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 |
|---|---|---|---|---|---|---|---|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#
# ------------------------------------------------------------------------------
# Copyright (C) 2006-2016 University of Dundee. All rights reserved.
#
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General P... | dpwrussell/openmicroscopy | components/tools/OmeroPy/src/omero/util/ROIDrawingUtils.py | Python | gpl-2.0 | 11,817 | [
"VisIt"
] | 0f37a44747b34ecf3c99c8c491114c96f2b8be30407277d7e0c1d36f7ea0de3d |
#!/usr/bin/python3
# Copyright 2017-2018 Brian Warner
#
# 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 ... | mkdolan/facade | utilities/import_gitdm_configs.py | Python | apache-2.0 | 7,057 | [
"Brian"
] | fbd1ea5c5e732d732493e7cb6dcd066e88fd03ed5ed514da2bece6827409a7fe |
"""Parse U.S. phone numbers
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/05 21:57:19 $"
__copyr... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/parsephone.py | Python | mit | 1,220 | [
"VisIt"
] | 5f0b8de542e4c24e021e6bd18aa6d6091ca54b5c6aa614c3a8682c3a2788f5e4 |
import numpy as np
from numpy import exp
from numpy import pi
from numpy import sqrt
from numpy import log
import numpy.testing as nut
import scipy.integrate as si
import mpmath as mp
import matplotlib.pylab as plt
# these three lines are in case you work with a specific software
try:
plt.switch_backend("Qt5Agg")
... | Evenity/py_psa | py_psa/psa_functions_numeric.py | Python | mit | 41,928 | [
"CRYSTAL",
"Gaussian"
] | 5157e12e4b5862c00288f267ec98b5c2d9d88dddc17d82683adea3fe4f3f2653 |
"""gibbsSampler.py
2D square lattice Gaussian MRF, naive Gibbs sampler.
"""
#import argparse
import numpy as np
from scipy import misc
#import matplotlib.pyplot as plt
def main():
M = 10
# Initialize arrays/matrices
nx = 10
ny = 10
iterNr = 1000
resultGibbs = np.zeros( (nx, ny) )
# ... | can-cs/smc-pgm | gmrf/gibbsSampler.py | Python | mit | 3,130 | [
"Gaussian"
] | 6ea5e4a84d91afe7c2a94d557e3eb395f979a5cc21b78cea9d904314e28ab247 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''The <output> and <file> elements.
'''
import os
import grit.format.rc_header
from grit import xtb_reader
from grit.node impor... | hujiajie/chromium-crosswalk | tools/grit/grit/node/io.py | Python | bsd-3-clause | 3,336 | [
"xTB"
] | 8137b533cdb4b5a58ca6523d93789c79c3bbc0162d9128e3363cccd69a16536c |
#!/usr/bin/env python
#
# This code was copied from the data generation program of Tencent Alchemy
# project (https://github.com/tencent-alchemy).
#
#
# #
# # Copyright 2019 Tencent America LLC. All Rights Reserved.
# #
# # Licensed under the Apache License, Version 2.0 (the "License");
# # you may not use this file e... | gkc1000/pyscf | pyscf/df/grad/rks.py | Python | apache-2.0 | 5,142 | [
"PySCF"
] | 825d07d653b70c0e3b2f9bff29af89e63f027c3481d914ef30116038ab8593ea |
# Copyright (c) 2012, Cloudscaling
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | mikalstill/nova | nova/hacking/checks.py | Python | apache-2.0 | 31,903 | [
"VisIt"
] | 8886667c390e39e23e7ee6c292af8b8eeee5a9461b578ddf461578e66ef3fe00 |
"""
AIRandomWalk1.py
The "random walk" AI. Possibly the worst AI (that makes legitimate moves).
Copyright 2016 Brian Romanchuk
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.apach... | brianr747/Simple4Xpygame | AI_randomwalk.py | Python | apache-2.0 | 2,184 | [
"Brian"
] | d10da4e6568d2cb74640c9595ba9c474a2719b7015e76d5ec60194542123f081 |
"""
It is used to compile the web framework
"""
from __future__ import print_function
import os
import tempfile
import shutil
import subprocess32 as subprocess
import gzip
import sys
from DIRAC import gLogger, gConfig, rootPath, S_OK, S_ERROR
from DIRAC.Core.Utilities.CFG import CFG
__RCSID__ = "$Id$"
class WebApp... | fstagni/DIRAC | FrameworkSystem/Client/WebAppCompiler.py | Python | gpl-3.0 | 14,059 | [
"DIRAC"
] | 385a95ee3e82db49911b536c7d7d875a5a75e199219c1def48f9fa78db14abf3 |
#!/usr/bin/env python
import sys
sys.path.insert(1,'/galaxy')
sys.path.insert(1,'/galaxy/lib')
from galaxy.model import User, APIKeys
from galaxy.model.mapping import init
from galaxy.model.orm.scripts import get_config
import argparse
def add_user(sa_session, security_agent, email, password, key=None, username="admi... | chambm/docker-galaxy-stable | compose/galaxy-server/files/create_galaxy_user.py | Python | mit | 2,139 | [
"Galaxy"
] | 442d0fe19c8f471c9c6652865f811faf795138fccbddd549bc733eb1b926882f |
# encoding: utf-8
import os
import numpy as np
import glob
import re
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import pyroms
import pyroms_toolbox
import _remapping
import matplotlib.pyplot as plt
import datetime
import pdb
def station_bound(varname, srcfile, srcgrd, dst_grd, \
... | kshedstrom/pyroms | examples/BC_from_sta/station_bound.py | Python | bsd-3-clause | 38,779 | [
"NetCDF"
] | f293f7249b336f27be1ec9dcd7401aa19cb48643a1872d826396698c3bf76119 |
"""
Feature calculations.
