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# -*- coding: utf8 -*-
#
# Copyright 2011 Kyrre Ness Sjøbæk
# This file is part of AcdOpti.
#
# AcdOpti 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 you... | kyrsjo/AcdOpti | src/acdOptiGui/infoFrames/MeshInstance.py | Python | gpl-3.0 | 20,096 | [
"ParaView"
] | 9a0274a85ae645989e8fa54bae5aedb9fbecdb9be2928f9bb797590823dfa761 |
#! /usr/bin/env python2.7
#Opens VMD with overlayed fields
import os
import numpy as np
import csv
import sys
import shutil
import glob
from .mdpostproc import MD_PostProc
from .mdfields import (MD_mField, MD_vField, MD_TField,
MD_momField, MD_dField)
from .headerdata import MDHeaderData
from .... | edwardsmith999/pyDataView | postproclib/vmdfields.py | Python | gpl-3.0 | 9,470 | [
"VMD"
] | d10d50814daca1a60ef453f3230fe9d4b2bf76df78a94aec4ebc97ed1f39a1fa |
# coding: utf-8
'''
------------------------------------------------------------------------------
Copyright 2016 Esri
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/... | jfrygeo/solutions-geoprocessing-toolbox | suitability/toolboxes/scripts/NAMDownload.py | Python | apache-2.0 | 8,637 | [
"NetCDF"
] | dce6cea09f66f09a61560b61646a03ccc5a2783a2b1323bb94b98623376e0ff0 |
#!/usr/bin/env python3
import sys
import os
import re
try:
import requests
import requests_cache
except Exception as e:
print("ERROR", "- You need to install missing dependencies: pip install requests requests-cache\n")
raise
assert sys.version_info.major == 3, "the script requires Python 3"
__author_... | juanmirocks/LocText | loctext/util/ncbi_global_align.py | Python | apache-2.0 | 3,601 | [
"BLAST"
] | 39a9f264a4bcc1f5e791ae76f44b9039a27ed240b85142ec834b4224c5856f01 |
"""
Some algorithms from the original skyline implementation are commented out and
the best combination of algorithms for NAB is included below.
"""
from datetime import datetime, timedelta
import numpy as np
import pandas
def tail_avg(timeseries):
"""
This is a utility function used to calculate the average o... | rhyolight/NAB | nab/detectors/skyline/algorithms.py | Python | agpl-3.0 | 9,540 | [
"ADF"
] | 976ef016b2439c35ac1b13a073b4d4cb657c71c547283a39f659e432fe8c8237 |
#!/usr/bin/env python
# Copyright 2008-2015 Nokia Networks
# Copyright 2016- Robot Framework Foundation
#
# 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.or... | jaloren/robotframework | src/robot/run.py | Python | apache-2.0 | 29,254 | [
"VisIt"
] | 9dbff30f68c75cd12dcef36e323afae8567c54bcc511f5b1bbb8b3a2d85ff81f |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | gertingold/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 108,314 | [
"Gaussian"
] | 526c4433b42676ef8bc3124eef7a7a3d45755167c53c242a0184a4df9c85e93e |
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 17 13:10:52 2012
Author: Josef Perktold
License: BSD-3
"""
import numpy as np
import scipy.sparse as sparse
from scipy.sparse.linalg import svds
from scipy.optimize import fminbound
import warnings
from statsmodels.tools.tools import Bunch
from statsmodels.tools.sm_exc... | bashtage/statsmodels | statsmodels/stats/correlation_tools.py | Python | bsd-3-clause | 32,295 | [
"Gaussian"
] | b66b89c6a4110499b90df6f14ccf60135f02c4f5b1e23bc54b91b16eeada1b34 |
# This file is part of Androguard.
#
# Copyright (C) 2014 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
... | reox/androguard | androguard/decompiler/dad/dast.py | Python | apache-2.0 | 23,908 | [
"VisIt"
] | a8bd397bac60144caeb1ae967a5d38bf1146d4b105fc6e42dc749f25bf6d7ad2 |
#!/usr/bin/env python
# encoding: utf-8
"""Wrapper of ELLIPSE."""
import os
import gc
import sys
import copy
import warnings
import argparse
import subprocess
import numpy as np
from scipy.stats import sigmaclip
# Astropy related
from astropy.io import fits
from astropy.table import Table, Column
from kungpao impo... | dr-guangtou/KungPao | kungpao/sbp.py | Python | gpl-3.0 | 68,174 | [
"Galaxy"
] | 822d32f737e99dd03fe4c048802cd419bea958008cb5392d4aec4657322cfa2c |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import Directive
from docutils.statemachine import ViewList
from sphinx import addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.directives.code import CodeBlo... | ar4s/django | docs/_ext/djangodocs.py | Python | bsd-3-clause | 13,834 | [
"VisIt"
] | 66e9b0ab157cad653b13a15830d98eaf5ff6222f273fdababf0052270064aa09 |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## 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 v... | graik/biskit | archive_biskit2/Biskit/StructureMaster.py | Python | gpl-3.0 | 3,752 | [
"Amber"
] | f779d1cd71c4268336d0b7259e7c100110732903403050f0c48864d39622170d |
"""
Test functions for genmod.families.family
"""
import pytest
import statsmodels.genmod.families as F
import statsmodels.genmod.families.links as L
all_links = {
L.Logit, L.logit, L.Power, L.inverse_power, L.sqrt, L.inverse_squared,
L.identity, L.Log, L.log, L.CDFLink, L.probit, L.cauchy, L.LogLog,
L.lo... | bashtage/statsmodels | statsmodels/genmod/families/tests/test_family.py | Python | bsd-3-clause | 1,603 | [
"Gaussian"
] | b669c5f4c667dde4189241a15004fbcaf70a9ba8522c46ccb5b999e8776730a3 |
import platform
from PyQt4.QtCore import *
from PyQt4.QtGui import *
StyleSheet = '''
QLineEdit[valid="false"] {background-color: rgb(255, 80, 80);}
'''
#TODO: add formatting to general, field, run and time options
#TODO: split up classes into separate files
#TODO: set tool tips
class ParamsForm(QDialog):
d... | rymurr/cpp-class | pygui/paramsform.py | Python | gpl-3.0 | 22,869 | [
"GAMESS",
"Gaussian"
] | 4b94790c5bb7f0ed9b6dc8897a26a2ca678bff4bc4cb11ca2d86828698446717 |
# Copyright (c) 2012 Spotify AB
#
# 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, s... | rayrrr/luigi | setup.py | Python | apache-2.0 | 3,689 | [
"VisIt"
] | 5c4a4a5d786b65e6586a8a7ece0f1011a53522eca3492fe8475d5d09b5507a2a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Concatenates the seamed and bandmerged fields into the final catalogue.
