text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import re
from constance import config
from django.views.generic import FormView, TemplateView
from haystack.views import SearchView
from recipes.models import Recipe, RecipeTag
class Home(TemplateView):
"""The first page that users see when they visit the site"""
template_name = "home.html"
def ge... | kamni/nodonuts | recipes/views.py | Python | agpl-3.0 | 1,560 | [
"VisIt"
] | 6e30a796259d7ab4b48859b86f7bdb21edf730cd5548cb6b489c567f574008c1 |
from __future__ import division # needed for 1/2 = 0.5
import numpy as np
from accelerator import Lattice, Element, LinearElement, Quad, Drift, LieAlgebra, LieAlgElement, leapfrog, Dipole, Cavity
#from sympy.parsing.sympy_parser import parse_expr
#from sympy import *
from particleFactory import straight, scanned, rando... | OscarES/Differential-Algebra-Tracker | testfacility.py | Python | gpl-3.0 | 13,073 | [
"Gaussian"
] | 251d4053ab89eab89c4fbee7a7d8fd02fb642f1825a87e42bf3bbbf7b8f38c70 |
#!/usr/bin/env python
"""
Convert data from Genbank format to GFF.
Usage:
python gbk_to_gff_conv.py in.gbk > out.gff
Requirements:
BioPython:- http://biopython.org/
"""
import os, sys, re
import collections
from Bio import SeqIO
from common_util import _open_file
def feature_table(chr_id, source, orient, gene... | ratschlab/oqtans_tools | GFFtools/0.1/gbk_to_gff_conv.py | Python | mit | 6,462 | [
"Biopython"
] | b4faafb4261031e92a6e09f6711c7243aec718cf26a09b7a59599fc53dd31362 |
import numpy as np
from ase.optimize import Optimizer
class MDMin(Optimizer):
def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
dt=None):
Optimizer.__init__(self, atoms, restart, logfile, trajectory)
if dt is not None:
self.dt = dt
def initia... | freephys/python_ase | ase/optimize/mdmin.py | Python | gpl-3.0 | 977 | [
"ASE"
] | a412cd7c6cc52f0ef9248471cdf27c2e522a0a08a12b27aee4197a0154174b8b |
from setuptools import setup, find_packages
import os
import glob
package_dir = {'': 'src'}
for pkg in [pkg for pkg in find_packages("src") if pkg.find('.') > -1]:
package_dir['rocketblast' + "." + pkg] = "src" + os.sep + pkg
datadir = os.path.join('data')
data_files = [(datadir, [f for f in glob.glob(os.path.joi... | rocketblast/rcon-troller | setup.py | Python | agpl-3.0 | 1,414 | [
"BLAST"
] | bd1969795ca65e924b3ee2c4940b475883570bb36f33b91812eb7e241d7c49ed |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, Matthew Har... | tcmoore3/mdtraj | mdtraj/tests/test_topology.py | Python | lgpl-2.1 | 8,412 | [
"MDTraj",
"OpenMM"
] | efcc9fa460e0aa81e18c9b648dd4d59b020c174ee836e20180e6bb62d5badc7e |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requ... | evenmarbles/rlglued | tests/test_message_agent.py | Python | bsd-3-clause | 1,608 | [
"Brian"
] | e4e72f998b3a6b70e809acb0430cdf27011efd71939b08740c67c2d4994e1abe |
#!/usr/bin/env python
""" update local cfg
"""
import os
from DIRAC.Core.Base import Script
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
' %s [option|cfgFile] ... DB ...' % Script.scriptName]))
Script.parseCommandLine()
arg... | arrabito/DIRAC | tests/Jenkins/dirac-cfg-update-server.py | Python | gpl-3.0 | 8,700 | [
"DIRAC"
] | 0b0fb2e5a96f0bb9712fd670b3b800ec21954e81e2ecf61530895716db1313ec |
#
# Copyright 2014-2015 University of Southern California
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
#
"""Synapse detection in 3D microscopy images using size-specific blob detection.
The method uses several convolution kernels which have been
experimentally derived:
Low: a gaussia... | informatics-isi-edu/synspy | synspy/analyze/__init__.py | Python | bsd-3-clause | 1,816 | [
"Gaussian"
] | 57025956a7ec1a7fc1b0039bfca3e0f80bcf34551bfc2e42b4ec280f6686134a |
"""
==================================
Constants (:mod:`scipy.constants`)
==================================
.. currentmodule:: scipy.constants
Physical and mathematical constants and units.
Mathematical constants
======================
============ ================================================================... | sargas/scipy | scipy/constants/__init__.py | Python | bsd-3-clause | 9,817 | [
"Avogadro"
