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 |
|---|---|---|---|---|---|---|---|
# -*- encoding:ascii -*-
from mako import runtime, filters, cache
UNDEFINED = runtime.UNDEFINED
__M_dict_builtin = dict
__M_locals_builtin = locals
_magic_number = 6
_modified_time = 1392055148.655435
_template_filename=u'templates/webapps/galaxy/base_panels.mako'
_template_uri=u'/webapps/galaxy/base_panels.mako'
_temp... | MGEScan/mgescan | galaxy-modified/base_panels.mako.py | Python | gpl-3.0 | 20,651 | [
"Galaxy"
] | 510778a823f42955a3ee8bca6c6475ed93e6a505d97cd6b4e9ad08ba7863f93c |
from __init__ import __version__, BLAST, BLAST_BIN_ROOT, BLAST_DB_ROOT, DEFAULT_DB
from services.classes import Procedure, Argument
from options import ALLOWED_OPTIONS, ALLOWED_FLAGS, SPECIAL_OPTIONS
from utility import SCRYError
from rdflib.term import Literal
... | bas-stringer/scry | services/BLAST/run_blast.py | Python | mit | 8,841 | [
"BLAST"
] | 01c5d23933f2833c217aac1f6861c25a8d7e58f4e38d7e9d51ec6d71dc855aaa |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines site transformations which transforms a structure into
another structure. Site transformations differ from standard transformations
in that they operate in a site-specific manner.
All transformations should inherit the AbstractT... | Dioptas/pymatgen | pymatgen/transformations/site_transformations.py | Python | mit | 21,082 | [
"pymatgen"
] | edae337469068acfa1e5798fd32f0089c5ff83f3b840a62e800930af5f2f2443 |
# (c) 2016, Adrian Likins <alikins@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later vers... | jmehnle/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 19,273 | [
"Galaxy"
] | 6b29f1154cd66f52ff4e4a2bde7a9ae81e7d87a648b693aaf4d3cd2f8198c68c |
from header_quests import *
####################################################################################################################
# Each quest record contains the following fields:
# 1) Quest id: used for referencing quests in other files. The prefix qst_ is automatically added before each quest-i... | nycz/useful-sisters | module_quests.py | Python | mit | 16,896 | [
"VisIt"
] | eb6da34fd9eb4a3587ac76465c7e63c81c92d2eb6fb17e207077ffe5ba2f91b3 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2012, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.zenoss.Notifications | ZenPacks/zenoss/Notifications/info.py | Python | gpl-2.0 | 2,078 | [
"VisIt"
] | 3dad417541ef428ebf6828e27ce71069e9d6f453a3de49cff5f5b35b6e1c6d34 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007,2012,2014,2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public versio... | ghutchis/cclib | test/method/testpopulation.py | Python | lgpl-2.1 | 2,809 | [
"Gaussian",
"cclib"
] | bf1ee7c13400a53166a98a76f7e5375fea13b80e5043b7ed5265cd3e5d283344 |
#
# https://github.com/ajjackson/ase-tutorial-symmetry/blob/master/ase-symmetry.md#getting-the-symmetry-operations
#
import ase.spacegroup
spg = ase.spacegroup.Spacegroup(152)
print("Is a-quartz centrosymmetric? {}".format("yes" if spg.centrosymmetric else "no"))
print("Is the a-quartz lattice primitive? {}".format(... | miroi/open-collection | theoretical_chemistry/software_runs/ase/runs/ase-symmetry/symmetry_operations.py | Python | mit | 702 | [
"ASE"
] | b79757a84ee6ec55b4180bbade454ae8f0ad172dac1b74a4b00315f578755b14 |
#!/usr/bin/env python
"""
Updates dataset.size column.
Remember to backup your database before running.
"""
import sys, os, ConfigParser
import galaxy.app
assert sys.version_info[:2] >= ( 2, 4 )
def main():
ini_file = sys.argv.pop(1)
conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
conf_pa... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/cleanup_datasets/update_dataset_size.py | Python | gpl-3.0 | 1,230 | [
"Galaxy"
] | aef2764e4643401c8dcd0cda25bfca5593bce8ad73f65af054571067297adb4a |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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
#
# ... | jeffrey4l/nova | nova/tests/unit/network/test_manager.py | Python | apache-2.0 | 168,360 | [
"FEFF"
] | a1d6fb60b0b24336c318c7039c1477bf6bf0817d517d5f23c90a030c52745d5b |
#!/usr/bin/python
import math
import os,sys
ncs_lib_path = "../../../"
sys.path.append(ncs_lib_path)
import ncs
def run(argv):
voltage_channel = {
"type": "voltage_gated_ion",
"m_initial": 0.0,
"reversal_potential": -80,
"v_half": -44,
"deactivation_slope": 40,
"activation_slope": 20,
"e... | BrainComputationLab/ncs | python/samples/models/lif/ncs_neuron_test.py | Python | bsd-2-clause | 1,973 | [
"NEURON"
] | 1923271e6bf875ff1d1b23a4a43b342fd42357f21f5e0d62255a8c48d78420bf |
import requests, json
import pandas as pd
from requests_api import requestsApi
from configparser import ConfigParser, NoSectionError
from datetime import datetime as dt
API_BASE_URL = 'https://api.meetup.com/'
EVENTS_URL = 'https://api.meetup.com/2/events'
RSVPS_URL = 'https://api.meetup.com/2/rsvps'
POST_RSVP_URL =... | mudragada/util-scripts | meetup.com/rsvper.py | Python | mit | 3,597 | [
"VisIt"
] | ec9ad5cdc7981c7c1251eaa34be824b062e55e1cb0d640e15d01e86b32cace35 |
#! /usr/bin/env python
import sys
import soundcloud # Get it with: pip install soundcloud Source: https://github.com/soundcloud/soundcloud-python, docs at https://developers.soundcloud.com/docs/api/reference
import time
import glob
import os
import itertools
try:
import credentials
except ImportError:
print... | motoom/scaup | scaup.py | Python | gpl-2.0 | 6,879 | [
"VisIt"
] | 553b824355fe3ef366b2ba1d9786111341b16d5141ff7dad7e397e128db67ee2 |
# Copyright 2012 OpenStack Foundation
# 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 requ... | SamYaple/neutron | neutron/tests/unit/agent/linux/test_ip_lib.py | Python | apache-2.0 | 56,817 | [
"Brian"
] | 647c727148b5182b7eefdd472f25f828be8983ded788916750bcddcb32f6f61e |
#!/usr/bin/env python
# coding: utf-8
"""
Slidecasting Recorder, a Product of Elpa Corp. www.elpacorp.com
Copyright (c) 2011 , Narendra Sisodiya , narendra@narendrasisodiya.com www.elpacorp.com
Released under GPLv3
Visit - http://code.google.com/p/slidecasting-recorder to know more about team
Dependency -
sudo ... | nsisodiya/slidecasting-recorder | SlideCasting.py | Python | mit | 15,919 | [
"VisIt"
] | 809da9b7df899f2771713eba32d2e2b50c8aa844f09554bbc0f2505a1469b895 |
from __future__ import absolute_import
import bisect
import plotutils.bounded_kde as bk
import bz2
import gzip
import plotutils.log_kde as lk
import numpy as np
import matplotlib.pyplot as pp
import os.path
import scipy.interpolate as si
import scipy.stats as ss
import scipy.stats.mstats as sm
def load_header_data(f... | farr/plotutils | plotutils/plotutils.py | Python | mit | 21,316 | [
"Gaussian"
