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# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | Karaage-Cluster/karaage | karaage/management/commands/lock_expired.py | Python | gpl-3.0 | 2,023 | [
"Brian"
] | 5d330c78e987f3d6c9d52cb38de9c43a78d23f145ecaf898dd4d3494c6bee57d |
"""
The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts a thread for execution of the job
and a Watchdog Agent that can monitor its progress.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN JobWrapper
:end-before: ##END
:caption: JobW... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 65,651 | [
"DIRAC"
] | 50736f93096484150a239672621683243f94c7f7017bef8b440f0a5246e5e6c5 |
import numpy as np
import os
from .sfr import SFR
from .solar_abundance import solar_abundances
import time
from .data_to_test import likelihood_function, wildcard_likelihood_function, elements_plot, arcturus, sol_norm, plot_processes, save_abundances, cosmic_abundance_standard, ratio_function, star_function, gas_rese... | jan-rybizki/Chempy | Chempy/cem_function.py | Python | mit | 40,611 | [
"ChemPy",
"Gaussian"
] | f2b9e83411e946240f02b84007824f45f7889694499f6b40ec8567093dec99ab |
# 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... | pvagner/orca | src/orca/scripts/apps/soffice/structural_navigation.py | Python | lgpl-2.1 | 3,942 | [
"ORCA"
] | ee9160e08078dadd5a71e8d8f7e981704b03e89cbf5ed6e81c47ed39b412d8f8 |
#
# Copyright 2016 The BigDL 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 applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/learn/spark/test_estimator_openvino.py | Python | apache-2.0 | 6,137 | [
"ORCA"
] | 23e2a3bbb42d046ba1e8bab39483ea9d96f038565e886ad16745e2ad40a860c0 |
"""
Socket abstraction module
Allows reusing previously opened sockets.
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
import time
import errno
import os, platform
im... | runefriborg/pycsp | pycsp/parallel/ossocket.py | Python | mit | 9,785 | [
"Brian"
] | 3f50f7ce19dcd610fc8b98acbb88ab599008dcd0de871631d35176b20c690c14 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import math
import numpy as np
import pandas as pd
from statsmodels.tsa.stattools import adfuller
import matplotlib.pyplot as plt
# Split time series into two (or more) partitions and compare the mean and variance of each group.
# If they differ and the difference is stat... | sangwook236/general-development-and-testing | sw_dev/python/rnd/test/statistics/statsmodels/statsmodels_tsa_stationarity.py | Python | gpl-2.0 | 2,150 | [
"ADF"
] | 9a68a642545d4827bea134ec2525dc9a637376ab008df964df4d1143098d8d8a |
import logging
import calendar
import copy
import dateutil
import numpy
import datetime
from couchdbkit.ext.django.schema import Document, StringProperty, IntegerProperty, DateTimeProperty
from couchdbkit.schema.base import DocumentSchema
from couchdbkit.schema.properties import LazyDict
from casexml.apps.case.models i... | SEL-Columbia/commcare-hq | corehq/apps/indicators/models.py | Python | bsd-3-clause | 33,596 | [
"VisIt"
] | dc22e1c087ba3a45856510a41a907f6ed50fc7adb621601302f77672c72ed434 |
import re
import warnings
from datetime import datetime
from functools import partial
import numpy as np
import pandas as pd
from ..core import indexing
from ..core.common import contains_cftime_datetimes
from ..core.formatting import first_n_items, format_timestamp, last_item
from ..core.variable import Variable
fro... | chunweiyuan/xarray | xarray/coding/times.py | Python | apache-2.0 | 16,949 | [
"NetCDF"
] | 170868b9fe5d5ba24a7627929cd814c95542c2e56d9b97f702bfdb7d50bae379 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# sssadmin - SSS sandbox generator and monitor for individual users
# Copyright (C) 2003-2015 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/shared/functionality/sssadmin.py | Python | gpl-2.0 | 13,548 | [
"Brian"
] | 7bbb5bcfff9c3bbd9655da21399aa136b1a1a330e921ca83040392f9f1e51b54 |
'''
An ALPR experiment runs in concert with MOE to find the optimal value for 'n' settings
Given a benchmark, and a list of settings, the ALPR experiment will communicate with MOE to manage
the next values to use. It also keeps track of the results and stops it when the experiment is complete.
'''
import sys, time
f... | openalpr/benchmarks | moe-experiments/moealpr/alpr_experiment.py | Python | agpl-3.0 | 2,590 | [
"MOE"
] | 7b23b636cfd2c4b0b8fcd22b0f8546cf0d5a633c344ffbb0da1285cc005d5cc3 |
# monitor.py
#
# Copyright (C) 2011-2015 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 progr... | maxamillion/lorax | src/pylorax/monitor.py | Python | gpl-2.0 | 6,808 | [
"Brian"
] | 5ae3a36290a435c4c97bb59931a8c73c1bdb21ee0b3b56933d20ab3706d58547 |
"""Tests for transforms.py."""
import textwrap
from pytype.pytd import transforms
from pytype.pytd.parse import builtins
from pytype.pytd.parse import parser_test
from pytype.pytd.parse import visitors
import unittest
class TestTransforms(parser_test.ParserTest):
"""Tests the code in transforms.py."""
