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from distutils.core import setup
packages_yambopy = ['yambopy',
'yambopy.io',
'yambopy.dbs',
'yambopy.bse',
'qepy',
'schedulerpy',
'yamboparser']
if __name__ == '__main__':
setup(name='yambopy',... | henriquemiranda/yambopy | setup.py | Python | bsd-3-clause | 580 | [
"Yambo"
] | 473833673a066c5106220b27911d7230ee70462cf65216b2a943e4f25e433e37 |
# Copyright 2016 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... | neilhan/tensorflow | tensorflow/contrib/bayesflow/python/ops/special_math.py | Python | apache-2.0 | 7,692 | [
"Gaussian"
] | 4ff48c042621e00057fca812ecdb5b0d39c6798d85b6d3a34db5bbf00a284ae3 |
import os
import sys
import DsaArrayResolutionCy3 as ARes
import cx_Oracle
import DsaTools3 as DsaTool
from DsaGetCycle3 import get_all_apdm, get_apdm
from collections import namedtuple
from DsaXmlParsers3 import *
from DsaConverter3 import *
prj = '{Alma/ObsPrep/ObsProject}'
val = '{Alma/ValueTypes}'
sbl = '{Alma/O... | itoledoc/gWTO3 | DsaDataBase3.py | Python | gpl-2.0 | 44,632 | [
"VisIt"
] | 98fc104629b5652343cfe5cfbbadf9def1166bebafb15cb3d3b5b0be0fa163f4 |
# goal: find an embedding based on RMSD (dis)similarities
import numpy as np
import pylab as pl
import numpy.random as npr
pl.rcParams['image.cmap'] = 'gray'
# import data
from msmbuilder.example_datasets import AlanineDipeptide
dataset = AlanineDipeptide().get()
ala_trajectories = dataset.trajectories
from msmbuil... | maxentile/msm-learn | projects/rmsd/rmsd_dr.py | Python | mit | 1,196 | [
"MDTraj"
] | 057a9d045a3c0a811b97df19e2ba2294b6b56c2c300ada26f1c501b6df2af603 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division
from ase.units import kJ
from sklearn.metrics import mean_squared_error
from math import sqrt
#rms = sqrt(mean_squared_error(y_actual, y_predicted))
import numpy as np
try:
from scipy.optimize import curve_fit
except ImportError:
try:
... | joshgabriel/dft-crossfilter | CompleteApp/eos.py | Python | mit | 13,301 | [
"ASE"
] | ebd40b85eb23fdeca09c73d42f5bb34d285edd228145c02c762e0f37f10777dd |
"""Gaussian Mixture Model."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
import numpy as np
from scipy import linalg
from .base import BaseMixture, _check_shape
from ..externals.six.moves import zip
from ..utils import check_arra... | sonnyhu/scikit-learn | sklearn/mixture/gaussian_mixture.py | Python | bsd-3-clause | 26,908 | [
"Gaussian"
] | b8648531e9f58979c64011a11200f37d3f7421940504b24325ea3007ace78b6a |
# -*- coding: utf-8 -*-
r"""Tests lattice math
"""
import numpy as np
import pytest
from neutronpy.crystal import lattice
unitcell = lattice.Lattice(4, 4, 4, 90, 90, 90)
def test_get_angle_between_planes():
"""Tests get angle between planes defined by two vectors
"""
assert (unitcell.get_angle_between_p... | granrothge/neutronpy | tests/test_lattice.py | Python | mit | 3,524 | [
"CRYSTAL"
] | 2155b72dc70050cea492476796c6cbc5c9af9ba507d41e6098d8e652d2f97791 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# 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 PyBioMed source tree.
"""
#####... | gadsbyfly/PyBioMed | PyBioMed/PyMolecule/topology.py | Python | bsd-3-clause | 19,317 | [
"RDKit"
] | 159752873753e0d712e3b93ac56b22914e6e120c8f4eec90f0eec96927b00691 |
""" Utility for loading plotting types.
Works both for Accounting and Monitoring.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import re
from DIRAC.Core.Utilities.Plotting.ObjectLoader import loadObjects
from DIRAC.AccountingSystem.Client.Types.... | yujikato/DIRAC | src/DIRAC/Core/Utilities/Plotting/TypeLoader.py | Python | gpl-3.0 | 1,594 | [
"DIRAC"
] | c6edac440a5f3c3d633924985802f78d3b4602be60f54bd974a790093693c9c5 |
# proxy module
from __future__ import absolute_import
from mayavi.components.ui.actor import *
| enthought/etsproxy | enthought/mayavi/components/ui/actor.py | Python | bsd-3-clause | 95 | [
"Mayavi"
] | e2d30cd6bb45593c2f4aaa4a3578bc09d02a0827978859f6dab64a6721cd3bbc |
import numpy as np, SimPEG as simpeg, vtk, sys, os, time
import vtk.util.numpy_support as npsup
# import polydata, extraction
def findZofXYOnPolydata(points,vtkPolydata):
# Make the cell locator
cellLocator = vtk.vtkCellLocator()
cellLocator.SetDataSet(vtkPolydata)
cellLocator.BuildLocator()
# Find the min/max ... | grosenkj/telluricpy | telluricpy/modelTools/surfaceIntersect.py | Python | mit | 982 | [
"VTK"
] | 57d5132dc1146c03ad3c23054c45e77ded92c132ebb83fb7d70ed5ed5581cb17 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views import defaults as default_views
from course.views import CourseManageView, CourseCre... | Wetrain/mmu-course-api | config/urls.py | Python | mit | 1,491 | [
"VisIt"
] | 00e5505ad876ac3f9192221234b5b5c6a0cb35b53c30127c4d54b0d2f41a44b1 |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors and contributors
# For license information, please see license.txt
from __future__ import unicode_literals
import frappe
from frappe.model.document import Document
from frappe.utils import flt, cstr
import os
import sys
import subprocess
import ge... | gangadhar-kadam/laganerp | erpnext/setup/doctype/site_master/site_master.py | Python | agpl-3.0 | 27,892 | [
"VisIt"
] | 164ad1e04afb9daf8d201fed4822a0695ad5be0f9930486eff838cf8a65595d8 |
import os
import sys
from setuptools import setup, find_packages
from tethys_apps.app_installation import custom_develop_command, custom_install_command
### Apps Definition ###
app_package = 'ssw_downloader'
release_package = 'tethysapp-' + app_package
app_class = 'ssw_downloader.app:SswDownloader'
app_package_dir = o... | CI-WATER/tethysapp-ssw_downloader | setup.py | Python | bsd-2-clause | 1,153 | [
"NetCDF"
] | e806381e09f60ba3184f79e07028f816e31cf2cf3595fa3c60502f8bee29e3f1 |
'''Grid cell network neuron definitions.
