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import numpy as np
import math
import sys
sys.path.insert(0,'../..')
import os
import classifier_eval_simplified
from sklearn import tree
from sklearn.ensemble import AdaBoostClassifier
from sklearn.svm import SVC
for dim in range(2,11):
comp_file_list=[]
######################################################... | weissercn/MLTools | Dalitz_simplified/evaluation_of_optimised_classifiers/nn_gaussian_same_projection/nn_Gaussian_same_projection_evaluation_of_optimised_classifiers.py | Python | mit | 1,678 | [
"Gaussian"
] | bd7e7763f3be47116d380470a86cedb1cbacbf3dc17d974e4c0f9fccd058a1ba |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module provides classes for plotting Pourbaix objects.
"""
import six
from six.moves import map
from six.moves import zip
__author__ = "Sai Jayaraman"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "1.1"
__maintainer__... | Dioptas/pymatgen | pymatgen/analysis/pourbaix/plotter.py | Python | mit | 24,049 | [
"pymatgen"
] | 7a5d7c7e7f2b2ee304bdda3552e42ba6654b65ec73402d6c100d7ebc652013da |
"""
Module for gathering and managing information about MooseFS
"""
import salt.utils.path
def __virtual__():
"""
Only load if the mfs commands are installed
"""
if salt.utils.path.which("mfsgetgoal"):
return "moosefs"
return (
False,
"The moosefs execution module cannot b... | saltstack/salt | salt/modules/moosefs.py | Python | apache-2.0 | 3,966 | [
"MOOSE"
] | 385b7cbef1456f7260913861356275b292bce94e5d427e4876e983f7bc2f6a30 |
#! /usr/bin/env python
#
# Copyright (C) 2015-2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD
import pytest
from rdkit.Chem.rdDepictor import Compute2DCoords
import numpy as np
from . import example_mol #for m fixture
from ...core import Mol
from ...core.conformer import Conformer
@pytest.fixture(name='... | richlewis42/scikit-chem | skchem/test/test_core/test_conformer.py | Python | bsd-3-clause | 4,703 | [
"RDKit"
] | 428f542b4230bf2db282aab04304a0216984b661140e16cce39fb31f17ee9f20 |
"""Some common utils"""
# pylint: disable = C0301, C0103, C0111
import os
import pickle
import shutil
import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mnist_estimators
import celebA_estimators
from sklearn.linear_model import Lasso... | AshishBora/csgm | src/utils.py | Python | mit | 18,887 | [
"Gaussian"
] | 146ffdcbc4d0c47cf43d687af18d87c483ea8661ec22c616efe8c5a4797381f8 |
import numpy as np
import pytest
from sklearn.utils._testing import assert_allclose
from sklearn.neighbors import KernelDensity, KDTree, NearestNeighbors
from sklearn.neighbors._ball_tree import kernel_norm
from sklearn.pipeline import make_pipeline
from sklearn.datasets import make_blobs
from sklearn.model_selection... | manhhomienbienthuy/scikit-learn | sklearn/neighbors/tests/test_kde.py | Python | bsd-3-clause | 9,605 | [
"Gaussian"
] | a6f725be25e9a18af1120b02d3c8455587ccab34811a4ef2b4e3bec55c8dba26 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
Module for reading Lobster output files. For more information
on LOBSTER see www.cohp.de.
"""
import collections
import fnmatch
import os
import re
import warnings
from collections import defa... | mbkumar/pymatgen | pymatgen/io/lobster/outputs.py | Python | mit | 52,716 | [
"VASP",
"pymatgen"
] | b59f3180218cbfe285bccfa63570ad6d30c7ad5f335da1c47426f750a03d1aff |
#pylint: skip-file
from flask_testing import TestCase
import yawtext
from yawt import create_app
from yawt.utils import save_file, remove_file
from yawtext.facebook import post_fb
from yawtext.test import fake_facebook
access_token = """ACCESS_TOKEN
"""
class TestFacebook(TestCase):
YAWT_EXTENSIONS = ['yawtext.... | drivet/yawt | yawtext/test/test_facebook.py | Python | mit | 1,325 | [
"Desmond"
] | c43fe7561cabba57e0024bdfc7df76c769da6042b872d5087da9660fea3b7015 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a neutron diffraction (ND) pattern calculator.
"""
from math import sin, cos, asin, pi, degrees, radians
import os
import numpy as np
import json
from .core import DiffractionPatte... | gVallverdu/pymatgen | pymatgen/analysis/diffraction/neutron.py | Python | mit | 7,972 | [
"CRYSTAL",
"pymatgen"
] | 4365421ee764d26f17e04a0d40ebe030e1aff2f760453d05be97dc42bdf328c8 |
# 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... | tensorflow/tensorflow | tensorflow/python/autograph/converters/slices.py | Python | apache-2.0 | 2,745 | [
"VisIt"
] | b1ba43ec0c810b164c43cfb6ad53773d4083202b08cdce7aaef7a0a48c30ba25 |
#!/usr/bin/env python
"""Run and view a kMC model. For this to work one needs a
kmc_model.(so/pyd) and a kmc_settings.py in the import path."""