def Par... | pombredanne/pytype | pytype/pytd/transforms_test.py | Python | apache-2.0 | 2,438 | [
"VisIt"
] | 4f9e864a5a93807822cb1b76fe314066793624d812310257cda441d28c229f81 |
#!/usr/bin/env python
"""add DMPs to jbrowse as gff3 and bigbed files"""
import argparse
import os
import gzip
import cPickle as pickle
import xml.etree.cElementTree as ET
from Bio import SeqIO
from nested_dict import nested_dict
def parse_args():
"""Parse command line arguments"""
parser = argparse.ArgumentP... | thomasvangurp/epiGBS | jbrowse/add_dmp.py | Python | mit | 15,139 | [
"BLAST"
] | ed9b60c37219343085a93dc4090b7b37ea2d55c2854137977133ebfa0ce15593 |
# Copyright 2016 Mycroft AI, Inc.
#
# This file is part of Mycroft Core.
#
# Mycroft Core is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | JarbasAI/JarbasAI | jarbas_skills/skill_translate_skills/__init__.py | Python | gpl-3.0 | 10,660 | [
"VisIt"
] | 77e28572fb944901d912a0a864f18d7dc858baefacc071982f99473ef8c38b0d |
import fileinput, os, random, math
from bs_utils.utils import *
from bs_align_utils import *
#----------------------------------------------------------------
def extract_mapping(ali_file):
unique_hits = {}
non_unique_hits = {}
header0 = ""
family = []
for header, chr, no_mismatch, location1, cigar... | BSSeeker/BSseeker2 | bs_align/bs_pair_end.py | Python | mit | 49,840 | [
"Bowtie"
] | 1bd8b45d08871350f6c30412086caca078442e28ea87552330697dc0f8468e0c |
import math, random
from pysparse.sparse import spmatrix
def bytesToString(n):
if n < 1024:
return '%d Bytes' % n
n /= 1024.0
if n < 1024:
return '%.1f Kbytes' % n
n /= 1024.0
if n < 1024:
return '%.1f Mbytes' % n
n /= 1024.0
return '%.1f Gbytes' % n
def printInfo(... | rspeer/csc-pysparse | pysparse/tools/spmatrix_util.py | Python | bsd-2-clause | 3,753 | [
"VTK"
] | 9124cb42d0e896c2372dd38d6d35859cfb6851fb036ade96cc6529f449c7bde7 |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# simple.py
# Purpose: mimic operation of examples/COUPLE/simple/simple.cpp via Python
# Serial syntax: simple.py in.lammps
# in.lammps = LAMMPS input script
# Parallel syntax: mpirun -np 4 simple.py in.lammps
# ... | arielzn/lammps | python/examples/simple.py | Python | gpl-2.0 | 2,272 | [
"LAMMPS"
] | 3b0f2cc727c2340626dfdf66fab78c3a524ee186cc10b43393fb00bbcd8838b6 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon
#
# MDTraj i... | marscher/mdtraj | MDTraj/tests/test_topology.py | Python | lgpl-2.1 | 3,980 | [
"MDTraj",
"OpenMM"
] | a3bb4150dccdfc715ee3704e018a30ff86878bc3143a8f2be1acebef7faebaf9 |
"""
This module provides GOCDB2CSAgent code.
The agent is used to synchronize information between GOCDB and DIRAC configuration System (CS)
Right now it only adds perfosonar endpoints
The following options can be set for the GOCDB2CSAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN GOCDB2CSAge... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/Agent/GOCDB2CSAgent.py | Python | gpl-3.0 | 10,495 | [
"DIRAC"
] | 4ff7f13dbc8543567a72766ddb1e64620821c9e87b43acfb7ce5a4348287d68c |
#!/usr/bin/env python
from __future__ import print_function
import os
import re
import subprocess
import sys
from distutils.command.build import build
from distutils.command.sdist import sdist
from distutils.errors import DistutilsExecError
from distutils.version import StrictVersion
from setuptools.command.build_ext i... | baoilleach/openbabel | scripts/python/setup.py | Python | gpl-2.0 | 6,283 | [
"Open Babel"
] | b9545f6b78f1c8e4301cb40c9a3cf0624d800a3e7aecf9fc5f8495ec8ab37167 |
# -*- coding: utf-8 -*-
##
##
## This file is part of Indico.
## Copyright (C) 2002 - 2014 European Organization for Nuclear Research (CERN).
##
## Indico 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; eith... | pferreir/indico-backup | indico/core/config.py | Python | gpl-3.0 | 43,294 | [
"CRYSTAL"
] | 3fdff824f823edd41882587dcd8456ebfb6d635747cd07e563c1f2670342ed99 |
"""
argparse for mail-style headers
``headerparser`` parses key-value pairs in the style of RFC 822 (e-mail)
headers and converts them into case-insensitive dictionaries with the trailing
message body (if any) attached. Fields can be converted to other types, marked
required, or given default values using an API base... | jwodder/headerparser | src/headerparser/__init__.py | Python | mit | 1,984 | [
"VisIt"
] | 92fbd2c6b71400923b8cd7273544c14ed292a064ea1b7be493ee9bad09f05a53 |
'''
Created on 28/8/2014
@author: victor
'''
import json
import sys
import hivprotmut.tools as tools
from hivprotmut.sequences.fastaFile import FastaFile
from hivprotmut.external.blast.blastpCommands import BlastpCommands
if __name__ == '__main__':
parameters = json.loads(tools.remove_comments(open(sys.argv[1]).r... | victor-gil-sepulveda/PhD-HIVProteaseMutation | hivprotmut/blastDBIds.py | Python | mit | 907 | [
"BLAST"
] | 08d0e8fdfaa7ca297c6b61dec4df8978ee5fde4ec841d2efd2eeaba4e143d760 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import math
import numpy as np
import cv2 as cv
from matplotlib import pyplot as plt
# REF [site] >> https://docs.opencv.org/master/d7/d4d/tutorial_py_thresholding.html
def thresholding():
img = cv.imread('../../../data/machine_vision/gradient.png', cv.IMREAD_GRAYSCALE)
... | sangwook236/SWDT | sw_dev/python/rnd/test/machine_vision/opencv/opencv_image_processing.py | Python | gpl-3.0 | 10,457 | [
"Gaussian"
] | b434fbb3cef6916ee856434b19b4b3579a500df0417f4aa95cb8dddd89e1fb9c |
import mock
import unittest
import stat
from types import ListType
from DIRAC import S_OK, S_ERROR
import DIRAC.DataManagementSystem.DB.FileCatalogComponents.SecurityPolicies.VOMSPolicy
# This just defines a few groups with their VOMSRole
diracGrps = {'grp_admin' : None,
'grp_data' : 'vomsProd',
... | vmendez/DIRAC | DataManagementSystem/DB/FileCatalogComponents/SecurityPolicies/test/testVOMSPolicy.py | Python | gpl-3.0 | 64,054 | [
"DIRAC"
] | 548c37d45235dda4225240a32b88b30487e1770ef19cb819040ec1e4613921ba |
from mayavi import mlab
from BDSpace import Space
from BDSpace.Figure.Sphere import *
from BDSpace.Curve.Parametric import Arc
from BDSpace.Coordinates import Cartesian
import BDSpaceVis as Visual
solar_system = Space('Solar System')
sun = Sphere('Sun', r_outer=0.2)
mercury = Space('Mercury', Cartesian(origin=[0.5,... | bond-anton/Space_visualization | demo/05_space_visualization_planets.py | Python | apache-2.0 | 2,261 | [
"Mayavi"
] | 9b3a8ea95e28023cc2e03207f2c5bc2fe1e890d521bafce94999f71d4acdf7d9 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
%prog infile [options]
This script combines pairwise alignments, sort and filter the alignments.