.. currentmodule:: grid_cell_model.models.gc_neurons
A helper module to set up parameters of E and I populations.
Functions
---------
.. autosummary::
getENeuronParams
getINeuronParams
'''
from __future__ import absolute_import, print_function, division
import num... | MattNolanLab/ei-attractor | grid_cell_model/models/gc_neurons.py | Python | gpl-3.0 | 3,301 | [
"NEURON"
] | 035e4a0090d27cd965ddbadfdc2c2672bf431b6c93052e15d797b3a53970e6b2 |
#### PATTERN | GRAPH ###############################################################################
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
####################################... | krishna11888/ai | third_party/pattern/pattern/graph/__init__.py | Python | gpl-2.0 | 65,658 | [
"VisIt"
] | d60091af7f97544b3a4396d4df25644dc74f673789b6089639bfd597a9f51b38 |
"""
Implementation of Harwell-Boeing read/write.
At the moment not the full Harwell-Boeing format is supported. Supported
features are:
- assembled, non-symmetric, real matrices
- integer for pointer/indices
- exponential format for float values, and int format
"""
# TODO:
# - Add more support (symmet... | teoliphant/scipy | scipy/io/harwell_boeing/hb.py | Python | bsd-3-clause | 18,387 | [
"exciting"
] | 62dd7d2a5b80efc50b531eb4462b0f47d8c7da9d44d99b82fa50fa210814b0f7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestImageThresholdConnectivity.py | Python | gpl-3.0 | 4,029 | [
"VTK"
] | bcb4e8c1bf3ff70df8c9979d5fdfecfc9ced7a646329a6497bc9cf24a1712999 |
"""
inflect.py: correctly generate plurals, ordinals, indefinite articles;
convert numbers to words
Copyright (C) 2010 Paul Dyson
Based upon the Perl module Lingua::EN::Inflect by Damian Conway.
The original Perl module Lingua::EN::Inflect by Damian Conway is
available from http://... | dantebarba/docker-media-server | plex/Sub-Zero.bundle/Contents/Libraries/Shared/inflect.py | Python | gpl-3.0 | 97,744 | [
"CASINO",
"ESPResSo",
"Elk",
"MOOSE",
"Octopus"
] | 8a9d8963bd5055a8d03c99f8e8171e4b405611dcc31b6d8a8b45d78361b276f0 |
########################################################################
# File : Watchdog.py
# Author: Stuart Paterson
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system resource consumption. The Watchdog... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/JobWrapper/Watchdog.py | Python | gpl-3.0 | 43,077 | [
"DIRAC"
] | 8a7140368b808149c942a5f5bcae5ceb4280417cd509a4cd28431f5d48a4e01f |
import pylab
import nest
neuron1 = nest.Create("iaf_neuron")
#nest.SetStatus(neuron1, {"I_e": 376.0})
neuron2 = nest.Create("iaf_neuron")
multimeter = nest.Create("multimeter")
nest.SetStatus(multimeter, {"withtime":True, "record_from":["V_m"]})
multimeter2 = nest.Create("multimeter")
nest.SetStatus(multimeter2, {"wit... | nmsutton/MemoryModule | python_version/examples/nestTest3.py | Python | mit | 1,555 | [
"NEURON"
] | 0d221b8b28287135745971a0c56f5946d5deb6ca2cd5448a08ff92c481107a92 |
"""
A setuptools based setup module.
See:
https://packaging.python.org/guides/distributing-packages-using-setuptools/
https://github.com/pypa/sampleproject
"""
from setuptools import setup # Always prefer setuptools over distutils
# from os import path
VERSION = '0.0.9'
LAST_MODIFIED_DATE = '2020-04-30' # by RJH — wh... | openscriptures/Biblelator | setup.py | Python | gpl-3.0 | 10,916 | [
"VisIt"
] | db3c06c2687305d77465660c2a00034ed3a5e1234cfe291bb3b656a9058fe803 |
#!/usr/bin/env yamtbx.python
"""
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
"""
Convert XPARM.XDS information for labelit programs.
Use PHENIX_TRUST_OTHER_ENV=1 to start this script.
"""
import re, sys, os, pickle, math
impor... | keitaroyam/yamtbx | yamtbx/dataproc/xds/command_line/xds2labelit.py | Python | bsd-3-clause | 7,054 | [
"CRYSTAL"
] | 0a9c878e06f52024ebd6d941eb62ec6e661e45016d86e53da41fbcdc9533df3c |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
#########
Reporting
#########
*Created on Thu Jun 8 14:40 2017 by A. Pahl*
Tools for creating HTML Reports."""
import time
import base64
import os
import os.path as op
from string import Template
from io import BytesIO as IO
import pandas as pd
from rdkit.Chem imp... | apahl/cellpainting | cellpainting/reporting.py | Python | mit | 19,241 | [
"RDKit"
] | b2a15e9fbdc0c7a734dbc74372b4c8bac0ba9bc7fb3cb6083a02772658535a19 |
import cProfile
import pstats
import math
import string
import sys
import struct
import matplotlib
import numpy as np
import scipy.ndimage
import scipy.stats as ss
import scipy.signal
import scipy as sp
import scipy.odr as odr
import glob
import os
import gzip
import tarfile
import shutil
import congrid
import astropy.... | gsnyder206/synthetic-image-morph | candelize_enzo.py | Python | gpl-2.0 | 11,398 | [
"Galaxy"
] | 613027250d2d27b4f7fc5587f3ffcff9eb196b403376bb3977f5557e32b4288c |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Sun Mar 1 19:51:42 2015
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.
