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import os
import time
import shlex
import subprocess as sp
import multiprocessing as mp
from . import blender
from . import freesurfer
from .database import db
def init_subject(subject, filename):
"""Run the first initial segmentation for a subject's anatomy. This function runs
autorecon-all, then imports th... | CVML/pycortex | cortex/segment.py | Python | bsd-2-clause | 5,976 | [
"Mayavi",
"VTK"
] | 830a677ccd60bd2336637fb37dda53b99ebf345527641ceda98e1df2e0f1d4e4 |
# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Various storage (molecular and othe... | adalke/rdkit | rdkit/Dbase/StorageUtils.py | Python | bsd-3-clause | 7,346 | [
"RDKit"
] | 06b31bd4702035ade2344fa6e9e44e553c300ebdca85af381bcb97d960410a3d |
#!/usr/bin/env python
########################################################################
# $HeadURL$
""" File Catalog Client Command Line Interface. """
__RCSID__ = "$Id$"
import cmd
import sys
import pprint
import os
from DIRAC.Core.Utilities.ColorCLI import colorize
from DIRAC.FrameworkSystem.Client.SystemAdm... | Sbalbp/DIRAC | FrameworkSystem/Client/SystemAdministratorClientCLI.py | Python | gpl-3.0 | 30,144 | [
"ASE",
"DIRAC"
] | 694bed203d12c691346a9065ed15f185c3c17e70f12322df734c484fa4e32219 |
# -*- coding: utf-8 -*-
#
# String constants for the RHN Register TUI/GUI.
# Copyright (c) 2000--2015 Red Hat, Inc.
#
# Author:
# James Slagle <jslagle@redhat.com>
import gettext
t = gettext.translation('rhn-client-tools', fallback=True)
_ = t.ugettext
COPYRIGHT_TEXT = _(u"Copyright © 2006--2010 Red Hat... | xkollar/spacewalk | client/debian/packages-already-in-debian/rhn-client-tools/src/up2date_client/rhnreg_constants.py | Python | gpl-2.0 | 19,573 | [
"VisIt"
] | 09fd5ee2f379e0f1b9f1eb56ee5c806675b3a000f6b64cfe18d4a02c38ea2525 |
import os
import numpy as np
import moose
print( 'Using moose from %s' % moose.__file__ )
import time
os.environ['MOOSE_SHOW_PROFILING_INFO'] = '1'
def test_ksolver_parallel( nthreads = 4 ):
"""
This example implements a reaction-diffusion like system which is
bistable and propagates losslessly. It is base... | BhallaLab/moose-core | tests/core/test_ksolve_parallel.py | Python | gpl-3.0 | 3,825 | [
"MOOSE",
"NEURON"
] | 295ce74ffca7c95b2c790174d8353db91faf48b7f4b4f76486889d4174113d62 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | 0x0all/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 54,955 | [
"Brian"
] | 9baf34594229a94c371b8713a95d81f32c0fb836f6a433b9efc71eec39de8505 |
import numpy
import sys
import math
import unittest
try:
import stile
except ImportError:
sys.path.append('..')
import stile
def funcname():
import inspect
return inspect.stack()[1][3]
class TestStats(unittest.TestCase):
def setUp(self):
self.rand_seed = 314159 # random seed for tes... | msimet/Stile | tests/test_stats.py | Python | bsd-3-clause | 6,150 | [
"Gaussian"
] | 09f349910b98abc53e31b0b1c4d5d7854df6bce9a4a8b280d826ea849a86976e |
# YouTube Playlist Bot
# Maintains a YouTube playlist that contains all submissions to a set of sub-reddits that are YouTube links
"""YouTube Playlist Reddit Bot
Usage:
$ python youtubeplaylistbot.py
You can also get help on all the command-line flags the program understands
by running:
$ python youtubeplaylist... | jonminter/youtubeplaylistbot | youtubeplaylistbot.py | Python | mit | 9,547 | [
"VisIt"
] | 1c6bfd8acde4ec21b94e004af3e8be28a46363436dba5edd154974bc9b834327 |
#! /usr/bin/env python3
#
# Copyright (c) 2017, Forschungszentrum Juelich GmbH
# Author: Yann Leprince <y.leprince@fz-juelich.de>
#
# This software is made available under the MIT licence, see LICENCE.txt.
import gzip
import re
import sys
import numpy as np
import pyvtk
# See description of OFF file format at
# http... | HumanBrainProject/neuroglancer-scripts | experimental/off_to_vtk.py | Python | mit | 5,164 | [
"VTK"
] | c851e382e3437bb4c2bfa7480c5a8909be65aec3f38f4908bacfe774a345e563 |
'''
This file is part of the 3CU Source code.
3CU - organizational tool helping you to categorize files in folders,
combine folder content, clean up folders.
Copyright (C) 2016 Timofei Tonu <timofei.tonu@gmail.com>
This program is free software: you can redistribute it and/or mod... | timton/3CU | Source-code/categorize_GUI_helpers.py | Python | gpl-3.0 | 72,008 | [
"ADF"
] | 630b90b0abd1320a9d4fa61d9021fd206a3fd0fe7fc9baf2ff9ac74fd759555a |
#!/usr/bin/env python
""" This script is used to submit the jobs on the grid.
It uses an executable (first argument), creates
a directory in which it will store all the job ids (<jobName> args),
and submit a configurable amount of jobs.