] | 5f0f94df449d04ccfe9711477fa22569527c2b990213058f877e0aebf30f6518 |
#-----------------------------------------------------------------------------
# Copyright (c) 2010-2012 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distributed as part of this software.
#-----... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/tests/test_pair.py | Python | lgpl-3.0 | 1,895 | [
"Brian"
] | b53078ad1568e668b6c909d51d2bba901b9a2d35ec01a07652f28ecbf7d5bc84 |
#!/usr/bin/env python
import sys
sys.path.append("../")
import numpy as np
import pandas as pd
import scipy.io
from functions import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import neuroseries as nts
import sys
import scipy.ndimage.filters as filters
from sklearn.mixture import GaussianMixtu... | gviejo/ThalamusPhysio | python/figure_talk/main_talk_3_tsne3.py | Python | gpl-3.0 | 9,905 | [
"Gaussian",
"NEURON"
] | dfbc2e68f7b57bba3295b385928901644c628e14e614e5e9ddc1eda1592d3198 |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe import session, _
from frappe.utils import today
from erpnext.utilities.transaction_base import TransactionBase
class ... | gangadharkadam/office_erp | erpnext/support/doctype/customer_issue/customer_issue.py | Python | agpl-3.0 | 2,229 | [
"VisIt"
] | 739fc599e00e1c9c0f5baf13eff92f0dcc31bdd39f52f7a346154a0bd531d0c5 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import random
import unittest
from pymatgen.core.composition import Composition
from pymatgen.core.ion import Ion
from pymatgen.core.periodic_table import Element
class IonTest(unittest.TestCase):
def setUp(self):
... | vorwerkc/pymatgen | pymatgen/core/tests/test_ion.py | Python | mit | 7,462 | [
"pymatgen"
] | 6c8d6e958256f0de90502117b0582e89ae1ee297bb6ae88d5875164867687108 |
"""Handlers for GROMACS trajectories xtc and trr formats
"""
from .base import IOHandler
import numpy as np
from ...libs.pyxdr import XTCReader
class BlockedArray(np.ndarray):
def __init__(self, *args, **kwargs):
super(BlockedArray, self).__init__(*args, **kwargs)
self.block_size = 1000 # It prea... | swails/chemlab | chemlab/io/handlers/xtctrr.py | Python | gpl-3.0 | 2,906 | [
"Gromacs"
] | 09dc5cdfb5c50e1d3294e2223b98059d54fe68e0418cf48b06dff5458d87cc49 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | juju-solutions/kubernetes | cluster/juju/layers/kubernetes-common/lib/charms/layer/kubernetes_common.py | Python | apache-2.0 | 18,539 | [
"CDK"
] | 48ed84ffae6a3c9be5882d7c63811f1494eef98ab839084ad2ab284f3638a20f |
'''@package docstring
@author: Jyh-Miin Lin (Jimmy), Cambridge University
@address: jyhmiinlin@gmail.com
Created on 2013/1/21
================================================================================
This file is part of pynufft.
pynufft is free software: you can redistribute it and/or modify
it un... | jyhmiinlin/cineFSE | CsTransform/fessler_nufft.py | Python | gpl-3.0 | 39,917 | [
"Gaussian"
] | fb24bd66be55f1cf2ae1a50bb3219dfc9c4b5ff5540b1ac46ab2d3fa01eca0e4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# arcresources - list arc resources and queues
# Copyright (C) 2003-2014 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 the GNU General Public... | heromod/migrid | mig/shared/functionality/arcresources.py | Python | gpl-2.0 | 9,096 | [
"Brian"
] | f278ecfade3c89d0b4f0f7c97f1123adedf7b8c976029676b2defdc721d14360 |
import sys
sys.path.insert(1, "../../")
import h2o, tests
def metric_accessors():
cars = h2o.import_file(path=tests.locate("smalldata/junit/cars_20mpg.csv"))
r = cars[0].runif()
train = cars[r > .2]
valid = cars[r <= .2]
# regression
response_col = "economy"
distribution = "gaussian"
... | kyoren/https-github.com-h2oai-h2o-3 | h2o-py/tests/testdir_misc/pyunit_metric_accessors.py | Python | apache-2.0 | 42,219 | [
"Gaussian"
] | 7bfb26fb734e7b6b7a5a3f1b6044071d3ddb6ef6851c14a12dedf438633f463a |
#!/usr/bin/env python
#
# This file is part of g_mmpbsa.
#
# Author: Rajendra Kumar
#
# Copyright (C) 2013-2015 Rashmi Kumari and Andrew Lynn
#
# g_mmpbsa 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 Foundati... | RashmiKumari/g_mmpbsa | tools/mutate_traj_tpr.py | Python | gpl-3.0 | 25,256 | [
"CHARMM",
"Gromacs"
] | 203a47b423c565b46883687cc85c92af5bd0ce48e49f6182732224ae01e4fde7 |
#-------------------------------------------------------------------------------
# Cloud-COPASI
# Copyright (c) 2013 Edward Kent.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available... | edkent/cloud-copasi | cloud_copasi/web_interface/task_plugins/plugins/parameter_estimation_repeat/plugin.py | Python | gpl-3.0 | 18,223 | [
"COPASI"
] | 3cecd1f91eaa14974bf91d3f57b8b775590ee1312af95836805b3405a91cc6cf |
import six
from fastidious.expressions import (Not, ZeroOrMoreExpr, LabeledExpr, SeqExpr,
ChoiceExpr, MaybeExpr, OneOrMoreExpr,
ExprProxi)
from fastidious.compiler.astutils import Visitor
from fastidious.compiler.action.base import Action
class... | lisael/fastidious | fastidious/compilers/gendot.py | Python | gpl-3.0 | 6,338 | [
"VisIt"
] | c97c38418e0ea783d604d2d875bc3a19c59244c03fa8a047a6013383edaf5d89 |
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use ... | cryptickp/libcloud | libcloud/common/google.py | Python | apache-2.0 | 29,712 | [
"VisIt"
] | 8d9eaa6125f26a0705125de05badb9a5f30539a67283c9de113a5a8474eb717d |
# coding: utf-8
"""Wrappers for ABINIT main executables"""
from __future__ import unicode_literals, division, print_function
import os
from subprocess import Popen, PIPE
from monty.os.path import which
from pymatgen.util.string_utils import list_strings
from six.moves import map, cStringIO
import logging
logger = lo... | Dioptas/pymatgen | pymatgen/io/abinitio/wrappers.py | Python | mit | 9,009 | [
"ABINIT",
"pymatgen"
] | fbb5697970d966388a888180878495a3e7b14751fa780d6801a0777d42f7979b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This pro... | magic-trip/hfinder | hfinder.py | Python | gpl-2.0 | 37,882 | [
"BLAST"
] | b8de757b389b255d7ab5a9b6cd6c07bba36adbadd29731c0c56f0a9cdaf4257e |
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Environment setup and teardown for remote devices."""