... | SamWitte/Codds_DarkMatter | src/experiment_HaloIndep.py | Python | gpl-2.0 | 55,784 | [
"DIRAC",
"Gaussian"
] | 9279561fd4389c7722f36c41bd2eab0677169cca985d1beadb3f40fdc3d9f1b3 |
"""Handle extraction of final files from processing pipelines into storage.
"""
import datetime
import os
import toolz as tz
from bcbio import log, utils
from bcbio.upload import shared, filesystem, galaxy, s3
from bcbio.pipeline import run_info
import bcbio.pipeline.datadict as dd
_approaches = {"filesystem": files... | guillermo-carrasco/bcbio-nextgen | bcbio/upload/__init__.py | Python | mit | 16,723 | [
"Galaxy"
] | f1ca5d9b102f997856b23788df7c7565f24141c5bad4e6e7d33a1f07edc557c1 |
#! /usr/bin/env python
########################################################################
# File : dirac-wms-jobs-select-output-search
# Author : Vladimir Romanovsky
########################################################################
"""
Retrieve output sandbox for DIRAC Jobs for the given selection and ... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_jobs_select_output_search.py | Python | gpl-3.0 | 3,510 | [
"DIRAC"
] | 2f00c829becab1d5b7bb5d1f205ef8f5b2d608248b684d7fb4313a7517c879b9 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
# pylint: disable=E1111
import unittest
import json
import requests
import datetime
import ddt
import random
from urllib import quote
from django.test import TestCase
from nose.tools import raises
from mock import Mock, patch
from django.conf import... | adlnet-archive/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 132,870 | [
"VisIt"
] | 51500d8bab4c3e52c183e5798571811649808112e13d3da0de23ad1d8d990983 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Provides class BaseVisualStim and mixins; subclass to get visual stimuli
"""
# Part of the PsychoPy library
# Copyright (C) 2002-2018 Jonathan Peirce (C) 2019-2022 Open Science Tools Ltd.
# Distributed under the terms of the GNU General Public License (GPL).
from path... | psychopy/psychopy | psychopy/visual/basevisual.py | Python | gpl-3.0 | 66,313 | [
"Gaussian"
] | 721de89cd44b9e4cec78378578e8f56887c69df28fa77ee85ed10e7e8c1e7d09 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/PotentialVSpherePair.py | Python | gpl-3.0 | 3,610 | [
"ESPResSo"
] | a75b852ae292935ffc345fe8e0765f43d90e8506880e76cd4ab265ad67da3700 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import json
from monty.json import MontyDecoder
import numpy as np
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.xas.spectrum import XAS
from pymatgen.vis.plo... | gVallverdu/pymatgen | pymatgen/vis/tests/test_plotters.py | Python | mit | 1,657 | [
"pymatgen"
] | 4b9e6ffc8ab32492dd10383f7908dc17f7e8353ffe40c619040db977ceaf6e8c |
#!/usr/bin/env python
"""
PYTHONPATH="." luigi-deps-tree --module test_luigi ReactionPath --id- 1
PYTHONPATH="." luigi --module test_luigi ReactionPath --local-scheduler --id- 1
python test_luigi.py inp/input.xyz 53 9 -1 11 54 -1 9 11 1
"""
import argparse
import os
from pathlib import Path
import shutil
... | eljost/pysisyphus | scripts/batchnt_multi.py | Python | gpl-3.0 | 11,910 | [
"xTB"
] | 11e33f1006168bff5e461fe1988175fb106b05802dcb9162920a83ecddb5d917 |
# -*- coding: utf-8 -*-
##########################################################################
# #
# Eddy: a graphical editor for the specification of Graphol ontologies #
# Copyright (C) 2015 Daniele Pantaleone <danielepantaleone@me.com> ... | ashwingoldfish/eddy | eddy/ui/session.py | Python | gpl-3.0 | 111,490 | [
"VisIt"
] | fae2fc900d47050624198f5c6179668f0f1ad7a9645e460aa8fdc14b8cd2b666 |
"""
KeepNote
Editor widget in main window
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@alum.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 Sof... | yngfng/keepnote-0.7.8 | keepnote/gui/editor_sourceview.py | Python | gpl-2.0 | 17,284 | [
"VisIt"
] | 4c8eaae85ef24f6fe3b7748069cd3dbfa739e007e964693dd91801d35c1a6caf |
# -*- coding: utf8 -*-
"""
"""
__author__ = "Jérôme Samson"
__copyright__ = "Copyright 2014, Mikros Image"
import os
import sys
import csv
import time
import datetime
from optparse import OptionParser
import numpy as np
import pygal
from pygal.style import *
try:
import simplejson as json
except ImportEr... | mikrosimage/OpenRenderManagement | src/pulitools/stats/trace_farm.py | Python | bsd-3-clause | 7,375 | [
"Octopus"
] | b45536c786ce521507a0badd99d2fd042453231ebbc82627bc59c9068630d87d |
"""
The B{0install list-feeds} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _
from zeroinstall.cmd import UsageError
from zeroinstall.injector import model, reader
synta... | AlexanderRyzhko/0install-TUF | zeroinstall/cmd/list_feeds.py | Python | lgpl-2.1 | 1,108 | [
"VisIt"
] | d5d6a77d731a6384c0e1c6b82e3121f213b2ad9461c46898e25417c9beca7afa |
#!/usr/bin/env python
# pmx Copyright Notice
# ============================
#
# The pmx source code is copyrighted, but you can freely use and
# copy it as long as you don't change or remove any of the copyright
# notices.
#
# ----------------------------------------------------------------------
# pmx is Copyright (C... | dseeliger/pmx | scripts/mutate_v2.py | Python | lgpl-3.0 | 22,705 | [
"Amber",
"CHARMM"
] | df601afdd88c61fc91bd1e16b570f23a31339417761a17989b4005ff0be71ee4 |
import sys
import csv
import blastparser
import screed
def collect_best_hits(filename):
d = {}
for n, record in enumerate(blastparser.parse_fp(open(filename))):
if n % 25000 == 0:
print >>sys.stderr, '...', filename, n
best_score = None
for hit in record.hits:
f... | jrherr/bioinformatics_scripts | python_scripts/blast_to_ortho_csv.py | Python | mit | 2,394 | [
"BLAST"
] | 266d9e14b72cb2038c9cc4a61af3dff8b309b162dc4a9c21eb8acdfd84e07afe |
"""
Test the mio parametrization of Frauenheim and co-workers.