"""
from __future__ import print_function
from __future__ import ab... | yujikato/DIRAC | tests/Performance/DFCPerformance/submitJobs.py | Python | gpl-3.0 | 1,284 | [
"DIRAC"
] | 0196f575ddcf3ee66ae692da92780aeb4d4effe3f0d5713075c30a06359b7002 |
#!/usr/bin/env python
import argparse
from Bio import SeqIO
from Bio.Alphabet import IUPAC, Gapped
from Bio.Seq import Seq
import os
# Create datasets by codon and 1st&2nd from an input nucleotide alignment.
# The output file is in fasta format, but that can be easily converted to phylip with MFAtoPHY.pl
#
# Matt Git... | Cactusolo/ToolBox | alignment_codon_parser.py | Python | mit | 1,980 | [
"Biopython"
] | 0c73d680e023ad4318568ff266577f73b75f8feadf823f0f8ba1fb8c76fb3a08 |
#__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 ... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/scipy/optimize/optimize.py | Python | agpl-3.0 | 114,645 | [
"Gaussian"
] | f8db11411fec8ee15644c3bb8643e812386e35d7bb4bce64d85400c9fc397878 |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2012 OpenStack 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.org/licenses/LICENSE-2.0
#
# Unless required by... | levythu/swift | test/unit/proxy/test_server.py | Python | apache-2.0 | 419,099 | [
"MOOSE"
] | 9a3b6aba78ebc65852fc6e00f4ba66b6eeb8129f35f7fe270d593d47721f9e1a |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | sidheshenator/autopsy | pythonExamples/fileIngestModule.py | Python | apache-2.0 | 7,526 | [
"Brian"
] | 428408ac4a603a3a60e4707b9b694ac5ec42f784ffe72b728a5246ecd0e833e4 |
"""
This module contains classes for representing Contest object
For further information visit http://codeforces.com/api/help/objects#Contest
"""
from enum import Enum
from . import BaseJsonObject
__all__ = ['Contest', 'ContestType', 'ContestPhase']
class ContestType(Enum):
cf = 'CF'
ioi = 'IOI'
icpc ... | soon/CodeforcesAPI | codeforces/api/json_objects/contest.py | Python | mit | 11,845 | [
"VisIt"
] | 696c56838b8d110a61ed81d53688111a385e6755f1cfd1d2cac2e48743d7b3bf |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | Freeseer/freeseer | src/freeseer/__main__.py | Python | gpl-3.0 | 981 | [
"VisIt"
] | dad92bb5c0b4479afd84e36874611e82a584b97a0d33c4bf116f29b3914a18d7 |
__author__ = 'tylin'
__version__ = '2.0'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that
# assists in loading, parsing and visualizing the annotations in COCO.
# Pleas... | DeepRNN/image_captioning | utils/coco/coco.py | Python | mit | 13,920 | [
"VisIt"
] | 21003cd7969ea4aee3d6a90011be97cabc1c1af9c15a0def4c58b32820528d34 |
# PDB Ion Survey
# Copyright (c) 2016 Kacey Clark
# Published under the GPL v3
# https://github.com/Becksteinlab/PDB_Ion_Survey/
'''
Functions for analyzing ion coordination in PDB structures
'''
import os.path
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import MDAnalysis as mda
import wa... | Becksteinlab/PDB_Ion_Survey | src/pdbionsurvey/coordination.py | Python | gpl-3.0 | 12,819 | [
"MDAnalysis"
] | 2c622d6ee40202c9eb93008dc8d080ce21162d37d7f4d87385ffe2ea7cbc854c |
#!/usr/bin/python
#
"""
Holiday simulator server and Python development platform
Using a named pipe to pass data locally (for IoTAS testing mostly)
Homepage and documentation: http://dev.moorescloud.com/
Copyright (c) 2013, Mark Pesce.
License: MIT (see LICENSE for details)
"""
__author__ = 'Mark Pesce'
__version__ ... | moorescloud/holideck | simpype/simpype.py | Python | mit | 4,795 | [
"BLAST"
] | b6873ad28da02f62a23aac2cb302c48e039bbcac652f31d43b172499b64d8019 |
"""
Elastic basis pursuit
"""
import numpy as np
import numpy.linalg as nla
import leastsqbound as lsq
import sklearn.linear_model as lm
import scipy.optimize as opt
def err_func(params, x, y, func):
"""
Error function for fitting a function
Parameters
----------
para... | arokem/elastic_basis_pursuit | ebp/elastic_basis_pursuit.py | Python | mit | 7,933 | [
"Gaussian"
] | 2b39833a81c920f68b96b8533f4e8a4a8d05f7c6295bb652b2f4c0afe3b92784 |
# Copyright (C) 2010-2019 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 v... | psci2195/espresso-ffans | testsuite/python/analyze_distance.py | Python | gpl-3.0 | 4,418 | [
"ESPResSo"
] | 82fdda7f95e1f4be0e101ff99ca513b8a71106128be701cc4d491fb010c036cf |
# tests 19926 weighted paths of log-transformed TGF_beta pathway
plRead = open("TGF_beta-weighted-paths-pathlinker.txt", "r")
csRead = open("TGF_beta-weighted-paths-cytoscape.txt", "r")
# dict that stores path: weight
pl = {}
epsilon = 0.0001
def sameFloat(a, b):
return abs(a - b) <= epsilon
for line in plRead:
... | tmmurali/PathLinker | data/TGF_beta/test-files/TGF_beta-weighted-paths-comparison.py | Python | gpl-3.0 | 720 | [
"Cytoscape"
] | d612a491f734b364033ad97eec4ea4b4712ccb9a1a35ecff225bc3e4e5c2924f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/writing mcsqs files following the rndstr.in format.
