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 |
|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
This ... | gadsbyfly/PyBioMed | PyBioMed/PyGetMol/Getmol.py | Python | bsd-3-clause | 6,259 | [
"Pybel",
"RDKit"
] | e44bac603c292e4b0b1c9a658223bc9bfae53111aa7a3a5f53cac2baed75995c |
""" General Message Queue Interface to create Consumers and Producers
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK
from DIRAC.Resources.MessageQueue.MQProducer import MQProducer
from DIRAC.Resources.MessageQueue.MQConsumer import MQConsumer
from DIRAC.Resources.MessageQueue.MQConnectionManager import MQConn... | arrabito/DIRAC | Resources/MessageQueue/MQCommunication.py | Python | gpl-3.0 | 3,051 | [
"DIRAC"
] | d4d36f31a72e5ff46c883a33ee52d4adcf01f7a8130c55917583909637af19fd |
#!/usr/bin/env python
# to call from bash, use:
# source /usr/local/uvcdat/1.2.0/bin/setup_cdat.sh
## \author Bruno Combal
## \date June 2013
import cdms2
from cdms2 import MV
import numpy
import glob
import sys
import os
from os import path
import re
import string
# ___________________________
def usage():
text=... | IOC-CODE/cmip5_projections | make_warmpool.py | Python | gpl-2.0 | 15,360 | [
"NetCDF"
] | 80e5789e3344351ca6bb9542c25345c987b0e4443f90a244d20d759a7e999f1a |
from ase import *
from ase.structure import molecule
from gpaw import *
from gpaw.mpi import serial_comm
from gpaw.test import equal
from gpaw.xc.fxc_correlation_energy import FXCCorrelation
ecut = 50
He = Atoms('He')
He.center(vacuum=1.0)
calc = GPAW(mode='pw',
dtype=complex,
xc='PBE',
... | robwarm/gpaw-symm | gpaw/test/ralda_C6_He.py | Python | gpl-3.0 | 644 | [
"ASE",
"GPAW"
] | cc6d00c07dc60318762df3f66c2f29ee95b3794d16556c4b83fd4d2efafea580 |
# -*- coding: utf-8 -*-
# Copyright (C) 2017-2020 The Project X-Ray Authors.
#
# Use of this source code is governed by a ISC-style
# license that can be found in the LICENSE file or at
# https://opensource.org/licenses/ISC
#
# SPDX-License-Identifier: ISC
#
# Project X-Ray documentation build configuration file, crea... | SymbiFlow/prjxray | docs/conf.py | Python | isc | 8,980 | [
"Amber"
] | fe6b9f5d03edb45fc00c7f9a4fe9bb5f48c478d9bedcac36e630e624564af2ff |
# -*- coding: utf-8 -*-
"""Define pRF finding parameters here."""
# Part of py_pRF_motion library
# Copyright (C) 2016 Marian Schneider, Ingo Marquardt
#
# 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 Fo... | MSchnei/py_pRF_motion | pyprf_feature/simulation/configs/pRF_sim_config_circleBar2.py | Python | gpl-3.0 | 4,236 | [
"Gaussian"
] | 51f6b9ac7e25c3f956b5864734275c2a114e7c334881cf0486560a1fe3608dcc |
import os
import shutil
import logging
import re
from functools import partial, wraps
import netCDF4
import numpy as np
from django.db import models, transaction
from django.core.exceptions import ValidationError
from django.core.files.uploadedfile import UploadedFile
from django.template import Template, Context
fro... | RENCI/xDCIShare | hs_file_types/models/netcdf.py | Python | bsd-3-clause | 43,703 | [
"NetCDF"
] | 3e2fbf21e00883679d2b96be0fc873e6cab91ae25d7787d2d7c42c3f6bb26f7a |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-02-14 22:51:01 by Brian McFee <brian.mcfee@nyu.edu>
'''Unit tests for display module'''
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except KeyError:
pass
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as p... | yunque/librosa | tests/test_display.py | Python | isc | 9,629 | [
"Brian"
] | 5786df06aaed348b62c4fd4ae8f8d486e9ffebf750155dbb55dc7d247f05961d |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Pair potentials."""
import copy
import warnings
import hoomd
from hoomd.md import _md
from hoomd.md import force
from hoomd.md.nlist import NList
from hoomd... | joaander/hoomd-blue | hoomd/md/pair/pair.py | Python | bsd-3-clause | 70,945 | [
"Gaussian",
"HOOMD-blue"
] | c3a0ea94eeb79a9434fef6e2fce80a29a81acaec039e524e93cdd858bad65cd6 |
"""FileDescriptorProto visitor interface for api_proto_plugin implementations."""
class Visitor(object):
"""Abstract visitor interface for api_proto_plugin implementation."""
def VisitService(self, service_proto, type_context):
"""Visit a service definition.