"""
import os
import glob
import numpy as np
from ase import read, FIRE, QuasiNewton, molecule
from hotbit import Hotbit, database_from_path
###
FMAX = 0.005
OPT = FIRE
debug = False
###
# From Elstner et al., Phys. Rev. B 58, 7260
noscc_db = {
... | pekkosk/hotbit | hotbit/test/pbc.py | Python | gpl-2.0 | 4,916 | [
"ASE"
] | 3caf962c7e52e55c41d53b061831f483bb8259a4372eb948c1a6c95026afea43 |
# -*- coding: utf-8 -*-
import sys
import os
sys.path.insert(0, os.path.abspath("."))
from custom_directives import *
from datetime import datetime
# Mocking modules allows Sphinx to work without installing Ray.
mock_modules()
assert (
"ray" not in sys.modules
), "If ray is already imported, we will not render d... | ray-project/ray | doc/source/conf.py | Python | apache-2.0 | 7,916 | [
"VisIt"
] | 96725ce3c689e13037a7355823f788866c1e82b97188af2ad33f1f94baf732f3 |
"""
#;+
#; NAME:
#; galaxy.core
#; Version 1.0
#;
#; PURPOSE:
#; Core routines for galaxy analysis
#; 29-Nov-2014 by JXP
#;-
#;------------------------------------------------------------------------------
"""
from __future__ import print_function, absolute_import, division, unicode_literals
import os, copy,... | astronomeara/xastropy-old | xastropy/galaxy/core.py | Python | bsd-3-clause | 1,859 | [
"Galaxy"
] | 3985c97c8677747053e9a9b6258d881e5fae11ea693ce3628d96ba127700627f |
# 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... | frreiss/tensorflow-fred | tensorflow/python/ops/control_flow_grad.py | Python | apache-2.0 | 9,572 | [
"VisIt"
] | 65fa436f5d916eb0d82a01a6d928d7d34c8a973b6a65acafe9e035ab3c8c530c |
# -*- coding: utf-8 -*-
"""
OficinaActivity.py
Create Oficina Activity
Copyright 2007, NATE-LSI-EPUSP
Oficina is developed in Brazil at Escola Politécnica of
Universidade de São Paulo. NATE is part of LSI (Integrable
Systems Laboratory) and stands for Learning, Work and Entertainment
Research Group. Visit our web p... | samdroid-apps/paint-activity | OficinaActivity.py | Python | gpl-2.0 | 10,961 | [
"VisIt"
] | 76e4f765e1904e4c1388adbe2ee0a6abbcb1073004819dcfb277abaa5de3f403 |
# $HeadURL: $
''' LogPolicyResultAction
'''
from DIRAC import S_OK, S_ERROR
from DIRAC.ResourceStatusSystem.Client.ResourceManagementClient import ResourceManagementClient
from DIRAC.ResourceStatusSystem.PolicySystem.Actions.BaseAction import BaseAction
__RCSID__... | avedaee/DIRAC | ResourceStatusSystem/PolicySystem/Actions/LogPolicyResultAction.py | Python | gpl-3.0 | 2,857 | [
"DIRAC"
] | bf9cb7e84fafc53de4c6107150902580b4a1b163c7f4cd9f91db76ff67612f46 |
import time
from math import sqrt
import numpy as np
from ase.utils import rotate
from ase.data import covalent_radii
from ase.data.colors import jmol_colors
class EPS:
def __init__(self, atoms,
rotation='', show_unit_cell=False, radii=None,
bbox=None, colors=None, scale=20):
... | slabanja/ase | ase/io/eps.py | Python | gpl-2.0 | 6,231 | [
"ASE"
] | 5a23ba7609e06203f707ef53877c90d04b5e4ef54b3a9a3878c30c00c75ab9a1 |
#
# Copyright (C) 2001-2004 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" The "parser" for compound descriptors.
I almost hesitate to document this, because it's not the prettiest
thing the world has ever seen... but it does work (for at least some
definitions of the word).
Rather than getti... | rdkit/rdkit-orig | rdkit/ML/Descriptors/Parser.py | Python | bsd-3-clause | 12,237 | [
"RDKit"
] | e8ba8e3703018478f9442fd10bab489a9a57567ad48bf12311c830ba2741ad0c |
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function, unicode_literals)
import os
import sys
sys.path.append(os.getenv('HOME') + '/bin/python/libs')
# just in case notebook was not launched with the option
# %pylab inline
import pylab as plt
import numpy as np
from scipy import spa... | mfouesneau/iasbs2017 | figrc.py | Python | mit | 107,856 | [
"Gaussian"
] | 45ecc4e5037a7b428cd82cfb785375a0705787e9f96066ee5de8530944d5989a |
# Author: Michele Mattioni
# Mon Jan 26 05:54:30 GMT 2009
import math
from neuron import h, nrn
import ecellControl as eC
from synapse import Synapse
import logging
logger = logging.getLogger(__name__)
class Spine():
"""
Class spine. Create a spine with head neck and psd
"""
def __init__(self, ... | mattions/TimeScales | neuronControl/spine.py | Python | bsd-3-clause | 8,023 | [
"Avogadro",
"NEURON"
] | 8cd7131ed2530f9551087154408ffc2740e47ebd27943e2f4b1afd4e33ab5430 |
from sympy.abc import x, y
from sympy import lambdify, sin, exp, pi
import numpy as np
from mayavi import mlab
import matplotlib.pyplot as plt
import invariants
## Start by setting up the function and transformed function
f = invariants.SymbolicImage(exp(-2*x**2 - 4*sin(0.5*x**2 + y)**2))
theta = np.pi/4
c = np.cos(th... | rgbrown/invariants | code/test_symbolic.py | Python | mit | 1,073 | [
"Mayavi"
] | 36c8197b0e91adf386feff1489cb5e0d18a7ad1dbcb965d1da7621a791f78eae |
"""
===============================
Ordinary Least Squares with SGD
===============================
Simple Ordinary Least Squares example with stochastic
gradient descent, we draw the linear least
squares solution for a random set of points in the plane.
