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from __future__ import annotations
from typing import TYPE_CHECKING, Callable, Dict, Tuple, Any, cast
import functools
import numpy as np
import math
import types
import warnings
# trapezoid is a public function for scipy.integrate,
# even though it's actually a NumPy function.
from numpy import trapz as trapezoid
fro... | zerothi/scipy | scipy/integrate/_quadrature.py | Python | bsd-3-clause | 33,347 | [
"Gaussian"
] | 9f08fd5837920348cb2511cc036198d53265c3c26cf4a3271cbb8a3c6efa24d1 |
# Storage filtering classes
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed... | akozumpl/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 23,929 | [
"VisIt"
] | 2738f94dc0da72d88166087a647ccd244e750977c947b7c70aab3d0ea2516944 |
import theano
import numpy as np
from theano.tensor.shared_randomstreams import RandomStreams
from time import time
from nn.opMap import convertActivation
class Layer () :
# rng is across all layer types
_randStream = RandomStreams(int(time()))
def __init__ (self, layerID, learningRate=0.001,
... | mbojrab/playbox | trunk/modules/python/nn/layer.py | Python | mit | 7,882 | [
"NEURON"
] | dbe883559eb924217179c84e61fea0814bbfa34bea2ffb31570c131188eea30b |
# -*- coding: utf-8 -*-
# PEP8 asserts
from copy import deepcopy
import httplib as http
import mock
import time
from nose.tools import * # noqa
from modularodm.exceptions import ValidationValueError
from tests.base import OsfTestCase, fake
from tests.factories import (
UserFactory, NodeFactory, ProjectFactory,... | fabianvf/osf.io | website/addons/wiki/tests/test_wiki.py | Python | apache-2.0 | 48,876 | [
"VisIt"
] | 8ad9c0598b7ac44cd739ac838de16607c4eb7c3d63acf743e3eea7ea14f87e87 |
"""Parse monthly IDOT Maint Report.
1. Only sites in `CALSITES` get calibrated as others will just have their
entire sensors replaced when outside of bounds.
2. There is no flag that denotes if a calibration even happened :/
"""
import sys
import re
import datetime
import pandas as pd
from pyiem.util import get_dbcon... | akrherz/iem | scripts/ingestors/awos/parse_monthly_maint.py | Python | mit | 3,060 | [
"VisIt"
] | 6f97e8d78f907c59a55a1c72e0ca1f81ea68a1b9e3c6f6d63713d659e0a740dd |
# 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 required by applica... | jbedorf/tensorflow | tensorflow/python/keras/utils/kernelized_utils_test.py | Python | apache-2.0 | 5,129 | [
"Gaussian"
] | cf561e3cfdebf45bb0c7a5b97a2ba128a44836ee3a10f16e09d8b0e3d3353243 |
#! python
# encoding: utf-8
# Wellcome Trust Sanger Institute and Imperial College London
# Copyright (C) 2020 Wellcome Trust Sanger Institute and Imperial College London
#
# 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 t... | sanger-pathogens/gubbins | python/scripts/mask_gubbins_aln.py | Python | gpl-2.0 | 3,305 | [
"Biopython"
] | 0610f33a7cb823baa033e9d3ab38de2a22999d43c3cd114896d078a00034317d |
#! /usr/bin/python
#
# Copyright (C) 2003-2021 ABINIT group
#
# Written by Gabriel Antonius in python (compatible v2.7).
# This is free software, and you are welcome to redistribute it
# under certain conditions (GNU General Public License,
# see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).
... | abinit/abinit | scripts/post_processing/merge_ddb_nc.py | Python | gpl-3.0 | 4,948 | [
"ABINIT"
] | be87d8121bda230e7a45954050c97e29cfef0c07fa3fdf5a6b953ab23a662eb6 |
#!/usr/bin env python
# Copyright (C) 2000-2006 B. Malengier
#
# 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.
#
# Thi... | bmcage/stickproject | stick/lib/diff/diffusion.py | Python | gpl-2.0 | 44,436 | [
"Mayavi",
"ParaView",
"VTK"
] | 6e2992510b57e9a0c3a9d87b663a710ebfe74e878392eed45fb2481e027aeff1 |
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, WOK, asyncGen
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.DISET.TransferClient import TransferClient
from DIRAC import gConfig, S_OK, S_ERROR, gLogger
from DIRAC.Core.Security import CS
from DIRAC.Core.Utilities import Time, List, DictCache
... | chaen/WebAppDIRAC | WebApp/handler/AccountingPlotHandler.py | Python | gpl-3.0 | 12,016 | [
"DIRAC"
] | 4b6c2caa8f5462a2f73f0650c642cf59450a41290fc33fafd1e4d4ae20fab688 |
from __future__ import print_function
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import collections
import json
import logging
import sys
import time
try:
from urllib.request import urlopen
from urllib.parse import urlencode
from urllib.error import URLError
except ImportError:
f... | fbudin69500/SlicerDeveloperToolsForExtensions | ExtensionStats/ExtensionStats.py | Python | apache-2.0 | 24,739 | [
"VTK"
] | 5b6abe8e4d5636632d9a4c78ea10e2c1259a184541bbba7d906e27321c0ae5e7 |
from __future__ import print_function
import numpy as np
from bokeh.browserlib import view
from bokeh.document import Document
from bokeh.models.glyphs import *
from bokeh.models import (
Plot, Range1d, LinearAxis, Grid, ColumnDataSource, PanTool, WheelZoomTool
)
from bokeh.session import Session
document = Docu... | zrhans/python | exemplos/Examples.lnk/bokeh/glyphs/prim_server.py | Python | gpl-2.0 | 1,835 | [
"VisIt"
] | 5029708ff40aac5f475d3bf79fd50ce7cf5065328fa2b31d9c38bfce6bbeb597 |
#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
from itertools import repeat
import numpy as np
import datetime
from random import randrange
import csv
class DataGenerator:
def __init__(self, _delta_seconds=1200, _data_schema_type='1t', _noise_schema='1t', _with_noise=True):
self.delta_seconds = _delta_sec... | pwcz/ml_embedded | simulation_tool/generate_data.py | Python | mit | 4,858 | [
"Gaussian"
] | 7576b59c7978de6690a9a1d8dd4179a075eb64dc1ccc53705ce664a5b480e25a |
#!/usr/bin/env python
"""
PyVISSIM for PTV VISSIM v8+
========================
PyVISSIM is a Python package for the creation, manipulation, and
automation of traffic models created using PTV's VISSIM
microsimulation modeling software.