] | 7a985404ae6474ce6159af02fc88a13208a7b69c557268127c2294fd88c5a1a7 |
#-------------------------------------------------------------------------------
#
# Define classes for (uni/multi)-variate kernel density estimation.
#
# Currently, only Gaussian kernels are implemented.
#
# Written by: Robert Kern
#
# Date: 2004-08-09
#
# Modified: 2005-02-10 by Robert Kern.
# Contr... | pizzathief/scipy | scipy/stats/kde.py | Python | bsd-3-clause | 21,561 | [
"Gaussian"
] | 4e03fa0a948212fee7c1f401a4004813311cac885eccf0761a0857b03eebec82 |
# swift_build_support/build_graph.py ----------------------------*- python -*-
#
# This source file is part of the Swift.org open source project
#
# Copyright (c) 2014 - 2017 Apple Inc. and the Swift project authors
# Licensed under Apache License v2.0 with Runtime Library Exception
#
# See https://swift.org/LICENSE.tx... | apple/swift | utils/swift_build_support/swift_build_support/build_graph.py | Python | apache-2.0 | 6,374 | [
"VisIt"
] | bdba42c74fb8f266ca89bbbf6b9379131bdceab09a2ccbf49fe9723563a7247b |
from datetime import datetime
from urllib import urlencode
from jinja2 import Environment, FileSystemLoader
import cherrypy
from libbe import storage
from libbe import bugdir
from libbe.command.depend import get_blocked_by, get_blocks
from libbe.command.target import add_target, remove_target
from libbe.command.targe... | yanshuaicao/yabbe | interfaces/web/web.py | Python | gpl-2.0 | 8,189 | [
"VisIt"
] | d82ae93472c2af60625cfff42ba2f59e185dc7ee4fc75f1a4e1d9c7e9d0a9b41 |
import inspect
from functools import partial
from typing import Callable, Dict, List, Optional, Tuple, Union, Any, Sequence
import numpy as np
import tensorflow as tf
from six import string_types
from tensorflow.keras.optimizers.schedules import LearningRateSchedule
from odin.fuel import IterableDataset
from tensorflo... | imito/odin | odin/networks/image_networks.py | Python | mit | 36,609 | [
"Gaussian"
] | 0e334f4eb12f35bdca0ff359af65f169b6e3bd20a9606a51d4011f7353da1260 |
""" manage PyTables query interface via Expressions """
from __future__ import annotations
import ast
from functools import partial
from typing import Any
import numpy as np
from pandas._libs.tslibs import (
Timedelta,
Timestamp,
)
from pandas.compat.chainmap import DeepChainMap
from pandas.core.dtypes.comm... | datapythonista/pandas | pandas/core/computation/pytables.py | Python | bsd-3-clause | 19,792 | [
"VisIt"
] | 98d9e0e0ef3e2fe4431251ddab683098fccc30799d5610ac6cd4f455a63e9887 |
# Orca
#
# Copyright 2004-2009 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... | h4ck3rm1k3/orca-sonar | src/orca/formatting.py | Python | lgpl-2.1 | 41,897 | [
"ORCA"
] | 7be3a167b66a11dfd1816f2b34e3bb40cd8512541f83eacb6a7be8514876a5b6 |
import morb
from morb import rbms, stats, updaters, trainers, monitors, units, parameters
import theano
import theano.tensor as T
import numpy as np
import gzip, cPickle
import matplotlib.pyplot as plt
plt.ion()
from utils import generate_data, get_context, one_hot
# DEBUGGING
from theano import ProfileMode
# mo... | benanne/morb | examples/example_mnist_labeled.py | Python | gpl-3.0 | 6,200 | [
"Gaussian"
] | 859f4e70c2b2152cfe4593606202140b22c538590767b01aab33516b17783495 |
#!/usr/bin/env python
import datetime, time, re
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib import gridspec
# load own modules
import spring_dynamics as _sd
__author__ = 'Rhys Whitley, Douglas Kelley, Martin De Kauwe'
__email__ = 'rhys.whitle... | rhyswhitley/phendulum | src/model_plotting.py | Python | apache-2.0 | 7,543 | [
"Gaussian"
] | 059cb0a802e624fb5b99ebe31f4656cdd05b306916ac1ccdb6e0c1cb4b837d0e |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import functools
import types
import warnings
import numpy as np
from astropy.units.core import Unit, UnitsError
from astropy.units.quantity import Quantity
from astropy.utils import lazyproperty
from astropy.utils.exceptions import AstropyUserWarning
_... | stargaser/astropy | astropy/constants/constant.py | Python | bsd-3-clause | 8,565 | [
"Gaussian"
] | a2c088549b8d32938896145e290494307115db2d3fa95c3586964ea80bc7c499 |
import json
import specialcases
RESULTS_FILE = "output.json"
OUTPUT_FILE = "cleanoutput.json"
def cleanDay(day):
"""
Cleans the day string, but returns an OBJECT, to handle cases such as
"first Sunday of the month" or "TBD"
"""
results = {}
day = day.strip().upper() #capitalize so we only hav... | Bcpoole/ClubLife | util/cleanresults.py | Python | mit | 7,649 | [