Infile expect BLAST tabular format (-m8) or nucmer .coords file.
In order to handle dups, we have to run two monotonic chains in both genomes,
first chain using ref, and ... | tanghaibao/jcvi | jcvi/algorithms/supermap.py | Python | bsd-2-clause | 4,999 | [
"BLAST"
] | bc4d9d4281dbdb95283766b4c80bedd159c33cd7132806410d91bf2ce92ed830 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of th... | Forage/Gramps | gramps/plugins/drawreport/timeline.py | Python | gpl-2.0 | 18,803 | [
"Brian"
] | 4ae1dac4be5fc386b36fcfd02b187e3249f2008b33bf00f66958103179fa8e6d |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits, load_iris
from sklearn.cross_validation import cross_val_score, train_test_split
from sklearn.externals.six.moves import zip
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.te... | WangWenjun559/Weiss | summary/sumy/sklearn/tests/test_naive_bayes.py | Python | apache-2.0 | 17,496 | [
"Gaussian"
] | 4adae637c4392224423ddc0a6969e7e66e1288af8e1ec1063c40fd21444dd13c |
"""
Data structure for 1-dimensional cross-sectional and time series data
"""
from __future__ import annotations
from io import StringIO
from shutil import get_terminal_size
from textwrap import dedent
from typing import (
IO,
TYPE_CHECKING,
Any,
Callable,
Hashable,
Iterable,
Literal,
S... | dsm054/pandas | pandas/core/series.py | Python | bsd-3-clause | 169,359 | [
"Elk"
] | a589e4105bcd5725b0d1fef8d4c9799cc08e9c8b0d2719c40ba546e97a824472 |
tests = [
("python", "UnitTestSDFToCSV.py", {}),
]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
doLong = 0
if '-l' in sys.argv:
doLong = 1
failed, tests = TestRunner.RunScript('test_list.py', doLong, 1)
sys.exit(len(failed))
| ptosco/rdkit | rdkit/Chem/ChemUtils/test_list.py | Python | bsd-3-clause | 282 | [
"RDKit"
] | 652313b1da0073aa491a0443055fb8343c8f28097adbbc5f2864a77abf224a91 |
from simphony_mayavi.tests.testing_utils import DummyEngine
from simphony.visualisation import mayavi_tools
# GUI for Interacting with the engine and mayavi
gui = mayavi_tools.EngineManagerStandaloneUI()
gui.show_config()
# you can add an engine from the python shell
engine_wrapper = DummyEngine()
# "test" is used ... | simphony/simphony-mayavi | examples/engine_manager_standalone_ui.py | Python | bsd-2-clause | 593 | [
"Mayavi"
] | 23e97f8c5229ee732e2bcf17cc80fa260072280435161179d6f436a556e6483b |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""DataPlatform module for the management of multimodal mechanical datasets.
The `samples` module provides a base class `SampleData` implementing a generic
data model and data paltform API, allowing to define by inheritance specific
data platform classes for specific mech... | heprom/pymicro | pymicro/core/samples.py | Python | mit | 218,980 | [
"ParaView"
] | d2c47b4d42bf43de2c23f55bd95b2657b6013187122f989ff147644a78af020f |
# -----------------------------------------------------------------------
# OpenXenManager
#
# Copyright (C) 2009 Alberto Gonzalez Rodriguez alberto@pesadilla.org
# Copyright (C) 2014 Daniel Lintott <daniel@serverb.co.uk>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of t... | mruse/openxenmanager | src/OXM/window_vm_performance.py | Python | gpl-2.0 | 4,123 | [
"FLEUR"
] | b5099d86f698b6cbfa51f8fc86219e332d70f45903d31c07e0a5fced2d399f37 |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 30 08:57:31 2016
@author: nicholas
The Goal of this is to have a unified place to put the useful
python 3.5 functions or templates
Minor version changes:
- added explicit if logger:
- added hashlib, re, various bits and bobs
- found bug in combine_contigs that ignored dir... | nickp60/pyutilsnrw | pyutilsnrw/utils3_5.py | Python | mit | 27,392 | [
"BLAST",
"BWA",
"Biopython"
] | 04356a9762664ab3ebe657bf1828201fdae0ee8ae643ee0c1d43fca77353dad9 |
from galaxy.web.base.controller import *
from galaxy.model.orm import *
from galaxy.datatypes import sniff
from galaxy import util
from galaxy.util.streamball import StreamBall
import logging, tempfile, zipfile, tarfile, os, sys
if sys.version_info[:2] < ( 2, 6 ):
zipfile.BadZipFile = zipfile.error
if sys.version_... | dbcls/dbcls-galaxy | lib/galaxy/web/controllers/library.py | Python | mit | 93,539 | [
"Galaxy"
] | c821898fe0dcab34bac99291fbc56711499f0c46530c76b1c6a3929d1d41a4e1 |
#!/usr/bin/python
# (C) 2010, Markus Wildi, markus.wildi@one-arcsec.org
# (C) 2011, Petr Kubanek, Institute of Physics <kubanek@fzu.cz>
# usage
# img_astrometry.py fits_filename
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as pu... | jstrobl/rts2 | scripts/rts2-f/astrometry.py | Python | lgpl-3.0 | 5,017 | [
"VisIt"
] | 25cad3430e187f28e748f13b6d0e566a791e6ae0d8bd24bca1c911a2f51bad1b |
"""ABCs."""
