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#!/usr/bin/env python
# Copyright 2014-2019 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/df/fft.py | Python | apache-2.0 | 13,481 | [
"PySCF"
] | bef94cdb3e97e3fe5dd899ba5d698e379c17604bb8abd19767e42a5e19bf59b3 |
def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
# FIXME: this function is duplicated in the DynamicOptions class. It is used here only to
# set data.name in exec_after_process().
microbe_info= {}
orgs = {}
filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR
for i, line... | lappsgrid-incubator/GalaxyMods | tools/data_source/microbial_import_code.py | Python | apache-2.0 | 7,277 | [
"Galaxy"
] | 40a526ca31ffe7d38ff112cfe7770d5654d1bee2251d00b658e4ec697dc2155c |
#
# Handle the special case of the first scenario
#
self.notebook.switchScenario(0,scenarioType="Powder")
#
#
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'castep'
tab.settings['Output file name'] = 'phonon.castep'
tab.settings['Excel file name'] = 'analysis_bruggeman.xlsx'
tab.settings['Script file name'] =... | JohnKendrick/PDielec | Examples/Castep/MgO/application_note_bruggeman.py | Python | mit | 12,568 | [
"CASTEP"
] | 4d6925ce6b43d5a74447f452b211ef0bc88b99eea7e24eb30bd76522972e3f51 |
#!/usr/local/bin/python2.6
###AltAnalyze
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to... | wuxue/altanalyze | AltAnalyze_new.py | Python | apache-2.0 | 558,055 | [
"Cytoscape"
] | 6616a48e50116b6c24510c5567e26ec3244aff51248975e41bd08866fbe8acd4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2014 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the L... | iwm911/plaso | plaso/parsers/popcontest_test.py | Python | apache-2.0 | 5,715 | [
"ORCA"
] | bf4783015849541b82d6cf2e83b8eec2b579a5e943443123e9ca902e08a48049 |
#
# cmdline.py
#
# Copyright (C) 2016 Red Hat, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program ... | Be-ing/lorax | src/pylorax/cmdline.py | Python | gpl-2.0 | 17,016 | [
"Brian"
] | 94708b418bb7c32ff9b1b6e43afe1ef39560f298f808a627faa8538e233bfae0 |
__all__ = ["create_settings_from_template"]
from scm.plams import Molecule
from qmflows.settings import Settings
from os.path import join
import os
import json
import pkg_resources as pkg
import yaml
path_valence_electrons = pkg.resource_filename(
"nac", "basis/valence_electrons.json")
path_aux_fit = pkg.resour... | felipeZ/nonAdiabaticCoupling | nac/workflows/templates.py | Python | mit | 7,349 | [
"CP2K"
] | 7a5cc974582c193842f4968d30845ba5dc6c71df98a522c62687c3c8c93c1bff |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 Brian Langenberger
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licens... | tuffy/python-audio-tools | audiotools/ape.py | Python | gpl-2.0 | 39,279 | [
"Brian"
] | 1381100cf4fa8343f4ce3e551fc38e96c51a12d27bb4652d84480807187a49ae |
"""
Copyright (C) 2014, 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/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
import datetime, pytz
from d... | klooer/rvi_backend | web/tracking/models.py | Python | mpl-2.0 | 7,824 | [
"Jaguar"
] | 59a35cb2b6369925ceb6a31247ceaca6a4e177e284d7a0376ac433584e245fbe |
# Copyright 2008-2010 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Multiple sequence alignment input/output as alignment objects.
The Bio.AlignIO interface... | ktokolwiek/Genetic-Stability-Tool | Bio/AlignIO/__init__.py | Python | gpl-3.0 | 20,217 | [
"BioPerl",
"Biopython"
] | e61cc3540fdd2d25453899264adc9d08a41e22c7b10b1e0f568f46b0d7be479f |
from django.test import SimpleTestCase
from corehq.apps.app_manager.tests.app_factory import AppFactory
from corehq.apps.app_manager.tests.util import TestXmlMixin
from corehq.util.test_utils import flag_enabled
@flag_enabled('GRID_MENUS')
class GridMenuSuiteTests(SimpleTestCase, TestXmlMixin):
def test_that_grid... | qedsoftware/commcare-hq | corehq/apps/app_manager/tests/test_grid_menus.py | Python | bsd-3-clause | 8,516 | [
"VisIt"
] | 7803445be5efe3aac5ef3e9c3363290878311f5150b2524857a98d94f391e7cf |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
####################################################################################
### Copyright (C) 2015-2019 by ABLIFE
####################################################################################
########################################################... | ablifedev/ABLIRC | ABLIRC/bin/public/mapping_distribution_statics_v2.py | Python | mit | 27,283 | [
"HTSeq"
] | d135816e276f6a955ef087661f4e21f0ee5ce27ebbd07b1cd2223b2b7fbef25d |
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free softw... | fedepad/espressopp | src/interaction/TabulatedAngular.py | Python | gpl-3.0 | 5,631 | [
"ESPResSo"
] | 07163143a3560beff7371c3b505b822938e2f93b255a901c98db6140db927888 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""Provides functions for creating a python classes from the cp2k_input.xml
file.
