text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/encore/bootstrap.py | Python | gpl-2.0 | 4,911 | [
"MDAnalysis"
] | bbfa8f670036f1494ae19aecab0a18ed3150818ed5b1cd9082f61fef54f2be82 |
# Copyright (C) 2016 The ESPResSo project
# Copyright (C) 2014 Olaf Lenz
#
# 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
# (a... | Smiljanic/espresso | src/python/espressomd/__init__.py | Python | gpl-3.0 | 1,106 | [
"ESPResSo"
] | 5d74f5da3cbac43cca0384ae7e4181dc1715befc1d91c5ca74e6b85098830196 |
"""
Vector Autoregression (VAR) processes
References
----------
Lutkepohl (2005) New Introduction to Multiple Time Series Analysis
"""
from __future__ import division, print_function
from statsmodels.compat.python import (range, lrange, string_types, StringIO, iteritems,
cStringIO)
fr... | phobson/statsmodels | statsmodels/tsa/vector_ar/var_model.py | Python | bsd-3-clause | 50,532 | [
"Gaussian"
] | c0ed4994782e4c05b143997c70374058ea2ec08659c0be0054a58b7a480258a6 |
# -*- coding: utf-8 -*-
"""
Unit tests for masquerade.
"""
import json
import pickle
from datetime import datetime
import ddt
from django.conf import settings
from django.urls import reverse
from django.test import TestCase
from mock import patch
from pytz import UTC
from capa.tests.response_xml_factory import Option... | ahmedaljazzar/edx-platform | lms/djangoapps/courseware/tests/test_masquerade.py | Python | agpl-3.0 | 21,981 | [
"VisIt"
] | 4aeceb7b888e91158a14ec1a4a5b7343f1803e5ba718e16cb66c39d2ecf04c25 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009-2010 Benny Malengier <benny.malengier@gramps-project.org>
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2010 Tim Lyons
# Copyright (C) 2... | beernarrd/gramps | gramps/plugins/docgen/htmldoc.py | Python | gpl-2.0 | 22,564 | [
"Brian"
] | 5a01215aa0a429200bde04e7b0d7f08a82ef3b81bd6e70b19c99abf61f822b96 |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for the
IDL version is:
... | artemic/Bubbly | mpfit.py | Python | gpl-3.0 | 78,402 | [
"Gaussian"
] | 5d60569c41b81511b2ff3a592250113f123685e92bb32f8d976cff8023c4b97b |
# License: BSD 3 clause
import pickle
import itertools
import numpy as np
import pytest
from sklearn.metrics import DistanceMetric
from sklearn.neighbors._ball_tree import (
BallTree,
kernel_norm,
DTYPE,
ITYPE,
NeighborsHeap as NeighborsHeapBT,
simultaneous_sort as simultaneous_sort_bt,
n... | sergeyf/scikit-learn | sklearn/neighbors/tests/test_neighbors_tree.py | Python | bsd-3-clause | 9,078 | [
"Gaussian"
] | 4001018fd5c575b8f4cce37b8165570eed3e8fdf5ba8df2794d1ad7f75fd006a |
#!/usr/bin/env python
#
# Unit tests for sites manipulation in samba
# Copyright (C) Matthieu Patou <mat@matws.net> 2011
#
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of t... | sathieu/samba | source4/dsdb/tests/python/sites.py | Python | gpl-3.0 | 22,483 | [
"TINKER"
] | 005d3c1697afd7e794933c03745b93e78dd89c05ecb53bd65cd3f128ddb3978a |
"Demonstrates molecular dynamics with constant energy."
from ase.calculators.emt import EMT
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.langevin import Langevin
from ase.io.trajectory import PickleTrajectory
from ase import units
from asap3 import EMT # Way too slow with ase.EMT !
size = 10
T = 150... | grhawk/ASE | tools/doc/tutorials/md/moldyn3.py | Python | gpl-2.0 | 1,439 | [
"ASE",
"CRYSTAL"
] | ba870f9f7dd3b00da0817dfcfd60e06453d164c0bfb4615cbb2e21d5a2d77113 |
#!/usr/env/python
import numpy as np
from ..utils import arrays as ar
# from ..utils import sliding_window as window
def distsToVectors(X, V):
"""Returns the distances between each row of X and each row of V. If X is
n x m and v is p x m, returns an n x p matrix of L2 distances.
>>> n, m, p = 100, 40, 10
>>> X... | dblalock/flock | python/algo/dist.py | Python | mit | 2,920 | [
"Gaussian"
] | 8d283e4f175d2f7c71179df7d2510ea505e9f4e1bcf93c9ae30e786454e08dd1 |
from unittest import skipUnless
from bok_choy.web_app_test import WebAppTest
from acceptance_tests import ENABLE_OAUTH_TESTS
from acceptance_tests.mixins import LoginMixin
from acceptance_tests.pages import LoginPage
@skipUnless(ENABLE_OAUTH_TESTS, 'OAuth tests are not enabled.')
class OAuth2FlowTests(LoginMixin, W... | edx/edx-analytics-dashboard | acceptance_tests/test_auth.py | Python | agpl-3.0 | 1,122 | [
"VisIt"
] | 6319d2a5ebf3f10bd8cb8a4cef049d80e4413d82ed07f6fccd84a739dabd8334 |
from codecs import getwriter
from collections import defaultdict
from errno import ENOENT
from json import load
import os
from os.path import abspath, relpath, splitext, sep
import subprocess
from tempfile import TemporaryFile, NamedTemporaryFile
from six import string_types
from sphinx.errors import SphinxError
from... | erikrose/sphinx-js | sphinx_js/doclets.py | Python | mit | 8,437 | [
"VisIt"
] | 74b9abc5f8365ad8e62ee464401bcc20dde5309db6dd8b15100625f13fc2d452 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2014-2017 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# 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 S... | lahwaacz/qutebrowser | scripts/dev/pylint_checkers/qute_pylint/config.py | Python | gpl-3.0 | 2,880 | [
"VisIt"
] | 6d88bb9a4480d7bb242b791795a602c7028051ac28df2d0d4cb12cee38f90583 |
import logging
from simtk.unit import nanometers, picoseconds
import numpy as np
logger = logging.getLogger('InterMolLog')
class GromacsGroParser(object):
"""GromacsGroParser reads and writes Gromacs .gro files
A .gro file also contains some topological information, such as elements and
residue names, ... | ctk3b/InterMol | intermol/gromacs/grofile_parser.py | Python | mit | 4,947 | [
"Gromacs",
"LAMMPS"