Args:
service_proto: ServiceDescriptorP... | lizan/envoy | tools/api_proto_plugin/visitor.py | Python | apache-2.0 | 1,604 | [
"VisIt"
] | 8c46e3efecd5fb1016662f3cf96baa81331d522694021be964032c2698077c4e |
#!/usr/bin/python2.4
# -*- coding: iso-8859-15 -*-
import sys, os
import MySQLdb
import MySQLdb.cursors
import traceback
import pickle
import time
from datetime import datetime, date
from string import join, letters
import math
import getpass
import itertools
import urllib, urllib2
import pprint
from klab.db.mysql im... | Kortemme-Lab/kddg | kddg/api/dbi.py | Python | mit | 157,608 | [
"FoldX"
] | a98c3b72c45a2b906261749c6a9be8e735f23c957dbba2e93c34c87e784939b5 |
# -*- 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-compute | tests/unit/gapic/compute_v1/test_forwarding_rules.py | Python | apache-2.0 | 136,480 | [
"Octopus"
] | 41afb9d7319d3e14ce5c5c330b61001d78b2fb4591c80064a977a648955b6b7c |
"""
Student Views
"""
import MySQLdb
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import... | cognitiveclass/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 98,446 | [
"VisIt"
] | 5e8570114d0e3c2d7eaecfdd037df735aa4f838b730aa62669686a859f81cd9e |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('uninstall_repository_revision')
@click.argument("name", type=str)
@click.argument("owner", type=str)
@click.argument("changeset_revision", type=str)
@click.argument("tool_shed_url",... | galaxy-iuc/parsec | parsec/commands/toolShed/uninstall_repository_revision.py | Python | apache-2.0 | 961 | [
"Galaxy"
] | 426ee482caa843df940f4239754ede88f60ef1d8c48c06531551852590fb76d3 |
"""Extensions to the ase Atoms class
"""
import numpy as np
from ase import Atoms
from ase.io import read, write
from ase.data import covalent_radii
from ase.calculators.neighborlist import NeighborList
class Cluster(Atoms):
"""A class for cluster structures
to enable simplified manipulation"""
def __in... | robwarm/gpaw-symm | gpaw/cluster.py | Python | gpl-3.0 | 6,122 | [
"ASE",
"GPAW"
] | 7573e4c834f9c15c71dd8da22a00aa5aad81d0b815628b43a2948a132c61ad69 |
import numpy as np
from .utils import overrides
import theano.tensor as T
import theano
from scipy.sparse import rand
class Distribution(object):
"""
interface for distributions
"""
def __init__(self, ndims=2, nbatch=100):
self.ndims = ndims
self.nbatch = nbatch
self.init_X()
... | rueberger/MJHMC | mjhmc/fast/distributions_T.py | Python | gpl-2.0 | 6,917 | [
"Gaussian"
] | 9967cea8823dd2297d96bd1a1e5ee14742702db64fe129f8c8a5469f8689183b |
# $HeadURL$
#
""" SystemLoggingDB class is a front-end to the Message Logging Database.
The following methods are provided
insertMessage()
getMessagesByDate()
getMessagesByFixedText()
getMessages()
"""
__RCSID__ = "$Id$"
import re
import os
import sys
from types import ListType, StringTypes
fro... | vmendez/DIRAC | FrameworkSystem/DB/SystemLoggingDB.py | Python | gpl-3.0 | 27,012 | [
"DIRAC"
] | d713105bd27f0527145706de85c51ad754f228672fa1c7088e754801032cb175 |
#!/usr/bin/env python
import logging
import copy
import argparse
import tsv
from Bio import SeqIO
from Bio.Seq import Seq
from CPT_GFFParser import gffParse, gffWrite
from gff3 import feature_lambda, feature_test_contains
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)
def mutate(gff3, fast... | TAMU-CPT/galaxy-tools | tools/gff3/genome_editor.py | Python | gpl-3.0 | 5,146 | [
"Biopython"
] | a6464b31098461f1ff2795fe61bdbf4a077b1c38f5ffb989d5719306c0cec179 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""local_browser
NOTICE: Close Crawl runs its browser form submissions through Mechanize.
The module, however, is deprecated and does not support Python 3. The more
stable and maintained Mechanize and BeautifulSoup wrapper, MechanicalSoup,
will be replacing the Mechanize ... | BNIA/Close-Crawl | close_crawl/modules/local_browser.py | Python | mit | 3,815 | [
"VisIt"
] | 8123c8b02a54ad4071accbf29285d9b69ab1d7f71fb94d46cf015418486df6a2 |
"""A linter for docstrings following the google docstring format."""