"ADF"
] | b684ce2f9e6e274ab922d66c0fbcc7580cec1a7fd73b593ce686b09eac616efb |
import string
import random
import json
from collections import defaultdict
from django.conf import settings
from django.http import HttpResponse
from catmaid.fields import Double3D
from catmaid.models import Log, NeuronSearch, CELL_BODY_CHOICES, \
SORT_ORDERS_DICT, Relation, Class, ClassInstance, \
... | catsop/CATMAID | django/applications/catmaid/control/common.py | Python | gpl-3.0 | 11,564 | [
"NEURON"
] | 2f470fa3782e4bc7a9d0b3f776b18bf54d9cd28450b6fa1cec211d5b5c5ff0c5 |
##
# Copyright 2009-2021 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... | akesandgren/easybuild-easyblocks | easybuild/easyblocks/w/wrf.py | Python | gpl-2.0 | 18,692 | [
"NetCDF"
] | 4e2d7870206a1d579934524ac686c84b9d181353351aa65425f107fa46b58e9e |
from ..utils import *
##
# Minions
# Goblin Auto-Barber
class GVG_023:
play = Buff(FRIENDLY_WEAPON, "GVG_023a")
# One-eyed Cheat
class GVG_025:
events = Summon(CONTROLLER, PIRATE - SELF).on(SetTag(SELF, {GameTag.STEALTH: True}))
# Iron Sensei
class GVG_027:
events = OWN_TURN_END.on(Buff(RANDOM(FRIENDLY_MINION... | butozerca/fireplace | fireplace/cards/gvg/rogue.py | Python | agpl-3.0 | 1,030 | [
"TINKER"
] | 0d3bc35094104ec9c854c39c4e3817a9e0d54ac4359dabfcf728728d6ddefca1 |
""" The CountryMapping module performs the necessary CS gymnastics to resolve country codes """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import gConfig, S_OK, S_ERROR
def getCountryMapping(country):
""" Determines ... | yujikato/DIRAC | src/DIRAC/Core/Utilities/CountryMapping.py | Python | gpl-3.0 | 1,151 | [
"DIRAC"
] | 11bd30db16bd1e7c007131c13a6df17ea2c68f3421a0f95d19f7c65dcc68589e |
# -*- coding: utf-8 -*-
#
# This file is part of the python-chess library.
# Copyright (C) 2012-2017 Niklas Fiekas <niklas.fiekas@backscattering.de>
#
# 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 Foundat... | DManuel010/Chess-Bot | Pascal-Drew Bot/chess/pgn.py | Python | gpl-3.0 | 32,527 | [
"VisIt"
] | 266af3c49379b89d27313b88b42ba2ad2dc0dfbd96017b3d5f13923d38f34deb |
import numpy as np
from math import pi
def _gaussian2d(xlen, ylen=None, xstd=0.5, ystd=None):
# Calculate the unnormalized Gaussian 2D matrix
#
# Parameters
# ----------
# xlen : int
# Length of x / width of the window
# ylen : int
# Length of y / height of the window
# xst... | caiotaniguchi/super-zoom-it | superzoomit/misc/filter.py | Python | gpl-3.0 | 1,839 | [
"Gaussian"
] | cdd8ebbc3d9a8a0469f72cd5b414cffe2f23e60db5aae779b477732b2d2d9628 |
"""
This library allows you to quickly and easily use the Twilio SendGrid Web API v3 via Python.
For more information on this library, see the README on GitHub.
http://github.com/sendgrid/sendgrid-python
For more information on the Twilio SendGrid v3 API, see the v3 docs:
http://sendgrid.com/docs/API_Reference... | sendgrid/sendgrid-python | sendgrid/sendgrid.py | Python | mit | 2,264 | [
"VisIt"
] | 10ad0292bef6cf721551de431bb92561b9b5e7a5b12053a42f8a4d1d930943ed |
#!/usr/bin/python
from django.shortcuts import render, render_to_response, get_object_or_404, HttpResponseRedirect
from openmoldbmolecules.models import Molecule
from openmoldbmolecules.search import smiles_search, properties_search, id_search, smarts_search, fast_fp_search
from openmoldbmolecules.forms import SearchFo... | samoturk/openmolDB | openmoldb/views.py | Python | bsd-3-clause | 15,287 | [
"Pybel"
] | b275c421386078b92508d709625cfbf262cf787d698f5e74e46b0d7758c05c68 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import glob
import itertools
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib2
import xmlrpclib
import zlib
from xml.etree import ElementTree
from cStringIO import StringIO
import b... | ksrajkumar/openerp-6.1 | openerp/addons/web/controllers/main.py | Python | agpl-3.0 | 78,698 | [
"VisIt"
] | 2b78de0664a84f224e23ac5fc75476cbe0cd74830557695e45bf4bd7cbb8b557 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
import os
from django.conf import settings
from django.test import Client, TestCase
from django.test.utils import ContextList
from django.core.urlresolvers import reverse
from django.core.exceptions import Suspi... | Smarsh/django | tests/regressiontests/test_client_regress/models.py | Python | bsd-3-clause | 39,461 | [
"VisIt"
] | ba55e5960dfc9498e2ca42ef7b2385605069f8094a97539e22262a62dc36b3d1 |
#!/usr/bin/env python
"""This example shows how you can produce contours on an IsoSurface.