"""
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.core.lattice import Lattice
from pymatgen.core.per... | mbkumar/pymatgen | pymatgen/io/atat.py | Python | mit | 4,520 | [
"CRYSTAL",
"pymatgen"
] | 1278661c46b512ba169fc3de450aef022b4c4c34462734be275b1b4f4f879260 |
#############################
##
## The SireMM library.
##
## This contains all of the classes that are used to
## provide a molecular mechanics forcefield (partial
## charges, LJ terms, bond, angle, dihedral terms,
## MM parameter database classes etc). It also
## contains all of the MM forcefields.
##
import Sire.F... | michellab/Sire | wrapper/MM/__init__.py | Python | gpl-2.0 | 3,237 | [
"Amber"
] | 313f8bf5148f1707f2319d41b803545e70992071a34d1c34ea23753656f8fd11 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-configure
# Author : Ricardo Graciani
########################################################################
"""
Main script to write dirac.cfg for a new DIRAC installation and initial downl... | rajanandakumar/DIRAC | Core/scripts/dirac-configure.py | Python | gpl-3.0 | 18,495 | [
"DIRAC"
] | 4b7062c0869de6dd18dc3e7c5927815bc897caa74a7b6cbb19f3cb69410b8b8b |
import ast
import sys
class RemoveObject(ast.NodeTransformer):
def __call__(self, node):
if sys.version_info < (3, 0):
return node
return self.visit(node)
def visit_ClassDef(self, node):
node.bases = [b for b in node.bases if not isinstance(b, ast.Name) or (isinstance(b, a... | listyque/TACTIC-Handler | thlib/side/python_minifier/transforms/remove_object_base.py | Python | epl-1.0 | 430 | [
"VisIt"
] | 9a15cef5d938b8b46bc57dc03a54dcac9cad1086915b790bff8476554c81d905 |
import ase
from ase.utils.geometry import cut, stack
from ase import io
from ase import atoms
# Read in the configurations
substrate = ase.io.read('POSCAR.SnO.vasp',format='vasp')
epilayer = ase.io.read('POSCAR.NiO.vasp',format='vasp')
# Rotate the epilayer
angle_of_rotation = 0.5 # The increment of rotation... | keeeto/Sodom | SodomStack.py | Python | gpl-3.0 | 751 | [
"ASE",
"VASP"
] | 606d872079a2910be1fd6427c7952fdaff8c537735f3a28cbb8c30770804455a |
#!/usr/bin/env python
# pygeo - a distribution of tools for managing geophysical data
# Copyright (C) 2011, 2012 Brendan Smithyman
# This file is part of pygeo.
# pygeo 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 Sof... | bsmithyman/pygeo | util/fast2paraview.py | Python | gpl-3.0 | 2,005 | [
"ParaView"
] | 3af868fb57e24f76f5e7950a33a19bf7f5d531e505db107a0b6b6f3bb79110cd |
#!/usr/bin/env python
"""
Auroral Phantom Generator
# stationary vertical bar
./AuroraPhantom.py -t vertbar -n 1
"""
import argparse
import scipy.ndimage as nd
import imageio
from pathlib import Path
import cvphantom
import cvphantom.plots as cp
if __name__ == "__main__":
p = argparse.ArgumentParser(description=... | scienceopen/cv-phantom-gen | AuroraPhantom.py | Python | gpl-3.0 | 2,377 | [
"Gaussian"
] | b3a49cba2cb3945f4844998ede0deafb9a59e165eb0f53c15cad5d2faa60467d |
# -c
# I/O check for ability to read & write PDB files in order and with atom names preserved
#
from glob import glob
import traceback
import threading
import time
from pymol import cmd
import sys, os, os.path
ent_dir = "pdb/*"
ref_file = "tmp/ref.pdb"
out_file = "tmp/out.pdb"
cmp_file = "tmp/cmp.pdb"
dif_fil... | gratefulfrog/lib | python/pymol/pymol_path/test/inp/B04.py | Python | gpl-2.0 | 2,041 | [
"PyMOL"
] | a8eaab09c5b9cb8688512e3fcf49b76a4238c3790c087def3e413d15fa20e5f8 |
from ase.test import cli, require
require('aims')
# warning! parameters are not converged - only an illustration!
cli("""ase-build -x bcc -a 3.6 Li | \
ase-run aims -s 0.3 -p \
kpts=1.5,xc=LDA,sc_accuracy_eev=5.e-2,relativistic=none,compute_analytical_stress=True,sc_accuracy_forces=5.e-2""")
| grhawk/ASE | tools/ase/test/aims/aims_cmdline.py | Python | gpl-2.0 | 294 | [
"ASE"
] | 3e97c26f3159247af8d48ee11657bdb57c24c17f8485982c3ed43e24b99a1511 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Views tests for the OSF."""
from __future__ import absolute_import
import datetime as dt
import httplib as http
import json
import math
import time
import unittest
import urllib
import datetime
import mock
from nose.tools import * # noqa PEP8 asserts
from modularodm... | jnayak1/osf.io | tests/test_views.py | Python | apache-2.0 | 185,117 | [
"Brian"
] | 3df18d9421d3cdef42b37ab0e740fde2a616085476e30854dbfba54897f80b87 |
import numpy as np
from scipy.stats import bernoulli
import random
def generateWignerMatrix(matrix_size):
matrix = np.zeros((matrix_size, matrix_size)) #Form a symmetric matrix
newSize = (matrix_size*(matrix_size+1))/2
bern = bernoulli.rvs(0.5, size=newSize) #Get the random bernoulli variates
for i in ... | krishnasripada/HighDimDataSet | Assignment1/problem22_bak.py | Python | gpl-2.0 | 1,775 | [
"Gaussian"
] | 33fd1409668c4572893853ff815a0129200f406d4971dda8da6a37f8486cff1b |
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | maestro-hybrid-cloud/horizon | horizon/base.py | Python | apache-2.0 | 38,614 | [
"VisIt"
] | a0b8cb8e4adb355ec89331221608d56517f4154b585263ad501e3560e4dd1233 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a MolecularOrbital class to represent band character in
solids. Usefull for predicting PDOS character from structural information.