import ast
from collections import deque
import sys
from enum import Enum
from typing import (
Callable,
Iterator,
List,
Set,
Tuple,
Optional,
Union,
Type,
Any,
)
from .analysis.analysis_visitor import (
Analys... | terrencepreilly/darglint | darglint/function_description.py | Python | mit | 6,095 | [
"VisIt"
] | bcbb4e9372972448e66d52c84610918532c3ca87083784a33d6397a7b1fb9a1c |
# Copyright (C) 2014
# Pierre de Buyl
# 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... | BackupTheBerlios/espressopp | src/interaction/MirrorLennardJones.py | Python | gpl-3.0 | 3,543 | [
"ESPResSo"
] | 0f278043fb11dad0e208aa2cb427dcbdabe6535c74ab4c2266cc7f0110145896 |
# Copyright (C) 2010-2019 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 v... | KaiSzuttor/espresso | testsuite/python/ek_common.py | Python | gpl-3.0 | 2,865 | [
"ESPResSo"
] | db37e89e3d164f24325967982bb2a7fc8dcb46897ed781029b92cb2e8bd96b89 |
import pytest
import sys, os
import time
import shlex
import shutil
import glob
import numpy as np
import subprocess as sp
import netCDF4 as nc
from helpers import setup_test_input_dir
from helpers import calc_regridding_err
from namcouple import namcouple as nam
def build_oasis(oasis_dir):
oasis3mct_dir = o... | DoublePrecision/oasis-grids | test/test_oasis.py | Python | apache-2.0 | 11,145 | [
"NetCDF"
] | 9821635eced43d68e94ecb21470a014a205c70ad6e090d6bd14ef9afe69bd0e7 |
import base64
import hashlib
import json
import os
import sys
import unittest
import warnings
from unittest import mock
from urllib.parse import urlencode
import requests
from flask import Flask, Response, current_app
import data
import routes
from oceannavigator import DatasetConfig, create_app
from plotting.class4 ... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | tests/disabled/test_api_v0_0_plot_area.py | Python | gpl-3.0 | 21,270 | [
"Gaussian"
] | 8b864257759a5b37c9dd1a0d9e456aa088de421f3713524a26eabad2667f6b58 |
import sys
import warnings
import numpy as np
from scipy import stats, linalg
from sklearn.covariance import EmpiricalCovariance
from sklearn.datasets.samples_generator import make_spd_matrix
from sklearn.externals.six.moves import cStringIO as StringIO
from sklearn.metrics.cluster import adjusted_rand_score
from sk... | imaculate/scikit-learn | sklearn/mixture/tests/test_gaussian_mixture.py | Python | bsd-3-clause | 36,087 | [
"Gaussian"
] | 2a2b32548956f2c84903a671eca73546fad39d0137fb7d773e1122341be0c216 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.core.surface import SlabGenerator
from pymatgen import Lattice, Structure
from pymatgen.core.surface import Slab
from itertools import product
import numpy as np
from pymatgen.symmetry.analyzer im... | blondegeek/pymatgen | pymatgen/analysis/interface.py | Python | mit | 47,521 | [
"VASP",
"pymatgen"
] | 385666767fae9a2d1a597a7502026a93ecfe76295735a5fb9c15a3624e926833 |
from collections import OrderedDict
import logging
import os
import parmed.unit as units
from intermol.utils import which, run_subprocess
from intermol.gromacs.gromacs_parser import load, save
GMX_PATH = ''
logger = logging.getLogger('InterMolLog')
to_canonical = {
'Bond': 'bond',
'Angle': 'angle',
'... | mrshirts/InterMol | intermol/gromacs/__init__.py | Python | mit | 4,855 | [
"Gromacs"
] | 05483f8b259ba890220d5a8515e4c7be4fa37856e68a5b26d54ce704a35fb426 |
"""A simple routine to load in a FASTQ file and give us the distribution of qname lengths, because I was curious"""
import numpy as np
import pysam
from mitty.benchmarking.alignmentscore import load_qname_sidecar
def main(fastq_fname, qname_overflow_fname, max_expected_qname_length=500):
long_qname_table = load_qn... | sbg/Mitty | mitty/empirical/qnamestats.py | Python | apache-2.0 | 652 | [
"pysam"
] | 3ce9dadb0373804997be4a727b2806d0d35e86bc7b19db43741ed3f357b64d38 |
SKIP_ABUNDANCES = False
ABUNDANCE_DENOM = ['H','Fe','O','Mg']
# do the following to limit computation a lot
NONEQFIELDS = None
METALS = ["N","O","Mg","Fe","Ba"]
ABUNDANCES = ["O_over_H", "O_over_Mg", "O_over_Fe",
"Fe_over_H", "Fe_over_Mg", "Fe_over_O",
"Mg_over_H... | aemerick/galaxy_analysis | analysis/gas_abundance.py | Python | mit | 32,947 | [
"Galaxy"
] | a7224167a6d84b877ce184d56b4921ea7c6facfd1391d8a1c6b7dd50f10f5a3c |
r"""OS routines for NT or Posix depending on what system we're on.
