text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
HTML reader/writer for RichText
"""
# python imports
import re
from HTMLParser import HTMLParser
from xml.sax.saxutils import escape
# keepnote imports
from rednotebook.gui.keepnote.gui.richtext.textbuffer_tools import \
iter_buffer_contents, \
buffer_contents_iter_to_offset, \
normalize_tags, \... | tomka/rednotebook | rednotebook/gui/keepnote/gui/richtext/richtext_html.py | Python | gpl-2.0 | 36,691 | [
"VisIt"
] | 364a47091797423ddf223488d0c554c1e9026643349899bf88e80bc33d6800e6 |
import pytest
from json import load
from GroupIBTIA import fetch_incidents_command, Client
with open('test_data/example.json') as example:
RAW_JSON = load(example)
with open('test_data/results.json') as results:
RESULTS = load(results)
# Because of errors with markdown tables
RESULTS.update({
'osi/git_le... | demisto/content | Packs/GroupIB_ThreatIntelligenceAttribution/Integrations/GroupIBTIA/GroupIBTIA_test.py | Python | mit | 7,954 | [
"Amber"
] | 2fa08971dfe1d39d2737d66baae258fa80817cb371e7eb2d2b0529b2fddde398 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
day_names = (
"Prometheus",
"Hercules",
"Orpheus",
"Ulysses",
"Lycurgus",
"Romulus",
"Numa",
"Belus",
"Sesostris",
"Menu",
"Cyrus",
"Zoroaster",
"The Druids",
"Buddha",
"Fuxi",
"Laozi",
"Mencius",
"The... | mpercich/Calendarize | ios/dateparser/lib/python2.7/site-packages/convertdate/data/positivist.py | Python | mit | 12,459 | [
"COLUMBUS",
"Dalton"
] | 5c72b059c91fd34ea2c2d6cec038689e6ca5cffe1666a6a1ff787d54a9d5965d |
""" The Matcher service provides an XMLRPC interface for matching jobs to pilots
It uses a Matcher and a Limiter object that encapsulated the matching logic.
It connects to JobDB, TaskQueueDB, and PilotAgentsDB.
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.Thread... | arrabito/DIRAC | WorkloadManagementSystem/Service/MatcherHandler.py | Python | gpl-3.0 | 4,882 | [
"DIRAC"
] | 2bdb53b5c27aee1e46e85f76276b8f9297a7c99fde9db0a180aff3acf4ce6315 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from parsimonious.grammar import Grammar
from parsimonious.nodes import NodeVisitor
import sys
grammar = """
#grammar HTML
document = (tag / anyword)*
# document = (doctype / text / tag)*
# tag = open_tag (text / tag)* close_tag
open_t... | codeyash/plugins | PyPlugins/PhpParser/py/html.py | Python | apache-2.0 | 1,709 | [
"VisIt"
] | 1849b5662531bdec7cc078c02edd77b4267d926a1e7667c829da949aa4aef98d |
""" Some utilities for FTS3...
"""
import json
import datetime
import random
import threading
from DIRAC.DataManagementSystem.Client.DataManager import DataManager
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilities.Decorators import deprecated
from DIRAC.Core.Utilities.ReturnValues impo... | fstagni/DIRAC | DataManagementSystem/private/FTS3Utilities.py | Python | gpl-3.0 | 9,882 | [
"DIRAC"
] | cae5aa31f6e78d09052fec3cfdad8d38ac7211f8b0a880f411b4295ffbacc9b1 |
from forte.solvers import solver_factory, HF, CallbackHandler
def test_hf_callback():
"""Example of using a callback to localize HF MOs."""
xyz = """
H 0.0 0.0 0.0
H 0.0 0.0 1.0
H 0.0 0.0 2.0
H 0.0 0.0 3.0
symmetry c1
"""
input = solver_factory(molecule=xyz, basis='sto-3g')
st... | evangelistalab/forte | tests/pytest/hf/test_hf_callback.py | Python | lgpl-3.0 | 948 | [
"Psi4"
] | 6c24f28236d82fc9a056d7978ed63e02ee429075b834758ca4c6f0c564ee0c10 |
#!/usr/bin/env python3
""" Computer-based immigration office for Kanadia """
__author__ = 'Susan Sim'
__author__ = 'Zhao'
__email__ = "ses@drsusansim.org"
__copyright__ = "2014 Susan Sim"
__license__ = "MIT License"
__status__ = "Prototype"
# imports one per line
import re
import datetime
import json
def decide... | ZhaoH/inf1340_2014_asst2_Halie_Zhao | papers.py | Python | mit | 7,417 | [
"VisIt"
] | e04c6bd957be5b89626cf335be575cec34c957cced62d7d64cf13b070959d75f |
from __future__ import division
from __future__ import print_function
import argparse
from astropy.io import fits
import json
import numpy as np
from numpy.polynomial import Polynomial
import os
from uuid import uuid4
from numina.array.display.polfit_residuals import polfit_residuals
from numina.array.display.polfit_... | nicocardiel/xmegara | refine_master_wlcalib.py | Python | gpl-3.0 | 14,977 | [
"Gaussian"
] | 841e7e55c109a01654622575ec4aba233a021a3740e315cdac77adb3698edbf3 |
#!/usr/bin/python
# coding: utf-8
# Ubuntu Tweak - PyGTK based desktop configuration tool
#
# Copyright (C) 2007-2008 TualatriX <tualatrix@gmail.com>
#
# Ubuntu Tweak 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 Found... | 0x7E/ubuntu-tweak | ubuntutweak/admins/sourcecenter.py | Python | gpl-2.0 | 47,382 | [
"VisIt"
] | 28cc386cf8eab7d9736579979a181a4bc0a90fc44b59c2aa32a9cd41bc5a1825 |
from base64 import urlsafe_b64encode, urlsafe_b64decode
import copy
import datetime
import sha
import hmac
import os
import pickle
import random
import re
import stat
from string import lower, count
import time
from django.contrib.auth import authenticate, login, logout
from django.contrib.auth.models import U... | hack4impact/Givology | mainSite/source/proj/giv/models.py | Python | mit | 54,236 | [
"VisIt"
] | 99724722fb82d4a594886abbbe726fbd49c89ffc610dea26774f77891d37a9d4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import random
import urllib
import json
from google.appengine.api import urlfetch
emoji_dic = {
"happy": "😀",
"winking": "😉",
"kissing": "😗",
"smirking": "😏",
"crying": "😢",
"woman": "👩",
"peach": "🍑",
"eggplant": "�... | ivanasamy/OGE-CSSI | dear-oge/OGE.py | Python | mit | 4,056 | [
"VisIt"