"""
import xml.etree.cElementTree as cElementTree
import utilities
import textwrap
#===============================================================================
def validify_section(st... | SINGROUP/pycp2k | inputparser.py | Python | lgpl-3.0 | 14,369 | [
"CP2K"
] | 9d98f7f80251c8c63798ae6b97c7a2f3efea8101278abbb1586f35421d84e8de |
#!/usr/bin/env python
"""
Find regions of first bed file that overlap regions in a second bed file
usage: %prog bed_file_1 bed_file_2 out_file
-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
-2, --cols2=N,N,N,N: Columns for start, end, strand in second file
-m, --mincols=N: Require this m... | volpino/Yeps-EURAC | tools/new_operations/gops_intersect.py | Python | mit | 2,542 | [
"Galaxy"
] | 871d07310a63187a2476231f8d71bf7d591018c69902470626969fd2379056ba |
#!/usr/bin/env python
import click
import os
import requests
import sys
import leagueids
import teamnames
import writers
BASE_URL = 'http://api.football-data.org/alpha/'
LIVE_URL = 'http://soccer-cli.appspot.com/'
LEAGUE_IDS = leagueids.LEAGUE_IDS
TEAM_NAMES = teamnames.team_names
try:
api_token = os.environ['... | nare469/soccer-cli | soccer/main.py | Python | mit | 5,464 | [
"VisIt"
] | 54200b07c71fdd0182d4c7d3b21b8089d657d70c4b33cfdc508066e43fe0706b |
from argparse import ArgumentParser
from singlecell import barcode, align, count, cluster
from singlecell.barcode import barcodes_to_plate_well
import os
import glob
from collections import OrderedDict
def get_sample(line, sample_map_filename):
keys = ["sample_id", "subsample_id", "r1_path", "r2_path"]
sample_... | roryk/singlecell | scripts/run_analysis.py | Python | mit | 5,635 | [
"BWA"
] | 15219eabbb39d435a3a1e3830be29b1a30913a38b490db72fdbf5951b5ad9889 |
def itemTemplate():
return ['object/tangible/item/quest/force_sensitive/shared_fs_crystal_force.iff'] # needs correct iff still
def customItemName():
return "Synapse Focus Crystal"
def requiredLevelForEffect():
return 80
def biolink():
return 1
def lootDescriptor():
return 'rarebuffitem'
def itemS... | agry/NGECore2 | scripts/loot/lootItems/legendarylootchest/synapse_focus_crystal.py | Python | lgpl-3.0 | 544 | [
"CRYSTAL"
] | 54dce3bd20e3a07081f04d92708c78d53f52268ad92274cc58c2f6936166bbdd |
# -*- coding: utf-8 -*-
"""
Created on Tue Jun 30 20:56:07 2015
@author: agiovann
Updated on Fri Aug 19 17:30:11 2016
@author: deep-introspection
"""
import cv2
import os
import sys
import scipy.ndimage
import scipy
import sklearn
import warnings
import numpy as np
import scipy as sp
from sklearn.decomposition import ... | agiovann/CalBlitz | calblitz/movies.py | Python | gpl-3.0 | 47,510 | [
"Gaussian"
] | 72c2e502e5e49788a9b86e2b608e8557b742307bf41bb45aa4da67c55ba65e42 |
# proxy module
from __future__ import absolute_import
from mayavi.preferences.bindings import *
| enthought/etsproxy | enthought/mayavi/preferences/bindings.py | Python | bsd-3-clause | 96 | [
"Mayavi"
] | 526125a7ca190292a5858243f657d0d8b07b0cfdf2b9cacb5534cfa0a5a4df2b |
"""
********************************************************************************
* Name: app_base.py
* Author: Nathan Swain and Scott Christensen
* Created On: August 19, 2013
* Copyright: (c) Brigham Young University 2013
* License: BSD 2-Clause
*********************************************************************... | CI-WATER/tethys | tethys_apps/base/app_base.py | Python | bsd-2-clause | 58,404 | [
"VisIt"
] | cf1d338f37d48620479b313a3ce0679de8a9ac63c7db45a159cde01f5cd21ced |
# Copyright 2010 United States Government as represented by the
# Administrator of the National Aeronautics and Space Administration.
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the L... | Metaswitch/calico-nova | nova/tests/unit/matchers.py | Python | apache-2.0 | 18,977 | [
"VisIt"
] | c37a0740eda9409b2896784b0c08848024481c6e6346aa535bd3f66e106edcb0 |
# functions for plotting and fitting gaussians
from math import sqrt, pi, log10
import numpy as N
def g_residuals(p, x, y):
ampl, centre, sigma = p
g = gaussian(x, ampl, centre, sigma)
return y - g
def multi_g_residuals(p, n, x, y):
ampl = p[0::3]
centre = p[1::3]
sigma = p[2::3]
g = multi... | bamford/astrobamf | gaussian.py | Python | mit | 3,797 | [
"Gaussian"
] | 433f41aa8d24322617d6205092545dbbb5bf0ae9c27d7b4903dabf3d06d6fa10 |
from __future__ import division, print_function
import numpy as np
from dipy.denoise.denspeed import nlmeans_3d
def nlmeans(arr, sigma, mask=None, patch_radius=1, block_radius=5,
rician=True, num_threads=None):
""" Non-local means for denoising 3D and 4D images
Parameters
----------
arr ... | JohnGriffiths/dipy | dipy/denoise/nlmeans.py | Python | bsd-3-clause | 2,157 | [
"Gaussian"
] | cfb04526e5a13d5d53aa6b6987e0ac9be15dd6735ee19323dbc59f7c94f63e29 |
import numpy as np
import psi4
import time
psi4.core.set_output_file("output.dat", False)
mol = psi4.geometry("""
He 0 0 1
He 0 0 -1
no_reorient
symmetry c1
""")
psi4.core.set_global_option("SCF_TYPE", "PK")
e, wfn = psi4.energy("B3LYP/6-31G", molecule=mol, return_wfn=True)
# Yank some things from the wavefunctio... | rmcgibbo/psi4public | tests/libxc/devl/cpks.py | Python | lgpl-3.0 | 5,150 | [
"Psi4"
