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# -*- coding: utf-8 -*-
#
# test_siegert_neuron.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 Lic... | terhorstd/nest-simulator | pynest/nest/tests/test_siegert_neuron.py | Python | gpl-2.0 | 4,880 | [
"NEURON"
] | f4a36947f5e9240d9b031f73de44b6fb588a7af5339a57e37255080885ec046c |
"""Constants and convenience functions for interacting with the library"""
from typing import Dict, List, TypeVar, Union
"""
Attributes
----------
"""
angstrom_per_bohr = 0.5291772086
"""float : The conversion factor from Bohr radii (a₀) to angstrom (Å)
Value used by Gaussian 09, based on:
P. J. Mohr, B. N. Taylor,... | jszopi/repESP | repESP/util.py | Python | gpl-3.0 | 5,529 | [
"Gaussian"
] | ab693f724ad325f56108e4c7a328ef8746b16b47ecc9059a5dffad1a557aa959 |
""" Computes the Control Flow Graph of a function. """
from pythran.passmanager import FunctionAnalysis
from pythran.utils import isnum
from pythran.graph import DiGraph
import gast as ast
def is_true_predicate(node):
# FIXME: there may be more patterns here
if isnum(node) and node.value:
return Tru... | pombredanne/pythran | pythran/analyses/cfg.py | Python | bsd-3-clause | 6,097 | [
"VisIt"
] | 4d6c488d28360363476eb133d4f07c3411d121244b146547585fdbe03095b107 |
#!/usr/bin/python
import os,sys
ncs_lib_path = ('../../../../python/')
sys.path.append(ncs_lib_path)
import ncs
def run(argv):
sim = ncs.Simulation()
bursting_parameters = sim.addNeuron("bursting","izhikevich",
{
"a": 0.... | BrainComputationLab/ncs | python/samples/models/test/flat_test.py | Python | bsd-2-clause | 1,681 | [
"NEURON"
] | c6b03c63c041f1f9ad48c1afcd9d2ba36b144f7e30fdbeaa7d0a7032ccaabf51 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@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 publish... | jjneely/ansible | lib/ansible/runner/action_plugins/assemble.py | Python | gpl-3.0 | 5,881 | [
"Brian"
] | 09533e06adec6d5666a4d82e7fb716583b7a6299e92919602b61572a9e008874 |
import matplotlib.pyplot as plt
import numpy as np
from numpy.testing import assert_array_almost_equal
from exponential_families import *
from utils import *
def test_bernoulli():
expfam = Bernoulli()
assert(expfam.num_params == 1)
p = np.array([0.1, 0.5, 0.9, 0.25])
eta = np.log(p / (1-p))
... | redreamality/vsmrfs | vsmrfs/test_exponential_families.py | Python | mit | 1,625 | [
"Gaussian"
] | 5a815a1317f1837f091468f3e21811bbfd2377a9c67d533c4d3c02c4e6cfb89f |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
from unittest import skipIf, skip
from ..helpers import UniqueCourseTest, is_youtube_available, YouTubeStubConfig
from ...pages.lms.video.video import VideoPage
from ...pages.lms.tab_nav import TabNavPage
from ...pages.lms.course_nav import CourseNavPage
fro... | xiandiancloud/edxplaltfom-xusong | common/test/acceptance/tests/video/test_video_module.py | Python | agpl-3.0 | 36,583 | [
"VisIt"
] | ae941596a2d23823178fce12aaf0c11aacb974a73a99db08385f31322b6cd235 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-lfn-replicas
# Author : Stuart Paterson
########################################################################
"""
Obtain replica information from file catalogue client.
Usage:
dirac-admin-lfn-re... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_dms_lfn_replicas.py | Python | gpl-3.0 | 1,740 | [
"DIRAC"
] | c26ec9f8c7c6495297f6fb8fe8ec2c21985bc7030913c9abc26030a5ce7d02f3 |
#!/usr/bin/env python
import sys
import importlib
import math
Unit = object()
World = object()
class IdrisError(Exception):
pass
def _idris_error(msg):
raise IdrisError(msg)
def _idris_pymodule(name):
return importlib.import_module(name)
def _idris_call(f, args):
return f(*list(args))
def _idris_foreach(... | nickgeoca/idris-py | examples/example.py | Python | bsd-3-clause | 106,390 | [
"exciting"
] | e41bd42c019efb516838b2ce3f2ec32e1b7e4563516d72eb5217cd14dbb39b1e |
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/containers/tables.py | Python | gpl-3.0 | 18,903 | [
"CRYSTAL"
] | 3cb27d86882529c17fbce613931cf0099aa4bbcbcab6881494d6661647ccd8e5 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | mkuron/espresso | testsuite/scripts/tutorials/test_10-reaction_ensemble__scripts__RE_vs_cpH_poly.py | Python | gpl-3.0 | 1,097 | [
"ESPResSo"
] | 99b11b11888ca3fb7a27d3ab4ae27c5d9e25dbeb840d7fc86fe61e48d5ba7c9f |
# -*- coding: utf-8 -*-
#
# Copyright © 2014 Brian Schmidt
# Licensed under the terms of the MIT License
"""Create a stand-alone executable"""
try:
from guidata.disthelpers import Distribution
except ImportError:
raise ImportError, "This script requires guidata 1.4+"
import spyderlib
import git as git
impor... | bps10/LM-Ratio | setup.py | Python | mit | 1,081 | [
"Brian"
] | 52f3986def997fc0a87966841c32877c6ee3815542d1f3c1497b42e0f6991eb2 |
# Copyright 2017 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/data/kernel_tests/rejection_resample_test.py | Python | apache-2.0 | 6,427 | [
"DIRAC"
] | 190c41efe530afc2bb181980eb40834967acc95d3163ec9e2e7762d82e5652dc |
#- Converted from:
#- http://svn.apache.org/repos/asf/httpd/httpd/trunk/docs/conf/mime.types
#- (excluding vnd. tree types)
__author__ = "Graham Klyne (GK@ACM.ORG)"
__copyright__ = "Copyright 2011-2013, University of Oxford"
__license__ = "MIT (http://opensource.org/licenses/MIT)"
FileMimeTypes = (
{ (... | wf4ever/ro-manager | src/MiscUtils/FileMimeTypes.py | Python | mit | 22,403 | [
"NetCDF"
] | 9436adee9ee6d56857dc0b4d15c54555bd17b93672f9462ff4bb15498fbadf42 |
"""
.. _statsrefmanual:
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. currentmodule:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each univari... | person142/scipy | scipy/stats/__init__.py | Python | bsd-3-clause | 10,188 | [
"Gaussian"
] | a70f65344bfedf8144370d6ec17eb56fe5589683f915dd77f3d4650c548e4068 |
from property import *
# Layer GLu GABA
L2_ratio = ( 2, 2, 0)
L3_ratio = (16, 2, 2)
L4_ratio = (16, 16, 8)
L5_ratio = ( 8, 0, 0)
L6_ratio = (12, 0, 0)
# Neuron number in layer
L2_NN = GlobalColumns * sum(L2_ratio)
L3_NN = GlobalColumns * sum(L3_ratio)
L4_NN = GlobalColumns * sum(L4_ratio)
L5_NN = GlobalColumn... | research-team/NEUCOGAR | NEST/visual/V1/scripts/data.py | Python | gpl-2.0 | 2,499 | [
"NEURON"
] | c1f3d24c4443238790c5441cd0d1c5636fce8229ea9dbbd908cf24c83c9bec39 |
"""
Bootstraps from the fix recoli vcf.