] | 3cfff32a5137ca3486773dd47dc77b41a343e29d9f4997bc36ebd08b36a7db4b |
from splinter import Browser
from splinter import Browser
class AbstractPage:
url = "NO_URL_FOR_ABSTRACT_SCREEN"
def load(self):
self.browser = Browser()
self.browser.visit(self.url)
return self
def close_page(self):
self.browser.quit()
| mbanje/ureport_uganda | functional_test/fixtures/abstract_page.py | Python | bsd-3-clause | 286 | [
"VisIt"
] | 9b2fd53bc3283dc1176335f74b65fc8e34d55e830d6ab111749438e59a23548e |
# $HeadURL$
__RCSID__ = "$Id$"
import os
import time
import re
import threading
import zipfile
import zlib
import DIRAC
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData, ConfigurationData
from DIRAC.ConfigurationSystem.private.Refresher import gRefresher
from DIRAC.FrameworkSystem.Clie... | avedaee/DIRAC | ConfigurationSystem/private/ServiceInterface.py | Python | gpl-3.0 | 11,873 | [
"DIRAC"
] | 892d09d4ec7fd05f102114471361cc556b00b9a2794711963d9c1e09b1d1a801 |
from copy import deepcopy
import numpy as np
from numpy.polynomial.chebyshev import chebval
from ..utils.smoothing import smoothspec
from .constants import cosmo, lightspeed, jansky_cgs, to_cgs_at_10pc
try:
import fsps
from sedpy.observate import getSED
except(ImportError):
pass
__all__ = ["SSPBasis", "F... | bd-j/prospector | prospect/sources/ssp_basis.py | Python | mit | 15,977 | [
"Galaxy"
] | ef045c1bf00dfb718ba0c6f3a45740d993b18c332b87ff1d663b07d053c1a3cb |
def endl(*args):
"""
endl(ostream s) -> ostream
Insert a newline character into the given C++ stream @p s.
This is a wrapper around the underlying C++ OStream method
<code>endl</code>. It inserts a newline into the stream
passed as argument. Additionally, it flushes buffered
streams.
... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/docs/src/python-substitutions/libsbml.py | Python | bsd-3-clause | 479,413 | [
"Avogadro"
] | 5072b8521607376bc2af252a75fed3610ff7ba53b3208c2281bef4a3f8f51635 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Classes and functions to simulate an Ornstein-Uhlenbeck process for the instantaneous growth rate
See also
--------
:mod:`tunacell.simu.base` for base classes to parameterize numerical simulations
"""
from __future__ import print_function
from builtins import input #... | LeBarbouze/tunacell | tunacell/simu/ou.py | Python | mit | 22,612 | [
"DIRAC",
"Gaussian"
] | 7b65e4685938c9aaa423940514a6dc8e594d15968605073b6da9a04412f96141 |
# shelve.py - save/restore working directory state
#
# Copyright 2013 Facebook, Inc.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
"""save and restore changes to the working directory
The "hg shelve" command saves changes made ... | ya790206/temp_hg | hgext/shelve.py | Python | gpl-2.0 | 25,713 | [
"VisIt"
] | e0d1e573cbfb884c1445006c3abca5ee0c540de102b14a073b73e3f574c4706d |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-site-info
# Author : Stuart Paterson
########################################################################
"""
Print Configuration information for a given Site
"""
from __future__ import print_fu... | fstagni/DIRAC | Interfaces/scripts/dirac-admin-site-info.py | Python | gpl-3.0 | 1,179 | [
"DIRAC"
] | c77f09bff1c451005de054a7054214e5831ef19dd61d951764f2cd5cacb48eb9 |
"""
Spatial Error Models module
"""
__author__ = "Luc Anselin luc.anselin@asu.edu, \
Daniel Arribas-Bel darribas@asu.edu, \
Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
from numpy import linalg as la
import ols as OLS
from pysal import lag_spatial
from utils import power_expansion, set_end... | spreg-git/pysal | pysal/spreg/error_sp.py | Python | bsd-3-clause | 45,973 | [
"COLUMBUS"
] | f7e7ef67c54f5b81df48ca15cc1f105f6c62d9b1ee2c88111071ac97ddec7a49 |
# -*- 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-dataflow-client | tests/unit/gapic/dataflow_v1beta3/test_messages_v1_beta3.py | Python | apache-2.0 | 56,970 | [
"Octopus"
] | a70c4b8206b1af32531009cee4e030c3ed3af0d59e34c45faf141411f87d1085 |
import ddapp
import math
import textwrap
import drc as lcmdrc
import bot_core as lcmbotcore
import vtkAll as vtk
from ddapp import transformUtils
from ddapp import visualization as vis
from ddapp import objectmodel as om
from ddapp import lcmUtils
from ddapp import ik
from ddapp import cameraview
from ddapp import affo... | gizatt/director | src/python/ddapp/drivingplanner.py | Python | bsd-3-clause | 68,779 | [
"VTK"
] | e1aae6ab9523ad98dfca7f204ba2695d6e919294d4d70a017ec045fcc44dbc04 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=too-many-branches
from __f... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/BASISCrystalDiffraction.py | Python | gpl-3.0 | 26,717 | [
"CRYSTAL"
] | c627a69a01bf31699d96001a05b104e6c313291afcdf31040a36b6eb6fce49c6 |
#!usr/bin/python
import matplotlib.pyplot as plt
import matplotlib.widgets as widgets
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
import e_field_gen as e_field
import odeint_solve as ode
import sys as sys
import matplotlib.cm as col
ELEC_MASS = 9.10938356E-31
ELEC_CHARGE = -1.60217662E-19
FU... | KavuriG/classical-calc-three-color | plot-all-paths/tester.py | Python | gpl-3.0 | 5,731 | [
"Gaussian"
] | 60c879df66ebecdaede8ca267507859f58f259b92753c0b41906cf49aefc35f9 |
import sys
import pytest
from gm_base.model_data import DataNode, Loader, NotificationHandler
from gm_base.model_data.yaml.resolver import resolve_scalar_tag
from ModelEditor.meconfig import MEConfig as cfg
import testing.ModelEditor.mock.mock_config as mockcfg
from gm_base.geomop_util import Position
# TODO: origin... | GeoMop/GeoMop | testing/ModelEditor/data/test_data_node.py | Python | gpl-3.0 | 6,377 | [
"VTK"