] | af75744a137eab57a96391cab58f849770e83b379a8a797a0c2c2769a5d18ad0 |
#
# Copyright (C) 2013 Stanislav Bohm
#
# This file is part of Kaira.
#
# Kaira 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, version 3 of the License, or
# (at your option) any later versi... | mec059/kaira | gui/textview.py | Python | gpl-3.0 | 2,807 | [
"FLEUR"
] | 48dac36efba0d86badb465f4982669e9e0ae5f2372dec64243795906a8b4cb8f |
# posix.py - Posix utility function implementations for Mercurial
#
# Copyright 2005-2009 Olivia Mackall <olivia@selenic.com> and others
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from __future__ import absolute_import
impo... | smmribeiro/intellij-community | plugins/hg4idea/testData/bin/mercurial/posix.py | Python | apache-2.0 | 23,605 | [
"FEFF"
] | 67aaeddf372b48cfa45488aca0d1e0388b572e870b149cf6fe17ccedbcc35f77 |
#
# Copyright (C) 2013,2014,2015,2016 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 ... | Marcello-Sega/espresso | tools/blockfile.py | Python | gpl-3.0 | 7,495 | [
"ESPResSo"
] | 7b43b5fb56f4a9b433443364b8379ee1125a73ed3cc83c2c96ec107a257e53d0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
An interface to the excellent spglib library by Atsushi Togo
(http://spglib.sourceforge.net/) for pymatgen.
v1.0 - Now works with both ordered and disordered structure.
v2.0 - Updated for spglib 1.6.
v3.0 ... | gVallverdu/pymatgen | pymatgen/symmetry/analyzer.py | Python | mit | 64,034 | [
"CRYSTAL",
"pymatgen"
] | 958ca83eef6f1b29e5adfcee4a11ef991cbcf8377a7d493966c1004feaf012fe |
import os
import sys
import collections
def sam_linkage_claster (linkage_info, output):
"""
blast_linkage_claster takes 2 arguments:
1) linkage_info file which was generated from self blast allignments.
it has 2 tab seperated columns: seq_id(link1), seq_id(link2)
link1 and link2 are lated in... | NIASC/VirusMeta | blast_module/blast_linkage_claster.py | Python | gpl-3.0 | 3,813 | [
"BLAST"
] | e81f82fe8453c68f27fbf31de5c688332a660e88348d94852a8e5d90b9be20f2 |
"""Helpful utilities for building analysis pipelines.
"""
import gzip
import os
import tempfile
import time
import shutil
import contextlib
import itertools
import functools
import random
from six.moves import configparser
import fnmatch
import subprocess
import sys
import types
import toolz as tz
import yaml
try:
... | biocyberman/bcbio-nextgen | bcbio/utils.py | Python | mit | 26,720 | [
"Galaxy"
] | d5d3a68a78db9c17e16bc3f152981551f84bd5be46f975ef9040567ea69b0757 |
#
# Copyright (C) 2017 Peter Gedeck
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
'''
Collection of utilities to be used with descriptors
'''
i... | greglandrum/rdkit | rdkit/Chem/ChemUtils/DescriptorUtilities.py | Python | bsd-3-clause | 1,903 | [
"RDKit"
] | cb801d1bb6fa88907ab09a71cd01a174a87b120d073312ec393da55997aeed75 |
########################################################################
# File : Watchdog.py
# Author: Stuart Paterson
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system resource consumption. The Watchdog... | fstagni/DIRAC | WorkloadManagementSystem/JobWrapper/Watchdog.py | Python | gpl-3.0 | 37,268 | [
"DIRAC"
] | 7da5f8bca4e39bc1d48637f9876923de989d20169f9b5a4539ca719e164a1099 |
"""
@name: Modules/Housing/Pool/pool_data.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2018-2020 by D. Brian Kimmel
@note: Created on Feb 13, 2018
@license: MIT License
@summary:
"""
__updated__ = '2019-12-30'
# Import system type stuff
# Import PyMh files
from Modu... | DBrianKimmel/PyHouse | Project/src/Modules/House/Pool/pool_data.py | Python | mit | 620 | [
"Brian"
] | 9318218a5af966558df9a56b7aa0eaa021c2ec3953f478771961284c70e0ed90 |
import os
from lan_ast import *
debug = False
class CGenerator(object):
""" Uses the same visitor pattern as the NodeVisitor, but modified to
return a value from each visit method, using string accumulation in
generic_visit.