# Copyright 2009-2013 Max J. Hoffmann (mjhoffmann@gmail.com)
# This file is part of kmos.
#
# kmos is free software: you can redistribute it and/or modify
# it unde... | mieand/kmos | kmos/view.py | Python | gpl-3.0 | 16,192 | [
"ASE"
] | 4dc9178b1fb3b1fbd63e3bd21ba5d779492c6ae0d30eee2bbaf1e8df190408e1 |
import os, re
from copy import copy
from difflib import unified_diff
from ming.orm import ORMSession
from sprox.test.mg import model_relational
from sprox.test.mg.model_relational import *
from io import StringIO
from cgi import FieldStorage
try:
from ming import create_datastore
def create_ming_datastore():
... | gjhiggins/sprox | sprox/test/mg/base.py | Python | mit | 6,544 | [
"VisIt"
] | 5c229a6b396acb20a04694c3655911665f7c0b774df199dad43514691b875658 |
'''
Created on Nov 28, 2012
@author: sean
'''
from ast import NodeVisitor
import _ast
import sys
node_name = '0__node_name__'
not_py3 = sys.version_info.major < 3
class DictAst(NodeVisitor):
def generic_visit(self, node):
dct = {node_name: type(node).__name__}
for attr in node._attributes:
... | enthought/Meta | meta/asttools/serialize.py | Python | bsd-3-clause | 1,405 | [
"VisIt"
] | 633fa98d6c28ac416efdfe793f27d985395f9d32726f76da04ba7968f6a74775 |
from __future__ import division
from __future__ import absolute_import
import numpy as np
import pandas as pd
from rankit.Table import Table
from scipy.stats import norm
import math
import warnings
pdf = norm.pdf
cdf = norm.cdf
ppf = norm.ppf
PI = math.pi
class TimeSeriesRanker(object):
"""Base class for all time... | wattlebird/ranking | rankit/Ranker/TimeSeriesRanker.py | Python | mit | 26,806 | [
"VisIt"
] | 118d12caf2acd700367ecc74ff70195e83fd473d73fa048ba8660f663bf32966 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "' 취소 ' 자산 로그 항목을 표시합니다 발생하지 않았습니다．",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for the area.": "위치 이... | collective/eden | languages/ko.py | Python | mit | 244,195 | [
"VisIt"
] | dca705096627873e8ea2cbd946fa4788d7a27f9bf3bb07deda9ee75a8b3c3f6e |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El, time
n0 = 50
n1 = 50
display = False
worldRa... | justusc/Elemental | examples/interface/CP.py | Python | bsd-3-clause | 3,170 | [
"Gaussian"
] | ce33ca2e301a2f369c89b6cd6f275e3a8b5f12c774d9e57271ed8704472fe024 |
# 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 u... | Laurawly/tvm-1 | python/tvm/te/hybrid/parser.py | Python | apache-2.0 | 23,814 | [
"VisIt"
] | ff22cc284bbba28e118b36bcf828084e7c85044e6a1a40ec74034be45d324871 |
from ..utility import settings
import bpy
from bl_ui import (
properties_render,
properties_data_camera,
#properties_data_lamp,
#properties_material,
)
class PhotonRenderer(bpy.types.RenderEngine):
# These three members are used by blender to set up the
# RenderEngine; define its internal name, visible na... | TzuChieh/Photon-v2 | BlenderAddon/PhotonBlend/bmodule/renderer.py | Python | mit | 5,810 | [
"Gaussian"
] | 2213be7cf434ac6d493b0a2071c54dc188ad48a8db94128c51318717f7cfe319 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import datetime
import itertools
import logging
import os
import shutil
import sys
from collections import defaultdict
import configargparse
import six
from jinja2 import FileSystemLoader
from jinja2.environment import Environment
s... | compbiol/CAMSA | camsa/run_camsa.py | Python | mit | 23,351 | [
"Cytoscape"
] | a707322dbed0bc45126292dd2794b4ff53904ff407900c4a2bd0c369fee9f44d |
#!/usr/bin/env python
# Copyright (c) 1996-2002 Denis G. Pelli
# Copyright (c) 1996-9 David Brainard
# Copyright (c) 2004-7 Andrew D. Straw
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# ... | psychopy/versions | psychopy/contrib/quest.py | Python | gpl-3.0 | 19,574 | [
"Gaussian"
] | 8c46c8a59490d15a0960f54c5a631b491a844124158d1ac42bfd775aa5fb73a3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#Project Musica main definition module
import json
try:
from . import *
except:
pass
from __init__ import *
from MU_GUI import *
COMBO_TEXT = \
"""\
COMBO
{0}\
"""
def randomID(size=6, chars=string.ascii_uppercase + string.digits):
return ''.join(random.choice(chars) fo... | MU-Software/Project_Musica_for_Contest | client/software/resources/modules/MU_Musica.py | Python | mit | 21,392 | [
"Galaxy"
] | 435d22746f253b5b1cf2ee1c888f4805badc9a4f362ce162a021a83ac558be03 |
# Taken from https://raw.githubusercontent.com/lennax/biopython/f_loc5/Bio/SeqUtils/Mapper/CoordinateMapper.py
# AUTHOR: Reece Hart <reecehart@gmail.com>
# Modifications copyright 2012 Lenna X. Peterson <arklenna@gmail.com>
# This code is part of the Biopython distribution and governed by its
# license. Please see ... | kantale/MutationInfo | biopython_mapper/CoordinateMapper.py | Python | mit | 12,744 | [
"BioPerl",
"Biopython"
] | 90f5aedc5b4a9afd9cd18a27f79ed7592484109c0951c092d4a0ce72ac88ad7c |
#!/usr/bin/env python
# -*- coding=utf-8 -*-
"""
Slater Module
-------------
This module implement several classes in order to deal with atomic orbital,
electronic configuration and compute atomic orbital energies using the slater's
rule.