"""
print(__doc__)
import pylab as pl
from sklearn.linear_mode... | florian-f/sklearn | examples/linear_model/plot_sgd_ols.py | Python | bsd-3-clause | 797 | [
"Gaussian"
] | c82a300e13b7916168dd332b2aa12350d16e03ccae33d145a24a87ac3b835369 |
import sys
import time
import os
import scipy
import numpy
import collections
import csv
import operator
import math
import itertools
import utils
mdir = "%s/work/partis/datascripts/meta/goo-dengue-10x" % os.getenv('HOME')
fabio_fname = '%s/fabio-pb-markers.tsv' % mdir
waickfname = '%s/waickman-markers.csv' % mdir
ms... | psathyrella/partis | python/gex.py | Python | gpl-3.0 | 24,326 | [
"BLAST"
] | 686560ac003050104cdca8f41719125978e61bdfb3b74ed6a8f40d1f8bfc59fa |
from __future__ import print_function, division
import unittest
class KnowValues(unittest.TestCase):
def test_water_si_wgth(self):
""" This is for initializing with SIESTA radial orbitals """
from pyscf.nao import gw as gw_c
from pyscf.nao import mf as mf_c
from pyscf.nao.m_x_zip import detect_maxim... | gkc1000/pyscf | pyscf/nao/test/test_0093_water_si_wght.py | Python | apache-2.0 | 2,872 | [
"PySCF",
"SIESTA"
] | ae451062d0659bf8e33dc7168611cfe3acecad7592e1747de2b28360540d76e3 |
""" :mod: SRM2Storage
=================
.. module: python
:synopsis: SRM v2 interface to StorageElement
"""
# # imports
import os
import re
import time
import errno
from stat import S_ISREG, S_ISDIR, S_IMODE, ST_MODE, ST_SIZE
# # from DIRAC
from DIRAC import gLogger, gConfig
from DIRAC.Core.Utilities imp... | Andrew-McNab-UK/DIRAC | Resources/Storage/SRM2Storage.py | Python | gpl-3.0 | 81,950 | [
"DIRAC"
] | 564624ee1a9699ecb9bcdf9b12e42c40ad1932ca3e155257b77136438bbfe480 |
#! /usr/bin/env python
"""Generate C code from an ASDL description."""
# TO DO
# handle fields that have a type but no name
import os, sys, traceback
import asdl
TABSIZE = 8
MAX_COL = 80
def get_c_type(name):
"""Return a string for the C name of the type.
This function special cases the default types prov... | TathagataChakraborti/resource-conflicts | PLANROB-2015/seq-sat-lama/Python-2.5.2/Parser/asdl_c.py | Python | mit | 25,788 | [
"VisIt"
] | 75f77e7378cd62a1f1d07dbb33b8c1f9b5c35b0ffbf7a18ca28bfe1f7a9d4612 |
# -*- coding: utf-8 -*-
"""
NeuroTools.signals.spikes
==================
A collection of functions to create, manipulate and play with spikes signals.
Classes
-------
SpikeTrain - object representing a spike train, for one cell. Useful for plots,
calculations such as ISI, CV, mean rate(), ... | NeuralEnsemble/NeuroTools | src/signals/spikes.py | Python | gpl-2.0 | 111,721 | [
"NEURON"
] | 0a806b0f90fe8652f01bf908504f6506057b5d6637430632f8ef5a6b26b57619 |
agencies = ["aaa","bbb","ccc","ddd"]
# abbreviation of agencies
agenciesAb = []
agenciesAb[0]='ALL';
agenciesAb[1]='USDA';
agenciesAb[2]='DOC';
agenciesAb[3]='DoD';
agenciesAb[4]='ED';
agenciesAb[5]='DOE';
agenciesAb[6]='HHS';
agenciesAb[7]='DHS';
agenciesAb[8]='HUD';
agenciesAb[9]='DOI';
agenciesAb[10]='DOJ';
age... | sunlightlabs/foia-data | python/python-for-loop-years.py | Python | gpl-3.0 | 5,890 | [
"ADF"
] | a24a4e862a30c7e9a80f9661efed3f1c9991f2df731932134b6f2ae900732845 |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, poly, _polify_basic,
_construct_domain,
_init_poly_from_dict,
_init_poly_from_list,
_init_poly_from_poly,
_init_poly_from_basic,
degree, degree_list,
pdiv, prem, pquo, pexq... | tarballs-are-good/sympy | sympy/polys/tests/test_polytools.py | Python | bsd-3-clause | 65,988 | [
"Gaussian"
] | 56f41739507668d076f36b733e56072be10aaa9f24ec3873b372320cee3d5077 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | liesbethvanherpe/NeuroM | neurom/fst/tests/test_neuronfunc.py | Python | bsd-3-clause | 6,299 | [
"NEURON"
] | 370fae49e4b1787b564ab6ab85def73ac9dd4b7e4b8c04cfd527c83455990bcb |
from numpy import array, arange, frombuffer, load, asarray, random, \
fromstring, expand_dims, unravel_index, prod
try:
buffer
except NameError:
buffer = memoryview
from ..utils import check_spark, check_options
spark = check_spark()
def fromrdd(rdd, nrecords=None, shape=None, index=None, labels=None, d... | thunder-project/thunder | thunder/series/readers.py | Python | apache-2.0 | 14,550 | [
"Gaussian"
] | 0d3c9a71a6548493a2c0c9f614a20e58f0207bd5e1a7c7157b7705d542f5ff03 |
# $HeadURL: $
''' TransferCommand module
'''
from datetime import datetime, timedelta
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
fr... | marcelovilaca/DIRAC | ResourceStatusSystem/Command/TransferCommand.py | Python | gpl-3.0 | 8,013 | [
"DIRAC"
] | ed595ae8deb0cd2bae31224b13fb3203b7747d0dc6f4e6c06c8453ebcf08b0ed |
from vtk import *
source = vtkRandomGraphSource()
view = vtkGraphLayoutView()
view.AddRepresentationFromInputConnection(source.GetOutputPort())
view.GetRenderWindow().SetSize(600, 600)
view.ResetCamera()
view.Render()
view.GetInteractor().Start()
| collects/VTK | Examples/Infovis/Python/hello_world.py | Python | bsd-3-clause | 253 | [
"VTK"
] | 722bba4f7955bd3df814ee2bf415493001d8da256eff4ed8909b1affb0b98388 |
from itertools import chain
from tools import indent
from visitor import Visitor
from expr import ExpresionOut
from alias import AliasOut
class StatementOut(Visitor):
level = 2
@classmethod
def handle_body(self, body, *a, **k):
body = (self.visit(stmt, *a, **k) for stmt in body)
body = chain.from_ite... | Neppord/py2py | py2py_lib/out/stmt.py | Python | mit | 7,125 | [
"VisIt"
] | b4bbfc4bbe8603792581f223dd22fbbe5e5848d8bd56126f8eb0bc54c819fba1 |
import unittest, os
import numpy as np
import warnings
warnings.simplefilter('error')
from nose.plugins.attrib import attr
from moltools import Generator, Water, Molecule
FILE_XYZ =os.path.join( os.path.dirname( os.path.realpath( __file__ ) ), "tmp.xyz" )
@attr(speed = 'fast' )
class GeneratorTestCase( unittest.Te... | fishstamp82/moltools | moltools/test/test_use_generator.py | Python | mit | 2,571 | [
"Dalton"
] | 700393602cffbb81c473832b1b4e4c5dc07db23079cd5d3515647cc065996f7a |
"""
Module to provide RabbitMQ compatibility to Salt.
