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# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.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... | thica/ORCA-Remote | src/ORCA/utils/Platform/win/win_GetUserDownloadsDataPath.py | Python | gpl-3.0 | 1,350 | [
"ORCA"
] | c3be80940d2f09a75f362a34a7e476c18b386a757b6ff4e608ea81e6c5f39d68 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import random
from collections import OrderedDict
import gzip
import json
import numpy as np
import pandas as pd
from ruamel.yaml import YAML
from pymatgen import Molecule, Element, La... | gVallverdu/pymatgen | pymatgen/io/lammps/tests/test_data.py | Python | mit | 48,451 | [
"CHARMM",
"LAMMPS",
"pymatgen"
] | 076e1ea195070f824bae18d821abb447ae88a324a53f4a69da17fe0641296706 |
"""
Copyright (C) 2015, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Barbara Harmon (bharmon@jaguarlandrover.com)
"""
from django.conf.urls import patterns, u... | PDXostc/rvi_backend | web/dynamicagents/urls.py | Python | mpl-2.0 | 606 | [
"Jaguar"
] | db49f09f40cf9e6525ce3e9d29e871bfca656dac457b7288995b3ad154bddf40 |
"""Lineshapes."""
# --- import -------------------------------------------------------------
import numpy as np
from scipy.special import wofz
# --- define -------------------------------------------------------------
__all__ = ["gaussian", "lorentzian_complex", "lorentzian_real", "voigt"]
# --- functions --... | wright-group/WrightTools | WrightTools/kit/_lineshapes.py | Python | mit | 3,564 | [
"Gaussian"
] | cb031f967969aa6b5992bda1b0a7371f35aa902efa72165ffe3858a6548870a5 |
#-------------------------------------------------------------------------------
# Copyright (c) 2011, Kafti team
#
# Released under the MIT license. See the LICENSE file for details.
#-------------------------------------------------------------------------------
"""Simple visitor which can be used for counting nasl... | kafti/pynasl | pynasl/visitors/countcverefs.py | Python | mit | 2,144 | [
"VisIt"
] | 6dd36c4b0929c9b7015c712b5c5be7a8a33bb705447260d2b70790cb8dacd201 |
from __future__ import annotations
import json
import math
import procrunner
import pytest
import scitbx.matrix
from cctbx import sgtbx, uctbx
from dxtbx.model import Crystal, Experiment, ExperimentList, Scan
from dxtbx.serialize import load
from dials.algorithms.symmetry.cosym._generate_test_data import (
gene... | dials/dials | tests/command_line/test_symmetry.py | Python | bsd-3-clause | 20,098 | [
"CRYSTAL"
] | 8587d7e3f1cbb0cad73479aef11cd159c4dd11beca302c85877163e1d2d421e6 |
import equadratures.distributions.template
import equadratures.distributions.gaussian
import equadratures.distributions.truncated_gaussian
import equadratures.distributions.chebyshev
import equadratures.distributions.cauchy
import equadratures.distributions.chisquared
import equadratures.distributions.beta
import equad... | psesh/Effective-Quadratures | equadratures/distributions/__init__.py | Python | mit | 682 | [
"Gaussian"
] | 6fdceab876ae95788c1eabca21eb68593ee1d4dc60ae8774d6ca4c0f764d377a |
import PythonQt
from PythonQt import QtCore, QtGui, QtUiTools
from ddapp import applogic as app
from ddapp.timercallback import TimerCallback
from ddapp.simpletimer import FPSCounter
from ddapp import ioUtils as io
import ddapp.vtkAll as vtk
import os
import glob
import time
import datetime
import itertools
def addWid... | gizatt/director | src/python/ddapp/screengrabberpanel.py | Python | bsd-3-clause | 10,245 | [
"VTK"
] | 37f1f3bc03987791d31c859c950477d4ae0650395502f67737a0b4f188a241e5 |
import json
import urllib2
tokens = {1725:["Ascalonian Tears",4],
1723:["Seals of Beetletun",7],
1721:["Deadly Blooms",9],
1722:["Manifestos of the Moletariate",8],
1714:["Flame Legion Charr Carvings",11],
1718:["Symbols of Koda",10],
1719:["Knowledg... | LutherEngelsnot/gw2_dungeon_tokens_collection | dungeon_tokens_func.py | Python | mit | 3,001 | [
"CRYSTAL"
] | 11d16fe66da06bc275fb11c9a6999aedf9d49830d223781676cbbd8ae635df4d |
from collections import namedtuple
from django.conf import settings
Junction = namedtuple('Junction',
['ref', 'ref_count', 'contig', 'contig_count'])
def get_ref_jbrowse_link(contig, loc):
sample_alignment = contig.experiment_sample_to_alignment
# This is a workaround to using type=Dataset.TYPE.BWA... | woodymit/millstone | genome_designer/genome_finish/contig_display_utils.py | Python | mit | 1,693 | [
"BWA"
] | 129ad8d54ef6ff7e772fa9f9ea76d0a4fcf2f5622d0a5b85a1c2ec495171d052 |
"""Character-based language model using LSTM.
This example demonstrates recurrent networks with BNAS, using an LSTM with
variational dropout (Gal 2016) and layer normalization (Ba, Kiros and Hinton
2016).