"""
def __init__(self):
self.output = ''
self.qu... | dikujepsen/OpenTran | v2.0/framework/cgen.py | Python | mit | 8,784 | [
"VisIt"
] | 83a7525e97e1d75c51b42d1efd07d77ea27fa3ad7537313ad83bfd9f333a68e7 |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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,... | govarguz/espressopp | testsuite/python_tools/complex/test_python_tools_complex.py | Python | gpl-3.0 | 3,613 | [
"ESPResSo"
] | 3ccdad8151b42620bc6661d93c913582083b1d35b45a52863fef4cd59680fd41 |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
int_or_none,
remove_end,
)
class MailRuIE(InfoExtractor):
IE_NAME = 'mailru'
IE_DESC = 'Видео@Mail.Ru'
_VALID_URL = r'https?://(?:(?:www|m)\.)?my\.mail\.ru/(?:video/.*#video=... | Tithen-Firion/youtube-dl | youtube_dl/extractor/mailru.py | Python | unlicense | 5,086 | [
"Galaxy"
] | ee9a69845b2131dcd8aa81c2411ded78895cd640eb74ed3aa28952769f6d2b68 |
##############################################################################
# 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/r-altcdfenvs/package.py | Python | lgpl-2.1 | 2,040 | [
"Bioconductor"
] | 309bd4f5977eb4bf0c974a22cf2667077973973138e71d425e10415252a5d708 |
#!/usr/bin/python
# Copyright 2017 Google Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later vers... | britcey/ansible | lib/ansible/modules/cloud/google/gcp_healthcheck.py | Python | gpl-3.0 | 16,066 | [
"VisIt"
] | 70c48e0c7b359809f694cfd7ac2ee67c2690f6e183a41e48363f18e02ed7ebc6 |
from flask import Flask, jsonify, request, g, redirect, url_for, \
abort, render_template, flash
import pika
from lxml import etree
from lxml.builder import ElementMaker
import random
import string
DATABASE = '/tmp/flaskr.db'
DEBUG = True
SECRET_KEY = 'development key'
USERNAME = 'admin'
PASSWORD = 'default'
app... | Advisory-iRound/StatusMapManager | app.py | Python | gpl-2.0 | 2,526 | [
"VisIt"
] | 9eacc8c565f3917db35d5ddd50bbe2278c93c23ce722516441f0974fb9ba99ef |
#!/usr/bin/env python
import os
import sys
sys.path.insert(1, os.path.abspath('..'))
#---------------------------------------------------------------------------------------------------
# SMT SYNTHESIS OF ARTIFICIAL NEURAL NETWORKS
#------------------------------------------------------------... | iwob/pysv | examples/synth_ann_xor.py | Python | mit | 8,840 | [
"NEURON"
] | 6930f67ff32ff05b0b94c8878cf0eb085d5a3b718aa077e6ec73b39b5bcba919 |
import datetime
import json
from sqlalchemy import orm
from DIRAC.DataManagementSystem.Client.FTS3Job import FTS3Job
from DIRAC.DataManagementSystem.private import FTS3Utilities
from DIRAC.DataManagementSystem.Client.DataManager import DataManager
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Re... | arrabito/DIRAC | DataManagementSystem/Client/FTS3Operation.py | Python | gpl-3.0 | 18,250 | [
"DIRAC"
] | e2e37c0cac556944a6ded729fc38cdeb77eb04c10c90980f914bc85d06bf614f |
# Copyright (c) 2012 Luke McCarthy <luke@iogopro.co.uk>
#
# This is free software released under the MIT license.
# See COPYING file for details, or visit:
# http://www.opensource.org/licenses/mit-license.php
#
# The file is part of FSMonitor, a file-system monitoring library.
# https://github.com/shaurz/fsmonitor
imp... | shaurz/fsmonitor | fsmonitor/polling.py | Python | mit | 6,513 | [
"VisIt"
] | a4d4c414c8c7d9333cc16686a6f3cb6b5d12d1383a5c959c3ead86498dc1a4ae |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009-2010 Benny Malengier <benny.malengier@gramps-project.org>
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2011 Adam Stein <adam@csh.rit.ed... | Nick-Hall/gramps | gramps/plugins/docgen/asciidoc.py | Python | gpl-2.0 | 17,549 | [
"Brian"
] | aa8bcf353520a18fbb6683a65acdc0fa5a32d75440e64425a6cb10de6644deff |
from netCDF4 import Dataset
import numpy as np
import os
#initializes a netCDF file to hold a single variable with dimensions x, y, z, time
#dimension lengths are specified by user
def initialize_ncFile(filename, varname, xlen, ylen, zlen, tlen):
#an error is thrown if the file already exists, delete it fi... | nchaparr/Sam_Output_Anls | initialize_ncFile.py | Python | mit | 1,159 | [
"NetCDF"
] | 437b3a95af9b74961b21a45d190a9a734ceedc21f7966857d5271b8f01ee3305 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/speech_generator.py | Python | gpl-3.0 | 79,095 | [
"ORCA"
] | e818c178cf63bc192924b4a262393b891ba7bec65b88ee100104a0c07210ab7e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2007 Donald N. Allingham
# Copyright (C) 2008 Lukasz Rymarczyk
# Copyright (C) 2008 Raphael Ackermann
# Copyright (C) 2008-2011 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011-2013 Paul Franklin
#
# This pro... | prculley/gramps | gramps/cli/plug/__init__.py | Python | gpl-2.0 | 35,372 | [
"Brian"
] | fced3ef4ba7adadc6a2ffbc7884b486d69951e194ea0b2295b007630d679ecf6 |
#!/usr/bin/env python
import json
import logging
import os
import string
import subprocess
import sys
import time
import uuid
from random import choice
from twisted.internet import reactor, defer
from twisted.internet.task import deferLater
from twisted.internet.defer import CancelledError
from twisted.python import... | msmolens/VTK | Web/Python/vtk/web/launcher.py | Python | bsd-3-clause | 26,514 | [
"ParaView",
"VTK"
] | 7238102393d60b7e170282939206e77b25f07abe2241250491140154ffec7ac6 |
#!/usr/bin/env python
'''
The expressions module contains classes to represent an expression. The main
class is ExpressionNode. ExpressionNode's most useful method is py_string(),
which returns a Python string representing that expression.
'''
import sys
from ctypedescs import *
import keyword
# Right now, the obje... | pombredanne/ctypesgen | ctypesgencore/expressions.py | Python | bsd-3-clause | 10,115 | [
"VisIt"
] | e44c638f02b2ce6cf26e020b60fc509a38694643364028156d2b730e1ac78df3 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Index.py
This module provides a way to create indexes to text files.