"""
import os
import pickle
import shutil
# Setup Django environment.
sys.path.append(
os.path.join(os.path.dirname(os.path.realpath(__file__)), '../'))
os.environ['DJANGO_SETTINGS_MODULE'] = 'settings'
from main.models import AlignmentGroup
from main.models import Dat... | woodymit/millstone | genome_designer/scripts/bootstrap_large_vcf_example.py | Python | mit | 2,959 | [
"BWA"
] | 85d39dbd6c8899e0ddc04ee04946c76981de00d05c101047f7c4a0619b6e6ccc |
"""
Performance test created using multi-mechnize to analyze time
for query processing with ElasticSearch.
"""
from __future__ import print_function
import random
import time
from DIRAC.WorkloadManagementSystem.DB.ElasticJobDB import ElasticJobDB
class Transaction(object):
def __init__(self):
self.ElasticJo... | fstagni/DIRAC | tests/Performance/ESJobMonitoring/test_scripts/query.py | Python | gpl-3.0 | 748 | [
"DIRAC"
] | 5350577f476190982914a3f3bac4e45997eb03d8653b94e2c3ee54a4bad462bd |
import warnings
from collections import OrderedDict
from distutils.version import LooseVersion
import numpy as np
from .. import Variable, coding, conventions
from ..core import indexing
from ..core.pycompat import integer_types
from ..core.utils import FrozenOrderedDict, HiddenKeyDict
from .common import AbstractWri... | shoyer/xray | xarray/backends/zarr.py | Python | apache-2.0 | 25,410 | [
"NetCDF"
] | 3148b30fca059811d965cfbcb1894dadb182fa65d8ce6ed74ed07b7857e79b0c |
import cv2
import numpy as np
__author__ = 'Daniel'
def imshow(mat, img_name="Image Name"):
"""
Display the image and wait
:param mat: normally the data type is 8-bit int, for other cases:
http://docs.opencv.org/modules/highgui/doc/user_interface.html?highlight=imshow#cv2.imshow
:param img_name:
... | idf/scipy_util | scipy_util/image/image.py | Python | bsd-3-clause | 942 | [
"Gaussian"
] | f24506fefd1c8da1970972991fd3ebb404aad91b4701cf173bfcd785c0c7a07a |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | jbonofre/beam | sdks/python/apache_beam/runners/portability/maptask_executor_runner.py | Python | apache-2.0 | 17,721 | [
"VisIt"
] | a658ee031aea240dbcda275ae2e12653f50898fd4d6c26b20316d3fbbbacfb4c |
########################################################################
# $HeadURL$
########################################################################
""" Proxy Renewal agent is the key element of the Proxy Repository
which maintains the user proxies alive
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Agen... | Sbalbp/DIRAC | FrameworkSystem/Agent/MyProxyRenewalAgent.py | Python | gpl-3.0 | 3,014 | [
"DIRAC"
] | f7f706903995bffed0a8de7fb4e0775cb4744e5a38ad918835573aeaa5dfaee4 |
# Version: 0.21
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
* [![Latest Version][pyp... | codl/forget | versioneer.py | Python | isc | 80,044 | [
"Brian"
] | ff1a437e396a25a3dd607fbe3da3f5ac5973ebd3d23459aa65161f59ed436567 |
import logging
from pathlib import Path
import h5py
import numpy as np
from pysisyphus.calculators.Calculator import Calculator
from pysisyphus.helpers import rms, get_tangent_trj_str
from pysisyphus.intcoords.helpers import get_weighted_bond_mode
from pysisyphus.linalg import perp_comp, make_unit_vec
from pysisyphus... | eljost/pysisyphus | pysisyphus/calculators/Dimer.py | Python | gpl-3.0 | 24,113 | [
"Gaussian"
] | 23977c3119b3f2f4614e19ddc075227f3a1e5303738092d3a5753f9fad1f0615 |
import uuid
from datetime import datetime
from django.test import TestCase
from sqlalchemy import Date, Integer, SmallInteger, UnicodeText
from casexml.apps.case.mock import CaseBlock
from casexml.apps.case.tests.util import delete_all_cases, delete_all_xforms
from casexml.apps.case.util import post_case_blocks
fro... | dimagi/commcare-hq | corehq/apps/aggregate_ucrs/tests/test_aggregation.py | Python | bsd-3-clause | 18,646 | [
"VisIt"
] | 29cd665e160fbd0eb9b1d719ad7b51969930b0429e31ff2d79f1eaf8075d67ae |
from typing import Tuple
import numpy as np
import pytest
import gpflow
from gpflow.base import AnyNDArray, RegressionData
from gpflow.models.vgp import VGP_deprecated, VGP_with_posterior
from gpflow.posteriors import PrecomputeCacheType
def make_models(
regression_data: RegressionData, likelihood: gpflow.likel... | GPflow/GPflow | tests/gpflow/models/test_vgp_posterior.py | Python | apache-2.0 | 2,757 | [
"Gaussian"
] | a7a243e64509efeb43666efe48256e209346e07e2b1ae96a8adf579ffa0eea97 |
from fabric.api import *
from fabric.exceptions import NetworkError as _NetworkError
from fabric.colors import green as _green, blue as _blue, red as _red, yellow as _yellow
from fabric.contrib.files import append as _fab_append, exists as _fab_exists
