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 |
|---|---|---|---|---|---|---|---|
from degas.gridding import gridGalaxy
datadir='/mnt/bigdata/erosolow/surveys/DEGAS/'
datadir = '/mnt/bigdata/erosolow/surveys/DEGAS/'
ppo = False
gridGalaxy(galaxy='IC0342', setup='12CO',
release='QA0', datadir=datadir,
PostprocOnly=ppo)
gallist = ['IC0342',
'NGC0337',
'NG... | low-sky/degas | degas/examples/gridgals.py | Python | gpl-3.0 | 3,461 | [
"Galaxy"
] | 82217dfb0a9f466161fba0552f2114fbd1c727fe84c7af203ef493493074d575 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | src/rmock/runners/http/protocols/jsonrpc.py | Python | lgpl-3.0 | 2,257 | [
"VisIt"
] | c5d477836ba13dc8df99b5138f4e92679efc41020f0fa0c1f25f41132c3e046e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/procrouting/solvent/__init__.py | Python | lgpl-3.0 | 1,057 | [
"Psi4"
] | e145264a1ccbc0e51214e9b334f413cda8c33feb0a619aae68d1399f4ed4cd51 |
import sys
import gobject
import gtk
import goocanvas
import math
import random
import re, db_conf
from phamerator_manage_db import *
class PhamCircle:
"""a class for drawing phamily circles on a pygoocanvas"""
def __init__(self, phamName, c,**kargs):
"""initializes circle center and radius"""
p... | byuphamerator/phamerator-dev | phamerator/PhamDisplay.py | Python | gpl-2.0 | 24,040 | [
"BLAST"
] | 8590e617295d60c2919eb6286b388e96471674f399f335d3a9c9f9f535314de2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
from pymatgen.core.structure import Structure
"""
This module implements symmetry-related structure forms.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials ... | dongsenfo/pymatgen | pymatgen/symmetry/structure.py | Python | mit | 2,764 | [
"pymatgen"
] | 020f8a0765c94c7379f5c2e54b5d390dbbd4de46eeb7bd3631b86aafa904b759 |
"""
Generate a hints database file from RNAseq/IsoSeq alignments for AugustusTMR/AugustusCGP.
"""
import collections
import itertools
import os
import logging
import pyfasta
import pysam
try:
from toil.fileStores import FileID
except ImportError:
from toil.fileStore import FileID
from toil.common import Toil
... | ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit | cat/hints_db.py | Python | apache-2.0 | 23,705 | [
"pysam"
] | ffd7e247e263807e723da1952632c8a2a42d79a93a7674b1d4aba6ece6c7051c |
__author__ = 'Matteo'
__doc__ = ''''''
N = "\n"
T = "\t"
# N="<br/>"
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast import NCBIXML
import csv
import math
import re
from difflib import Differ
import itertools
de... | matteoferla/Geobacillus | geo_prot_eq2.py | Python | gpl-2.0 | 2,897 | [
"BLAST"
] | 45f17d9f87d8d51627c31f8ac840fc6cc3b627eee71b553e0eebff00f32082d1 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | dgasmith/psi4 | psi4/driver/util/__init__.py | Python | lgpl-3.0 | 913 | [
"Psi4"
] | 869f86b115eca439325f14c3aa410f42b787f358bd8b0e8ec63063094ad22d4c |
# loadKineticModel.py ---
#
# Filename: loadKineticModel.py
# Description:
# Author: Upi Bhalla
# Maintainer:
# Created: Sat Oct 04 12:14:15 2014 (+0530)
# Version:
# Last-Updated: Tue Apr 18 17:40:00 2017(+0530)
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change ... | BhallaLab/moose-examples | snippets/loadKineticModel.py | Python | gpl-2.0 | 3,284 | [
"MOOSE"
] | 7de109b8ba6cff8d2440907c6e73af47d139a3a14fb639299fc76be6f3b467a6 |
"""
:class:`ASE_OTF` is the on-the-fly training module for ASE, WITHOUT molecular dynamics engine.
It needs to be used adjointly with ASE MD engine.
"""
import os
import json
import sys
import inspect
import pickle
from time import time
from copy import deepcopy
import logging
import numpy as np
from flare.ase.npt i... | mir-group/flare | flare/ase/otf.py | Python | mit | 14,797 | [
"ASE",
"ESPResSo",
"LAMMPS",
"VASP"
] | f81d24d0ee65efba37b975a438f4ae9f5634d857607fb769287b60262ef60091 |
"""
Manipulate HTML or XHTML documents.
Version 1.1.0. This source code has been placed in the
public domain by Connelly Barnes.
Features:
- Translate HTML back and forth to data structures.
This allows you to read and write HTML documents
programmably, with much flexibility.
- Extract and modify URLs in a... | mjhea0/feedzilla | feedzilla/util/htmldata.py | Python | bsd-3-clause | 49,864 | [
"CDK"
] | 18012ccd4d037c5e1e0665a74d2afb80f32843c29ca1c68950ef3d9ac1d16563 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | testsuite/python/langevin_thermostat.py | Python | gpl-3.0 | 8,806 | [
"ESPResSo"
] | fcdf1cc6edb1d6d3a0e3aa7c19f23b323517c4b568537779258f4e90acf9ed32 |
#!/usr/bin/env python
# filename: alignment.py
#
# Copyright (c) 2015 Bryan Briney
# License: The MIT license (http://opensource.org/licenses/MIT)
#
# 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 Sof... | briney/abtools | abtools/alignment.py | Python | mit | 33,992 | [
"Biopython"