Usage:
python3 lm.py model.bin corpus.txt
If model.bin exists, the corpus filename can be left out to genera... | robertostling/bnas | examples/lm.py | Python | gpl-3.0 | 7,042 | [
"Gaussian"
] | c2e93e01f7ee0347f3a0f2adffb769d2757ebac7e8359fdfadc2d5b1dd753cc7 |
#!/usr/bin/python
import datetime
import praw #pip install praw #remove the --pre if it's now the future and praw4 is standard
import os
import time
import socket
import sys
homedir = os.getenv("HOME")
sys.path.append(homedir + '/Pigrow/scripts/')
script = 'reddit_settings_ear.py'
import pigrow_defs
from cr... | Pragmatismo/Pigrow | scripts/autorun/reddit_settings_ear.py | Python | gpl-3.0 | 26,625 | [
"VisIt"
] | 3741b53d11bc4b4375755cffe090d1ba374ff89878c882dff4402fc50c2e25c2 |
#! /usr/bin/env python
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import os
def configuration(parent_package='', top_path=None):
if os.path.exists('MANIFEST'):
os.remove('MANIFEST')
from numpy.distutils.misc_util import Configuration
config = Configurati... | jmetzen/skgp | setup.py | Python | bsd-3-clause | 1,855 | [
"Gaussian"
] | d52a2941a4a1b58f12b8859ac24e9ede15968ae960cedcb4f5c931fa295bfbf5 |
# -*- coding: utf-8
#------------------------------------------------------------------#
"""
.. inheritance-diagram:: xtd.core.stat.counter
:parts: 1
"""
__author__ = "Xavier MARCELET <xavier@marcelet.com>"
#------------------------------------------------------------------#
import threading
import sys
impo... | psycofdj/xtd | xtd/core/stat/counter.py | Python | gpl-3.0 | 10,574 | [
"VisIt"
] | 61f5de1abd8fc1c19b320d9eed276b0021565a0b80f77784bbbefa221ec72f9e |
########################################################################
# $HeadURL $
# File: StrategyHandler.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/05/25 07:49:30
########################################################################
""" :mod: StrategyHandler
=======================
.. m... | sposs/DIRAC | DataManagementSystem/private/StrategyHandler.py | Python | gpl-3.0 | 24,691 | [
"DIRAC"
] | d117c88ea5cf914c040c6a306b0c26c0d8765da726ec5ec1cdaa321dad557e6d |
def get_annotation_axioms(entity, ontologies):
"""
:param entity: an owlapy.model.OWLEntity object to look for
:param ontologies: a list/set of owlapy.model.OWLOntology objects to search
:return: a set of annotation axioms containing the given entity
"""
result = set()
for ontology in ontol... | patrickwestphal/owlapy | owlapy/util/__init__.py | Python | gpl-3.0 | 1,661 | [
"VisIt"
] | f3eb42ffa2524883a332103f9d4011855a1267aea1a4696a5ba773f8aa4c4e10 |
"""
This pipeline is intended to extract Haralick features from T2W images.
"""
import os
import numpy as np
from protoclass.data_management import T2WModality
from protoclass.data_management import GTModality
from protoclass.preprocessing import RicianNormalization
from protoclass.preprocessing import GaussianNorm... | I2Cvb/mp-mri-prostate | pipeline/feature-extraction/t2w/pipeline_extraction_haralick_t2w.py | Python | mit | 4,151 | [
"Gaussian"
] | bd01c7799f097d484db8d5881610fb5fa6ec4f282e1e0cbfd8b707b6683804cd |
from __future__ import division, absolute_import, print_function
import warnings
import sys
import collections
import operator
import numpy as np
import numpy.core.numeric as _nx
from numpy.core import linspace, atleast_1d, atleast_2d
from numpy.core.numeric import (
ones, zeros, arange, concatenate, array, asarr... | MyRookie/SentimentAnalyse | venv/lib/python2.7/site-packages/numpy/lib/function_base.py | Python | mit | 150,005 | [
"Gaussian"
] | 27ca4c1ad329648f633557ee1df2ffe0a27363ede408ae2ff6c0c8edfb5e8fe6 |
#!/usr/bin/python2.4
#
# Copyright 2009 Google 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... | Alwnikrotikz/marinemap | lingcod/common/uaparser/regexes.py | Python | bsd-3-clause | 4,764 | [
"ORCA"
] | 64dbb1f045ceccecbbd9ae89b14ca65ee1702b9e7544805ec2a36790f54bb08d |
import re
import numpy
from orbkit.qcinfo import QCinfo
from orbkit.orbitals import AOClass, MOClass
from orbkit.tools import l_deg, lquant
from orbkit.display import display
from .tools import descriptor_from_file, spin_check
def read_aomix(fname, all_mo=False, spin=None, i_md=-1, interactive=True,
c... | orbkit/orbkit | orbkit/read/aomix.py | Python | lgpl-3.0 | 11,610 | [
"TURBOMOLE"
] | 51bd3382ae94a9d827c265258bb52ebeb35254b54b6f79fbb9fd8ffcc080e98e |
__author__ = 'sibirrer'
from astrofunc.LensingProfiles.dipole import Dipole, Dipole_util
import numpy as np
import numpy.testing as npt
import pytest
class TestDipole(object):
"""
tests the Gaussian methods
"""
def setup(self):
self.dipole = Dipole()
self.dipole_util = Dipole_util()
... | sibirrer/astrofunc | test/test_dipole.py | Python | mit | 3,716 | [
"Gaussian"
] | 63eaf032b90c792598acebac6da9ad24434859dbaa4f56e2beaf61f83c63858f |
"""audio_read reads in a whole audio file with resampling."""
# Equivalent to:
#import librosa
#def audio_read(filename, sr=11025, channels=1):