This script takes the output from the seaming script and concatenates the
results into the final source catalogue products, which contains one entry
for each unique source and is generated in 5x5 de... | barentsen/iphas-dr2 | dr2/concatenating.py | Python | mit | 16,803 | [
"Galaxy"
] | 36eaa1d124413fb3ef825bbb1b385fc1a4d92132f7559ea00ada692539057d04 |
import os
import sys
from xml.etree import ElementTree as ET
from collections import defaultdict
# Todo: ""
# execute from galaxy root dir
tooldict = defaultdict(list)
def main():
doc = ET.parse("tool_conf.xml")
root = doc.getroot()
# index range 1-1000, current sections/tools divided between 2... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/extract_toolbox_sections.py | Python | gpl-3.0 | 5,474 | [
"Galaxy"
] | 7bcb98922bf06ad64817ced054b4d835b78c27d27866ce9b7710fab477f36e15 |
import vtk, qt, slicer
from math import sqrt, cos, sin
from .CircleEffect import AbstractCircleEffect
class AbstractPointToPointEffect(AbstractCircleEffect):
def __init__(self, sliceWidget):
# keep a flag since events such as sliceNode modified
# may come during superclass construction, which will
# ... | andreashorn/lead_dbs | ext_libs/SlicerNetstim/WarpDrive/WarpDriveLib/Effects/PointToPointEffect.py | Python | gpl-3.0 | 3,198 | [
"VTK"
] | 735043f1d7c24807d6d6d9e72722e4be71ae3f24b048ea26bf9f49c8347e36c0 |
from __future__ import print_function
from .objs import *
from .axes import *
__displayname__ = 'Visualization'
def hideAll():
"""This hides all sources/filters on the pipeline from the current view"""
import paraview.simple as pvs
for f in pvs.GetSources().values():
pvs.Hide(f)
return None
... | banesullivan/ParaViewGeophysics | pvmacros/vis/__init__.py | Python | bsd-3-clause | 390 | [
"ParaView"
] | 7b2d2bd2e2b45f3d034f549d3c6f6353793ca7ae762c597f739fcccf7e88ace9 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import sys
class Visitor:
def defaultVisit(self, node):
raise Exception, "INTERNAL ERROR: no visitor for no... | wilebeast/FireFox-OS | B2G/gecko/ipc/ipdl/ipdl/ast.py | Python | apache-2.0 | 12,921 | [
"VisIt"
] | 52363490252db6994c8610bf546dc6f40664e0a6472ea6b3a21beb2195be6836 |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, PurePoly, poly,
parallel_poly_from_expr,
degree, degree_list,
LC, LM, LT,
pdiv, prem, pquo, pexquo,
div, rem, quo, exquo,
half_gcdex, gcdex, invert,
subresultants,
resu... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/sympy/polys/tests/test_polytools.py | Python | gpl-3.0 | 105,502 | [
"Gaussian"
] | 78b6ecab67df417e15d1cb969999fa8ae751320ccacba3a576ac104dc53a5b9d |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# read data
#
reader = vtk.vtkGene... | berendkleinhaneveld/VTK | IO/EnSight/Testing/Python/EnSightOfficeASCII.py | Python | bsd-3-clause | 1,997 | [
"VTK"
] | 5636553f2a5c872c611d40eb5aaf041f23e1cefabde4329bb3a6a547650f1a6b |
"""
This file contains miscellaneous.
"""
import os
import random
from propargs.propargs import PropArgs
from registry.registry import set_propargs
def gaussian(mean, sigma, trim_at_zero=True):
sample = random.gauss(mean, sigma)
if trim_at_zero:
if sample < 0:
sample *= -1
return samp... | gcallah/Indra | indra/utils.py | Python | gpl-3.0 | 1,694 | [
"Gaussian"
] | 86b4617eb199a5cc1bd8e876dbd7db809af2716eb7b94eb37a2d9b6992321b60 |
"""
Tags Controller: handles tagging/untagging of entities
and provides autocomplete support.
"""
from galaxy import web
from galaxy.web.base.controller import BaseUIController, UsesTagsMixin
from sqlalchemy.sql import select
from sqlalchemy.sql.expression import and_, func
import logging
log = logging.getLogger( __... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tag.py | Python | gpl-3.0 | 10,048 | [
"Galaxy"
] | c62a47469dc80f2910cbf188a8dfe96620774a82f0ad2440c4db3071987047eb |
"""
prototype for a pymel ipython configuration
Current Features:
tab completion of depend nodes, dag nodes, and attributes
automatic import of pymel
Future Features:
tab completion of PyNode attributes
color coding of tab complete options:
- to differentiate between methods and attributes
... | CountZer0/PipelineConstructionSet | python/maya/site-packages/pymel-1.0.3/pymel/tools/ipymel.py | Python | bsd-3-clause | 20,452 | [
"VisIt"