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports
from os.path import join, abspath, dirname
# Mayavi imports.
from may... | dmsurti/mayavi | examples/mayavi/advanced_visualization/contour_contour.py | Python | bsd-3-clause | 1,825 | [
"Mayavi"
] | 15375055f947de37041308cef44919ce5bd076aa5911bd4450b7c77df2c7c404 |
import sys
import pysam
from collections import defaultdict
bamFile = pysam.Samfile(sys.argv[1], 'rb')
#for chrom in [str(x) for x in range(1,23)] + ["X"] + ["Y"]:
for chrom in [str(x) for x in range(20,21)]:
nBroken = 0
nReads = 0
chromsWithBrokenPairs = {}
for index,read in enumerate(bamFile.fetch(... | andyrimmer/Platypus | scripts/countBrokenPairs.py | Python | gpl-3.0 | 836 | [
"pysam"
] | 409c05daec6f647ee24d11a22fa3f5fd6ea31f73e6c65613766d59fcad1b1a4b |
from fabric.api import *
# the user to use for the remote commands
env.user = 'vagrant'
env.key_filename = '~/.ssh/id_rsa'
# the servers where the commands are executed
# env.hosts = ['foodbeazt.in']
env.hosts = ['192.168.33.10']
def pack():
# create a new source distribution as tarball
local('python setup.... | cackharot/fbeazt | src/fabfile.py | Python | apache-2.0 | 2,033 | [
"GULP"
] | 740683ef31f9b304b9139693aaee3685694dd4732fed12b246a9368a8a550987 |
#
#-*- coding:utf-8 -*-
"""
Gentoo-Keys - Log.py
Logging module, placeholder for our site-wide logging module
@copyright: 2012 by Brian Dolbec <dol-sen> <dol-sen@users.sourceforge.net>
@license: GNU GPL2, see COPYING for details.
"""
import logging
import time
import os
NAMESPACE = 'gentoo-keys'
l... | dol-sen/gentoo-keys | gkeys/log.py | Python | gpl-2.0 | 2,035 | [
"Brian"
] | 5d6e887ca6a151b3613d147c324cd4e8ea6b5664e62f85f402bd6ac9c5ca7e5e |
# Copyright (c) 2012-2016 Seafile Ltd.
from importlib import import_module
import os
from uuid import uuid4
from django.core.cache import cache
from django.urls import reverse
from django.conf import settings
from django.http import SimpleCookie
from django.test import RequestFactory
from django.test import TestCase
f... | miurahr/seahub | seahub/test_utils.py | Python | apache-2.0 | 16,682 | [
"VisIt"
] | ae29760b880435ed6bbf18001cb04863d4b33729e0143f4884f72271b674cdea |
import numpy
from pyscf import gto, scf, mcscf
'''
Scan BeH2 molecule symmetric dissociation curve
Note the CI wave function might change symmetry in the scanning. Adjust
fcisolver parameters to maintain the right symmetry.
'''
def run(i, dm0, mo0, ci0):
x = i
y = (2.54 - 0.46 * x)
x = x * 0.529177249
... | gkc1000/pyscf | examples/mcscf/32-beh2_scan/BeH2-scan.py | Python | apache-2.0 | 1,127 | [
"PySCF"
] | 34a7269c3bf399f03829ee85b465a4fc5d6c5c5e399f3c6f0991c0d6677e0591 |
#!/usr/bin/python2
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that... | StuntsPT/4Pipe4_validator | validator.py | Python | gpl-3.0 | 1,954 | [
"pysam"
] | d9e23296b3db69004bca80661b9435ec6f91f93a61762010ff96536918fa828b |
# Copyright 2004-2012 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, m... | MSEMJEJME/Get-Dumped | renpy/display/behavior.py | Python | gpl-2.0 | 46,412 | [
"VisIt"
] | ff0aa456a9ebe9689450cbad5026f3174fa693fee41cbfcb7975aaaa3f1bde7b |
"""
Constructs for grouping tool parameters
"""
from basic import ToolParameter
from galaxy.util.expressions import ExpressionContext
import logging
log = logging.getLogger( __name__ )
import StringIO, os, urllib
from galaxy.datatypes import sniff
from galaxy.util.bunch import Bunch
from galaxy.util.odict import odi... | volpino/Yeps-EURAC | lib/galaxy/tools/parameters/grouping.py | Python | mit | 19,677 | [
"Galaxy"
] | b17f26334ad20ab61028278e5055a39fb6cdf8bca4b5ae65142c3bb767d6e18a |
from __future__ import absolute_import, division
from django.core import urlresolvers
from django.db import connection
from django.db.models import Sum
from django.db.models.query import QuerySet
from django.http import HttpResponseNotFound, HttpRequest, HttpResponse
from django.template import RequestContext, loader
... | sharmaeklavya2/zulip | analytics/views.py | Python | apache-2.0 | 32,900 | [
"VisIt"
] | a0696a98ac03614bbad77317d0ab63142ef806e600daed6bb071a05497b4bce0 |
from armstrong.utils.backends import GenericBackend
from django.db import models
from django.template import Context
from django.template.loader import select_template
try:
from django.utils.text import slugify
except ImportError:
from django.template.defaultfilters import slugify
from . import utils
class... | texastribune/tt_dailyemailblast | tt_dailyemailblast/models.py | Python | apache-2.0 | 3,047 | [
"BLAST"