from fabric.contrib.console import confirm
from StringIO import Stri... | jollysean/solr-scale-tk | fabfile.py | Python | apache-2.0 | 119,007 | [
"VisIt"
] | 08ac3f8c24f68af96643b173dca21e70747a2146d53b95f647dc1faae6caa0c8 |
# vim:set ff=unix expandtab ts=4 sw=4:
from typing import Callable, Tuple, Sequence, Set, Dict
from functools import lru_cache, _CacheInfo, _lru_cache_wrapper
import numpy as np
import matplotlib.pyplot as plt
import inspect
from collections import namedtuple
from numbers import Number
from scipy.integrate import odein... | MPIBGC-TEE/CompartmentalSystems | src/CompartmentalSystems/helpers_reservoir.py | Python | mit | 45,988 | [
"DIRAC"
] | 03b257ecf7080ac9186cc770870122f6bd3cf2d9f01df452f269e424f8641067 |
from numpy.testing import TestCase, assert_equal, assert_almost_equal
import unittest
import os
import numpy as np
import MDAnalysis
from lintools.lintools import Lintools
from lintools.testdata.datafiles import *
################ AMI in P-gp with -ro 30 #################
class TestBasic1(TestCase):
def setUp(sel... | ldomic/lintools | lintools/testdata/test_topol.py | Python | gpl-3.0 | 3,677 | [
"MDAnalysis"
] | 12a86d29b3429f2bff8c382189de874b2905f4fc5b423fb6964360ef0dc39522 |
# for rgenetics - lped to pbed
# where to stop with converters
# pbed might be central
# eg lped/eigen/fbat/snpmatrix all to pbed
# and pbed to lped/eigen/fbat/snpmatrix ?
# that's a lot of converters
import sys,os,time,subprocess
prog = os.path.split(sys.argv[0])[-1]
myversion = 'Oct 10 2009'
galhtmlpre... | volpino/Yeps-EURAC | lib/galaxy/datatypes/converters/pbed_to_lped_converter.py | Python | mit | 2,643 | [
"Galaxy"
] | bcf812658f8f7450fd8efa362c939d6c87158276847ae6054ebc745acf6550eb |
from Tkinter import *
def quit3(event=None):
root3.destroy()
root3=Tk()
root3.title("Manual for NOMA...")
sss1=Scrollbar(root3)
T=Text(root3)
T.focus_set()
sss1.pack(side='right',fill='y')
T.pack(side='left',fill='y')
sss1.config(command=T.yview)
T.config(yscrollcommand=sss1.set)
T.insert(END,"""
If you use the applic... | marmy28/NOMA | manual.py | Python | gpl-2.0 | 4,356 | [
"VMD"
] | 36eb6b6deb012cdafb8332a967d7e5bf41e0ed2e7266adb0b1119949f818635c |
# proxy module
from __future__ import absolute_import
from mayavi.plugins.script import *
| enthought/etsproxy | enthought/mayavi/plugins/script.py | Python | bsd-3-clause | 90 | [
"Mayavi"
] | b9c7ec7eede2e41018ff16b7cce9ebe1470488f551d666601c57e3132983b4cb |
# $Id$
#
# Copyright (C) 2011 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" unit testing code for molecule drawing
"""
from ... | rdkit/rdkit-orig | rdkit/Chem/Draw/UnitTestDraw.py | Python | bsd-3-clause | 3,985 | [
"RDKit"
] | 55aa28e8ec4348f7ae32b0b05d9a66d3be2e7277347cd890df453595f024bd15 |
from __future__ import print_function
# from __future__ import unicode_literals
def read_sequence_data(
handle,
data_format,
ret_type='list',
key='accession', # accession gi description
alphabet=None
):
'''
Read sequence data from Entrez.efetch or file handle and return a list of
... | karolisr/krpy | krpy/krbioio.py | Python | gpl-3.0 | 7,513 | [
"Biopython"
] | 2b9a7f42770d194c5f4649f63d77be4b7c2d853477a4f33980e860a5c0136a98 |
########################################################################
# This example illustrates molecular transport of an oscillatory reaction
# system, along a closed-end cylinder. The concentrations along the entire
# length of the cylinder start out uniform. It shows an interesting
# combination of propagating... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex7.4_travelling_osc.py | Python | gpl-2.0 | 1,272 | [
"MOOSE"
] | b02b51b0a1dd30656d78a57371f04f9274194cd2fecb330989152a01b8f14de5 |
from django.conf.urls.defaults import *
# You'd want to change this to wherever your app lives
urlpatterns = patterns('pyfacebook.views',
# Some functionality - users can post text to their homepage
(r'^canvas/post/', 'post'),
# For the mock AJAX functionality
(r'^canvas/ajax/', 'ajax'),
# This i... | CollabQ/CollabQ | pyfacebook/urls.py | Python | apache-2.0 | 723 | [
"VisIt"
] | 86b2ff06e6cbc5896df638196e9e03d581379f4920cb143019a9dc0d33f00b05 |
from jinja2.compiler import CodeGenerator, Frame, EvalContext
from jinja2.parser import Parser
from jinja2 import nodes
import os
META = os.path.join(os.path.dirname(__file__), 'meta.js')
FILTER_ARGS = {
'attr': ('name',),
'batch': ('linecount', 'fill_with'),
'center': ('width',),
'default': ('default_value', 'boo... | djc/jasinja | jasinja/codegen.py | Python | bsd-3-clause | 12,466 | [
"VisIt"
] | 06a9a578b8932db05bb34724dafc6ea595daecd16549a25ed6f17faa5a31afa1 |
from pprint import pprint