Todo: A lot, need to add cluster support, logging, and minion configuration
data.
"""
import logging
import os
import random
import re
import string
import salt.utils.itertools
import salt.utils.json
import salt.utils.path
import salt.utils.platform
import salt.ut... | saltstack/salt | salt/modules/rabbitmq.py | Python | apache-2.0 | 39,358 | [
"VisIt"
] | 83530a6fe2aefcf1b4062d69ccc2bcc8fa8b8b347bdb15c37bd99ac070775c08 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os
im... | harterj/moose | python/moosesyntax/nodes.py | Python | lgpl-2.1 | 8,090 | [
"MOOSE"
] | d531946f67f02721f24d128f5d25b5e48dfd58fab074ecf52837d9cba039a1c4 |
'''
#=============================================================================
# FileName: extract_structures.py
# Desc:
# Author: jlpeng
# Email: jlpeng1201@gmail.com
# HomePage:
# Version: 0.0.1
# Created: 2015-04-09 20:18:19
# LastChange: 2015-04-09 20:29:39
# Hist... | Jianlong-Peng/pytools | miscellaneous/extract_structures.py | Python | gpl-2.0 | 1,610 | [
"Pybel"
] | 7043b0657045fa69c79de78cfa9e19756cbcc19e14f82378fb9b8a681446316f |
# proxy module
from __future__ import absolute_import
from mayavi.sources.builtin_surface import *
| enthought/etsproxy | enthought/mayavi/sources/builtin_surface.py | Python | bsd-3-clause | 99 | [
"Mayavi"
] | 2a9db5fd162654b1c5fd882ad0f22c32ea47b19b8ab3026c4bc7253dd88c9fc7 |
from gpiozero import TrafficLights
import time
def british_lights_cycle(lights, cycle_time):
lights.off()
# Red
lights.red.on()
time.sleep(cycle_time)
# Red and Amber
lights.amber.on()
time.sleep(cycle_time)
# Green
lights.red.off()
lights.amber.off()
lights.green.on()
... | claremacrae/raspi_code | hardware/gpio/TrafficLights_gpiozero.py | Python | mit | 667 | [
"Amber"
] | 2ef992af399efbe3f6ab9dc7f5f19d920d246c75b8d28f868ec69d0a0b244070 |
#!/usr/bin/env python
"""gitchangelog: Generate a change log based on closed pull requests."""
from __future__ import unicode_literals
__version__ = '1.6.0'
import six
from six.moves import input
import sys
import os
import os.path
import json
import codecs
import argparse
import re
from pygithub3 import Github
cl... | kirsle/github-changelog | gitchangelog.py | Python | mit | 11,969 | [
"VisIt"
] | 8f0a282e71587d9f5623837bc6bd3dac39f46f803f6b89d9d1089ac1f5fd929f |
"""
.. module:: analyze
:synopsis: Extract data from chains and produce plots
.. moduleauthor:: Karim Benabed <benabed@iap.fr>
.. moduleauthor:: Benjamin Audren <benjamin.audren@epfl.ch>
Collection of functions needed to analyze the Markov chains.
This module defines as well a class :class:`Information`, that sto... | baudren/montepython_public | montepython/analyze.py | Python | mit | 93,542 | [
"Gaussian"
] | 9b0ace6d2080c8a8a9cbb78a0b1aadb7a507975ba1f4cd2dd24ba172a1c21f6e |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/cluecode/test_years.py | Python | apache-2.0 | 4,079 | [
"VisIt"
] | 816ffcc976afc0be70073dd884b42ac4bff489a8c9a1c7a19007bd4b8fe2a4e7 |
#!/usr/bin/env python
from __future__ import division, print_function
from collections import defaultdict
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
import parmed as pmd
# ParmEd Imports
from parmed import load_file, unit as u
from parmed.charmm import CharmmParameterSet
from... | leelasd/OPLS-AAM_for_Gromacs | GMX_TEST/DIP/R/test_OMM_GMX.py | Python | mit | 1,580 | [
"CHARMM",
"OpenMM"
] | 891d90a3fe8fbe9cf2098c72b54054732a3f87a7cf09e85c8bb00668f0163e47 |
from numpy.random import normal
from scipy.signal import gausspulse
from gwpy.timeseries import TimeSeries
# Generate a `TimeSeries` containing Gaussian noise sampled at 4096 Hz,
# centred on GPS time 0, with a sine-Gaussian pulse ('glitch') at
# 500 Hz:
noise = TimeSeries(normal(loc=1, size=4096*4), sample_rate=4096... | gwpy/gwpy.github.io | docs/0.8.1/api/gwpy-timeseries-TimeSeries-7.py | Python | gpl-3.0 | 579 | [
"Gaussian"
] | 9d0dcf500880207910619d43d5ccbf57948ed23962bbbc9060488de5c2e90985 |
import numpy as np
from deepchem.utils.typing import RDKitMol
from deepchem.feat.base_classes import MolecularFeaturizer
class PubChemFingerprint(MolecularFeaturizer):
"""PubChem Fingerprint.