import distutils.version
import json
import logging
import os
import random
import sys
from devil.... | Teamxrtc/webrtc-streaming-node | third_party/webrtc/src/chromium/src/build/android/pylib/remote/device/remote_device_environment.py | Python | mit | 13,391 | [
"Galaxy"
] | 92247364820ec4972ca614ac04d77452c954f8141578896091ffa394dd0b84bb |
# RABDAM
# Copyright (C) 2020 Garman Group, University of Oxford
# This file is part of RABDAM.
# RABDAM 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 3 of
# the License, or (at your... | GarmanGroup/RABDAM | rabdam/Subroutines/makeDataFrame.py | Python | lgpl-3.0 | 8,239 | [
"PyMOL"
] | a70725699548c4d6b00db36741b6b8067526b7dc9e1030fcb047baf8f8968339 |
# Copyright (c) 2000-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | JetChars/vim | vim/bundle/python-mode/pymode/libs/pylint/pyreverse/diadefslib.py | Python | apache-2.0 | 8,381 | [
"VisIt"
] | 95a148d9b2574e424ceaba6f8ca44eec0d6b4cc1e32585aa965de38209fca26b |
"""Generate the storage of NARR 3 hourly products"""
import datetime
import sys
import os
import numpy as np
import pygrib
from pyiem.util import ncopen, logger
# This exists on dev laptop :/
TEMPLATE_FN = (
"/mesonet/ARCHIVE/data/1980/01/01/model/NARR/apcp_198001010000.grib"
)
BASEDIR = "/mesonet/data/iemre"
LOG... | akrherz/iem | scripts/iemre/init_narr.py | Python | mit | 2,984 | [
"NetCDF"
] | 218f4900546c48e96f759d955ebea9940240fda6dcf5b4f5ced6ef64d39e8994 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyGpyopt(PythonPackage):
""" Performs global optimization with different acquisition funct... | LLNL/spack | var/spack/repos/builtin/packages/py-gpyopt/package.py | Python | lgpl-2.1 | 1,089 | [
"Gaussian"
] | 71d82ead1fd6b3c17d132d3f2798b6d8b8c11970b2d5a72fa5a78c2416c4e676 |
BOARDS = {
'arduino' : {
'digital' : tuple(x for x in range(14)),
'analog' : tuple(x for x in range(6)),
'pwm' : (3, 5, 6, 9, 10, 11),
'use_ports' : True,
'disabled' : (0, 1, 14, 15) # Rx, Tx, Crystal
},
'arduino_mega' : {
'digital' : tuple(x for x in range(54... | hatchetation/pyFirmata | pyfirmata/boards.py | Python | bsd-3-clause | 508 | [
"CRYSTAL"
] | 8113b05843a48c71fac02e5a46050bf4daf115bccdd1b62aa513c4dd5070c5da |
"""
EvMenu
This implements a full menu system for Evennia. It is considerably
more flexible than the older contrib/menusystem.py and also uses
menu plugin modules.
To start the menu, just import the EvMenu class from this module,
```python
from evennia.utils.evmenu import EvMenu
EvMenu(caller, menu_module_... | emergebtc/evennia | evennia/utils/evmenu.py | Python | bsd-3-clause | 27,667 | [
"VisIt"
] | 7ddfc01dfa0f127601d62b02790912557e1a7f7b4b665948ad6aebca3651886a |
"""
Copyright (c) 2014 Brian Muller
Copyright (c) 2015 OpenBazaar
"""
import time
import sqlite3 as lite
from collections import OrderedDict, MutableMapping
from zope.interface import implements, Interface
from protos.objects import Value
from threading import RLock
class IStorage(Interface):
"""
Local stora... | the9ull/OpenBazaar-Server | dht/storage.py | Python | mit | 9,488 | [
"Brian"
] | 698a1679dcc112c5f3f5bd539864f54876e3fd6020dd330ade7708f0045f1397 |
"""
Push test that pushes actual data to widgets set up on a geckoboard dashboard.
gecko_settings.json should contain the widget keys and api keys for corresponding
widgets.
"""
import geckopush
from tests import pull_keys
WIDGET_KEYS = pull_keys.get_keys()
API_KEY = WIDGET_KEYS['api_key']
d = geckopush.Dashboard(AP... | patleeman/geckopush | tests/push_test.py | Python | mit | 10,551 | [
"Amber"
] | 44551939103cbd149f81a262fb765b44075a09959e4779b8f6cbcc859badd749 |
#!/usr/bin/env python
import pylab as pyl
from mpl_toolkits.axes_grid1 import AxesGrid
import cPickle as pickle
from colsort import colsort
def plot_uvj_vs_icd():
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ICD_IH != None, galaxies)
galaxies = filter(lambda ... | boada/ICD | sandbox/legacy_plot_code/plot_icd_n_ssfr.py | Python | mit | 2,741 | [
"Galaxy"
] | 8434857d6f7db27467d42e1045f02be414e90b2c586fa01feb401018cbd6f5af |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides utility classes for string operations.
"""
import re
from fractions import Fraction
from monty.dev import deprecated
SUBSCRIPT_UNICODE = {
"0": "₀",
"1": "₁",
"2": "₂",
... | richardtran415/pymatgen | pymatgen/util/string.py | Python | mit | 14,409 | [
"pymatgen"
] | 7c9e10c140684f95da9744dad0324c09b4ffb6f83f4c3e1e9f6f07ccfb55cdb3 |
import subprocess
import sys
usage = """
python prepareMicroarrayProbes.py MODE ...