] | 5cca155062ea5a7955f1f42e6ed6370b43ef85ecb309b65c211c7b8c75b143a5 |
from bayes_opt import BayesianOptimization
# Example of how to use this bayesian optimization package.
# Lets find the maximum of a simple quadratic function of two variables
# We create the bayes_opt object and pass the function to be maximized
# together with the parameters names and their bounds.
bo = BayesianOptim... | ysasaki6023/NeuralNetworkStudy | examples/usage.py | Python | mit | 1,879 | [
"Gaussian"
] | 62009f5811cfdca0279f0c29254f0f43e8c2c4ffcae75b200e370d66a944fb1a |
# -*- coding: utf-8 -*-
# Dioptas - GUI program for fast processing of 2D X-ray diffraction data
# Principal author: Clemens Prescher (clemens.prescher@gmail.com)
# Copyright (C) 2014-2019 GSECARS, University of Chicago, USA
# Copyright (C) 2015-2018 Institute for Geology and Mineralogy, University of Cologne, Germany
... | erangre/Dioptas | dioptas/tests/unit_tests/test_PatternModel.py | Python | gpl-3.0 | 2,962 | [
"Gaussian"
] | 6f9412252bf60cb1e028473861c1a66c0076d88ef4066591fd0789ff5a1153b2 |
import numpy as np
import imblearn.over_sampling
import sklearn.preprocessing
import astropy.convolution
START = 6519
END = 6732
def air2vacuum(air_waves):
'''Convert air wavelengths to vacuum wavelengths'''
# http://www.astro.uu.se/valdwiki/Air-to-vacuum%20conversion
vac_waves = np.zeros_like(air_waves)... | podondra/bt-spectraldl | notebooks/spectraldl/preprocessing.py | Python | gpl-3.0 | 1,684 | [
"Gaussian"
] | 7ae9ee2525650fbba0af0e52f45a6b85b64e9117b71f5e109a6f3f1fe7d421f8 |
"""
Acceptance tests for Studio's Settings Details pages
"""
from datetime import datetime, timedelta
from unittest import skip
from .base_studio_test import StudioCourseTest
from ...fixtures.config import ConfigModelFixture
from ...fixtures.course import CourseFixture
from ...pages.studio.settings import SettingsPage... | inares/edx-platform | common/test/acceptance/tests/studio/test_studio_settings_details.py | Python | agpl-3.0 | 9,782 | [
"VisIt"
] | 8617ac0ab3679029c65b9bf7c4a8c5fcf1a7f3aefcc400f3a2204936575196b3 |
# Copyright 2013-2014 Mitchell Stanton-Cook Licensed under the
# Educational Community 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.osedu.org/licenses/ECL-2.0
#
# Unless required by ... | BeatsonLab-MicrobialGenomics/SeqFindR | SeqFindr/blast.py | Python | apache-2.0 | 6,984 | [
"BLAST"
] | 5a29540ab3c9bf29b5320369d6fe5d736afcacfb276fd5f7465ccf5df984f436 |
# -*- coding: utf-8 -*-
"""test email sending"""
from unittest import skipIf
from django.conf import settings
from django.test.utils import override_settings
from django.urls import reverse
from coop_cms.models import Newsletter
from coop_cms.settings import is_localized, is_multilang
from coop_cms.tests import Base... | ljean/coop_cms | coop_cms/apps/newsletters/tests/test_view_online.py | Python | bsd-3-clause | 8,054 | [
"VisIt"
] | 84bbb3e3dd74835a6db6668836acbf3cbef0301d9493db99783437af8a6ebfcc |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2008 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by t... | DeadBugEngineering/myHDL_shenanigans | ssd1306_8x64bit_driver/myhdl_10dev/lib/python2.7/site-packages/myhdl-1.0.dev0-py2.7.egg/myhdl/_instance.py | Python | lgpl-2.1 | 3,993 | [
"VisIt"
] | 960629d44c884b0c9580b1091304f4d25b64ceb2989acf520a34c567a361436b |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Base class for Residue, Chain, Model and Structure classes.
It is a simple container ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/PDB/Entity.py | Python | apache-2.0 | 8,749 | [
"Biopython"
] | 4b0464bdd09e629452790fd09804e22ab063e8a7368db470309eb94f699bf299 |
#!/usr/bin/env python2.7
# Copyright 2014 Virantha Ekanayake 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 ... | virantha/scanpdf | scanpdf/scanpdf.py | Python | apache-2.0 | 18,680 | [
"ADF"
] | 64c33ce6b1372fe8f32f8d9da9e37fdf690f0b8fb2a5d785ebef6b3ec157d199 |
from flask import flash
from flask.ext.login import current_user
from octopus.models import CaseStaffMap, User
__author__ = 'MartinoW'
def create_query(args, q):
conditions = []
joins = set()
valid = True
user_id = args.get('user_id')
if user_id:
if user_id == "me":
user = User.get_by_id(curren... | quaintm/octopus | octopus/case/utils.py | Python | bsd-3-clause | 629 | [
"Octopus"
] | c0d4ccc730839d2afc9dd1f300e2986ce21431ddd44feda5936108d13c4ebc1f |
import re
from cfnviz.model import Parameter
from cfnviz.model import Mapping
from cfnviz.model import Condition
from cfnviz.model import Output
from cfnviz.model import Attribute
from cfnviz.model import Edge
from cfnviz.model import Model
def visit(value, fn, context={"path": []}):
path = context.get("path")
... | devquixote/cfnviz | cfnviz/factories.py | Python | mit | 6,899 | [
"VisIt"
] | 33a0e8319691651f06f271638f5c9c2afae088c4d170a63e7963c7b6c7b5274a |
"""
====================================
Outlier detection on a real data set
====================================
This example illustrates the need for robust covariance estimation
on a real data set. It is useful both for outlier detection and for
a better understanding of the data structure.