] | 2d9df1ac615d7a322571bb0ccdec4f22fe26a5ffe421b65dcb8f80043a278730 |
#-------------------------------------------------------------------------------
# Copyright (c) 2011, Kafti team
#
# Released under the MIT license. See the LICENSE file for details.
#-------------------------------------------------------------------------------
"""
Visitor for collecting nasl scripts family statis... | kafti/pynasl | pynasl/visitors/statistic/scripts_family.py | Python | mit | 3,741 | [
"VisIt"
] | aef8d56a43ac473870aa2bef358fbb4df24e7eedf46f40d510492cdfba47b177 |
import numpy as np
import ase
from pyemto.utilities import distort, rotation_matrix
from pyemto.examples.emto_input_generator import *
from pymatgen import Lattice
from ase.visualize import view
from ase.build import cut, make_supercell
import sys
find_primitive = False
make_supercell = None
coords_are_cartesian = Tru... | hpleva/pyemto | example_projects/fcc_elastic_constants/input_scripts/equilibrium_volume/input.py | Python | mit | 4,206 | [
"ASE",
"pymatgen"
] | bde7b44bdc45f7f0a16a9883e2693856a2c04df216f9fd38bbb198350d0842c2 |
from typing import Optional
from urllib.parse import urlparse
import click
from click.exceptions import Exit
from valohai_cli import __version__
from valohai_cli.api import APISession
from valohai_cli.consts import default_app_host, yes_option
from valohai_cli.exceptions import APIError
from valohai_cli.messages impo... | valohai/valohai-cli | valohai_cli/commands/login.py | Python | mit | 5,072 | [
"VisIt"
] | e21124139497ac68c947e8721c9567d7745d5875beb5ae3127d302a03eb52e29 |
#!/usr/bin/env python
# to run the script with the correct version of uvcdat:
# source /usr/local/uvcdat/1.4.0/bin/setup_runtime.sh
import cdms2
from cdms2 import MV2
import numpy
import glob
import sys
import os
from os import path
import shutil
import re
import string
import random
import gc
import logging
import ... | IOC-CODE/esgf_ensemble_mean | ensemble_stats/bin/make_ensembleMean_tzyx.py | Python | gpl-2.0 | 25,104 | [
"NetCDF"
] | 0524452cdddf53c88057262494e78515625b5393afb752d731dacfd7611d2dd5 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.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 lat... | t794104/ansible | lib/ansible/template/safe_eval.py | Python | gpl-3.0 | 5,339 | [
"VisIt"
] | 617a7f9cb7df209f30b1d5ff35b25bd02afec02f8470f683abff8372b64ef9a8 |
# encoding: utf-8
# Copyright (c) 2001-2016, Canal TP and/or its affiliates. All rights reserved.
#
# This file is part of Navitia,
# the software to build cool stuff with public transport.
#
# Hope you'll enjoy and contribute to this project,
# powered by Canal TP (www.canaltp.fr).
# Help us simplify mobility... | Tisseo/navitia | source/jormungandr/jormungandr/realtime_schedule/siri.py | Python | agpl-3.0 | 8,180 | [
"VisIt"
] | c10660650b57caa8930d1b40960fc2e83cdab0f8aef4995cee8b3cbd1bb14041 |
''' ``traverse`` statement parsing and evaluation. '''
import syntax
import exp_parser
from collections import deque
from spidy.document import *
from spidy.common import *
from tokenizer import *
from nodes import Node
from nodes import NumberNode
from skip_node import SkipNode
# traverse ident in @path_string [mo... | AlexPereverzyev/spidy | spidy/language/traverse_node.py | Python | bsd-3-clause | 7,985 | [
"VisIt"
] | f86f50af50f77c72f1fd6cde222bd85bb5de55f72dd18890c505a5bd7e3be0b0 |
from ase import Atoms
from gpaw import GPAW
from gpaw.test import equal
# Self-consistent calculation:
a = 2.5
slab = Atoms('Li', cell=(a, a, 2 * a), pbc=1)
slab.calc = GPAW(kpts=(3,3,1), txt='li.txt')
slab.get_potential_energy()
slab.calc.write('Li.gpw')
# Gamma point:
e1 = slab.calc.get_eigenvalues(kpt=0)[0]
# Fi... | ajylee/gpaw-rtxs | gpaw/test/fixdensity.py | Python | gpl-3.0 | 869 | [
"ASE",
"GPAW"
] | 8e27953ac1f1cce87326e8ecf9b06ce75352b94e7cfa79cc6966e6b9a1d6fd35 |
from gui.views.EMITView import EMITView
from sprint import *
from utilities import gui
import wx
from gui import events
from coordinator.engineManager import Engine
import coordinator.engineAccessors as engine
from emitLogging import elog
import threading
from gui.controller.NetcdfCtrl import NetcdfCtrl
from gui.contro... | Castronova/EMIT | gui/controller/EMITCtrl.py | Python | gpl-2.0 | 11,268 | [
"NetCDF"
] | 10f48d131c8d48c5da2e4185b49392c4145543525fe4016afe23ca567312a847 |
#!/usr/bin/env python3
# pylint: disable=line-too-long
"""
Various functions for annotating genomes.