] | 023361bd833683eb148c7b2e1dd87fba11d96f6c8a128d286a26e35e6d61dbae |
#!/usr/bin/env python
#
# PDBList.py
#
# A tool for tracking changes in the PDB Protein Structure Database.
#
# Version 2.0
#
# (c) 2003 Kristian Rother
# This work was supported by the German Ministry of Education
# and Research (BMBF). Project http://www.bcbio.de
#
# Contact the author
# homepage : http://www.rub... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PDB/PDBList.py | Python | gpl-2.0 | 14,525 | [
"Biopython"
] | 5b8d8c091f51fb8e9e17de5ede8c7f239c5ed4a0bd23d0332fc873033e0e8c6c |
"""
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)
"""
from django.contrib import ad... | rstreif/rvi_backend | web/devices/admin.py | Python | mpl-2.0 | 3,806 | [
"Jaguar"
] | 5fdbc1591d03ff86298f52460d01454c6f7e6154fb7c9a30919c70b08af61015 |
Symbol
TFSC
TFSCR
TFSCU
TFSCW
PIH
FLWS
FCTY
FCCY
SRCE
VNET
TWOU
JOBS
SIXD
CAFD
EGHT
AVHI
SHLM
AAON
ABAX
ABY
ABGB
ABEO
ABEOW
ABIL
ABILW
ABMD
AXAS
ACTG
ACHC
ACAD
ACST
AXDX
XLRN
ANCX
ARAY
VXDN
VXUP
ACRX
ACET
AKAO
ACHN
ACIW
ACRS
ACNB
ACOR
ACTS
ACPW
ATVI
ACTA
ACUR
ACXM
ADMS
ADMP
ADAP
ADUS
AEY
IOTS
ADMA
ADBE
ADTN
ADRO
AAAP
A... | computerpencils/ScraXBRL | scrape_lists/stock_exchanges/nasdaq.py | Python | mit | 15,608 | [
"CDK"
] | f4cab10bdd46cc2f377290a463823acaf49c40101f92c3064555af1252dabc88 |
import numpy as np
from astroNN.lamost.lamost_shared import lamost_default_dr
def wavelength_solution(dr=None):
"""
To return wavelegnth_solution
:param dr: data release
:type dr: Union(int, NoneType)
:return: wavelength solution array
:rtype: ndarray
:History: 2018-Mar-15 - Written - He... | henrysky/astroNN | astroNN/lamost/chips.py | Python | mit | 2,586 | [
"Gaussian"
] | 384975d97dcaaf44748add2bbe50d4e27108b2cc078628e3acd0043a6809090c |
# -*- coding: utf-8 -*-
# The defaults dict should contain all application-wide default keys, with their default value.
# Each key must have a value. If it is optional, the empty string will suffice.
defaults_dict = {
# Example default settings set by the EbaTableSpider
'app/scraping_application_name': 'Scrapy... | tenforce/ods-scraper | ods/dictionary.py | Python | apache-2.0 | 10,013 | [
"BWA"
] | 54adcb6dd341d9dab5621377a85c17971ff12cef69304217a17fb6509392925a |
# -*- coding: UTF-8 -*-
"""A module with Gaussian h-sssi process generators.
"""
import numpy as np
from pyfftw import FFTW, empty_aligned
from sklearn.base import BaseEstimator as BaseGenerator
from sklearn.utils import check_random_state
class FractionalGaussianNoise(BaseGenerator):
"""A class to generate frac... | ivannz/crossing_paper2017 | crossing_tree/processes/gaussian.py | Python | mit | 8,114 | [
"Gaussian"
] | ecc5cbbd8d18b07d92ab09ed892c8943d6ed35685471420eb5dc8914c67453eb |
#!/usr/bin/env python
#
# Copyright 2008,2009,2011,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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, or (at ... | geosphere/gr-osmosdr | apps/osmocom_siggen_base.py | Python | gpl-3.0 | 21,193 | [
"Gaussian"
] | 94c3060d94fcb7f4256c204c8c83716c3fd6ae0bb1faa8e38d137734a3d7f1b3 |
import pytest
import json
import asyncio
from tornado import testing
from tornado import httpclient
from waterbutler.core import streams
from waterbutler.core import exceptions
from tests import utils
class TestCrudHandler(utils.HandlerTestCase):
HOOK_PATH = 'waterbutler.server.api.v0.crud.CRUDHandler._send_... | TomBaxter/waterbutler | tests/server/api/v0/test_crud.py | Python | apache-2.0 | 8,981 | [
"Brian"
] | ba315f60dc8a7b801a7e2e2dac7b4d461f85d683404acfd8be5a3a07f6d8622b |
from collections import OrderedDict
import os
from gym import error, spaces
from gym.utils import seeding
import numpy as np
from os import path
import gym
try:
import mujoco_py
except ImportError as e:
raise error.DependencyNotInstalled("{}. (HINT: you need to install mujoco_py, and also perform the setup i... | rail-berkeley/d4rl | d4rl/locomotion/mujoco_goal_env.py | Python | apache-2.0 | 6,751 | [
"TINKER"
] | bffef171df1d7f68231cbeaa8adaecd7c7eb10737f8369927abc8eea26880e76 |
import boardgame as bg
from .core import *
from . import action
from . import tags
class Hydra(VillainGroup):
name = 'HYDRA'
def fill(self):
self.add(HydraKidnappers, 3)
self.add(HydraArmies, 3)
self.add(HydraViper, 1)
self.add(HydraSupreme, 1)
class HydraKidnappers(Villain):
... | tcstewar/boardgame | boardgame/legendary/villains.py | Python | gpl-2.0 | 22,654 | [
"Octopus"