"""
# Copyright (C) 2015-2016 by
# S. Brian Huey (sbhuey@gmail.com... | brianhuey/vissim | vissim_v8/__init__.py | Python | mit | 613 | [
"Brian"
] | 491090b5becf5fd8ad85afc501a72a14bae65d583dd6461abde39f0290e09be4 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-ncdf4/package.py | Python | lgpl-2.1 | 2,621 | [
"NetCDF"
] | 3dec3205beef0a4e2177a4054388bd40b519465a412532122959d0888eb165e6 |
from __future__ import annotations
import pytest
from dials.command_line.frame_orientations import extract_experiment_data
def test_extract_experiment_data():
"""Test basic operation of the extract_experiment_data function. Does not
test extraction of data from scan-varying models"""
# Set up an Experi... | dials/dials | tests/command_line/test_frame_orientations.py | Python | bsd-3-clause | 2,030 | [
"CRYSTAL"
] | f0dcd2eff0d09552f766c76e3cf4e48f61c15ae0268b8ffc3a77493e7a530616 |
# ui.py -- A VTK "Widget" for displaying robots
# -*- coding: utf-8 -*-
#
# Written by Jonathan Kleinehellefort <jk@molb.org>.
#
# Copyright 2008 Lehrstuhl Bildverstehen und wissensbasierte Systeme,
# Technische Universität München
#
# This file is part of RoboView.
#
# RoboView is free software: you ca... | arcoslab/roboview | ui.py | Python | gpl-3.0 | 10,261 | [
"VTK"
] | 64684a5fe4c3f306563d40d4ac8314fee9713a093cae79ad1a9f38b156d1894a |
"""
Collection of physical constants and conversion factors.
Most constants are in SI units, so you can do
print '10 mile per minute is', 10*mile/minute, 'm/s or', 10*mile/(minute*knot), 'knots'
The list is not meant to be comprehensive, but just convenient for everyday use.
"""
"""
BasSw 2006
physical constants: imp... | pizzathief/scipy | scipy/constants/constants.py | Python | bsd-3-clause | 8,219 | [
"Avogadro"
] | b798d4464ddca530b57db7136e36f4cd5e4cd1f378c880749871e659936fda34 |
import codecs
import contextlib
import io
import locale
import sys
import unittest
import warnings
import encodings
from test import support
if sys.platform == 'win32':
VISTA_OR_LATER = (sys.getwindowsversion().major >= 6)
else:
VISTA_OR_LATER = False
try:
import ctypes
except ImportError:
ctypes = N... | PennartLoettring/Poettrix | rootfs/usr/lib/python3.4/test/test_codecs.py | Python | gpl-2.0 | 111,073 | [
"FEFF"
] | 1e17f7f97744c5bfc3bbda71fa8a8b440623fded470a9e966540f6fe030d181a |
#!/usr/bin/env python
#
# $Id$
#
# This python program/module creates a graphical VTK pipeline browser.
# The objects in the pipeline can be configured.
#
# This code is distributed under the conditions of the BSD license.
# See LICENSE.txt for details.
#
# Copyright (C) 2000 Prabhu Ramachandran
# Conversion to wxPyt... | chrisidefix/devide | external/vtkPipeline/vtkPipeline.py | Python | bsd-3-clause | 17,320 | [
"VTK"
] | fbcafa1b992285e22ae48048e8a1fae3bfb765b79bc5e9ded85802f6c9b998a6 |
import numpy as np
class Adaline(object):
"""
ADAptive LInear NEuron classifier
Params:
@learning_rate : float (Learning rate between 0.0 and 1.0)
@passes : int (Number of passes over the training data)
@random_state : int (Random state for initializing we... | MVilstrup/simple_neural_network | python/classifier/adaline.py | Python | mit | 3,995 | [
"NEURON"
] | 4298da35a5aba66b3393afc2e6f8aed94116091c7dd09ffab9de450b17d469e1 |
'''
Copyright (C) 2014 Pietro Sormanni
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is... | hmc-cs-rkretsch/Secondary-Protein-Structure | Lit/s2Dv2/s2D_class.py | Python | mit | 85,152 | [
"BLAST",
"NEURON"
] | 1a61b943576c0c4bea3baf4b8c935050d23b61cc31d64075b055efd69c417532 |
# -*- coding: utf-8 -*-
"""
Molecules Controller is submodule for *RootController*
"""
from tg import expose, flash, redirect, request
from tg.i18n import lazy_ugettext as l_
from molgears.model import DBSession, PCompound, PHistory, PStatus, Tags, SCompound, SFiles, LCompound, LPurity, LHistory
from molgears.model imp... | admed/molgears | controllers/molecules.py | Python | bsd-3-clause | 108,442 | [
"RDKit"
] | 0292426dba1e12fb9d1a04ec9e8d31319b75e5b93c271c350629a3c9290f8639 |
#!/usr/bin/python
#
# Copyright (C) 2011, 2012 Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this l... | leshchevds/ganeti | lib/ovf.py | Python | bsd-2-clause | 68,214 | [
"VisIt"
] | 7f92d2f4527f57a7f7d33d72e15ec19ac2873e3b6be03786780889b9d83c7515 |
from __future__ import print_function, division
import matplotlib
matplotlib.use('agg')
from nutils import *
import scipy
import numpy as np
import matplotlib.pyplot as plt
from scipy import sparse
import obspy
from mpl_toolkits.axes_grid1 import make_axes_locatable
@log.title
def makeplots( domain, geom, verts_x, ... | ManuelMBaumann/elastic_benchmarks | marmousi2.py | Python | mit | 8,930 | [
"VTK"
] | 53f8b8bda55d539deb93b2ad687bffef14d9cc6c76e97386e51a1be81c5c73eb |
import matplotlib
matplotlib.use('Agg')
import pyemma
import pyemma.coordinates as coor
import pyemma.plots as mplt
import numpy as np
import mdtraj as md
import matplotlib.pyplot as plt
from glob import glob
import os
# Source directory for MEK simulations
source_directory = '/cbio/jclab/projects/fah/fah-data/mung... | choderalab/MSMs | shanson/mek-10488/pyemma-finding4/pyemma-finding4-mek.py | Python | gpl-2.0 | 2,762 | [
"MDTraj"
] | 114c3c4e4d8e971c7b355b09f55410db772a35a409bbefcbe9e6229b99837413 |
"""
[2016-05-20] Challenge #267 [Hard] IDDQD
https://www.reddit.com/r/dailyprogrammer/comments/4k8m02/20160520_challenge_267_hard_iddqd/
Description
-----------
You are trapped in a room full of evil zombies. Some people might resign
themselves to their doom in this situation, but not you. You're a badass space
marin... | DayGitH/Python-Challenges | DailyProgrammer/DP20160520C.py | Python | mit | 3,453 | [
"BLAST"