import numpy as np
import pytest
from pysisyphus.cos.ChainOfStates import ChainOfStates
from pysisyphus.Geometry import Geometry
from pysisyphus.helpers import geom_loader
from pysisyphus.run import run_from_dict
from pysisyphus.testing import using
@using("pyscf")
def test_diels_alder_gro... | eljost/pysisyphus | tests/test_run/test_run.py | Python | gpl-3.0 | 4,676 | [
"PySCF"
] | e11feb5dfb0ee02224fe862df0f9e72f2e617448448c9a859cf64f47d9d3dcc1 |
################################################################################
# #
# Copyright (C) 2010-2017 The ESPResSo project #
# ... | KonradBreitsprecher/espresso | doc/tutorials/06-active_matter/SOLUTIONS/flow_field.py | Python | gpl-3.0 | 4,633 | [
"ESPResSo",
"VTK"
] | 257971bdfa31cc915b08f432db9c5a211307ddd37b2580ab9225b7c97ea71367 |
#! /usr/bin/env python
#
# conncomp.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (... | gewaltig/cython-neuron | topology/examples/conncomp.py | Python | gpl-2.0 | 4,197 | [
"NEURON"
] | d19b7c0030ff8eacefe0ca8318c20662fb5ff9a537fc51509332ae484e18fc26 |
import unittest
import pysal
import numpy as np
from scipy import sparse
from pysal.spreg import error_sp_het as HET
from pysal.common import RTOL
class TestBaseGMErrorHet(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("HOVAL")... | TaylorOshan/pysal | pysal/spreg/tests/test_error_sp_het_sparse.py | Python | bsd-3-clause | 19,869 | [
"COLUMBUS"
] | c63880103fc5bb260105398eaab8a07b107caabcf6aa6b981fb0382add89d6db |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor(... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/General/Testing/Python/splitVectors.py | Python | bsd-3-clause | 4,701 | [
"VTK"
] | 0bd8cc8687e4829010b2a32cd4462f633ea836cc5ef28107e2e6db2dfadf1c65 |
import paraBEM
from paraBEM.pan3d import doublet_3_0_vsaero, doublet_3_0_vsaero_v, doublet_3_0_sphere
from paraBEM.vtk_export import VtkWriter
import numpy
from paraBEM.utils import check_path
v1 = paraBEM.PanelVector3(-0.5, -0.5, 0)
v2 = paraBEM.PanelVector3(0.5, -0.5, 0)
v3 = paraBEM.PanelVector3(0.5, 0.5, 0)
v4 = p... | looooo/paraBEM | examples/vtk/vtk_panel_doublet.py | Python | gpl-3.0 | 1,009 | [
"VTK"
] | 8dc85773df5bad8bfe7b35aee51b58f8c2191c3e351cfaebb9f4566ede7eaf89 |
# Copyright 2017 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... | francoisluus/tensorboard-supervise | tensorboard/plugins/image/images_demo.py | Python | apache-2.0 | 11,511 | [
"Gaussian"
] | 3fbf81abac0c86c56398b033c3837f20a0a1a834db7a86b8138acee5a0df68c4 |
# The MIT License (MIT)
# Copyright (c) 2016-2017 Massachusetts Institute of Technology
#
# Authors: Victor Pankratius, Justin Li, Cody Rude
# This software has been created in projects supported by the US National
# Science Foundation and NASA (PI: Pankratius)
#
# Permission is hereby granted, free of charge, to any p... | skdaccess/skdaccess | skdaccess/geo/grace/mascon/cache/data_fetcher.py | Python | mit | 4,980 | [
"NetCDF"
] | 02c5a43a76115b64bb6fa973f97bd9fc2cea6de9e015e132b3b34e4fefdf26e6 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | smu/parser/smu_utils_lib.py | Python | apache-2.0 | 57,505 | [
"RDKit"
] | 113e2c478e694745f4314f427ac72eef5e63f79da0943994c13a0ff8b5d1ca94 |
# Copyright 2012, SIL International
# All rights reserved.
#
# This library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version 2.1 of License, or
# (at your option) any lat... | silnrsi/graide | lib/graide/makegdl/glyph.py | Python | lgpl-2.1 | 6,978 | [
"VisIt"
] | 9a71ed5fa62ac0f41664da00d0a092bf221bd0d0b0a3e9252a3445f1cee989fd |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
"""
Workflows for GW calculations:
VaspGWFWWorkFlow fireworks wf for vasp
SingleAbinitGWWorkFlow workflow for abinit
Under construction:
general GW workflow that should manage all the code independent logic
"""
__author__ = "Michie... | yanikou19/pymatgen | pymatgen/io/gwwrapper/GWworkflows.py | Python | mit | 15,024 | [
"ABINIT",
"VASP",
"pymatgen"
] | 04bb047be97f96995f92f74a6dc8852fd78b4f54171d886c7a236a8a49687c71 |
########################################################################
# $HeadURL $
# File: Request.py
# Date: 2012/07/16 13:43:45
########################################################################
"""
:mod: Request
.. module: Request
:synopsis: request implementation
request implementation
"""
# for proper... | fibbo/DIRAC | RequestManagementSystem/Client/Request.py | Python | gpl-3.0 | 15,135 | [
"DIRAC"
] | 86bf567c3c2544ab879a2e199248cb03519919324addd0378be877d11c2e27ce |
"""
CSB is a high-level, object-oriented library used to solve problems in the
field of Computational Structural Biology.