] | 8a5d707e8d21e852a88d3d802612034733cb7a45ef991efb0c0ac6518aed7da5 |
########################################################################
# File: MetaQuery.py
# Author: A.T.
# Date: 24.02.2015
# $HeadID$
########################################################################
""" Utilities for managing metadata based queries
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
... | coberger/DIRAC | DataManagementSystem/Client/MetaQuery.py | Python | gpl-3.0 | 8,932 | [
"DIRAC"
] | 1de090e2403fff0e6cf0751895ff5e216bc08492733002bcc65ff3f131ef28b8 |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pylab as pl
import Scientific.IO.NetCDF as IO
import matplotlib as... | CopyChat/Plotting | Downscaling/climatechange.clt2.py | Python | gpl-3.0 | 24,117 | [
"NetCDF"
] | f4b9be073134c0c52e65160aca151371e5af5c0a18052e4b5243cab3a8a1a819 |
import json
import shlex
import os
import socket
import heapq
from collections import OrderedDict, defaultdict
from libmproxy.protocol.http import decoded
from tabulate import tabulate
from recordpeeker import Equipment, ITEMS, BATTLES, DUNGEONS, slicedict, best_equipment
from recordpeeker.dispatcher import Dispatche... | jonchang/recordpeeker | recordpeeker/mitmdump_input.py | Python | mit | 6,758 | [
"VisIt"
] | bd11708e3dc382fee41aa8ee568b5943d4573506680f962ce5cde35365ad90a2 |
"""
Helper functions for the course complete event that was originally included with the Badging MVP.
"""
import hashlib
import logging
import six
from django.urls import reverse
from django.utils.text import slugify
from django.utils.translation import ugettext_lazy as _
from badges.models import BadgeAssertion, ... | msegado/edx-platform | lms/djangoapps/badges/events/course_complete.py | Python | agpl-3.0 | 4,555 | [
"VisIt"
] | 62ad6d23f54b92fef536f0ccd0d659d39145de48b28126a624ff8443a195538a |
from __future__ import division
import abc
import warnings
import numpy as np
import six
np.seterr('warn')
from scipy.special import gamma as scipy_gamma
from scipy.special import gammaln as scipy_gammaln
from astropy.modeling.fitting import _fitter_to_model_params
from astropy.modeling import models
from stingray... | pabell/stingray | stingray/modeling/posterior.py | Python | mit | 22,031 | [
"Gaussian"
] | 6b0da809dfec9a59f414d897a324806eca364fa5869ed98bfb5f50f4076c8c66 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | marmyshev/transitions | resources/pyinstaller/hook-openlp.core.ui.media.py | Python | gpl-2.0 | 2,265 | [
"Brian"
] | 0d5249eb9e032a886a49d3ecd574eedc7b6a53e366a601a404bc4c2ba1691d77 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# vgridforum - vgrid forum front end
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | heromod/migrid | mig/cgi-bin/vgridworkflows.py | Python | gpl-2.0 | 1,078 | [
"Brian"
] | 781c0051755adf0c5f3e7afea8b9d95789548e5212fb6044390e03d1ce28917b |
""" :mod: RegisterReplica
==================
.. module: RegisterReplica
:synopsis: register replica handler
RegisterReplica operation handler
"""
__RCSID__ = "$Id $"
from DIRAC import S_OK, S_ERROR
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.DataManagementSystem.Age... | vmendez/DIRAC | DataManagementSystem/Agent/RequestOperations/RegisterReplica.py | Python | gpl-3.0 | 5,244 | [
"DIRAC"
] | 9d33f15dadc664f11f2613ffd1ce59f55d958adc8af7e44c74e6ba85fda9817c |
import errno
import functools
import fnmatch
import json
import os
import os.path
import re
import shutil
import subprocess
import sys
import tarfile
import requests
import stat
from typing import (
Type, NoReturn, List, Optional, Dict, Any, Tuple, Callable, Union
)
from dbt.events.functions import fire_event
from... | analyst-collective/dbt | core/dbt/clients/system.py | Python | apache-2.0 | 18,396 | [
"exciting"
] | 8f918b9b7f1d39c0f3e7460c49a599876cd30c30b515365baef6611aa8b7fa5d |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/custom/forms/editcustomdialog.py | Python | gpl-2.0 | 7,205 | [
"Brian"
] | 03453ffca5320f7f044fae77211b452034aa8024f25c84228091b6f845b4db18 |
# Copyright 2020 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, s... | googleapis/python-kms | samples/snippets/encrypt_symmetric.py | Python | apache-2.0 | 2,966 | [
"VisIt"
] | 997311c21e98ef417530f6c654a84a6f5d662cc8e7e58ee9bc09efa132c66035 |
import os
import sys
import tempfile
import yaml
import zlib
import numpy as np
import simplejson as js
import subprocess as sb
from time import time,sleep
from os import path
from scipy.stats.mstats import mquantiles
try:
from sklearn.lda import LDA
from sklearn.svm import SVC
from sklearn.neighbors impor... | binarybana/samcnet | exps/fig_yj.py | Python | mit | 4,928 | [
"Gaussian"
] | 3236aed8022fa0bf404fb44eb44120444e1ef7e174ee2998512bb4ee7218b079 |
import numpy as np
from numpy.fft import fft2, ifft2, ifftshift
from templatetracker.correlationfilter.utils import pad, crop, fast2dconv
def gaussian_correlation(x, z, sigma=0.2, boundary='constant'):
r"""
Gaussian kernel correlation.
Parameters
----------
x : ``(channels, height, width)`` `nda... | jalabort/templatetracker | templatetracker/correlationfilter/kernelizedfilter.py | Python | bsd-3-clause | 5,605 | [
"Gaussian"
] | 80151dcc5eb6870987a77535382d710caa1a3a1474c102dca78e5742f7a0bea2 |
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLength
from ase.io import PickleTrajectory
from ase.optimize import BFGS
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0),
(b, b, 0),
(a, a, b)],
calc... | grhawk/ASE | tools/ase/test/emt1.py | Python | gpl-2.0 | 632 | [
"ASE"
] | 70e4d42ec86764b496acfc8cbbfbb12045ef300d9872c2f909413c1fc808f04b |
"""
TornadoREST is the base class for your RESTful API handlers.