This exports:
- all functions from posix or nt, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix' or 'nt'
- os.curdir is a string representing the current directory ('.' or ':')
- os.pardir is a strin... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.6.0/Lib/os.py | Python | mit | 39,122 | [
"VisIt"
] | cdc4b1c0db926eaf4524d59c73b938e9d73e0130966e140999ea8ef3b12730a1 |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# _generate_pyx.py to generate the docstrings for the ufuncs in
# scipy.special at the C level... | arokem/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 236,527 | [
"Gaussian"
] | e80f9d75d29d958c3404efafbdeac01883dc79494f1e1315b8c4adf91f41e9bd |
# -*- coding: utf-8 -*-
import os
from importlib import import_module
from collections import Counter
from pickle import HIGHEST_PROTOCOL as pickle_HIGHEST_PROTOCOL
import matplotlib
matplotlib.use('Agg')
from graphviz import Digraph
import numpy as np
import bayespy as bp
from django.db import models
from django.c... | math-a3k/django-ai | django_ai/bayesian_networks/models.py | Python | lgpl-3.0 | 31,062 | [
"Gaussian"
] | d94e14a4faf6d6ca53ef49bcc5a588a0873d21fa085c10935519e0a063b72618 |
from flask import Flask, render_template_string
app = Flask(__name__)
@app.route("/")
@app.route("/<path:path>")
def hello(path=None):
if not path:
body = "Visit hello.tghack.no/your_name"
else:
body = "Hello {}!".format(path)
template_str = """<html>
<head><body>
{}
</body></head>
</html>""".format(body... | tghack/tg17hack | web/friends/server.py | Python | mit | 507 | [
"VisIt"
] | ac8594268b658d5b3389c882ac2dd5659135c0bcf72c9374e4f570517ed9f1b5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module implements an interface to the Henkelmann et al.'s excellent
Fortran code for calculating a Bader charge analysis.
This module depends on a co... | migueldiascosta/pymatgen | pymatgen/command_line/bader_caller.py | Python | mit | 5,826 | [
"VASP",
"pymatgen"
] | a23f1aac249819efa4f4adac4fdeb381ee9ad59ee0a346e33c62d1ac535697d2 |
""" Author: Hongyang Cheng <chyalexcheng@gmail>
Test #2: 2D Pullout of membrane beneath granular material
"""
from esys.escript import *
from esys.weipa import saveVTK
from esys.finley import ReadGmsh
from esys.escript.pdetools import Projector
from esys.escript.linearPDEs import LinearPDE,SolverOptions
from msFEM... | chyalexcheng/multiscale | msTest2_explicit.py | Python | gpl-3.0 | 6,082 | [
"VTK"
] | 64c40c8ea43afab1390415e1221eda04911984eb18353737a0607b242a8e3673 |
""" ElasticDB is a base class used to connect an Elasticsearch database and manages queries.
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger
from DIRAC.Core.Utilities.ElasticSearchDB import ElasticSearchDB
from DIRAC.ConfigurationSystem.Client.Utilities import getElasticDBParameters
class ElasticDB(ElasticSearchDB... | arrabito/DIRAC | Core/Base/ElasticDB.py | Python | gpl-3.0 | 3,494 | [
"DIRAC"
] | 0d2a68d5ad68afae7e9363dc71909c757086e1b75d203e525fa45e10dad8448f |
"""This module provides functions for reading molecule positions,
radii, and connections from ASCII files.
Written by: Filip Malmberg
Modified by: Erik Vidholm and Johan Nysjo
"""
import os
import string
import vtk
def read_points(filename):
"""Reads molecule coordinates from an ASCII file."""
points = vtk... | RDeckers/ScientificVisualization-1TD389 | Assignments/Assignment 1/part2a/molecules_io.py | Python | gpl-3.0 | 1,624 | [
"VTK"
] | ac74e3be4a0dc9726e670761ad02a2f4384d1632f3bc53877aff69c453a73443 |
#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# viz_vmd.py
# Purpose: viz running LAMMPS simulation via VMD
# Syntax: viz_vmd.py in.lammps Nfreq Nsteps
# in.lammps = LAMMPS input script
# Nfreq = dump and viz shapshot every this many steps
# Nsteps = ... | jeremiahyan/lammps | python/examples/viz_vmd.py | Python | gpl-2.0 | 2,128 | [
"LAMMPS",
"VMD"
] | b5e0a5609e1faae5e2a1a3796476c2c3d7b73e47ace03135a2cdd7536e571854 |
"""
Courseware views functions
"""
import json
import logging
import urllib
from collections import OrderedDict
from datetime import datetime
import analytics
import newrelic.agent
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User, A... | alu042/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 68,532 | [
"VisIt"