"""
from itertools import chain, combinations
from pymatgen.core.c... | vorwerkc/pymatgen | pymatgen/core/molecular_orbitals.py | Python | mit | 4,651 | [
"CRYSTAL",
"pymatgen"
] | d1f738316f7036b8ed3189e3dcd926f19b97d3aaea18f18bc56aee184ef73614 |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
"""
Initialize server package... | rstreif/rvi_backend | server/__init__.py | Python | mpl-2.0 | 1,031 | [
"Jaguar"
] | 53122925cdfabbd39645c6339c45d082dd46d7677dc403c21929ef744ea709eb |
import numpy as np
import scipy.special as sp
import matplotlib.pyplot as plt
# radius of the oberservation circle
def NMLA_radius(omega,Rest=1):
# Input: omega--frequency; Rest--estimate of the distance from source to observation point
#
# Output: the radius of the oberservation circle
poly = [1,... | dinrker/MPM_NMLA | NMLA/NMLA.py | Python | mit | 2,968 | [
"Gaussian"
] | 5105488e7569d376563ea88a3fd672402dd6aba8f5945d4e0c453a85a896ce64 |
# changes 2019 new output format
# changes 2020 tube 7 is normalised to BM if ticked
# Script control setup area
# script info
__script__.title = 'KKB Plot and Reduction 25.1.2016'
__script__.version = '2.0'
# 15.6.2017 Allow to reduce the detector range
# 15.6. Throw out points below resoluti... | Gumtree/Kookaburra_scripts | Internal/KKB-Plot and Reduction_March2019_changeOutputFormat.py | Python | epl-1.0 | 65,928 | [
"CRYSTAL"
] | c85fbf07e9ab924e3a294bd4d2bb167f6bb950338d468acb919da5dd5c296b88 |
##
# Copyright 2013-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | boegel/easybuild-easyblocks | easybuild/easyblocks/f/foldx.py | Python | gpl-2.0 | 3,065 | [
"FoldX"
] | b2a57479f38f3586c4816658a5af1ffbab2a97035ee4116419ecb2b70233f3f9 |
# The Vision Egg: SphereMap
#
# Copyright (C) 2001-2004 Andrew Straw.
# Copyright (C) 2005-2008 California Institute of Technology
#
# Author: Andrew Straw <astraw@users.sourceforge.net>
# URL: <http://www.visionegg.org/>
#
# Distributed under the terms of the GNU Lesser General Public License
# (LGPL). See LICENSE.TXT... | visionegg/visionegg | VisionEgg/SphereMap.py | Python | lgpl-2.1 | 56,058 | [
"Gaussian"
] | a145bfc3dc6d36347b03d12065ab417ac04e6466cc4f3ba1e8ba259ce183be98 |
import argparse
import sys
from multiprocessing.spawn import freeze_support
import logging
from .version import __version__
def main(call_args=None):
"""
Main launcher function for the pipeline.
:param call_args: optional argument string to be passed to execute the commands.
Otherwise, the string wil... | lucventurini/mikado | Mikado/__main__.py | Python | lgpl-3.0 | 3,694 | [
"BLAST"
] | 139bdfe27f94c1ef2d1db8f932054894f596b4ea4700eddf67bfff87ee68518f |
# -*- coding: utf-8 -*-
# Generated by Django 1.11.20 on 2019-06-27 01:51
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('core', '0004_auto_20170502_0120'),
]
operations = [
migrations.AlterField(... | BridgeCityBicycleCoop/workstand | core/migrations/0005_auto_20190627_0151.py | Python | mit | 693 | [
"VisIt"
] | 50c225822d4b82ce0c655094774df703d629bead13841351a0d2731fc7553a2e |
# Copyright 2012 by Wibowo Arindrarto. 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.
"""Bio.SearchIO parser for HMMER domain table output format."""
from itertools import cha... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SearchIO/HmmerIO/hmmer3_domtab.py | Python | gpl-2.0 | 12,634 | [
"Biopython"
] | 43065f9eae8171dfe5979948ee0f81d48a662221e8004b5e75cbbca44ddba045 |
from piston.handler import BaseHandler
from emitters import *
from piston.utils import rc
from climatedata import models
import inspect
from slug import *
import climatedata.models
from climatedata.models import Archive
from climatedata.models import ClimateModel
from climatedata.models import Scenario
from climatedata... | OpenSource-/OpenClimateGIS | src/openclimategis/api/handlers.py | Python | bsd-3-clause | 12,016 | [
"NetCDF"
] | dc05bd7f2b76f81c94f3b2ab4aad9d33a40f25b1ac0a0fccee70e2dc8a4f4e3f |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import os
import re
import webapp2
import jinja2
import logging
from markupsafe import Markup, escape # https://pypi.python.org/pypi/MarkupSafe
import parsers
from google.appengine.ext import ndb
from google.appengine.ext import blobstore
from google.appengine.api impo... | twcctz500000/schemaorg | sdoapp.py | Python | apache-2.0 | 58,895 | [
"VisIt"
] | 207b6311e7754898c9b3249cb9c7b49aeaf0794fb1c42126d44f5875fffea9f9 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The main routine of this package that aims at performing the
extraction of ROIs from multisubject dataset using the localization
and activation strength of extracted regions.
This has been published in... | bthirion/nipy | nipy/labs/spatial_models/bayesian_structural_analysis.py | Python | bsd-3-clause | 14,826 | [
"Gaussian"
] | fbb0b1801e392c2509207d9b65730bb38267e5eaeb4d8e56be9912b70d230083 |
tests = [("testExecs/testDepictor.exe", "", {}), ]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| rvianello/rdkit | Code/GraphMol/Depictor/test_list.py | Python | bsd-3-clause | 224 | [
"RDKit"
] | 4f4e0a836b3c1a6b9545a9136e2fdd7695b2eb7620d8e000e0c8217c06df9994 |
"""
Utilities for PDB2PQR Suite
This module provides various utilities for the PDB2PQR suite to be
imported into other Python scripts.