"""
# System imports
import pickle
import shutil
import os
import tempfile
import logging
import subprocess
import multiprocessing as mp
from os import path, close, mkdir, listdir
from enrichm.genome import Genome, Ann... | geronimp/enrichM | enrichm/annotate.py | Python | gpl-3.0 | 35,214 | [
"BLAST"
] | 55df7056270ef20e7bd4af9a1a065259cc8006b15f68b787086b0235d8477fef |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | mtlchun/edx | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 53,923 | [
"VisIt"
] | c7831ccd67298cd8fe97826a50d3e58609bdacec7b6eed3d6d6c9f58af0d99ce |
# -*- coding: utf-8 -*-
# test_gc.py ---
#
# Filename: test_gc.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Mon May 19 10:25:13 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This prog... | dharmasam9/moose-core | tests/python/test_gc.py | Python | gpl-3.0 | 3,698 | [
"MOOSE"
] | 37dbf4d0f807e5d40bb097e7ec7ac4e8ba0ccfad6173d704018703fdeaa8e2f8 |
# 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.
"""WebsiteTest testing class."""
import logging
import time
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common... | guorendong/iridium-browser-ubuntu | components/test/data/password_manager/automated_tests/websitetest.py | Python | bsd-3-clause | 12,124 | [
"VisIt"
] | 27ea80fc18af8bfde3b91d208e944ed0a9463634cd2849f37f1dcef4572dec62 |
# -*- coding: utf-8 -*-
#
# hl_api_simulation.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 Licen... | jougs/nest-simulator | pynest/nest/lib/hl_api_simulation.py | Python | gpl-2.0 | 8,229 | [
"NEURON"
] | f5dc283597b35a3353f2d603c6be8d40777f6eaa35bbf6b3a9f5ca94b60e1ca4 |
"""
======================================
Plotting sensor layouts of MEG systems
======================================
In this example, sensor layouts of different MEG systems
are shown.
"""
# Author: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
import os.path as op
from mayavi import mlab
im... | nicproulx/mne-python | examples/visualization/plot_meg_sensors.py | Python | bsd-3-clause | 1,910 | [
"Mayavi"
] | 808599606bed6f79c0320c5f7bcfa50796de28b97b2c01a7131ceb50160481cd |
import sys
from redux.assignmentdeclare import AssignmentScopeAnalyzer
from redux.ast import BitfieldDefinition
from redux.callinliner import CallInliner
from redux.enuminliner import EnumInliner
from redux.intrinsics import get_intrinsic_functions
from redux.parser import parse
from redux.stringinliner import StringIn... | Muon/redux | redux/codegenerator.py | Python | mit | 7,154 | [
"VisIt"
] | 77c016d4b93074e3029a9b0416942b64abb03ea04d02e556119b9a93aab0bd1a |
"""
Acceptance tests for Studio related to the split_test module.
"""
import json
import math
from unittest import skip
from nose.plugins.attrib import attr
from selenium.webdriver.support.ui import Select
from xmodule.partitions.partitions import Group
from bok_choy.promise import Promise, EmptyPromise
from ...fixt... | dkarakats/edx-platform | common/test/acceptance/tests/studio/test_studio_split_test.py | Python | agpl-3.0 | 46,739 | [
"VisIt"
] | 111c101c4d17365eb727fe88952ded36923e39b5037794ca27034a3331dec539 |
from argparse import *
from sys import *
from struct import *
from os.path import *
from paraview.simple import *
from paraview.servermanager import *
parser = ArgumentParser(description = 'Process the arguments')
parser.add_argument('vtkFilePrefix', help = 'Path to the VTK file before the frame index')
parser.add_argu... | fercook/SciViz | Voxels/NETCDF_2_VTK_2_Blender/job/bvox/paraview/VTKVoxel2BVOX_prolog.py | Python | gpl-2.0 | 5,497 | [
"ParaView",
"VTK"
] | 2ad14b79f559c04d737931cfd555f8fd40511ea735c19e1f8d3be9deae3acae0 |
# -*- coding: utf-8 -*-
#
# test_refractory.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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... | mschmidt87/nest-simulator | pynest/nest/tests/test_refractory.py | Python | gpl-2.0 | 8,419 | [
"NEURON"
] | b523d1efddd1cff25b1f29882dc90c9d94c08f01473bc5b5260f79cddaf599e3 |
# A simple HTTP server implemented using h11 and Trio:
# http://trio.readthedocs.io/en/latest/index.html
# (so requires python 3.5+).
#
# All requests get echoed back a JSON document containing information about
# the request.
#
# This is a rather involved example, since it attempts to both be
# fully-HTTP-compliant ... | python-hyper/h11 | examples/trio-server.py | Python | mit | 13,993 | [
"VisIt"
] | c37a2a8c22a4afcf5f19ee5a9c182fb87f86575b58456e4690d3b073b2727b64 |
#!/usr/bin/env python
###############################################################################
#
# pytableaucreate - Python implementation of protein Tableau creator
#
# File: pytableaucreate.py
# Author: Alex Stivala
# Created: February 2008
#
# $Id: pytableaucreate.py 4291 2012-08-09 23:43:39Z astivala $
#... | NirBenTalLab/proorigami-ptgraph | pytableaucreate.py | Python | mit | 24,326 | [
"Biopython"
] | 5fd27c760569449ed099a294f2f65bdef3998007b11a5ed24bdd54f4794c4e4d |
import enum
import struct
class SpecialSectionNumber(enum.IntEnum):
UNDEFINED = 0
ABSOLUTE = -1
DEBUG = -2
class StorageClass(enum.IntEnum):
END_OF_FUNCTION = -1
NULL = 0
AUTOMATIC = 1
EXTERNAL = 2
STATIC = 3
REGISTER = 4
EXTERNAL_DEF = 5
LABEL = 6
UNDEFINED_LABEL = 7... | d3dave/cough | cough/symbol.py | Python | mit | 1,935 | [
"MOE"
] | 37c23a489ea0d683e78cdfd858f5be16bca3ece3678165479e911c5b9171971d |
#!/usr/bin/env python
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# 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 script is used to produce the dict... | updownlife/multipleK | dependencies/biopython-1.65/Scripts/Restriction/ranacompiler.py | Python | gpl-2.0 | 39,012 | [
"Biopython"
] | afbd3f0a644e4358579ae8053660e00a35a90bde0a4cf92d0ae20d816bcf9814 |
"""Performance comparison between the Tensor / Numba implementations."""