It directly inherits from :py:class:`tornado.web.RequestHandler`
"""
import os
import inspect
from tornado.escape import json_decode
from tornado.web import url as TornadoURL
from urllib.parse import unquote
from functools import partial
from DIRAC impo... | ic-hep/DIRAC | src/DIRAC/Core/Tornado/Server/TornadoREST.py | Python | gpl-3.0 | 16,483 | [
"DIRAC"
] | fde4591975677bc9ecd6b73479f497c20d02fa39eb940786a2fdc9711d1b8733 |
"""
Load and Plot from a File
~~~~~~~~~~~~~~~~~~~~~~~~~
Read a dataset from a known file type.
"""
###############################################################################
# Loading a mesh is trivial - if your data is in one of the many supported
# file formats, simply use :func:`pyvista.read` to load your spa... | akaszynski/vtkInterface | examples/00-load/read-file.py | Python | mit | 2,859 | [
"VTK"
] | f43249fa89c8689f48473df21aaf87edaa327fff91b26d270f4c12af5a75ac92 |
#!/usr/bin/env python3
import gensafeprime
import contextlib
import textwrap
import hashlib
import fuckpy3 #pylint:disable=unused-import
import random
import numpy as np
import ast
import os
import re
banner = r"""
___ ___ ___ _____ _
/ _ \ / _ \ / _ \ | ___|... | Qwaz/solved-hacking-problem | DEFCON/2020 Quals/ooo-flag-sharing/chal.original.py | Python | gpl-2.0 | 8,529 | [
"exciting"
] | 5f5ea357d2504d94f620b8f16f3cea408521e7b7634372537f897ec6c416f9e9 |
##########################################################################
#
# Copyright 2010 VMware, Inc.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without res... | apitrace/apitrace | retrace/retrace.py | Python | mit | 26,739 | [
"VisIt"
] | c7bae1f6ab79297373cbae3eec0d97535f8bef93ee7d4d477663be0e8ca191f0 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2013-2014 CRS4.
#
# This file is part of vispa.
#
# vispa 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
#... | crs4/vispa | bl/tiget/repeats.py | Python | gpl-3.0 | 1,643 | [
"BLAST"
] | efdcbc696cef1f4265d02ce2efcff91accc0b1ca4a31fca80b2bf16375b1c1ca |
from __future__ import annotations
from scitbx import matrix
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalOrientationMixin,
CrystalUnitCellMixin,
)
from dials.algorithms.refinement.parameterisation.scan_varying_model_parameters import (
GaussianSmoother,
ScanVar... | dials/dials | algorithms/refinement/parameterisation/scan_varying_crystal_parameters.py | Python | bsd-3-clause | 7,512 | [
"CRYSTAL"
] | 3de3d350ae42d1e3cc1eed7e4ad66e2087c825bae90ee4015dfc3ab8c3953779 |
"""
Tests for elliptical Gaussian fitting code in the TKP pipeline.
"""
import unittest
import numpy
from sourcefinder.extract import source_profile_and_errors
from sourcefinder.fitting import moments, fitgaussian, FIT_PARAMS
from sourcefinder.gaussian import gaussian
# The units that are tested often require inform... | transientskp/pyse | test/test_gaussian.py | Python | bsd-2-clause | 10,816 | [
"Gaussian"
] | 4df13f39de888eeb98ea2637085a0cd85e06ffc694bc96fd150989b24941fef5 |
#!/usr/bin/env python
import argparse
from rdkit import Chem
from rdkit.Chem import rdFMCS
def _process_input():
"""Define and parse the command line arguments"""
parser = argparse.ArgumentParser()
parser.add_argument(
'-target',
'--target_file',
required=True,
help='Path... | amjjbonvin/haddocking.github.io | education/HADDOCK24/shape-small-molecule/scripts/calc_mcs.py | Python | mit | 3,372 | [
"RDKit"
] | 185e06419a34ecf2d9813a5954924bce54d996d4dc075065d3b9c69b74c37769 |
# Copyright 2015 SAP AG or an SAP affiliate company.
#
import operator
import re
import decimal
import itertools
import sqlanydb
from sqlalchemy.sql import compiler, expression, text, column, bindparam
from sqlalchemy.engine import default, base, reflection, url
from sqlalchemy import types as sqltypes
from sqlalch... | sqlanywhere/sqlalchemy-sqlany | sqlalchemy_sqlany/base.py | Python | apache-2.0 | 30,247 | [
"ASE"
] | 803c5169206a63069962ff5721754fc34b12bac053e25963dd124cc29a08e0ed |
# transform_counts_with_normalization_factor/transform_counts_with_normalization_factor.py - a self annotated version of DockerToolFactory.py generated by running DockerToolFactory.py
# to make a new Galaxy tool called transform counts with normalization factor
# User m.vandenbeek@gmail.com at 14/01/2015 21:18:10
# Doc... | JuPeg/tools-artbio | unstable/local_tools/local_shed_backup/transform_counts_with_normalization_factor-default/transform_counts_with_normalization_factor/transform_counts_with_normalization_factor.py | Python | mit | 32,081 | [
"Galaxy"
] | a164918184e8888be157ca046ea99fdbc21cd6b4eaaa4a605ec7c5e9844f6a51 |
# -*- encoding: utf-8 -*-
from scriptorium.base.test import SeleniumTestCase
from scriptorium.base.test.mixin import MailerTesterMixIn
from scriptorium.models import User
class AuthTesterMixin(object):
def login(self: SeleniumTestCase, email, password):
self.tester.visit('login')
self.tester.fill_... | alex20465/open-scriptorium | apps/frontpage/tests/test_auth.py | Python | mit | 1,588 | [
"VisIt"
] | d0e55ba3170c3b1b842d00b7f475a961887b0b832f660e7646dd3edcba67736f |
#!/usr/bin/env python
from vtk import *
source = vtkRandomGraphSource()
source.SetNumberOfVertices(150)
source.SetEdgeProbability(0.01)
source.SetUseEdgeProbability(True)
source.SetStartWithTree(True)
view = vtkGraphLayoutView()
view.AddRepresentationFromInputConnection(source.GetOutputPort())
view.SetVert... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/random3d.py | Python | bsd-3-clause | 899 | [
"VTK"
] | 808c0d295b64de24bfce4d9929243435c76a81a95ce97f9b1f776d36abbfeebc |
../../../../share/pyshared/orca/dectalk.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/dectalk.py | Python | gpl-3.0 | 42 | [
"ORCA"
] | ec58a1bde0458685ce88b6b3a95183d5cb7526d860589c30009c7affd27aced6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Count and export redundancy of sequences found in a fasta file.