] | a332db13ea9931ca18a9792ec5448fbeb4275192bba4a6a75ab39ee7f5e72fdd |
# goal = make a table of ase values for each gene.
import sys
import scipy.stats
import vcf
if len(sys.argv) != 6:
print('python aseValuesByGene.py [DNA vcf] [RNA vcf] [out file] [min snps per gene] [list of median expression levels]')
sys.exit()
dnaDict = {} #keys are (scaffold,pos) and value is a list of all the ... | emjosephs/eQTL | aseValuesByGene.py | Python | mit | 2,135 | [
"ASE"
] | 5c220f3f2d96855936457126afa18d474fea0554758197d54bed3f152350b5a2 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe import session, _
from frappe.utils import today
from erpnext.utilities.transaction_base import TransactionBase
class War... | mahabuber/erpnext | erpnext/support/doctype/warranty_claim/warranty_claim.py | Python | agpl-3.0 | 2,169 | [
"VisIt"
] | f5c5f70365e36abe0345d2f721686bf4120f18e0fb28143869eba18bb10d38ab |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup
import os.path
SETUP_DIR = os.path.dirname(__file__)
README = os.path.join(SETUP_DIR, 'README.md')
readme = open(README).read()
setup(
name='regate',
version='0.10.0',
description='Registration of Galaxy Tools in Elixir',
long... | C3BI-pasteur-fr/ReGaTE | setup.py | Python | gpl-2.0 | 1,091 | [
"Galaxy"
] | 405b042400a466d996ead05cab1d792e77c6ea22f2504259479a35d1fa379d9a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import re
import numpy as np
import warnings
from pymatgen.core.operations import SymmOp
from pymatgen import Element, Molecule, Composition
from monty.io imp... | johnson1228/pymatgen | pymatgen/io/gaussian.py | Python | mit | 55,956 | [
"Gaussian",
"pymatgen"
] | db84c5fe07a5a8f290599905a87adc161d0551104c1e654e1386c73493a2bf68 |
import numpy as np
import dolfin
from dolfin import *
from mpi4py import MPI as pyMPI
from leopart import StokesStaticCondensation, FormsStokes
import geopart.stokes.incompressible
import dolfin_dg as dg
comm = pyMPI.COMM_WORLD
mpi_comm = MPI.comm_world
#mark whole boundary, inflow and outflow will overwrite)
clas... | BradHub/SL-SPH | hdg_test/anistropic/hdg_test.py | Python | mit | 2,697 | [
"ParaView"
] | e5c822465fdc0f2510eb3952b1879c6c55d5e8cef3d2acfb50af0990bd206657 |
# sybase/base.py
# Copyright (C) 2010-2014 the SQLAlchemy authors and contributors <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is part ... | jessekl/flixr | venv/lib/python2.7/site-packages/sqlalchemy/dialects/sybase/base.py | Python | mit | 28,800 | [
"ASE"
] | 0ced06ff7f120ed6e6e0e0ea9bda2755b649a43e91c5b5d155e20d26f4183288 |
#!/usr/bin/env python
"""An object that provides various utilities for Gaussian random variables. Ben, 1 May 2008"""
import numpy as np
#import pylab
from scipy.linalg import eigh
from scipy.linalg import solve
from scipy.linalg import inv
from scipy.linalg import det
from scipy import randn
class Gauss(object):
... | bhrzslm/uncertainty-reasoning | my_engine/others/GrMPy/lib/GrMPy/gauss.py | Python | mit | 12,617 | [
"Gaussian"
] | 79824fec275528b0b36394cba347536475db9ef4b04cbc5c5fd06ca07a159f2c |
from urlparse import urlparse, parse_qs
from django.test import TransactionTestCase
from django.contrib.auth.models import Group
from django.http import HttpRequest
from hs_core.hydroshare import resource
from hs_core import hydroshare
from hs_tools_resource.models import RequestUrlBase, ToolVersion, SupportedResTy... | FescueFungiShare/hydroshare | hs_tools_resource/tests/test_web_app.py | Python | bsd-3-clause | 12,169 | [
"NetCDF"
] | 0d7aa4de4242ad0ffa48bb44291bbcdea9520cc18e0778c59863feab58c1a24f |
# Copyright 2015 Google Inc. All Rights Reserved.
"""A collection of CLI walkers."""
import cStringIO
import os
from googlecloudsdk.core.util import files
from googlecloudsdk.calliope import cli_tree
from googlecloudsdk.calliope import markdown
from googlecloudsdk.calliope import walker
from googlecloudsdk.core.doc... | wemanuel/smry | smry/server-auth/ls/google-cloud-sdk/lib/googlecloudsdk/calliope/walker_util.py | Python | apache-2.0 | 8,744 | [
"VisIt"
] | 66e57c313ba7e82da4e661a69e045a88ca1e870cf4616a029ca55fe980a94509 |
import pytest
from pysisyphus.calculators import XTB
from pysisyphus.cos.NEB import NEB
from pysisyphus.helpers import geom_loader
from pysisyphus.run import run_tsopt_from_cos
from pysisyphus.testing import using
@pytest.fixture
def cos(this_dir):
geoms = geom_loader(this_dir / "input.cycle_019.trj")
for i... | eljost/pysisyphus | tests/test_run_tsopt_from_cos/test_run_tsopt_from_cos.py | Python | gpl-3.0 | 1,486 | [
"xTB"
] | 1ea882bcc63d65dd71265631fce8a10d687722a37c29b713fea9662b92bb7bec |
"""
@name: Modules/Computer/Nodes/_test/test_nodes_sync.py
@author: D. Brian Kimmel
@contact: d.briankimmel@gmail.com
@copyright: 2016-2020 by D. Brian Kimmel
@date: Created on Jun 2, 2016
@licencse: MIT License
@summary:
Passed all 8 tests - DBK - 2019-01-19
"""
__updated__ = '2020-01-24'
# I... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Nodes/_test/test_nodes_sync.py | Python | mit | 1,875 | [
"Brian"
] | b70327163820bd3ae84566fdc14326a9898715e522fda631c042e41c717ecefe |
# CamJam Edukit 1 - Basics
# Worksheet 7 - Traffic Lights - Solution
# Import Libraries
import os
import time
import RPi.GPIO as GPIO
# Set the GPIO pin naming mode
GPIO.setmode(GPIO.BCM)
GPIO.setwarnings(False)
# Set up variables for the LED, Buzzer and switch pins
PinGreen = 24
PinAmber = 23
PinRed = 18
PinBuzzer ... | CamJam-EduKit/EduKit1 | CamJam Edukit 1 - RPI.GPIO/Code (RPI.GPIO)/7-TrafficLights-solution.py | Python | mit | 4,708 | [
"Amber"
] | 7d93f4d7ccef0f1fdf2688464443c2c9b4aadcaece1dbed29afa958a2b731c23 |