We selected two sets o... | glemaitre/scikit-learn | examples/applications/plot_outlier_detection_wine.py | Python | bsd-3-clause | 5,819 | [
"Gaussian"
] | 3715b450f94b3b9dacd369b16b8c4272ac492e60b34869cc741bf03d161ffed4 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | ened/scancode-toolkit | src/scancode/__init__.py | Python | apache-2.0 | 1,380 | [
"VisIt"
] | e15257c0c52cee9e12bb94ba9e7e91fe41b1d92c4b2162e81817439df28d0d49 |
import tensorflow as tf
import numpy as np
from skimage.segmentation import felzenszwalb as skimage_felzenszwalb
SCALE = 1.0
SIGMA = 0.0
MIN_SIZE = 20
def felzenszwalb(image, scale=SCALE, sigma=SIGMA, min_size=MIN_SIZE):
"""Computes Felsenszwalb's efficient graph based image segmentation.
Args:
ima... | rusty1s/graph-based-image-classification | segmentation/algorithm/felzenszwalb.py | Python | mit | 2,086 | [
"Gaussian"
] | 65265c802c2e233255c5cd34aa6716ec29d9d6e3cf31290d970cbdd70868cc36 |
#!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test a variety of custom integrators.
DESCRIPTION
TODO
COPYRIGHT AND LICE... | choderalab/YankTools | testsystems/test_custom_integrators.py | Python | gpl-2.0 | 31,219 | [
"Gaussian",
"OpenMM"
] | 29e3dce498ce1c3949bf339e2fa1765bd4ef0c26c8584713aa21f7fec9896750 |
"""
Example to generate a .fit, .mod and .dat file to feed in MrMoose for
demonstration. The model consists of a double power-law and and a break frequency
six data points from a source at z=4, but will be fitted as a free parameter
"""
import sys
# adding the path
sys.path.insert(0, '/Users/guillaume/Desktop/MrMoose... | gdrouart/MrMoose | examples/example_1cz.py | Python | gpl-3.0 | 3,478 | [
"Gaussian"
] | 75191677b57edfe0837bf45a588f7bc91c6926f8664ac0330da06afa2b725ca0 |
# Copyright (C) 2014 Pierre de Buyl
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or ... | acfogarty/espressopp | src/analysis/TotalVelocity.py | Python | gpl-3.0 | 2,655 | [
"ESPResSo"
] | 7f6d91ef253c7c2c8e5bb9041bb3a3544e08812e2e016657b4a48d425ea6bb45 |
#!/usr/bin/env python
# Copyright 2014-2019 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/grad/__init__.py | Python | apache-2.0 | 1,723 | [
"PySCF"
] | c5dcaf61e68a8744a4db538eaa84b34e1aa22cc55ae5abc37058005992bb4d80 |
import cdms2
import os, sys
from harmonic_util import harmonic
# setting the absolute path of the previous directory
# getting the this py module path by __file__ variable
# pass that __file__ to the os.path.dirname, returns the path of this module
__curDir__ = os.path.dirname(__file__)
previousDir = os.path.abspath(os... | arulalant/mmDiagnosis | diagnosis1/miso/harmonic/cal_harmonic_climatology.py | Python | gpl-3.0 | 2,875 | [
"NetCDF"
] | bd18fcf2f15f6cfc977682a44e08031f3915525172fc2d89ac13e4706b1864fb |
import numpy as np
from ase import Atoms, Atom
a = Atoms([Atom('Cu')])
a.positions[:] += 1.0
print(a.get_positions(), a.positions)
a=a+a
a+=a
a.append(Atom('C'))
a += Atoms([])
a += Atom('H', magmom=1)
print(a.get_initial_magnetic_moments())
print(a[0].number)
print(a[[0,1]].get_atomic_numbers())
print(a[np.array([1,1... | suttond/MODOI | ase/test/build.py | Python | lgpl-3.0 | 509 | [
"ASE"
] | c5833bc9d4fc17590caa668371c04b0473e405f39b556471a9f754cb0ddf00c3 |
"""
Gaussian Mixture Models.
This implementation corresponds to frequentist (non-Bayesian) formulation
of Gaussian Mixture Models.
"""
# Author: Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Bertrand Thirion <bertrand.thirion@inria.fr>
import warnings
import numpy as... | ssaeger/scikit-learn | sklearn/mixture/gmm.py | Python | bsd-3-clause | 30,702 | [
"Gaussian"
] | e440c09286574d29490f9f8430ba67e68b612a63f5c8969907c704f1fe4e1121 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/licensedcode/test_query.py | Python | apache-2.0 | 30,761 | [
"VisIt"
] | e40b94291d06f71c02d479ccf452e121c607891f9b716b122da08d65605b9bea |
from jinja2 import Template
import os
class ConfigBcbio(object):
def __init__(self):
# some runs from ERP002442 study
# normal, cancer
self.list_of_runs = [('ERR256781', 'normal'), ('ERR256782', 'cancer'),
('ERR256783', 'normal'), ('ERR... | kern3020/incubator | cancer-normal-setup/generate_conf.py | Python | mit | 1,760 | [
"BWA"
] | f66da6f75babacc268bab1f61aa9c8b8705cbc4dfbe218aa14a847c36bce342a |
#-*- coding: utf-8 -*-
'''
GATK-based variant calling pipeline
It implements a workflow pipeline for next generation
sequencing variant detection using the Broad Institute's GATK
for variant calling.