] | 59b86fe4f37e1c520e5b5e65f214eb03f1e9895c546390efaa4f6cb5fb680f6d |
#!/usr/bin/env python
#
# PDBList.py
#
# A tool for tracking changes in the PDB Protein Structure Database.
#
# (c) 2003 Kristian Rother
# This work was supported by the German Ministry of Education
# and Research (BMBF). Project http://www.bcbio.de
#
# Contact the author
# homepage : http://www.rubor.de/bioinf
# ... | zjuchenyuan/BioWeb | Lib/Bio/PDB/PDBList.py | Python | mit | 13,494 | [
"Biopython"
] | 85848f9d97692419dda915ff2a04d99b4bc8c2c924eefacfbefa817c21d29058 |
from BaseHTTPServer import BaseHTTPRequestHandler,HTTPServer
from SocketServer import ThreadingMixIn
from urlparse import urlparse
import json
import threading
import argparse
import re
import cgi
import random
import sys
import math
import random
class HTTPRequestHandler(BaseHTTPRequestHandler):
def randomTaxiDri... | paulomendes/mock-server-easytaxi | simpleserver.py | Python | mit | 2,884 | [
"MOE"
] | 78246eea8aed776308a30f1e88a2fabc8cec5c31cf810abcb6c2b7d31fef0890 |
# -*- coding: iso-8859-15 -*-
"""
routes
======
This module establishes and defines the Web Handlers and Websockets
that are associated with a specific URL routing name. New routing
associations must be defined here.
Notes
-----
For more information regarding routing URL and valid regular expressions
visit: http://w... | TiMed-dev/TIMed-backend | routes.py | Python | mit | 745 | [
"VisIt"
] | 2d415f8847a1ea6d046a348be42cd087bc71d07e8602bed7fd3a05ce059e7677 |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | strets123/rdkit | rdkit/Chem/Pharm2D/UnitTestMatcher.py | Python | bsd-3-clause | 2,881 | [
"RDKit"
] | 388ea6d982c6744f0b10a9ac170afd8ec5690a19485cdb123e586c4fc5a38411 |
# MIT License
#
# Copyright (c) 2017, Stefan Webb. All Rights Reserved.
#
# 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 us... | stefanwebb/tensorflow-models | tensorflow_models/models/vae_mubeta_obs.py | Python | mit | 5,753 | [
"Gaussian"
] | 5b7f78176c0e32a03132a6a6a76fc9227d1b77c95a446455739331a44dceb89b |
#!/usr/bin/env python2.7
"""
Computes and prints the RMS error between the variable named var1 in netcdf file1
and variable var2 in netcdf file2. If var2 isn't specified then it defaults to var1.
This script assumes that the data arrays associated with var1 and var2 either have
the same shape or else are broadcastable,... | rockdoc/grabbag | netcdf/ncrmse.py | Python | bsd-3-clause | 1,728 | [
"NetCDF"
] | ea49740e50b0d0b640f3b44e207f9b713dceff38728963db4c357c6ecc8cab06 |
# -*- coding: utf-8 -*-
#
# ConnPlotter.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, or... | stinebuu/nest-simulator | extras/ConnPlotter/ConnPlotter.py | Python | gpl-2.0 | 83,966 | [
"Gaussian",
"NEURON"
] | 076f6523d9952bb798f7fc1ea4a701f5c87737a08e17b84a2b68bf2f6ad24d70 |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import urllib
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.core.mail import send_mail
from django.core.urlresolv... | JioEducation/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 60,641 | [
"VisIt"
] | ad0c3d5ec186c815f996d0fcb95b04987e5c38edf98374b66b40dc3690d7da82 |
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
import DIRAC
__RCSID__ = "$Id$"
class DataOperation(BaseAccountingType):
def __init__(self):
BaseAccountingType.__init__(self)
self.definitionKeyFields = [('OperationType', "VARCHAR(32)"),
... | fstagni/DIRAC | AccountingSystem/Client/Types/DataOperation.py | Python | gpl-3.0 | 1,590 | [
"DIRAC"
] | 56e8a1436a97344fb7d8684baddc3178b7bd431268ed9dc7f40c0b6023c17f43 |
# -*- coding: utf-8 -*-
import os
# 2nd-order accurate finite-volume implementation of linear advection with
# piecewise linear slope reconstruction
#
# We are solving a_t + u a_x = 0
#
# M. Zingale (2013-03-24)
import numpy
import pylab
import math
class ccFVgrid:
def __init__(self, nx, ng, xmin=0.0, xmax=1.... | NicovincX2/Python-3.5 | Analyse (mathématiques)/Analyse à plusieurs variables/Équation aux dérivées partielles/Équation en dynamique des fluides/Advection/fv_advection.py | Python | gpl-3.0 | 5,409 | [
"Gaussian"
] | f56beae9954682f966bd8815b371bff40f238f1a5e9b123ef815f7caa4d3dd78 |
"""
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. module:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each included distribution is an instanc... | teoliphant/scipy | scipy/stats/__init__.py | Python | bsd-3-clause | 8,511 | [
"Gaussian"
] | d14776e175c205b5116172978a8bbde2b8402b8a5169d453f8ef1566b850aca5 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
"""
Check that only chemfiles symbols are exported by the shared library.