The PubChem fingerprint is a 881 bit structural key,
which is used by PubChem for similarity searching.
Please confi... | lilleswing/deepchem | deepchem/feat/molecule_featurizers/pubchem_fingerprint.py | Python | mit | 1,454 | [
"RDKit"
] | 7a276dde275b80765d60522570cf2a053e54d196819eaf8bf4613307509e5f83 |
#!/usr/bin/env python
# Copyright (C) 2012 Tianyang Li
#
# 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 progr... | tianyang-li/meta-transcriptome | uniform-test/contig_bowtie2_uniform_test_multinomial.py | Python | gpl-3.0 | 3,255 | [
"HTSeq"
] | 5844bf537ba62da0ea94c7933e8cb73973b3b832349f6f072141a2e54390a089 |
"""
Test course update
"""
from uuid import uuid4
from bok_choy.web_app_test import WebAppTest
from regression.pages.studio.course_info_studio import CourseUpdatesPageExtended
from regression.tests.helpers.api_clients import LmsLoginApi
from regression.tests.helpers.utils import get_course_info
class CourseUpdateT... | edx/edx-e2e-tests | regression/tests/studio/test_course_update.py | Python | agpl-3.0 | 4,097 | [
"VisIt"
] | 874041e943ddd47d45a14e4c97e8e59852b18007fdc98347350db02e461e72db |
from LOTlib.Miscellaneous import Infinity, normlogpdf
from math import isnan
class GaussianLikelihood(object):
def compute_single_likelihood(self, datum):
""" Compute the likelihood with a Gaussian. Wraps to avoid nan"""
ret = normlogpdf(self(*datum.input), datum.output, datum.ll_sd)
if... | piantado/LOTlib | LOTlib/Hypotheses/Likelihoods/GaussianLikelihood.py | Python | gpl-3.0 | 784 | [
"Gaussian"
] | 16e80e66fcadd6ad98cc0d65a3d49070f2fd58f33043ac2e63b5b18fb566574c |
# Copyright (C) 2017,2018,2019,2020 Luiz Felippe S. Rodrigues <luizfelippesr@alumni.usp.br>
#
# This file is part of GalMag.
#
# GalMag 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 L... | luizfelippesr/galmag | galmag/Observables.py | Python | gpl-3.0 | 15,729 | [
"Galaxy"
] | 6c8100294789bec90627808a21af17c2322f9718f81d3800212f93867aa77c60 |
#!/usr/bin/env python
# encoding: utf-8
#
# bpt.py
#
# Created by José Sánchez-Gallego on 19 Jan 2017.
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
import warnings
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.axes_grid1 import ... | albireox/marvin | python/marvin/utils/dap/bpt.py | Python | bsd-3-clause | 19,622 | [
"Galaxy"
] | 07f6b80cb0cf3ffa3079e8a8d47195ccb8f3743b7d7113eeb2d76bb435c2d2d5 |
# 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 a... | panmari/tensorflow | tensorflow/contrib/distributions/python/ops/gaussian.py | Python | apache-2.0 | 3,593 | [
"Gaussian"
] | e8355fc65cdb9c61257a2ce14401b7855872a909f7dffa6f2b00e4085a804414 |
"""
This module contains code for storing the output of tabular HMMer parses, in
analogy to the BLAST record class of BioPython. Idea is to hold on to all of the
possible attributes of a HMMer result so that they can be iterated over after
"""
class HMMerRecord:
def __init__(self, hmmer_type):
self.hmmer_t... | chris-klinger/Goat | searches/hmmer/hmmer_record.py | Python | gpl-3.0 | 2,362 | [
"BLAST",
"Biopython"
] | 14e13727cdd19ffbe32bfe502c9f43a0f61976fb0afe594e9021f2bed9e8c183 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/snippets/funcRateHarmonicOsc.py | Python | gpl-2.0 | 3,873 | [
"MOOSE"
] | 81b5e190974bba55155f78aec6ba7782da5ddb76433fafbc9e633a10845edbf5 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | test/tests/outputs/format/test_hit_output.py | Python | lgpl-2.1 | 5,797 | [
"MOOSE"
] | 94d55a2fcf2cbd766baeb9e7893a1792adbc137ff3b78f5276c0e0731c504db9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
OpenBabel interface module, which opens up access to the hundreds of file
formats supported by OpenBabel. Requires openbabel with python bindings to be
installed. Please consult the
`openbabel documentation... | gVallverdu/pymatgen | pymatgen/io/babel.py | Python | mit | 13,465 | [
"Open Babel",
"Pybel",
"pymatgen"
] | e6a6ea07e9883e3c1b1f9fcd7d0eed02af48b49894f12b03be1772d620d73b4d |
#
# libtcod 1.5.1 python wrapper
# Copyright (c) 2008,2009,2010 Jice & Mingos
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright... | deeredman1991/CreepSmash | tools/libtcod/libtcodpy.py | Python | mit | 60,784 | [
"Amber"
] | 52ee1f5374f1beb32d1f8e851a2d4c20d05f4e2ff22c641b31e0cfd8f9cf3e48 |
r"""
===============
Decoding (MVPA)
===============
.. contents:: Contents
:local:
:depth: 3
.. include:: ../git_links.inc
Design philosophy
=================
Decoding (a.k.a. MVPA) in MNE largely follows the machine
learning API of the scikit-learn package.