Introduction
============
The library is composed of a set of highly branched python packages
(namespaces). Some of the packages are meant to be directly used by
the clients (core library), while... | csb-toolbox/CSB | csb/__init__.py | Python | mit | 9,278 | [
"Gaussian"
] | 100c568aff72b01f88c5bd263f63da0caa8bd7b315992fa69424fc0daa7de52e |
# -*- coding: utf-8 -*-
''':class:`blade` filtering operations'''
from collections import namedtuple
from inspect import getmro, isclass
from itertools import chain, tee, groupby
from operator import attrgetter, itemgetter
from stuf.base import identity
from stuf.six.moves import filterfalse # @UnresolvedImport
from... | lcrees/blade | blade/xfilter.py | Python | bsd-3-clause | 10,691 | [
"MOE"
] | a838e1d95d034fc225f444d647548351ca2a83b0e30646e1ca9082e163d9307f |
'''
Created on Oct 25, 2012
@author: Shunping Huang
'''
from distutils.core import setup
import lapels.version
setup(
name = 'lapels',
version = lapels.version.__version__,
description = 'Lapels - A remapper and annotator of in silico (pseudo) genome alignments',
author = 'Shunping Huang',
author... | andrewparkermorgan/lapels | setup.py | Python | mit | 1,362 | [
"pysam"
] | ac76e4ec8fd70dd0f43938c037e9888795f8e241358655af1c2e3c234f663018 |
"""Tests for algorithms for partial fraction decomposition of rational
functions. """
from sympy.polys.partfrac import (
apart_undetermined_coeffs,
apart_full_decomposition,
apart,
apart_list_full_decomposition,
apart_list, assemble_partfrac_list
)
from sympy import (S, Poly, E, pi, I, Matrix, Eq,... | amitjamadagni/sympy | sympy/polys/tests/test_partfrac.py | Python | bsd-3-clause | 4,915 | [
"Gaussian"
] | edc452a5e834e1d758b71db12833fef9adf4e4db95f32a39cc8ee12435c72f92 |
import json
import pytest
import re
import yaml
# Functions
# ==============================================================================
# Common checks
def common_tests(data, result):
# General assert
assert result.exit_code == 0
assert result.exception is None
# Structure assert
assert_ro... | infOpen/cookiecutter-ansible-role | tests/test_run.py | Python | mit | 5,186 | [
"Galaxy"
] | d9a081cbf1482748350ab32503911665530d55d4b6f1c71fedccd8946e3fc638 |
#!/usr/bin/env python
"""Installer for geminicassandra: a lightweight db framework for disease and population genetics.
https://github.com/bgossele/geminicassandra
Handles installation of:
- Required third party software
- Required Python libraries
- Gemini application
- Associated data files
Requires: Python 2.7 (... | bgossele/geminicassandra | geminicassandra/scripts/gemini_install.py | Python | mit | 15,544 | [
"Galaxy",
"pysam"
] | fbf66f8002a0d131dfa35ba1cc737dac5c491d00d22cc4d5d4658a31542cb508 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2014 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | Freeseer/freeseer | src/freeseer/frontend/qtcommon/dpi_adapt_qtgui.py | Python | gpl-3.0 | 7,981 | [
"VisIt"
] | e951a089a47998f026f2f5870fc9b56c117169adfed891fe81caf0b9802379db |
# 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... | junghans/espressopp | src/integrator/LangevinThermostatHybrid.py | Python | gpl-3.0 | 3,383 | [
"ESPResSo"
] | 84609062452e23392a9bc1ffba9ed71cfcc2611fb5b178c9bf0bc549a7212a2d |
#!/usr/bin/env python
#-*- coding: utf-8 -*-
from viennagrid import Domain
from viennagrid import config
from viennagrid import io
import os
file_path = os.path.join(os.path.split(__file__)[0], '../data/half-trigate.mesh')
#################
# Netgen reader #
#################
# In case we want to read only the dom... | jonancm/viennagrid-python | doc/examples/viennagrid/io.py | Python | mit | 1,595 | [
"VTK"
] | b715e725e06214a57b363565e10122eff62b42633764bf6696895cc6aab1ced9 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
# Copyright 2011 Igalia, S.L.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your optio... | h4ck3rm1k3/orca-sonar | src/orca/input_event.py | Python | lgpl-2.1 | 17,556 | [
"ORCA"
] | 30788e17c44bced052b0f97914655e85692cc6492b11838b02fadd33b9f3537f |
from agui.backends.pyside.extras.about import About
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public ... | bhdouglass/agui | agui/backends/pyside/extras/__init__.py | Python | gpl-3.0 | 1,082 | [
"Brian"
] | 94634b5616609eacd5db8c04243cbe4838797bc2d9e2a1514b5307e876c9320e |
from ase import *
from ase.constraints import *
from ase.dft.bee import BEEF_Ensemble
from ase.io import read
from ase.optimize import QuasiNewton
from espresso import espresso
import cPickle as pickle
# read in trajectory file
# it can be the clean surface or
# with atoms adsorbed
atoms = read('surface.traj')
####... | chemeng444/chemeng444.github.io | ASE/Adsorption/opt.py | Python | gpl-2.0 | 3,151 | [
"ASE",
"ESPResSo",
"Quantum ESPRESSO"
] | 8e70b8a95f2f599760fb04248285e139503274f4a256a83c79964f6ddecf327b |
# The MIT License (MIT)
# Copyright (c) 2016, 2017 by the ESA CCI Toolbox development team and contributors
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including wi... | CCI-Tools/cate-core | cate/util/im/tilingscheme.py | Python | mit | 15,755 | [
"NetCDF"
] | d31c93d848c380d62537d863d223cdd716a4f31991cfc2dd0b6808eaf8412e8c |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# License: MIT License (See LICENSE.md)
# Copyright (c) 2013
"""
renumber the integers at the beginning of ever line in the file
to make sure these numbers are contiguous.