there are four modes:
BUILD:
builds a bowtie index and requires two additional arguments:
(i) the cDNA sequence fasta file
(ii) the bowtie index name/path
example:
python prepareMicroarrayProbes.py BUILD myCDNA.fasta myBowtieIndex
... | MWSchmid/microarray | prepareMicroarrayProbes.py | Python | gpl-3.0 | 4,846 | [
"Bowtie"
] | bd4dd48487112446b900f11a229dc1f395b23d4d108987190a1ec472e0844501 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kevin-coder/tensorflow-fork | tensorflow/python/autograph/converters/call_trees.py | Python | apache-2.0 | 5,417 | [
"VisIt"
] | 820405f0ce6f2802dc6f786f16b587e167cc51f154a6ad0ca01af1f1e4b7bc76 |
# -*- Python -*-
# Converted by ./convert_mime_type_table.py from:
# /usr/src2/apache_1.2b6/conf/mime.types
#
content_type_map = {
'css': 'text/css',
'js': 'text/javascript',
'log': 'text/plain',
'ai': 'application/postscript',
'aif': 'audio/x-aiff',
'aifc': 'audio/x-aiff',
'aiff': 'audi... | hansroh/skitai | skitai/handlers/mime_type_table.py | Python | mit | 3,687 | [
"NetCDF"
] | d2c975bee79f94025e2c864ab86be113f1c46f3d549b0d3c8d951d05f37cfba2 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | retrography/scancode-toolkit | src/commoncode/system.py | Python | apache-2.0 | 3,647 | [
"VisIt"
] | 4814790f4421c5678be8b26317837f00387655f19fbd8c541bcf061372afdfc1 |
import os
import re
import shutil
import sys
if sys.version_info[:2] < (2, 6):
sys.exit('virtualenv requires Python 2.6 or higher.')
try:
from setuptools import setup
from setuptools.command.test import test as TestCommand
class PyTest(TestCommand):
user_options = [('pytest-args=', 'a', "Argu... | boardman/sphinx-buildpack | vendor/virtualenv-13.1.0/setup.py | Python | mit | 3,693 | [
"Brian"
] | 88f5a0fe8853626cf5f940c4409833b88aa6215677111e8327b0e8e61a46a358 |
# sql/visitors.py
# Copyright (C) 2005-2012 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Visitor/traversal interface and library functions.
SQLAlchemy schema and expressio... | fredericmohr/mitro | mitro-mail/build/venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py | Python | gpl-3.0 | 9,614 | [
"VisIt"
] | f882cc925a479cecb8357afe73d08260e6b70c636bb7edfd34c81257dafa5ea3 |
"""SCons.Util
Various utility functions go here.
"""
#
# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 The SCons Foundation
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the So... | rwatson/chromium-capsicum | third_party/scons/scons-local/SCons/Util.py | Python | bsd-3-clause | 52,579 | [
"VisIt"
] | e52c6b600485a6806b057af1336a5a54f60f20f511db9ab6b52e628a8943d278 |
"""
Basic operations for BRI Mongo databases.
"""
import logging
import re
from functools import wraps
import datetime
from .. import util
logger = logging.getLogger(__name__)
def find_objects(collection):
"""
Return a decorator that retrieves objects from the specified
collection, given a db connection... | jaeddy/bripipetools | bripipetools/database/operations.py | Python | mit | 7,760 | [
"Galaxy"
] | 01ee6e1e095d2f599de537912411cf858ac5df5a4787af270e55eb7ea4a494e5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Run this test like so:
# vtkpython TestParametricFunctions.py -D $VTK_DATA_ROOT \
# -B $VTK_DATA_ROOT/Baseline/Graphics/
import vtk
import vtk.test.Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# ------------------------------------... | aashish24/VTK-old | Common/ComputationalGeometry/Testing/Python/TestParametricFunctions.py | Python | bsd-3-clause | 25,521 | [
"VTK"
] | 758ca412fed9592df6eefb97c4edbebb31cbba71944f68e32bf048a145b6e77b |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
#
# Impressive, a fancy presentation tool
# Copyright (C) 2005-2008 Martin J. Fiedler <martin.fiedler@gmx.net>
# portions Copyright (C) 2005 Rob Reid <rreid@drao.nrc.ca>
# portions Copyright (C) 2006 Ronan Le Hy <rlehy@free.fr>
# portions Copyright (C) 2007 Luke Campag... | geekq/impressive | impressive.py | Python | gpl-2.0 | 160,901 | [
"VisIt"
] | fffdc6fcb8de76d7e57df3f20f54f13ceb38cc738f306a65ea11b34faacf2cb4 |
import time
from netCDF4 import Dataset
from oceansar.ocs_io.netcdf import NETCDFHandler
class SkimRawFile(NETCDFHandler):
""" Raw data file generated by the OASIS Simulator
:param file_name: File name
:param mode: Access mode (w = write, r = read, r+ = read + append)
:param raw_dim: Raw ... | pakodekker/oceansar | oceansar/ocs_io/raw.py | Python | gpl-3.0 | 8,090 | [
"NetCDF"
] | 0a0c094ae5e647fa77ab22e6158ab61854ddcfa6a7587247f7ebd64606cf787a |
#
# Copyright 2008 The ndb Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | GoogleCloudPlatform/datastore-ndb-python | samples/columbus.py | Python | apache-2.0 | 2,388 | [
"COLUMBUS"
] | 2189fc93c1f0273aa804882fcdd2d16f50b99278d5f5abd82eb900f7719d48a1 |
import string
import AST
from Memory import *
from Exceptions import *
from visit import *
class Interpreter(object):
def __init__(self):
self.memory_stack = MemoryStack()
@on('node')
def visit(self, node, create_memory=True):
pass
@when(AST.BinExpr)
def visit(self, node, create_... | salceson/kompilatory | lab4/Interpreter.py | Python | mit | 5,461 | [
"VisIt"
] | dbd30f92e8c6a64fbebd1024a76489b64dfe2f4e5d1f88656f96f70d75a65fd3 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | annarev/tensorflow | tensorflow/python/ops/nn_ops.py | Python | apache-2.0 | 238,507 | [
"Gaussian"
] | 402706303b388a11d6667adeff92ec69d19c9fa1ad7bca22c48b9b646012da13 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#-------------------------------------------------------------------------------
# Name: adawaty
# Purpose: web interface tools for manipulating arabic texts.
#
# Author: Taha Zerrouki (taha.zerrouki[at]gmail.com)
#
# Created: 31-10-2011
# Copyright: (c) Ta... | linuxscout/mishkal | interfaces/web/adawaty.py | Python | gpl-3.0 | 6,234 | [
"VisIt"
] | 1af9f500381e4ae25f49c19031c09c50ac0f7ae10306c50a204f5fa9802996dc |
import sys
import time
import numpy as np
from ase.parallel import world
from asap3.Tools.ParameterOptimization.Optimization import ParameterOptimization
def now():
"Time as a string."
return time.strftime("%H:%M:%S")
class ParameterSearch(ParameterOptimization):
"""Parallel parameter optimization."""