The pipeline is configured by an options file in a python file
including the actual command which are run at each sta... | marcelcaraciolo/nextgen-pipeline | pipeline.py | Python | mit | 11,293 | [
"BWA"
] | 39ca639b32a87bab180db11b6a30ad0e44e4a70eb5b7b196abdfe3a589ccec4e |
#!/usr/bin/env python
from numpy import deg2rad, rad2deg
from traits.api import HasTraits, Range, Instance, \
on_trait_change, Float, Property, File, Bool, Button
from traitsui.api import \
View, Item, VSplit, VGroup, HSplit, HGroup, Group, Label
from mayavi.core.ui.api import MayaviScene, MlabSceneM... | chrisdembia/yeadon | yeadon/gui.py | Python | bsd-3-clause | 17,580 | [
"Mayavi"
] | dda67caa69e6e151e47ec8e2cdbafd0ab8427fd6e5d652ec9177f968ac97fac0 |
"""Command-line interface for crowdastro.
Matthew Alger
The Australian National University
2016
"""
import argparse
import logging
import sys
from crowdastro import __description__
from crowdastro import __version__
from crowdastro import compile_cnn
from crowdastro import consensuses
from crowdastro import generate... | chengsoonong/crowdastro | crowdastro/__main__.py | Python | mit | 4,138 | [
"Galaxy"
] | 0e55f02934e0bb1fb2e9442a2faa8c533116521b8ed59449bda8320924ef8624 |
from build.management.commands.base_build import Command as BaseBuild
from django.conf import settings
from protein.models import Protein, ProteinSegment, ProteinConformation, ProteinState, ProteinFamily
from structure.models import Structure, Rotamer
from structure.functions import BlastSearch
from Bio.Blast import NC... | protwis/protwis | protein/management/commands/blastp.py | Python | apache-2.0 | 2,860 | [
"BLAST"
] | 5039f05de929ea269aac2e3f4b117feb2c65e6d136bdb7918cf54d5032800b49 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/orca/learn/pytorch/pytorch_ray_estimator.py | Python | apache-2.0 | 17,478 | [
"ORCA"
] | f0952ed54b5d2d0483ae3a3fff2d74b4e03913635b20c127636b343a37424a4e |
"""
Histogram-related functions
"""
import contextlib
import functools
import operator
import warnings
import numpy as np
from numpy.core import overrides
__all__ = ['histogram', 'histogramdd', 'histogram_bin_edges']
array_function_dispatch = functools.partial(
overrides.array_function_dispatch, module='numpy')
... | WarrenWeckesser/numpy | numpy/lib/histograms.py | Python | bsd-3-clause | 39,865 | [
"Gaussian"
] | 060184fbc835d1b041b8fd9571c55aa8fbf607bb44aa89814ffe6684e884cec9 |
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------
# Copyright (c) 2009 Jendrik Seipp
#
# RedNotebook 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 vers... | pakesson/rednotebook | rednotebook/info.py | Python | gpl-2.0 | 26,888 | [
"Brian",
"VisIt"
] | 4408aeeb24d459b4aa3f7d77225dce566e33154c26d6604bbf858619641848a2 |
"""
Manage Telemetry alert configurations
=====================================
.. versionadded:: 2016.3.0
Create, Update and destroy Mongo Telemetry alert configurations.
This module uses requests, which can be installed via package, or pip.
This module accepts explicit credential (telemetry api key)
or can also r... | saltstack/salt | salt/states/telemetry_alert.py | Python | apache-2.0 | 7,205 | [
"ORCA"
] | da7d46f8a66e55c7fc80f0527a3f6dd43a274abc68540a7215dd7eea9a44bde2 |
#!/usr/bin/env py27
from ecmwfapi import ECMWFDataServer
import numpy as np
import datetime as dt
import calendar
server = ECMWFDataServer()
dir = "/automount/agh/Projects/skiefer/"
# date_first_start = dt.date(1958, 1, 1)
# date_first_end = dt.date(1958, 1, 31)
# date_last_end = dt.date(1978, 12, 1)
# date_last_... | sebaki/clim-jet-stream | 01-code/01-ecmwf-py/b-get-era-int-daily-by-year.py | Python | mit | 1,239 | [
"NetCDF"
] | 7f4b8394e9b8475b45b8091d5b1b5e3af3d97f04df4c13082cabacb224ebd7f7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License... | sparkslabs/kamaelia | Sketches/MPS/BugReports/FixTests/Kamaelia/Kamaelia/UI/Pygame/VideoSurface.py | Python | apache-2.0 | 9,230 | [
"DIRAC"
] | 54b8491a464c9ee8fc87b5d0a843242a360e5040c66bef14794e594fc36c46b8 |
# -*- coding: utf-8 -*-
#
# conncomp.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# ... | tobikausk/nest-simulator | topology/examples/conncomp.py | Python | gpl-2.0 | 4,303 | [
"NEURON"
] | a6b119383a968a761a117995929a512a2220796bb5c92f04e71d48bff2af2ed7 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/base/test_lexers.py | Python | lgpl-2.1 | 5,154 | [
"MOOSE"
] | e93d78b49e4ffd85c5fe8bc1cc91ac1afe874a8b283db3b0b41e6a1793cc348a |
#
# 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... | psci2195/espresso-ffans | testsuite/python/p3m_gpu.py | Python | gpl-3.0 | 1,621 | [
"ESPResSo"
] | b6c033757af26dcdf58764ae46d06113eaa43de9a3b915f85e563e9a02ad71a0 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 1000
n = 2000
k = 1500
testMe... | justusc/Elemental | examples/interface/QPAffineDense.py | Python | bsd-3-clause | 3,907 | [
"Gaussian"
] | b17c723bfa4d60d06489a277a3e9f291771a0b7f496f08d3e95c0c4a82949997 |
import unittest
from pyaria2 import PyAria2
from random import choice
from time import sleep
import os
import shutil
ENABLE_LONG_TESTS = False
ENABLE_VERY_LONG_TESTS = False
def setUpModule():
try:
os.mkdir("tests/trash")
except OSError:
pass
def tearDownModule():
... | alfateam123/pyaria2 | tests/test_pyaria2.py | Python | mit | 2,870 | [
"MOE"