Each estimator implements ``fit``, ``transform``, `... | mne-tools/mne-tools.github.io | 0.17/_downloads/34a6d4fd8dc9f5e092fe81327a209348/plot_sensors_decoding.py | Python | bsd-3-clause | 18,160 | [
"VisIt"
] | df5486f7727a71ff69da397e28854e86d3be5cc4adb4df63b03f82641b2362fc |
#!/usr/bin/env python3
import sys
from antlr4 import *
from llvmlite import ir
from LucyLexer import LucyLexer
from LucyParser import LucyParser
from LucyVisitor import LucyVisitor
class SymbolTable:
def __init__(self):
self._symbols = [dict()]
def push_frame(self, symbols=None):
symbols = d... | AndreaOrru/Lucy | compiler/lucyc.py | Python | bsd-2-clause | 5,689 | [
"VisIt"
] | 7f678e7c144348e4975bb8769330edc62caf024a4902953486002a21371f38c1 |
from setuptools import setup
import glob,os,sys
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspath(path.dirname(__file__))
scriptlist =glob.glob(os.path.join('bin', '*.py'))
scriptlist+=glob.glob(os.path.join('sbin', '*.py'))
from PyFoam import versionString
# with open(... | mortbauer/openfoam-extend-Breeder-other-scripting-PyFoam | setup.py | Python | gpl-2.0 | 1,967 | [
"ParaView"
] | 5d6bacf6ac03de24ec05d00ad62afaf1f02a74b66dd0570d2fd4812791ba39f6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Mathias Hauser
# Date: 08.2014
# USAGE: CONVERT clm history files in xy-format (lat, lon) to col format
try:
import netCDF4 as nc
except: # netCDF4 is not available on cscs
import scipy.io.netcdf as nc
nc.Dataset = nc.netcdf_file
import shutil
# DEFINE F... | IACETH/prescribeSM_cesm_1.2.x | clm_col_to_xy_example.py | Python | mit | 2,286 | [
"NetCDF"
] | d3a046fbf94c4d184be11f92aa4682da8f331d84ff5f69da84eef66ec36f86d3 |
# coding: utf-8
texto = '''
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Fotos BIXURRASCO - XV Edicao - FATEC - 14/09/2013 - Afterfest</title>
<meta http-equiv="Content-Type... | renebentes/Python4Zumbis | Códigos/TWP415.py | Python | mit | 119,764 | [
"Dalton"
] | 726ae569eb07dc2b7b6988d7fd78fc9828bee7c2abb8695d9d411caa25cc85c0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
import scipy.constants as const
from pymatgen.core.structure import Structure
from pymatgen.util.coord import get_linear_interpolated_value
from monty.json import MSONable
from monty.functoo... | fraricci/pymatgen | pymatgen/phonon/dos.py | Python | mit | 13,471 | [
"Avogadro",
"Gaussian",
"pymatgen"
] | 4fdfb12f84969cb4d9b554e3373316e6603cb0ae070827f1821991760008ff82 |
# Lint as: python3
# Copyright 2021 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/jax/layers/transformer_models_test.py | Python | apache-2.0 | 28,346 | [
"MOE"
] | b9fbca0da53e9f4b9b190a63f2896381b6238f1b723858cacec4373b1b6565b2 |
#! Tests out the CG solver with CPHF Polarizabilities
import time
import numpy as np
import psi4
#psi4.set_output_file("output.dat")
# Benzene
mol = psi4.geometry("""
0 1
O 0.000000000000 0.000000000000 -0.075791843589
H 0.000000000000 -0.866811828967 0.601435779270
H ... | amjames/psi4 | samples/psi4numpy/cphf/input.py | Python | lgpl-3.0 | 2,446 | [
"Psi4"
] | 2012341d4343943070e3daaa7ade51eeda9cd5a032a7a4525f7ec91ff4a84862 |
general_issue_codes = {
"ACC": "Accounting",
"ADV": "Advertising",
"AER": "Aerospace",
"AGR": "Agriculture",
"ALC": "Alcohol & Drug Abuse",
"ANI": "Animals",
"APP": "Apparel/Clothing Industry/Textiles",
"ART": "Arts/Entertainment",
"AUT": "Automotive Industry",
"AVI": "Aviation/A... | influence-usa/lobbying_federal_domestic | ref/sopr.py | Python | cc0-1.0 | 5,786 | [
"CASINO"
] | 3bc4094b426fc27075e29b9c7c12444265ed868bd423ba21237c7b027d087723 |
"""
.. _tut-sensor-locations:
Working with sensor locations
=============================
This tutorial describes how to read and plot sensor locations, and how
the physical location of sensors is handled in MNE-Python.
As usual we'll start by importing the modules we need and loading some
:ref:`example data <sample... | rkmaddox/mne-python | tutorials/intro/40_sensor_locations.py | Python | bsd-3-clause | 14,370 | [
"Mayavi"
] | a482a3ac51d52a03bb3879f30c6f0f6d32afbf9b16083372878a330c629f6973 |
''' file name : simple_linear_blender.py
Discription : This sample shows how to blend two images.
This is Python version of this tutorial : http://opencv.itseez.com/doc/tutorials/core/adding_images/adding_images.html#adding-images
Level : Beginner
Benefits : 1) Learns usage of cv2.addWeighted and 2) its numpy imple... | asrob-uc3m/rpc_rpi | src/python/opencv_python_tutorials/Official_Tutorial_Python_Codes/2_core/add_images.py | Python | gpl-3.0 | 1,423 | [
"VisIt"
] | 90cfe6d52f966cf9a550b825603f73610ad618c5d4d1b4c49d093fb10e115363 |
# LOFAR IMAGING PIPELINE
#
# BBS Source Catalogue List
# Bart Scheers, 2011
# L.H.A.Scheers@... | jjdmol/LOFAR | CEP/GSM/src/gsmutils.py | Python | gpl-3.0 | 48,216 | [
"Gaussian"
] | 0a4a8ed9c7d4245064b26bfb7707baf7e4dc202b27117c5691dd4af1b7c64342 |
"""Utilities to help Computing Element Queues manipulation
"""
import os
import hashlib
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.List import fromChar
from DIRAC.Core.Utilities.ClassAd.ClassAdLight import ClassAd
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getDIRACPlatform
from DIRAC... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/Utilities/QueueUtilities.py | Python | gpl-3.0 | 12,592 | [
"DIRAC"
] | 7fa9d7af58da5d60701c3c601de925672590fbaea1de71315fc79dea9213a788 |
# author: brian dillmann
# for rscs
from context import Timer
import unittest
import time
class test_time_input(unittest.TestCase):
def test_start_on_init(self):
input = Timer('timer')
t = input.read()
self.assertGreater(t, 0)
def test_seconds_interval(self):
input1 = Timer('timer')
input2 = Timer('time... | dillmann/rscs | test/devicetests/time_input_test.py | Python | mit | 976 | [
"Brian"
] | 4aa2258916196867ee7563a109307f5e6f0a694e2ae70ac93825d25c9dce0be8 |
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