] | c72d77884f6e2932de3636e592872ee6e2cd7d2be52089d405e5a8219b017df5 |
#
# This file is part of postpic.
#
# postpic 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.
#
# postpic is distributed in the hope th... | skuschel/postpic | postpic/datareader/__init__.py | Python | gpl-3.0 | 7,297 | [
"VisIt"
] | e845ae932c22f5560b14d45582d2cce83fc8b4f4b52ac23a4850555b4558d50b |
from DIRAC import S_ERROR, S_OK
from DIRAC.DataManagementSystem.private.FTSAbstractPlacement import FTSAbstractPlacement, FTSRoute
from DIRAC.DataManagementSystem.private.FTS2.FTS2Strategy import FTS2Strategy
# from DIRAC.DataManagementSystem.private.FTS2Graph import FTS2Graph
class FTS2Placement(FTSAbstractPlacemen... | Andrew-McNab-UK/DIRAC | DataManagementSystem/private/FTS2/FTS2Placement.py | Python | gpl-3.0 | 3,859 | [
"DIRAC"
] | 5c62e57e9248bca06b5b4985af6587e15dd511e12d67e543f3cf1d513411d842 |
import time
import utils as utils
import numpy as np
import numpy.random as npr
import theano
import theano.tensor as T
##################################
# MISCELLANEOUS HELPER FUNCTIONS #
##################################
def reparametrize(z_mean, z_logvar, rng=None, rvs=None):
"""
Gaussian reparametrizati... | Philip-Bachman/Sequential-Generation | HelperFuncs.py | Python | mit | 6,554 | [
"Gaussian"
] | 7685cd4dc605681d84e99c521e08313d8556d3c7338f035ac0f7920fbca11930 |
from sfepy import data_dir
filename_meshes = ['/meshes/3d/cylinder.mesh',
'/meshes/3d/cylinder.vtk',
'/meshes/various_formats/small2d.mesh',
'/meshes/various_formats/small2d.vtk',
'/meshes/various_formats/octahedron.node',
'... | olivierverdier/sfepy | tests/test_meshio.py | Python | bsd-3-clause | 6,008 | [
"VTK"
] | 3d691b80099fcdd49cb06a80beea94b79d398cbc2922995c5b36e7bd48886389 |
#%% IMPORTS
import matplotlib.pyplot as plt
import numpy as np
import addcopyfighandler
#%% FUNCTIONS
def SW_IL(maxIL=1, distribution='uniform', size=1):
if distribution=='uniform':
return np.random.uniform(0,maxIL,size=size)
elif (distribution=='gaussian') or distribution=='normal':
return np.... | OSHI7/Learning1 | sim_SW_repeatability.py | Python | mit | 1,004 | [
"Gaussian"
] | 1d22ae5fe4a4f5140009ea5bc55896edfe548f62cf39f378f008638743e04916 |
"""
Module to set up run time parameters for Clawpack -- amr code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#-----------------------------------------------
# Set these parameters for adjoint flagging...... | clawpack/adjoint | paper2_examples/acoustics_1d_ex1/setrun.py | Python | bsd-2-clause | 13,708 | [
"Gaussian",
"NetCDF"
] | 9ea26da9960330c3cc0537499bc1f3c7baf68fd4972efcd904975dafb0d0dfe8 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import glob
import itertools
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib
import urllib2
import urlparse
import xmlrpclib
import zlib
from xml.etree import ElementTree
from cStri... | Johnzero/OE7 | openerp/addons/web/controllers/main.py | Python | agpl-3.0 | 68,170 | [
"VisIt"
] | b0a6e3924afc3d6230b4a526149156178a63b6811ec6b454d3892eca950b0710 |
# -*- coding: utf-8 -*-
"""A plugin that extracts browser history from events."""
import re
from urllib import parse as urlparse
from plaso.analysis import interface
from plaso.analysis import logger
from plaso.analysis import manager
from plaso.containers import analysis_results
class BrowserSearchPlugin(interfac... | joachimmetz/plaso | plaso/analysis/browser_search.py | Python | apache-2.0 | 9,546 | [
"VisIt"
] | f12c849f14cdbf8e82715f856acb7737a9b28bfcbfe482b5e0ca508a1fbd2be2 |
# Copyright 2021 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/distributions/markov_chain_test.py | Python | apache-2.0 | 18,847 | [
"Gaussian"
] | 5f73332da7ea5e8649914176cca7b065348db5e988a34ab82219ed381961c87a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | pmghalvorsen/gramps_branch | gramps/gui/plug/_windows.py | Python | gpl-2.0 | 50,813 | [
"Brian"
] | b969e24321763c19dab59909ab5f3544f29949ec28a41726e69ae2a4eff4350b |
'''
Created on 29.04.2017
@author: Mr. Jones
'''
#TODO this codes messes up for variable, by substituting the loop variable inside the loop
class ConstantVisitor():
'''used on flow graph basic blocks'''
def __init__(self):
#for each variable save the
self.var_declarations = dic... | mrj0n3s/jimplify | Jimplify/jimplify/visitors/constantvisitor.py | Python | mit | 1,612 | [
"VisIt"
] | 7f96be94aafab65e7bd456b7ce75bdb31db735d953460e94ee4e6b5c9fa35855 |
# thic code is used to test parcellation
from MNNparcellation import Python2Vtk as PY
import tempfile as TP
import numpy as np
from MNNparcellation import CSParcellation as CSP
from termcolor import colored
import warnings
warnings.filterwarnings("ignore")
def co_shape(A, B):
if np.shape(A) == np.shape(B):
... | BBELAOUCHA/dMRIParcellation | test/test_parcellation.py | Python | bsd-3-clause | 3,826 | [
"VTK"
] | 34760c592de44fa4cd4e783fd0abfb84c77d5037259996f5d486655bd562a2ab |
from Firefly import logging
from Firefly.const import LUX, MOTION, MOTION_ACTIVE, MOTION_INACTIVE
from Firefly.helpers.device import *
from Firefly.helpers.device.device import Device
from Firefly.helpers.metadata.metadata import action_motion, action_text
# TODO: Add support for temp reporting.
# from Firefly.service... | Firefly-Automation/Firefly | Firefly/helpers/device_types/multi_sensor.py | Python | apache-2.0 | 4,411 | [
"Firefly"
] | a6749ad5224bef03c6d58de26d24dc869892ba0b1251976a8954af04ec9c1abe |
## Run the pymol server
from __future__ import print_function
import xmlrpclib
try:
serv = xmlrpclib.Server('http://%s:%d'%('localhost',9123))
serv.ping()
except:
print('\nStarting PyMol as server... ')
import subprocess as sp
import os
import time
FNULL = open(os.devnull, 'w')
sp.Popen... | grhawk/IChemiton | dot.ipython/profile_ichemiton/startup/49PyMolServer.py | Python | gpl-2.0 | 452 | [
"PyMOL"
] | 7b7cf63f59f0aa4bdf1812c566fa82ee4c9492ca8b14da2954f066c34a02f043 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/vasp/nlep/__init__.py | Python | gpl-3.0 | 1,284 | [
"CRYSTAL",
"VASP"
] | 60701dc6845648aee7a250c7f11a67ced9df58762be490d4a296de605bf86a27 |
"""
This project connects to Trello via their API, then iterates through a given board, downloading lists, cards,
and comments and put the resulting data into a tabbed spreadsheet.