] | 7533fc72a01234cf69ce6dbb063a5f5b2572c7ad0ed0c16a5091543dada74a75 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | kkreis/espressopp | src/tools/analyse.py | Python | gpl-3.0 | 2,918 | [
"ESPResSo"
] | 04e45ab9357c3b7d840cb58f78e82d6696f5894f8c98a668847f0c36fdd38f81 |
# Copyright 2012 Patrick Varilly, Stefano Angioletti-Uberti
#
# 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... | patvarilly/DNACC | dnacc/units.py | Python | gpl-3.0 | 7,113 | [
"Gromacs"
] | 7a82b3cdbcbeb74e0435d243b0ebc7ed87e15bc9a04d9a8473e41d6a7067a895 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 2000
n = 4000
testMehrotra = True
testIPF... | birm/Elemental | examples/interface/LPDirect.py | Python | bsd-3-clause | 3,471 | [
"Gaussian"
] | 0da09b6defe420afcf655ae32961d29a22cbf82129eec8a381a44ae425c5a006 |
'''
Arthur Glowacki
APS ANL
10/17/2014
'''
import vtk
from Model import Model
from random import random
class CubeModel(Model):
def __init__(self):
Model.__init__(self)
self.source = vtk.vtkCubeSource()
self.source.SetCenter(0.0, 0.0, 0.0)
self.source.SetXLength(1.0)
self.source.SetYLength(1.0)
self.sour... | aglowacki/ScanSimulator | PrimitiveModels.py | Python | gpl-2.0 | 1,340 | [
"VTK"
] | 8dbbf19f3d86e416de37fe5f7efbb4482059a9a96f8766c82d207f76c3e43cef |
symbols = [
["Lower-case Greek",
5,
r"""\alpha \beta \gamma \chi \delta \epsilon \eta \iota \kappa
\lambda \mu \nu \omega \phi \pi \psi \rho \sigma \tau \theta
\upsilon \xi \zeta \digamma \varepsilon \varkappa \varphi
\varpi \varrho \varsigma \vartheta"""],
["Upper-case Gree... | M-R-Houghton/euroscipy_2015 | stats/_sphinxext/math_symbol_table.py | Python | mit | 7,432 | [
"Bowtie"
] | 813deaaf3d2eb277de295cb150a4b8d1e347d342e43c3df31d8187c7f94fe25c |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
from datetime import date
try:
import json
except:
import simplejson as json
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','versi... | benbahrenburg/benCoding.SMS | build.py | Python | apache-2.0 | 6,402 | [
"VisIt"
] | 286654d5dbf933a79307fe922d684b3926fc027e8163e1933b0828bfe6f90481 |
"""riboSeqR Galaxy unit tests"""
import unittest
from riboseqr import utils
class PrepareTestCase(unittest.TestCase):
def test_process_args(self):
"""Test processing arguments. """
# "ATG" -> c("ATG")
rs = utils.process_args('ATG', ret_mode='charvector')
self.assertEqual(rs, 'c("A... | vimalkvn/riboseqr_wrapper | tests/test_riboseqr.py | Python | gpl-2.0 | 2,326 | [
"Galaxy"
] | 5dcd0e18a12721c8f9b5cea53ed96b10e7a72c31bb200f2cc36d8fdc3999c575 |
#!/usr/bin/env python
# (c) 2012, Jan-Piet Mens <jpmens () gmail.com>
#
# This file is part of Ansible
#
# Modified to support stand-alone Galaxy documentation
# Copyright (c) 2014, Juniper Networks Inc.
# 2014, Rick Sherman
#
# Ansible is free software: you can redistribute it and/or modify
# it under th... | lamoni/ansible-junos-stdlib | docs/ansible2rst.py | Python | apache-2.0 | 6,013 | [
"Galaxy"
] | 813ea9743d80a1821681f66dd51e5ec18039d61c4598eaf4e6ee0c17f2f5a8d4 |
#!/usr/bin/env python3
########################################################################
# Solving this with Biopython, because I might as well get used to
# the libraries here.
from Bio.SeqUtils.ProtParam import ProteinAnalysis
import sys
if __name__=="__main__":
print("The Biopython values are differen... | andrew-quinn/rosalind-exercises | problems/level-5/prtm/prtm-biopython.py | Python | mit | 532 | [
"Biopython"
] | 89db8c4e4c3b6c3823d4654cb65b7c0133d5c5b857592e5d1d9f357fad5c4319 |
# -*- coding: UTF-8 -*-
"""
Based on ``behave tutorial``
Scenario Outline: Blenders
Given I put <thing> in a blender
When I switch the blender on
Then it should transform into <other thing>
Examples: Amphibians
| thing | other thing |
| Red Tree Frog | mush |
| apples... | raulpush/monitorizare-site | bin/features/steps/blender.py | Python | apache-2.0 | 1,217 | [
"Galaxy"
] | cd6d529f23fdc6ecf159a88970d29f5f010df0f0aeac21add76b78ab6e42986e |
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 08 15:06:17 2016
@author: Pedro Leal
"""
import matplotlib.pyplot as plt
import scipy.signal as signal
import scipy.interpolate as interpolate
import numpy as np
from xfoil_module import output_reader
stress = "50MPa"
raw_data = output_reader("flexinol_isobaric_trained_... | Mecanon/morphing_wing | experimental/sma_database/read_data.py | Python | mit | 5,064 | [
"Gaussian"
] | 260f600c8737b93be3232d51a03615d111a36a0541acadfcfde4890e804855dc |
#!/usr/bin/env python
import vtk
red = [255, 0, 0]
green = [0, 255, 0]
blue = [0, 0, 255]
# Setup the colors array
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
colors.SetName("Colors")
# Add the colors we created to the colors array
colors.InsertNextTypedTuple(red)
colors.InsertNextTypedTuple(... | tjssmy/CuviewerPy | vtkTests/quad.py | Python | mit | 2,817 | [
"VTK"
] | efe81608bddb1dab401e1463f8ed7ee1fc8b93ec4c5120fbdc3309c866681e5e |
import sys
from ase import Atoms
from gpaw import GPAW, FermiDirac
from gpaw import KohnShamConvergenceError
from gpaw.utilities import devnull, compiled_with_sl
from ase.structure import molecule
# Calculates energy and forces for various parallelizations
tolerance = 4e-5
parallel = dict()
basekwargs = dict(mode... | ajylee/gpaw-rtxs | gpaw/test/parallel/fd_parallel_kpt.py | Python | gpl-3.0 | 4,339 | [
"ASE",
"GPAW"