# Authors: Guillaume Favelier <guillaume.favelier@gmail.com
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
from abc import ABC, abstractmethod, abstractclassmethod
from contextlib import nullcontext
import warnings
from ..utils import tight_layout
class _AbstractRenderer(A... | bloyl/mne-python | mne/viz/backends/_abstract.py | Python | bsd-3-clause | 26,175 | [
"Mayavi"
] | dcd8a73ec2ff35279621ce604bece2e0c2a16e199529403ab3e8bdedea2c1aaf |
import random, pylab
#set line width
pylab.rcParams['lines.linewidth'] = 4
#set font size for titles
pylab.rcParams['axes.titlesize'] = 20
#set font size for labels on axes
pylab.rcParams['axes.labelsize'] = 20
#set size of numbers on x-axis
pylab.rcParams['xtick.labelsize'] = 16
#set size of numbers on y-axis
pylab.... | johntauber/MITx6.00.2x | Unit3/Lecture7Video3Notes.py | Python | mit | 1,404 | [
"Gaussian"
] | 4e6b4d7ffc3e0a4c14d98d565ea6cbff986453b5009cc8cf10887166d5b406fa |
#! /usr/bin/env python
"""This program plots the energies of each kohn-sham state along the MD trajectory
Note that you have to provide the location of the folder where the NAMD
hamiltonian elements are stored using the -p flag
"""
import numpy as np
import matplotlib.pyplot as plt
import glob
import argparse
import ... | SCM-NV/qmworks-namd | scripts/hamiltonians/plot_mos_energies.py | Python | mit | 2,077 | [
"NAMD"
] | 298fb20ad38378c2ded72da57d91c74ddf62558e06c7f233c9701038d1af8206 |
# -*- coding: utf-8 -*-
"""
.. _ex-tfr-comparison:
======================================================================
Time-frequency on simulated data (Multitaper vs. Morlet vs. Stockwell)
======================================================================
This example demonstrates the different time-frequency... | mne-tools/mne-python | examples/time_frequency/time_frequency_simulated.py | Python | bsd-3-clause | 7,927 | [
"Gaussian"
] | cc7da8f471c77c64dc5c4f42396c2d94863cc898d762a5b9b6c0fb7935dd5637 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import tempfile
import unittest
import warnings
import numpy as np
from pymatgen import Structure
from pymatgen.electronic_structure.core import Spin, Orbital
from pymatgen.io.lobster im... | mbkumar/pymatgen | pymatgen/io/lobster/tests/test_lobster.py | Python | mit | 105,105 | [
"Gaussian",
"VASP",
"pymatgen"
] | 240d8f24ee3e6ab783f6c71f9b7d4c4f5622156bb0ee346ec923a4c1c7105fdf |
tests = [
("python", "testBV.py", {}),
("python", "testDiscreteValueVect.py", {}),
("python", "testSparseIntVect.py", {}),
]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| rvianello/rdkit | Code/DataStructs/Wrap/test_list.py | Python | bsd-3-clause | 303 | [
"RDKit"
] | 4f42e1bda218503f5c91c2aaf5bac74df2ccc7cfde880dbdea6ee02dd458cafe |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/analysis/component.py | Python | agpl-3.0 | 114,213 | [
"Galaxy"
] | 344e1ce82d060d3774bb3a021f39e33bae8969011c922ec4e42e63dc5b590a08 |
'''
Individual stages of the pipeline implemented as functions from
input files to output files.
The run_stage function knows everything about submitting jobs and, given
the state parameter, has full access to the state of the pipeline, such
as config, options, DRMAA and the logger.
'''
from utils import safe_make_d... | bjpop/crpipe | src/stages.py | Python | bsd-3-clause | 11,910 | [
"BWA"
] | d1413179d4ca44da6a935b0ee901028e9874cb49a0da635c985dd64d16731d3b |
###############################################################################
##
## Copyright 2011-2013 Tavendo GmbH
##
## 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
##
## ... | bzero/bitex | libs/autobahn/websocket.py | Python | gpl-3.0 | 156,783 | [
"VisIt"
] | 770eff8e6a6d1835d5f4cae580a6447fde562c5e537e52dfe355e94186647761 |
#!/usr/bin/python
# Surface deforming according to a damped oscillation consisting
# of bezier patches.
#
# Copyright (C) 2007 "Peter Roesch" <Peter.Roesch@fh-augsburg.de>
#
# This code is licensed under the PyOpenGL License.
# Details are given in the file license.txt included in this distribution.
import math
impo... | mgood7123/UPM | Sources/PyOpenGL-Demo-3.0.1b1/PyOpenGL-Demo/proesch/bezier/bezier.py | Python | gpl-3.0 | 4,125 | [
"Gaussian"
] | 30c7d134bc7d79954a5e7b918f91cc58c0e181fb7c48d08867ca73c63b9ecc11 |
import operator as op
import exceptions as ex
import itertools
import re
import networkx as nx
import numpy as np
import elements as elem
from rotamer.io.amber import read_amber_restart
class Atom(object):
""" Atom defined from the AMBER topology file. """
def __init__(self, index, name, mass, amber_atom_t... | khs26/rotamer_library | rotamer/topology/read_amber_prmtop.py | Python | mit | 13,877 | [
"Amber"
] | 7245f8f6b7fd15ee555621814f62886604265a7463c8798f5c583e97038b55a0 |
""" Definition for WMSHistory Monitoring type.
Drop-in replacement for the Accounting/WMSHistory accounting type.