... | auag92/n2dm | Asap-3.8.4/Python/asap3/Tools/ParameterOptimization/SearchParallel.py | Python | mit | 11,614 | [
"ASE"
] | 7b953885eb85cef02fdd1c220091bc57a23c0af2b3f5f50b4d915bb79a78978c |
from typing import Any
import importlib
from ..core.legacy_plugin_wrapper import LegacyPlugin
class PluginConfig:
"""Plugin Configuration Metadata
This class holds the information needed to lazy-import plugins.
Parameters
----------
name : str
The name of the plugin.
class_name : st... | imageio/imageio | imageio/config/plugins.py | Python | bsd-2-clause | 20,029 | [
"VTK"
] | c213322054999619168d430fabbca7df18a4795bed031698e2cbd0c2a822d439 |
from PyQt4 import QtCore, QtGui, uic
import vtk
import os
import sys
from MovePlanet import updateSunsystem
class PlanetSimulation(QtGui.QDialog):
__timer = QtCore.QTimer()
__renderer = vtk.vtkRenderer()
__list_of_planets = []
__list_of_actors = []
__scale_sun_radius = 0.00000006
__scale_... | tscholze/ts-py-planet-sim | stable/planetSim.py | Python | mit | 9,343 | [
"VTK"
] | 1163dde28c3fc70921318b48e53260f2fda544bf9b0249c92da4fa2cd78d5d01 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Subliminal post-processing script for NZBGet and SABnzbd
#
# Copyright (C) 2015-2019 Chris Caron <lead2gold@gmail.com>
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by
... | caronc/nzbget-subliminal | Subliminal.py | Python | gpl-3.0 | 102,462 | [
"VisIt"
] | e266fdd1bb439a57c4a80f644e180f24514edbe3c105436d786ecb532fe3584b |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
import input_array_choice_mixin # need this for constants
reload(input_array_choice_mixin)
from input_array_... | chrisidefix/devide | modules/filters/warpPoints.py | Python | bsd-3-clause | 3,444 | [
"VTK"
] | 0ab44018522e02f92f3b8a8df68ac5c5ec6cbc665676854ed42957077e4e2b47 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/util/_decorator.py | Python | bsd-3-clause | 11,769 | [
"scikit-bio"
] | 4091320b0196e9e7716814c5ae0532e1daf8f4c25a5eac30b60ace8b93ce0091 |
"""Expression for IPI format.
IPI is nearly swissprot, but contains some differents which makes the
Swissprot parsers choke.
"""
import warnings
warnings.warn("Bio.expressions was deprecated, as it does not work with recent versions of mxTextTools. If you want to continue to use this module, please get in contact wit... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/expressions/swissprot/ipi.py | Python | apache-2.0 | 2,637 | [
"Biopython"
] | 83aeb52de2d6e426df0516880b524f4e9f19b8b0524620da8da804a82b6b827b |
from __future__ import division
from __future__ import print_function
from mpop.satellites import GeostationaryFactory
from mpop.projector import get_area_def
import datetime
import numpy as np
# in this example we read parallax corrected data
# from an netCDF file, do some modifications to it.
# you could also use a... | meteoswiss-mdr/monti-pytroll | scripts/demo_add_channel.py | Python | lgpl-3.0 | 6,339 | [
"NetCDF"
] | d5e0f62df8ded3a8019c28bc63c0585689c6dc7163751b537ae1d2e68666d2b6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#==============================================================================
# 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 th... | JoaoVasques/aws-devtool | eb/macosx/python2.7/scli/resources.py | Python | apache-2.0 | 16,173 | [
"VisIt"
] | 9844b927a3fd99604bfbc4d03f232cb09da7cf9889a50d03c2ef01175ab3604c |
##
# Copyright 2013-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/d/dl_poly_classic.py | Python | gpl-2.0 | 4,824 | [
"DL_POLY"
] | 623f7033a76628395955c57fc2c4b88de9f71de85b417e2d6d9f3e0729e87eab |
"""Handle extraction of final files from processing pipelines into storage.