import matplotlib
matplotlib.use('Agg')
import cPickle
from matplotlib import pyplot as plt
import os
data_dir = '/Volumes/Storage/models'
img_save_dir = '/Volumes/Storage/weights'
models = [('clean', 'AE1110_Scale_Warp_Blocks_2049_500_tanh_tanh_gpu_sgd_clean_continue_20141110_1235_21624029'),
('gaussian... | hycis/Pynet | scripts/nii/show_weights.py | Python | apache-2.0 | 1,681 | [
"Gaussian"
] | 2c5f8f60a0e350d37bd20384d544dce5c7b4525e597162367677322b590a8352 |
# 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_rsphar.py | Python | apache-2.0 | 2,649 | [
"PySCF"
] | fcc4d8697622409a40b665cccb31982847d2e6bafa20fc8a4ac83d11ad6940f5 |
#!/usr/bin/env python
import logging
import apache_beam as beam
from apache_beam.io import ReadFromAvro
from apache_beam.utils.pipeline_options import GoogleCloudOptions
from apache_beam.utils.pipeline_options import PipelineOptions
from apache_beam.utils.pipeline_options import SetupOptions
from apache_beam.utils.pi... | chrisbangun/dataflow-appengine | recsys_data_pipeline/ingestion.py | Python | apache-2.0 | 3,269 | [
"COLUMBUS"
] | 63b70f295a661963f8450d8b4f2d835fa6cfadc864bb5f7ead6e72058c70ea21 |
"""The MIT License (MIT)
Copyright (c) 2016-2017 Marcus Ottosson
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 restriction, including without limitation the rights
to use, copy, modify, m... | alijafargholi/prman_rfmPrimVarTool | src/gui/Qt.py | Python | gpl-3.0 | 26,880 | [
"VisIt"
] | 8273a1074fd21481b5bf6339c3adaa99909172dcdc30724b18ace0846430a146 |
'''This example uses a convolutional stack followed by a recurrent stack
and a CTC logloss function to perform optical character recognition
of generated text images. I have no evidence of whether it actually
learns general shapes of text, or just is able to recognize all
the different fonts thrown at it...the purpose ... | baojianzhou/DLReadingGroup | keras/examples/image_ocr.py | Python | apache-2.0 | 20,934 | [
"Gaussian"
] | 0b116d3d718b819303e0b390bcade2117a5d87de5f1cd6e147cb9bda98cd9a1e |
#! /usr/bin/env python
from MDAnalysis import *
#from MDAnalysis.analysis.align import *
import numpy
import math
import sys
my_traj = sys.argv[1]
end = my_traj.find('.pdb')
u = Universe("init.pdb",my_traj)
v = Universe("init.pdb")
# linker 1
a1 = u.selectAtoms("segid J and resid 123")
b1 = u.selectAtoms("segid N a... | demharters/git_scripts | dist_DA10_linker.py | Python | apache-2.0 | 750 | [
"MDAnalysis"
] | 3bfe4e1236d5771828b6f8e34c18bb62d2f12098254c461fa02355940e514dec |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | susilehtola/psi4 | psi4/share/psi4/basis/primitives/diff_gbs.py | Python | lgpl-3.0 | 4,694 | [
"Psi4"
] | 8f36a5ba18710e80414a7b5f5ba89658f718028d697cb7a3329930d45cd332d5 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | rmcgibbo/mdtraj | tests/test_lh5.py | Python | lgpl-2.1 | 4,056 | [
"MDTraj"
] | cf010878d724b89ff50e4ebb17f653795ea1d342ed0803ed1e43a45d7da81bc2 |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | antonve/s4-project-mooc | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 24,093 | [
"VisIt"
] | 33fc5472c851d7032e3b250d4e0b922342dca1a7e8225f06e629e69d28264bf8 |
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright (C) 2014 Dave Hocker
#
# 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, version 3 of the Lic... | dhocker/athomepowerlineserver | commands/__init__.py | Python | gpl-3.0 | 387 | [
"xTB"
] | 9d999f524f5e3079621296a4f91a33c5dc00d8e90e50b6d3457d2555254714b1 |
""" manage PyTables query interface via Expressions """
import ast
from functools import partial
import numpy as np
import pandas as pd
from pandas.core.dtypes.common import is_list_like
import pandas.core.common as com
from pandas.compat import u, string_types, DeepChainMap
from pandas.core.base import StringMixin
f... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/pandas/core/computation/pytables.py | Python | mit | 18,930 | [
"VisIt"
] | 3b92f3203718f3190dbdd0bb7a1eba150e0837b113933924d45b0bb11a738c19 |
# ======================================================================
# Given the following input data w.r.t. a mitral valve setup:
# - a 3D volume mesh (vtu),
# - a 2D surface mesh representation of the MV segmentation (vtp), and
# - an Annuloplasty Ring representation including vertex IDs (vtp)
# this script co... | CognitionGuidedSurgery/msml | src/msml/ext/mvrBCdataProducer.py | Python | gpl-3.0 | 6,923 | [
"VTK"
] | 34b48d1a3d0bad22faa17648e2e5b7b53e2be7ab2837bea48f239129c38effb3 |
"""LAMMPS data format."""
import itertools as it
from collections import OrderedDict
from warnings import warn
import numpy as np
from parmed.parameters import ParameterSet
from scipy.constants import epsilon_0
from mbuild import Box
from mbuild.utils.conversion import RB_to_OPLS
from mbuild.utils.sorting import natu... | iModels/mbuild | mbuild/formats/lammpsdata.py | Python | mit | 38,981 | [
"Amber",
"CHARMM",
"LAMMPS",
"MDTraj"
] | d34ed777f3abe136ca36f41be2dd325867446670684b2dff2b9764ea4f093820 |
"""
Some useful tools for dealing with the oddities of XML serialisation
"""
import re, sys
from octopus.core import app
###########################################################
# XML Character encoding hacks
###########################################################
_illegal_unichrs = [(0x00, 0x08), (0x0B, 0x0... | JiscPER/jper-oaipmh | service/xml.py | Python | apache-2.0 | 2,928 | [
"Octopus"
] | 732da3b213b5b9c1b5c0614ddb14bfbe2bbcfc83ec8f95840d94a684df949084 |
"""Multiprocessing module to handle parallelization.