# """Read a soundfile, return (d, sr)."""
# d, sr = librosa.load(filename, sr=sr, mono=(channels == 1))
# return d, sr
# The code below is adapted from:
# https://gi... | piotrwicijowski/whistler | audio_read.py | Python | mit | 15,179 | [
"Brian"
] | f89f4399a377e8faa0a30d928f8aeb148d528074ea5a16a51fb7d4aeffabaa83 |
from satistjenesten.utils import load_area_def
from satistjenesten.image import add_graticules_to_img
from satistjenesten.image import add_caption_to_img
from satistjenesten.image import save_reduced_jpeg
from copy import deepcopy, copy
from pyresample import kd_tree, geometry
from osgeo import gdal, osr
from PIL impor... | metno/satistjenesten | satistjenesten/scene.py | Python | mit | 10,071 | [
"Gaussian"
] | 285e93ab59bc30269dd444c1d9bdfa113f6956c02e4f5976b30c6391a9a82c6c |
"""
Copyright 2020 Kat Holt
Copyright 2020 Ryan Wick (rrwick@gmail.com)
https://github.com/katholt/Kleborate/
This file is part of Kleborate. Kleborate 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 versi... | katholt/Kleborate | kleborate/blastn.py | Python | gpl-3.0 | 5,485 | [
"BLAST"
] | 07153c91ee47a22f1fd41f7ed76e1ff258026937a5028f28199e9e74320d0366 |
import unittest
from fixtures.sample_asts import *
from ctree.transformations import *
from ctree.c.nodes import *
from ctree.frontend import get_ast
class TestCtxScrubber(unittest.TestCase):
def _check(self, tree):
for node in ast.walk(tree):
if isinstance(node, ast.Name):
se... | ucb-sejits/ctree | test/test_xforms.py | Python | bsd-2-clause | 10,981 | [
"VisIt"
] | 46c34e4e21a14c0cf252e219732890fb9336362649250f20ef4e40ea14d24c45 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Joan Massich <mailsik@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
import os
import sys
import pytest
import numpy as np
from mne.utils import... | pravsripad/mne-python | mne/viz/backends/tests/test_renderer.py | Python | bsd-3-clause | 6,893 | [
"Mayavi"
] | b04981b4458137a9adcfb0698e65a349642d269cf4584b45c9cce4f7df900007 |
""" TSCatalogClient class represents the Transformation Manager service
as a DIRAC Catalog service
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK
from DIRAC.Core.Utilities.List import breakListIntoChunks
from DIRAC.Resources.Catalog.Utilities ... | fstagni/DIRAC | Resources/Catalog/TSCatalogClient.py | Python | gpl-3.0 | 1,830 | [
"DIRAC"
] | 201cca1f3451bf65bc8004e94605342f2984fa8226527fe0f9eea2336a6e2892 |
import numpy
import os
import argparse
import rotatexyz
parser = argparse.ArgumentParser(description="Take an XYZ file as input, rotate it in various directions and output a bunch of XYZ files into separate folders")
parser.add_argument("-i", "--input_file", default="input.xyz", help="the path to the input file (defau... | SINGROUP/readAFM | databaseCode/dostuff.py | Python | gpl-3.0 | 3,555 | [
"CHARMM"
] | 0409707bcb189ff2b4f7945bc892d929e3195ad04592ec51f14f96f3e018ff62 |
## begin license ##
#
# "Meresco Harvester" consists of two subsystems, namely an OAI-harvester and
# a web-control panel.
# "Meresco Harvester" is originally called "Sahara" and was developed for
# SURFnet by:
# Seek You Too B.V. (CQ2) http://www.cq2.nl
#
# Copyright (C) 2006-2007 SURFnet B.V. http://www.surfnet.nl
# ... | seecr/meresco-harvester | meresco/harvester/deleteids.py | Python | gpl-2.0 | 3,881 | [
"xTB"
] | 6f4fbebe7bc5b139c9e29a5e181d66646f9b11d04b41584b13706d9a1b197068 |
# 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.
"""Integration tests for loading and saving netcdf files."""
# Import iris.tests first so that some things can be initialised ... | SciTools/iris | lib/iris/tests/integration/test_climatology.py | Python | lgpl-3.0 | 3,735 | [
"NetCDF"
] | 22a7d6c9c8b4f677386b01f2d3d609181963b768391e0f539a200bf6be1afb64 |
#!/usr/bin/python
"""
Tracking of rotating point.
Rotation speed is constant.
Both state and measurements vectors are 1D (a point angle),
Measurement is the real point angle + gaussian noise.
The real and the estimated points are connected with yellow line segment,
the real and the measured points are... | HDLynx/sharingan | KalmanExample.py | Python | gpl-2.0 | 3,304 | [
"Gaussian"
] | 030269cfc83849258ecfb3b6b287fd85a5aa2dfaeb58d9e1aeb500d5040a1417 |
#!/usr/bin/env python
# Convolve PRE spin label rotamers with MD trajectories.
# Copyright (c) 2011-2017 Philip Fowler and AUTHORS
# Published under the GNU Public Licence, version 2 (or higher)
#
# Includes a rotamer library for MTSSL at 298 K by Gunnar Jeschke,
# which is published under the same licence by permissio... | MDAnalysis/RotamerConvolveMD | scripts/convolve-mtss-rotamers_pre.py | Python | gpl-2.0 | 5,460 | [
"MDAnalysis"
] | c31ee5fbf5f97e89dadf906d3f2250877e4db7937ddd36d675e5d9498f5b91c5 |
import os
import sys
import optparse
import lib.vcrparser as vcrparser
import lib.spider_stats as spider_stats
import lib.html_lib as html
#########################################################################
# PARSER
#########################################################################
desc = "aRNApipe: SPIDE... | HudsonAlpha/aRNAPipe | spider.py | Python | mit | 15,141 | [
"HTSeq"
] | 2bcf6602f413299fdac3bd6a8a18b0cdef8facf3b8a5a37c4ceede9d7352c66e |
#!/usr/bin/env python
__requires__ = ['pysam>=0.8.1']
import pysam
import sys
import time
from optparse import OptionParser
import radiaUtil
import collections
import logging
from itertools import izip
import os
'''
' RNA and DNA Integrated Analysis (RADIA):
' Identifies RNA and DNA variants in NGS data.