] | 993593669a572e94cc962f3b19750dcbd4ff33601a5186ef04e6c728a3c1e003 |
# -*- coding: utf-8 -*-
#
# Copyright © 2016 Mark Wolf
#
# This file is part of Scimap.
#
# Scimap 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 lat... | m3wolf/scimap | scimap/exceptions.py | Python | gpl-3.0 | 4,504 | [
"CRYSTAL"
] | 6c996c9830049808634db0bdd53c5c773c3e83c91a6480dcab74206cbc60554f |
import discord
from .nodes.upgrades import upgrade_list
def calculate_upgrade(up_id, level):
up_table = {
'stamina': {
'amount': -(60 - (int(60 - ((60 / 100) * (level * 0.5))))),
'end': 'Seconds'
},
'luck': {
'amount': level * 250,
'end': 'B... | AXAz0r/apex-sigma-core | sigma/modules/minigames/professions/upgrades.py | Python | gpl-3.0 | 1,781 | [
"CASINO"
] | d59456ded9e44afe25e4a26fd34847b8e671f9af23780734beaa3320ea2e8128 |
from pyseeyou.grammar import ICUMessageFormat
from pyseeyou.node_visitor import ICUNodeVisitor
def format(msg, values, lang):
'''
:param msg: String, The message to parse
:param values: Dict, The values to use in forming the final message
:param lang: String, The language code for the language to use ... | rolepoint/pyseeyou | pyseeyou/__init__.py | Python | mit | 842 | [
"VisIt"
] | c0dc4b71d93fd9b934ddb710af71555594c855cb1ff77516e7dd4279c46a64d7 |
#
# Parse tree nodes for expressions
#
from __future__ import absolute_import
import cython
cython.declare(error=object, warning=object, warn_once=object, InternalError=object,
CompileError=object, UtilityCode=object, TempitaUtilityCode=object,
StringEncoding=object, operator=object,
... | mrGeen/cython | Cython/Compiler/ExprNodes.py | Python | apache-2.0 | 498,361 | [
"VisIt"
] | 8b08754e359c0404f485012e8b0446e5a3258299623159b4e4f6018c4cfca368 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | gagoncal/Selenium | Selenium with python/Selenium_with_python_config_files/setuptools-12.0.1/setuptools/command/easy_install.py | Python | lgpl-2.1 | 85,584 | [
"VisIt"
] | b6fe3f4927ea9298217bcf1ab1f1861f3b91db92835a3705792f4f0869ee7f6b |
#! /usr/bin/env python
#adam-does# matches the redshifts from our pipeline/bpz to external reference redshifts
#adam-example# ipython -i -- ./match_specz_and_bpz_cats.py nedcat bpzcat =astropy.io.ascii.read("/u/ki/awright/bonnpipeline/adam_ned_MACS1226+21_galaxies.tsv")
#adam-example# ipython -i -- ./match_specz_and_bp... | deapplegate/wtgpipeline | adam-nedgals2mygals/match_specz_and_bpz_cats.py | Python | mit | 8,999 | [
"Galaxy"
] | 6a85b028524859f831411bd44998780744521a0f99fe07838922834cc48b8b16 |
#!/usr/bin/env python
import sys
if sys.version_info.major != 3:
sys.exit('ERROR: This script must be run using Python v3.')
from datetime import datetime, timedelta
import multiprocessing
from numpy import arcsin, array, cos, isnan, pi, radians, sin, sqrt, tan
import numpy as np
from netCDF4 import Dataset
import ... | mmb-carb/GATE | GATE.py | Python | gpl-3.0 | 73,403 | [
"NetCDF"
] | 777945af8eaee4e8ed9cab7c19294a9b9c01605f90e51bba876ce7af6b4ffb77 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | RackSec/ansible | lib/ansible/modules/network/avi/avi_dnspolicy.py | Python | gpl-3.0 | 3,647 | [
"VisIt"
] | 4af71086237de5db99014bf4d68fb12e777b2ddb24ada7fc182057f9484c5bdc |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/qcdb/libmintsmolecule.py | Python | lgpl-3.0 | 121,856 | [
"Elk",
"Psi4"
] | 800e7d78631a1f62ce23483ffd68bb8313d737d238dc0882a6164527139a2959 |
from django.test import TestCase
from django.core.urlresolvers import reverse
from django.core import mail
from django.conf import settings
from datetime import *
from tradeschool.models import *
class RegistrationTestCase(TestCase):
"""
Tests the process of registering and unregistering
to a course using... | orzubalsky/tradeschool | ts/apps/tradeschool/tests/registration.py | Python | gpl-3.0 | 8,207 | [
"VisIt"