This module can optionally update a statusbar and can divide tasks
between cores using weights (so that each core gets a set of tasks with
the same total weight).
Adapted from a module by Brian Refsdal at SAO, available at AstroPython
(http://www.astropython.org/sn... | lofar-astron/PyBDSF | bdsf/multi_proc.py | Python | gpl-3.0 | 7,726 | [
"Brian"
] | 2c3257de94ee2c3d1b17b9534add53df0f048ab7c00ad9df65b2e82d66f348a1 |
"""
Container page in Studio
"""
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise, Promise
from common.test.acceptance.pages.common.utils import click_css, confirm_prompt
from common.test.acceptance.pages.studio import BASE_URL
from common.test.acceptance.pages.studio.utils import... | pepeportela/edx-platform | common/test/acceptance/pages/studio/container.py | Python | agpl-3.0 | 24,434 | [
"VisIt"
] | 38818e7b607443545799e32864cdafca9ea9b7503755b9ab791dfc525e7ef488 |
# This is a main file to run the diceseq software, which will return the
# isoform proportions ratio for each gene at all time points.
import os
import sys
import gzip
import time
import pysam
import numpy as np
import multiprocessing
from optparse import OptionParser, OptionGroup
# import pyximport; pyximport.insta... | huangyh09/diceseq | diceseq/diceseq.py | Python | apache-2.0 | 9,351 | [
"pysam"
] | aeb0a256deb6bcbe1f8e04c2254d947a1a4d2c717d4b4382a226e54647cf4a80 |
#!/usr/bin/env python3
# ver 0.1 - coding python by Hyuntae Jung on 03/29/2018
import argparse
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='conver MC input file to npy trajectory files')
## args
parser.add_argument('-i', '--input', default='traj.trr'... | jht0664/Utility_python_gromacs | python/mc_ic_2_npy.py | Python | mit | 3,788 | [
"MDAnalysis"
] | c44abe9bde50bcbb0cecaf95808095398752aa9bef0ff50c96bf1be09fc77e38 |
from __future__ import unicode_literals
import unittest
from django.utils import html
class TestUtilsHtml(unittest.TestCase):
def check_output(self, function, value, output=None):
"""
Check that function(value) equals output. If output is None,
check that function(value) equals value.
... | mammique/django | tests/regressiontests/utils/html.py | Python | bsd-3-clause | 6,494 | [
"ADF"
] | 7cb30e3c54fb2d4a7b21947e8ce3a1ef5a04c9365682e08c6740265e01eba481 |
## Copyright (c) 2012-2015 Aldebaran Robotics. All rights reserved.
## Use of this source code is governed by a BSD-style license that can be
## found in the COPYING file.
import os
import subprocess
import qisys.command
def check_gettext():
gettext = qisys.command.find_program("xgettext", raises=False)
if n... | dmerejkowsky/qibuild | python/qilinguist/test/test_gettext.py | Python | bsd-3-clause | 4,505 | [
"Brian"
] | eaa56c6b320698dcf4df12a34e612e85526cd81022f535dbcfc494ee8192a5bf |
"""
Copyright (c) 2011-2015 Nathan Boley
This file is part of GRIT.
GRIT is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
GRIT is distribut... | nboley/grit | bin/bam2wig.py | Python | gpl-3.0 | 12,286 | [
"pysam"
] | 38fdbf0c34adefe68d613c441a7be1d585833a8c39eef0380728a670913ec3f7 |
#! /usr/bin/env python
import roslib; roslib.load_manifest('ist_tasks')
import rospy
import actionlib
from perception_msgs.msg import *
from ist_grasp_generation_msgs.srv import *
from ist_grasp_generation_msgs.msg import *
import numpy
from orca_proxy.srv import *
from geometry_msgs.msg import Point
import math
from ... | kuri-kustar/seekur_jr_perception | ist_object_detection/scripts/detect_clusters_client.py | Python | lgpl-3.0 | 11,760 | [
"ORCA"
] | 9e389c1c8aa6cbd938e3ffa1f97429906dfec98da17cb87dab044d7c9b022285 |
#!/usr/bin/env
"""
epic_make_monthly.py
From a list of netcdf files calculate for chosen parameter
30.42 day average and output
year month var_ave number_of_samples
2001 1 30.1 15
2001 2 30.0 14
2001 3 1e35 0
print output to screen to be captured
... | shaunwbell/FOCI_Analysis | ReanalysisRetreival_orig/CB_monthly_aves/epic_make_monthly.py | Python | mit | 4,676 | [
"NetCDF"
] | f032cdfa9b4af31c1e44e7cfa39241852a9d67b10b30c431362a8c21e5b56abd |
########################################################################
# $HeadURL $
# File: FileCatalogProxyHandler.py
########################################################################
""" :mod: FileCatalogProxyHandler
================================
.. module: FileCatalogProxyHandler
:synopsi... | avedaee/DIRAC | DataManagementSystem/Service/FileCatalogProxyHandler.py | Python | gpl-3.0 | 3,492 | [
"DIRAC"
] | 04d95d95f75518a7460b1e2dd3044f102febea1e7a80c3084b65665ad55b143d |
import click
from functools import update_wrapper
from PIL import Image, ImageFilter, ImageEnhance
@click.group(chain=True)
def cli():
"""This script processes a bunch of images through pillow in a unix
pipe. One commands feeds into the next.