] | 8810c0ce8b6b84ebd7bf1666f03771116b6c41f8796a2b916ba233d1317f9361 |
# This file is part of COFFEE
#
# COFFEE is Copyright (c) 2014, Imperial College London.
# Please see the AUTHORS file in the main source directory for
# a full list of copyright holders. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided ... | gmarkall/COFFEE | coffee/utils.py | Python | bsd-3-clause | 24,020 | [
"VisIt"
] | e8e15bbf888f65918959262c09ce0c02a87ae96b08c57be028c8f5895be2d1fa |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# startfe - [insert a few words of module description on this line]
# 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 t... | heromod/migrid | mig/cgi-bin/startfe.py | Python | gpl-2.0 | 1,102 | [
"Brian"
] | c71031638b0884ceb55b6a1b53c90b90edc898c217eee00a3da2253403f23c88 |
#!/usr/bin/env python
# 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
#
# U... | gkc1000/pyscf | pyscf/prop/gtensor/test/test_uks.py | Python | apache-2.0 | 2,552 | [
"PySCF"
] | 321d8a6c51ed6c0cad7cf0dcfd4c9b62aaf2dbd4768d5445bb6f3c4a26ec9c52 |
# -*- coding: utf-8 -*-
"""So much practical programming involves string manipulation, which
Python readily accomodates. Still, there are dozens of basic and
common capabilities missing from the standard library, several of them
provided by ``strutils``.
"""
from __future__ import print_function
import re
import sys
... | doublereedkurt/boltons | boltons/strutils.py | Python | bsd-3-clause | 32,963 | [
"MOOSE",
"Octopus"
] | f8191e66ca6d27739e4fbbd7080ab377386bfd93de656818f6dbbf0351706a11 |
########################################################################
# File : BOINCComputingElement.py
# Author : J.Wu
########################################################################
""" BOINC Computing Element
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import os
import bz2
import ba... | fstagni/DIRAC | Resources/Computing/BOINCComputingElement.py | Python | gpl-3.0 | 13,553 | [
"DIRAC"
] | a412137b03b1eb557a0feaaa8a2c0a324055f5d1f961f12807f2c9fc98741a27 |
"""Generators for classes of graphs used in studying social networks."""
import itertools
import math
import networkx as nx
from networkx.utils import py_random_state
# Accommodates for both SciPy and non-SciPy implementations..
try:
from scipy.special import zeta as _zeta
def zeta(x, q, tolerance):
r... | SpaceGroupUCL/qgisSpaceSyntaxToolkit | esstoolkit/external/networkx/generators/community.py | Python | gpl-3.0 | 34,550 | [
"Gaussian"
] | aee5b986ae638f256e7b832b0e2143dca39343943ed9e67dbddb11ae8245681f |
from __future__ import absolute_import, division, print_function
import warnings
from typing import Optional
from typing_extensions import Literal
import numpy as np
from odin.utils.crypto import md5_checksum
from odin.utils.mpi import MPI, cpu_count
from sklearn.decomposition import PCA
_cached_values = {}
__all__... | imito/odin | odin/ml/fast_tsne.py | Python | mit | 10,451 | [
"Gaussian"
] | d79b6a445d6d36287ed554d0671fe45692ba00d97dfc6d1a5de00702de86daff |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | marmyshev/transitions | openlp/__init__.py | Python | gpl-2.0 | 2,254 | [
"Brian"
] | f55cbba6ec159600bd475c4efcf22fcae8b7edc25d5790c090e3225a4e425e8f |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
# BEGIN PYTHON 2/3 COMPATIBILITY BOILERPLATE
from __future__ import absolute_import
from __future__ import with_statement
from __future__ import division
from __future__ import nested_scopes
from __future__ import generators
from __future__ import unicode_literals
from __future... | michaelerule/neurotools | gpu/cu/graph.py | Python | gpl-3.0 | 6,957 | [
"Gaussian"
] | 6c931eb115dfdacb5f2799a2fcd2bfc28e7cd1dea78f3441fd583b080384d381 |
#!/usr/bin/python
import httplib
import httplib2
import os
import random
import sys
import time
from apiclient.discovery import build
from apiclient.errors import HttpError
from apiclient.http import MediaFileUpload
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage
from oau... | siavashk/ClassicalRNN | scripts/uploadVideo.py | Python | mit | 6,711 | [
"VisIt"
] | 6f5f04129bb90b08c82d5a95745af324294e9cec81842a5a51790c5b4cc5efed |
r'''
Overlap of the cell-periodic part of AO Bloch function.