Filled by the agent "WorkloadManagement/StatesAccountingAgent"
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Monitorin... | yujikato/DIRAC | src/DIRAC/MonitoringSystem/Client/Types/WMSHistory.py | Python | gpl-3.0 | 1,409 | [
"DIRAC"
] | 79986804100e712afb804113be6c4b456ac1ad96190d4ded0727d7ef928c1f10 |
# -*- coding: utf-8 -*-
import sys
sys.path.insert(0, '../algo')
from src.trie import Trie
# 1. Implement Reverse DNS Lookup Cache
# http://www.geeksforgeeks.org/implement-reverse-dns-look-cache/
class ReverseDNS(object):
def __init__(self):
self.storage = Trie()
def insert(self, ip, url):
... | topliceanu/learn | interview/geeksforgeeks/geeksforgeeks.py | Python | mit | 15,476 | [
"VisIt"
] | a2430a3b6f3910546147bf8124054b0d81ef9588336f4555a3b1d5c3dcb9d0f5 |
from rdkit import RDConfig
import sys, os
from time import sleep
from multiprocessing import Process, Value
import unittest
from rdkit import Chem
from rdkit.Chem import ChemicalForceFields
from rdkit.Chem import rdMolTransforms
class OptSafe:
def __init__(self):
self.minInfLoop = """minInfLoop
RDKit ... | rvianello/rdkit | Code/ForceField/Wrap/testConstraints.py | Python | bsd-3-clause | 12,190 | [
"RDKit"
] | d57c3f9b97d49f782c5668434a76c8fb1ba8a086b8caf36de2c366bef551d308 |
#!/usr/bin/python
"""
Copyright 2010 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 of th... | clreinki/GalaxyHarvester | dbSession.py | Python | agpl-3.0 | 1,761 | [
"Galaxy"
] | 1228d70607a5edc934abf35800b0145b18752f21ede70a95b7c2cd683469fcf0 |
##########################################################################
#
# Copyright (c) 2013-2015, Image Engine Design Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redi... | lucienfostier/gaffer | python/GafferImageTest/ImageTransformTest.py | Python | bsd-3-clause | 20,296 | [
"Gaussian"
] | f48abcd86c9c62861b8ae717ff423cd88db3fba09bad02e27d10f3d58e0d3418 |
"""
A plugin for reading converted ICARTT files
"""
from cis.data_io.products import AProduct
import logging
class CARIBIC(AProduct):
def get_file_signature(self):
return [r'.*\.nc']
def create_coords(self, filenames, usr_variable=None):
from cis.data_io.netcdf import read_many_files_individ... | duncanwp/cis_plugins | CARIBIC.py | Python | lgpl-3.0 | 3,631 | [
"NetCDF"
] | bb62856b559e23a123f555cc5c133c83a289e183bb806e605875bea9fdbe1a61 |
import gzip
import csv
import re
import os
###############################################################################
# Base Classes
###############################################################################
class FeatureBuilder:
def __init__(self, debug=False):
self.debug = debug
def b... | TurkuNLP/CAFA3 | learning/featureBuilders.py | Python | lgpl-3.0 | 15,619 | [
"BLAST"
] | bd526c2525f2ac3e7e2f117883e3f2f7cd413a1020b8035ce84dafa3e0329b6c |
##############################################################################
# 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/scripts/_run_.py | Python | lgpl-2.1 | 1,882 | [
"MDTraj"
] | e49a5cdc89c7d4a504e2dbb7d6d9119b30a2de284735e3a652460c26a4232349 |
"""
Migration script to add the tool_test_errors, do_not_test, tools_functionally_correct, and time_last_tested columns to the repository_metadata table.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
# Need our custom types, but don't import anything e... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py | Python | gpl-3.0 | 5,322 | [
"Galaxy"
] | 8a4a607d088c17091b81359f44d1c072f3263e5eaf4a7182b931d53a6541dd80 |
# 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... | capoe/espressopp.soap | src/tools/decomp.py | Python | gpl-3.0 | 6,174 | [
"ESPResSo"
] | 7dbc9805b89f5bd2effc084c66188169884f1020a7d17a08c3a5a3b1d4d53fb8 |
import web
from web import form
import paramiko
#paramiko.util.log_to_file('/tmp/filename.log')
# install web.py
# use pip install or easy_install web.py
# or download source
# wget http://webpy.org/static/web.py-0.37.tar.gz
# tar xvf web.py-0.37.tar.gz
# cd web.py-0.37
# python setup.py install
##############
# run ... | shantanuo/easyssh | code.py | Python | gpl-2.0 | 13,733 | [
"VisIt"
] | f1d6fc40eafa120856a99a8d67cb7681f2d916c3c64bab1f86a488614f602d65 |
import numpy as np
import theano
import theano.tensor as T
from collections import OrderedDict
def simulate_dynamics(initial_pos, initial_vel, stepsize, n_steps, energy_fn):
"""
Return final (position, velocity) obtained after an `n_steps` leapfrog
updates, using Hamiltonian dynamics.
Parameters
-... | rueberger/MJHMC | mjhmc/fast/hmc.py | Python | gpl-2.0 | 14,473 | [
"Gaussian"
] | cc7b123d9b135bcbae80d9fe140189b23a56d54a406c55bffb0474bc8aabb31c |
"""
Take a processed dataframe, generate features, add classification label, make
validation set, predict class.
"""
import pandas as pd
from scipy.ndimage import gaussian_filter
from sklearn.ensemble import RandomForestClassifier
from sklearn.cross_validation import cross_val_score
from sklearn.metrics import accur... | sbussmann/sensor-fusion | Code/learnposition.py | Python | mit | 3,061 | [
"Gaussian"
] | 8199f2c93c795f56587b601e523314859586bc793cc0221d9d77660d4e223771 |
#
# 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 your option)... | KonradBreitsprecher/espresso | samples/lj-demo.py | Python | gpl-3.0 | 19,950 | [
"ESPResSo",
"Mayavi"
] | 1dc643f863ec741e93e575a4c5f1a28614a42ff99878b2306501cb686f954244 |
"""
Check for updates in a background process. If we can start a program immediately, but some of our information
is rather old (longer that the L{config.Config.freshness} threshold) then we run it anyway, and check for updates using a new
process that runs quietly in the background.