The file is read from sys.stdin.
This program does not parse an ... | jewettaij/moltemplate | moltemplate/renumber_DATA_first_column.py | Python | mit | 2,298 | [
"LAMMPS"
] | 520880fde956963a1932970b9ce58eb2193a23f43bae2b153066fd7db5e95170 |
from paraview.simple import *
from paraview import coprocessing
#--------------------------------------------------------------
# Code generated from cpstate.py to create the CoProcessor.
# ParaView 4.2.0-15-g46ac001 64 bits
# ----------------------- CoProcessor definition -----------------------
def CreateCoProce... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/CoProcessing/Adaptors/CamAdaptor/fv_coprocess.py | Python | gpl-3.0 | 4,575 | [
"ParaView"
] | bb1b4e4b842894734ed4ae813e59742288359e4504fe0d0d09ec2818701be1ae |
import numpy
from pyscf import lib
from pyscf.pbc import gto, df
import scipy.special
cell = gto.M(
atom = '''H 0 0 0;
H 0 -1 1
H 0 1 1
H 1 0 -1''',
basis = {'H': [[0, (2., .8), (1.5, .3)],
[0, (.625, 1)],
[1, ( .8, 1)],
[2, (1.2, 1)]
]},
dimension = 0,
a = nu... | sunqm/libcint | testsuite/test_f12_with_aft.py | Python | bsd-2-clause | 8,754 | [
"PySCF"
] | 147802f31ad6a4586059c6cb4aa22deb5ac3478825bb5765837862a0e17340b2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to represent all xas and stitching methods
"""
import math
import warnings
from typing import List
import numpy as np
from scipy.interpolate import interp1d
from pymatgen.analy... | gmatteo/pymatgen | pymatgen/analysis/xas/spectrum.py | Python | mit | 11,139 | [
"pymatgen"
] | 4bf0bfd8419dc87868d4a06b240e8c18fbc48dd5d2ba35b4cac79080c711c638 |
#! /usr/bin/env python
"""
Module containing functions for cubes frame registration.
"""
__author__ = 'Carlos Alberto Gomez Gonzalez, V. Christiaens, G. Ruane'
__all__ = ['frame_shift',
'cube_shift',
'frame_center_radon',
'frame_center_satspots',
'cube_recenter_satspots',
... | carlgogo/vip_exoplanets | vip_hci/preproc/recentering.py | Python | bsd-3-clause | 65,675 | [
"Gaussian"
] | 8b43ef2d36c14525eba82c3d1a23b5e4db808c4391dc67f435fd8085869a8bf8 |
# -*- coding: utf-8 -*-
import application
documentation = []
documentation.append(_(u"""Documentation for TWBlue - {0}""").format(application.version))
# Translators: This is the new line character, don't change it in the translations.
documentation.append(_(u"""
"""))
documentation.append(_(u"""## Table of contents""... | codeofdusk/ProjectMagenta | doc/strings.py | Python | gpl-2.0 | 41,853 | [
"Brian",
"VisIt"
] | 9cd655cae86bbf1a78ef10c98b89bb695768d6052d696b38e3b2778efc87e22b |
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | VisTrails/VisTrails | vistrails/packages/ImageMagick/init.py | Python | bsd-3-clause | 11,223 | [
"Gaussian"
] | 4f915343d9139f256b0a6df9535f3926d67fceb643c065538cd52a8ce45d0a23 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import math
import numpy as np
from pymatgen.core.periodic_table import Element
"""
Utilities for generating nicer plots.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Proj... | tschaume/pymatgen | pymatgen/util/plotting.py | Python | mit | 21,466 | [
"pymatgen"
] | e1d7b05e7c13fa0472b6c0ee1c44a5c4b6adf18a8d0ff504cacff4c7521d955e |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | soulmachine/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 25,165 | [
"Gaussian"
] | 3d5eb967a328331011f75641b068a9210d787ee76c1537796eb4ba83d06fdd1c |
import os
from upseto import manifest
from upseto import gitwrapper
import collections
Dependency = collections.namedtuple(
"Dependency", "requirement projectDir manifest parentOriginURL basename level")
class Traverse:
def __init__(self, baseDir=".."):
self._baseDir = baseDir
self._visitedO... | Stratoscale/upseto | upseto/traverse.py | Python | apache-2.0 | 1,828 | [
"VisIt"
] | a1bedadbdfa18415ec279a1eaf747fefb3e216e7d751271eaac7c45af48bac4f |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | cmelange/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 99,201 | [
"VisIt"