Warning: may crash by using the whole memory.
Usage:
%program <input_file> <output_file> [data_column]"""
import sys
import re
from collections import defaultdict
try:
from Bio import SeqIO
exce... | enormandeau/Scripts | fasta_distribution.py | Python | gpl-3.0 | 917 | [
"Biopython"
] | 1be7c634d65e606ca98967800ff373b72a61ebb2ebb03785d5c51769f2ac4890 |
'''
Unittests for pysal.model.spreg.error_sp_hom module
'''
import unittest
import pysal.lib
from pysal.model.spreg import error_sp_hom as HOM
import numpy as np
from pysal.lib.common import RTOL
import pysal.model.spreg
class BaseGM_Error_Hom_Tester(unittest.TestCase):
def setUp(self):
db=pysal.lib.io.op... | lixun910/pysal | pysal/model/spreg/tests/test_error_sp_hom.py | Python | bsd-3-clause | 17,463 | [
"COLUMBUS"
] | 975ff913be46336ade7716f2eed3bef8ea09306ed7cfc8954c6d33c793396cae |
from ase import Atoms
# Setup a chain of H,O,C
# H-O Dist = 2
# O-C Dist = 3
# C-H Dist = 5 with mic=False
# C-H Dist = 4 with mic=True
a = Atoms('HOC', positions=[(1, 1, 1), (3, 1, 1), (6, 1, 1)])
a.set_cell((9, 2, 2))
a.set_pbc((True, False, False))
# Calculate indiviually with mic=True
assert a.get_distance(0, 1,... | askhl/ase | ase/test/atoms_distance.py | Python | gpl-2.0 | 1,192 | [
"ASE"
] | fd105633f7de177283bd41e0c7a8828d23ea1ac7397ddf7e61da42a86da33f8f |
#!/usr/bin/env python3
# coding: utf-8
from __future__ import unicode_literals
from collections import Counter
from molbiox.algor import interval
def find_next_contigs(samfile, contig, lendict, insertmax,
direction='next', orientation='fr'):
"""
:param samfile: pysam.calignmentfile... | frozflame/molbiox | molbiox/algor/mapping.py | Python | gpl-2.0 | 2,293 | [
"pysam"
] | 28b471ec16a7f7e2b66bf39184f11cfc90480f230ce4646415d48a36645a1c6e |
"""Fabric deployment file to install genomic data on remote instances.
Designed to automatically download and manage biologically associated
data on cloud instances like Amazon EC2.
Fabric (http://docs.fabfile.org) manages automation of remote servers.
Usage:
fab -i key_file -H servername -f data_fabfile.py inst... | chapmanb/cloudbiolinux | data_fabfile.py | Python | mit | 3,179 | [
"Galaxy"
] | b92d34c9a2283cc54684728b513637e2ac9ead2ca80ca616c613edf75ba93e28 |
# -*- coding: utf-8 -*-
#
# Author: Taylor Smith <taylor.smith@alkaline-ml.com>
#
# Utils for autoencoders
from __future__ import print_function, absolute_import, division
import tensorflow as tf
__all__ = [
'cross_entropy',
'kullback_leibler'
]
def cross_entropy(actual, predicted, eps=1e-10):
"""Binary ... | tgsmith61591/smrt | smrt/autoencode/_ae_utils.py | Python | bsd-3-clause | 1,213 | [
"Gaussian"
] | ad8817ac6fc9f96e38809a4eeffd9762163e9081b672888a74a4560e499be456 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
#
# 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 ) any... | SNoiraud/gramps | gramps/gen/plug/menu/__init__.py | Python | gpl-2.0 | 1,586 | [
"Brian"
] | a54af05a5c807911132fa63cb844570938c7fab127d2b63fa5b50d2997c0a024 |
"""Test the DataRecoveryAgent"""
import unittest
from collections import defaultdict
from mock import MagicMock as Mock, patch, ANY
from parameterized import parameterized, param
import DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.TransformationSystem.Agent.DataRecoveryAgent import DataRecoveryAgent
fr... | fstagni/DIRAC | TransformationSystem/test/Test_DRA.py | Python | gpl-3.0 | 24,555 | [
"DIRAC"
] | 1bbc3b94d4ce33d62d23ac54a21a4b5015f61b2fbe329e03b3bcbc3aa3c452ca |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | snippets/scaleVolumes.py | Python | gpl-2.0 | 6,386 | [
"MOOSE"
] | ff7bc079ed53cf37931c9112f0fa2fb7f543dff4f034d1479b7b105f3bf216b9 |
from __future__ import print_function
from __future__ import absolute_import
import sys
from copy import copy
import numpy as nm
from sfepy.base.base import (complex_types, dict_from_keys_init,
assert_, is_derived_class, ordered_iteritems,
insert_static_method... | lokik/sfepy | sfepy/discrete/fem/meshio.py | Python | bsd-3-clause | 97,709 | [
"VTK"
] | 75f575d839a461551744cd54a962ce3a66881bc5860456fc2e356554858caf4a |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#
# pylint: disable=no-member
"""Wrapper for netCDF readers."""