import json
with open("../../paper.json", 'r') as f: cfg = json.load(f) # noqa
import numpy as np
import pandas as pd
from time import time as tst
from tensorpac.signals import pac_signals_wavelet
from tensorpac import Pac
from tensorpac.spectr... | EtienneCmb/tensorpac | paper/reviews/code/r2_numba_performance.py | Python | bsd-3-clause | 3,659 | [
"Gaussian"
] | c03a8052094b54019e135266d8316f2535b8887a2f41e2e13432faea51319134 |
from __future__ import annotations
import http.server as server_base
import json
import logging
import multiprocessing
import sys
import time
import urllib.parse
import libtbx.phil
from cctbx import uctbx
from dxtbx.model.experiment_list import ExperimentListFactory
from libtbx.introspection import number_of_processo... | dials/dials | command_line/find_spots_server.py | Python | bsd-3-clause | 13,148 | [
"CRYSTAL"
] | b7a046c98ac38c4c98e8541c6abb1041443a7f3f7de9bb1d46b6889dab488d64 |
import matplotlib
import matplotlib.gridspec as gridspec
import pylab as plt
from scipy.stats import gaussian_kde, norm
from Pyheana.load.fit_data import *
from Pyheana.load.load_data import *
def plot_particles(x, y, z):
plt.figure(figsize=(12,10))
# pdf2, bins2, patches = plt.hist(x[:,0], 100, histtype='s... | like2000/Pyheana | display/plot_particles.py | Python | gpl-2.0 | 5,332 | [
"Mayavi"
] | e4510fe861deae8ae12bad9af177657160ed2cd04d671922b59dca5f3e7403a3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Adds KO annotation to each gene ID that passes the specified thresholds
(max. e-value, min. bitscore, min. identity) in the BLAST results file.
Usage: annotate.py <file> <max log e-value> <min bitscore> <min identity>
"""
from config import *
import sys
import itertools
fr... | pseudonymcp/keggmapping | annotate.py | Python | gpl-3.0 | 4,449 | [
"BLAST"
] | 6d6ab9749dd3bdde643bca4f236ddf937535134868e92a536b8a578976215890 |
"""
Job control via a command line interface (e.g. qsub/qstat), possibly over a remote connection (e.g. ssh).
"""
import os
import logging
from galaxy import model
from galaxy.jobs import JobDestination
from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner
from .util.cli import CliInterface, spl... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/runners/cli.py | Python | gpl-3.0 | 10,834 | [
"Galaxy"
] | 17cf2376721eabb91e1ca26291b9cb7b566037029ab39fbce120daba4131da26 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import csv
import itertools
import logging
import os
import shutil
import sys
import tempfile
import numpy as np
from pathlib import Path
from shutil import which
from collections import defaultdict
from superfocus_app.do_alignment import align_reads, p... | metageni/SUPER-FOCUS | superfocus_app/superfocus.py | Python | gpl-3.0 | 16,374 | [
"BLAST"
] | 77c0dd1175117e441310a9db2020e05e2eb60aadfa0b97c0b33cd6f100d056f4 |
import ast
import datetime
import re
import secrets
import time
from collections import defaultdict
from datetime import timedelta
from typing import (
AbstractSet,
Any,
Callable,
DefaultDict,
Dict,
Iterable,
List,
Optional,
Sequence,
Set,
Tuple,
TypeVar,
Union,
)
im... | showell/zulip | zerver/models.py | Python | apache-2.0 | 130,376 | [
"VisIt"
] | c8969092bee37da0d84957dcdfa49a907039a911e0ba4edf3d8e519cb8ce22b1 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | brianmay/karaage | karaage/plugins/kgapplications/urls.py | Python | gpl-3.0 | 2,686 | [
"Brian"
] | 7ea31a83ee69f81c340db3ea60464c5e094c5baa491cdc67b9c08a1225fabc49 |
import logging
from cgi import escape
import galaxy.util
from galaxy import model
from galaxy import web
from galaxy import managers
from galaxy.datatypes.data import nice_size
from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
from galaxy.model.orm import and_, eagerload_all, func
from galaxy import... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py | Python | gpl-3.0 | 78,352 | [
"Galaxy"
] | 882cd407fc209f6335b8a6126e91919c079da02eff9f24ce48d74f56f58397c7 |
#!/usr/bin/env python
"""
Scalars
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RI... | ddempsey/PyFEHM | pyvtk/Scalars.py | Python | lgpl-2.1 | 2,099 | [
"VTK"
] | ba8dd8c79952f192c2cc232637448a34f1a5392c7163aa342f178f3bcd9f208e |
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
#
# This file is part of ChemLab
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (... | cgchemlab/chemlab | src/tests/test_reaction_parser.py | Python | gpl-3.0 | 2,211 | [
"ESPResSo"
] | e2fdcb0685e12e5e8e3d705097aa7fbba350d4c55f654b3aa07eb28af08935b6 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2011 Tim G L Lyons
#
# 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
#... | sam-m888/gramps | gramps/gen/proxy/private.py | Python | gpl-2.0 | 41,102 | [
"Brian"
] | 2c173b8893df023abc1208667f1cafec788fb78a993c158bba02ad63a045337e |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Rudolf Streif (rstreif@jaguarlandrover.com)
"""
from django.contrib import admin
from sec... | rstreif/rvi_backend | web/security/admin.py | Python | mpl-2.0 | 1,149 | [
"Jaguar"
] | ac7a9d23cbaba4ef80766949c7adc2c7e43512e82a030a31218648b1634d245d |
#!/usr/bin/env python3
# coding: utf-8
"""
Subprogram that constitutes the first step of the Mikado pipeline.
