcb98d28ea636d024bfa20b592b8 |
import numpy as np
from skynet.neural_network.layers import *
from skynet.neural_network.fast_layers import *
from skynet.neural_network.layer_utils import *
class ThreeLayerConvNet(object):
"""
A three-layer convolutional network with the following architecture:
conv - relu - 2x2 max pool - affine - relu - a... | Alexoner/skynet | skynet/neural_network/classifiers/cnn.py | Python | mit | 27,801 | [
"Gaussian"
] | e97e3fd5de51df4bcfad32b3a8c61cec43fbda78c8a8617a2259da177441dc15 |
"""
.. sectionauthor:: Asher Bender <a.bender.dev@gmail.com>
.. codeauthor:: Asher Bender <a.bender.dev@gmail.com>
.. |bool| replace:: :class:`.bool`
.. |callable| replace:: :func:`.callable`
.. |False| replace:: :data:`.False`
.. |float| replace:: :class:`.float`
.. |int| replace:: :class:`.int`
.. |ndarray| replace:... | asherbender/bayesian-linear-model | linear_model.py | Python | apache-2.0 | 35,023 | [
"Gaussian"
] | 331bb2aa276d40eb1ded9bc74766ecd1b9636546d883ef7895c6a98e6cf02905 |
#!/usr/bin/python
import numpy as np
from math import sqrt, exp, ceil
from decimal import Decimal
from ase.dftd.dftd_native import check_interaction_group_input
from ase.dftd.dftd_native import dft_d_pbc
from ase.dftd.dftd_native import maxdist
from ase.dftd.dftd_native import minbox
# General parameters
AU_TO_ANG ... | alexei-matveev/ase-local | ase/dftd/dftd_interface.py | Python | gpl-2.0 | 17,910 | [
"ASE"
] | 6ffc62411e12afaa8c6223aaf458d7a886d34ff4dcbe0c84342168ba12e474ce |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
import warnings
from io import open
from monty.serialization import loadfn
import numpy
from pymatgen.core.lattice import Lattice
from pymatgen.electronic_structure.band... | richardtran415/pymatgen | pymatgen/electronic_structure/tests/test_bandstructure.py | Python | mit | 24,247 | [
"VASP",
"pymatgen"
] | 54c3cec7a655c13b146a74c60517931dd732ea982279d98f6136206e1dc96a00 |
# coding=utf-8
'''Define Schema'''
from __future__ import absolute_import
from datetime import datetime
from flask import url_for, g
from firefly.ext import db
from firefly.views.utils import timesince
from firefly.models.consts import CATEGORY_COLORS
from .user import User
__all__ = ["Category", "Post", "Video", "... | matrixorz/firefly | firefly/models/topic.py | Python | mit | 3,718 | [
"Firefly"
] | e5d321758e8aa097fde89cb9682069b2353394b3ffc239ef11ba64d899c1e5e1 |
#!/usr/bin/env python3
## INFO ########################################################################
## ##
## pypp ##
## ==== ... | petervaro/pypp | build.py | Python | gpl-3.0 | 3,589 | [
"VisIt"
] | 905b358cf0e254cc9bb8f5f54be6c402cb9b50167cd98333dd9a8e5fc13287ae |
"""
Utility functions for simulations using openeye toolkits
"""
__author__ = 'John D. Chodera'
from simtk import unit
from simtk.openmm import app
import simtk.unit as unit
import numpy as np
import logging
logging.basicConfig(level=logging.NOTSET)
_logger = logging.getLogger("utils.openeye")
_logger.setLevel(lo... | choderalab/perses | perses/utils/openeye.py | Python | mit | 17,579 | [
"OpenMM"
] | b58ee886043d6504a345b47c6261534dab9f1ad61053220f524fed722be9c48f |
"""
This is our testing framework.
Goals:
* it should be compatible with py.test and operate very similarly
(or identically)
* doesn't require any external dependencies
* preferably all the functionality should be in this file only
* no magic, just import the test file and execute the test functions, that's it
* po... | wdv4758h/ZipPy | edu.uci.python.benchmark/src/benchmarks/sympy/sympy/utilities/runtests.py | Python | bsd-3-clause | 77,728 | [
"VisIt"
] | 850a00cd1e5b73694584ed76ebe02cffb8c1c43d243cff416aa8f0658318fb95 |
# encoding: utf-8
import sys
import os
import numpy as np
from mpl_toolkits.basemap import Basemap
from datetime import datetime
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import pyroms
from pyroms.hgrid import *
from pyroms.vgrid import *
from pyroms.grid import *
from pyroms import io
#defi... | kshedstrom/pyroms | pyroms/pyroms/grid.py | Python | bsd-3-clause | 23,655 | [
"NetCDF"
] | 2f911a5186ded0ceba45cb3e11190376326adc2514c5badb83849d90b7cc4bcd |
#!/usr/bin/env python
#
# Select and extract JPL/NAIF SPICE toolkit for local OS and Architecture
#
# Run this command to extract appropriate JPL/NAIF SPICE toolkit
# into ./cspice/:
#
# getnaiftoolkit.py extract
#
# Author: Brian Carcich, drbitboy@gmail.com
# Original date: 2013-01-05
#
# Released under the BSD lic... | rca/PySPICE | getnaifspicetoolkit.py | Python | bsd-3-clause | 7,654 | [
"Brian"
] | cd24fc315d622763ea88e144c3070a1f3e143a4fbf89df412b028b97a4310444 |
#!/usr/bin/env python
# The GIMP PAL plugin - PAL effect plugin for The GIMP.
# Copyright (C) 2009 Dave Jeffery <david.richard.jeffery@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 Softwar... | IrregularShed/newoldtv | pal.py | Python | gpl-3.0 | 8,583 | [
"Gaussian"
] | fc07d24a8db2e3c2424d25ca6e901b8a66e22a714fe664ec30b5347a12bf77ef |
# Copyright: 2005 Gentoo Foundation
# Author(s): Brian Harring (ferringb@gentoo.org)
# License: GPL2
from portage.cache import cache_errors
from portage.cache.cache_errors import InvalidRestriction
from portage.cache.mappings import ProtectedDict
import sys
import warnings
if sys.hexversion >= 0x3000000:
basestring ... | Neuvoo/legacy-portage | pym/portage/cache/template.py | Python | gpl-2.0 | 7,197 | [
"Brian"
] | ac2c2ede7faa3c7d1f3d1b7414391a3e865e83562c686cf6faccba26174cef04 |
import polypasswordhasher
import sys
THRESHOLD = 10
# require knowledge of 10 shares to decode others. Create a blank, new
# password file...
pph = polypasswordhasher.PolyPasswordHasher(threshold = THRESHOLD, passwordfile = None)
# create three admins so that any two have the appropriate threshold
pph.create_accoun... | shaunstanislaus/PolyPasswordHasher | python-reference-implementation/testpolypasswordhasher_nopartialverification.py | Python | mit | 2,034 | [
"MOE"
] | f9303e79465c4afe76ab1da2698aaa1111fe6f5cc82c2537cd141ec64116ab5d |
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