import logging
import os.path
import warnings
import numpy as np
from monty.collections import AttrDict
from monty.dev import requires
from monty.functools impor... | materialsproject/pymatgen | pymatgen/io/abinit/netcdf.py | Python | mit | 17,462 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | 15c1cafd7ec55f867429d9a89a3ff2709409c7a3359abe423b0621268079148e |
# -*- test-case-name: pyflakes -*-
# (c) 2005-2010 Divmod, Inc.
# See LICENSE file for details
try:
import __builtin__ # NOQA
except ImportError:
import builtins as __builtin__ # NOQA
import os.path
import _ast
import sys
from flake8 import messages
from flake8.util import skip_warning
__version__ = '... | fivestars/flake8 | flake8/pyflakes.py | Python | mit | 25,440 | [
"VisIt"
] | 8516b5089e560cb3e8b79d628a87938db24cb2e115223db51c16c12f2d366838 |
__author__ = 'ddeconti'
import FileHandler
import numpy
import random
import sys
from bokeh.plotting import figure, output_file, show, VBox, HBox
from rdkit import DataStructs
from rdkit.Chem import AllChem, SDMolSupplier
from sklearn.decomposition.pca import PCA
from sklearn.cross_validation import train_test_split
... | dkdeconti/PAINS-train | training_methods/clustering/pca_plots_on_fp.py | Python | mit | 3,717 | [
"RDKit"
] | 96cd1e86e67e10a1950d60800b2da661ed379cd66bf82cc557b9424132296779 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/model/type_and_status.py | Python | gpl-2.0 | 9,374 | [
"VisIt"
] | 4de075c8c445791589cb19725e84c1109e69a8e185fa3fc92b3602436d0c287d |
#!/usr/bin/env python
import glob
import os
try:
from setuptools import setup
have_setuptools = True
except ImportError:
from distutils.core import setup
have_setuptools = False
kwargs = {'name': 'openmc',
'version': '0.7.1',
'packages': ['openmc', 'openmc.mgxs'],
'script... | mjlong/openmc | setup.py | Python | mit | 1,289 | [
"VTK"
] | 0ffe8900cb9724bd740b4c6e428f11dae24e9cecfb8180e55c93df3f271dfbc8 |
import lb_loader
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
n_steps = 3000
temperature = 300. * u.kelvin
collision_rate = 1.0 / u.picoseconds
timestep = 1.0 * u.femtoseconds
steps... | kyleabeauchamp/HMCNotes | code/old/test_vv.py | Python | gpl-2.0 | 3,374 | [
"OpenMM"
] | f5006055283f8f31816c86a9934cce9f4d8861edad4368dc7637f5e4813c7023 |
import numpy as np
from ..filters import gaussian
def binary_blobs(length=512, blob_size_fraction=0.1, n_dim=2,
volume_fraction=0.5, seed=None):
"""
Generate synthetic binary image with several rounded blob-like objects.
Parameters
----------
length : int, optional
Linear... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/skimage/data/_binary_blobs.py | Python | gpl-3.0 | 2,068 | [
"Gaussian"
] | 56c3d95856ff5609044e6bcfeb9fcdd09632d08e0ac81cd0875360c66e37562f |
# Licensed under an MIT open source license - see LICENSE
from __future__ import print_function, absolute_import, division
import pytest
import numpy as np
import numpy.testing as npt
import astropy.units as u
import astropy.constants as const
import os
try:
import emcee
EMCEE_INSTALLED = True
except ImportE... | e-koch/TurbuStat | turbustat/tests/test_pca.py | Python | mit | 11,070 | [
"Gaussian"
] | e3f2d941b914ed3f605b6940971484def1d2b975c29a2a93e6ff220969033ed7 |
# Copyright 2000-2002 by Andrew Dalke.
# Revisions copyright 2007-2008 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Alphabets used in Seq objects etc to de... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/Alphabet/__init__.py | Python | mit | 11,346 | [
"Biopython"
] | ee5aeaf3c62b823f2c6a3bf64351a6f74719ca5752ff97945153cdfb646bf344 |
# Natural Language Toolkit: Feature Structures
#
# Copyright (C) 2001-2013 NLTK Project
# Author: Edward Loper <edloper@gmail.com>,
# Rob Speer,
# Steven Bird <stevenbird1@gmail.com>
# URL: <http://nltk.sourceforge.net>
# For license information, see LICENSE.TXT
"""
Basic data classes for representing ... | TeamSPoon/logicmoo_workspace | packs_sys/logicmoo_nlu/ext/pldata/nltk_3.0a3/nltk/featstruct.py | Python | mit | 102,180 | [
"VisIt"
] | 4e272441614737b0ae8d21a23ad23c1a6900845214b83b7112956fe51f7c57dd |
"""
Newick format (:mod:`skbio.io.format.newick`)
=============================================
.. currentmodule:: skbio.io.format.newick
Newick format (``newick``) stores spanning-trees with weighted edges and node
names in a minimal file format [1]_. This is useful for representing
phylogenetic trees and taxonomies... | kdmurray91/scikit-bio | skbio/io/format/newick.py | Python | bsd-3-clause | 20,466 | [
"scikit-bio"
] | cc72453c28a9bea6a6a80cab53a8889756abb762b4243f8caa0414e33fec53dd |
"""
canny.py - Canny Edge detector
Reference: Canny, J., A Computational Approach To Edge Detection, IEEE Trans.
Pattern Analysis and Machine Intelligence, 8:679-714, 1986
Originally part of CellProfiler, code licensed under both GPL and BSD licenses.
Website: http://www.cellprofiler.org
Copyright (c) 2003-2009 M... | chintak/scikit-image | skimage/filter/_canny.py | Python | bsd-3-clause | 10,380 | [
"Gaussian"
] | de5148e32a853d49f8e62f2c5f710911e3811bb06b52b0f1bf316acab60f2925 |
# 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 uniq... | zjuchenyuan/BioWeb | Lib/Bio/SCOP/Hie.py | Python | mit | 2,745 | [
"Biopython"
] | d8b0fdea4cd71707c51581b4ff59bc8debedd2eafb50e403e394116675dccc57 |
# -*- coding: utf8
"""Random Projection transformers
Random Projections are a simple and computationally efficient way to
reduce the dimensionality of the data by trading a controlled amount
of accuracy (as additional variance) for faster processing times and
smaller model sizes.