"""
import datetime
import os
import toolz as tz
from bcbio import log, utils
from bcbio.upload import shared, filesystem, galaxy, s3, irods
from bcbio.pipeline import run_info
from bcbio.variation import vcfutils
import bcbio.pipeline.datadi... | biocyberman/bcbio-nextgen | bcbio/upload/__init__.py | Python | mit | 30,250 | [
"Galaxy"
] | 19034e60d41885e8bb90954b93ffec867aea6ae330304fd3222cf8c9ae12a056 |
# Copyright (c) 2012, Cloudscaling
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | bswartz/manila | manila/hacking/checks.py | Python | apache-2.0 | 11,630 | [
"VisIt"
] | ca358c3f2095882526e972a0dc86a2113cd4fdcce7bc06976b1078bda61aa75d |
#!/usr/bin/env python
# encoding: utf-8
#| Copyright Inria May 2015
#| This project has received funding from the European Research Council (ERC) under
#| the European Union's Horizon 2020 research and innovation programme (grant
#| agreement No 637972) - see http://www.resibots.eu
#|
#| Contributor(s):
#| - Jean-Bap... | jbmouret/limbo | waf_tools/sferes.py | Python | gpl-3.0 | 3,417 | [
"Gaussian"
] | e579897f039328c33b3d840cb3666830b436906c6d60f83a8b5ea7c643045da8 |
'''
Created on May 27, 2014
@author: Francesco Nero
'''
from . import settings
network = None
class Network():
def __init__(self, name):
global network
print "Creating network: "+name
self.name = name
self.nodes = {}
self.connections = []
network = self
... | francesconero/nengo2nest | nengo2nest/nef.py | Python | gpl-2.0 | 2,126 | [
"NEURON"
] | c843e298a120c09b8bb2235e5f0f114d402da88c1563c2a4d267af94d34c4758 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""SPM wrappers for preprocessing data
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path... | mick-d/nipype_source | nipype/interfaces/spm/preprocess.py | Python | bsd-3-clause | 67,777 | [
"Gaussian"
] | e41e99b50addd1a43999021c81d07336b2fa7679670f5a717f181e28301b8757 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# 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 Licens... | tsdmgz/ansible | lib/ansible/modules/network/cnos/cnos_factory.py | Python | gpl-3.0 | 5,254 | [
"VisIt"
] | 504d6efd103082ce4989f7e45c1016bf34df8fa09f7def9bd64e354d80f23190 |
#!/usr/bin/env python
#coding: utf-8
class Solution:
def _bfs(self, board, cr, cc, row, col, visit, live):
if cr < 0 or cr >= row or cc < 0 or cc >= col: return
if visit[cr][cc]: return
visit[cr][cc], live[cr][cc] = True, True
queue = [(cr,cc)]
while queue:
cr, ... | wh-acmer/minixalpha-acm | LeetCode/Python/surrounded_regions.py | Python | mit | 2,345 | [
"VisIt"
] | a084c3a67ce71ea928ecac595582314f8b63d9adf24d86be31ad277dc455f1ae |
"""
WSGI config for ase project.
This module contains the WSGI application used by Django's development server
and any production WSGI deployments. It should expose a module-level variable
named ``application``. Django's ``runserver`` and ``runfcgi`` commands discover
this application via the ``WSGI_APPLICATION`` sett... | epcoullery/ase | repart/wsgi.py | Python | agpl-3.0 | 1,049 | [
"ASE"
] | a65de21ea4fab815362a29a76247023372e5dd8ba882fcb2eee8fef2e04f7fb6 |
import os
import numpy as np
import deepchem as dc
def load_gaussian_cdf_data():
"""Load example with numbers sampled from Gaussian normal distribution.
Each feature and task is a column of values that is sampled
from a normal distribution of mean 0, stdev 1."""
current_dir = os.path.dirname(os.path.ab... | deepchem/deepchem | deepchem/trans/tests/test_cdf_transform.py | Python | mit | 3,446 | [
"Gaussian"
] | 92fa8dae05a44c02b7bfcf812b1cd9bc2d6d8d2668546b98346f590cc2136f65 |
# ******************************** #
# Double pole balancing experiment #
# ******************************** #
import math
import random
import cPickle as pickle
from neat import config, population, chromosome, genome, visualize
from cart_pole import CartPole
def evaluate_population(population):
simulation = Cart... | anuragpapineni/Hearthbreaker-evolved-agent | neat-python-read-only/examples/pole_balancing/double_pole/cpExp.py | Python | mit | 1,609 | [
"NEURON"
] | b69831dcedb1c191a1e571f0e28d234941cde7555688bcce0d9d4656415fa2e3 |
#!/usr/bin/env python3
import os
import pathlib
from pathlib import Path
import cloudpickle
from natsort import natsorted
import numpy as np
from pysisyphus.helpers import geom_from_library, geom_from_xyz_file, geoms_from_trj
from pysisyphus.calculators.Turbomole import Turbomole
from pysisyphus.optimizers.Conjugate... | eljost/pysisyphus | tests_staging/test_turbo_butadien_td_opt/test_turbo_butadien_td_opt.py | Python | gpl-3.0 | 9,847 | [
"TURBOMOLE"
] | 57ce17634c223d22db791fd23f3598174f9dc04dfff490b008415a68065bfd79 |
'''
This is the main program loop. This generates the front end and generates all URLS for the user to visit.
'''
# TODO: 2 Generate all food URLS once the database is done
#
import web_scraper
from flask import *
#from flask_bootstrap import Bootstrap
DC_menu=web_scraper.Webget()
DC_menu=DC_menu.format_to_HTML()
ap... | SalehHindi/DC-Killer | web_frontend.py | Python | gpl-2.0 | 1,006 | [
"VisIt"
] | 8d4c58c6fca95d8f64a4871c75d2f3f8f20e611dff9a20fbcb6d2c5b933da66a |
"""Module created to test the library on MNIST digits.
Contains:
* ANN/ DBN network training.
* RBM training and feature exposure.
* CNN network training.
"""
__author__ = "Mihaela Rosca"
__contact__ = "mihaela.c.rosca@gmail.com"
import argparse
import cPickle as pickle
import matplotlib
import numpy as np
imp... | mihaelacr/pydeeplearn | code/MNISTdigits.py | Python | bsd-3-clause | 36,365 | [
"Gaussian"
] | 4ab9c62d6b03dfdf66d631d94ed792be116d10395a2de2dc69f8c5b74dff4f08 |
""" Definition for WMSHistory Monitoring type.
Drop-in replacement for the Accounting/WMSHistory accounting type.