Classes:
Index D... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Index.py | Python | gpl-2.0 | 4,883 | [
"Biopython"
] | 17edaab3112425b80c75cb18918b0a5b44796115083644872bb5ca42ce395b06 |
#!/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/pbc/scf/ghf.py | Python | apache-2.0 | 4,343 | [
"PySCF"
] | 9a38def7f301a18d1b3fd11a0fad78a2145a40eed3e6cd1f16e31e67ed787c55 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
from itertools import product
from fractions import Fraction
from abc import ABCMeta, abstractmethod
from collections.abc import Sequence
import numpy as np
import warnings
import re
from monty.serial... | dongsenfo/pymatgen | pymatgen/symmetry/groups.py | Python | mit | 18,798 | [
"pymatgen"
] | 02043a1e6317ebf284c4dc7e79e1ca1741a679068cb216e7b1a11b80734ebe78 |
#!/usr/bin/env python
# This example demonstrates the use of vtk3DSImporter.
# vtk3DSImporter is used to load 3D Studio files. Unlike writers,
# importers can load scenes (data as well as lights, cameras, actors
# etc.). Importers will either generate an instance of vtkRenderWindow
# and/or vtkRenderer or will use th... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/IO/Python/flamingo.py | Python | gpl-3.0 | 1,534 | [
"VTK"
] | 5830c391f7b71ebbd4b56b45fbbf4eef68b7cc54b2faba243c2e35085d0d9d5e |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jun 12 20:20:03 2018
@author: BallBlueMeercat
"""
import time
import dnest4
import numpy as np
import numpy.random as rng
import matplotlib.pyplot as plt
import pickle
import datasim
import results
import tools
import matplotlib as mpl
mpl.style.use('d... | lefthandedroo/Cosmo-models | Models/Bfactor.py | Python | mit | 10,727 | [
"Amber",
"Gaussian"
] | d64f2bdc192d69163c418696db530b2e1fefa44a61d8e0980f66c7a14874276d |
# ***************************************************************************
# *
# * Copyright (C) 2013-2016 University of Dundee
# * All rights reserved.
# *
# * This file is part of SAMoS (Soft Active Matter on Surfaces) program.
# *
# * SAMoS is free software; you can redistribute it and/or modify
# * it unde... | sknepneklab/SAMoS | utils/read_param.py | Python | gpl-3.0 | 24,144 | [
"Gaussian"
] | bc6badbaecce45c6469eb669cedb7548b31550fa59449e00423c2f0c1f0e0b0b |
# $Id$
#
# Copyright (C) 2011 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" unit testing code for molecule drawing
"""
from ... | soerendip42/rdkit | rdkit/Chem/Draw/UnitTestDraw.py | Python | bsd-3-clause | 5,233 | [
"RDKit"
] | 7e78da78564f056ffcde3fd0c52414986b1d17e8c065c9d392ed1747e63c4cdc |
# Copyright 2018 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 agreed to in writing, ... | brain-research/deep-molecular-massspec | feature_utils_test.py | Python | apache-2.0 | 3,719 | [
"RDKit"
] | 5fb9eb4bb1ce1a49e3129246154282acfb002412e870254d7cd7a0fad593dd05 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/lenovo/cnos_showrun.py | Python | bsd-3-clause | 4,911 | [
"VisIt"
] | 37a8ac32fa651a9448cf4008b1276b308c3a3a3474582acd2d9367b92b05be90 |
def cell_array_slicer(data):
""" Iterate over cell components on a vtk cell array
VTK stores the associated point index for each cell in a one
dimensional array based on the following template::
[n, id0, id1, id2, ..., idn, m, id0, ...]
The iterator takes a cell array and returns the point indi... | simphony/simphony-mayavi | simphony_mayavi/core/cell_array_tools.py | Python | bsd-2-clause | 620 | [
"VTK"
] | 25a2fa6c80b17a5081dd14703a8501f98f49b9c0b59af21f7cd05953738d1e3e |
"""\
Create general Channel Proto, pass in name, x and y power, and params
Also, create the library of channels
Might need a few other chan_proto types, such as
inf-tau channels
Ca dep channels
chan_proto quires alpha and beta params for both activation and inactivation
If no inactivation, just send in empty... | subhacom/moose-core | tests/python/chan_proto.py | Python | gpl-3.0 | 4,834 | [
"MOOSE"
] | af4b535c7659a7b5cc086da050e533c64dfe65b77887755d8a0281dcb3b870f9 |
#
# Copyright (C) 2013,2014 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... | rbardak/espresso | testsuite/python/electrostaticInteractions.py | Python | gpl-3.0 | 4,650 | [
"ESPResSo"
] | acbb23120da9f9c51c2798d511c8879edac3030e570f1dce08e74777f7eadc5f |
r"""
brew install libtiff libjpeg webp little-cms2
sudo easy_install pip
sudo pip install Pillow
"""
import sys, os, json, math, gzip, shutil
import numpy as np
from PIL import ImImagePlugin
from PIL import Image
from vtk import *
from tonic.paraview import data_converter
def extractFloatArrays(directory, ranges):
... | Kitware/tonic-data-generator | python/tonic/cinema/spec-b-converter.py | Python | bsd-3-clause | 5,917 | [
"ParaView",
"VTK"
] | 9f3809926be2ef4604068dba68eb2433b8158d549c1214178e31165e94f6d6b4 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/changeFriend.py | Python | gpl-3.0 | 3,145 | [
"Galaxy"
] | f5820992de0a0fd2ac5cb85ebe906c72c2bca7d024377f936e01011a139923ba |
"""
This sample demonstrates a simple skill built with the Amazon Alexa Skills Kit.