Use this project to create "point in time" snapshots of your Trello data.
This process will download each list in the board, creating a spr... | scaine/TrelloExport | trelloexport.py | Python | gpl-2.0 | 9,424 | [
"VisIt"
] | 6a5c5b135796529a6411347685f92208abf855d03e15125e8d2b4141d1b7198a |
# Copyright 2016 Facundo Batista, Nicolás Demarchi
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General
# Public License version 3, as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ... | jcabdala/fades | tests/test_multiplatform.py | Python | gpl-3.0 | 2,995 | [
"BLAST"
] | 271e6e47f9ca63598d8aabd2161c36614fd6cb64efa44290d3893ea80a30b41f |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-many-arguments
# pylint: disable=too-many-locals
import random
import sys
... | neilswainston/PathwayGenie | twist/client.py | Python | mit | 7,797 | [
"VisIt"
] | f1ea80085cebb3b56de46f7052e75c9cb3b3cd1c03316df8c27b59446df10fec |
# Hungarian algorithm (Kuhn-Munkres) for solving the linear sum assignment
# problem. Taken from scikit-learn. Based on original code by Brian Clapper,
# adapted to NumPy by Gael Varoquaux.
# Further improvements by Ben Root, Vlad Niculae and Lars Buitinck.
#
# Copyright (c) 2008 Brian M. Clapper <bmc@clapper.org>, Gae... | futurulus/scipy | scipy/optimize/_hungarian.py | Python | bsd-3-clause | 9,295 | [
"Brian"
] | 9dc46b6f7b6b50e4353292bd87929c153d771dd8b42d1494b0b44386660b1c85 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-appengine-admin | tests/unit/gapic/appengine_admin_v1/test_domain_mappings.py | Python | apache-2.0 | 82,477 | [
"Octopus"
] | eca6a200774a161d0c0df6efdb1769bb41764f1c401b34526fa66790fb53facb |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source
##
## 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 the Free Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/gui/utils/idle.py | Python | gpl-2.0 | 6,012 | [
"VisIt"
] | 4e80e98bd871537c21a8ebb04505d7f7642f788902a44706ed7162dfa2cf1f77 |
# Copyright 2021 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... | google/differential-privacy | python/dp_accounting/rdp/rdp_privacy_accountant_test.py | Python | apache-2.0 | 17,532 | [
"Gaussian"
] | b5b32f184b1391f02261338a40ef988b912d40bc62c91b391ad04c2b8fe39b1b |
"""
Caffe network visualization: draw the NetParameter protobuffer.
.. note::
This requires pydot>=1.0.2, which is not included in requirements.txt since
it requires graphviz and other prerequisites outside the scope of the
Caffe.
"""
from caffe.proto import caffe_pb2
"""
pydot is not supported under p... | dbishai/DeepRGB | python/caffe/draw.py | Python | mit | 7,604 | [
"NEURON"
] | 27b1161ac86c45e353e17c7451365df2c5442f7844f2880c52ff69a1f5415d24 |
"""A frontend web server with load balanced request handlers.
This example shows how to use zmq.web to run a Tornado web server with
individual request handlers in separate backend processes. This file implements
the frontend logic and needs to be run with 1 or more instances of
backend_stream.py.
This version uses ... | ellisonbg/zmqweb | examples/frontend_stream.py | Python | bsd-3-clause | 2,041 | [
"Brian"
] | 5c8483aacc6e2187c78baced43c77579a7bfdb4f32c6309c3da5439eb7ffb287 |
# pylint: disable=missing-docstring
from lettuce import world
import time
import json
import re
import platform
# django_url is assigned late in the process of loading lettuce,
# so we import this as a module, and then read django_url from
# it to get the correct value
import lettuce.django
from textwrap import de... | louyihua/edx-platform | common/djangoapps/terrain/ui_helpers.py | Python | agpl-3.0 | 21,719 | [
"VisIt"
] | b459109e3bb8e4619d7e170adba908ced99ad53d20c6b8a969b613902a6814aa |
# simple proof-of-concept exercise in PyMOL synchronization
# NOT FOR PRODUCTION USE! HIGHLY INSECURE!
# You need to launch two PyMOL simultaneously as follows...
# MASTER/SLAVE (on same machine):
# pymol syncmol.py -- recv 8000
# pymol syncmol.py -- send 8000
# MUTUAL SYNCHRONIZATION (on same machine):
# pymol s... | gratefulfrog/lib | python/pymol/pymol_path/examples/devel/syncmol.py | Python | gpl-2.0 | 6,442 | [
"PyMOL"
] | eb01ad0d9c8bacce6bfaf679cbfd041243e0e688051a02d903fb2cec9108f15f |
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# 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 L... | lahnerml/espresso | src/core/gen_featureconfig.py | Python | gpl-3.0 | 3,849 | [
"ESPResSo"
] | 433b9ca8bdeccb752705f7cf4d3610e0bd1bfe92d122707d61ba416e96e11d64 |
import numpy as np
from .control import model_setup
from .cp_confocal import twod
from .cp_mix import double_pnum
# 2D + 2D Gauß
# Model 6037
def CF_Gxyz_gauss_2D2D(parms, tau):
u""" Two-component, two-dimensional diffusion with a Gaussian laser
profile, including a triplet component.