Important note: In the following, electronic sub-shell such as 2s, 3d ... are
... | gVallverdu/Slater | slater.py | Python | gpl-2.0 | 12,723 | [
"pymatgen"
] | d93b014ae76dc93760151c429d50b8b854870f6dfaf5f6ab4aaed9825114a472 |
# (c) 2013-2016, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.com>
# Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under t... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/plugins/action/assemble.py | Python | bsd-3-clause | 6,243 | [
"Brian"
] | 9cd519caa202b52116aa7ab43cc898aa2f97836408056ab3c86eef2a174480d9 |
# $HeadURL$
""":mod:`Pfn`
.. module: Pfn
:synopsis: pfn URI (un)parsing
.. moduleauthor:: Krzysztof.Ciba@NOSPAMgmail.com
"""
__RCSID__ = "$Id$"
## imports
import os
import re
## from DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
def pfnunparse( pfnDict ):
""" create pfn URI from pfnDict
:param ... | avedaee/DIRAC | Core/Utilities/Pfn.py | Python | gpl-3.0 | 4,103 | [
"DIRAC"
] | 75a1d55b5d0de2e1a2191111cd5bff62d5236575cfd2bf028c44536dd9df7663 |
#!/usr/bin/env python
# ===============================================================
# date : 30 novembre 2016
# author : fmv
# decription : convert POSCAR (vasp) to POSFF (mdff)
# ===============================================================
import datetime
import argparse
from config import Config
fr... | FilipeVasconcelos/mdff | bin/cartoff.py | Python | gpl-2.0 | 1,230 | [
"VASP"
] | 4be8aa4f91ff260fbd5d0e0a47bf21fec71be3234ec8a83683b3a66c94b3aea0 |
# -*- coding: utf-8
# pylint: disable=line-too-long
"""
Low-level db operations.
"""
import os
import time
import math
import numpy
import pandas as pd
import sqlite3
import warnings
import anvio
import anvio.tables as tables
import anvio.terminal as terminal
import anvio.filesnpaths as filesnpaths
from anvio.er... | meren/anvio | anvio/db.py | Python | gpl-3.0 | 42,573 | [
"GULP"
] | bfa2c3af67e693d2cb7fe7f6492dda46b4d030f1fa2210a30a4a5201ff9b9421 |
# Copyright 2002 Gary Strangman. All rights reserved
# Copyright 2002-2016 The SciPy Developers
#
# The original code from Gary Strangman was heavily adapted for
# use in SciPy by Travis Oliphant. The original code came with the
# following disclaimer:
#
# This software is provided "as-is". There are no expressed or... | anntzer/scipy | scipy/stats/_stats_py.py | Python | bsd-3-clause | 315,337 | [
"DIRAC"
] | 2b3fa9f1053783e2e5ec7152ada7e10d5923d3dcca7a3ac2b85c9c1eb6362f2e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | evangelistalab/forte | forte/proc/fcidump.py | Python | lgpl-3.0 | 15,649 | [
"Molpro",
"Psi4"
] | 6532325744505f7cd9aa0adff6bdc275fb3e303f8cc82e8e464f8ab411805c8a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A reproduction of Figure 5.6 from Rasmussen & Williams (2006).
http://www.gaussianprocess.org/gpml/
"""
from __future__ import division, print_function
import sys
import time
import emcee
import numpy as np
import cPickle as pickle
import statsmodels.api as sm
import... | jbernhard/george | docs/_code/hyper_sample.py | Python | mit | 1,964 | [
"Gaussian"
] | 9a92fcc85e88fa14b0c565a0c35ea6c197959212d6dddbc04d32ff083dde48fd |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | marscher/PyEMMA | pyemma/coordinates/data/featurization/util.py | Python | lgpl-3.0 | 10,654 | [
"MDTraj"
] | 2c7e6003d8f57f2bba765c4c3bf4294b8c9427fdc206ef79e688c4214ffb4323 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/mass-and-rinertia_per_particle.py | Python | gpl-3.0 | 22,973 | [
"ESPResSo"
] | bf3f0249347a49179d83e88a5b6e5abd42c05fabc077bd2a9fc2a874950c5243 |
import os
import sys
import pandas as pd
from pyspark.sql.types import *
from pyspark.sql import Row, Column
from pyspark.sql.functions import *
from datetime import datetime
from pyspark import SparkConf, SparkContext
from pyspark.sql import SQLContext
from pyspark.sql.functions import udf
import numpy as np
import ma... | RBDA-F17/crime | src/Tables_for_Questions.py | Python | gpl-3.0 | 8,639 | [
"Gaussian"
] | 08071582c6ca83c202a3aade1b86cf6704bf5a6cc52853001c38366f6d455fc5 |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2019 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | dursobr/Pythics | pythics/lib.py | Python | gpl-3.0 | 11,508 | [
"Brian"
] | ffb36c1dec0d3b88e7b6b5ed59e00d28ec685e8566df77a408201bba8a3c8b92 |
"""This demo program solves an elastodynamics problem."""
# Copyright (C) 2010 Garth N. Wells
#
# This file is part of DOLFIN.
#
# DOLFIN 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 ... | alogg/dolfin | demo/undocumented/elastodynamics/python/demo_elastodynamics.py | Python | gpl-3.0 | 4,789 | [
"VTK"
] | bd7c4ba41e3ce5fb47a9b67fc06e5e464449c66ba2a19bf8667f3d39c734f46d |
# -*- coding: utf-8 -*-
from __future__ import print_function
import pandas as pd
import os
import argparse
import sys
import numpy as np
from copy import copy
from bokeh.io import curdoc
from bokeh.layouts import layout,column,row
from bokeh.models.layouts import Row,Column
from bokeh.models import (
ColumnDataSou... | sandipde/Interactive-Sketchmap-Visualizer | app-base/main.py | Python | mit | 20,904 | [
"Jmol"
] | 9612a69a423b631663cb5765d8dda5052ae9e4b99f35f5cb69ed1d79b8920c7a |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://ww... | echohenry2006/tvb-library | tvb/simulator/demos/surface_deterministic_stimulus.py | Python | gpl-2.0 | 5,675 | [
"Gaussian",
"Mayavi"
] | 61060acd76d1e24923b196583c1602a2f057ad427a9b4ffba6a8e153ab2975b0 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-dialogflow | tests/unit/gapic/dialogflow_v2/test_contexts.py | Python | apache-2.0 | 98,853 | [
"Octopus"
] | 492dc9e6c4c0f31da57182ace314375586f8afce82fdc9403a93df8932696ab3 |
import os
from warnings import warn
import datajoint as dj
import numpy as np
import sh
from pipeline.notify import temporary_image
import gc
from .. import experiment
from ..utils.signal import mirrconv
from ..utils import galvo_corrections
import matplotlib.pyplot as plt
from ..import notify
from distutils.version ... | cajal/pipeline | python/pipeline/legacy/preprocess.py | Python | lgpl-3.0 | 67,438 | [
"Gaussian",
"NEURON"
] | 372554685cd5cad69e18b827a8438512e165332b96fe59cec1f53a853fed1fb9 |
""" This is a test of the chain
DataStoreClient -> DataStoreHandler -> AccountingDB
It supposes that the DB is present, and that the service is running
this is pytest!