Filled by the agent "WorkloadManagement/StatesAccountingAgent"
"""
from DIRAC.MonitoringSystem.Client.Types.BaseType import BaseType
__RCSID__ = "$Id$"
class WMSHistory(BaseType):
"""
... | ic-hep/DIRAC | src/DIRAC/MonitoringSystem/Client/Types/WMSHistory.py | Python | gpl-3.0 | 1,432 | [
"DIRAC"
] | 1b491c082acaa5f0fa7cbb8696177b5be4332fef75f20fc59fd085ce037bf4eb |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | xhochy/arrow | python/pyarrow/parquet.py | Python | apache-2.0 | 74,846 | [
"VisIt"
] | 29f4abe0b9fb56b3c26f866b1e07ce7782565d189797b64a018f57bd9fd3c102 |
#!/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... | gkc1000/pyscf | pyscf/scf/dhf.py | Python | apache-2.0 | 28,936 | [
"DIRAC",
"PySCF"
] | 6ee9c97318dd90390292f07ba482d7a51957ff17efc2188c2890c4c9a46820ca |
# SYSTEM LIBS
from matplotlib.colors import LogNorm
import matplotlib.pyplot as plt; plt.ion();
import matplotlib
import numpy as np
import pandas as pd
# from root_pandas import read_root
import sys
from itertools import islice
from scipy import signal # To find peaks, for edge-detecting the crystal
from scipy.optimiz... | f-forcher/crystal-channeling-analysis | channeling_efficiency_autooffset.py | Python | gpl-3.0 | 25,655 | [
"CRYSTAL",
"Gaussian"
] | 817d74bc5fe2f5606d6abc0155f963fbada94a965d8733529bccf8b0c50515d6 |
"""This module tests various ways how to set up the provisioning using the provisioning dialog."""
import re
from datetime import datetime
from datetime import timedelta
import fauxfactory
import pytest
from widgetastic.utils import partial_match
from widgetastic_patternfly import CheckableBootstrapTreeview as CbTree
... | izapolsk/integration_tests | cfme/tests/infrastructure/test_provisioning_dialog.py | Python | gpl-2.0 | 19,319 | [
"VisIt"
] | 0247831c708e4ea4b8bafe79b77fba6fee7a6a5f8ce6a374ff67c46baf37ebaa |
"""
Structure contains the description of a set of atoms in space, for periodic structures it adds a lattice.
"""
try:
import itertools.izip as zip
except ImportError:
pass
import json
import os
import struct
import sys
import numpy as np
from collections.abc import MutableSequence
from itertools import combin... | MaterialsDiscovery/PyChemia | pychemia/core/structure.py | Python | mit | 49,235 | [
"CRYSTAL"
] | e53568e58943dd2eeb383a70c939d5f869d93174f73ae338f453484faf941148 |
# -*- coding: utf-8 -*-
#############################################################################
# SRWLIB Example: Virtual Beamline: a set of utilities and functions allowing to simulate
# operation of an SR Beamline.
# The standard use of this script is from command line, with some optional arguments,
# e.g. for ... | mkeilman/sirepo | tests/template/srw_import_data/chx.py | Python | apache-2.0 | 32,127 | [
"CRYSTAL"
] | 403d5539c88b7ff2a8b6ff8da921a8bc21b0241619cf1dce372e5d5973a04536 |
# coding=utf-8
# Copyright 2022 RigL 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 agree... | google-research/rigl | rigl/experimental/jax/pruning/symmetry.py | Python | apache-2.0 | 5,956 | [
"NEURON"
] | 9ab8bef5c9f87ec0930db047e54064aaff640da29d71dab2ca8143d422972748 |
import numpy as np
from ase.io.pupynere import NetCDFFile
# Write array
a1 = np.random.rand(5, 5)
a2 = a1 * 2 - 5
nc = NetCDFFile('test.nc', 'w')
nc.createDimension('dimx', a1.shape[0])
nc.createDimension('dimy', a1.shape[1])
nc.createVariable('matrix1', 'd', ('dimx', 'dimy'))[:] = a1
nc.createVariable('matrix2', 'd',... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/fio/netcdf.py | Python | gpl-2.0 | 556 | [
"ASE"
] | a5b55e85ab9f734c6fccddec0f4eeffae5b0e2348a5b842ecedf36dea16a7dc3 |
"""Removes hanging LogicalFiles in composite resources. Hanging LogicalFiles do not have a
Resource nor reference any files.
"""
from django.core.management.base import BaseCommand
from hs_file_types.models.generic import GenericLogicalFile
from hs_file_types.models.geofeature import GeoFeatureLogicalFile
from hs_f... | hydroshare/hydroshare | hs_core/management/commands/delete_hanging_logical_files.py | Python | bsd-3-clause | 2,806 | [
"NetCDF"
] | 28e8ee6e4346af94cf01e1dcfa48337ac56678d7ad8ae3ceece8046e844ba124 |
# Awn Applet Library - Simplified APIs for programming applets for Awn.
#
# Copyright (C) 2007 - 2008 Pavel Panchekha <pavpanchekha@gmail.com>
# 2008 - 2010 onox <denkpadje@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public ... | gilir/awn-extras-debian | shared/python/awnlib.py | Python | gpl-3.0 | 47,971 | [
"VisIt"
] | 3b06477e669cd450240c0572b1c0ac1b6a43ede672fe10984fe018643b3e75b7 |
#!/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/recipe.py | Python | gpl-3.0 | 9,692 | [
"Galaxy"
] | 70793a8d4187d63133d5eee97d26a7b4428bd210e3450fa6ac1b6f34dbea97d5 |
import torch
import torch.nn as nn
from mushroom_rl.utils.features import uniform_grid
from mushroom_rl.utils.torch import to_float_tensor, to_int_tensor
class GaussianRBFTensor(nn.Module):
"""
Pytorch module to implement a gaussian radial basis function.