'
' ... | aradenbaugh/radia | scripts/createBlatFile.py | Python | agpl-3.0 | 41,837 | [
"pysam"
] | 36d2be20c96a4b9e5d554e1ec777f17e6028948f7290f988d2c5738127898b04 |
#!/usr/bin/env python3
import matplotlib as m
import matplotlib.pyplot as plt
from matplotlib.mlab import griddata
import numpy as np
import sys
import pdb
import os
import random
def file_len(full_path):
""" Count number of lines in a file."""
f = open(full_path)
nr_of_lines = sum(1 for line ... | FluidityStokes/fluidity | examples/hokkaido-nansei-oki_tsunami/raw_data/plotbathymetry.py | Python | lgpl-2.1 | 3,548 | [
"NetCDF"
] | 2989e9d2204b984a04d62f7fac867e3553436eb0bbac15cd597cac2aa34e34fd |
from __future__ import unicode_literals
import hashlib
import hmac
import re
import time
from .common import InfoExtractor
from ..compat import compat_str
from ..utils import (
ExtractorError,
js_to_json,
int_or_none,
parse_iso8601,
try_get,
unescapeHTML,
update_url_query,
)
class ABCIE(... | steebchen/youtube-dl | youtube_dl/extractor/abc.py | Python | unlicense | 7,393 | [
"VisIt"
] | 45736d3b453b9b30cd37e84f8487e25481b5c550a49c9f96c842fbea1292016f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/topology/test_tprparser.py | Python | gpl-2.0 | 6,511 | [
"Gromacs",
"MDAnalysis"
] | f84309dba2fe8c6a7fc22504d604ddc8815170ac2c2e5c653d9402c5b1642544 |
# -*- coding: utf-8 -*-
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Python
abstract syntax grammar. The abstract syntax itself might change with
each Python release; this module helps to find out programmatically what
the current grammar looks like and allows... | antb/TPT----My-old-mod | src/python/stdlib/ast.py | Python | gpl-2.0 | 11,840 | [
"VisIt"
] | 4cc8fe1dcff73c996247e7c4b0a9e63b428fd5e1dbf1795771df91e391fff049 |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import Directive
from docutils.statemachine import ViewList
from sphinx import addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.directives.code import CodeBlo... | theo-l/django | docs/_ext/djangodocs.py | Python | bsd-3-clause | 13,798 | [
"VisIt"
] | 46db07ee55d83f3354ca635a3d686615e4f3f025cf9fe9ee1f404ebff12c220c |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Implementation of defect correction methods.
"""
import logging
import matplotlib.pyplot as plt
import numpy as np
import scipy
from scipy import stats
from pymatgen.analysis.defects.core import DefectCorrection
from py... | materialsproject/pymatgen | pymatgen/analysis/defects/corrections.py | Python | mit | 38,761 | [
"VASP",
"pymatgen"
] | 95dd5f205ae989ec67d42f32f8d81a2881dbda96120f0dd923ff46d491d35349 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | anksp21/Community-Zenpacks | ZenPacks.AndreaConsadori.Raytalk/ZenPacks/AndreaConsadori/Raytalk/modeler/plugins/RaytalkCPEDeviceMap.py | Python | gpl-2.0 | 1,315 | [
"VisIt"
] | ae9823524b15920d3a784f05a5d7377d29e7189b09eec2424c4767772f990f22 |
#!/usr/bin/env python
# Computes exact similarity solution "test Q" at an initial time and after
# a specified runtime. Suggests a PISM run for this runtime. The exact
# solution for velocity and for thickness can be compared to PISM output.
#
# For the similarity solution see equation (3.19) in
# [\ref PeglerLister... | talbrecht/pism_pik06 | src/verif/tests/exactQ.py | Python | gpl-3.0 | 6,087 | [
"NetCDF"
] | d6a481e86f971eb049b7b75fa04d4352a3a93696630a5161099d74d2d82eb5a3 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2015 Rodrigo Silva (MestreLion) <linux@rodrigosilva.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, ... | MestreLion/pyrogue | pyrogue/things.py | Python | gpl-3.0 | 3,227 | [
"Amber"
] | b402c462de08a73053fe8399122a0f0e437d849e4f6d668984d9ac2dc52bb6f2 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from datetime import datetime
from unittest import skip
from bok_choy.page_object import XSS_INJECTION
from nose.plugins.attrib import attr
from pytz import timezone, utc
from common.test.acceptance.pages.common.auto_auth import AutoAuthP... | Stanford-Online/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 22,158 | [
"VisIt"
] | 02eb85b4ddfad2b1a6e724f69a3ffa747a4a1c476077973ca533e03ea247bcde |
from __future__ import absolute_import
from __future__ import print_function
from six import iteritems
from builtins import range
from os import path
import numpy as np
from netCDF4 import Dataset
from pyproj import Proj
from pyproj import transform
from shyft import api
from shyft import shyftdata_dir
from .. import... | felixmatt/shyft | shyft/repository/netcdf/cf_geo_ts_repository.py | Python | lgpl-3.0 | 15,302 | [
"NetCDF"
] | 79e895c3f70fb00d3d421516d827a2188b981f41254d224d0959403845c28253 |
#
# Test executable to exercise the Gauss-Hermite class
#
# Copyright (c) 2013 RadiaBeam Technologies. All rights reserved
#
# python imports
import math
# SciPy imports
import numpy as np
import matplotlib.pyplot as plt
# RadiaBeam imports
from radtrack.fields import RbGaussHermiteMN
from radtrack.util import plotTo... | radiasoft/radtrack | experimental/hermite/testHermite08.py | Python | apache-2.0 | 3,053 | [
"Gaussian"
] | adc5e50c37ea88f5417f7d9d58d9308cfae367bf57d22d4945fc94b92422a718 |
#!/usr/bin/env python
###############################################################################
##
## 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.
##
## "Redistribution and use in... | celiafish/VisTrails | scripts/dist/mac/fix_qtplugin_libs.py | Python | bsd-3-clause | 6,555 | [
"ParaView"