"""
import os
import sys
import subprocess
ROOT = os.path.join(os.path.dirname(__file__), "..", "..")
ERRORS = 0
def error(message):
global ERRORS
ERRORS += 1
print(message)
def list_s... | chemfiles/chemfiles | scripts/ci/check-exported-symbols.py | Python | bsd-3-clause | 1,155 | [
"Chemfiles"
] | d24b29be0ebb202f07bc8488829acef9fa21916953dfcbfdcb801f01723aafee |
# Jython Database Specification API 2.0
#
# $Id: jndi.py 4185 2008-02-28 16:55:33Z cgroves $
#
# Copyright (c) 2001 brian zimmer <bzimmer@ziclix.com>
"""
This script is used to bind a JNDI reference for testing purposes only.
"""
from java.util import Hashtable
from org.gjt.mm.mysql import MysqlDataSource
fro... | babble/babble | include/jython/Lib/test/zxjdbc/jndi.py | Python | apache-2.0 | 898 | [
"Brian"
] | 0f36ad7e94570d5dadca527d8fe614eddd8dbeff9fede6bfd0aa4bec2bcac6d6 |
import numpy as np
import pandas as pd
import sys, os
from functions import *
from pylab import *
from sklearn.manifold import TSNE
store_fourier = pd.HDFStore("/mnt/DataGuillaume/MergedData/FOURIER_OF_AUTOCORR.h5", 'r')
fte = {}
for e in ['wak', 'rem', 'sws']:
fte[e] = store_fourier[e]
store_fourier.close()
firing... | gviejo/ThalamusPhysio | python/main_make_TSNE_FOURIER.py | Python | gpl-3.0 | 1,465 | [
"Gaussian"
] | f52ae29f20df1b28ad3326d72de7684bc6d7418505a9cd0cd65562847a7ff723 |
# -*- coding: utf-8 -*-
#
# PMDA documentation build configuration file
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commente... | MDAnalysis/pmda | docs/conf.py | Python | gpl-2.0 | 7,800 | [
"MDAnalysis"
] | 8e56186d1647dc1f893e0828b4601ec1eaab4737592aa321f094fa24e4b65853 |
#!/usr/bin/env python
import os
import logging
import argparse
import subprocess as sp
import sys
logging.basicConfig(level=logging.DEBUG)
logger = logging.getLogger(os.path.basename(__file__))
HERE = os.path.dirname(os.path.realpath(__file__))
BLUE = '\033[94m'
GREEN = '\033[92m'
YELLOW = '\033[93m'
RED = '\033[91m... | lcdb/lcdb-workflows | lcdb/lcdb-init.py | Python | mit | 2,055 | [
"Bioconda"
] | 9c7d8c7650b172337e3640b33e0056cbce3912ca407d32a3eac9186ab630f285 |
import os
import re
import shutil
import sys
try:
from setuptools import setup
setup_params = {
'entry_points': {
'console_scripts': [
'virtualenv=virtualenv:main',
'virtualenv-%s.%s=virtualenv:main' % sys.version_info[:2]
],
},
'z... | alex/virtualenv | setup.py | Python | mit | 2,973 | [
"Brian"
] | 8ffe287676758ada890fb503f2e1e08de35915c4053e599845b11552f8f46477 |
""" ProxyManagementAPI has the functions to "talk" to the ProxyManagement service
"""
__RCSID__ = "$Id$"
import os
import datetime
import types
from DIRAC.Core.Utilities import ThreadSafe, DIRACSingleton
from DIRAC.Core.Utilities.DictCache import DictCache
from DIRAC.Core.Security import Locations, CS, File
from DIRAC... | vmendez/DIRAC | FrameworkSystem/Client/ProxyManagerClient.py | Python | gpl-3.0 | 19,703 | [
"DIRAC"
] | ceb4dfb6830277b16dcb45fcda239d1eaa72592de2beb4275bd7751ce9e87833 |
""" Base url for the API calls """
BASE = "http://bowtie.mobi:8080/"
""" Used to get data that is ready to be sent """
SEND = BASE + "send/"
""" Checks if there is anything new to send """
CHECK = BASE + "check/"
""" Used to pass a message from the SMS server to the main server """
RECEIVE = BASE + "receive/"
| wallarelvo/unicef-sms-server | smsserver/url.py | Python | apache-2.0 | 316 | [
"Bowtie"
] | 307be9f42a99fa1fb3f679215e82b6b9d85310a2fcc59dca015972e3dec94a58 |
'''Convenience functions for use in package hooks.'''