"""
import inspect
import logging
import numpy as np
import multiprocessing
from typing import Any, Dict, List, Iterable, Sequence, Tuple, Union
from deepchem.utils import get_print_threshold
from deepchem.utils.typing import PymatgenStructure
logger = logging.getLogger(__name__)
class Fea... | lilleswing/deepchem | deepchem/feat/base_classes.py | Python | mit | 13,696 | [
"CRYSTAL",
"RDKit",
"matminer",
"pymatgen"
] | 7fa2fb442a01442b62e92260e914dcc523d63ef785253385f1dd2210e9d10fe0 |
from __future__ import absolute_import
from __future__ import print_function
from PyOpenWorm.data import DataUser
from .DataTestTemplate import _DataTest
from PyOpenWorm.cell import Cell
class CellTest(_DataTest):
ctx_classes = (Cell,)
def test_DataUser(self):
do = Cell('', conf=self.config)
... | gsarma/PyOpenWorm | tests/CellTest.py | Python | mit | 2,893 | [
"BLAST"
] | bcbd5be039908ae06ed2e8f83b3c7809a7ecf60e0d2108f23b8b2eaf8666c71e |
# -*- coding: utf-8 -*-
# Copyright (C) 2005-2006 Joe Wreschnig
# Copyright (C) 2006-2007 Lukas Lalinsky
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
#... | nwokeo/supysonic | venv/lib/python2.7/site-packages/mutagen/asf/_util.py | Python | agpl-3.0 | 10,780 | [
"CRYSTAL"
] | 9825d5cfe3dcb4cd9516adea62896c6aa21b0c5a3e1d72c621a9d3bb93dae1e4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2014, SIL International
# All rights reserved.
#
# This library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version 2.1 o... | thresherdj/shrinkypic | lib/shrinkypic/icon/__init__.py | Python | mit | 986 | [
"VisIt"
] | 5707cfda186070acef2768c627607b467fa5f65150c1e08f1463bd03dc1ad663 |
from __future__ import annotations
class ProfileModelExt:
"""
The definition for a profile model.
"""
@staticmethod
def create(
params, reflections, crystal, beam, detector, goniometer=None, scan=None
):
"""
Create the profile model from data.
:param params: T... | dials/dials | model/experiment/profile.py | Python | bsd-3-clause | 2,922 | [
"CRYSTAL"
] | 3dfb4a974f380b8e372418da0db9dc262dfeb4075eac841927f1c952b5dd92f7 |
# -*- coding: utf-8 -*-
"""
.. _tut-artifact-ica:
Repairing artifacts with ICA
============================
This tutorial covers the basics of independent components analysis (ICA) and
shows how ICA can be used for artifact repair; an extended example illustrates
repair of ocular and heartbeat artifacts. For conceptu... | rkmaddox/mne-python | tutorials/preprocessing/40_artifact_correction_ica.py | Python | bsd-3-clause | 31,805 | [
"Gaussian"
] | b9142b817e437f9bb5afe345d9df8d8186198e7ef4cc1afd17b2d322d4bcb3be |
import sys
import json
import pprint
import numpy as np
import pytest
import qcelemental as qcel
import psi4
from .utils import *
pp = pprint.PrettyPrinter(width=120, compact=True, indent=1)
pytestmark = pytest.mark.quick
@pytest.fixture(scope="function")
def result_data_fixture():
return {
"molecule"... | psi4/psi4 | tests/pytests/test_qcschema.py | Python | lgpl-3.0 | 8,092 | [
"Psi4"
] | cfa5368631ecc55cbcba762551329ed1bea3d5c6196bcb4735b987b1fc26a0a9 |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
import os
from twilio.rest import Client
from datetime import datetime
# Your Account Sid and Auth Token from twilio.com/user/ac... | TwilioDevEd/api-snippets | notifications/rest/bindings/list-binding/list-binding.7.x.py | Python | mit | 736 | [
"VisIt"
] | befda6f692d75d98fbe6ae409a6b8a43287774d1c650cc69166fdb103835bb1e |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/forms.py | Python | gpl-2.0 | 25,448 | [
"VisIt"
] | 4145ecf9bacfd9c75e64875ef2928b0cb48cbde70cd3aacf0230b81c89ddfa17 |
from collections import OrderedDict
from django.utils import html
from corehq.apps.users.models import CouchUser
from custom.succeed.reports.patient_task_list import PatientTaskListReport
from custom.succeed.reports import *
from custom.succeed.reports.patient_details import PatientDetailsReport
from dimagi.utils.decor... | qedsoftware/commcare-hq | custom/succeed/reports/patient_interactions.py | Python | bsd-3-clause | 8,037 | [
"VisIt"
] | 3a6eac957b4d0421e7094f12222e3e974f21a6c47ff889d4fb03cbde2a33dd84 |
#!/usr/bin/env python
#############
#
# Cluster molecules in MOL files by similarity using Tanimoto coefficients
# based on Open Babel FP2 fingerprints using the DBSCAN algorithm.
#
# 1. Read all MOL files in the current directory
# 2. Calculate all FP2 fingerprints with Open Babel's pybel module
# 3. Construct distan... | johncfaver/clulig | cluster_ligands.py | Python | gpl-2.0 | 2,360 | [
"Open Babel",
"Pybel"
] | 11f76190ab940251fe791d990de281b3fcf39d3643fd5d10c275a5a89b2f34f3 |
# Copyright (C) 2010-2018 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... | hmenke/espresso | testsuite/python/constraint_homogeneous_magnetic_field.py | Python | gpl-3.0 | 3,725 | [
"ESPResSo"
] | 4c8f0ac6418e4cc340e47b95d533423e776ee80927656dcef2b9ab7cd497e8b9 |
#just an possible use, we can use it to replace H**.py, treat fliC and fljB as the target genes?
from __future__ import division
import sys
import os
from Bio.Blast import NCBIXML
from Bio import SeqIO
def special_gene(target_fie,database,gene_list):
database=database.split("/")[-1]##########1/27/2015
... | denglab/SeqSero | libs/special_gene_test_assemblies.py | Python | gpl-2.0 | 2,142 | [
"BLAST"
] | 1297bee3af06b01fb58d6178caeddef62989da4ec48c440a1f8308c9e740bca0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/util/mpl.py | Python | lgpl-3.0 | 2,263 | [
"Psi4"
] | e599d3a25038cacf6ae11f9932638465b783d21329eb16cce96b8e7785677662 |
# -*- coding: utf-8; mode: python -*-
# pylint: disable=C0103, R0903, R0912, R0915
u"""
scalable figure and image handling
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Sphinx extension which implements scalable image handling.