AO(k,r) = \sum_T e^{i k \dot T} \mu(r-T)
AO_{Bloch}(k,r) = e^{-i k\dot r) AO(k,r)
S_{k1,k2} = \int AO(k1,r) AO(k2,r) dr
'''
import numpy as np
from pyscf.pbc import gto
from pyscf.pbc import df
cell = gto.M(atom='H 0 0 0; H 1 0 1; H 0 1 0; H 1 .5 .5',
... | gkc1000/pyscf | examples/pbc/30-overlap_periodic_cell.py | Python | apache-2.0 | 1,055 | [
"PySCF"
] | ab3842e64f244b2283ae4cf547e954e71f661419328b77c7f12caca4a9543b4e |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Standard module
import math
import operator
# Third-party modules
import numpy
# =============================================================================
# Classes
# =============================================================================
class AtomError(... | pierrepo/PBxplore | pbxplore/structure/structure.py | Python | mit | 12,329 | [
"MDAnalysis"
] | 7e4961a7070aeb6226e3f8caab31f024047d764ac0a12b4de53199be1666b62c |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-service-ports
# Author : Stuart Paterson
########################################################################
"""
Print the service ports for the specified setup
Usage:
dirac-admin-service-port... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_service_ports.py | Python | gpl-3.0 | 1,434 | [
"DIRAC"
] | 7ecdac9e05c4945f234b248e04c115cf82f9ecd943bd5e571c668de7979d10a4 |
#!/usr/bin/python
######################################################################
# Ascii TMS Viewer
#
#--------------------------------------------------------------------
# Brian Hone | Initial Release
#--------------------------------------------------------------------
# ... | flailingsquirrel/asciimapper | TileLoader.py | Python | bsd-3-clause | 6,172 | [
"Brian"
] | d067561dde03be4164a262ab261c1492e1f98b0d1a5e212473fabe55fed2441a |
"""
Views for user API
"""
from completion.exceptions import UnavailableCompletionData
from completion.utilities import get_key_to_last_completed_block
from django.contrib.auth.models import User # lint-amnesty, pylint: disable=imported-auth-user
from django.contrib.auth.signals import user_logged_in
from django.sho... | eduNEXT/edunext-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 14,887 | [
"VisIt"
] | 93d206d0c45db85050e601b1d4f193632490a7c6d0c0cb1c35ccc14cd41f0060 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'Abbrechen' zeigt an, dass ein Asset Log Eintrag nicht eingetreten ist",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has... | flavour/eden | languages/de.py | Python | mit | 385,698 | [
"VisIt"
] | 1489ffde34d0e663ccb54bc94b26d350fdd761163cd9adc32a5d6db5a6ae87e5 |
#!/usr/bin/env python
# -*- coding=utf-8 -*-
import sys
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib.gridspec import GridSpec
# import pymatgen.io
# print(dir(pymatgen.io))
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure... | dimonaks/siman | siman/bands.py | Python | gpl-2.0 | 16,329 | [
"VASP",
"pymatgen"
] | dc3fb2e28601f7152fa8f3ce8b344e4818559ea154a999c0832e82ab5dcbf165 |
"""
Details of how the data model objects are mapped onto the relational database
are encapsulated here.
"""
import logging
log = logging.getLogger( __name__ )
import sys
import datetime
from galaxy.model import *
from galaxy.model.orm import *
from galaxy.model.orm.ext.assignmapper import *
from galaxy.model.custom... | dbcls/dbcls-galaxy | lib/galaxy/model/mapping.py | Python | mit | 53,116 | [
"Galaxy"
] | a27c687e566e4a5c8199fac0ff10e22f50006891e957b6fbd92803cf60480c51 |
from fabric.api import env, run, sudo, cd, abort, roles, execute, warn_only
env.use_ssh_config = True # username, identity file (key), hostnames for machines will all be loaded from ~/.ssh/config
# This means that you run this script like this:
# fab -H <host1,host2> <task_name>
# E.g.:
# Update app to HEAD of curre... | CottageLabs/sysadmin | fabric/oacwellcome/fabfile.py | Python | mit | 4,611 | [
"Octopus"
] | 606c5378c4480ffcfad9701b75480761b912cf6cf35464e3c07c415b93232fd5 |
"""
Basic support for running library as script
"""
import errno
import os
import time
import os.path as op
import shutil
import signal
import sys
import logging
import fnmatch
from more_itertools import flatten
from http.client import HTTPSConnection
from urllib.parse import urlencode
from configparser import (
C... | tanghaibao/jcvi | jcvi/apps/base.py | Python | bsd-2-clause | 66,758 | [
"BWA",
"Bowtie"
] | 7ce4223fd402e78e811cb4eb09233ace8681abd115e5358f1f44ea28d45a76d9 |
# -*- coding: utf-8 -*-
# imports here
from aiida.parsers.plugins.vasp.instruction import BaseInstruction
__copyright__ = u'Copyright © 2016, Mario Zic, Trinity College Dublin. All Rights Reserved.'
__license__ = "Apache, Version 2.0, see LICENSE.txt file"
__version__ = "0.0.1"
__contributors__ = "Mario Zic"
__contac... | abelcarreras/aiida_extensions | plugins/parsers/vasp/instruction/structure/dummy_structure_parser.py | Python | mit | 894 | [
"VASP"
] | c34e14c3b0eb0ff6fe4d1a807367aff3a0cb04b9e9d258329026398bed64eff6 |
'''
SPADE is the combination of a mining technique and multiple statistical tests
to detect and asses the statistical significance of repeated occurrences of
spike sequences (spatio-temporal patterns, STP).