Example:
\b
imagepipe open -i example01.jpg resi... | staranjeet/fjord | vendor/packages/click/examples/imagepipe/imagepipe.py | Python | bsd-3-clause | 8,425 | [
"Gaussian"
] | 1f2f5b8700c3c03d88e71ca1128aeccecadf3214651751f8e0abd7f4b16f782c |
"""
File format detector
"""
import logging, sys, os, csv, tempfile, shutil, re, zipfile
import registry
from galaxy import util
log = logging.getLogger(__name__)
def get_test_fname(fname):
"""Returns test data filename"""
path, name = os.path.split(__file__)
full_path = os.path.join(path, 'test',... | dbcls/dbcls-galaxy | lib/galaxy/datatypes/sniff.py | Python | mit | 9,773 | [
"Galaxy"
] | e91919f7b98f33ba1a4823e419be6e43789e2264ecfdda9f4669b6c71ef9a01d |
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Prabhu Ramachandran
# License: BSD Style.
# Enthought library imports.
from traits.api import HasTraits, List, Str, Instance
from apptools.preferences.api import PreferencesHelper
################################################... | liulion/mayavi | mayavi/tools/preferences_mirror.py | Python | bsd-3-clause | 2,102 | [
"Mayavi"
] | efbf7fc6e297951bf928dfde0f5c4b0c5924fa98f154986a43453b1de64351d7 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import filecmp
import os
import re
import shutil
import unittest
import pandas as pd
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.io.lammps.data import LammpsData
from ... | vorwerkc/pymatgen | pymatgen/io/lammps/tests/test_inputs.py | Python | mit | 4,338 | [
"Gaussian",
"LAMMPS",
"pymatgen"
] | da9452b9dbbf585a6820efe3c29c31805439d322489cddbc3d2077394499f364 |
# Copyright 2013 the V8 project authors. All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditi... | h0x91b/redis-v8 | redis/deps/v8/test/benchmarks/testcfg.py | Python | mit | 6,634 | [
"Gaussian"
] | 6445dd9a5930d7e95952b22010b3d792489b2ba6eebdaa1ab7eb5969e9339007 |
import sys
import numpy as np
try:
# Matplotlib is not a dependency
import matplotlib as mpl
mpl.use('Agg') # force the antigrain backend
except (ImportError, RuntimeError):
mpl = None
from ase.units import Bohr
from gpaw.mpi import world, distribute_cpus
from gpaw.utilities.tools import md5_array
f... | robwarm/gpaw-symm | gpaw/test/parallel/ut_invops.py | Python | gpl-3.0 | 19,632 | [
"ASE",
"GPAW",
"Gaussian"
] | 38242e33c204e158b4ab7997fe117751114dfc8d10ce5e7b2f198df3a680c5df |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
import json
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST,require_GET
from djang... | TheMOOCAgency/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 52,741 | [
"VisIt"
] | 1944ba5f719c43b9efe1464bf278a916a070111cc7a70ba4c0409b185e83f011 |
#!/usr/bin/env python
import sys
lines_gaff = sys.stdin.readlines()
#pair_style = 'lj/charmm/coul/long'
# NOTE: Long-range coulombic forces were disabled intentionally. (See below)
# If you want to use long-range electrostatics, uncomment these lines:
# Instead I use hybrid lj/charmm/coul/charmm b... | slitvinov/lammps-swimmer | tools/moltemplate/common/amber/amberparm_pair_to_lt.py | Python | gpl-2.0 | 1,072 | [
"CHARMM",
"LAMMPS"
] | c913b04ae90e1f47237523af84e70e8a48e739783ca73a1510e45c13f6486c1c |
# Created by DrLecter, based on DraX' scripts
# This script is part of the L2J Official Datapack Project
# Visit us at http://www.l2jdp.com/
# See readme-dp.txt and gpl.txt for license and distribution details
# Let us know if you did not receive a copy of such files.
import sys
from com.l2scoria.gameserver.model.ques... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/village_master/elven_human_mystics_2/__init__.py | Python | gpl-3.0 | 4,139 | [
"VisIt"
] | 78500fe02d75c2d6739f213f5aeb0ad6a8c41ae6bb3cd5002173214fb8d2f683 |
from common import Modules, data_strings, load_yara_rules, AndroidParseModule, ModuleMetadata
from base64 import b64decode
from string import printable
class dendroid(AndroidParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="dendroid",
bot_name="Dendroid",
... | bwall/bamfdetect | BAMF_Detect/modules/dendroid.py | Python | mit | 2,007 | [
"Brian"
] | ac48112ca2713a20c8cc4c30601257d2d1811cf6d8e2233ba6beaec9f5047f30 |
"""Test Axis event instance API.
pytest --cov-report term-missing --cov=axis.event_instances tests/test_event_instances.py
"""
import pytest
from axis.event_instances import EventInstances, URL, get_events
import respx
from .conftest import HOST
from .event_fixtures import (
EVENT_INSTANCES,
EVENT_INSTANCE_... | Kane610/axis | tests/test_event_instances.py | Python | mit | 9,698 | [
"VMD"
] | ca4ab2f583d2b7883f9c867c44b13d493dbdd49058d40f7c53e66f73cc41e9bc |
"""
Timothy James Lang
tjlangco@gmail.com
Last Updated 04 September 2015 (Python 2.7/3.4)
Last Updated 26 July 2005 (IDL)
csu_kdp v1.4
Change Log
----------
v1.4 Major Changes (09/04/2015):
1. Added window keyword to enable stretching the FIR window (e.g.,
use a 21-pt filter over 5 km with 250-m gate spacing
2. F... | jjhelmus/CSU_RadarTools | csu_radartools/csu_kdp.py | Python | gpl-2.0 | 10,457 | [
"Gaussian"
] | a11e26c2634cdffdbe9998879d52c48d0c1870d79186a20f76585b3add9a9d75 |
#
# Copyright (C) 2006-2007 Cooper Street Innovations Inc.
# Charles Eidsness <charles@cooper-street.com>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License,... | fuesika/teispice | module/waveform.py | Python | gpl-2.0 | 6,850 | [
"Gaussian"
] | f859c8dcc29654b5ec5d921023fe4e05217aed14a7137f5c4c1f751048b3e148 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ---------------------... | Jorge-C/bipy | skbio/core/tests/test_alignment.py | Python | bsd-3-clause | 25,230 | [
"scikit-bio"
] | de96dc82988421196574d98c068657cbb7c6a9aa143e2eceac43a4c816e09d6c |
"""Test Register for Family Camp Bookings.