This avoids the need to annoy peop... | dsqmoore/0install | zeroinstall/injector/background.py | Python | lgpl-2.1 | 9,970 | [
"VisIt"
] | d44fccd69ac5e3308526e523098be8f3212a530a45dbd4a23a140b6cfd143dc6 |
# -*- coding: utf-8 -*-
# IV_curve.py analysis class for IV like transport measurements
# Micha Wildermuth, micha.wildermuth@kit.edu 2019
# 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 ... | qkitgroup/qkit | qkit/analysis/IV_curve2.py | Python | gpl-2.0 | 57,685 | [
"Gaussian"
] | 6410d35ccf40d5c5421020293c6bf60a6c63d53889f5a61f046908adbee7a22d |
"""Various network tools (w3m, w3c validator, curl, traceurl, ...)"""
# PYTHON STUFFS #######################################################
import logging
import re
from nemubot.exception import IMException
from nemubot.hooks import hook
from nemubot.module.more import Response
from . import isup
from . import p... | nbr23/nemubot | modules/networking/__init__.py | Python | agpl-3.0 | 6,175 | [
"VisIt"
] | d8b1eaaa4e141f909b3d1091ac701f856a1b6e6ea909a0975ac2236ab40318d0 |
# Copyright (c) 2002 Zooko, blanu
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: tristero.py,v 1.2 2002/12/02 19:58:54 myers_carpenter Exp $"
nodeSchema='http://tristero.sourceforge.net/mnet/Meta... | zooko/egtp_new | egtp/tristero.py | Python | lgpl-2.1 | 687 | [
"VisIt"
] | e7114e69fefd6dc3a6824cce71c3afc3cf589a07e9d241694d8014f60180508c |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
TDDFT NTO analysis.
'''
from pyscf import gto, dft, tddft
mol = gto.Mole()
mol.build(
atom = 'H 0 0 0; F 0 0 1.1', # in Angstrom
basis = '631g',
symmetry = True,
)
mf = dft.RKS(mol)
mf.xc = 'b3lyp'
mf.kernel()
mytd = tddft.TDDFT... | sunqm/pyscf | examples/tddft/01-nto_analysis.py | Python | apache-2.0 | 574 | [
"PySCF"
] | 8d91325689506c89694654150ff8d1da0659eb15481945066e6d744d7bfe9d56 |
import os
import glob
from setuptools import setup, find_packages
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name='Assembly_tools',
version='0.1.2',
description='Scripts relating to genome assembly',
long_description=read('README.md'),
packages =... | martinghunt/Assembly_tools | setup.py | Python | gpl-3.0 | 626 | [
"pysam"
] | ec57c18e607a9f246de8ba01cc5c240b2c27a42c4547b29d1df1989a80a02863 |
import tensorflow as tf
import numpy as np
from neuralFuncs import add_art_layers
from optimizationFuncs import optimize
from inputFuncs import get_Samples, MNIST_Data_Get, generate_Random_Samples
from printFuncs import network_Architecture
from errorCheck import error_Check
def create_Simple_Artificial_Network(laye... | modelarious/Artificial_Net_Simple | Main.py | Python | mit | 7,614 | [
"NEURON"
] | 63f20206dd35609d14ed91c030ea02159b79b2c987a62e8ae3cd5987a6c6a90e |
from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
TableToPoints1 = TableToPoints()
TableToPoints1.XColumn = 'x0'
TableToPoints1.YColumn = 'x1'
TableToPoints1.a2DPoints = 1
# SpreadSheetView1 = GetRenderView()
# DataRepresentation2 = Show()
# DataRepresentation2.FieldAssociation = 'Point... | davidshepherd7/oomph-lib-micromagnetics | etc/paraview_helpers/csv2points.py | Python | gpl-2.0 | 2,020 | [
"ParaView"
] | b89ebb9690de224c86bc0c26029b1779a47b69c67c97aef84d89508b9abc7f36 |
"""Module for interacting with Cytoscape."""
from pathlib import Path
from typing import Any
from py2cytoscape.data.cyrest_client import CyRestClient # type: ignore
from requests.exceptions import ConnectionError # type: ignore
from sbmlutils import log
logger = log.get_logger(__name__)
def visualize_sbml(sbml_... | matthiaskoenig/sbmlutils | src/sbmlutils/cytoscape.py | Python | lgpl-3.0 | 841 | [
"Cytoscape"
] | 98db05eb4cf40a7d55cd4768ba37994223dda8498993b6f4947701e2dd9eb7d0 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
import warnings
from scipy.special import comb
from scipy.misc.doccer import inherit_docstring_from
from scipy import special
from scipy import optim... | larsmans/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 123,899 | [
"Gaussian"
] | f377dcaa906951f309a60decaf853efe35cb59384c22194e5f529cb0cec8e01e |
"""
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... | shadanan/hevante-points | src/lambda_function.py | Python | mit | 9,555 | [
"VisIt"
] | 30ba8c4336f4bad594fb6da103dcb319431f05299e11c876195ec59c138ad716 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | gph82/PyEMMA | pyemma/coordinates/api.py | Python | lgpl-3.0 | 65,189 | [
"Amber",
"CHARMM",
"Gromacs",
"LAMMPS",
"MDTraj",
"NAMD",
"NetCDF",
"TINKER"