"""
# pylint: disable=invalid-name,wrong-import-position
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DI... | arrabito/DIRAC | tests/Integration/AccountingSystem/Test_DataStoreClient.py | Python | gpl-3.0 | 1,546 | [
"DIRAC"
] | 61fb2609f31c29e94658016117b2686f7c9b57b429055a8a9d353c66d93b28c4 |
from build.management.commands.base_build import Command as BaseBuild
from django.db.models import Q
from django.conf import settings
from protein.models import Protein, ProteinConformation, ProteinAnomaly, ProteinState, ProteinSegment
from residue.models import Residue
from residue.functions import dgn, ggn
from stru... | cmunk/protwis | structure/management/commands/structure_anomaly_recognition.py | Python | apache-2.0 | 6,977 | [
"CRYSTAL"
] | ead29ab061eaf0ace0c9750f5570b3dc0009b30d3ffa6ae1f11ea643c1b76d74 |
import os.path
from pulsar.client import PathMapper
from pulsar.client.action_mapper import path_type
from .test_utils import TempDirectoryTestCase
from galaxy.util.bunch import Bunch
class PathMapperTestCase(TempDirectoryTestCase):
def test_input(self):
local_path = os.path.join(os.path.dirname(self.t... | natefoo/pulsar | test/path_mapper_test.py | Python | apache-2.0 | 3,549 | [
"Galaxy"
] | ee8d3be2144eb61e6cc31a220b4a925ceb2f9c79f9db7022ed1fee8327bac809 |
########################################################################
# File : LocalComputingElement.py
# Author : Ricardo Graciani, A.T.
########################################################################
""" LocalComputingElement is a class to handle non-grid computing clusters
"""
from __future__ import a... | yujikato/DIRAC | src/DIRAC/Resources/Computing/LocalComputingElement.py | Python | gpl-3.0 | 11,400 | [
"DIRAC"
] | 1cbdc9d72737cedb9aa58014c4a5e9267157248b1a3b0dc0d1d8d28eb48a302d |
""" DIRAC FileCatalog plugin class to manage file metadata
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.Time import queryTime
from DIRAC.Core.Utilities.List impor... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/FileMetadata/FileMetadata.py | Python | gpl-3.0 | 24,516 | [
"DIRAC"
] | 8bff548dfe9c6337cbe78a261b8aefbb4fb92914d1349e273e57828046097290 |
""" SingularityCE is a type of "inner" CEs
(meaning it's used by a jobAgent inside a pilot).
A computing element class using singularity containers,
where Singularity is supposed to be found on the WN.
The goal of this CE is to start the job in the container set by
the "ContainerRoot" config option... | yujikato/DIRAC | src/DIRAC/Resources/Computing/SingularityComputingElement.py | Python | gpl-3.0 | 18,193 | [
"DIRAC"
] | ac83026ada241f677b8b5d43c5fad9c95f2b908656c98cb0919d852df2f9ab51 |
__author__ = 'Mike McCann'
__copyright__ = '2012'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
STOQS Query manager for building ajax responses to selections made for QueryUI
@undocumented: __doc__ parser
@status: production
@license: GPL
'''
from collections import defaultdict, Ma... | duane-edgington/stoqs | stoqs/utils/STOQSQManager.py | Python | gpl-3.0 | 136,384 | [
"NetCDF"
] | b31a425d9ed88ef294113052550b927e9ab38b8d1cd3e74bbde285d893be2d77 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
import gyn.common
import gyn.simple_copy
import multiprocessing
import os.path
import re
import shlex
import signal
import s... | saghul/gyn | gyn/input.py | Python | bsd-3-clause | 112,705 | [
"VisIt"
] | a17874b074b57a6430efec75488ca0c836dcfd35eb2ab7cd0241541c5a31a965 |
"""
Use Mayavi to visualize the structure of a VolumeGrid
"""
from enthought.mayavi import mlab
import numpy as np
from enthought.tvtk.api import tvtk
dims = (4, 4, 4)
x, y, z = np.mgrid[0.:dims[0], 0:dims[1], 0:dims[2]]
x = np.reshape(x.T, (-1,))
y = np.reshape(y.T, (-1,))
z = np.reshape(z.T, (-1,))
y += 0.3*np.sin... | yarikoptic/NiPy-OLD | doc/neurospin/datasets/viz_volume_grid.py | Python | bsd-3-clause | 900 | [
"Mayavi"
] | e5e7df1a214f39cc691ca7faaed0e82440417b1ff4c1e228c3b8db455c6995b8 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/eph/test/test_uks.py | Python | apache-2.0 | 2,131 | [
"PySCF"
] | c1a93d7867fea63a9c7834ca3423d2332fbdfdb1bcfa412cb48c185445365763 |
# -*- coding: utf-8 -*-
# @author: Mike Reinhardt
# @email: mreinhardt@gmail.com
# @license: BSD
"""Convert emoji aliases to unicode emoji.