Usage:
test_register_family.py
test_register_family.py <email> <adults> <children> <infants>
Options:
-d,--debug Turn on debug output.
-h,--help Show this screen.
--version Show version.
"""
from splinter import Browser
from time import sleep
impor... | hippysurfer/family-camp | family_camp/test/test_register_family.py | Python | mit | 8,847 | [
"CRYSTAL",
"VisIt"
] | 8082e1a03636fdef50712a93f61019f77d9dae9601d62f8fd4c332a4c27c7e2c |
from __future__ import absolute_import, division, unicode_literals
named_entities = {
"AElig": "\xc6",
"AElig;": "\xc6",
"AMP": "&",
"AMP;": "&",
"Aacute": "\xc1",
"Aacute;": "\xc1",
"Abreve;": "\u0102",
"Acirc": "\xc2",
"Acirc;": "\xc2",
"Acy;": "\u0410",
"Afr;": "\U0001d50... | kevinhendricks/ePub3-itizer | src/html_namedentities.py | Python | lgpl-2.1 | 57,273 | [
"Bowtie"
] | 1252f47bbef9008c8540df0c7242fcd7eb2ec2f7aba523a286c141265062b3fd |
#!/usr/bin/env python
"""
Install.py tool to download, unpack, build, and link to the n2p2 library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, os, platform, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from ... | lammps/lammps | lib/hdnnp/Install.py | Python | gpl-2.0 | 4,218 | [
"LAMMPS"
] | 5fe8ac67441a3eafac6823448bc5900874dd16f5f6a7d8c08813eeb7cc04fe0c |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/commoncode/test_version.py | Python | apache-2.0 | 9,896 | [
"VisIt"
] | 2696ab93019aba9ac00e30e8f5ac521599f901f56ddf38ebeb235ee69536539d |
# 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... | pkreissl/espresso | testsuite/python/icc.py | Python | gpl-3.0 | 6,336 | [
"ESPResSo"
] | c28bc5c44cd0a442703ba6c82192a5acb8ae0bcf02db4e8f6e704f275bfaff20 |
from models import Entry
from models import User
from models import Project
from models import Vendor
from models import Objective
from models import EvaluationCriteria
from models import DEFAULT_PROJECT_NAME
from models import project_db_key
from functools import wraps
import json
import time
import datetime
from fla... | paddyvishnubhatt/daranalysis | utils.py | Python | apache-2.0 | 24,212 | [
"Amber"
] | dbfae0cbd424b5afe4decd6375c1ef7d60e5e7edc540b3e94b0a6ecdf282f2aa |
#!/usr/bin/env python
"""
tree_encode.py
Contains methods that convert a binary tree (NetworkX DiGraph)
into a bit string.
Henrik Ronellenfitsch 2013
"""
#import sys
#sys.path.append('../')
#import analyzer
import networkx as nx
import matplotlib.pyplot as plt
import numpy.random
from numpy import... | hronellenfitsch/nesting | tree_encode.py | Python | mit | 15,060 | [
"VisIt"
] | aecae1792fe9eadc6341dda11359945eac9752263c216ce8754608a5057b7df9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/wrapper_database.py | Python | lgpl-3.0 | 26,159 | [
"Psi4"
] | dc400b6f4adba275bd01fb0ed1e6a3f50eb44ed55fc0d0fd9806246aedf64a7d |
# -*- coding: utf-8 -*-
import numpy as np
from numpy.core.numeric import isscalar
import copy
from pyorderedfuzzy.ofnumbers import branch
from pyorderedfuzzy.ofnumbers import defuzzy
__author__ = "amarszalek"
class OFNumber(object):
def __init__(self, branch_f, branch_g):
super(OFNumber, self).__init_... | amarszalek/PyOrderedFuzzyTools | pyorderedfuzzy/ofnumbers/ofnumber.py | Python | mit | 12,894 | [
"Gaussian"
] | b9ba3792a554fe79075100e92326e120504aed5017a695047cb69f98980b69ed |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import numpy as np
from pymatgen.optimization.linear_assignment import LinearAssignment # type: ignore
class LinearAssignmentTest(unittest.TestCase):
def test(self):
w0 = np.ar... | gmatteo/pymatgen | pymatgen/optimization/tests/test_linear_assignment.py | Python | mit | 9,635 | [
"pymatgen"
] | 364c369a09984fd2d5e256d4a0ce0aeffd324fbee67959eabf9c5053b42fb460 |
"""
Unit tests for `dbgroup` module.