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
... | MonZop/BioBlender | bin/pdb2pqr-1.6/src/utilities.py | Python | bsd-2-clause | 12,031 | [
"Amber",
"CHARMM"
] | 1a8ed507285b93f49808984a6909c629c216df95e4213bdef285f44304330980 |
#!/usr/bin/env python
# Author: Jason Buenrostro, Stanford University
# modified from plotV_vC.py (Alicia)
# Will make a V-plot from bed regions
##### IMPORT MODULES #####
# import necessary for python
import os
import sys
import numpy as np
import re
import pysam
import matplotlib
matplotlib.use('Agg')
from multip... | buenrostrolab/proatac | proatac/bin/python/py3_bedCount.py | Python | mit | 2,571 | [
"pysam"
] | 3efd69fdbd5a615aeb3f6b9e86556706032aba59484ffdd7df393ab862b7342e |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2014-2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This p... | elkingtonmcb/nupic | src/algorithms/anomaly_likelihood.py | Python | agpl-3.0 | 25,045 | [
"Gaussian"
] | 3d1f4d0720430aecd8e03c65932297be96db6c44d4288e0548db6cd54cb36152 |
import sys
from pyneuroml import pynml
####################################################################
# Choose a LEMS/NeuroML2 file and run it with jNeuroML
example_lems_file = "LEMS_NML2_Ex5_DetCell.xml"
print("Running with jNeuroML...")
results1 = pynml.run_lems_with_jneuroml(
example_lems_file, nogui... | NeuroML/pyNeuroML | examples/run_jneuroml_plot_matplotlib.py | Python | lgpl-3.0 | 1,827 | [
"NEURON"
] | dfe8474ee9a4278c2905e76866b3392580469367ab96ba4ce601f4a3ee025f19 |
# -*- coding: utf-8 -*-
#
# network.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
# (... | heplesser/nest-simulator | pynest/examples/Potjans_2014/network.py | Python | gpl-2.0 | 21,146 | [
"NEURON"
] | e49e3611c2540400d7a1c8a5c0cbbdea0cc3b6c0271b9318e2af1a927ff74900 |
# -*- coding: utf-8 -*-
"""
\mainpage Thoth – Scanning Probe Microscopy (SPM) Analysis Tools
Thoth is a SPM data analysis tools handling 1d, 2d and 3d data types. It is
based on Guidata and Guiqwt (Qt based) for the GUI. Thoth is written in
order to be able to use scripted analysis on large bunch of ... | fbianco/thoth | thoth.py | Python | gpl-3.0 | 21,553 | [
"Gaussian"
] | 61a9e8a887b06f17c4f0b4bf17f06406afd764b0fecea3f44777b04bcefc38ff |
# This script processes MIMIC-III dataset and builds longitudinal diagnosis records for patients with at least two visits.
# The output data are cPickled, and suitable for training Doctor AI or RETAIN
# Written by Edward Choi (mp2893@gatech.edu)
# Usage: Put this script to the foler where MIMIC-III CSV files are locate... | mp2893/retain | process_mimic.py | Python | bsd-3-clause | 5,376 | [
"VisIt"
] | 0569b4ae922779f434e76b92b3b6b6f8968d1ab6d46b4833f9c296d514c5e441 |
# $Id$
#
# Copyright (C) 2004-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit import rdBase
from rdkit.D... | bp-kelley/rdkit | rdkit/DataStructs/__init__.py | Python | bsd-3-clause | 1,628 | [
"RDKit"
] | a54aae192708ece560df9e6c8aba736720dc06f4500c17f70cc8cc9d8dd6d64e |
#!/usr/bin/env python
"""
print DCommands session environment variables
"""
import os
import DIRAC
from COMDIRAC.Interfaces import critical
from COMDIRAC.Interfaces import DSession
if __name__ == "__main__":
import sys
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__.split( '... | pigay/COMDIRAC | Interfaces/scripts/dgetenv.py | Python | gpl-3.0 | 1,447 | [
"DIRAC"
] | 3c1506d096859192397734773a15d02c002b17c3fd6df2296bd0d154be33f5b8 |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
"""
The :mod:`sklearn.hmm` module implements hidden Markov models.
**Warning:** :mod:`sklearn.hmm` is orphaned, undocumented and has known
numerical stability issues. If nobody volunteers to write documentation and
make it more stable, this module will... | cdegroc/scikit-learn | sklearn/hmm.py | Python | bsd-3-clause | 40,928 | [
"Gaussian"
] | 150ec840f23677b37f81f8982d95a0011f344a223a682f7ae534b0da4f0a8786 |
# Copyright 2013-2016 Tom Eulenfeld, MIT license
"""
obspyh5
=======
HDF5 write/read support for obspy
---------------------------------
Welcome!
Writes and reads ObsPy streams to/from HDF5 files.
Stats attributes are preserved if they are numbers, strings,
UTCDateTime objects or numpy arrays.
Its best used as a plug... | trichter/obspyh5 | obspyh5.py | Python | mit | 10,485 | [
"VisIt"
] | c3074f01e43910a0702bfc51debe3f16244b3fb5a37383233c4967d51af0f8f2 |
# cython: infer_types=True
#
# Tree visitor and transform framework
#
from __future__ import absolute_import, print_function
import sys
import inspect
from . import TypeSlots
from . import Builtin
from . import Nodes
from . import ExprNodes
from . import Errors
from . import DebugFlags
from . import Future
impor... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Cython/Compiler/Visitor.py | Python | apache-2.0 | 28,932 | [
"VisIt"
] | 2fc40933fda1ab9f2819e79278828d070788a47ff29d81561e1209a15a826856 |
#
# Copyright (C) 2014-2022 S[&]T, The Netherlands.
#
from __future__ import absolute_import, division, print_function
from muninn._compat import string_types as basestring
from muninn.schema import *
from muninn.visitor import TypeVisitor
class _ConfigParser(TypeVisitor):
def visit(self, type, value):
... | stcorp/muninn | muninn/config.py | Python | bsd-3-clause | 2,744 | [
"VisIt"
] | fa0e4be6fdfabc376f6afb6e13f0ddbebc530d62b69089a42d21100dc2da8e04 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 9 10:44:56 2015
@author: amminex
"""
from yade import plot, pack, qt, export, ymport#, vtk #,utils
from yade.pack import *
import numpy as np
#from yade import heat_ as heat
from yade import heat2 as heat
import os
O.materials.append(FrictMat(young=... | bcharlas/mytrunk | examples/thermalFlowEngine/02-trial_Heat_python_c.py | Python | gpl-2.0 | 2,936 | [
"VTK"
] | ba43a32885654ce1d82d3937fc3a2347a275e2738158605cda25d03fbf1160d6 |
#!/usr/bin/python
# -*- coding: iso-8859-1 -*-
"""Use VTK to display an HMatrix graphically.