The dimensions and distribution of Ra... | BiaDarkia/scikit-learn | sklearn/random_projection.py | Python | bsd-3-clause | 22,853 | [
"Gaussian"
] | b87a5392e855aa46a9591d823b522174e140f8d5bbb4c9aa90ec068dd7647440 |
## This file is part of Scapy
## See http://www.secdev.org/projects/scapy for more informations
## Copyright (C) Philippe Biondi <phil@secdev.org>
## This program is published under a GPLv2 license
"""
Packet sending and receiving with libdnet and libpcap/WinPcap.
"""
import time, struct, sys, platform
import socket
... | CodeNameGhost/shiva | thirdparty/scapy/arch/pcapdnet.py | Python | mit | 26,496 | [
"VisIt"
] | 9e73ee8fc86f647f30dcdf3174d1168acdb769ce97073e9beabf1ed663387478 |
import datetime
import json, yaml
import io
import csv
from bson import json_util, ObjectId
from collections import OrderedDict
from dateutil.parser import parse
from django.conf import settings
try:
from django.urls import reverse
except ImportError:
from django.core.urlresolvers import reverse
from django.te... | Magicked/crits | crits/core/crits_mongoengine.py | Python | mit | 105,301 | [
"Amber"
] | 00c9f59919acdfaf5237c3258cf18795c4370e8c8c876f10d1f2205a7ae47254 |
#!/usr/bin/env python
# Copyright (C) 2011-2012, 2014, 2016 The PISM Authors
# script to generate figure: results from SeaRISE experiments
# usage: if UAFX_G_D3_C?_??.nc are result NetCDF files then do
# $ slr_show.py -m UAFX
# try different netCDF modules
try:
from netCDF4 import Dataset as CDF
except:
pri... | citibeth/twoway | pism/std-greenland/slr_show.py | Python | gpl-3.0 | 3,893 | [
"NetCDF"
] | b0247e0d85c54625d57db3c0ac5ea9936e712e5817225181617436469fd143cf |
from topo.pattern import Gabor, SineGrating, Gaussian
import __main__
import numpy
import pylab
import matplotlib
from numpy import array, size, mat, shape, ones, arange
from topo import numbergen
#from topo.base.functionfamily import IdentityTF
from topo.transferfn.misc import PatternCombine
from topo.transferfn.misc ... | ioam/svn-history | contrib/modelfit.py | Python | bsd-3-clause | 198,364 | [
"Gaussian"
] | 505eda46203f60dbdd3d996479e196fc14b710183cfc5fc0e2fb3e41bc6bf36d |
"""Factor Analysis.
A latent linear variable model, similar to ProbabilisticPCA.
This implementation is based on David Barber's Book,
Bayesian Reasoning and Machine Learning,
http://www.cs.ucl.ac.uk/staff/d.barber/brml,
Algorithm 21.1
"""
# Author: Christian Osendorfer <osendorf@gmail.com>
# Alexandre Gramfor... | depet/scikit-learn | sklearn/decomposition/factor_analysis.py | Python | bsd-3-clause | 7,690 | [
"Gaussian"
] | e6911d046dbad612dd432fcc2aad020bb7b40a4c66ba6c7b8d756f07bd790f4e |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010 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 Software F... | tiagocardosos/stoq | stoqlib/gui/slaves/taxslave.py | Python | gpl-2.0 | 20,452 | [
"VisIt"
] | 28bec556226977559affdda6121bc975d6659d3daf4437dc1a99bde367e76b13 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2017-2019 Satpy developers
#
# This file is part of satpy.
#
# satpy 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 Licens... | pytroll/satpy | satpy/readers/fci_l1c_nc.py | Python | gpl-3.0 | 23,583 | [
"NetCDF"
] | ceab32c442de1819937c807cc40fabc9171d7ec39cee248ce6f66817d031ddf2 |
#!/usr/bin/python
# -*- coding: iso-8859-1 -*-
from telegram import (ReplyKeyboardMarkup, ReplyKeyboardRemove)
from telegram.ext import (Updater, CommandHandler, MessageHandler, Filters, RegexHandler,
ConversationHandler)
from config import Telegram_BOTID
import logging
# Enable logging
logg... | giuva90/TreeBot | TEST/botConversation.py | Python | gpl-3.0 | 4,255 | [
"VisIt"
] | 618c5b2a42304d1a98b9c71ef1b87a34d0673211ea53ce460f32862d12470973 |
# -*- coding: utf-8 -*-
"""
Main module for mito network normalization
@author: sweel_lim
"""
import os
import os.path as op
import cPickle as pickle
import re
from collections import defaultdict
from post_mitograph import mkdir_exist
from pipeline import pipefuncs as pf
import Tkinter
import TkClas
# pylint: disable=C... | moosekaka/sweepython | pipeline/write_raw_vtk.py | Python | mit | 3,736 | [
"VTK"
] | b0ec7d36ad1ad597a8a0cf0034ca1cf250ba248d5fe9ba4ab5329d7eebba4ba5 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-clusterprofiler/package.py | Python | lgpl-2.1 | 2,199 | [
"Bioconductor"
] | e3fe004ece779e729c991b2b72a0b5ecb5f84c53d7bbf467175ab1f9454c952b |
# 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_dipole_coo.py | Python | apache-2.0 | 2,518 | [
"PySCF"
] | bda25d01aef86ea2da05ae76a2f516b9c4acaec2d9da54dbbe926481fe1d9788 |
################################################################
#
# kim_compare_lammps
#
################################################################
#
# Copyright 2018 the potfit development team
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated doc... | potfit/potfit | util/kim/kim_compare_lammps/lammps.py | Python | gpl-2.0 | 5,179 | [
"LAMMPS"
] | 36207409d0e75898a112a0697b26b921d2b3be7df3c51359abb095ea05c5deaa |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2012 Paul Franklin
#
# This program... | arunkgupta/gramps | gramps/gen/plug/docgen/drawdoc.py | Python | gpl-2.0 | 3,990 | [
"Brian"
] | 5c14dd1cfb8d8667d619700b6b326bb27fc61ee1d56fa61a4d7f84769f778501 |
# cell.py ---
#
# Filename: cell.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Fri Jul 24 10:04:47 2009 (+0530)
# Version:
# Last-Updated: Fri Oct 21 17:17:50 2011 (+0530)
# By: Subhasis Ray
# Update #: 225
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
# This is an ... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/traub2005/py/cell.py | Python | lgpl-2.1 | 11,594 | [
"MOOSE",
"Mayavi"
] | 1f409d50d31a1d797c400974b5fc4fbcc7441e991e1f4175b6ea020a6fa9c20d |
import io
from useful import reverse, remove_dashes, complement
file = [line.rstrip('\n') for line in open("results_RCM.txt", 'r')] #'''input("What's the file you want to read?")'''