:copyright: Copyright (C) 2016 Markus Heiser
:license: GPL Version 2, June 1... | rperier/linux-rockchip | Documentation/sphinx/kfigure.py | Python | gpl-2.0 | 18,793 | [
"VisIt"
] | b75cba430020ef53966eac8db41ad97a134503d3019005dfe67d5965b95c7a43 |
#!/bin/env python
# -*- coding: utf-8 -*-
"""
| This file is part of the web2py Web Framework
| Copyrighted by Massimo Di Pierro <mdipierro@cs.depaul.edu>
| License: LGPLv3 (http://www.gnu.org/licenses/lgpl.html)
| Thanks to ga2arch for help with IS_IN_DB and IS_NOT_IN_DB on GAE
Validators
-----------
"""
import os
... | ShySec/scrimmage-scoreboard | web2py/gluon/validators.py | Python | gpl-2.0 | 136,563 | [
"CASINO",
"MOE"
] | 7ad869e91beac9375d19fc98d28686ac330f6495515b95732ebf489ccf45ce29 |
from errno import ENOENT
from os import remove, getcwd
from sys import argv, exit
from collections import OrderedDict
from pandas import DataFrame, read_csv
from astropy.io.fits impo... | Delosari/dazer | bin/lib/ssp_functions/ssp_synthesis_tools.py | Python | mit | 42,976 | [
"Gaussian"
] | cd3d828e35975a4956ae32f02e3bddf9417db4f3218db63864f3e06f7d5eefaa |
# Lint as: python3
# Copyright 2018 The TensorFlow Authors. 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 ... | tensorflow/lingvo | lingvo/tasks/punctuator/input_generator_test.py | Python | apache-2.0 | 3,127 | [
"Elk"
] | f902df261cbf2cde3805f390a880e9e0b7e12c4804d086405b9afa8884332592 |
# Note that the lat and lon positions below correspond to the center point of the maps you want to download
# Proper zoom level selection determines total viewable area
MAPPING_LOCATIONS = {
"Graf Hall": {
"latitude": 44.5675721667,
"longitude": -123.2750535,
"default_zoom": 18,
"va... | caperren/Archives | OSU Robotics Club/Mars Rover 2017-2018/software/ros_packages/ground_station/src/Resources/Settings/MappingSettings.py | Python | gpl-3.0 | 2,002 | [
"CRYSTAL"
] | 3d9262862f70b035baf225945c7f66112099e958195750043217b0691d50ae81 |
##
# Copyright 2009-2018 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... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/d/dirac.py | Python | gpl-2.0 | 5,950 | [
"DIRAC"
] | 33c9bbef4dc209b197890e8111258b5e30016c422d710b33cf400bfdde904eeb |
import datetime
import logging
import os
import re
from os.path import join
import pytest
from PIL import Image as PILImage
from sigal.gallery import Album, Gallery, Image, Media, Video
from sigal.video import SubprocessException
CURRENT_DIR = os.path.dirname(__file__)
REF = {
'dir1': {
'title': 'An exa... | saimn/sigal | tests/test_gallery.py | Python | mit | 13,546 | [
"Galaxy"
] | 9dbac36f1bb500b6da4fbd4f31747e6abadc1844741a43c2f7de7e5c51331496 |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | almarklein/visvis.dev | vvmovie/images2gif.py | Python | bsd-3-clause | 36,746 | [
"NEURON"