"""
import sys
import os
import argparse
import logging
import logging.handlers
from ._utils import check_log_settings_and_create_logger
from ..configuration import MikadoConfiguration, DaijinConfiguration, p... | lucventurini/mikado | Mikado/subprograms/prepare.py | Python | lgpl-3.0 | 15,276 | [
"pysam"
] | e049ff4b89dfe4a583224530c6fa1aedaf0a9eb3baf871c714fca90c68d05b4d |
def visit_Call(self, node):
""" The visit of a call node.
Is an overwrite of Visit_Call ignoring all calls
except for those we need to modify.
:param node: A call node
"""
name = self.__find_call_name(node)
if name in ATOMIC_SOURCES:
id = self.__... | Betaboxguugi/P6 | documentation/presentation/code/CallNode.py | Python | gpl-3.0 | 658 | [
"VisIt"
] | e6d2e0bd2358bcbe7b2c0fe9eb976314f9eee159571f67b5dab9d7abf3bace5f |
# -*- 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 ... | mrakitin/sirepo | tests/template/srw_import_data/chx.py | Python | apache-2.0 | 32,265 | [
"CRYSTAL"
] | 06614c7e389d91736ead1e58960f747e88bb11986ef56b21779c9e3939f0c065 |
"""Factor Analysis.
A latent linear variable model.
FactorAnalysis is similar to probabilistic PCA implemented by PCA.score
While PCA assumes Gaussian noise with the same variance for each
feature, the FactorAnalysis model assumes different variances for
each of them.
This implementation is based on David Barber's B... | ashhher3/scikit-learn | sklearn/decomposition/factor_analysis.py | Python | bsd-3-clause | 11,908 | [
"Gaussian"
] | d2ae9dc1ae5da7c3629637ecdee28954770930e54f115edaf56ec04b0a06485f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import, print_function
import logging
import re
import time
from datetime import datetime, timedelta
from builtins import * # pylint: disable=unused-import, redefined-builtin
from dateutil.parser import parse as dateutil_parse
from ... | qvazzler/Flexget | flexget/plugins/api_trakt.py | Python | mit | 54,456 | [
"VisIt"
] | 7822269bd84f994cdc32ee550dbdd283ea74087710a8700097693235331afb6f |
# -*- coding: utf-8 -*-
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Andrew I Baznikin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General P... | sam-m888/gprime | gprime/plugins/rel/rel_da.py | Python | gpl-2.0 | 7,385 | [
"Brian"
] | 47f36e573f2244fc26259c692354817e67a7e8aaf90942f7a306fb634f5ddc80 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageGaussianSmooth(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkImageGaussianSmooth.py | Python | bsd-3-clause | 501 | [
"VTK"
] | d52d490cc7c00b0409c66cbd260dae950a279caa76e82d4f0f4d54aa849698a7 |
"""
DIRAC.WorkloadManagementSystem.Agent package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
| yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Executor/Base/__init__.py | Python | gpl-3.0 | 185 | [
"DIRAC"
] | cd9d6cb0c0bc5ffe9da2b423909b2b541740942b0d46b140898911ca5bb2032b |
import numpy as np
class GMM:
"""
Implements the expectation-maximisation (EM) algorithm for the
Gaussian mixture model (GMM). The algorithm is based on the
pseudo-code described in the book by C. Bishop "Pattern Recognition
and Machine Learning", chapter 9.
"""
def __init__(self,
... | kubkon/gmm | gmm/algorithm.py | Python | mit | 6,433 | [
"Gaussian"
] | 0a0cc7fdc0350182a8b8cf140b537e189c59974decb01679d04a60cdbd91c4aa |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016-2017 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtainin... | aytekaman/appleseed | src/appleseed.python/test/testentitymap.py | Python | mit | 4,820 | [
"VisIt"
] | a041d11034328a00a9f71c20ea726ad4b88ea788311b17b8165ae875c23834cb |
#!python
#coding= latin-1
# This script implements the Double Metaphone algorythm (c) 1998, 1999 by Lawrence Philips
# it was translated to Python from the C source written by Kevin Atkinson (http://aspell.net/metaphone/)
# By Andrew Collins - January 12, 2007 who claims no rights to this work
# http://atomboy.isa... | zedshaw/librelist | lib/metaphone.py | Python | agpl-3.0 | 14,779 | [
"Brian"
] | 0e971c6e9257d7425ca109ade8bfd3ec98d58368bf92ca2d1811f7558fc7c524 |
#!/usr/bin/env python
# Python module for simulated annealing - anneal.py - v1.0 - 2 Sep 2009
#
# Copyright (c) 2009, Richard J. Wagner <wagnerr@umich.edu>
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright ... | KevinNJ/Projects | Sallen Key Solver/anneal.py | Python | mit | 13,636 | [
"COLUMBUS",
"VisIt"
] | 73364631f50e7c0709a0b9f31fdd44753cafeb271547e2a1d103957e89381224 |
# 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... | dmordom/nipype | nipype/interfaces/spm/preprocess.py | Python | bsd-3-clause | 68,149 | [
"Gaussian"
] | c61af248891a3323b0cd2bf3b409c544f3ca6b6f5297a3f07f3f20b618097642 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_siesta_eig.py | Python | apache-2.0 | 872 | [
"PySCF",
"SIESTA"
] | 61ddd51535d5d7d32f701cca7b3d8cba91a9fbcf0f79624aacc71fa2f87d9a72 |
#!/usr/bin/python3.4
# -*- coding: utf-8 -*-
# vim:ts=4:sw=4:softtabstop=4:smarttab:expandtab
# 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
... | kdart/pycopia3 | net/pycopia/http/useragents.py | Python | apache-2.0 | 8,690 | [
"VisIt"
] | 448dc1a016675746decaa131b921c1ca06cdb1effb790e32e40e00bddea0aee0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from lib.meos import MEoS
from lib import unidades
class Cyclohexane(MEoS):
"""Multiparameter equation of state for cyclohexane"""
name = "cyclohexane"
CASNumber = "110-82-7"
formula = "cyclo(CH2)6"
synonym = ""
rhoc = unidades.Density(271.33016352)
... | edusegzy/pychemqt | lib/mEoS/Cyclohexane.py | Python | gpl-3.0 | 10,322 | [
"Jmol"
] | 306b67753b21e1acd6578930dd8ae8012b13f464a7051bec01eb6722253effbd |
"""Class for making a redMaGiC galaxy selection."""