"""
import logging
import optparse
import sys
import vtk
import random
from hmat_json_parser import *
from vtk_utils import *
def badLeaves(hmat):
"""Return a list of big, badly-compressed Rk leaves.
"""
# leav... | BenoitLBen/runtime | tools/display_tree.py | Python | mit | 9,511 | [
"VTK"
] | b1481bb3c90da16a92a7eba33350157987233e2d79fd5a2332694b4f2880259e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/share/psi4/databases/RSE42.py | Python | gpl-2.0 | 77,132 | [
"Psi4"
] | 84a86a5e1f88f62200c2a117992660978e3bf90e9265bed0c6ff8e1da0f47b9c |
"""
Utilities to execute one or more functions with a given proxy.
:func:`executeWithUserProxy` decorator example usage::
@executeWithUserProxy
def testFcn(x, i, kw='qwerty'):
print "args", x, i
print "kwargs", kw
print os.environ.get('X509_USER_PROXY')
return S_OK()
...
result = testFcn( 1... | chaen/DIRAC | Core/Utilities/Proxy.py | Python | gpl-3.0 | 10,067 | [
"DIRAC"
] | 827ca297fb03c86a819e513d941a8c690ed1eca05d2befeaadac0ea14d9fb23b |
#!/usr/bin/env python
import sys
import os
import getopt
import numpy as np
import lcg
import time
import subprocess as sub
class ColorFactory:
RED = '\033[91m'
GREEN = '\033[92m'
BLUE = '\033[94m'
YELLOW = '\033[93m'
ENDC = '\033[0m'
def __init__(self):
pass
def __color__(self, co... | danielelinaro/dynclamp | python/lcg/correlations.py | Python | gpl-3.0 | 19,107 | [
"Gaussian"
] | 451ef043da9a190a1f6afdb8c0aeb3eecaf0cf3d14b75dca141a2d13576ce8e6 |
"""
A module for finding context genes associated with bacteriocins
using a training dataset and blast
Output
1. bacteriocin ID
2. organism
3. bacteriocin start
4. bacteriocin end
5. bacteriocin strand
6. annotated gene organism
7. annotated gene locus
8. annotated gene protein id
9. annotated gene s... | idoerg/BOA | src/genome/context_gene.py | Python | gpl-3.0 | 5,910 | [
"BLAST"
] | 0aa0ff8bd714201fb4b2c962536d7421668171626b1c0bba49ef0d84e29f923c |
#!/usr/bin/env python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free ... | GustavoHennig/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 32,676 | [
"Galaxy"
] | ac3a8bfbe2af450d131de488046eaa6b6f52b075266ff3d3b6a79288915619cc |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test logfiles with core electron data in cclib"""
import os
import unittest
import numpy
from cclib.parser.utils imp... | Schamnad/cclib | test/data/testCore.py | Python | bsd-3-clause | 1,500 | [
"ADF",
"cclib"
] | 2e02c4d7ce19c9d13733dabc588b2e6bc52e3048f0b13f2d6a390e45a5278003 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Tests for the SkyCoord class. Note that there are also SkyCoord tests in
test_api_ape5.py
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import copy
import n... | AustereCuriosity/astropy | astropy/coordinates/tests/test_sky_coord.py | Python | bsd-3-clause | 51,951 | [
"Galaxy"
] | 2b0fa11e406cf3f0fb3471caf2760ed8f4c69221442fd72273b33b116b0f0869 |
from __future__ import absolute_import
input_name = '../examples/navier_stokes/stokes_slip_bc.py'
output_name = 'test_stokes_slip_bc.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| vlukes/sfepy | tests/test_input_stokes_slip_bc.py | Python | bsd-3-clause | 205 | [
"VTK"
] | f1db94df23f9db72fec43cbee15e03a9163b7051c61a64e044d3eb060cfc9e36 |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_HTTPError,
compat_http_client,
compat_urllib_error,
co... | xydinesh/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 49,261 | [
"VisIt"
] | f5a7cd27fd82ee626dd502e3255e270a5d63ac55dcfe83f2d268f778f8f403aa |
"""Smooth model maps with Gaussian kernels of HERA specs"""
from __future__ import print_function
import argparse
from multiprocessing import Pool, Manager
import numpy as np
from astropy import constants as const
from astropy.io import fits
from archive.modules.convolution import convolve_gaussian2d
from opstats im... | piyanatk/sim | scripts/archive/gaussian_smooth_hera.py | Python | mit | 4,057 | [
"Gaussian"
] | c857147d203f8431bef26d683b3b28f25077c640a08bbc6e5f5626d936df285a |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2015-2016 lamarpavel