Primarily intended to support Slack chat over IRC or XMPP. Contains many extra
aliases found in other programs as well.
See http://www.emoji-cheat-sheet.com/ for supported sit... | qguv/config | weechat/plugins/python/emoji_aliases.py | Python | gpl-3.0 | 57,565 | [
"FLEUR",
"Octopus"
] | b3ba12c1b28eac13d5380d7dbdaf2280246911865026cf6771bf66d24827bd00 |
from flask import Flask, render_template, session, request, redirect
import random #added import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
... | jiobert/python | Smith_Ben/Assignments/flaskolympics/olympics6/server.py | Python | mit | 697 | [
"CASINO"
] | 96f6b53b8bafd827ec4625d315adb9c0bd19a6a4c0c54cefdd1cca08788c13d3 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# u... | jtulach/mx | mx_urlrewrites.py | Python | gpl-2.0 | 5,473 | [
"VisIt"
] | 6dd758b2bd02ce5c4a64f23dc88e2925ac85453f639e0d87faba2f007de4ad5e |
from DIRAC import S_OK
from DIRAC.Core.Utilities import DEncode
from DIRAC.WorkloadManagementSystem.Client.JobState.CachedJobState import CachedJobState
from DIRAC.WorkloadManagementSystem.Client.JobState.JobManifest import JobManifest
class OptimizationTask( object ):
def __init__( self, jid ):
if isinstance( ... | avedaee/DIRAC | WorkloadManagementSystem/Client/JobState/OptimizationTask.py | Python | gpl-3.0 | 1,474 | [
"DIRAC"
] | 955259d2269f1c50bb72043587c784f41ceffcfc56d1f5d7283a6f40575e9812 |
#! /bin/usr/env python
# D.J. Bennett
# 24/03/2014
"""
pglt download tools
"""
# PACKAGES
import os
import re
import random
import entrez_tools as etools
import alignment_tools as atools
from special_tools import getThreads
from Bio.SeqFeature import SeqFeature
# CLASSES
class Downloader(object):
"""Download seq... | DomBennett/pG-lt | pglt/tools/download_tools.py | Python | gpl-2.0 | 14,873 | [
"BLAST"
] | 0ce89416682fb4a811857ce07bfc61bcf6c8b916931063dfd742304b93fb3322 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
# Generated automatically. To regenerate:
# ./bin/generate-tlds > yelp_uri/tlds/all.py
all_tlds = '|'.join((
'aaa',
'aarp',
'abarth',
'abb',
'abbott',
'abbvie',
'abc',
'able',
'abogado',
'abudhabi',
'ac',
... | Yelp/yelp_uri | yelp_uri/tlds/all.py | Python | unlicense | 22,808 | [
"CASINO",
"Jaguar",
"MOE"
] | 0622d08fd9773ea0de02a9d0869599bb7c6f9f22a1c116c05cff478691370687 |
''' this is the module for the hamiltonian '''
import numpy as np
import os
import pickle
import datetime
from quantumpropagator import (printDict, printDictKeys, loadInputYAML, bring_input_to_AU,
warning, labTranformA, gaussian2, makeJustAnother2DgraphComplex,
fromHartreetoCmMin1, makeJustAnother2Dg... | acuzzio/GridQuantumPropagator | src/quantumpropagator/TDPropagator.py | Python | gpl-3.0 | 30,840 | [
"Gaussian"
] | 21b0d899d01b0703d3e162a22301ce99598d6e9f5f977e7bbc0193644a8ec169 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
# ---------------------------------------------------------------------------
# ___ __ ___ ___ ____ ____ __
# | \ | \ | | / | | | \ Automatic
# |__/ |__/ | | | |__ |__ | | Conference
# | |\... | brigittebigi/proceed | proceed/src/wxgui/manager.py | Python | gpl-3.0 | 23,631 | [
"VisIt"
] | e3ae4f2490c96ca747267f6bf681326edd056fd18ba052bf0398a00879c8f28f |
# Game: Use cowboys to have a good time and play some music on a Piano, while brawling with enemy Cowboys.
# DO NOT MODIFY THIS FILE
# Never try to directly create an instance of this class, or modify its member variables.
# Instead, you should only be reading its variables and calling its functions.
from typing impo... | siggame/Joueur.py | games/saloon/game.py | Python | mit | 7,430 | [
"SIESTA"
] | 07a5b8888a79210100552645433ce55417b2660c93a59c077c2a6c15460f183a |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Provides the infrastructure to support the common metadata API.
"""
from abc import ABCMeta
from collections import name... | rcomer/iris | lib/iris/common/metadata.py | Python | lgpl-3.0 | 53,849 | [
"NetCDF"
] | 0c22d01e8b1e640d61aae61848f0a9f920f351a8fd798b90aac10145b48f0552 |
# -*- coding: utf-8 -*-
"""
This file contains the Qudi logic which controls all pulsed measurements.
Qudi 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 ... | tobiasgehring/qudi | logic/pulsed_measurement_logic.py | Python | gpl-3.0 | 58,081 | [
"Gaussian"
] | f222cd809c338c547805b5ae21eb0df7bd304e2d350d20f86c1f13538a5b5fb5 |
#!/usr/bin/env python3
# coding=utf-8
"""
GPS3 (gps3.py) is a Python 2.7-3.5 GPSD interface (http://www.catb.org/gpsd)
Default host='127.0.0.1', port=2947, gpsd_protocol='json' in two classes.
1) 'GPSDSocket' creates a GPSD socket connection & request/retrieve GPSD output.