from collections import OrderedDict
import os
import numpy as np
import fitsio
import time
import scipy.optimize
import esutil
import healpy as hp
from ..catalog import Entry, Catalog
from ..galaxy import GalaxyCatalog
from ..configuration import Configuration
from ... | erykoff/redmapper | redmapper/redmagic/redmagic_selector.py | Python | apache-2.0 | 10,043 | [
"Galaxy"
] | 323595018a156fb9ba22a290eab283c486942508098ed6597a7da089fc583192 |
#!/usr/bin/python3
# -*- coding: UTF-8 -*-
# Introduction: 本程序用于
# Created by galaxy on 2016/9/8 10:50
import os
my_path = os.getcwd()
gbk_dir = os.path.join(my_path, 'gbk')
batch_lines = []
for root, dirs, files in os.walk(gbk_dir):
for each_file in files:
gbk_path = 'gbk/{0}'.format(each_file)
e... | cvn001/RecentHGT | src/convertGenbank2table_InBatch.py | Python | mit | 691 | [
"Galaxy"
] | 43121bc20ba222b0f9f203439e926489129d4199dd8fac9fbabee5dd567feed8 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009-2010 Benny Malengier <benny.malengier@gramps-project.org>
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2011 Adam Stein <adam@csh.rit.ed... | beernarrd/gramps | gramps/plugins/docgen/asciidoc.py | Python | gpl-2.0 | 17,303 | [
"Brian"
] | bb658db6bbc4a8624650ee26c21d24dff056988fbbaefd21f3eeeb7913411c9a |
#!/usr/bin/python
"""
Script for parsing Gaussian input files (obtained from the EMSL website for
example) and converting them into PyQuante's (http://pyquante.sourceforge.net/)
format.
It reads a file from the stdin and outputs to the stdout (so you should redirect
it to a file). This file should then be put in th... | aalopes/atomicCI | parseGaussian/parseGauss.py | Python | bsd-3-clause | 5,423 | [
"Gaussian"
] | c5e455def00509ce94cb03f8dc818615c2eefab23e3a9b0486d24ef6fcc34dab |
"""
Dropbox API Storage object.
"""
import pickle
import os
import tempfile
from shutil import copyfileobj
from .base import BaseStorage, StorageError
from dropbox.rest import ErrorResponse
from django.conf import settings
from dropbox.client import DropboxClient
from dropbox import session
DEFAULT_ACCESS_TYPE = 'app_... | nimbis/django-dbbackup | dbbackup/storage/dropbox_storage.py | Python | bsd-3-clause | 8,496 | [
"VisIt"
] | 5251fb73d13afbd95c065f56ba93fb3f0dd91bdc3232b2809d65fc0706cf0aae |
import matplotlib.pyplot as plt
import argparse
import warnings
from orcanet.history import HistoryHandler
from orcanet.utilities.visualization import TrainValPlotter
class Summarizer:
"""
Summarize one or more trainings by giving their orcanet folder(s).
- Plot the training and validation curves in a si... | ViaFerrata/DL_pipeline_TauAppearance | orcanet/utilities/summarize_training.py | Python | agpl-3.0 | 7,103 | [
"Gaussian"
] | 55eddc47b7d45f303dc081aa7eae463fac20002eb4bb9bed84ca1a9f19f91e46 |
import pandas as pd
import numpy as np
import os
from sys import argv
import copy
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import proj3d
from matplotlib.patches import FancyArrowPatch
plot_angle = 0 # plot histogram of maxmimum angle between NN atom vectors.
class POSCAR:
theta = 90 ... | cwandtj/A2P2 | SurfaceExtraction_PCA_180419.py | Python | mit | 27,865 | [
"VASP"
] | b0f111e6718550460b545700255f0be6dd5d88a29d2527fb3bac62fc14385a16 |
# Copyright (C) 2013-2017 Paulo V. C. Medeiros
# This file is part of BandUP: Band Unfolding code for Plane-wave based calculations.
#
# BandUP 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 ... | paulovcmedeiros/band_unfolding | src/python_interface/bandupy/runners.py | Python | gpl-3.0 | 3,192 | [
"ABINIT",
"CASTEP",
"VASP"