# Copyright (C) 2008 - 2012 Canonical Ltd.
# Authors:
# Matt Zimmerman <mdz@canonical.com>
# Brian Murray <brian@ubuntu.com>
# Martin Pitt <martin.pitt@ubuntu.com>
#
# This program is free software; you can redistribute it and/or modify it
# under the terms o... | windflyer/apport | apport/hookutils.py | Python | gpl-2.0 | 31,108 | [
"Brian"
] | 83871084b0f2ce9353b6281c0129d460c68d17b551c1838a847e5cb1ca117365 |
'''
Unit-tests for full learning for zero-mean, full-covariance Gaussian models
'''
import numpy as np
import unittest
import bnpy
from AbstractEndToEndTest import AbstractEndToEndTest
import Util
class TestSimple(AbstractEndToEndTest):
''' Test basic functionality (run without crashing?) on very simple dataset.
... | daeilkim/refinery | refinery/bnpy/bnpy-dev/tests/end-to-end/TestMixZMGauss.py | Python | mit | 2,836 | [
"Gaussian"
] | fbeea88e60ab85580844c20c4ac52c225b0b7c3aad31aa983b91b25cca0fed30 |
from netCDF4 import Dataset
import tempfile, unittest, os
import numpy as np
file_name = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
xdim=None; ydim=121; zdim=169
datashape = (ydim,zdim)
data = np.ones(datashape,dtype=np.float64)
class ShapeTestCase(unittest.TestCase):
def setUp(self):
s... | Unidata/netcdf4-python | test/tst_shape.py | Python | mit | 1,126 | [
"NetCDF"
] | d26f9d530065776eef8a6702dcb04081c05d467b0e568b6128374f8fba0a4faa |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014-2017 CERN.
#
# INSPIRE 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 ... | kaplun/inspire-next | tests/unit/workflows/test_workflows_tasks_submission.py | Python | gpl-3.0 | 24,495 | [
"Galaxy"
] | 9d81ba7638a8101358bec862950307018bb140eb5a00d077ae3ae697fbc354e3 |
import copy
import itertools
from hyperopt.genson_helpers import (null,
false,
true,
choice,
uniform,
gaussian,
lognormal,
qlognormal,
... | yamins81/thor_model_exploration | thor_model_exploration/model_exploration_params.py | Python | mit | 12,724 | [
"Gaussian"
] | 4e85a4f24479891bab47d4b03777a36d5b21d6fbd8b1c6be1fd79a78dd1aeb94 |
#!/usr/bin/env python
# coding: utf-8
import libtcodpy as libtcod
import math
import time
import collections
import textwrap
from random import randrange, random, shuffle, getrandbits
import pprint
pp = pprint.PrettyPrinter(indent=4, width=200).pprint
from particle import Particle, ThrustExhaust, Fire, ExplosionFireB... | AnthonyDiGirolamo/heliopause | heliopause.py | Python | mit | 26,271 | [
"Galaxy"
] | 57ea16d938e5a2b121f728e4a62b60b665cdeaff45501f55d33576eb76907ae1 |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | crafty78/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 96,185 | [
"VisIt"
] | cc1d1f036ec3c8b9129758b4a93da94e9fa143a9b0fc07e05152cc4ddac4624e |
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | wemanuel/smry | smry/server-auth/ls/google-cloud-sdk/lib/oauth2client/tools.py | Python | apache-2.0 | 8,651 | [
"VisIt"
] | ed26dd5fccdb8dd1dc29d21f3f2a8d247e93b22133e1fb19ac7f343a5b2e671e |
# -*- coding: utf-8 -*-
## Copyright 2015-2016 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## This file is part of Nascent.
##
## Nascent is free software: you can redistribute it and/or modify
## it under the terms of the GNU Affero General Public License as
## published by the Free Software Fou... | scholer/na_strand_model | nascent/graph_sim_nx/reaction_utils.py | Python | gpl-3.0 | 7,469 | [
"Biopython"
] | 8679f3cd8f83ffe39e590ebf5f61f244a66b7404d18251bea27660efa4968eab |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2012, MBARI"
__license__ = "GPL"
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__doc__ = '''
Script to read data from Western Flyer Seabird profile ctd .asc files and
write them to netCDF files.
Use the conventions for ... | stoqs/stoqs | stoqs/loaders/CANON/toNetCDF/pctdToNetcdf.py | Python | gpl-3.0 | 12,284 | [
"NetCDF"
] | 136b397ef150dc59bb7dbed8df5d966f80f6aac320d3cf4d3ca29d8746fe0ac9 |
##########################################
# File: visualise_subdivision.py #
# Copyright Richard Stebbing 2014. #
# Distributed under the MIT License. #
# (See accompany file LICENSE or copy at #
# http://opensource.org/licenses/MIT) #
##########################################
# Imports
... | rstebbing/subdivision | examples/doosabin/visualise_subdivision.py | Python | mit | 4,213 | [
"VTK"