] | e556cba7d043a486cf806e59c0fffda525c8aae3c37d474bd753baecf9cf6392 |
##########################################################################
# This file is part of plom.
#
# plom 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
... | QCaudron/iterated-inference-pipeline | model_builder/Ccoder.py | Python | gpl-3.0 | 38,198 | [
"Gaussian"
] | 814cbd421af3ab3a59d79db432471fdd1088f73d6530304ced5a9e27dd05e69a |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkProjectedTerrainPath(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkProjectedTerrainPath.py | Python | bsd-3-clause | 516 | [
"VTK"
] | 780e909cce25221910bf3f0e70208d1513baa99669b08af744f62bb7ed71bfda |
from cosmos.lib.ezflow.tool import Tool, TaskFile
def _list2input(l, opt):
return opt + ("\n"+opt).join(map(lambda x: str(x), l))
cmd_init = r"""
set -e -o pipefail && tmpDir=$(mktemp -d --tmpdir={s[scratch]}) && export TMPDIR=$tmpDir;
printf "%s %s at %s\n" "{s[date]}" "$(hostname)" "$tmp... | LPM-HMS/GenomeKey | genomekey/tools/pipes.py | Python | mit | 15,799 | [
"BWA"
] | ea3477e116e174404bf6db0df6f6e35f18b926aca079984cecb91988453714e6 |
#
# Copyright (C) 2003-2005 Rational Discovery LLC
# All Rights Reserved
#
""" Defines the class SigTreeNode, used to represent trees that
use signatures (bit vectors) to represent data. As inputs (examples),
SigTreeNode's expect 3-sequences: (label,sig,act)
_SigTreeNode_ is derived from _DecTree.DecTreeNode_... | bp-kelley/rdkit | rdkit/ML/DecTree/SigTree.py | Python | bsd-3-clause | 1,772 | [
"RDKit"
] | 59f18eee05044de02e5d6adfdc570a14f73b9edd62a963752d80cbd1e0970978 |
import copy
import json
import threading
import time
from common.log import logUtils as log
from constants import dataTypes
from constants import matchModModes
from constants import matchScoringTypes
from constants import matchTeamTypes
from constants import matchTeams
from constants import serverPackets
from constan... | osuripple/pep.py | objects/match.py | Python | agpl-3.0 | 24,956 | [
"MOE"
] | fbf28c62e9bd34f4f34b0276e72deff82d84cdc5e35763304e04b715ad944df6 |
#!/usr/bin/env python3
#
# Argument Clinic
# Copyright 2012-2013 by Larry Hastings.
# Licensed to the PSF under a contributor agreement.
#
import abc
import ast
import atexit
import collections
import contextlib
import copy
import cpp
import functools
import hashlib
import inspect
import io
import itertools
import os
... | anbangleo/NlsdeWeb | Python-3.6.0/Tools/clinic/clinic.py | Python | mit | 152,205 | [
"VisIt"
] | 443db90ed2cc56cee48d0a90b0d72a2236314ee3e4e5a8c8452568a6c33e463f |
#! usr/bin/env python #
# -*- coding: utf-8 -*-
"""
Posical is a Python 3 module that models a generalized calendar reform with regularly-sized weeks and months and an intercalary period, based on August Comte's Positivist Calendar.
"""
import datetime,operator
from calendar import isleap as std_isleap
from nonzero i... | subsetpark/posical | posical.py | Python | bsd-2-clause | 20,175 | [
"COLUMBUS",
"Dalton"
] | 132dd5033e52bd4e62897b3ce177ad7137b43f8f3eb78a4f7d84adcfeaa3a5c5 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
This module defines plotting functions for the statistics of the dynamics.
"""
from __future__ import print_function
import os
import numpy as np
import collections
import logging
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib import ticker
... | LeBarbouze/tunacell | tunacell/plotting/dynamics.py | Python | mit | 34,918 | [
"Gaussian"
] | 8137102aac58b8cf0e68b4cb7dd82a496319aa92e3acedbe98c8b70a787e4de1 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | eljefe6a/incubator-beam | sdks/python/apache_beam/pipeline_test.py | Python | apache-2.0 | 18,194 | [
"VisIt"
] | e491d1909f5cff1efd84e52826b5b4a5375c3f5c08b6c17e693d2764e1d780e8 |
"""
MORE INFO AT: http://code.google.com/p/django-rest-interface/wiki/RestifyDjango
"""
from django.http import HttpResponse
from django.utils.translation import ugettext as _
import time, random
from hq.authentication import get_username_password, get_auth_dict
from hashlib import md5
def djangouser_auth(username, ... | icomms/wqmanager | apps/django_rest_interface/authentication.py | Python | bsd-3-clause | 8,478 | [
"Brian"
] | 629f832a25871505d0fd8fe78b0f84d552230dacad376e5e687f48e65733b9e6 |
""" Tests for ProxyProvider modules module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import sys
import pytest
from diraccfg import CFG
import DIRAC
from DIRAC.Core.Security.X509Chain import X509Chain # pylint: disable=import-error
from... | ic-hep/DIRAC | tests/Integration/Resources/ProxyProvider/Test_DIRACCAProxyProvider.py | Python | gpl-3.0 | 3,954 | [
"DIRAC"
] | e34762c9e89b1f31971f20e44b7c55de3bb2a7a50a2e2107548faaa14f17c02e |
#!/usr/bin/env python3
# Copyright (c) 2016 ghst659@github.com
# All rights reserved.
import queue
import sys
import threading
import unittest
import dag
class TestBase(unittest.TestCase):
def setUp(self):
self.dag = dag.Graph()
def tearDown(self):
del self.dag
class TestGraphNodes(TestBase):... | ghst659/topopy | tc/dag_test.py | Python | gpl-3.0 | 6,951 | [
"VisIt"
] | bb58deb4c054827e67c4b1de2c8b4f7e2f033a83101f857ac0c7eea8cf6d1de9 |
#pylint: disable=missing-docstring
#* 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/... | nuclear-wizard/moose | python/chigger/filters/TubeFilter.py | Python | lgpl-2.1 | 2,274 | [
"MOOSE",
"VTK"
] | 530a318f6f2da49499c678d16ce41106aa931b3afb013827457fbf91c42f061d |
#!/usr/bin/env python
import sys
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def Gather(c, arr, root):
vtkArr = vtk.vtkDoubleArray()
count = len(arr)
vtkArr.SetNumberOfTuples(count)
for i in range(count):
vtkArr.S... | hlzz/dotfiles | graphics/VTK-7.0.0/IO/MPIParallel/Testing/Python/Plot3DMPIIO.py | Python | bsd-3-clause | 1,867 | [
"VTK"