] | c32b2f26d7b9db66c1ca9a5666d55ba43807b80c991add258549f761e3fc9822 |
#
# Copyright (c) 2017 Luis F. Simoes (github: @lfsimoes)
#
# Licensed under the MIT License. See the LICENSE file for details.
from collections import deque
import numpy as np
# ==================================== ## ==================================== #
class tsp_path(object):
"""
Handler for Travelling ... | lfsimoes/beam_paco__gtoc5 | paco/paco.py | Python | mit | 22,135 | [
"VisIt"
] | 95413b9c27a712de859f1c32f45b8dd80ff55e47185bf53b7a99e1d1a8ec3428 |
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2015 Uni.Lu/LCSB, NTUA
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Kenneth Hoste
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>
# License:: MIT/GPL
# $Id... | torbjoernk/easybuild-easyblocks | easybuild/easyblocks/b/bwa.py | Python | gpl-2.0 | 2,735 | [
"BWA"
] | 66a0a4d95d8b60a4c0b8a7893ebf09787b5f8a1ff74cd5f0b145cf1c5d63f96a |
import sys
import numpy as np
from ase.test.tasks.htb import HaasTranBlahaBulkTask
class Task(HaasTranBlahaBulkTask):
def __init__(self, xc='LDA', **kwargs):
HaasTranBlahaBulkTask.__init__(self, xc, **kwargs)
def calculate(self, name, atoms):
data = HaasTranBlahaBulkTask.calculate(self, name... | robwarm/gpaw-symm | doc/devel/ase_optimize/htb_pw.py | Python | gpl-3.0 | 1,938 | [
"ASE",
"GPAW"
] | 73ba9cdfb574a212904b3cfadd8de7bf400622c71b3b3d5fc84fb37f100de909 |
# -*- coding: utf-8 -*-
import sys
sys.path[0:0] = [""]
import bson
import os
import pickle
import unittest
import uuid
from datetime import datetime
from bson import DBRef
from tests.fixtures import PickleEmbedded, PickleTest, PickleSignalsTest
from mongoengine import *
from mongoengine.errors import (NotRegistered... | closeio/mongoengine | tests/document/instance.py | Python | mit | 78,634 | [
"exciting"
] | d976c0cdf9d6ecb78aa1169f2b19adefc5fe30bc72b1f86bd10ce0fa577d2507 |
# 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/test/test_0157_bse_h2o_rhf_cis.py | Python | apache-2.0 | 2,109 | [
"PySCF"
] | b404fc91cefd4995ffb9db5e813ba3b9adb6488dbdbf707b0ed3148147a75bce |
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
import os
import errno
import logging
from decorator import decorator
... | jtoppins/beaker | Server/bkr/server/identity.py | Python | gpl-2.0 | 10,592 | [
"VisIt"
] | 817dec150b409609296b1075cace4835d467272c17b10d472867ae4cf2d28335 |
import numpy as np
from astropy.io import fits
from astropy.wcs import WCS
from astropy.wcs.utils import proj_plane_pixel_scales
def computeBaryshift(header):
from astropy.coordinates import FK5, solar_system, UnitSphericalRepresentation, CartesianRepresentation
from astropy.time import Time
import astrop... | darioflute/sospex | sospex/specobj.py | Python | gpl-3.0 | 64,074 | [
"Gaussian"
] | 09a0c6368e60ddd9cd312d996365106b910ef4f8f4e0a919d12a835482a3482c |
"""
This is our testing framework.
Goals:
* it should be compatible with py.test and operate very similarly
(or identically)
* doesn't require any external dependencies
* preferably all the functionality should be in this file only
* no magic, just import the test file and execute the test functions, that's it
* po... | NikNitro/Python-iBeacon-Scan | sympy/utilities/runtests.py | Python | gpl-3.0 | 82,274 | [
"VisIt"
] | 49c2ba8f07cb2ddf888c37631865a85341ecc9c9721c4f40da3183e962cffd66 |
"""
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. module:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each univariate distribution is an insta... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/scipy/stats/__init__.py | Python | apache-2.0 | 8,937 | [
"Gaussian"
] | 4d0256c53915218d4bb23a0f828dd0e950505a0a319da801b8b7477fa54e481a |
#!/usr/bin/env python3
#
# Copyright (C) 2020(H)
# Institute Jozef Stefan
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++ -> Powered by HeSpaDDA algorithm developed by horacio.v.g@gmail.com
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under th... | espressopp/espressopp | testsuite/HeSpaDDA/nodeGrids/testHeSpaDDAv1p1.py | Python | gpl-3.0 | 2,097 | [
"ESPResSo"
] | 277118d8d3830dbed3f08f5a9a1fbd1a8af16041f3ea05d0ea4160132cb10f66 |
from python.src.neurons.neurons import Neuron
from python.src.neurons.activation_functions.tanh_activation import TanhActivation
from python.src.neurons.activation_functions.sigmoid_activation import SigmoidActivation
from python.src.neurons.activation_functions.sine_activation import SineActivation
# This type is ... | DomenicD/dom_ml_playground | python/src/neurons/receive_all_neuron.py | Python | mit | 1,652 | [
"NEURON"
] | a765bb825d61d7a22492afd9721edce80a4d1f671ef0f01e2cde564ac4e48311 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module implements classes (called Fitters) which combine optimization
algorithms (typically from `scipy.optimize`) with statistic functions to perform
fitting. Fitters are implemented as callable classes. In addition to the data
to fit, the ``__c... | MSeifert04/astropy | astropy/modeling/fitting.py | Python | bsd-3-clause | 57,416 | [
"Gaussian"
] | 8b94907e471dff129d5c09af2f2a18dadcafea0b78c2c487889edc0060440262 |
"""
This module adapted ANUGA
https://anuga.anu.edu.au/
"""
#FIXME: Ensure that all attributes of a georef are treated everywhere
#and unit test
import types, sys
import copy
import numpy as num
DEFAULT_ZONE = -1
TITLE = '#geo reference' + "\n" # this title is referred to in the test format
DEFAULT_PROJECTION = ... | tridge/MAVProxy | MAVProxy/modules/lib/ANUGA/geo_reference.py | Python | gpl-3.0 | 16,586 | [
"NetCDF"
] | fb5a536025f95d66971b538e6e772acccc569e18217ed5cd1099726cbd82ff61 |
"""
CBMPy: CBRead module
====================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2009-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public ... | SystemsBioinformatics/cbmpy | cbmpy/CBRead.py | Python | gpl-3.0 | 40,518 | [
"PySCeS"
] | 37d568cfa4e28cfb2dcee52cc1da9f2feb8f9dd5a2a6f98192f1ba1ca0c849c4 |
"""
State Space Analysis using the Kalman Filter
References
-----------
Durbin., J and Koopman, S.J. `Time Series Analysis by State Space Methods`.
Oxford, 2001.
Hamilton, J.D. `Time Series Analysis`. Princeton, 1994.
Harvey, A.C. `Forecasting, Structural Time Series Models and the Kalman Filter`.
Cambrid... | wwf5067/statsmodels | statsmodels/tsa/kalmanf/kalmanfilter.py | Python | bsd-3-clause | 30,936 | [
"Gaussian"
] | 29a14037770180e14b467f4c91cba5237dbcb55549bce4e6b4ba89ba4c37ef0e |
#!/usr/bin/env python
"""This peak-caller script is part of the CLAM pipeline.
This subcommand will call peaks using permutation by randomly placing reads along the gene.
More details about the permutation procedure is described in our NAR paper.