The triplet... | paulmueller/PyCorrFit | pycorrfit/models/model_confocal_2d_2d.py | Python | gpl-2.0 | 3,205 | [
"Gaussian"
] | acb53eb991a707376454055aedb8faf03e1aa8c383b25b89343035742b00dc88 |
import argparse
from ast import (fix_missing_locations, iter_fields, parse, Add, Assign, AST,
Attribute, BitAnd, BitOr, BitXor, Call, Div, Ellipsis,
ExceptHandler, Expr, ExtSlice, FloorDiv, ImportFrom, Index,
List, Load, LShift, Mod, Mult, Name, NodeTransformer, Num,
... | brandm/live-py-plugin | plugin/PySrc/code_tracer.py | Python | mit | 47,862 | [
"VisIt"
] | c9baefd16f081ea98913b3fa3c9cd8d44233f36a25351d52f99c8536329d10fc |
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2017-06-07 14:59:50
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-20 15:15:09
import aces.tools as tl
from aces import config
import numpy as np
def minimize(m):
if m.engine == "lammps":
minimize_lammps(m)
elif m.engine == "vasp"... | vanceeasleaf/aces | aces/runners/minimize.py | Python | gpl-2.0 | 3,204 | [
"LAMMPS",
"VASP"
] | 3ef2b74041a8d78106a1b286a30cc932e5b4b4e379b86adaf8039ee2c498b723 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/gtk/widgets/checkbox.py | Python | gpl-3.0 | 1,324 | [
"Brian"
] | 81cb2c0218a7e25ba0c1fb3ba64fe89931cab6a0f3f60710eeb581ac3a4fe575 |
# GNU Solfege - free ear training software
# vim: set fileencoding=utf-8 :
# Copyright (C) 2000, 2001, 2002, 2003, 2004, 2006, 2007, 2008, 2011 Tom Cato Amundsen
#
# 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 So... | RannyeriDev/Solfege | solfege/gu.py | Python | gpl-3.0 | 43,835 | [
"VisIt"
] | 0910724e763ac80fd739e234d8d31bbcd7d771d5430165d88fd0e602bb3aee0d |
#Standard dependencies
import os
import sys
import inspect
import time
try:
import cPickle as pickle
except:
import _pickle as pickle
import re
from copy import copy
from string import Template
#Non-standard dependencies
import numpy as np
try:
from scipy.interpolate import InterpolatedUnivariateSpline as... | mhoffman/catmap | catmap/__init__.py | Python | gpl-3.0 | 3,120 | [
"ASE"
] | 616b9b280b36c6a1f34c379a0b908f2c1511ede96dadacc7e832a65ef8595e65 |
# Copyright (c) 2014 Evalf
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, s... | joostvanzwieten/nutils | nutils/expression.py | Python | mit | 63,056 | [
"DIRAC"
] | 1880adb81b54841304cbcc15fe340e27b52ffc5db7e0f65af56fd3d7554b2c14 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Scaled_Features/results/objects/test10_cross_validate_objects_1200ms_scaled_method_iv.py | Python | mit | 4,553 | [
"Mayavi"
] | 792a92ed78100cbae268d4125cb23c6e96ac54bbbabfc32a10286cb01212bbae |
#!/usr/bin/env python
import argparse
import eutils
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='EPost', epilog='')
parser.add_argument('db', help='Database to use')
parser.add_argument('--user_email', help="User email")
parser.add_argument('--admin_email', help="Admin em... | nekrut/tools-iuc | tools/ncbi_entrez_eutils/epost.py | Python | mit | 1,772 | [
"Biopython"
] | 2f1f0890060b0e05ae1d0c20002f794e1dc588484ae66e186c6152da8afd4b08 |
#!/usr/bin/env python
import vtk
import numpy as np
from vmtk import vmtkscripts
import argparse
import itertools
import os
def addPolyLine(pts_ids):
new_line = vtk.vtkPolyLine()
new_line.GetPointIds().SetNumberOfIds(pts_ids.GetNumberOfIds())
for i in range(pts_ids.GetNumberOfIds()):
new_line.Ge... | kayarre/Tools | vmtk/clipcenterlines.py | Python | bsd-2-clause | 8,879 | [
"VTK"
] | 1d3432ff67684422ed4de5321e05113ad1852d5a4f5d7bd63d880e2481e7eb5c |
#!/usr/bin/env python
#coding: utf-8
#### CLASSES ####
class fasta():
"""
"""
def __init__(self):
"""
"""
self.fastaDict = {}
#### FUNCTIONS ####
def fasta_reader(self, fastaFile):
"""
"""
fastaDict = {}
subHeader("Fasta reader")
... | brguez/TEIBA | src/python/clusterClippedReads.sim.py | Python | gpl-3.0 | 26,944 | [
"pysam"
] | cb72c468c24d0adc1e42551b57a19aba0120d0c81f327a635fd61443a6a3884a |
""" manage PyTables query interface via Expressions """
import ast
import time
import warnings
from functools import partial
from datetime import datetime, timedelta
import numpy as np
import pandas as pd
import pandas.core.common as com
from pandas.compat import u, string_types, DeepChainMap
from pandas.core.base imp... | BigDataforYou/movie_recommendation_workshop_1 | big_data_4_you_demo_1/venv/lib/python2.7/site-packages/pandas/computation/pytables.py | Python | mit | 20,296 | [
"VisIt"
] | 165f6374fc70e6293f045b5a320b44191a1a50352b49f6d82753bcbcb979cf3b |
"""
Find intermediate evalutation results in assert statements through builtin AST.
This should replace _assertionold.py eventually.
"""
import sys
import ast
import py
from py._code.assertion import _format_explanation, BuiltinAssertionError
def _is_ast_expr(node):
return isinstance(node, ast.expr)
def _is_ast... | UK992/servo | tests/wpt/web-platform-tests/tools/third_party/py/py/_code/_assertionnew.py | Python | mpl-2.0 | 11,450 | [
"VisIt"
] | e760031726645b66a4b3988514a4ad20dc33ff67c54e8981073e34029959e2f2 |
'''
Creates a feature location index (FLI) for a given BED/GFF file.