The Intent Schema, Custom Slots, and Sample Utterances for this skill, as well
as testing instructions are located at http://amzn.to/1LzFrj6
For additional samples, visit the Alexa Skills Kit Getting Started guide at
http://amzn.to/1LG... | ItsNotABugItsAFeature/transcribe | alexa/stopTranscribe.py | Python | mit | 7,197 | [
"VisIt"
] | b85566bc644d64804f8d3af467c2c2c3c453e357ffa7e31e56b634d5ea3b4f4d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
__author__ = "Bharat Medasani"
__copyright__ = "Copyright 2013, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "bkmedasani@lbl.gov"
__date__ = "Aug 2, 2013"
import os... | gmatteo/pymatgen | pymatgen/io/tests/test_zeopp.py | Python | mit | 11,239 | [
"VASP",
"pymatgen"
] | ca6d0f60364eb3f91f123f3c8811b3ffa75065f777959c0611a87b31c1e9b3a4 |
#!/usr/bin/env python
#==============================================================================
# Copyright 2012 Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Amazon Software License (the "License"). You may not use
# this file except in compliance with the License. A copy of the... | singlebrook/AWS-ElasticBeanstalk-CLI | eb/macosx/python3/lib/elasticbeanstalk/eb_utils.py | Python | apache-2.0 | 12,340 | [
"BLAST"
] | c918b3524103aee3c292f5687e5b2b4c172d43d00673207538eb066837aac921 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | google/uncertainty-baselines | baselines/jft/sngp.py | Python | apache-2.0 | 33,350 | [
"Gaussian"
] | 6ad9b38df7084c4ebc5bea2fbe18e346d2771c46febb327ad1731190a4ea7c50 |
"""
====================================================================
Probabilistic predictions with Gaussian process classification (GPC)
====================================================================
This example illustrates the predicted probability of GPC for an RBF kernel
with different choices of the hy... | chrsrds/scikit-learn | examples/gaussian_process/plot_gpc.py | Python | bsd-3-clause | 3,993 | [
"Gaussian"
] | 5ab696e817b3ac9bb481c9efb17924a5cc882836e466f7c8ce0cec50cc6f1dcf |
"""
Subpackage with functions to plot all kind of results from runs.
"""
import numpy as np
import math, sys, os
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import matplotlib.colors as colors
from matplotlib.ticker import MultipleLocator, FormatStrFormatter, MaxNLocator
import scipy.ndimage
import ... | COSMOGRAIL/PyCS | pycs/sim/plot.py | Python | gpl-3.0 | 70,485 | [
"Bowtie"
] | 83581d7c569188bd6a2e91fd7d93404fb14d2f4ff454d3381b2590ff822b1bab |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import directives
from sphinx import addnodes, __version__ as sphinx_ver
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.writers.html import SmartyPantsHTMLTranslato... | Beeblio/django | docs/_ext/djangodocs.py | Python | bsd-3-clause | 11,807 | [
"VisIt"
] | 410c15ea2fec7935d0cc332a2122ddbb46b01ef4d8bb3f1437d952d808e6f517 |
"""
This app is intended to provide the core functionality for tracking user
engagement with content and Kolibri in general. As such, it is intended
to store details of user interactions with content, a summary of those
interactions, interactions with the software in general, as well as user
feedback on the content and... | jayoshih/kolibri | kolibri/logger/models.py | Python | mit | 8,175 | [
"VisIt"
] | 9e7e609b0be89458597e1d8363cb7a79dfdf96f065985d9c54fd1fe817ffdd0d |
# -*- coding: utf-8 -*-
import re
import os
import sys
from os import path
import traceback
#TODO:
# support #else
# support #define
# support constrainttypes
GMXLIB = ["/usr/local/gromacs/share/gromacs/top/","/usr/share/gromacs/top/"]
if("GMXLIB" in os.environ):
GMXLIB = os.environ["GMXLIB"].split(":")
#==========... | CMD-at-ZIB/ZIBMolPy | ZIBMolPy_package/ZIBMolPy/io/topology.py | Python | lgpl-3.0 | 13,427 | [
"Gromacs"
] | 674a31dd06b2753a63d216f91561f5c9ef95c98752d478287ff71e7eacee1f1f |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | MrTheodor/espressopp | testsuite/unittest/TestEsLogging.py | Python | gpl-3.0 | 2,198 | [
"ESPResSo"
] | 3f33ffa0c5bfdc7611c4c8f5f016868316a61edf940c2f813a7e2ec271514a7e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, Ve... | sparkslabs/kamaelia | Sketches/MH/dirac/Dirac.py | Python | apache-2.0 | 10,508 | [
"DIRAC"
] | 5c274cebd8c0f5f62962b86fa87062e5745795cd01f2b079a2711ed55760ffb4 |
from mdtraj import element
from mdtraj.testing import assert_raises
def test_immutable():
def f():
element.hydrogen.mass = 1
def g():
element.radium.symbol = 'sdfsdfsdf'
def h():
element.iron.name = 'sdfsdf'
assert_raises(AttributeError, f)
assert_raises(AttributeError, g)
... | casawa/mdtraj | mdtraj/tests/test_element.py | Python | lgpl-2.1 | 482 | [
"MDTraj"
] | aff558ba8135f6fa0fbc518ed288d0671d7174e5ceaee116d1b567c9a2eabd4b |
########################################################################
# File: RequestExecutingAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/12 15:36:47
########################################################################
""" :mod: RequestExecutingAgent
===========================
..... | miloszz/DIRAC | RequestManagementSystem/Agent/RequestExecutingAgent.py | Python | gpl-3.0 | 15,238 | [
"DIRAC"
] | 87d8baee86ec8bf3090f98d72538712b8955765af574938c53699c354290e5f2 |
"""
Generalized linear models currently supports estimation using the one-parameter
exponential families
References
----------
Gill, Jeff. 2000. Generalized Linear Models: A Unified Approach.