Example run:
```
CLAM permutation_callpeak -i path/to/outdir/unique.... | Xinglab/CLAM | CLAM/permutation_peakcaller.py | Python | gpl-3.0 | 15,129 | [
"pysam"
] | 77411e17b1f3e2148edd65632e3bcf475cee485d410fe7d2f858495e148523f1 |
#!/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_tree.py | Python | bsd-3-clause | 30,416 | [
"scikit-bio"
] | 4f946bba067067e42569067012bea5124668ac641220082c19afbdc0aba82492 |
#
# Copyright (C) 2007-2017 by Greg Landrum
# All rights reserved
#
from __future__ import print_function
import math
import numpy
from rdkit import Geometry
from rdkit.Chem.Subshape import SubshapeObjects
def ComputeGridIndices(shapeGrid, winRad):
if getattr(shapeGrid, '_indicesInSphere', None):
return sha... | rvianello/rdkit | rdkit/Chem/Subshape/BuilderUtils.py | Python | bsd-3-clause | 10,895 | [
"RDKit"
] | 494c9d0d31e0a31a9bd35dda775caadf4643f90c16c3951b2a765c5342b31525 |
""" (Sample) workload definition file for .
"""
# ATTENTION:
#
# Read the tutorial instructions:
# https://github.com/radical-cybertools/HT-BAC/blob/master/README.md
#
# You can download the sample data from:
# http://testing.saga-project.org/cybertools/sampledata/BAC-MMPBSA/mmpbsa-sample-data.tgz
import os
WOR... | radical-cybertools/HT-BAC | examples/fecalc/workload.py | Python | mit | 1,923 | [
"NAMD"
] | 327ba5f7035625831034433867adf9a327ebbee3ced83b92a344e127b06f0ed7 |
# -*- coding: utf-8 -*-
import mds.ordered_set
import convention
import units
class Generic(convention.Convention):
"""
This class can be used in case there is no convention attribute present
in the netcdf file, or if the convention that is mentioned is unsupported.
This class implements the `generic... | jfrygeo/solutions-geoprocessing-toolbox | suitability/toolboxes/scripts/MultidimensionSupplementalTools/MultidimensionSupplementalTools/Scripts/mds/netcdf/convention/generic.py | Python | apache-2.0 | 2,266 | [
"NetCDF"
] | 8d4f1eef66c955109da3e5837d6d56c57ee2f5ee07da6da845133d7e89888aa3 |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
ImageCheckerboard()
| jeromevelut/Peavip | Testing/ImageCheckerboard.py | Python | gpl-3.0 | 130 | [
"ParaView"
] | 5d8679c02c556a5413bc6b2704ed1be34b527f87f951129fcbccebc763983d56 |
# -*- coding: utf-8 -*-
#
# gif_pop_psc_exp.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... | mschmidt87/nest-simulator | pynest/examples/gif_pop_psc_exp.py | Python | gpl-2.0 | 13,893 | [
"NEURON"
] | 44ce20e17ef891d46f5e01b466150c529b11cc1a190a9ae2961c0706eacf4414 |
""" This is for transfers what RPCClient is for RPC calls
"""
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import File
from DIRAC.Core.DISET.private.BaseClient import BaseClient
from DIRAC.Core.DISET.private.FileHelper import FileHelper
class TransferClient(BaseClient):
def _sendTransferHe... | DIRACGrid/DIRAC | src/DIRAC/Core/DISET/TransferClient.py | Python | gpl-3.0 | 7,636 | [
"DIRAC"
] | 21c8a5420bf9c3b8eeac4d73b658c596cc4e5227e81e774ecdc9c911ded8100d |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import numpy as np
from pymatgen.core.sites import PeriodicSite
from pymatgen.core.structure import Molecule, Structure
from pymatgen.io.cif import CifParser
from pymatgen.io.vasp.inputs import Pos... | materialsproject/pymatgen | pymatgen/symmetry/tests/test_analyzer.py | Python | mit | 31,174 | [
"VASP",
"pymatgen"
] | bc06603018f093b5657ed12a218c993dd8e3dc931a30022be8065a5720b452cc |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2006 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | prculley/gramps | gramps/gen/filters/rules/event/__init__.py | Python | gpl-2.0 | 2,333 | [
"Brian"
] | 0856836100fda7251f425bdc427a08498d357143e35ff2e101094afa3706d67e |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | brandond/ansible | lib/ansible/modules/network/avi/avi_actiongroupconfig.py | Python | gpl-3.0 | 5,492 | [
"VisIt"
] | f78b7e50f674d8d9ce35605c323df65c45714e85262bb3fb8b037da68729ee2c |
"""Support for package tracking sensors from 17track.net."""
from datetime import timedelta
import logging
from py17track import Client as SeventeenTrackClient
from py17track.errors import SeventeenTrackError
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA
from homeassistant.const... | tboyce021/home-assistant | homeassistant/components/seventeentrack/sensor.py | Python | apache-2.0 | 11,089 | [
"VisIt"
] | c72f45b5124ddde577a260622ee52a1f4a2f8dde6a335f27b0219185939a9439 |
import game.controllers
import game.constants
from entities.player import Player
from entities.solarsystem import SolarSystem
from entities.starbase import StarBase
from game.renderer import Renderer
from game.input import Input
from game.matrix import Matrix
from game.genesis import Genesis
from game.coordinates impor... | dmalatesta/spaceterm | game/game.py | Python | gpl-3.0 | 11,924 | [
"Galaxy"
] | 22be9207eaed63008b752a2aebc4e34585853096740987d6f75a6c0404b472f5 |
import matplotlib.pyplot as plt
import colormaps as cmaps
import numpy as np
import pretty_plotting as pp
def raster(spike_times,
ax = None,
figsize = (12,8),
ylabel = "Cell Id",
title = None,
color="k"):
"""
Raster plot
"""
if not isinstance(spi... | miladh/lgn-simulator | tools/analysis/plotting_tools.py | Python | gpl-3.0 | 18,502 | [
"Gaussian"
] | 76f50dd4c0d9c80278bad88d359994c0bd70aa439ad9418088c179499a63c0e6 |
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | slai11/youtube-8m | frame_level_models.py | Python | apache-2.0 | 60,647 | [
"MOE"