FLI index has the form::
[line_length]
<symbol1_in_lowercase><tab><symbol1><tab><location>
<symbol2_in_lowercase><tab><symbol2><tab><location>
...
where location is formatted as:
contig:start-end
and symbols are sorted in lexig... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py | Python | gpl-3.0 | 3,535 | [
"Galaxy"
] | 0e13235993f57790675315ac07765c5416e02480c9da2e25f65b67a45674ca71 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on March 25, 2013
@author: geoffroy
"""
import numpy as np
import warnings
from math import ceil
from math import cos
from math import sin
from math import tan
from math import pi
from warnings im... | fraricci/pymatgen | pymatgen/symmetry/bandstructure.py | Python | mit | 31,772 | [
"pymatgen"
] | 03294d7fb7d1685c1946e86c38dc3ad34197170713b31ab4887f793e82cd37d2 |
import re
import string
class Node(object):
def accept(self, visitor, create_memory=True):
return visitor.visit(self, create_memory)
#Function definitions
class Arg(Node):
def __init__(self, t, idd, lineno):
self.t = t
self.idd = idd
self.lineno = lineno
class ArgList(Node)... | salceson/kompilatory | lab4/AST.py | Python | mit | 4,960 | [
"VisIt"
] | abfe4c54d9c0db8c833df1e79f7b9c227aed55e0686cd283e749478daf72bb3e |
#! /usr/bin/python
'''pysam - a python module for reading, manipulating and writing
genomic data sets.
pysam is a lightweight wrapper of the htslib C-API and provides
facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ
files as well as access to the command line functionality of the
samtools and bcft... | bioinformed/pysam | setup.py | Python | mit | 17,532 | [
"pysam"
] | afa5956d61904e2c2270cd0f208229611275fa9ea3e24f16dd82999db9fc03af |
import argparse
from director.consoleapp import ConsoleApp
from director import cameraview
from director import vtkAll as vtk
import PythonQt
from PythonQt import QtCore, QtGui, QtUiTools
def addWidgetsToDict(widgets, d):
for widget in widgets:
if widget.objectName:
d[str(widget.objectName)] =... | RobotLocomotion/director | src/python/scripts/cameraViewer.py | Python | bsd-3-clause | 2,349 | [
"VTK"
] | 3100bdf98f48ceeb9621e25bc50a2d0ea8a5001060ad7722e3fa379c895499ae |
import numpy as _n
import time as _t
import spinmob as _s
from spinmob import egg
##### GUI DESIGN
# create the main window
w = egg.gui.Window(autosettings_path='example_daq_w.cfg')
# add the "go" button
b = w.place_object(egg.gui.Button("Pretend to Acquire Data", checkable=True)).set_width(135)
i = w.place_o... | correlator/spinmob | egg/examples/example_daq.py | Python | gpl-3.0 | 5,108 | [
"MOOSE"
] | 7f0a5bb1bcfb82674742f3910d57eb65c076aae133c77f6a71bf59c635217fe5 |
##
# title: RAMS.py
# by: Brian Kim
# description: a wrapper class to encapsulate all the roams stuff
#
class RAMS():
pass
| briansan/rams | RAMS/app/RAMS.py | Python | bsd-3-clause | 126 | [
"Brian"
] | 3fc9b4b630c4e045542ea0e909bb518b0bf352832eddc0397bad520fafec66f4 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2013 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 yo... | AlbertoPeon/invenio | modules/docextract/lib/refextract_regression_tests.py | Python | gpl-2.0 | 109,322 | [
"DIRAC"
] | 5ff7fed8bc5440a390400d19cfff4bd75b62f8962526ec8a0205c6ac335569ab |
# Copyright 2014, Egan McComb
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
from scipy import ndimage
from skimage import filter
# Load image into np.array.
img = plt.imread('mussels-gray.png')
# Apply Gaussian blur with 3 pixel std. deviation.
# TODO: Determine proper blur radius [interactiv... | RoboticsatUCD/MateROV | test/countmatron/thresholding.py | Python | gpl-3.0 | 521 | [
"Gaussian"
] | fb00bc406ea25bd33c025c0d4233bacc9bd4cdac2e64a2d6b5bdc29be80ccf4b |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 y... | hyperspy/hyperspy | hyperspy/utils/peakfinders2D.py | Python | gpl-3.0 | 20,036 | [
"Gaussian"
] | 4a5cca4d4bb9bc987bea4cd79109511001b4a76180fd53926db49c57ae82b9aa |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, PurePoly, poly,
parallel_poly_from_expr,
degree, degree_list,
total_degree,
LC, LM, LT,
pdiv, prem, pquo, pexquo,
div, rem, quo, exquo,
half_gcdex, gcdex, invert,
subre... | kaushik94/sympy | sympy/polys/tests/test_polytools.py | Python | bsd-3-clause | 114,574 | [
"Gaussian"
] | 18ff1b3203302c8a588649f697206688f5ea68ced1e04324e52b67f0df12050e |
"""Tool for handling delivery of JWST ETC files
Authors
-------
- Varun Bajaj, Brian Brooks August 2017
Use
---
This script is intended to be run from the comand line:
::
python jwst_etc_check.py [-d <destination> -f <files> -i <instrument> -u -m]
-d <destination> - Path to current Pandeia direc... | Vb2341/ReDCaT | jwst_etc_check.py | Python | gpl-3.0 | 19,527 | [
"Brian"
] | ac22a4278a5bddaad63fc95f01c16d733f9952dc4690c7e3154fa495275164f9 |
#!/usr/bin/env python
import argparse
import pysam
def Parser():
parser = argparse.ArgumentParser(description='miRNAs counts and coverages')
parser.add_argument('-a', '--alignment', metavar='FILE', type=str,
dest='alignment_file', help='Alignment bam file')
parser.add_argument('--... | chamaelj/tools-artbio | tools/mircounts/mircounts.py | Python | mit | 4,846 | [
"pysam"
] | 0d3f621d80ae5de07ec3493addea64bda44599a4b2ce30bbee56b4fc203a6097 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.