SAGE QASS Series.
Green, PJ. 1984. "Iteratively reweighted least squares for maximum
likelihood estimation, and some ... | jseabold/statsmodels | statsmodels/genmod/generalized_linear_model.py | Python | bsd-3-clause | 84,593 | [
"Gaussian"
] | 5ab3815e483dd58b2cb7dbd69540b4dabb9734064fc12742999440b72f21d344 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
from datetime import date
try:
import json
except:
import simplejson as json
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','versi... | plainprogrammer/timobile-streaming_metadata | build.py | Python | mit | 6,493 | [
"VisIt"
] | 5eaa2ceafce4be6b95725ca0686d448038b5209706ae704188bffdbc908d44f0 |
#!/usr/bin/env python3
"""
weatherBot tests
Copyright 2015-2019 Brian Mitchell under the MIT license
See the GitHub repository: https://github.com/BrianMitchL/weatherBot
"""
import configparser
import datetime
import logging
import os
import pickle
import sys
import unittest
import forecastio
import pytz
import twe... | bman4789/weatherBot | test.py | Python | mit | 45,908 | [
"Brian"
] | dda4d914f2ea54c4ec93a170660fe2388d4bed934a9954d31e3c94ae6d87e7ed |
#!/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/gccsd_t_lambda.py | Python | apache-2.0 | 5,864 | [
"PySCF"
] | dad326b75945f817fd50f11c8e4c9ac2eaa7e08fd8dee015cd0d44f1a5cb531b |
# Copyright (C) 2015-2022: The University of Edinburgh
# Authors: Craig Warren and Antonis Giannopoulos
#
# This file is part of gprMax.
#
# gprMax 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 Foundatio... | gprMax/gprMax | gprMax/input_cmds_multiuse.py | Python | gpl-3.0 | 47,381 | [
"VTK"
] | d790e52a2bd81d95e751d57f33e404afa0a3d1a8b129e97d9fb9fd7530486edc |
"""
This module contains the necessary tools to discover and load
the handlers for serving HTTPS
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from tornado.web import url as TornadoURL, RequestHandler
from DIRAC import gConfig... | yujikato/DIRAC | src/DIRAC/Core/Tornado/Server/HandlerManager.py | Python | gpl-3.0 | 7,117 | [
"DIRAC"
] | 649733668fdfd34985941adde6c59eda3cadf818d44f80dfdf3c43de4422b768 |
#!/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/forge/reservoir_and_water_3.py | Python | lgpl-2.1 | 2,604 | [
"MOOSE"
] | 0dbf9920762f3cd27cce781c68c80d22dad2356a0e0afa954574cbbbedf16830 |
#!/usr/bin/env python
"""Prevent unwanted files from being added to the source tree."""
import os
import sys
def main():
"""Main entry point."""
paths = sys.argv[1:] or sys.stdin.read().splitlines()
allowed_extensions = (
'.cs',
'.ps1',
'.psm1',
'.py',
)
skip = (
... | albertomurillo/ansible | test/sanity/code-smell/no-unwanted-files.py | Python | gpl-3.0 | 1,137 | [
"Galaxy"
] | b6458c8e935d8e9a37d4d4db347c04c6f811f677be0e003883854437312d2cd9 |
#!/usr/bin/env python3
import numpy as np , pylab, tkinter
import math
import matplotlib.pyplot as plt
import mpmath as mp
hbar=0.658212 # Planck's constant (eV.fs/rad)
J0=0.05 # per-neighbor exchange interaction (eV)
S1 = np.array([1.0, 0.0, 0.0])
S2 = np.array([0.0, 1.0, 0.0])
alpha=0.01 ... | pastewka/lammps | examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py | Python | gpl-2.0 | 2,292 | [
"LAMMPS"
] | 4d382288625501c53f628de9d9ec347d41216a752808f85164e3766b2dbb876c |
#!/usr/bin/env python3
from distutils.core import setup
from glob import glob
# Scripts whose names end in a-z or 1-9 (avoids emacs backup files)
scripts = glob('scripts/*[a-z,1-9]')
setup(name='vasputil',
version='master',
description='VASP utilities',
author='Janne Blomqvist',
author_email=... | jabl/vasputil | setup.py | Python | lgpl-2.1 | 467 | [
"VASP"
] | 06978cc40a56f730a29c0f060ee59288146e5a6cf87b5302062aa8e8f6c67635 |
import argparse
import os
import string
import sys
__author__ = 'Rob Edwards'
"""
Newick format:
((15:0.04110,((16:0.03869,17:0.11891):0.00888,14:0.10566):0.00609):0.09345,
(((6:0.00000,7:0.00000):0.01537,13:0.00839):0.00229,((1:0.00011,
4:0.00065):0.01946,(11:-0.01252,(10:0.00692,(8:0.00463,(((2:0.00178,
(3:0.00192... | linsalrob/EdwardsLab | roblib/newick.py | Python | mit | 6,633 | [
"Biopython"
] | b0c78ada944b4742e13003d0414a0afcc01715f1a37c24136c83f68d5b255d2f |
# -*- coding: utf-8 -*-
import re
import scrapy
from scrapyproject.showingspiders.showing_spider import ShowingSpider
from scrapyproject.items import (ShowingLoader, init_show_booking_loader)
from scrapyproject.utils import UnitedUtil
class UnitedSpider(ShowingSpider):
"""
united site spider.