] | 4ef17194a6a8ecd5a13845206843cc40fb837113844ea6e00013918488342e2d |
#!/usr/bin/python
# Copyright 2017 Google Inc.
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['preview'],
... | hryamzik/ansible | lib/ansible/modules/cloud/google/gcp_healthcheck.py | Python | gpl-3.0 | 15,302 | [
"VisIt"
] | 177281d9b423665593b251f24d17c22950a323c84765291aa82a403c2ded12e6 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/metacity/__init__.py | Python | gpl-3.0 | 844 | [
"ORCA"
] | 3f4da953558a9ff8beb35f766bd970425eb16c4baa4be621d3e22036565f756a |
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from ase.visualize.fieldplotter import *
clean = True
plotlog = "fieldplotter.log"
atoms = FaceCenteredCubic(size=(50,50,5), symbol="Ag")
def xy(a=atoms):
r = atoms.get_positions()
return r[:,0] + r[:,1]
plotter = FieldPlotter(atoms, xy, ve... | auag92/n2dm | Asap-3.8.4/Test/FieldPlotter.py | Python | mit | 659 | [
"ASE"
] | c9d25f3a86014636b99fe57de4da294a90d73bf92eae25f621ff1c9c8a795cfc |
# Copyright 2007 by Tiago Antao. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
PopGen: Population Genetics and Genomics library in Python
"""
| Ambuj-UF/ConCat-1.0 | src/Utils/Bio/PopGen/__init__.py | Python | gpl-2.0 | 293 | [
"Biopython"
] | d26c851a0606a508aa1604d57448f4ac05404e638e2fd19c5f49e520bb26f155 |
import os
import re
import imp
from copy import deepcopy
import pyfits as pf
import pywcs
import numpy as np
from astrodata import AstroData
from astrodata.adutils import gemLog
from detSources import detSources
class DetectSources(object):
"""
Find x,y positions of all the objects in the input
i... | pyrrho314/recipesystem | trunk/devel/fluxcal/detectSources.py | Python | mpl-2.0 | 10,654 | [
"Gaussian"
] | 8ac5cf69f824fd57db84c752088fab6d73f9f52109c31652d6d5345c90719778 |
import numpy as np
from numba import i4
from pyiid.adp import has_adp
from pyiid.experiments.elasticscatter. \
kernels.cpu_flat import (get_d_array,
get_r_array,
get_normalization_array,
get_omega,
g... | CJ-Wright/pyIID | pyiid/experiments/elasticscatter/cpu_wrappers/flat_serial_cpu_wrap.py | Python | bsd-3-clause | 5,091 | [
"ASE"
] | 5ed6adafd22cdefd6789e98a67a65745140318af8cbc922bfae378f89b159aca |
print("""
FEM simulation using getfem++ and siconos.
""")
import siconos.kernel as kernel
import numpy as np
import getfem as gf
from matplotlib.pyplot import *
import math
class SiconosFem:
""" The set of matrices required by Siconos, from a Finite Element Model
"""
def __init__(self):
sel... | siconos/siconos-deb | examples/Mechanics/FEM/python/block_extrude.py | Python | apache-2.0 | 8,591 | [
"ParaView",
"VTK"
] | 23486c24d310c63c8017e1176600956ba71d13318d56bff13e5fbd74cad6a1c7 |
from itertools import chain
from optparse import make_option
from django.core import serializers
from django.core.management.base import BaseCommand, CommandError
from catmaid.control.tracing import check_tracing_setup
from catmaid.models import Class, ClassInstance, ClassInstanceClassInstance, \
Relation, Con... | AdaEne/CATMAID | django/applications/catmaid/management/commands/catmaid_export_data.py | Python | gpl-3.0 | 12,461 | [
"NEURON"
] | 107934f030d6e1e5f4d3a0b0e93bd31d9ea9faac36c93c473fe164b42df25fcb |
__author__ = 'tylin'
__version__ = '1.0.1'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that
# assists in loading, parsing and visualizing the annotations in COCO.
# Ple... | meppe/ros-ort | src/frcnn/src/lib/pycocotools/coco.py | Python | gpl-3.0 | 14,881 | [
"VisIt"
] | 48d30a569b5611c8670ce2d96f6075d305269b36442dec9b510c8299e3538170 |
import math
from pyvolution.EvolutionManager import *
from pyvolution.GeneLibrary import *
"""
This example attempts to find a solution to the following system of equations:
a + b + c + d - 17 = 0
a^2 + b^2 - 5 = 0
sin(a) + c - d - 20 = 0
"""
def fitnessFunction(chromosome):
"""
Given a "chromosome", this ... | littley/pyvolution | examples/EquationSolver_simple.py | Python | apache-2.0 | 2,566 | [
"Gaussian"
] | 54777a15ee032125b323c3047dbf00d26b7beea705197d36cde16b0ea78cdbb7 |
import random
import requests
from django.conf import settings
from django.contrib.auth.models import User
from django.db.models import Prefetch, Q
from django.utils.http import urlencode
from kitsune.dashboards import LAST_7_DAYS
from kitsune.dashboards.models import WikiDocumentVisits
from kitsune.wiki.models impor... | mozilla/kitsune | kitsune/wiki/utils.py | Python | bsd-3-clause | 5,618 | [
"VisIt"
] | 61a7fc05c9df1c1cf09cd65234e4161bd36d2262c9ee157c4687f638fa7244d1 |
# -*- coding: utf-8 -*-
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import abel
import os
import bz2
import matplotlib.pylab as plt
# This example demonstrates ``linbasex`` inverse Abel transform
# of a velocity-map image of photoel... | PyAbel/PyAbel | examples/example_linbasex.py | Python | mit | 3,486 | [
"Gaussian"
] | 2ede136e2a00b57eb532136778ad29c9c659cfd562890e3b01833f5f2b4fb32f |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-04-28 14:07:58
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-04-28 14:07:58 by Brian Cherinka
Last Modified On: 2016-04-28 14:07:58 by Brian
'''
from __future__ import print_function
from __future__... | albireox/marvin | python/marvin/web/controllers/plate.py | Python | bsd-3-clause | 2,933 | [
"Brian"
] | 6e18bd5fa57c5ad7719666b9adb34c394a590bd4d36aa5813d8d46c270d64fbc |
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