#
# This file is part of qutebrowser.
#
# qutebrowser 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 th... | flv0/qutebrowser | tests/unit/browser/test_cache.py | Python | gpl-3.0 | 13,028 | [
"VisIt"
] | d002be3edbcace8217083f4af25f348af70c5315c91e12467fce6f917a58a576 |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# ---------------------------... | wasade/qiita | setup.py | Python | bsd-3-clause | 3,898 | [
"scikit-bio"
] | 96a2b98e0b545d1f58f907012f251e02c6ee88fdb021765dcf12f84f628dfb85 |
"""Test the dirac-transformation-replication script and helper"""
import unittest
from mock import MagicMock as Mock, patch
from DIRAC import S_OK, S_ERROR
from DIRAC.TransformationSystem.Utilities.ReplicationTransformation import createDataTransformation
from DIRAC.TransformationSystem.Utilities.ReplicationCLIParam... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/test/Test_replicationTransformation.py | Python | gpl-3.0 | 10,827 | [
"DIRAC"
] | e314cb193d704bde7c56a299d7e26274961974aafabfcd5a22b60b3d28848567 |
#!/usr/bin/env python3
from octopus.server.DBInterface import DBInterface
projectName = 'coreutils.tar.gz'
query = "queryNodeIndex('type:Function').name"
db = DBInterface()
db.connectToDatabase(projectName)
result = db.runGremlinQuery(query)
for x in result:
print(x)
| octopus-platform/joern | python/examples/dummy.py | Python | lgpl-3.0 | 276 | [
"Octopus"
] | 84f1725a502755a9f640f4dedc1e145b0d5501b76427c38bb89a571879d683e2 |
# Natural Language Toolkit: Feature Structures
#
# Copyright (C) 2001-2017 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 ... | sdoran35/hate-to-hugs | venv/lib/python3.6/site-packages/nltk/featstruct.py | Python | mit | 102,182 | [
"VisIt"
] | fec797877a43f5da531104d11c7d4dbf477a91bbeb0162f0b88126a397ebe382 |
#!/usr/bin/env python
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COP... | JWDebelius/scikit-bio | skbio/draw/tests/test_distributions.py | Python | bsd-3-clause | 28,920 | [
"scikit-bio"
] | 0d01ebee7aa6f62e32d3721091c61f062dbf991c48a4eb040600992060fc9b41 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
__author__ = "firesun"
__license__ = "GPL"
from selenium import webdriver
import requests
import os
import time
from pyvirtualdisplay import Display
display = Display(visible=0, size=(800,800))
display.start()
while True:
try:
r = requests.get('A url wher... | firesunCN/My_CTF_Challenges | bctf_2017/diary/bot/bot.py | Python | gpl-3.0 | 2,410 | [
"VisIt"
] | 3c7c25ab50bf303a8e4bbe0a11579e2f5c72acb46fe3aa5d499953bb066813a3 |
#!/usr/bin/env python
import os
import logging
import argparse
import subprocess
logging.basicConfig(level=logging.INFO,
format="%(asctime)s %(levelname)s %(message)s")
script_dir = os.path.dirname(os.path.realpath(__file__))
root_dir = os.path.join(script_dir, "../")
def main():
parser = cre... | teanet/Nazabore | Script/bootstrap.py | Python | mit | 1,545 | [
"VisIt"
] | c56668eb50b2cb1bf64e8907f460c985845d5bb5f292fb128920f090d9ec59b4 |
"""
Tests for Coulomb matrix calculation.
"""
import numpy as np
import unittest
from rdkit import Chem
from vs_utils.features import coulomb_matrices as cm
from vs_utils.utils.rdkit_utils import conformers
class TestCoulombMatrix(unittest.TestCase):
"""
Tests for CoulombMatrix.
"""
def setUp(self):... | rbharath/vs-utils | vs_utils/features/tests/test_coulomb_matrices.py | Python | gpl-3.0 | 2,130 | [
"RDKit"
] | 3896a8e09c3157b6b10a5ae6c4ff5b35d83dc82b436e57704feb5c779de7084b |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2009-2013 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 Softw... | andrebellafronte/stoq | stoqlib/domain/production.py | Python | gpl-2.0 | 25,759 | [
"VisIt"
] | 30e21c7df8787975e072dbb5ad5335a7a3585656e4aa76ba81195813c3fef21b |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008-2010, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License ... | NetNow/wmi-samba | pysamba/ndr.py | Python | gpl-2.0 | 821 | [
"VisIt"
] | 9c39041e16fd4cffadae77051e0cd494f35da77353f81fd01e1f7ac89f04ddd9 |
#!/usr/bin/env python3
"""
1.3-finalize_assignments.py
This script parses the BLAST output from 1.1-blast-V_assignment.py and
1.2-blast_J.py. Sequences with successful assignments are
output into fasta files and a master table is created summarizing the
properties of all input sequences.
Usage: 1.... | scharch/SONAR | annotate/1.3-finalize_assignments.py | Python | gpl-3.0 | 16,043 | [
"BLAST"
] | f94e4246f02ddf40c351a1e1bc37d84495436ef1fb3a019098f42abe0aa1c48f |
#! /usr/bin/python
import sys
import time
import os
import traceback
import argparse
from biokbase.probabilistic_annotation.DataParser import DataParser
from biokbase.probabilistic_annotation.Helpers import get_config, now
from biokbase.probabilistic_annotation.DataExtractor import *
desc1 = '''
NAME
pa-gendata... | kbase/probabilistic_annotation | scripts/pa-gendata.py | Python | mit | 10,215 | [
"BLAST"
] | 19b35246d06a7a4bc9bf2fb1e1d5f22feb2a64f75e72bc605e6b2308150e59c2 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
# import funkcí z jiného adresáře
import sys
import os.path
import numpy as np
# from scipy import signal
import matplotlib.pyplot as plt
# import skimage.exposure as skexp
path_to_script = os.path.dirname(os.path.abspath(__file__))
sys.path.append(os.path.join(path_to_scrip... | mjirik/lisa | lisa/lesions.py | Python | bsd-3-clause | 20,631 | [
"Mayavi"