] | 4cdd055ff21eba548491be90d1124727caf5ee4da4c5a74c9cd558f283bc3d5e |
#
## This file is part of INSPIRE.
## Copyright (C) 2015 CERN.
##
## INSPIRE is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
## I... | Lilykos/inspire-next | inspire/modules/authors/views.py | Python | gpl-2.0 | 9,301 | [
"VisIt"
] | d7edbe4a3a9cea3fcc5bb5f56e97b6b2b1de24a95b2c303f73a124f1f9d7b0b0 |
"""
Adaptfilt
=========
Adaptive filtering module for Python. For more information please visit
https://github.com/Wramberg/adaptfilt or https://pypi.python.org/pypi/adaptfilt
"""
__version__ = '0.2'
__author__ = "Jesper Wramberg & Mathias Tausen"
__license__ = "MIT"
# Ensure user has numpy
try:
import numpy
excep... | Wramberg/adaptfilt | adaptfilt/__init__.py | Python | mit | 1,258 | [
"VisIt"
] | dd10f5eb8c041bc27831cb85aba68f35011c4b4b7b15603d4a56cb4518c2c265 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | Forage/Gramps | gramps/gen/filters/rules/place/_hasnote.py | Python | gpl-2.0 | 1,764 | [
"Brian"
] | 86bc29f5f2ec2a1b4dc2ba967d7f45ffb99a79bd4a4e7686c59b3fc256c680bf |
#!/usr/bin/env python
import sys
import vtk
from vtk.test import Testing
useBelowRangeColor = 0
if sys.argv.count("--useBelowRangeColor") > 0:
useBelowRangeColor = 1
useAboveRangeColor = 0
if sys.argv.count("--useAboveRangeColor") > 0:
useAboveRangeColor = 1
cmap = vtk.vtkDiscretizableColorTrans... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Core/Testing/Python/TestOutOfRangeDiscretizableColorTransferFunction.py | Python | bsd-3-clause | 1,475 | [
"VTK"
] | 1bc56ec70ab88bb2276476ca70a22682b8ac67ea9b8baaf761f3e9b1f49ecccd |
#!/usr/bin/env python
import copy
import datetime
import dateutil.parser
import json
import logging
import os
import pytz
import re
import requests
from requests.packages.urllib3.util import Retry
from requests.adapters import HTTPAdapter
from six import string_types
try:
from urllib.parse import urlencode
except... | AlienVault-Labs/OTX-Python-SDK | OTXv2.py | Python | apache-2.0 | 42,419 | [
"Amber"
] | 8df25310dc811c3a9087834c9b0fd7bf30dfbdcbec8c273e8edb6fed782c4697 |
#!/usr/bin/env python
from DIRAC.Core.Base.Script import Script
@Script()
def main():
Script.parseCommandLine(ignoreErrors=False)
from DIRAC.WorkloadManagementSystem.Client.VirtualMachineCLI import VirtualMachineCLI
cli = VirtualMachineCLI(vo="enmr.eu")
cli.cmdloop()
if __name__ == "__main__":
... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_vm_cli.py | Python | gpl-3.0 | 327 | [
"DIRAC"
] | 58103f6b1bf9742e9a18f98a9d35e839df4d1382d2853a0ddc5bb2a5633dde9a |
import os
import re
import time
import gzip
import queue
import shutil
import threading
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.ThreadScheduler import gThreadScheduler
from DIRAC.Core.Utilities.File import mkDir
class SecurityFileLog(threading.Thread):
def __init__(self, basePath, daysT... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/private/SecurityFileLog.py | Python | gpl-3.0 | 4,231 | [
"DIRAC"
] | 57b330a25d7be83f6a08ff5a9b173704adc893735145f09fa250546e06625008 |
"""Tornado handlers for the notebook.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed as p... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/html/services/kernels/handlers.py | Python | bsd-3-clause | 6,225 | [
"Brian"
] | e8d33f279396b2cb1641e8221403b1adda7e5dc879363cf377491f536aba085f |
#Copyright 2009,2010 Alex Graves
#
# This file is part of RNNLIB.
#
# RNNLIB is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# RNNL... | j-briggs/rnnlib | utils/rescale_netcdf_binary_inputs.py | Python | gpl-3.0 | 1,582 | [
"NetCDF"
] | 8394a3ac5eec905a8260787df0643c66d736ba16f9741028d461e1df51b06023 |
"""
local path implementation.
"""
from __future__ import with_statement
from contextlib import contextmanager
import sys, os, atexit, io, uuid
import py
from py._path import common
from py._path.common import iswin32, fspath
from stat import S_ISLNK, S_ISDIR, S_ISREG
from os.path import abspath, normpath, isabs, exi... | pytest-dev/py | py/_path/local.py | Python | mit | 36,759 | [
"VisIt"
] | f9075323de47da0b403c07c4e1686f450abfdaa32394d055452a7afeb7a0ee41 |
# Copyright (c) 2014, Zhenwen Dai
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ...core import Model
from ...core.parameterization import variational
from ...util.linalg import tdot
from GPy.core.parameterization.variational import VariationalPosterior
def infer_newX(model, Y_new... | ptonner/GPy | GPy/inference/latent_function_inference/inferenceX.py | Python | bsd-3-clause | 8,076 | [
"Gaussian"
] | c1f5892aef09f9456d468dd1f94b37b9443f0f86df0f86e568393f69283277c0 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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
#
# Unle... | beyondblog/kubernetes | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 4,733 | [
"VisIt"