] | 1634a53d9d334644ab9afc5d41b2d49f10aecdfcfcd25d7a4a668657d982c20e |
import pytest
from selenium import webdriver
import os
# Fixtures are a way to setup data dependencies in automated tests.
@pytest.fixture(scope="function")
def driver(request):
desired_caps = {}
wd = None
if os.getenv('RUN_TARGET') == "SAUCE":
# sauce labs.
desired_caps['browserName'] = "... | dlai0001/appium-spike-running-tests-oncloud | tests/test_examply.py | Python | mit | 2,791 | [
"ADF"
] | a52a88961f9f2fa2b1ba6d5ef5bc5564a6bcb0babf6533ff3e20950124a86e86 |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-channel | scripts/fixup_channel_v1_keywords.py | Python | apache-2.0 | 8,723 | [
"VisIt"
] | 2cfe5ea6935cb5e12829f14fd6eee0dce4bdaaaa8a1540633e8afab0e46b5cee |
import pyspark
from pyspark import SparkContext
from pyspark.sql import SQLContext
from pyspark.sql.types import *
import pyspark.sql.functions as func
from pyspark.sql.functions import udf
import pandas as pd
import numpy as np
sc = SparkContext() # creating sparkcontext
sql = SQLContext(sc) # creating... | XInterns/IPL-PySpy | src/DreamTeam.py | Python | mit | 12,702 | [
"ADF"
] | 13569b69e03ef5e0c1b14746f73f8aab738ddc7a9b75560ed15a6b84e105bc02 |
# -*- coding: utf-8 -*-
###############################################################################
#
# PyLint tests that will never be applied by Trump.
#
# ... is not callable, ignored because a property that returns a callable
# becomes callable.
# pylint: disable-msg=E1102
# miss... | Asiant/trump | trump/orm.py | Python | bsd-3-clause | 71,147 | [
"ADF"
] | 3892c9567e0851ebff8e9fac4ef0f1184fdb9b01a41d402e465d0c759bce06eb |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Li... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/cache/cachebase.py | Python | gpl-2.0 | 11,283 | [
"VisIt"
] | 3bc1a7afe8162e46595596e66e0a9b5b0889085febf78e2702ec658008f6b1e6 |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/test/test_data.py | Python | gpl-3.0 | 11,110 | [
"Avogadro",
"CP2K",
"Gaussian"
] | d85c5bca43fbc62f076c6c8efedbe340b74978910ab93e9dea9f1e90b6536f20 |
''' Provide a base class for all objects (called Bokeh Models) that can go in
a Bokeh |Document|.
'''
from __future__ import absolute_import, print_function
import logging
logger = logging.getLogger(__file__)
from json import loads
from operator import itemgetter
from six import iteritems
from .core.json_encoder i... | Ziqi-Li/bknqgis | bokeh/bokeh/model.py | Python | gpl-2.0 | 25,598 | [
"VisIt"
] | 2a295c42b409e3ec9e24845537bf37e96bab0064bcfd06771dea5977efb1e0e4 |
#
# +!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!+!
# #
# selafin_io_pp.py #
# #
# +!+!+!+!+!+!+!+!+!+... | ArteliaTelemac/PostTelemac | PostTelemac/meshlayerparsers/libtelemac/selafin_io_pp.py | Python | gpl-3.0 | 16,829 | [
"ParaView",
"VTK"
] | 57c6443fdb4b26c1cd58015088a9a7a950b0709ffb9cdb857b6de042ec56087e |
# classifier - classification algorithms for Bregman toolkit
__version__ = '1.0'
__author__ = 'Michael A. Casey'
__copyright__ = "Copyright (C) 2010 Michael Casey, Dartmouth College, All Rights Reserved"
__license__ = "New BSD License"
__email__ = 'mcasey@dartmouth.edu'
import numpy as N
import scipy.linalg
from ran... | folkengine/bregman | classifier.py | Python | gpl-2.0 | 11,359 | [
"Gaussian"
] | 9e6606aba4d968eefca1044724bda84b2aa82ce8044431e0f1771c91d4ce94ce |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This module is also sponsored by E.T.A.I. (www.etai.fr)
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version... | 2ndQuadrant/ansible | lib/ansible/modules/cloud/vmware/vmware_guest.py | Python | gpl-3.0 | 146,527 | [
"VisIt"
] | 24c83b99a21f61e1a658a109167910d30ca26bedcf11c85fc43bee676c03ba33 |
# iCraft is Copyright 2010 both
#
# The Archives team:
# <Adam Guy> adam@adam-guy.com AKA "Adam01"
# <Andrew Godwin> andrew@aeracode.org AKA "Aera"
# <Dylan Lukes> lukes.dylan@gmail.com AKA "revenant"
# <Gareth Coles> colesgareth2@hotmail.com... | TheArchives/Nexus | core/entities/vodwhar.py | Python | bsd-2-clause | 6,691 | [
"VisIt"
] | 4e8536e6a1115cedba883011a1dbf573634f20ef3492943675bebc9fc67fa971 |
#!/usr/bin/env python3
# coding: utf-8
from __future__ import unicode_literals, print_function
import sys
import itertools
from molbiox.frame.command import Command
from molbiox.io import blast, tabular
"""
If your results come from more than 2 columns, use a SQL database instead.
"""
class CommandAggregate(Command)... | frozflame/molbiox | molbiox/execute/relational.py | Python | gpl-2.0 | 3,111 | [
"BLAST"
] | 611e2bec1f391b7c0c95ef48be6d2523ab8bd4b7740605b56c34a7e26536b09f |
import re
from lxml import html
try:
from pyokc import helpers
from pyokc import magicnumbers
from pyokc.objects import MessageThread, Question, Session
from pyokc.settings import USERNAME, PASSWORD
except ImportError:
import helpers
import magicnumbers
from objects import MessageThread, Que... | odkken/pyokc | pyokc/pyokc.py | Python | mit | 27,544 | [
"VisIt"
] | 891dba65fb66b1e7bf2384eda72cd50e97da38b5e4bec137bf70f7540b354b6d |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 3: Deep Learning and Neural Networks
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2015 by Jeff Heaton
Licensed under the Apache License, V... | PeterLauris/aifh | vol3/vol3-python-examples/examples/example_mnist_sigmoid.py | Python | apache-2.0 | 2,382 | [
"VisIt"
] | 31ef4334fccda0ae0f93d67e684e250ba30c68848eac280e3a6535c1bc4102b4 |
#! /usr/bin/env python
"""
Convert the results of a database search from one file format to another
Copyright:
convert_query_format.py Convert query format between databases
Copyright (C) 2016 William Brazelton
This program is free software: you can redistribute it and/or modify
it under the terms ... | Brazelton-Lab/lab_scripts | convert_query_format.py | Python | gpl-2.0 | 4,679 | [
"BLAST"
] | 30fe1066d44a7d71b5acd46b08f308bdcb58a4cbc0fe3b4da19b0ec1c1dd9ea2 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------------------