] | e0702954c4085a39910050a498d2f1f923a0541bec671ff0a6c61c577bbacf67 |
# Copyright (c) 2010-12, Pierre-Antoine Delsart, Kurtis Geerlings, Joey Huston,
# Brian Martin, and Christopher Vermilion
#
#----------------------------------------------------------------------
# This file is part of SpartyJet.
#
# SpartyJet is free software; you can redistribute it and/or modify
# ... | mickypaganini/SSI2016-jet-clustering | spartyjet-4.0.2_mac/python/SpartyJetConfig.py | Python | mit | 1,210 | [
"Brian"
] | 72641958e78034c8d07695962ad9af0e550e090d4e78922e4d133f2d5fbeadfd |
import os
import numpy as np
from astropy.io import fits
from astropy import wcs
from astropy.convolution import Gaussian2DKernel, convolve_fft, convolve
from skimage import restoration
import matplotlib.pyplot as plt
import blast.util
fwhm = 5.0
mapdir = "/home/wizwit/miscellaneous_projects/carina/carinaData"
mapfil... | sbg2133/miscellaneous_projects | carina/velocityMaps/smoothMopra_13.py | Python | gpl-3.0 | 1,544 | [
"BLAST",
"Gaussian"
] | 40a1313e34e4c8ab3ce2a562ba967c459a446e5b9033153a0a4bb7a6167497bd |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_compiled_0128.py | Python | gpl-3.0 | 3,911 | [
"Brian"
] | befa0256ea06c3256c04340d6e24e5b1f2ee7d55207fc1060e7c31cf6aec1936 |
# -*- coding: latin1 -*-
from __future__ import print_function
"""
.. currentmodule:: pylayers.antprop.rays
.. autosummary::
:members:
"""
import doctest
import os
import sys
import glob
try:
# from tvtk.api import tvtk
# from mayavi.sources.vtk_data_source import VTKDataSource
from mayavi import mlab
e... | pylayers/pylayers | pylayers/antprop/rays.py | Python | mit | 132,523 | [
"Mayavi"
] | cac3cafe33ef01707109df174c7d6c73a6f608db985cae225d8258e6e2837c64 |
"""
Implementation of Harwell-Boeing read/write.
At the moment not the full Harwell-Boeing format is supported. Supported
features are:
- assembled, non-symmetric, real matrices
- integer for pointer/indices
- exponential format for float values, and int format
"""
# TODO:
# - Add more support (symmetr... | pizzathief/scipy | scipy/io/harwell_boeing/hb.py | Python | bsd-3-clause | 19,230 | [
"exciting"
] | b60b79e9f5929314d15ddd120b67f19b56fccda43a91b7504012f538a1ffd466 |
__all__ = ['Neuron', 'Simulation', 'Integrator', 'Stimulus',
'plotting_tools', 'pretty_plotting',
'tuning_analysis', 'data_extractor']
| miladh/lgn-simulator | tools/analysis/__init__.py | Python | gpl-3.0 | 157 | [
"NEURON"
] | 226e7223a6bf1383e04ba753ebd1838c23575519fd37e22caa6df751873c4862 |
"""
OLD -- this module has not been fully modernized, and most likely will not
import.
forcing.py: construct forcing (and eventually initialization?) for suntans runs.
the total process is something like this:
1) Write a forcing_conf.py file that goes with a specific grid
This file constructs groups of ed... | rustychris/stompy | stompy/model/suntans/forcing.py | Python | mit | 103,813 | [
"NetCDF"
] | 97af0b18f9b2f43d3e4dd08b1776da6ac6cb71db58cfdd1206ee03c3089c06f5 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-dose/package.py | Python | lgpl-2.1 | 2,475 | [
"Bioconductor"
] | 702215a1837e54212e6d4d39353a3abe60025c4daf6aaf2aabd5fb5cc067451b |
# -*- coding: utf-8 -*-
"""This module contains functions to be called from console script entry points.
"""
# symbols which are imported by "from mse.command import *"
__all__ = ['bootstrap', 'ConfigurationError', 'start']
import sys
import optparse
from os import getcwd
from os.path import dirname, exists, join
i... | jinmingda/MicroorganismSearchEngine | mse/command.py | Python | mit | 4,370 | [
"VisIt"
] | a55ca05be16a95b2d317f6c7a71f470d6f74c646afef4b15ce6ad8e5f8e59938 |
"""
Acceptance tests for the teams feature.
"""
import json
import random
import time
from dateutil.parser import parse
import ddt
from flaky import flaky
from nose.plugins.attrib import attr
from selenium.common.exceptions import TimeoutException
from uuid import uuid4
from ..helpers import get_modal_alert, EventsTe... | IndonesiaX/edx-platform | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 82,589 | [
"VisIt"
] | a093fb62bda848c19ee52857c9a2053885ca7327cb2814044bd4d00c3637f17d |
# Copyright 2016 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | tkzeng/molecular-design-toolkit | setup.py | Python | apache-2.0 | 3,223 | [
"VisIt"
] | a4bc2e46adbe5866bfa6ff3ea31a6b793fb1acd88616953456b301df711cce71 |
# 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... | DavidNorman/tensorflow | tensorflow/python/ops/image_ops_test.py | Python | apache-2.0 | 203,147 | [
"Gaussian"
] | b929f99f53d0c27c85b10d3730ea0d33f8f14cd2c2f8ae51248a0eb80ddce4e2 |
# TO-DO: to be moved to tests directory
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import cmd
import sys
import os.path
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.AbstractFileSystem import UnixLikeFileSystem
from DIRAC.DataManagementSystem... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Client/test/new_dir_completion.py | Python | gpl-3.0 | 1,215 | [
"DIRAC"
] | e80fd082b1e3287b1502c647e8cc771802b6b51d7406894601ea3036263d0061 |
# -*- encoding: utf-8 -*-
import sys
import os.path
import logging
def precheck( configs ):
"""
checks configs for problems
return value specifies number of errors found
Checks:
- if the full path to the executables have not been provided are these the right ones?