] | b8d62f9ed56498da07ab1ae97040b21e152d97673f84305d122c16dba23cee33 |
# We only import librairies needed for plotting
# Other librairies are imported in the class definition file, G3D_class.py,
# which contains all process and variables function definition.
import matplotlib
matplotlib.use('pdf')
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
import datetime as dt
imp... | acapet/GHER-POSTPROC | Examples/NbottomClim.py | Python | gpl-3.0 | 4,091 | [
"NetCDF"
] | 0b6caa5f23c8256d8cbbf9e3bce69051c027b944e5dbe910146feaa1f89542bf |
"""
SnpFile datatype
"""
import galaxy.datatypes.data
import tempfile
import os
import json
from galaxy import util
from galaxy.datatypes.sniff import *
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.images import Html
from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import Meta... | gigascience/galaxy-genome-diversity | datatypes/wsf_datatypes/wsf.py | Python | gpl-3.0 | 8,020 | [
"Galaxy"
] | 62e34fceade59949205894a76c7b0a600c96703b6495978fba601d21d4e80d13 |
#coding=utf-8
#Introduction:聚超值签到
from splinter import Browser
import time
import logging
def qd():
## browser = Browser('firefox'
## , profile='D:\UsersDocuments\FFmissions')
browser = Browser('chrome')
browser.visit(juchaozhi)
time.sleep(1)
browser.find_by_name('username').fill(... | sveiow/doitpy | Autosign/juchaozhi.py | Python | gpl-2.0 | 2,001 | [
"VisIt"
] | 7488c7e57200e03da2d164c2b1c778c85d0299975c553038a46d2905eddcd86b |
# Maked by Mr. Have fun! Version 0.2
# Shadow Weapon Coupons contributed by BiTi for the Official L2J Datapack Project
# Visit http://forum.l2jdp.com for more details
import sys
from com.l2scoria.gameserver.model.quest import State
from com.l2scoria.gameserver.model.quest import QuestState
from com.l2scoria.gameserver.... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/quests/415_PathToOrcMonk/__init__.py | Python | gpl-3.0 | 15,358 | [
"VisIt"
] | 6e1d5ac29769047b86c65511b93210a4dcc458951e017e3a833d4c84283d0800 |
"""
Tests for target_utils.
"""
import numpy as np
import os
import shutil
import tempfile
import unittest
from rdkit import Chem
from rdkit_utils import serial
from .. import read_pickle, write_pickle
from ..target_utils import (AssayDataParser, Nci60Parser, PcbaParser,
Tox21Parser)
cl... | rbharath/pande-gas | vs_utils/utils/tests/test_target_utils.py | Python | bsd-3-clause | 14,885 | [
"RDKit"
] | baa644688b41e8a6f783a2830bfa6b52d0c2703787a07cb23a4f848598d6872d |
#!/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... | harterj/moose | modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep/exchanger.py | Python | lgpl-2.1 | 1,932 | [
"MOOSE"
] | 5049412f9ac8b86e00b72f7d9be5c1da2e5cb3842f99f93dd24159aa2b9894a7 |
# Copyright 2013, 2014, 2015, 2016, 2017 Kevin Reid <kpreid@switchb.org>
#
# This file is part of ShinySDR.
#
# ShinySDR 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
# ... | bitglue/shinysdr | shinysdr/i/network/app.py | Python | gpl-3.0 | 11,655 | [
"VisIt"
] | f84d63e8b05aaefcad8ec605c602ff1b0589d8120d61bbb007a96c4ec28749ac |
from builtins import object
import numpy as np
from code_base.layers import *
from code_base.layer_utils import *
class ThreeLayerConvNet(object):
"""
A three-layer convolutional network with the following architecture:
conv - relu - 2x2 max pool - affine - relu - affine - softmax
The network operates ... | coldmanck/Neural-Network-in-Python | assignment2/code_base/classifiers/cnn.py | Python | mit | 9,043 | [
"Gaussian"
] | 1e58cd9521481cba9d749e9f8d7690064f35d45c147ebc02b4d58d651f04bab6 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import unittest
import numpy as np
import pytest
import lisa.convert
import os.path as op
import os
class MyTestCase(unittest.TestCase):
@pytest.mark.interactive
def test_something(self):
seg = np.zeros([20,21,22], dtype=np.uint8)
seg [4:11, 3:15... | mjirik/lisa | tests/convert_test.py | Python | bsd-3-clause | 764 | [
"VTK"
] | c517993109be3f22c88d8f8a28574efa6fc2e0bc32b1d552f6b7bba582438baa |
import sys, random, math, re, os, itertools
# Need to extract moleculetypes, residues and atom lists
# Set the pattern for matching files to be included
includePattern = re.compile('#include "(.*)"')
# Gromacs force field directory
gmxlib = os.environ.get("GMXLIB")
if not gmxlib:
gmxdat = os.environ.get("... | Tsjerk/MartiniTools | gmx/top/top.py | Python | gpl-2.0 | 4,906 | [
"Gromacs"
] | b4ff710e082cc066e695ed646e02129e25e342b7042b12de86ebc4ecd19f50a8 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/reducer.py | Python | lgpl-2.1 | 11,955 | [
"MDTraj"
] | 428cbbc3d9909839e656d854a08ba2347ce9cf92d3cb446e129b82b988b0ed49 |
# -*- coding: utf-8 -*-
"""
Spot Stamp Class.
Created on Thu Apr 20 15:35:08 2017
:author: Ruyman Azzollini
"""
# IMPORT STUFF
from pdb import set_trace as stop
import numpy as np
from .shape import Shapemeter
from .photom import Photometer
from .gauss import Gaussmeter
from vison.datamodel.ccd import gain
# EN... | ruymanengithub/vison | vison/point/spot.py | Python | gpl-3.0 | 5,410 | [
"Gaussian"
] | 4e0d5c2e505dd3d91600dfe90c8b36f197c86ae13bb425adf7e715b0e8c6cfa4 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_compiled_0008.py | Python | gpl-3.0 | 3,909 | [
"Brian"
] | f77ae53df826139ca790ca602b86d25b7392c09e84e7a833b52441d0be6479f9 |
"""
The central component of the Neofelis pipeline.