] | 1d3ff50e4a43f52b203f2e1b11dc60093b4c693ccf0428aa83059c28a768bce1 |
# Copyright 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Kevin Reid and the ShinySDR contributors
#
# This file is part of ShinySDR.
#
# ShinySDR 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 vers... | kpreid/shinysdr | shinysdr/i/network/webapp.py | Python | gpl-3.0 | 11,530 | [
"VisIt"
] | a97b67159814ccb67c6bdb8287e4467c5c8f50222b5854fa3a8935746b3250ca |
# -*- coding: utf-8 -*-
"""
CPP数据结构定义
"""
from cppvisitattr import CppVisit
class CppData(object):
def __init__(self, ty, name, ptr=False, static=False, visit=CppVisit(CppVisit.NONE), init=None):
self.__type = ty
self.__name = name
self.__ptr = ptr
self.__static = static
... | lailongwei/llbc | tools/building_script/cpputils/cppdata.py | Python | mit | 745 | [
"VisIt"
] | 64f9441a94644e5788c371812ce6d55900921049f746e8500749658ac2327b96 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | KonradBreitsprecher/espresso | testsuite/pair_criteria.py | Python | gpl-3.0 | 4,765 | [
"ESPResSo"
] | f051f131f8c1f71590f7d7a24ef232a3229bc0da5ef7bb991fac6080c6cf6746 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# pymaid documentation build configuration file, created by
# sphinx-quickstart on Sun Jul 9 22:17:00 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# aut... | schlegelp/pymaid | docs/conf.py | Python | gpl-3.0 | 13,592 | [
"Cytoscape",
"NEURON"
] | 1bd34f3d04aa81d65e4796bded6d8c7e1c6ce86b5a66ebb5c1e5f4cc004a142c |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | PeterLauris/aifh | vol2/vol2-python-examples/examples/example_aco_iris.py | Python | apache-2.0 | 20,865 | [
"VisIt"
] | c645d116c805472547a353b031081af124a6c3876d7c69c4c9e8a755077f1616 |
#!/usr/bin/env python
"""BWA/samtools pileup tools"""
from jip import *
@tool('bwa_index')
class BwaIndex():
"""\
Run the BWA indexer on a given reference genome
Usage:
bwa_index -r <reference>
Inputs:
-r, --reference The reference
"""
def validate(self):
self.add_ou... | thasso/pyjip | examples/bwa/pileup.py | Python | bsd-3-clause | 5,658 | [
"BWA"
] | fc6168132d65b0a0da7b5d514985bed465f3a0c71dffdce8769b535d0decb12b |
import numpy as np
from ase import Atoms
from gpaw import GPAW
from gpaw.xc.sic import SIC
from gpaw.test import equal
a = 7.0
atom = Atoms('N', magmoms=[3], cell=(a, a, a))
molecule = Atoms('N2', positions=[(0, 0, 0), (0, 0, 1.14)], cell=(a, a, a))
atom.center()
molecule.center()
calc = GPAW(xc=SIC(),
txt... | qsnake/gpaw | gpaw/test/scfsic_n2.py | Python | gpl-3.0 | 553 | [
"ASE",
"GPAW"
] | c9fda28a6e65e3817773930d0d8071bf601e84b1e5a3bfee817f175ce4488ca8 |
# gridDataFormats --- python modules to read and write gridded data
# Copyright (c) 2009-2014 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Lesser General Public License, version 3 or later.
# See the files COPYING and COPYING.LESSER for details.
"""
:mod:`gridData` -- Handling grids of data
=========... | holocronweaver/GridDataFormats | gridData/__init__.py | Python | gpl-3.0 | 5,484 | [
"PyMOL",
"VMD"
] | e4a0662cfa2460fdd68739fa8916b4e818d0611df507ae0e6d313593d9019a69 |
###########################################################
# File: OpenStackEndpoint.py
# Author: A.T.
###########################################################
"""
OpenStackEndpoint is Endpoint base class implementation for the OpenStack cloud service.
"""
from __future__ import print_function
from __future__ ... | DIRACGrid/VMDIRAC | VMDIRAC/Resources/Cloud/OpenStackEndpoint.py | Python | gpl-3.0 | 17,476 | [
"DIRAC"
] | d0f3f2574a7a4f51ca523018ea17a9ec9fdac434f63211954722368c1defa147 |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
ORStools
A QGIS plugin
QGIS client to query openrouteservice
-------------------
begin : 2017-02-01
git sha ... | nilsnolde/ORStools | ORStools/gui/ORStoolsDialog.py | Python | mit | 19,930 | [
"VisIt"
] | cf6dc4f52be0a77dfa358346f220ecbbe8189d20f0452f3c2aefb3063c559829 |
"""
K-means clustering and vector quantization (:mod:`scipy.cluster.vq`)
====================================================================
Provides routines for k-means clustering, generating code books
from k-means models and quantizing vectors by comparing them with
centroids in a code book.
.. autosummary::
... | jamestwebber/scipy | scipy/cluster/vq.py | Python | bsd-3-clause | 27,263 | [
"Gaussian"
] | 416da765e78c22965d176b05d3a7c1580be3cc9719f0a8985da6e376fff61199 |
#!/usr/bin/env priithon
import os, sys, time, csv
import Chromagnon as ch
import numpy as N
from Priithon.all import F, Mrc
from PriCommon import imgGeo
from imgio import mrcIO
METHODS=['quadrisection', 'logpolar', 'simplex']
#PARM_EXT = 'csv'
NOISE_STATS=['Gaussian', 'Poisson']
def repeat(fns, n=10):
outs = ... | macronucleus/chromagnon | Chromagnon/test_compareReg.py | Python | mit | 6,944 | [
"Gaussian"
] | 4ba9aaa7bfe3ec89000d3ffc7c188d77e37f1bdb57818b1c773afc9ca30a20ac |
#!/usr/bin/env python
# Copyright 2014-2020 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/solvent/test/test_ddcosmo.py | Python | apache-2.0 | 19,467 | [
"PySCF"
] | 0f4f56a7cbbff5958c485c6de368efc3cd13932f0f0f93e0c1dc4ec559d18f57 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the Cp2k output parser along with a few other functions for parsing cp2k-related
outputs.
"""
import glob
import logging
import os
import re
import warnings
import numpy as np
import p... | gmatteo/pymatgen | pymatgen/io/cp2k/outputs.py | Python | mit | 55,516 | [
"CP2K",
"Gaussian",
"VASP",
"pymatgen"
] | a1b2a040ad7a239d8bdd36a6dc671e339366b43b704fd143c1d210c12d07144d |
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