] | d1c5b67d4f4a3ab3af6a6fb0f53a83826942c9aa9bc8a664fa031f15e75fe391 |
#
# The OpenDiamond Platform for Interactive Search
#
# Copyright (c) 2011-2019 Carnegie Mellon University
# All rights reserved.
#
# This software is distributed under the terms of the Eclipse Public
# License, Version 1.0 which can be found in the file named LICENSE.
# ANY USE, REPRODUCTION OR DISTRIBUTION OF T... | cmusatyalab/opendiamond | opendiamond/server/search.py | Python | epl-1.0 | 13,135 | [
"BLAST"
] | 15216b2ec33b7536e6d0b5ab041f8914572e49b570272d5a64c215eacfc48b51 |
"""
Algos.py
Basic building blocks of trading rules, like volatility measurement and
crossovers
"""
import warnings
import math as maths
import numpy as np
import pandas as pd
from syscore.genutils import sign
LARGE_NUMBER_OF_DAYS = 250 * 100 * 100
def calculate_weighted_average_with_nans(weights: list, data: li... | robcarver17/pysystemtrade | syscore/algos.py | Python | gpl-3.0 | 7,474 | [
"Gaussian"
] | 462f7a6ef233513f914e65804e362f8f7c2e886966c3a60c9f6aab2b0788b7f3 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songusage/forms/songusagedetailform.py | Python | gpl-2.0 | 6,151 | [
"Brian"
] | 466d64832326ae9a70c53481e941b7135a5a29395e4dbaedf370933c4cd0325f |
#! /usr/bin/python
import argparse
import ast
import os
import sys
import yaml
PATTERNS_V1 = []
PATTERNS_V2 = []
RESULT = {"v1": PATTERNS_V1, "v2": PATTERNS_V2}
class CallVisitor(ast.NodeVisitor):
def visit_Call(self, node):
if isinstance(node.func, ast.Name):
name = node.func.id
e... | matrix-org/synapse | scripts-dev/list_url_patterns.py | Python | apache-2.0 | 1,254 | [
"VisIt"
] | fa5c595024af923cd51d4e656f772036401b5aa41710f4def04016a2a1a88ea6 |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 21 12:30:45 2016
@author: Radu
"""
from Network import ClarkeNetwork
from neuron import h
thenet = ClarkeNetwork()
| penguinscontrol/Spinal-Cord-Modeling | ClarkesNetwork/test3.py | Python | gpl-2.0 | 165 | [
"NEURON"
] | ea075bb82fd0ecc8bb5c92929a4b0ea98808c6763f7a2b9b13bf9c67c9f514de |
"""
CBMPy: CBMultiEnv module
========================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2009-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General... | SystemsBioinformatics/cbmpy | cbmpy/CBMultiEnv.py | Python | gpl-3.0 | 41,374 | [
"PySCeS"
] | 39f444a3c3d2aca17568df46850f95729087adfa82fb7a99cc2866bcb28c1229 |
#!/usr/bin/python
# -*- coding: cp1252 -*-
# Telegraph Fantasy Football Team Picker
# version 1.2.1 (11 March 2011)
# by Ian Renton and Mark Harris
# For details, see http://www.onlydreaming.net/software/telegraph-fantasy-football-team-picker
# This code is released under the GPLv3 licence (http://www.gnu.org/licenses... | ianrenton/TelegraphFantasyFootballTeamPicker | telegraphpicker.py | Python | bsd-2-clause | 19,193 | [
"VisIt"
] | aae28aba1e5c0efbffcadf83c4cace51c6390195cab1f6ed7d3cbf39e141ee26 |
# 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 Libmesh(AutotoolsPackage):
"""The libMesh library provides a framework for the numerical s... | iulian787/spack | var/spack/repos/builtin/packages/libmesh/package.py | Python | lgpl-2.1 | 12,046 | [
"NetCDF",
"VTK"
] | 2c467d882d8d02c045c40de625fd4050b42a139bd90ac3d279a3520b63864ac6 |
import hashlib
import logging
import os
import subprocess
from clashchimeras.parsers import Fastq
logger = logging.getLogger('root')
class Bowtie:
"""Class for calling bowtie2 aligner
"""
def __init__(self, args=None):
self.parameters = []
self.inputFile = args.input
self.compre... | kashyapchhatbar/CLASHChimeras | clashchimeras/runners.py | Python | mit | 7,323 | [
"Bowtie"
] | 5167f8f0ce8064c5293ed5bc4c12b14732e35372542196e69b23842cc06b5ed8 |
# Copyright 2018 Open Source Robotics Foundation, 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... | ros2/launch | launch/test/launch/utilities/test_visit_all_entities_and_collect_futures.py | Python | apache-2.0 | 3,558 | [
"VisIt"
] | 826a69481d2125b0ff4f23a9183761541f6b54b94b6f48106a80d0ba13f93ac6 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/tree/_tree.py | Python | bsd-3-clause | 101,148 | [
"VisIt",
"scikit-bio"
] | 445acd96685ac3b0b935d921bd5c205f6e22028d8c6388be627e4f55f01dc663 |
# -*- coding: utf-8 -*-
# Krzysztof Joachimiak 2017
# sciquence: Time series & sequences in Python
#
# Symbolic Aggregate Approximation
# Author: Krzysztof Joachimiak
#
# License: MIT
import numpy as np
import scipy.stats
from sklearn.preprocessing import scale, StandardScaler
from paa import paa
from operator import... | krzjoa/sciquence | sciquence/representation/sax.py | Python | mit | 3,735 | [
"Gaussian"
] | 8acf983407b48dba88c3dc23ce8f2bb8b614bfc172216f15951c557753fb7801 |
#!/usr/bin/env python3
# Copyright 2021 Stanford University
#
# 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 applicab... | StanfordLegion/legion | tools/perf_chart.py | Python | apache-2.0 | 4,912 | [
"VisIt"
] | 4d40ee954104cd0dfc1c35939a12d842cb5210719bff0d77d45adb1e92c10f10 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and 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.