2) 'DataStream' Streamed gpsd JSON data liter... | wadda/gps3 | gps3/gps3.py | Python | mit | 9,199 | [
"MOE"
] | 1b8e91da47de6fdf458ce3702ad711c69003ad67cbacfdaa454d746e21b3f3a2 |
#
# tsne.py
#
# Implementation of t-SNE in Python. The implementation was tested on Python 2.5.1, and it requires a working
# installation of NumPy. The implementation comes with an example on the MNIST dataset. In order to plot the
# results of this example, a working installation of matplotlib is required.
# The ... | poldrack/openfmri | openfmri_paper/tsne.py | Python | bsd-2-clause | 5,245 | [
"Gaussian"
] | c3cc4dd611a643394a424b8891b4c79a88650fdbddbabf4c0baab5dfd2e603a3 |
"""\
MINDO3.py: Dewar's MINDO/3 Semiempirical Method
This program is part of the PyQuante quantum chemistry program suite.
Copyright (c) 2004, Richard P. Muller. All Rights Reserved.
PyQuante version 1.2 and later is covered by the modified BSD
license. Please see the file LICENSE that is part of this
distrib... | certik/pyquante | PyQuante/MINDO3.py | Python | bsd-3-clause | 28,067 | [
"MOPAC"
] | cc164ae21be08c9f935a712577e17493df0c941c5156819518650eefb945e417 |
global astrom
global tmpdir
import traceback, tempfile
tmpdir = '/tmp/pkelly/'
astrom='solve-field'
def length_swarp(SUPA,FLAT_TYPE,CHIPS):
import os, re, utilities, bashreader, sys, string
from copy import copy
from glob import glob
dict = get_files(SUPA,FLAT_TYPE)
search_params = initialize(dict... | deapplegate/wtgpipeline | non_essentials/calc_test/calc_tmpsave_from_pat_dir.py | Python | mit | 212,139 | [
"Galaxy"
] | b4545e6abc11a475c5f6595dfc2b210836288f50ae3364d956f669a2dd657855 |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/cc/rintermediates.py | Python | apache-2.0 | 12,070 | [
"PySCF"
] | 3d4631d034b094675fe6aeb147b2839e8b68a6cd91db64707b97a3291f3ff7dd |
# compartment_net_no_array.py ---
#
# Filename: compartment_net_no_array.py
# Description:
# Author:Subhasis Ray
# Maintainer:
# Created: Sat Aug 11 14:30:21 2012 (+0530)
# Version:
# Last-Updated: Tue May 7 18:26:26 2013 (+0530)
# By: subha
# Update #: 974
# URL:
# Keywords:
# Compatibility:
#
#
# Comm... | BhallaLab/moose | moose-examples/snippets/compartment_net_no_array.py | Python | gpl-3.0 | 15,353 | [
"MOOSE"
] | e334c717ba3587dcc22ccc6cefeccfef48264c28b05208be1ce37719fdc48008 |
#
# Copyright 2001 - 2016 Ludek Smid [http://www.ospace.net/]
#
# This file is part of Outer Space.
#
# Outer Space 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
# (... | dahaic/outerspace | client/osci/dialog/EmpireOverviewDlg.py | Python | gpl-2.0 | 12,429 | [
"Galaxy"
] | 515f4a0ecfe69bcb1deff25d61b833e836884197752dc699fe03ab29a35fe9b0 |
#!/usr/bin/env python
import os
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# NOTE: This test only works if the current directory is writable
#
try:
filename = "plyWriter.ply"
channel = open(filename, "wb")
channel.close()
... | hlzz/dotfiles | graphics/VTK-7.0.0/IO/PLY/Testing/Python/TestPLYReadWrite.py | Python | bsd-3-clause | 3,362 | [
"VTK"
] | 59ca7d5f20cc3890fb45da78fb0ab40d2870cc5e92fccd067c00f3096c5bb69e |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-kegggraph/package.py | Python | lgpl-2.1 | 2,027 | [
"Bioconductor"
] | 430494f5de0d6b75dfd067e071210f4a77815f660a9a26a8d937af18a2c637cb |
"""
Acceptance tests for Studio related to the asset index page.
"""
from ...pages.studio.asset_index import AssetIndexPage
from .base_studio_test import StudioCourseTest
from ...fixtures.base import StudioApiLoginError
from ..helpers import skip_if_browser
class AssetIndexTest(StudioCourseTest):
"""
Tests ... | analyseuc3m/ANALYSE-v1 | common/test/acceptance/tests/studio/test_studio_asset.py | Python | agpl-3.0 | 1,804 | [
"VisIt"
] | b71637876543a78ff2110b06cbd0d8efe9f402cc700af1effbb0bbddb59da795 |
# 2012 L. Amber Wilcox-O'Hearn
# real_word_vocabulary_extractor.py
import codecs, unicodedata
class RealWordVocabExtractor():
def __init__(self, vocabfile_obj, outfile_obj):
self.unicode_vocabfile_obj = codecs.getreader('utf-8')(vocabfile_obj)
self.unicode_outfile_obj = codecs.getwriter('utf-8')(... | ambimorph/malaprop | malaprop/error_insertion/real_word_vocabulary_extractor.py | Python | agpl-3.0 | 1,901 | [
"Amber"
] | 7215951d81e1b9fbc51d16743b6a8d52b1ec22d92337ce11ca520eee29ab7bfa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import os
import json
from pymatgen import Spin, Orbital
from pymatgen.electronic_structure.dos import CompleteDos
test_dir = os.path.join(os.path.dirn... | migueldiascosta/pymatgen | pymatgen/electronic_structure/tests/test_dos.py | Python | mit | 5,385 | [
"pymatgen"
] | 26496ab9e22f27aeafb14b2337abd238c31b64516b8f9b82530df96a792bc11c |
# -*- coding: utf-8 -*-
# TO DO: update for non-CGAT work
# test documentation build configuration file, created by
# sphinx-quickstart on Fri Feb 7 11:33:27 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in ... | AntonioJBT/genotype_tools | genotype_QC/pipeline_genotype_QC/conf.py | Python | gpl-3.0 | 13,257 | [
"pysam"
] | c604c8cf7a3fc3c4c8dca39f434d2f27c35c84d357bfdf3db8d03eef1d118976 |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/result/visitor.py | Python | mit | 3,246 | [
"VisIt"
] | fdb5df83eaca03a836aa14b52d843394a819b3254685abdf467334d01fc3a644 |
import pytest
from tests.utils import async
import io
import json
import aiohttpretty
from waterbutler.core import streams
from waterbutler.core import exceptions
from waterbutler.providers.figshare import metadata
from waterbutler.providers.figshare import provider
@pytest.fixture
def auth():
return {
... | cosenal/waterbutler | tests/providers/figshare/test_provider.py | Python | apache-2.0 | 17,418 | [
"Brian"
] | baff708871b7da15e64dc413249c44ff12690f3535a6b608175d1de0b8b610cb |
from . import gng2