"""
"""
Copyright 2010 Jarl Haggerty
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 r... | jarl-haggerty/profelis | src/main/jython/profelis/pipeline.py | Python | apache-2.0 | 12,209 | [
"BLAST"
] | 1ee6227966d145dd2185df495dcc22d2f68cda2abceb19e541691f6c2ddd8f1d |
import vtk
from vtk.util.misc import vtkGetDataRoot
import render_mpr
reader = vtk.vtkMetaImageReader()
reader.SetFileName("C:\\Users\\fei.wang\\PycharmProjects\\Rendering\\data\\org.mha")
reader.Update()
render_mpr = render_mpr.RendererMPR()
render_mpr.set_volume(reader)
render_mpr.set_output_image_siz... | comedate/VolumeRendering | test_mpr.py | Python | mit | 580 | [
"VTK"
] | 61cb44478643c7c102e8149b28f1c7e964ec85366e710f1a097839aaac4ac33e |
from __future__ import absolute_import
from builtins import range
from .belief_structure import BeliefStructure
class QTable(BeliefStructure):
"""
Creates a Q table and visit frequency table for quick and dirty Q learning
Indexing into the Q-table is done by
q_table[action_idx][state_idx] = Q(s,... | pemami4911/POMDPy | pomdpy/pomdp/q_table.py | Python | mit | 1,308 | [
"VisIt"
] | 13a737d339a40de50c6ea49e97ee5bcdde0195d7738e3b99841aaea188128627 |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
#
# CollisionWarningSelfTest
#
class CollisionWarningSelfTest(ScriptedLoadableModule):
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "CollisionWarni... | amirzolal/CollisionWarning | CollisionWarning/Testing/Python/CollisionWarningSelfTest.py | Python | bsd-2-clause | 9,555 | [
"VTK"
] | 2df221d509590f5f3be040b82614811847d73e872a8e43f33fc412bee51884d7 |
# -*- 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-notebooks | tests/unit/gapic/notebooks_v1/test_notebook_service.py | Python | apache-2.0 | 302,622 | [
"Octopus"
] | 9b6d05a7286d0b8f9d1fcc750f8b58b40d5e3e0ff502dc34c76980b1c5908d2e |
from __future__ import division
import numpy as np
from scipy.ndimage import uniform_filter, gaussian_filter
from ..util.dtype import dtype_range
from ..util.arraycrop import crop
from .._shared.utils import deprecated
from .._shared.utils import skimage_deprecation, warn
__all__ = ['compare_ssim']
def compare_ssi... | paalge/scikit-image | skimage/measure/_structural_similarity.py | Python | bsd-3-clause | 8,286 | [
"Gaussian"
] | 602f57c6ca3a12b1c247769ef0ee491f7f6623ca0b4da88c941b58380e0adf6c |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/lib/test/test_kpts.py | Python | apache-2.0 | 1,862 | [
"PySCF"
] | 5af949acd7c2cd06aa89c048668ec7f67420147a2a713b69d605e7b4c929f3dc |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/blast-plus/package.py | Python | lgpl-2.1 | 7,740 | [
"BLAST"
] | 86895068fa4ca88d1aa1cda69e6a0dfbc566e8360c5dd2ce06ed8d0b0f888f68 |
#!/usr/bin/env python
#
#
# A file which can be run in (Python enabled) NEURON to analyse the rate
# variables contained in a mod file
#
#
import argparse
import re
from math import log
import neuron
print("\n\n")
import matplotlib.pyplot as pylab
from pylab import *
from pyneuroml.analysis.NML2ChannelAnalysis... | NeuroML/pyNeuroML | pyneuroml/neuron/analysis/HHanalyse.py | Python | lgpl-3.0 | 18,353 | [
"NEURON"
] | 9b2da2eeaaea6f8045ce849749c2a86bf77311912ebed31f45e6357ce0d21ec0 |
import os
from setuptools import setup
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name = "django-safe-admin-emails",
version = "0.1",
author = "Brian Luft",
author_email = "brian@lincolnloop.com",
description = "Provides support for making sure s... | lincolnloop/django-safe-admin-emails | setup.py | Python | bsd-3-clause | 775 | [
"Brian"
] | ca16f634f470d62166377663e7590ba68c739132332c86261192d4e4a3a37737 |
import requests
import sys
import hashlib
import subprocess
import shlex
import shutil
import os.path
import os
from Bio.Blast import NCBIXML
import time
import math
import json
import re
# arg 1 input fasta file
# arg 2 output dir
# arg 3 base uri
# arg 4 blast bin path
# arg 6 blast settings string
# arg 5 blast db
#... | DanBuchan/cache_server | scripts/run_hhblits_legacy_blast.py | Python | gpl-2.0 | 12,820 | [
"BLAST"
] | 2a01b1f34174eeea19ad0208c5844e2a45dcc933c9327b7fea08022f19d89a43 |
'''
NFI -- Silensec's Nyuki Forensics Investigator
Copyright (C) 2014 George Nicolaou (george[at]silensec[dot]com)
Silensec Ltd.
This file is part of Nyuki Forensics Investigator (NFI).
NFI is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public Licen... | georgenicolaou/nfi | AndroidAuxiliary/FacebookContacts.py | Python | gpl-3.0 | 6,007 | [
"ORCA"
] | c9d1a164d2ae55b18bbea4b0a0aefe17c1837de332974d4ccf634f201f11417e |
#! /usr/bin/env python
# FIXME: if it requires a dirac.cfg it is not a unit test and should be moved to tests directory
import unittest
import time
import os
import shutil
import sys
import types
from DIRAC.Core.Base.Script import parseCommandLine, getPositionalArgs
parseCommandLine()
from DI... | andresailer/DIRAC | Resources/Storage/test/FIXME_Test_StorageElement.py | Python | gpl-3.0 | 38,619 | [
"DIRAC"
] | 8eedac6f130c351854173063092f461bca7daf44dee033f45050669d13c684af |
from __future__ import print_function
from pylearn2.models.dbm.dbm import DBM
from pylearn2.models.dbm.layer import BinaryVector, BinaryVectorMaxPool, Softmax, GaussianVisLayer
__authors__ = "Ian Goodfellow"
__copyright__ = "Copyright 2012, Universite de Montreal"
__credits__ = ["Ian Goodfellow", "Devon Hjelm"]
__lic... | JazzeYoung/VeryDeepAutoEncoder | pylearn2/pylearn2/models/tests/test_dbm.py | Python | bsd-3-clause | 37,752 | [
"Gaussian"
] | 9eeb04aa4954b9df9ed464306b766cfddcbc2708a81c994301835899c65a6b46 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# resman - Resource manager, json based UI for browsing resources
#
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of t... | heromod/migrid | mig/cgi-bin/resman.py | Python | gpl-2.0 | 1,101 | [
"Brian"
] | 7dcfe4956c912302964067e46fbc3e6db4efa9048f18673cd1f12e44200aac9b |
r'''
Module containing Colour Quantization for reducing an images down to a
selection of set colours.