# Created by: Lee Bergstrand
# Description: A simple python program that use BLASTn to search for 16S genes within a geneome.
# Extracts the aligned query sequence from the BLAST results (This ... | LeeBergstrand/Phylogenetic-Tree-Building | BLASTToFind16S/16SBLAST.py | Python | mit | 6,012 | [
"BLAST",
"Biopython"
] | a87da7961f4aca856645111a56e83cd3ef59b6331f8d893b164d854e17bc65ad |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2015 CERN.
#
# Invenio 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... | jirikuncar/invenio-search | invenio_search/walkers/elasticsearch.py | Python | gpl-2.0 | 6,499 | [
"VisIt"
] | 981ac9b8b411e739c0535400aff42836e0785be91ecf40dceb7f7b0b79ba5c55 |
import numpy as np
from ase import Atom, Atoms
from gpaw import GPAW, Mixer
from gpaw.test import equal
a = 4.0
n = 20
d = 1.0
x = d / 3**0.5
atoms = Atoms([Atom('C', (0.0, 0.0, 0.0)),
Atom('H', (x, x, x)),
Atom('H', (-x, -x, x)),
Atom('H', (x, -x, -x)),
Atom... | qsnake/gpaw | gpaw/test/CH4.py | Python | gpl-3.0 | 941 | [
"ASE",
"GPAW"
] | 07f7644b190b293c431f87974aca6c3ec8572ecfa493de054f9c188fbbf3302e |
#!/usr/bin/env python
from __future__ import print_function
import argparse
import glob
import sys
import numpy as np
import pysam
import math
# read keys
R_ID = "id"
R_START_POS = "start_pos"
R_END_POS = "end_pos"
R_LENGTH = "length"
R_SECONDARY = "secondary_alignment"
R_SUPPLEMENTARY = "supplementary_alignment"
R_MA... | benedictpaten/marginPhase | toil/src/toil_marginphase/scripts/bam_stats.py | Python | mit | 26,073 | [
"pysam"
] | 5da660ac0d2ef5423cc00672ed776930d78a9ad23053dc27d6f45e5d2579e171 |
import unittest
from httpclient import HttpClient, RelativeURIError, ServerNotFoundError
from setting import PARAM
from multiprocessing import Pool
class testHttpclient(unittest.TestCase):
def test_basicConnections(self):
httpclient = HttpClient()
# test for available hosts
avalaible_hosts... | princeedward/PyCrawler | src/pycrawler/pycrawler/Crawler/test/test_httpclient.py | Python | bsd-2-clause | 3,525 | [
"VisIt"
] | 6e9c71120574560ec580d142112a5bb01b3c5a805cdb08c42b36d772b9c7078f |
# -*- coding: utf-8 -*-
#
# Copyright © 2009-2013 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""
Spyder, the Scientific PYthon Development EnviRonment
=====================================================
Developped and maintained by Pierre Raybaut... | violasox/tellurium | spyder_mod/spyderlib/spyder.py | Python | apache-2.0 | 108,037 | [
"CRYSTAL"
] | b43abc3c1f9e04c4a880bda072a8fb2e1e53eb0fc965ad29b621a762ae630095 |
# ---
# jupyter:
# anaconda-cloud: {}
# jupytext:
# cell_metadata_filter: -all
# formats: ipynb,py:percent
# notebook_metadata_filter: all
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.6.0
# kernelspec:
# di... | ManchesterBioinference/BranchedGP | notebooks/Hematopoiesis.py | Python | apache-2.0 | 4,055 | [
"Gaussian"
] | 6f504a76cf9ceb4b0b03c56ff3867723536a595c385ddcf9acc05b692bd25810 |
import paramiko
import select
import argparse
import sys
import threading
import uuid
import tempfile
import os
import getpass
from ForwardSshTunnel import ForwardSshTunnel
class SecureRemoteLauncher(object) :
#-------------------------------------------------------------------------
# SecureRemoteLauncher... | scottwittenburg/web-hpc-manager | python/webserver/SecureRemoteLauncher.py | Python | bsd-3-clause | 5,903 | [
"ParaView"
] | 3cbc3491f096d6061c07911dcc799f9bcf61fcae32dcf41b6e6ff318a8cd3598 |
# KillerBee Device Support for:
# Sewio Open-Sniffer Radio Client
# (product previously known as Wislab Sniffer)
# This sniffer is a remote IPv4 host.
#
# (C) 2013 Ryan Speers <ryan at riverloopsecurity.com>
#
# For documentation from the vendor, visit:
# http://www.sniffer.wislab.cz/sniffer-configuration/
#
import... | EastL/killerbee | killerbee/dev_sewio.py | Python | bsd-3-clause | 19,377 | [
"VisIt"
] | 1bd841be5f292ea0d63fd005f40eae8627e5207278d15de22cfc7ad488d8a4be |
"""Test suite for the crystal field calculations in the Inelastic/CrystalField package
"""
from __future__ import (absolute_import, division, print_function)
import unittest
import numpy as np
from scipy.constants import physical_constants
# Import mantid to setup the python paths to the bundled scripts
import mantid
... | dymkowsk/mantid | scripts/test/CrystalFieldTest.py | Python | gpl-3.0 | 89,255 | [
"CRYSTAL",
"Gaussian"
] | fee2644959e585a4262a8b4a9921fef592985c13cc016c14221dadb02c7a41eb |
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