"""
def __init__(self, mu, scale, dim, use_cu... | carloderamo/mushroom | mushroom_rl/features/tensors/gaussian_tensor.py | Python | mit | 2,669 | [
"Gaussian"
] | fd6dfe75a5204aa05357f37bca916fcf8b8cb6df8798daee72668b7f761d55ae |
"""
Integration with native distribution package managers.
@since: 0.28
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import os, platform, re, subprocess, sys
from zeroinstall.injector import namespaces, model, arch, qdom
fr... | dsqmoore/0install | zeroinstall/injector/distro.py | Python | lgpl-2.1 | 38,221 | [
"VisIt"
] | f5a4087099f4f6b61b404382c6588c989209e69ba1e9ccda7be12bb87ad2bc3e |
import os
import shutil
import os.path as op
import pysam
# from collections import Counter
from bcbio.utils import splitext_plus, file_exists, safe_makedir, chdir
from bcbio.provenance import do
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
from bcbio import broad
from bcbio.bam import index
... | lbeltrame/bcbio-nextgen | bcbio/wgbsseq/align.py | Python | mit | 3,378 | [
"pysam"
] | d7fdea6cf3b9c7311b2b7397323fbbbef6f2a1219007fee29938f69b6209c5c6 |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2012 OpenPlans
#
# 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 versio... | GISPPU/GrenadaLandInformation | geonode/base/enumerations.py | Python | gpl-3.0 | 14,305 | [
"BWA"
] | 13974b6c1099c6cdc0d59b3ac411d0c97ed5855f16bbc0166ce05ec61c38d916 |
#!/usr/bin/env python
"""
SPAdes Contig Graph
This is a tool to combine the assembly graph and contigs made by the SPAdes
assembler. For more information, go to:
https://github.com/rrwick/spades_contig_graph
Author: Ryan Wick
email: rrwick@gmail.com
"""
from __future__ import division
from __future__ import print_f... | rrwick/SPAdes-Contig-Graph | spades_contig_graph.py | Python | gpl-3.0 | 56,862 | [
"BLAST"
] | a85d537680c7214d07508164fe044abdb2f6d8cd7b0b67285690b8bf983b7826 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting model 'GeoMapping'
db.delete_table('profiles_geomapping')
# Removing M2M table for fie... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0007_auto__del_geomapping.py | Python | mit | 11,245 | [
"MOE"
] | 180ce7b876ed648a7abb416bd3858d927aed80ae3539618e4039e2e7897cc7f7 |
#!/usr/bin/env python
from __future__ import absolute_import
#----------------------------------------------------------------------
# Copyright (c) 2013-2015 Raytheon BBN Technologies
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and/or hardware specification (th... | plantigrade/geni-tools | src/gcf/omnilib/stitchhandler.py | Python | mit | 207,229 | [
"ORCA"
] | 23ff9b738196fbee58a5600607c4e26a9cf72b3b178ef9f3a06c0625afff3201 |
""" ConanFile user tools, as download, etc
"""
from __future__ import print_function
import logging
import multiprocessing
import os
import platform
import re
import subprocess
import sys
from contextlib import contextmanager
import requests
from patch import fromfile, fromstring
from conans.client.output import C... | mropert/conan | conans/tools.py | Python | mit | 22,036 | [
"Jaguar"
] | 027bfb0c8a1ecfcde74f95bf7a7836b196de5cf813501ef0cf6ead81e0dcc867 |
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.ConfigurationSystem.Client.PathFinder import getAgentSection
from DIRAC.Core.Utilities.CFG import CFG
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.Core.Utilities.JDL import loadJDLAsCFG, d... | Sbalbp/DIRAC | WorkloadManagementSystem/Client/JobState/JobManifest.py | Python | gpl-3.0 | 8,989 | [
"DIRAC"
] | ee019c5c2e20746db7c902368f30011cc43c1bb16dbe759f76cdb985c1cb5911 |
'''
Created on 2012-09-29
A simple script that reads a WRF netcdf-4 file and displays a 2D field in a proper geographic projection;
application here is plotting precipitation in the inner WRF domain.
@author: Andre R. Erler
'''
## includes
# matplotlib config: size etc.
import numpy as np
import matplotlib.pylab as ... | aerler/WRF-Projects | src/archive/plotInnerPrecip.py | Python | gpl-3.0 | 6,163 | [
"NetCDF"
] | 4ff9c453eb3862d034264f14557b96d2c55d8b62be166c195d51c9ddd59475ad |
#!/usr/bin/env python
"""
Print list of users with proxies.
Example:
$ dirac-admin-users-with-proxy
* vhamar
DN : /O=GRID-FR/C=FR/O=CNRS/OU=CPPM/CN=Vanessa Hamar
group : dirac_admin
not after : 2011-06-29 12:04:25
persistent : False
-
DN : /O=GRID-FR/C=FR/O=CNRS/OU=CPPM/CN=Vanessa... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_admin_users_with_proxy.py | Python | gpl-3.0 | 2,813 | [
"DIRAC"
] | 1ff71a2faf284a118c3836b703eaf348ee59907d389d01c3e481ba228f3d9a17 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007,2008,2012,2014,2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version... | ghutchis/cclib | test/data/testTD.py | Python | lgpl-2.1 | 4,812 | [
"ADF",
"Dalton",
"cclib"
] | 9d5c3ec774f0a2fddf118fcda15ee9192e65eea5db63c2dda117f073fb7ebbfc |
# 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/convert/units.py | Python | gpl-3.0 | 3,557 | [
"ESPResSo"
] | 45a8d56067357b3933eb51ca2c973d29307470c7faf5adb70cdfaefc613439fa |
# Copyright 2008-2009 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.
#
# This module is for reading and writing PIR or NBRF format files as
# SeqRecord objects. ... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/SeqIO/PirIO.py | Python | gpl-2.0 | 7,219 | [
"Biopython"
] | fa18fbf915e9ae07cda21c56296ae15197e122a8e870d4555afd8d19d77cc7a1 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.