The idea behind this module is to replace the colours of an image with
the most likely matches from a set of colours specified by the user. This
module works in conjunction with PIL as it's mea... | JFDesigner/LichtensteinGenerator | bin/quantize.py | Python | apache-2.0 | 6,289 | [
"Gaussian"
] | 698d6b1190b1399e404d01e09c7d604c64fe1a1ac5d0d096223d5f38c91210d8 |
#uses modified cclib 1.00
import sys
sys.path.append(sys.argv[2])#add $RMG/source to the PYTHONPATH so that import statements below work properly
import logging
from cclib.parser import Mopac
myfile=Mopac(sys.argv[1])
myfile.logger.setLevel(logging.ERROR) #cf. http://cclib.sourceforge.net/wiki/index.php/Using_cc... | faribas/RMG-Java | scripts/MopacPM3ParsingScript.py | Python | mit | 1,340 | [
"MOPAC",
"cclib"
] | 138728546bdb3f9154eafa96180603356bc2bf650293787c88bd8321503ee061 |
#!/usr/bin/env python
import sys
import pysam
import argparse
parser = argparse.ArgumentParser(description='Filter BAM/SAM files for read coverage and mapping quality')
parser.add_argument('-s', dest='sam_input', default=False, action='store_true', help='Input is ASCII SAM format')
parser.add_argument('--mincov', type... | koadman/proxigenomics | simulation/pipeline/bin/filter_bam.py | Python | gpl-2.0 | 2,089 | [
"pysam"
] | 8fc9ec903f1e43d4f0fb8774a104d505a2267f9f84001f5fa7266f3838818a3c |
# -*- coding: utf-8 -*-
#
# This file is part of EventGhost.
# Copyright (C) 2005-2009 Lars-Peter Voss <bitmonster@eventghost.org>
#
# EventGhost is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License version 2 as published by the
# Free Software Foundation... | garbear/EventGhost | plugins/X10/__init__.py | Python | gpl-2.0 | 10,490 | [
"Firefly"
] | 354dcaa76afb49ee49e21611862513ae2c98c3ec12678ce24bceaca9a7e09753 |
# modified mexican hat wavelet test.py
# spectral analysis for RADAR and WRF patterns
# NO plotting - just saving the results: LOG-response spectra for each sigma and max-LOG response numerical spectra
# pre-convolved with a gaussian filter of sigma=10
import os, shutil
import time, datetime
import pickle
imp... | yaukwankiu/armor | tests/modifiedMexicanHatTest15_march2014_sigmaPreprocessing4.py | Python | cc0-1.0 | 7,832 | [
"Gaussian"
] | 24f0d148b7b11552debcec64cbf9d39c2f6df480485c900df32af36983c50f29 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import sys
import re
from collections import defaultdict
from copy import deepcopy
from datetime import datetime
class Vertex(object):
def __init__(self, v_id):
self._id = v_id
def __hash__(self):
return se... | PiJoules/Zombies-on-the-highways- | main.py | Python | isc | 4,231 | [
"BLAST"
] | 0a336568e30fda667f1ad2da243c52404de4fd621d8c68d66ffba62c92d83eee |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | arunkgupta/gramps | gramps/gen/filters/rules/family/_hassourcecount.py | Python | gpl-2.0 | 1,771 | [
"Brian"
] | 069bf34d2cb00312b4899aa6c6af72d0b78d677b9d0016be8f290d0ce8582241 |
import socket
import smtplib
import os
import base64
import werkzeug.security as ws
import pyotp,time
import datetime
from Crypto.Signature import PKCS1_v1_5
from Crypto.Hash import SHA
from Crypto.PublicKey import RSA
from Crypto.Cipher import AES
from flask import Flask, request, jsonify, abort, json
from simplekv.fs... | achamely/omniwallet | api/user_service.py | Python | agpl-3.0 | 27,185 | [
"exciting"
] | b3a98cacef6ad87d0d3c780efb508d882862d581fef78398a30a426233982ff6 |
#! /usr/bin/env python3
#
# Copyright (C) 2011, 2014, 2015, 2016, 2018 David Maxwell and Constantine Khroulev
#
# This file is part of PISM.
#
# PISM 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 vers... | pism/pism | examples/python/ssa_forward.py | Python | gpl-3.0 | 2,059 | [
"NetCDF"
] | 64b5576d9600b389bbf67d18af6e7c00fab5beece4e37ad1391a7f41e520c5d9 |
# 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... | Mega-DatA-Lab/mxnet | example/reinforcement-learning/dqn/utils.py | Python | apache-2.0 | 11,572 | [
"Gaussian"
] | 98ff478e225bacbd87e438534f668259f65b6b72df2b0ccf4a88bb28448a81ca |
#!/usr/bin/env python
from __future__ import division
'''
Created on Mar 14, 2012
'''
# XXX may need to downgrade to pymatgen 1.x (2.x introduced July 2012).
# Last commit from Anubhav was 2012-11-29, so could have used v2.3.0 at latest.
from pymatgen.core.periodic_table import Element
import logging
logging.basicCo... | mp-interns/ga_optimization_ternary | ga_optimization_ternary/simple_ga.py | Python | mit | 21,730 | [
"pymatgen"
] | a767afb8fdb9a523179d520534663f069b0a4ca16987ae446f77341074240647 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/pbc/tools/test/test_k2gamma.py | Python | apache-2.0 | 2,509 | [
"PySCF"
] | 6dd2f204109195a1f5c78fde9bd0a4e2cde5667b51f236133c84f22c98918d0d |
#! /usr/bin/env python
"""
Change status of replica of a given file or a list of files at a given Storage Element
"""
from DIRAC import exit as DIRACExit
from DIRAC.Core.Base.Script import Script
@Script()
def main():
# Registering arguments will automatically add their description to the help menu
Script.reg... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_change_replica_status.py | Python | gpl-3.0 | 1,787 | [
"DIRAC"
] | 3a81657e90ec380fb7a04a6877890a1862f4b8a4fc7b672d945309bb9f0f7eec |
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