"""
__author__ = "Dan Gunter"
__copyright__ = "Copyright 2014, The Materials Project"
__email__ = "dkgunter@lbl.gov"
__date__ = "2014-04-29"
import json
import mongomock
import os
import tempfile
import unittest
from pymatgen.db.dbgroup import ConfigGroup
from pymatgen.db import db... | materialsproject/pymatgen-db | pymatgen/db/tests/test_dbgroup.py | Python | mit | 4,724 | [
"pymatgen"
] | e539709386e1697921177c3146a3a570fa316e2e516335b637b5373883326e9c |
# -*- coding: utf-8 -*-
from __future__ import print_function
import unittest
import time
import os
import csv
from globalvalues import RPI
if RPI:
import RPi.GPIO as GPIO
import sensor
import sender
import auxiliaries
import cust_crypt
from auxiliaries import get_data
from manager import Manager
from globalv... | bearing/dosenet-raspberrypi | tests.py | Python | mit | 9,484 | [
"Brian"
] | 2cce0d532338c574ee6c6b3f39db07c3c5d37f123e8ef4db87330ea54d2393a1 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-asset | scripts/fixup_asset_v1_keywords.py | Python | apache-2.0 | 6,935 | [
"VisIt"
] | a30332cf9b41579fd38ff44daed4bc80d782e5f77e639f915a5df50087fa95e9 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2012 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by t... | cordoval/myhdl-python | myhdl/conversion/_toVHDL.py | Python | lgpl-2.1 | 74,347 | [
"VisIt"
] | b4680559850f66333a455139339e4c13dc7f9af5c2c6ad796b4953d0c67ac151 |
## \file
## \ingroup tutorial_roofit
## \notebook
##
## \brief Organization and simultaneous fits: easy interactive access to workspace contents - CINT
## to CLING code migration
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
def fillWorkspace(w):
... | karies/root | tutorials/roofit/rf509_wsinteractive.py | Python | lgpl-2.1 | 3,412 | [
"Gaussian"
] | c34be77d27f80544d81750ea804bcddcfb0556caae5667ffdc835f4b00f45a52 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# isjobactive - sandbox job kill helper
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | heromod/migrid | mig/cgi-sid/isjobactive.py | Python | gpl-2.0 | 1,116 | [
"Brian"
] | cd26cf9856e9a994b1bde8e772d91dda5e66b68afe0eab2695b101b1648124c8 |
import unittest
from circlator import external_progs
class TestExternalProgs(unittest.TestCase):
def test_canu_version(self):
'''Test canu version'''
self.assertEqual('1.6', self.check_regex_version_extraction('canu', """
Canu 1.6
""" ))
def test_spades_version(sel... | sanger-pathogens/circlator | circlator/tests/external_progs_test.py | Python | gpl-3.0 | 2,735 | [
"BWA"
] | 4f4f216ca42cdd206bd2867601fc23c4ef3a280ca81410a8e95283560a4ee7d7 |
import matplotlib.pyplot as plt
import numpy as np
gaussian_numbers = np.random.randn(1000)
plt.hist(gaussian_numbers)
plt.title("Gaussian Histogram")
plt.xlabel("Value")
plt.ylabel("Frequency")
fig = plt.gcf()
plt.show()
| andyraib/data-storage | python_scripts/Python_DS/histogram.py | Python | apache-2.0 | 226 | [
"Gaussian"
] | edd0317e1ae222f75cf4e3cf586b054915f5a649ac3994270eed26adaf572cbc |
# -*- coding: utf-8 -*-
#
# Bio-Formats documentation build configuration file, created by
# sphinx-quickstart on Wed Aug 29 15:42:49 2012.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
#... | ctrueden/bioformats | docs/sphinx/conf.py | Python | gpl-2.0 | 13,943 | [
"CRYSTAL"
] | 9ad998a59f42923cc8885932a7515750d1455eccf6ea256b03d35a1419a800dc |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | JWDebelius/scikit-bio | skbio/parse/sequences/factory.py | Python | bsd-3-clause | 4,532 | [
"scikit-bio"
] | 4c8ff35cdc3ff2fdc3f468415a7ebbd112c4e414b44cf825c71337bec39585ad |
import pandas as pd
import numpy as np
import myio as Mio
import mymath as Mmath
def getAndStoreDump(simname,increment,rootdir,dumpdir='Dump_Files/',pickledir='Pickle_Files/',override=False,bounds=None,**kwargs):
return Mio.getAndStore(readDumpFile,getDumpFilename,override=override,subdirstore=rootdir+pickledir,si... | varun-rajan/python-modules | mdutilities_io.py | Python | gpl-2.0 | 4,140 | [
"LAMMPS"
] | d80d65931b0c73a9eef1d312ebb581e3a451be785a356c877cdbfa23c620a4fb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
USAGE: python list_repos.py --url_galaxy_ref <url galaxy reference> --url_galaxy_target <url galaxy target>
--adminkey_galaxy_target <glaxy target admin api key> --url_toolshed <url toolshed with tools>
--output_yaml <yaml output file>
'''
from bioblend.toolshed import... | C3BI-pasteur-fr/Galaxy-playbook | galaxy-pasteur/roles/galaxy_tools/files/list_repos.py | Python | gpl-2.0 | 3,186 | [
"Galaxy"
] | 4ef9473ae02764d1c97ddffa3add6ebab402cc64dbd02b4c65bf2fa4bfac14c5 |
# coding=utf-8
from datetime import timedelta
from django.contrib.auth.tokens import default_token_generator
from django.core import mail
from django.test import TestCase, LiveServerTestCase
from django.utils.timezone import now
from selenium import webdriver
from alert.userHandling.models import UserProfile
class U... | shashi792/courtlistener | alert/userHandling/tests.py | Python | agpl-3.0 | 5,129 | [
"VisIt"
] | 41f16f75528ecba3bd61cf06c874d7119c91ece153794601ed1de18d160c0a83 |
# Licensed under an MIT open source license - see LICENSE
import numpy as np
import astropy.units as u
import networkx as nx
import warnings
import scipy.ndimage as nd
from astropy.nddata import extract_array
import astropy.modeling as mod
from astropy.modeling.models import Gaussian1D, Const1D
import sys
if sys.vers... | e-koch/FilFinder | fil_finder/filament.py | Python | mit | 56,431 | [
"Gaussian"
] | 32c2ba09624efb14b0d04ba85d4030f42f1bce65e6ba9e1fc20bf5d17d10894c |
########################################################################
# $HeadURL $
# File: RequestTask.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/13 12:42:45
########################################################################
""" :mod: RequestTask
=================
.. module: RequestT... | Sbalbp/DIRAC | RequestManagementSystem/private/RequestTask.py | Python | gpl-3.0 | 16,433 | [
"DIRAC"
] | cd6a6c0b12843711738ff5db04b9a0039c75972380be22317ea656f18e7a543d |
import unittest
import filecmp
import os
import logging
import numpy as np
from pycgtool.frame import Atom, Residue, Frame
from pycgtool.framereader import FrameReaderSimpleTraj, FrameReaderMDAnalysis, FrameReaderMDTraj
from pycgtool.framereader import FrameReader, get_frame_reader, UnsupportedFormatException
try:
... | jag1g13/pycgtool | test/test_frame.py | Python | gpl-3.0 | 7,943 | [
"MDAnalysis",
"MDTraj"
] | 2d412f1ed733ff94610a2b15535992136dcef5b751d94b3ca368e542ab0fa9f6 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.