Given a list of Neo Spiketrain objects, assumed to be recorded in parallel, the
SPADE analysis can be applied as... | pietroquaglio/elephant | elephant/spade.py | Python | bsd-3-clause | 67,974 | [
"NEURON"
] | 2e2cce5c6b2b5a833a84260c773b0e3cc67f831428c3e81b00452125c507d0b8 |
import subprocess
from flask import Flask, request, abort, render_template, redirect, make_response, jsonify, send_file, \
send_from_directory, url_for
from wtforms import Form, StringField, validators, SelectField
from wtforms.fields.html5 import EmailField
from werkzeug import secure_filename
from StringIO import... | CottageLabs/oacwellcome | service/web.py | Python | apache-2.0 | 7,585 | [
"Octopus"
] | a8be9b00c6bc70b6e168a6f5f2de96e664d32bc050859b24595b2e41235b008e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | cmelange/ansible | lib/ansible/modules/system/systemd.py | Python | gpl-3.0 | 16,941 | [
"Brian"
] | 9be2e6141444cca1c8498aad993cbfbce4f53334e0160f543b772c6bda9290a5 |
from qtpy.QtCore import Qt
from qtpy.QtWidgets import QMainWindow, QDockWidget, QTabWidget, QWidget, QVBoxLayout
from ert_gui.plottery.plots.ccsp import CrossCaseStatisticsPlot
from ert_gui.plottery.plots.distribution import DistributionPlot
from ert_gui.plottery.plots.ensemble import EnsemblePlot
from ert_gui.plotter... | joakim-hove/ert | ert_gui/tools/plot/plot_window.py | Python | gpl-3.0 | 7,729 | [
"Gaussian"
] | 9ab35dcfc68f1ca1fd475596ce11032e1b31e6a1a35d2423fd8007044a423963 |
"""
Acceptance Tests for Course Information
"""
from common.test.acceptance.pages.studio.course_info import CourseUpdatesPage
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest
from ...pages.common.auto_auth import AutoAuthPage
from ...pages.studio.index import DashboardPage
class User... | fintech-circle/edx-platform | common/test/acceptance/tests/studio/test_studio_course_info.py | Python | agpl-3.0 | 6,771 | [
"VisIt"
] | e44583581e6280b7040848af4fdf1b8434014fde77b9b16f5ebf20fbe6f3f906 |
#
# tsne.py
#
# Implementation of t-SNE in Python. The implementation was tested on Python 2.7.10, and it requires a working
# installation of NumPy. The implementation comes with an example on the MNIST dataset. In order to plot the
# results of this example, a working installation of matplotlib is required.
#
# The ... | val-iisc/deligan | src/modified_inception_scores/cifar10/tsne.py | Python | mit | 5,210 | [
"Gaussian"
] | 7c4387303e0faf1ebb2084fc8c84f4f5cf9629a5069d5bab0222b6027bd07615 |
../../../../share/pyshared/orca/settings.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/settings.py | Python | gpl-3.0 | 43 | [
"ORCA"
] | c4b6a14f303ed64b9e9732c3e9ac122375f023c8e385c1d6608e42e5642178a8 |
# Copyright 2014-2017 The ODL contributors
#
# This file is part of ODL.
#
# This Source Code Form is subject to the terms of the Mozilla Public License,
# v. 2.0. If a copy of the MPL was not distributed with this file, You can
# obtain one at https://mozilla.org/MPL/2.0/.
"""Functions to create noise samples of dif... | aringh/odl | odl/phantom/noise.py | Python | mpl-2.0 | 9,327 | [
"Gaussian"
] | 8f58c15148929fe4d85da7e7e091e5d37f77e61e99bc11a57c83b696d7f0de5c |
#!/usr/bin/env python
"""
Get the size of the given file or a list of files
Example:
$ dirac-dms-data-size /formation/user/v/vhamar/Example.txt
------------------------------
Files | Size (GB)
------------------------------
1 | 0.0
------------------------------
"""
i... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_data_size.py | Python | gpl-3.0 | 2,499 | [
"DIRAC"
] | aa28cafc5d66ea04fc096b5f6c306edbe0b3163bac946da18a826c723f90244b |
import logging
import warnings
from django.contrib.auth.models import User
from django.core.cache import cache
from django.core.exceptions import ObjectDoesNotExist
from django.db import models
from django.db.models import Count, Q
from django.utils import timezone
from django.utils.translation import ugettext_lazy as... | reviewboard/reviewboard | reviewboard/reviews/models/review_request.py | Python | mit | 59,355 | [
"VisIt"
] | 8478598f0c3c22066f799982b75e4dee6c87aabb37a74921a147f09aeca8b57f |
import numpy as np
import geostatsmodels.variograms as variograms
def opt( fct, x, y, c, parameterRange=None, meshSize=1000 ):
'''
Optimize parameters for a model of the semivariogram
'''
if parameterRange == None:
parameterRange = [ x[1], x[-1] ]
mse = np.zeros( meshSize )
a = np.linsp... | cjohnson318/geostatsmodels | geostatsmodels/model.py | Python | mit | 3,637 | [
"Gaussian"
] | 17002e329f077219b72f235f06e05f306e7327c1796653512ba891208b903022 |
"""
A headless Page Object pattern implementation.
Background reading: https://www.martinfowler.com/bliki/PageObject.html
"""
import django.shortcuts
from bs4 import BeautifulSoup
class WrongElementError(RuntimeError):
"""
A different PageObject element was expected by the getter from the
```elements`` d... | behave/behave-django | behave_django/pageobject.py | Python | mit | 4,098 | [
"VisIt"
] | 80b8a79fd33c21ab13f31604691d594ed7a65ac5008f9cfab2fbc32520e52fa5 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | h-hirokawa/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 23,698 | [
"Galaxy",
"MOOSE"
] | 8cdfb092fa19decac1bd5dc40d5547c3181c79b60e914f8be837fe89f74b2a39 |
import sys
from ase.test import NotAvailable
if sys.platform in ['win32']:
raise NotAvailable('Fails on Windows https://trac.fysik.dtu.dk/projects/ase/ticket/62')
from ase.visualize.vtk import requirevtk, probe_vtk_kilobyte
requirevtk()
vtk_kilobyte = probe_vtk_kilobyte(1024)
import numpy as np
import sys, un... | suttond/MODOI | ase/test/vtk_data.py | Python | lgpl-3.0 | 19,422 | [
"ASE",
"VTK"
] | 8ac3ff01787f1136cf19f51444fc38dcf3b83503087ee8705b7c24d6de8c68ce |
class SurveyResponse(object):
def __init__(self, master):
self.master = master
def create(self, person, score, person_properties=None, comment=None):
"""Create a survey response (i.e. a score and comment from a person).