"""
name... | gas1121/JapanCinemaStatusSpider | scrapyproject/showingspiders/united.py | Python | mit | 8,448 | [
"VisIt"
] | 11247f8a0de75c8c39a7413add487402306af43acf9e5e5bccaa9cbdf2978a35 |
# -*- coding: utf-8 -*-
"""
For a undirected graph with tree characteristics, we can choose any node as the root. The result graph is then a rooted tree. Among all possible rooted trees, those with minimum height are called minimum height trees (MHTs). Given such a graph, write a function to find all the MHTs and ret... | Ahmed--Mohsen/leetcode | minimum_height_trees.py | Python | mit | 2,530 | [
"VisIt"
] | 5538c4bd82f4ad42616b5658f23da8f2d291fd17e172189d96f4a29f7bdc8f0e |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import symp... | nuclear-wizard/moose | modules/navier_stokes/python/ins_calc_routines.py | Python | lgpl-2.1 | 8,672 | [
"MOOSE"
] | edcba0b09037f729857b1b4c68b75692d48b7b0ab769c79f70b56f3670506219 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# peakfinder.py
"""
Class for finding blobs. Encapsulates a difference of gaussians (DoG)
algorithm and exposes methods to easilyt interact with the data and
results.
Copyright (c) 2016, David Hoffman
"""
import logging
# need math log too, for arbitrary base
from math i... | david-hoffman/peaks | peaks/peakfinder.py | Python | apache-2.0 | 33,428 | [
"Gaussian"
] | ff7a81993d468b8f0311ba7c8fae37dcb45bbaf2cef3a6e4fdf5a50909237440 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/externing.py | Python | gpl-2.0 | 4,073 | [
"PyMOL"
] | b20e74502fd838eee511518f7ced367087a0ec08caf29fa6158f9cc677cdcb37 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import importlib
from importlib.metadata import version as get_version
from DIRAC import S_OK
from DIRAC.Core.Utilities.Extensions import extensionsByPriority
def getCurrentVersion():
... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/Version.py | Python | gpl-3.0 | 952 | [
"DIRAC"
] | 6cf2d61c050fa9549cbff4a922a53ce6b4c1598318ab30cfb349ad0dc5b3ae5d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as... | Freeseer/freeseer | src/freeseer/frontend/record/ReportDialog.py | Python | gpl-3.0 | 4,570 | [
"VisIt"
] | aefe8c22b7bf0ae290b0845d2f0a88e6a22141d8433b3cb28dd8c17e9783ca0e |
import numpy as np
from multiphenotype_utils import (get_continuous_features_as_matrix, add_id, remove_id_and_get_mat,
partition_dataframe_into_binary_and_continuous, divide_idxs_into_batches)
import pandas as pd
import tensorflow as tf
from dimreducer import DimReducer
from general_autoencoder import GeneralAuto... | epierson9/multiphenotype_methods | laplacian_variational_autoencoder.py | Python | mit | 4,025 | [
"Gaussian"
] | 37d2cd277e25160b12f2da04f624a9c1ac50bf978935b7735fa48fb8e24a847a |
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, WOK, asyncGen
from DIRAC.Core.DISET.RPCClient import RPCClient
import json
class NotepadHandler(WebHandler):
AUTH_PROPS = "authenticated"
def index(self):
pass | chaen/WebAppDIRAC | WebApp/handler/NotepadHandler.py | Python | gpl-3.0 | 228 | [
"DIRAC"
] | d3eb1ca7ada8496ff5f1b58558562b95c508b5f2873010a5b93325aa5b121823 |
import os.path as op
import gzip
import string
import logging
import urllib.request
import re
from functools import wraps
from tempfile import NamedTemporaryFile
from collections import defaultdict, OrderedDict
import six
import numpy as np
import Bio
from Bio.PDB import PDBIO, Select, NeighborSearch
from Bio.PDB.PDBPa... | ostrokach/elaspic | elaspic/structure_tools.py | Python | mit | 36,218 | [
"Biopython"
] | 1cc156a90fea2f6d62ec9e65e27f689e5da65584a65af7085a3af0bf645a93b4 |
####
#Copyright 2011 Samuel Volchenboum, Jonathan Goya, Gene Selkov, Chaim Kirby,
#
#This file is part of Validator.
#
#Validator 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,... | chicagohemeonc/Validator-Max | code/validator_mediator.py | Python | gpl-3.0 | 4,744 | [
"Galaxy"
] | 2cd1ff5952ff3df78d9a2890042ccc5ae2a8357ecd712d34ac7b76e49b0d94ed |
#!/usr/bin/env python
'''unit testing code for pysam.
Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''
import sys
import os
import shutil
import gzip
import pysam
import unittest
import itertools
import subprocess
import glob
import re
DATADIR = 'tabix_data'
IS_PY... | genome-vendor/python-pysam | tests/tabix_test.py | Python | mit | 29,309 | [
"pysam"
] | a37a4364a703adcb31fa928f4079b1410f177c94699a8d1fc03f94d243ea858e |
__author__ = "E. A. Tacao <e.a.tacao |at| estadao.com.br>"
__date__ = "12 Fev 2006, 22:00 GMT-03:00"
__version__ = "0.03"
__doc__ = """
ButtonTreeCtrlPanel is a widget where one can place check buttons, tri-state
check buttons, radio buttons, both, and the ability to display them
hierarchically.
Abou... | ktan2020/legacy-automation | win/Lib/site-packages/wx-3.0-msw/wx/lib/analogclock/lib_setup/buttontreectrlpanel.py | Python | mit | 10,055 | [
"VisIt"
] | 72d76c07440c2aeb3f5e7975674c127b2853fae6bd35968afe605fa6356c8132 |
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