left_distances = []
right_distances = []
circs = ["no circ at this position"]
for index, line in enumerate(file):
if ("Left intron... | alexandruioanvoda/autoBLAST | distance_analysis.py | Python | gpl-3.0 | 1,641 | [
"BLAST"
] | 1ffb5f82c4dba7091b135714a1539f60fb2a0eb2bb55cf33c934b92f81e85154 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | erh3cq/hyperspy | hyperspy/_components/skew_normal.py | Python | gpl-3.0 | 9,625 | [
"Gaussian"
] | 331a4d5f76f2358074cf4a455c48d00f230b6d97ae9bf866fad5ff2a0b7d28b5 |
import copy
import json
import multiprocessing
import os
import random
import shutil
import string
import tempfile
from contextlib import contextmanager
from os import chdir, getcwd, mkdir
from os.path import exists
import pkgpanda.build.constants
import pkgpanda.build.src_fetchers
from pkgpanda import expand_require ... | dcos/dcos | pkgpanda/build/__init__.py | Python | apache-2.0 | 52,595 | [
"VisIt"
] | 55517cb7f0bf5a8dcd118e5c916ca734d221eff00dcbd88fbca9556378106536 |
"""
Various bayesian regression
"""
from __future__ import print_function
# Authors: V. Michel, F. Pedregosa, A. Gramfort
# License: BSD 3 clause
from math import log
import numpy as np
from scipy import linalg
from .base import LinearModel
from ..base import RegressorMixin
from ..utils.extmath import fast_logdet, p... | RomainBrault/scikit-learn | sklearn/linear_model/bayes.py | Python | bsd-3-clause | 19,494 | [
"Gaussian"
] | 0d95a4bd1d3790d69e220b50bba48e4b2cd84e4568f9f5b18618b1610689bfdc |
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, ... | CMUSV-VisTrails/WorkflowRecommendation | vistrails/gui/shell.py | Python | bsd-3-clause | 30,589 | [
"VisIt"
] | 4a6583dcabf60d1b92ab555685d7ba729abe2a3d36862e35a752a72320a97207 |
#!/usr/bin/env python3
#
# DNSChef is a highly configurable DNS Proxy for Penetration Testers
# and Malware Analysts. Please visit http://thesprawl.org/projects/dnschef/
# for the latest version and documentation. Please forward all issues and
# concerns to iphelix [at] thesprawl.org.
DNSCHEF_VERSION = "0.4"
# Copy... | iphelix/dnschef | dnschef.py | Python | bsd-3-clause | 30,352 | [
"VisIt"
] | 126bc70a88c8a38d723ed78c1c31046d924e63597edf59ce0228681c4986affa |
import os,sys,re,fileinput
path=os.path.split(os.path.realpath(sys.argv[0]))[0]
filelst=os.listdir(path)
filelst_gjf = []
for filename in filelst:
if filename[-4:] == '.gjf':
filelst_gjf.append(filename)
filenumber=input()
for i in range(filenumber):
filename = str(i) + '.pbs'
fp = open(filename,'w')... | Yuxin-H/test | test3.py | Python | gpl-3.0 | 851 | [
"Gaussian"
] | 29aeff5cbf53f995958b09819f208b70edefc23409d226c9e4704d31340203bd |
import ast
import collections
import math
import numpy as np
import random
from copy import copy
import cgen as c
from parcels.field import Field
from parcels.field import NestedField
from parcels.field import SummedField
from parcels.field import VectorField
from parcels.grid import Grid
from parcels.particle import... | OceanPARCELS/parcels | parcels/codegenerator.py | Python | mit | 46,535 | [
"VisIt"
] | 975dcf2f8eecd8db52b629f6662d8499d59b91e630aec6c9210ea71be7f9dd15 |
# -*- coding: latin-1 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This 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 the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later ... | FedoraScientific/salome-hexablock | src/TEST_PY/test_unit/test_piquage.py | Python | lgpl-2.1 | 2,758 | [
"VTK"
] | 7d95a18ecfc4ee656855d964be6073cf9a3b2bc32b0362cddfa00dfbcf824132 |
"""Leetcode 142. Linked List Cycle II
Medium
URL: https://leetcode.com/problems/linked-list-cycle-ii/
Given a linked list, return the node where the cycle begins.
If there is no cycle, return null.
To represent a cycle in the given linked list, we use an integer pos which
represents the position (0-indexed) in the l... | bowen0701/algorithms_data_structures | lc0142_linked_list_cycle_ii.py | Python | bsd-2-clause | 4,455 | [
"VisIt"
] | 5816497dc11911cf6d973f9e269991dfd49499f0b4984d6c61cb672cb8a00423 |
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