Args:
person (string): The ID of the person responding... | meori/delighted-python | delighted/survey_response.py | Python | mit | 4,927 | [
"VisIt"
] | 761a59870a39a8509b939c738b691f2cf1c25efb48c54a2ab1d149b6f5c6a84a |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/io/test/test_molden.py | Python | gpl-3.0 | 5,971 | [
"ORCA",
"Psi4"
] | 8d20f6e3771dd41782bc6f83d89f191e61a8e3d9340b23e304c6aa71823dc275 |
BASE_URLS = [
"www.journals.elsevier.com/aasri-procedia/",
"www.elsevier.com/journals/abstract-bulletin-of-paper-science-and-technology/1523-388x",
"www.journals.elsevier.com/academic-pediatrics/",
"www.journals.elsevier.com/academic-radiology/",
"www.journals.elsevier.com/accident-analysis-and-prevention/",
"www.elsev... | CottageLabs/OpenArticleGauge | openarticlegauge/plugins/resources/elsevier_list.py | Python | bsd-3-clause | 184,321 | [
"CRYSTAL",
"NEURON"
] | d3ae6b5525783893fc309b7f681643a2d9aef39ea703f0c8368394da1725c343 |
# -*- coding: utf-8 -*-
#
# tsodyks_depressing.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 Lice... | weidel-p/nest-simulator | pynest/examples/tsodyks_depressing.py | Python | gpl-2.0 | 5,612 | [
"NEURON"
] | f36585bbdc2d26f8f3723cdb7a34c02d18650a65765ab448c568e5d4b5f5614a |
# -*- coding: utf-8 -*-
"""
jinja2.meta
~~~~~~~~~~~
This module implements various functions that exposes information about
templates that might be interesting for various kinds of applications.
:copyright: (c) 2017 by the Jinja Team, see AUTHORS for more details.
:license: BSD, see LICENSE fo... | facelessuser/sublime-markdown-popups | st3/mdpopups/jinja2/meta.py | Python | mit | 4,313 | [
"VisIt"
] | 505b7bf69d5eedf76f16c56f452af3b219e45989a4a6f6169eee35ce291efa69 |
"""Kernels for Gaussian process regression and classification.
The kernels in this module allow kernel-engineering, i.e., they can be
combined via the "+" and "*" operators or be exponentiated with a scalar
via "**". These sum and product expressions can also contain scalar values,
which are automatically converted to... | ClimbsRocks/scikit-learn | sklearn/gaussian_process/kernels.py | Python | bsd-3-clause | 66,623 | [
"Gaussian"
] | 10329cd3153a4a4b9252433fdac051ca099012cf077cd4d355ec939bda2baa9b |
# -*- coding:utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2010, 2011, 2012, 2013 CERN.
#
# Invenio 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 ... | kasioumis/invenio | invenio/modules/indexer/testsuite/test_indexer_engine_tokenizer.py | Python | gpl-2.0 | 18,585 | [
"Brian",
"Galaxy"
] | 284ec34757a7f25ea6f15170590d984b054d7e682c30e4f79c186c922fdb4980 |
# ==============================================================================
# Copyright 2019 - Philip Paquette
#
# NOTICE: 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 rest... | diplomacy/research | diplomacy_research/utils/tensorflow.py | Python | mit | 33,171 | [
"Gaussian"
] | b91c6638749e89c4a84d58de358071616370a58b01e458ce117e2f8e42001232 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-get-normalized-queue-length.py
# Author : Ricardo Graciani
########################################################################
"""
Report Normalized CPU length of queue
This scri... | avedaee/DIRAC | Interfaces/scripts/dirac-wms-get-normalized-queue-length.py | Python | gpl-3.0 | 1,319 | [
"DIRAC"
] | 5816fb9a43d092842e22389390d178194d01199a1e6cded9f2ce755f1dbd10cd |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/netcdf-cxx4/package.py | Python | lgpl-2.1 | 1,758 | [
"NetCDF"
] | 138a322ce12d84a9e5222c3753fb120e521e2a858feaccdbbbf2dbe3834403e3 |
# $Id$
#
# Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" unit testing code for composite models
"""
import unittest
import io
from rdkit.six.moves import cPickle
from rdkit.ML.Composite import Composite
from rdkit.ML.DecTree.DecTree import DecTreeNode as Node
from rdk... | rvianello/rdkit | rdkit/ML/Composite/UnitTestComposite.py | Python | bsd-3-clause | 7,247 | [
"RDKit"
] | ffb4fa86873eaae94b5adb332bd0497bff8c32457cc1828660a404b5897128d3 |
from splinter import Browser
from time import sleep
from selenium.common.exceptions import ElementNotVisibleException
from settings import settings
from lib import db
from lib import assets_helper
import unittest
from datetime import datetime, timedelta
asset_x = {
'mimetype': u'web',
'asset_id': u'4c8dbce552e... | ktorti/CWW | tests/splinter_test.py | Python | gpl-2.0 | 9,301 | [
"VisIt"
] | cbd8a8c983da25a40047fa222031ad9b178fe2c98aa94914005c272976993b3b |
#!/usr/bin/python
### TBLASTX formatting
### MATCH = Only the first match keeped
MATCH = 0 # Only 1rst match Wanted
#MATCH = 1 # All match wanted
### SUBMATCH = several part of a same sequence match with the query
SUBMATCH = 0 # SUBMATCH NOT WANTED (only the best hit)
#SUBMATCH =1 # SUBMATCH WANTED
###... | abice-sbr/adaptsearch | 05_scriptExtractMatch_v20_BLASTX.py | Python | gpl-3.0 | 24,772 | [
"BLAST"
] | 388cad06693df0719f1d71324a4b0d860ad0779176899d398769c5ae71c7f2a9 |
r"""
Gradient analyses (:mod:`skbio.stats.gradient`)
===============================================
.. currentmodule:: skbio.stats.gradient
This module provides functionality for performing gradient analyses.