from pygraph.classes.graph import graph
from pygraph.algorithms.minmax import cut_tree
from pygraph.algorithms.accessibility import connected_components
from .utils import __dict_reverse as dict_reverse
import itertools
import time
from numpy import array,sum,sqrt
class data_block:
"""This is th... | sbxzy/pygks | pygks/ui_gng.py | Python | bsd-3-clause | 8,630 | [
"NEURON"
] | 0dde968e4165e37a244bc8b1dca893fbf84ea17e2edd91393dc36d596fa37766 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Module: utilities
=================
"""
from __future__ import print_function
from timeit import default_timer as timer
from itertools import product
import numpy as np
from sys impor... | Marcello-Sega/pytim | pytim/utilities.py | Python | gpl-3.0 | 9,147 | [
"MDAnalysis"
] | e4a8561399791a6af595aeaa0beeb147e0f538206f2c1f20e2d20788df5e3d21 |
import os
import re
import subprocess
import numpy as np
import numbers
from ..codes import CodeRun
from pychemia.crystal import KPoints
from pychemia import Structure, pcm_log
from pychemia.utils.serializer import generic_serializer
class DFTBplus(CodeRun):
def __init__(self, workdir='.'):
if not os.pat... | MaterialsDiscovery/PyChemia | pychemia/code/dftb/dftb.py | Python | mit | 22,893 | [
"CRYSTAL"
] | 4394bbfab7022024811c144c0d6c97db6c5fa95903cdcb73a2860f0a06676dab |
# -*- coding: utf-8 -*-
#
# hl_api_connections.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Lice... | terhorstd/nest-simulator | pynest/nest/lib/hl_api_connections.py | Python | gpl-2.0 | 21,938 | [
"NEURON"
] | 2856cee7ce31028dd66d963841010e91355dc636b3fc874833d8e3b43d8aafb0 |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | ppanczyk/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 31,915 | [
"Galaxy"
] | 8d5f857b29159fe0aa37bd52bf2fe0dde0cfd8c955201e37f5f4855319518a44 |
#!/usr/bin/python
###############################################################################
#
# This script extracts RMSD fluctuations from chain sliding data and computes
# it on a per trajectory basis as well as over the complete dataset.
#
# Example: For 2+12-column data like (with reduced decimals for example... | cing/ChannelAnalysis | ChannelAnalysis/PoreAnalysis/Statistics.py | Python | mit | 6,199 | [
"MDAnalysis"
] | 0ad1ae660c5f501ffc9c153fbb12b06af6ba73ef1c18476ecc03016ceed174ef |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import urllib
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.core.mail import send_mail
from django.core.urlresolv... | waheedahmed/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 60,419 | [
"VisIt"
] | 878066fcc92686e9f8210dde9e34b931c9fe3e4ea6572cfc3dafa0b44cebaa41 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | jtyr/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 64,084 | [
"VisIt"
] | c6e5ffee2dc1fa19e131f9dc71893c994b7b65139bb6fef27848d7680ca223e7 |
"""
Calculate stresses over a rectangular geographic region on a regular
lat-lon-time grid.
L{gridcalc} allows you to specify a grid of times and locations (using a
L{Grid} object) at which to perform stress calculations using the L{satstress}
module. A L{GridCalc} object is created from a L{StressCalc} object and a
... | zaneselvans/satstress | satstress/gridcalc.py | Python | gpl-3.0 | 25,016 | [
"NetCDF"
] | 7d067088402957f6519d11a36c14e26526bbc9046d9558ad33e707ae224ce269 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alxgu/ansible | lib/ansible/modules/network/avi/avi_seproperties.py | Python | gpl-3.0 | 3,664 | [
"VisIt"
] | 054a910af961ee20633c9fe94724ddbcf38d0793bcf09512d4f52ba978e49bfd |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
##########... | rimbalinux/MSISDNArea | django/conf/global_settings.py | Python | bsd-3-clause | 21,619 | [
"VisIt"
] | 3c2fa252269b46e20d1af5cc3b00abce2019895b328a5c8d3aed5e201bac67c9 |
from __future__ import print_function, division, unicode_literals
import os
import operator
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
from math import sqrt
from scipy.spatial import Delaunay, ConvexHull
from pymatgen.core.composition import Composition
from pymatgen... | henniggroup/MPInterfaces | mpinterfaces/mat2d/intercalation/analysis.py | Python | mit | 22,981 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | d556b398d5e4d9e339c14eaeeecbb74907f5f2bcd7ccc1aaf731cabc0e7a33be |
# Copyright (c) 2015-2016 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | cimarron-pistoncloud/molecule | test/unit/conftest.py | Python | mit | 12,897 | [
"Galaxy"
] | 5c8f37ba7494dcb3e0f63f46dd152e6824136c25069783b13a3a8d183694854b |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: HSC Weak Lensing collaboration
"""
import os
import sys
import math
import numpy as np
import pyfits
import matplotlib.pyplot as plt
import healpy as hp
def removeDuplicatedVisits(d):
# Remove visits with the same pntgid. Those visits were retaken beca... | cassandra-sh/corrset | getFullAreaHealPixels.py | Python | mit | 5,066 | [
"VisIt"
] | 062def4ac7b06f700efc7d12d27f8d5c82e798a22b636847739571c672721f94 |
#!/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 | python/peacock/tests/input_tab/InputTreeWriter/test_InputTreeWriter.py | Python | lgpl-2.1 | 1,927 | [
"MOOSE"
] | b3c3b4bc49865a326c557e6fdd3150826d8adf9913a523896398065a8a201bde |
""" Client to interact with the S3Gateway """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Core.Base.Client import Client, createClient
@createClient('DataManagement/S3Gateway')
class S3GatewayClient(Client):
""" Client code to the S3Gatew... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Client/S3GatewayClient.py | Python | gpl-3.0 | 1,253 | [
"DIRAC"
] | b9ce36333f7b67171df48c408b55c24412fa3551e8b644118740dc1f504f13e4 |
'''A collection of tools to handle sequence manipulation.