- if bowtie/bowtie are the indexes bowtie/bowt... | polarise/breeze | breeze/precheck.py | Python | gpl-2.0 | 1,136 | [
"Bowtie"
] | 9349bc6f613856cd15f703c3837da4c89557aeb50a40f36be32d0d8e0d92011c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
from setuptools import setup
# Version number
version = '0.0.1'
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(name = 'GPSVI',
version = version,
author = 'Ziang Zhu',
author_email = 'zhu.ziang.1... | AlchemicalChest/Gaussian-Process-with-Stochastic-Variational-Inference | setup.py | Python | mit | 1,017 | [
"Gaussian"
] | 6261ad2951904d5a51912700284ed84c1e4f91f6f8df446c5a7f0eb67f1ef0b1 |
"""This demo program solves Poisson's equation
- div C grad u(x, y) = f(x, y)
on the unit square with source f given by
f(x, y) = 10*exp(-((x - 0.5)^2 + (y - 0.5)^2) / 0.02)
and boundary conditions given by
u(x, y) = 0 for x = 0 or x = 1
du/dn(x, y) = 0 for y = 0 or y = 1
The conductivity C is a sym... | akshmakov/Dolfin-Fijee-Fork | demo/documented/tensor-weighted-poisson/python/demo_tensorweighted-poisson.py | Python | lgpl-3.0 | 3,177 | [
"VTK"
] | 261f24153cca54e09c436d52fd31f2f49f77c5e5a8b8245a087e73903934a761 |
# Lint as: python3
# 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 ... | tensorflow/lingvo | lingvo/core/checkpointer_eager_test.py | Python | apache-2.0 | 7,045 | [
"Gaussian"
] | 4e147d6d980750617d6314c3169d803680e95282a700c9dd359e0d114d14ea2e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2005 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Peter Landgren
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012,2017 Paul Franklin
# Copyright (C) 2014 Nick Hall
#
# This program... | jralls/gramps | gramps/gui/plug/report/_styleeditor.py | Python | gpl-2.0 | 23,885 | [
"Brian"
] | 7aeeffb21516eade9bdb097db5fde16a00a5bb598c9e11d14f6b0defc5967a5f |
# Copyright 2000-2002 by Andrew Dalke.
# Revisions copyright 2007-2010 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Alphabets used in Seq objects etc to de... | zjuchenyuan/BioWeb | Lib/Bio/Alphabet/__init__.py | Python | mit | 14,959 | [
"Biopython"
] | 18f9dfb2fba8034131569836bc4a1e88e9133f2d41680baa0f35f08135e5be29 |
import os
from tempfile import mkdtemp, NamedTemporaryFile
import pytest
from numpy.testing import assert_array_equal, assert_array_almost_equal
import pandas as pd
import oddt
from oddt.utils import method_caller
from oddt.spatial import rmsd
from oddt.scoring import scorer
from oddt.scoring.functions import rfscor... | mkukielka/oddt | tests/test_virtualscreening.py | Python | bsd-3-clause | 10,272 | [
"RDKit"
] | 1bbf03ac0dc77c13dcc357191e53c18485b15a4d2c19c7c494823aa3e987ee19 |
# 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... | BackupTheBerlios/espressopp | src/tools/__init__.py | Python | gpl-3.0 | 1,523 | [
"ESPResSo",
"VMD"
] | d962969f2f8eea37a0f86379135785fcd83a73a1c297766089604aa4656b9d7e |
''' master file '''
''' imports needed for doing bash commands in python '''
import os
import shutil
''' imports needed for getRestartTime '''
from scipy.io import netcdf
import glob
''' imports needed for email '''
import smtplib
from email.MIMEMultipart import MIMEMultipart
from email.MIMEText import MIMEText
def... | wesleybowman/aidan-projects | placentia/master.py | Python | gpl-2.0 | 9,667 | [
"NetCDF"
] | e661d625a83f2cd17bae964a2a3652daf9e1a97c99306e1a55bcbe6f8f79443f |
"""
desitarget.lyazcat
==================
Post-redrock ML processing for LyA Quasar object identification.
"""
import os
import numpy as np
import time
import fitsio
from desitarget.geomask import match, match_to
from desitarget.internal import sharedmem
from desitarget.io import write_with_units
from desispec.io im... | desihub/desitarget | py/desitarget/lyazcat.py | Python | bsd-3-clause | 30,371 | [
"Gaussian"
] | 94b5d738f7fdd1fec41139523ae6673f0bbe007a02e8dd55c81bd669163f6246 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | markovmodel/adaptivemd | adaptivemd/engine/acemd/acemd.py | Python | lgpl-2.1 | 2,101 | [
"ACEMD",
"MDTraj"
] | 8cc7f777fe01fba588634e0374bf7de5c540b150943caaf711ca8858f5624b8b |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
#
# This file is part of solus-sc
#
# Copyright © 2014-2018 Ikey Doherty <ikey@solus-project.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Founda... | solus-project/evolve-sc | xng/details.py | Python | gpl-2.0 | 19,486 | [
"VisIt"
] | 3744d2ceb3a3faca59f29b7b196e2c966ba6b33ac129954c7b547761e3799872 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2015 Hans Hoogenboom, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any perso... | Vertexwahn/appleseed | scripts/oslextractmeta.py | Python | mit | 16,460 | [
"VisIt"
] | 88db088d6436a500423fab97f6287cbb0907f03a514ae58e7db23057a0a4f11b |
# This code simulates something the user would like to do. In this
# case the code allows a user to create a 3D cube of data (a numpy
# array), specify an equation for the scalars and view it using the
# mayavi plugin. The only "envisage bits" are the code that let one
# grab the running mayavi instance and script it... | dmsurti/mayavi | examples/mayavi/explorer/explorer_app.py | Python | bsd-3-clause | 8,360 | [
"Mayavi",
"VTK"
] | fb10371092649edb0209e5b8a43a6ae92651841ba2c4575549136e06d6330888 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.