The algorithms included in this module mainly allows performing analysis of
volatility on time series data, ... | jensreeder/scikit-bio | skbio/stats/gradient.py | Python | bsd-3-clause | 31,926 | [
"scikit-bio"
] | 532a987059ab1803c0f49cbbd5c4c7679c367f12a039361a0e0f406c1505aa4c |
# changelog bisection for mercurial
#
# Copyright 2007 Olivia Mackall
# Copyright 2005, 2006 Benoit Boissinot <benoit.boissinot@ens-lyon.org>
#
# Inspired by git bisect, extension skeleton taken from mq.py.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version ... | smmribeiro/intellij-community | plugins/hg4idea/testData/bin/mercurial/hbisect.py | Python | apache-2.0 | 11,155 | [
"VisIt"
] | 61aee4b00da721adc1bfa12e8dc222ee1047d70311a6c2cd9ce9054d0b212be5 |
import matplotlib.pyplot as plt
import sys
from scipy.optimize import curve_fit
import numpy as np
# alaz files
try:
alfile = sys.argv[1]
azfile = sys.argv[2]
except IndexError:
print 'Usage: python plotbeam.py alfile azfile'
print 'Will then use offsets and power values in both files to fit and plot b... | varenius/salsa | Developer_notes/Beam_measurements/Beam_2015-02-17/plotbeam.py | Python | mit | 3,716 | [
"Gaussian"
] | 25c37c48ca8b6f32f28e47cb332d00739839e4291cb01ddae4abef2c883d5fbe |
import sys
import warnings
from itertools import zip_longest
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Generator,
List,
Optional,
Set,
Tuple,
Union,
)
from antlr4 import TerminalNode
from .errors import InterpolationResolutionError
if TYPE_CHECKING:
from .ba... | omry/omegaconf | omegaconf/grammar_visitor.py | Python | bsd-3-clause | 16,055 | [
"VisIt"
] | 2fa2cea261b6e0670f035f9a63334e98a2eea799188ab1d3bb2a7ce7b57b4fb0 |
"""
Does the following:
1. Generates and saves random secret key
2. Removes the taskapp if celery isn't going to be used
3. Removes the .idea directory if PyCharm isn't going to be used
4. Copy files from /docs/ to {{ cookiecutter.project_slug }}/docs/
TODO: this might have to be moved to a pre_gen_hook
A portio... | drxos/cookiecutter-django-dokku | hooks/post_gen_project.py | Python | bsd-3-clause | 9,980 | [
"GULP"
] | 45150280e17f8f33dfb36354eaa05525e9f32d40bcc32099265a860432994fb2 |
import time
import random
import pickle
import os
from datetime import date
RANDOM_CHANNEL_ID = os.environ.get("MARVIN_SLACK_CHANNEL_ID")
FILE="plugins/animal.data"
ANIMALS = ['Adelie Penguin',
'African Bush Elephant',
'African Civet',
'African Clawed Frog',
'African Forest ... | BlackPepperSoftware/marvin | plugins/animal/animal.py | Python | mit | 12,451 | [
"Jaguar",
"MOOSE",
"Octopus"
] | 61be2a1b27f3c35b98ceead1ae29868197bc2b9e23cd2a8c78d1c5743bdfb5fb |
#!/usr/bin/python
#load simulated reads
sim=open('sim.21.hsa.fa','r')
data={}
dataseq={}
lendata={}
name=""
for line in sim:
line=line.strip()
if line.startswith(">"):
name=line.replace(">","")
slot=name.split("_")[0].split("-")
data[name]="-".join(slot[0:3])
else:
lendata[n... | lpantano/mypubs | mirna/mirannotation/check_mirna.py | Python | mit | 8,273 | [
"BWA",
"Bowtie"
] | 16bb7055845d4429b711d39b96fb5396d4f98c88c17fd0cdb53e3a2e40ad8cd0 |
import numpy as np
from neurons.activations import get_activation
class Neuron:
def __init__(self, number_of_inputs, weights_range, bias, activation):
self.number_of_inputs = number_of_inputs
self.weights = np.random.uniform(*weights_range, number_of_inputs)
self.bias = bias
self.... | PiotrGrzybowski/NeuralNetworks | networks/neurons/neuron.py | Python | apache-2.0 | 855 | [
"NEURON"
] | be686682082f8004e0e0b95f504f00314ac585b3a9f4cc2fafcfd1e5db34ca61 |
import numpy as np
import copy as cp
import struct as st
import math,os,sys,progressbar,pylab
import matplotlib as mpl
from matplotlib import pyplot as plt
from numpy.lib import recfunctions
from scipy import spatial as sp
from scipy import special
from scipy.interpolate import griddata,interp1d
from scipy.ndimage impo... | viswimmer1/PythonGenerator | data/python_files/33855489/pyInit.py | Python | gpl-2.0 | 31,552 | [
"Gaussian"
] | 3edb512d779f4882b0eea259ce24d045a860b6c8246c32d0cc94a93a53ff5f41 |
# c: 20.03.2008, r: 20.03.2008
from __future__ import absolute_import
input_name = '../examples/diffusion/sinbc.py'
output_name = 'test_sinbc.vtk'
from tests_basic import TestInput
class Test( TestInput ):
pass
| vlukes/sfepy | tests/test_input_sinbc.py | Python | bsd-3-clause | 216 | [
"VTK"
] | cc615b294d2bc5d4ce7ec639fcde265dcf6c102ae2019c1b481ca724644079bc |
import os
import vtkAll as vtk
class JointPropagator(object):
def __init__(self, parentRobotModel, childRobotModel, jointsToPropagate):
self.parentRobotModel = parentRobotModel
self.childRobotModel = childRobotModel
# Figure out which joint indices we're going to
# be propagating
... | patmarion/director | src/python/director/jointpropagator.py | Python | bsd-3-clause | 1,291 | [
"VTK"
] | 555a4e0526290729adb313a7a2365870107043d8d66d2d5259394093de65a00c |
from rdkit import RDConfig
import unittest
import random
import re
from os import environ
from rdkit import Chem
from rdkit.Chem import Draw, AllChem, rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit import Geometry
import numpy as np
class TestCase(unittest.TestCase):
def setUp(self):
pass
def... | rdkit/rdkit | Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py | Python | bsd-3-clause | 26,232 | [
"RDKit"
] | 6848bffaef2ed42df9f5a820ab43f15f3114617b8a08fd834c994be7c72cadb2 |
"""
Brian T. Bailey
ITM 513 - MP4
ServerThread Class File
"""
from socket import *
import threading
from crypto import *