#
""" Basic EState defini... | rdkit/rdkit-orig | rdkit/Chem/EState/EState.py | Python | bsd-3-clause | 1,801 | [
"RDKit"
] | 8402214d533cbc1e074540508eceee5650a31e649fc49c48e12501591ae63b84 |
import numpy as np
import datetime as dt
import matplotlib
import matplotlib.pyplot as plt
import os
#import smooth_2d as s2d
from scipy import signal
from scipy import misc
import warnings #To supress certain warnings.
from mpl_toolkits.basemap import Basemap
#Some module constant section.
default_figure_si... | gustfrontar/LETKF_WRF | scale_breeding/python/bred_vector_functions.py | Python | gpl-3.0 | 22,316 | [
"Gaussian"
] | 598c53d6fe4176f5310ac15c32d2c7ef4861aa8e158653b6c7fe4e1109366d98 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'dev/ui/about.ui'
#
# Created: Sat Mar 26 03:26:15 2011
# by: PyQt4 UI code generator 4.7.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
class Ui_DialogAbout(object):
def setupUi(self, Di... | BlackDragonHunt/Mangle | ui/about_ui.py | Python | gpl-3.0 | 4,829 | [
"VisIt"
] | bf038569e99f3490d8a28c97f1df806ac38051378d5fbf154e4d6d778f94ebb7 |
# -*- coding: utf-8 -*-
"""
Created on 5/10/2016
@author: david-hoffman
@copyright : David Hoffman
Package holding the necessary functions for generating SIM patterns for
the QXGA-3DM writing repz11 files and ini files for labVIEW
"""
import os
import numpy as np
from numpy.linalg import norm
from scipy.optimize imp... | david-hoffman/simpattern | __init__.py | Python | apache-2.0 | 34,845 | [
"Gaussian"
] | 24d567f9f9510360ff5b74c0bfdb4fbd17105c98c772ef6b0baca6752377f67b |
# proxy module
from __future__ import absolute_import
from mayavi.modules.skeleton_module import *
| enthought/etsproxy | enthought/mayavi/modules/skeleton_module.py | Python | bsd-3-clause | 99 | [
"Mayavi"
] | 9168ceba3c253eebd6054c3f337a4c3f336cda66ea2249131a3a5e61cc0112d7 |
"""
Acceptance tests for the teams feature.
"""
import json
import ddt
from flaky import flaky
from nose.plugins.attrib import attr
from uuid import uuid4
from ..helpers import UniqueCourseTest
from ...fixtures import LMS_BASE_URL
from ...fixtures.course import CourseFixture
from ...fixtures.discussion import (
T... | ahmadio/edx-platform | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 47,500 | [
"VisIt"
] | 81fe0ea7d71e7b66c782d4b326435e291292d47689b643abf9fd2056b272f212 |
# Copyright 2015 The TensorFlow Authors. 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 applica... | ghchinoy/tensorflow | tensorflow/tools/common/traverse.py | Python | apache-2.0 | 3,773 | [
"VisIt"
] | 8920d0f62c8e48533bdde83d5be36d3a0c46790913ccf82c08998c9c159e5ba4 |
#!/usr/bin/env python
import sys
from lib.ansible_base import AnsibleBaseRunner
__all__ = [
'AnsibleGalaxyRunner'
]
class AnsibleGalaxyRunner(AnsibleBaseRunner):
"""
Runs Ansible galaxy commands: install/remove/list.
See: http://docs.ansible.com/galaxy.html
"""
BINARY_NAME = 'ansible-galaxy'... | armab/st2contrib | packs/ansible/actions/ansible_galaxy.py | Python | apache-2.0 | 583 | [
"Galaxy"
] | 63302c2aacc879cb1edebadf5b8904c5e6462844ef347238c9091ff4e00fd61e |
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2021, 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 program is free software you can redistribute it and/or modify
# it under... | mrcslws/nupic.research | projects/dendrites/permutedMNIST/experiments/base.py | Python | agpl-3.0 | 6,498 | [
"Gaussian"
] | d62116c7eeaf3e2ac8c33d1148173ccc214bf74e0c0285e32c985e767c565d78 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/bibles/lib/versereferencelist.py | Python | gpl-2.0 | 5,336 | [
"Brian"
] | c45ce0b09f5d14fc3a9015e183f2df69620a8d75428e1f61083fc69f01d1d6bf |
# subsystemBonusAmarrOffensive2EnergyWeaponCapacitorNeed
#
# Used by:
# Subsystem: Legion Offensive - Drone Synthesis Projector
# Subsystem: Legion Offensive - Liquid Crystal Magnifiers
type = "passive"
def handler(fit, module, context):
fit.modules.filteredItemBoost(lambda mod: mod.item.requiresSkill("Medium Ene... | Ebag333/Pyfa | eos/effects/subsystembonusamarroffensive2energyweaponcapacitorneed.py | Python | gpl-3.0 | 513 | [
"CRYSTAL"
] | fe20905310eaee4fc182ecfd1545124171a79d5910343a76b6a300d4c9fd5ba9 |
import os
import StringIO
import sys
import unittest
try:
import hyperopt
except:
# TODO: Remove this Hackiness when installation fully works!
import HPOlib
hyperopt_path = os.path.join(os.path.dirname(os.path.abspath(
HPOlib.__file__)), "../optimizers/tpe/hyperopt_august2013_mod_src")
pri... | automl/HPOlib | tests/unittests/test_pyll_util.py | Python | gpl-3.0 | 29,539 | [
"BLAST"
] | 437a887183033fb701481546cd555caa7f23bdbe9644085391558fe8c4ea1f95 |
# -*- coding: utf-8 -*-
"""
@author: Philippe Giraudeau
Philippe Giraudeau <philippe@giraudeau.eu>
"""
#Modules
import math
import random
import pylab as pl
def rand(a, b):
return (b-a)*random.random() + a
# Number of neuron in Input, Hidden and output layer.
li = 24
lh = 30
lo = 1
iterations = 2000 # Number ... | masterchef8/IUT-PTUT | ia/lastMLP.py | Python | gpl-3.0 | 5,001 | [
"NEURON"
] | a0aab65c3df3862ad4717b664b5f3213619bb3da85ece49297f5571f6f876f8e |
from pyiid.sim import leapfrog
__author__ = 'christopher'
def classical_dynamics(atoms, stepsize, n_steps):
"""
Create a new atomic configuration by simulating the hamiltonian dynamics
of the system
Parameters
----------
atoms: ase.Atoms ase.Atoms
The atomic configuration
stepsize... | CJ-Wright/pyIID | pyiid/sim/dynamics.py | Python | bsd-3-clause | 679 | [
"ASE"
] | 6ec9c9a271e0cf4bdcf06c7436ccaacb7efb1841cfacda8d889b67014f6c42b2 |
"""Test a single point calculation using CP2K."""
import os
from pathlib import Path
import pytest
from assertionlib import assertion
from nanoqm.common import is_data_in_hdf5
from nanoqm.workflows.input_validation import process_input
from nanoqm.workflows.workflow_single_points import workflow_single_points
from .... | SCM-NV/qmworks-namd | test/test_workflow_single_points.py | Python | mit | 1,321 | [
"CP2K"
] | 6b124e1f43e60914f005cbc5ab34475025a3e905df4b80f5f1437f9443f920c2 |
'''Crops windowed particles from a micrograph
This script (`ara-crop`) crops windows containing particles from a micrograph based on coordinates from a particle picking
algorithm such as AutoPicker (`ara-autopick`).
It performs the following preprocessing on the micrograph:
- High pass filter with cutoff = sigma... | ezralanglois/arachnid | arachnid/util/crop.py | Python | gpl-2.0 | 35,274 | [
"Gaussian"
] | 4f90cf45c0c58f11e50d78b89b88e1d6305c3fa93676e87dabf5635249353ac7 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki,Danelle Cline'
__copyright__ = '2017'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all *postSeason* (after KISS/CANON April season) activities in 2017
Mike McCann, Duane Edgington, Danelle Cli... | stoqs/stoqs | stoqs/loaders/CANON/loadCANON_postSeason2017.py | Python | gpl-3.0 | 39,871 | [
"NetCDF"
] | 9bbb77734933b4b1ad59474747f6486a7bf187c51e87d07888806f1dfff1f3bc |
# Copyright (C) 2017
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2017
# Gregor Deichmann (TU Darmstadt, deichmann(at)cpc.tu-darmstadt.de)
# Copyright (C) 2017
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyrigh... | MrTheodor/espressopp | src/io/__init__.py | Python | gpl-3.0 | 1,486 | [
"ESPResSo"
] | a5e0f6e5494dc801935aa4dbf99951c58006dfb17d07313be8490e8a44709847 |
# Copyright (C) 2013-2015 Samuel Damashek, Peter Foley, James Forcier, Srijay Kasturi, Reed Koser, Christopher Reffett, and Fox Wilson
#
# 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 ve... | Polarcraft/KbveBot | commands/choose.py | Python | gpl-2.0 | 1,513 | [
"MOE"
] | 04742156f23cb7d982707b6d9220d99aedd42838f09495103a7ce69e39cd6163 |
# ICE Revision: $Id$
"""
Class that implements pyFoamPVSnapshot
"""
from optparse import OptionGroup
from PyFoamApplication import PyFoamApplication
from PrepareCase import PrepareCase
from CommonSelectTimesteps import CommonSelectTimesteps
from PyFoam.RunDictionary.SolutionDirectory import SolutionDirectory
from ... | Unofficial-Extend-Project-Mirror/openfoam-extend-Breeder-other-scripting-PyFoam | PyFoam/Applications/PVSnapshot.py | Python | gpl-2.0 | 39,876 | [
"ParaView",
"VTK"
] | 34d8e028d0c064dd38baca4475d98244f967e6377c56029c312b4497bf849a65 |
"""
"""
import errno
import os
import shutil
import subprocess
import time
from os.path import exists, join
from gravity.io import debug, error, info, warn
from gravity.process_manager import BaseProcessManager
from gravity.state import GracefulMethod
from gravity.util import which
from supervisor import supervisorct... | galaxyproject/gravity | gravity/process_manager/supervisor_manager.py | Python | mit | 18,198 | [
"Galaxy"
] | f438217c593f26289afce8f06b4549b150a2ef0fa35c2bdfd0a8f4ae866d9501 |
########################################################################
# $HeadURL$
# File : StalledJobAgent.py
########################################################################
""" The StalledJobAgent hunts for stalled jobs in the Job database. Jobs in "running"
state not receiving a heart beat signal for more... | rajanandakumar/DIRAC | WorkloadManagementSystem/Agent/StalledJobAgent.py | Python | gpl-3.0 | 19,698 | [
"DIRAC"
] | 75cd7895194c11059e83b27bbedca338030a1837484245acffaf02659c698ceb |
#
# This file is part of Bakefile (http://bakefile.org)
#
# Copyright (C) 2008-2013 Vaclav Slavik
#
# 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... | vslavik/bakefile | src/bkl/interpreter/passes.py | Python | mit | 11,402 | [
"VisIt"
] | e7bf8ab9a0b7693cf1998c233cc4be1735e7cc533c4e687f00b43c8472da5438 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.