] | bd719b0760662dbe81252b3d4fbb0590408276c57a73b8e9e9be706d36eb7477 |
# -*- coding: UTF-8 -*-
## Copyright 2011-2013 Luc Saffre
## This file is part of the Lino project.
## Lino 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 op... | MaxTyutyunnikov/lino | lino/modlib/cal/workflows/__init__.py | Python | gpl-3.0 | 4,199 | [
"VisIt"
] | b024e9cfdd3f4b53554b3a6f094ef736be3d002ba121dfb753ee9b9177e2f19e |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/tvbrowser.py | Python | gpl-2.0 | 5,168 | [
"VisIt"
] | b3a8b89fe80e35e041c6b7f33aab93811cc8fe5e14adc89bce8a71b64892fed7 |
from interspike_interval import *
from numpy import *
from matplotlib.pyplot import *
from numpy.random import randint
from matplotlib import rcParams
from scipy.io import savemat, loadmat
from switch import *
import UnrecognizedFormatError
class ISIpy(object):
#Constructor begins ---------------------------------... | mac389/brainpy | lib/analysis/ISI/ISIpy.py | Python | gpl-3.0 | 5,276 | [
"Brian",
"NEURON"
] | c5cf32aa39337eea2df785c7891ac1a6ef5219b94f69049f35ab740fa56d3c66 |
"""
Retrieve radar data from the NASA and plot a view of the Grand Canyon
landscape.
We cannot display the whole data, as it would be too big. To display
more, see the canyon decimation example.
This example is interesting as it shows how numpy can be used to load
and crop data completly foreign to Mayavi.
"""
# Auth... | liulion/mayavi | examples/mayavi/mlab/canyon.py | Python | bsd-3-clause | 1,774 | [
"Mayavi"
] | e8eeab3f6c873d097bf73df503dfb230d3ce721a0622d26d8489da5376b1e1ff |
#!/usr/bin/env python
"""This defines data processing and configuration helper functions.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
# Defins constant variables
UNK_TOKEN = '<UNK>'
EOS_TOKEN = '<EOS>'
PAD_TOKEN = '<PAD>'
GO_T... | hao-cheng/factored_neural | factored_neural/model/helper.py | Python | apache-2.0 | 5,825 | [
"Gaussian"
] | 223d8de29127704dcc1bfafa6561e02236df6efb498723c2d71bbaac498ffb4d |
"""Generate the yearly PRISM file to hold our data """
import datetime
import sys
import os
import numpy as np
from pyiem import prism
from pyiem.util import ncopen, logger
LOG = logger()
def init_year(ts):
"""
Create a new NetCDF file for a year of our specification!
"""
fn = "/mesonet/data/prism/... | akrherz/iem | scripts/prism/init_daily.py | Python | mit | 2,835 | [
"NetCDF"
] | 11c61cd5920b49949f125c9c0e46358ba57692ca0c289536f85d29df4d247714 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/io/cube.py | Python | gpl-3.0 | 5,382 | [
"Gaussian"
] | fe520e35d260384df222558283f6da9cf5dc502b8813968114609b754214bd01 |
# FreeCAD init script of the Fem module
# (c) 2001 Juergen Riegel
# ***************************************************************************
# * (c) Juergen Riegel (juergen.riegel@web.de) 2002 *
# * *
# * This fi... | wood-galaxy/FreeCAD | src/Mod/Fem/Init.py | Python | lgpl-2.1 | 2,615 | [
"VTK"
] | 05b40eaa09b07090e4e068a6e7cbc0c37b7fdb2d6837a7b339ad842a174590b3 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Converion between HF object and DFT (KS) object. The SCF energy and SCF
wavefunction are not changed during conversion.
'''
from pyscf import gto
mol = gto.M(
atom = '''
O 0 0 0
H 0 -.757 .587
H 0 .757 .587''',
basis = '6-31... | gkc1000/pyscf | examples/scf/33-convert_to_dft.py | Python | apache-2.0 | 597 | [
"PySCF"
] | 1e1ca1f80ce3d8dad1ce98689d006f38add61ede54727ac6ab0529ee8b581f6a |
# -*- coding: utf-8 -*-
# TODO: Port to pytest
# PEP8 asserts
from copy import deepcopy
import httplib as http
import time
import mock
import pytest
from nose.tools import * # noqa
from tests.base import OsfTestCase, fake
from osf_tests.factories import (
UserFactory, NodeFactory, ProjectFactory,
AuthUserF... | mluo613/osf.io | addons/wiki/tests/test_wiki.py | Python | apache-2.0 | 59,479 | [
"VisIt"
] | 8ca76bb08b545f2f6b838fbed9bba51f9c4a16ba580f16c1f072b730f52688a4 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RCategory(RPackage):
"""Category Analysis.
A collection of tools for performing ca... | iulian787/spack | var/spack/repos/builtin/packages/r-category/package.py | Python | lgpl-2.1 | 1,381 | [
"Bioconductor"
] | 89638fabad82a0e042813fd1c22415ad40c5ae7367edee850fa5decbe62540ec |
__RCSID__ = "$Id$"
from DIRAC import gConfig, S_OK, gLogger
from DIRAC.AccountingSystem.DB.AccountingDB import AccountingDB
from DIRAC.AccountingSystem.private.TypeLoader import TypeLoader
class MultiAccountingDB( object ):
def __init__( self, csPath, readOnly = False ):
self.__csPath = csPath
self.__readO... | Andrew-McNab-UK/DIRAC | AccountingSystem/DB/MultiAccountingDB.py | Python | gpl-3.0 | 3,414 | [
"DIRAC"
] | 2a36098c058d5148dc323a106b9a978955cbf64f4c85211b8421bea9b84e1895 |
import math
import numpy as np
import random
import matplotlib.pyplot as plt
from pylab import *
def initialize(population, minmax):
minmax_diff = minmax[1] - minmax[0]
values = [round(x)
for x in np.random.ranf(population) * minmax_diff - minmax[1]]
steps = [float("%.2f" % x)
... | VictorRodriguez/personal | GP_tutorial/homework3/common.py | Python | apache-2.0 | 954 | [
"Gaussian"
] | 9246f5c6d996bc0a73c3e3f782534ff0e45d7688feb70f65617fccf16472ff7b |
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