from ioutils import *
class ServerThread(threading.Thread):
"""Runable server thread to process messages from clients
A runnable thread class that allows the server program to be run ... | briantbailey/ITM-513 | mp4/src/mp4domain/ServerThread.py | Python | mit | 1,808 | [
"Brian"
] | bd0d0b30079515ce2a1897c5e15cfcfafa8ad15bfb801fbdac0befdd563062e4 |
"""
KeepNote
Base class for a viewer
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@mit.edu>
#
# 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 Found... | reshadh/Keepnote-LaTeX | keepnote/gui/viewer.py | Python | gpl-2.0 | 4,824 | [
"VisIt"
] | e565610d26168fc5439e97706e5956d36860d2dbfef66cf67e0205e296479fe8 |
#-------------------------------------------------------------------------------
# Cloud-COPASI
# Copyright (c) 2013 Edward Kent.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available... | edkent/cloud-copasi | cloud_copasi/web_interface/pools/task_views.py | Python | gpl-3.0 | 19,056 | [
"COPASI"
] | 46a831d55d904d7a878a80d50e174d60169de5c060251a5be8da0b44a22f99a7 |
import os
from django.core.files.uploadedfile import UploadedFile
from rest_framework import status
from hs_core.hydroshare import resource
from hs_core.hydroshare.utils import resource_file_add_process
from hs_core.views.utils import create_folder, move_or_rename_file_or_folder
from .base import HSRESTTestCase
c... | ResearchSoftwareInstitute/MyHPOM | hs_core/tests/api/rest/test_set_file_type.py | Python | bsd-3-clause | 7,061 | [
"NetCDF"
] | 35eb3a36b853bf8a39247b11308583593a8bb406752e60f774d67f7210bb1971 |
import bisect
import random
from typing import Any, List, Tuple
import cv2
import numpy as np
class VideosIndexer:
"""
Handles absolute indexing for a list of videos.
Attributes:
video_list (List([List[Any]])) :matrix with the frame ids for each video
video_lengths (List(int)): partial s... | googleinterns/keypoint-mot | src/dataset/dataset_utils.py | Python | apache-2.0 | 6,995 | [
"Gaussian"
] | 9281d6bace78692e1a38a62f2a1581ef00748a852106fd72f7bb93234eec91db |
"""Tools for VASP input and output"""
from io import *
from incar import *
from kpoints import *
from outcar import *
from oszicar import *
from poscar import *
from species import *
from vaspio import *
from vasprun import *
__all__ = dir()
| jbechtel/CASMcode | python/vasp/vasp/io/__init__.py | Python | lgpl-2.1 | 242 | [
"VASP"
] | 6ab5f7dedae69f8d4b1ad6f6f80ee9e52057cca7eeb6d87a0b8f90ed6f2d47df |
../../../../../../../share/pyshared/orca/scripts/apps/acroread/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/acroread/__init__.py | Python | gpl-3.0 | 74 | [
"ORCA"
] | 29e6e56096194fd8d1ee12f55267613b9bb35aec53e36ff8d0aad69292a41d44 |
""" The SLURM TimeLeft utility interrogates the SLURM batch system for the
current CPU consumed, as well as its limit.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Resources.Computing.... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/SLURMResourceUsage.py | Python | gpl-3.0 | 4,240 | [
"DIRAC"
] | 8440df3ece269b8aefcf6ea8a7c943b1f96324abdab7f16ea91aa66122414a4c |
import cPickle
import gzip
import os, sys, errno
import time
import math
# numpy & theano imports need to be done in this order (only for some numpy installations, not sure why)
import numpy
#import gnumpy as gnp
# we need to explicitly import this in some cases, not sure why this doesn't get imported with numpy its... | ronanki/merlin | src/work_in_progress/run_sdae.py | Python | apache-2.0 | 55,019 | [
"NEURON"
] | ed5774fe133a6e0460fbd057526f4f2eab70cd9cf50ec478a46b632b8bb2f860 |
import HFIR_4Circle_Reduction.fourcircle_utility as fourcircle_utility
from HFIR_4Circle_Reduction.integratedpeakview import GeneralPurposedPlotView
import os
from qtpy.QtWidgets import QMainWindow, QFileDialog
from mantid.kernel import Logger
try:
from mantidqt.utils.qt import load_ui
except ImportError:
Logge... | mganeva/mantid | scripts/HFIR_4Circle_Reduction/generalplotview.py | Python | gpl-3.0 | 3,492 | [
"Gaussian"
] | 1e2d7be0e4bf0ef25d01d8baee386a01acb63ce2d4da56a8cdfe842a0a968942 |
#!/usr/bin/env python
#----------------------------------------------------------------------------
#
# Monte Carlo simulation of the kinematic extraction with pPXF. It is useful
# to determine the desired value for the BIAS keyword of the pPXF procedure.
# This procedure generates a plot similar (but not identical) to... | cebarbosa/fossilgroups | ppxf/ppxf_simulation_example.py | Python | gpl-3.0 | 7,303 | [
"Galaxy",
"Gaussian"
] | 43717291dc59cc3c6d12e6ca3f5807d7278777772fad9397381401881dc6e14a |
""" Class Image
"""
# Author: Ilya Patrushev ilya.patrushev@gmail.com
# License: GPL v2.0
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.image import pil_to_array
import PIL as pil
from .find_embryo import find_embryo
from .extract_pattern import extract_pattern
zigzag_index = [ 0, 1, 5, 6, 1... | ilyapatrushev/isimage | isimage/Image.py | Python | gpl-2.0 | 7,753 | [
"Gaussian"
] | 413fe76de3604867145fb83ea204352fe67fcd4f5e5634b682d517c89ecf0f1a |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pprint
import sys
import textwrap
import py
import pytest
from _pytest.main import _in_venv
from _pytest.main import EXIT_NOTESTSCOLLECTED
from _pytest.main import Session
class TestCollector(object)... | hackebrot/pytest | testing/test_collection.py | Python | mit | 38,316 | [
"VisIt"
] | f8f4f7e7ae613d4a57da8d8087102cd38188e5836ea76ce8d5d41b2c9607fda2 |
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