Part of the biostructmap package.
'''
from __future__ import absolute_import, division, print_function
from io import StringIO
import operator
import re
import subprocess
import tempfile
import warnings
from Bio import AlignIO
from Bio.Blast.Applications import... | andrewguy/biostructmap | biostructmap/seqtools.py | Python | mit | 23,316 | [
"BLAST",
"Biopython"
] | d88b6c616758bbf957909e78508018713c430133fe7410c0121f69e36a7f5bde |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains the class describing the coordination geometries that can exist in a given structure. These
"model" coordination geometries are descri... | gpetretto/pymatgen | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | Python | mit | 52,555 | [
"Jmol",
"pymatgen"
] | ce549ddf7323b7a515e88dbefe01ee1a058faa9e5bc5d9f213a34b47e96a72d6 |
#!/usr/bin/python
import numpy as np
from scipy.integrate import odeint
import sys
ELEC_MASS = 9.10938356E-31
ELEC_CHARGE = -1.60217662E-19
FUND_FREQ = 3.7474057E14
SP_LIGHT = 3E8
FOCUS_RADIUS = 30E-6
PL_FWHM = 5E-15
PULSE_ENERGY = 0.6E-3
EPSILON_o = 8.85418782E-12
TIME_GRID = 5000
INTENSITY = 1.88... | KavuriG/classical-calc-three-color | odeint_solve.py | Python | gpl-3.0 | 5,163 | [
"Gaussian"
] | d3db9b6a0c8471d4f0e242b906998d513500cb59c6fc6b2c41aa682827083bd5 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Reads a list of intervals and a maf. Produces a new maf containing the
portions of the original that overlapped the intervals
NOTE: See maf_extract_ranges_indexed.py which works better / faster for many
use cases.
TODO: Combine with maf_extract_ranges, and possibly ... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_extract_chrom_ranges.py | Python | bsd-3-clause | 2,755 | [
"Galaxy"
] | f4639d6232d385314438f1470558c8ab5bc8de6543d861fa9123f4c49af2e1bb |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-annotationforge/package.py | Python | lgpl-2.1 | 2,180 | [
"Bioconductor"
] | fb363287ab3c1bb489518361fa970db97bc28e2df225ede66241df681b9ac992 |
# mk_amiga_exe.py
#
# Convert a raw binary into a simple AmigaDOS executable
# file with one loadable hunk and no relocations
#
# Written & released by Keir Fraser <keir.xen@gmail.com>
#
# This is free and unencumbered software released into the public domain.
# See the file COPYING for more details, or visit <http:/... | keirf/Amiga-Stuff | base/mk_amiga_exe.py | Python | unlicense | 859 | [
"VisIt"
] | 00ad5bd3ad56206b955a8932590a1fbfb26983cfba1baabab61a80c02cb768b1 |
# -*- coding: utf-8 -*-
from .base import BaseDataGenerator
from .single_file_3d import Gen3D
import logging
import threading
import queue
import traceback
import signal
import sys
import random
class SingleFileThread(threading.Thread):
"""
Wrapper thread for buffering data from a
single file
"""
# Lo... | HEP-DL/proton_decay_study | proton_decay_study/generators/threaded_gen3d.py | Python | mit | 7,573 | [
"VisIt"
] | e620279f590000ec116df6c250b356e5d113eb0ef84fa32823056feaddb4a373 |
# $HeadURL$
""" PlottingClient is a client of the Plotting Service
"""
__RCSID__ = "$Id$"
import types, tempfile
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.DISET.TransferClient import TransferClient
class PlottingClient:
def __init__( self, rpcClient = False,... | Sbalbp/DIRAC | FrameworkSystem/Client/PlottingClient.py | Python | gpl-3.0 | 4,017 | [
"DIRAC"
] | edb9d8c5b356e9d77a55abd5f932d357785078b1c17ef01440c4726cdbc2eea1 |
""" Aliases gather aliasing informations. """
from pythran.analyses.global_declarations import GlobalDeclarations
from pythran.intrinsic import Intrinsic, Class, NewMem
from pythran.passmanager import ModuleAnalysis
from pythran.syntax import PythranSyntaxError
from pythran.tables import functions, methods, MODULES
im... | pbrunet/pythran | pythran/analyses/aliases.py | Python | bsd-3-clause | 14,289 | [
"VisIt"
] | 469b3101b9309b1d4e10e8afed61b1c2190696fa90c956f93441b404da9d96ba |
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