] | 8add3df10b96ed1b184863304501589c78300ba37115c44060a3567fcd879187 |
# --------------------------------------------------------
# Iliass Tiendrebeogo Nov 2014
# program : Naive Gaussian elimination
#
# Desc : This program take 1 matrix and 1 vector as entry,
# perform the naive Gaussian elimination method.
# Return the vector result
#----------... | ledrui/Naive_Gauss_Elimination | Naive_Gauss.py | Python | gpl-2.0 | 3,402 | [
"Gaussian"
] | 6e189b6282b86bf0e6c47a63aa66b61d024fae5568f7f1a9ce7b13d3e0e6c261 |
# -*- coding:utf-8 -*-
# Copyright (c) 2015, Galaxy Authors. All Rights Reserved
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
# Author: wangtaize@baidu.com
# Date: 2015-04-06
import datetime
import logging
from sofa.pbrpc import client
from galaxy import master... | imotai/galaxy | platform/src/galaxy/sdk.py | Python | bsd-3-clause | 2,033 | [
"Galaxy"
] | d2726237d959632affc99c5f3dc093794c64421a66e19a0ec03541e3debf4f4b |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ---------------------... | Kleptobismol/scikit-bio | skbio/io/tests/test_clustal.py | Python | bsd-3-clause | 11,382 | [
"scikit-bio"
] | 32ad15a79c70176d40a479cbd8010c3cede9bd859a9a3e4be894c3f83267b008 |
"""The ants module provides basic functions for interfacing with ants functions.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(... | sgiavasis/nipype | nipype/interfaces/ants/segmentation.py | Python | bsd-3-clause | 58,559 | [
"Gaussian"
] | 82a739a793450b892defc646020891c7dcaf3faed17458315195547d0ac3ab61 |
""" core implementation of testing process: init, session, runtest loop. """
import os
import sys
import _pytest
import _pytest._code
import py
import pytest
try:
from collections import MutableMapping as MappingMixin
except ImportError:
from UserDict import DictMixin as MappingMixin
from _pytest.runner impor... | pdxwebdev/yadapy | yada/lib/python2.7/site-packages/_pytest/main.py | Python | gpl-3.0 | 27,248 | [
"VisIt"
] | bd8d7a9004a585812d701afafaee5a0106918db4e49b4d811ac3bd23556673f6 |
"""
merged implementation of the cache provider
the name cache was not choosen to ensure pluggy automatically
ignores the external pytest-cache
"""
import py
import pytest
import json
from os.path import sep as _sep, altsep as _altsep
class Cache(object):
def __init__(self, config):
self.config = config... | mhils/pytest | _pytest/cacheprovider.py | Python | mit | 7,978 | [
"VisIt"
] | 0c6cb08a8fb51b0d862bcdf4b10c81143265f5dfeb1aae7d7ed051536590a429 |
from django.core.urlresolvers import reverse
from django.utils.translation import ugettext_lazy as _
from horizon import exceptions
from horizon import forms
from horizon import messages
from crystal_dashboard.api import filters as api
from crystal_dashboard.dashboards.crystal import exceptions as sdsexception
class... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/filters/filters/forms.py | Python | gpl-3.0 | 15,443 | [
"CRYSTAL"
] | ef16c23e0489159c59657907627ceb45f7b26734d1b65e71a09b97dc84667d22 |
# ======================================================================
# Atomistica - Interatomic potential library and molecular dynamics code
# https://github.com/Atomistica/atomistica
#
# Copyright (2005-2020) Lars Pastewka <lars.pastewka@imtek.uni-freiburg.de>
# and others. See the AUTHORS file in the top-le... | Atomistica/atomistica | tests/coulomb.py | Python | gpl-2.0 | 1,993 | [
"ASE"
] | d4f2966a9c21a08e415f38e58f5ed42b5bac1786882fb0c6dd8b7d54df53799d |
"""
LMS Course Home page object
"""
from collections import OrderedDict
from bok_choy.page_object import PageObject
from bok_choy.promise import BrokenPromise
from six import text_type
from .bookmarks import BookmarksPage
from .course_page import CoursePage
from .courseware import CoursewarePage
from .staff_view im... | cpennington/edx-platform | common/test/acceptance/pages/lms/course_home.py | Python | agpl-3.0 | 12,146 | [
"VisIt"
] | 810b5eea04f0f1e6e39047809adba470db994ac9cc61a188f0bd4eb2d31d3b1c |
# -*- coding: utf-8 -*-
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
import warnings
from collections.abc import Iterable
import ctypes
import numpy as np
from scipy._lib.doccer import (extend_notes_in_docstring,
replace_notes_i... | WarrenWeckesser/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 288,872 | [
"CRYSTAL",
"Gaussian"
] | 08d4b526657070528deeae609398fa51aef8565d290299bf075bde74040ee1be |
import os, ipdb, json
def anfrage_token():
befehl = """curl -v https://api.sandbox.paypal.com/v1/oauth2/token -H "Accept: application/json" -H "Accept-Language: en_US" -u "AfmyoibNF5Q_5k_wO4jYEAY4Asz00wmybsk3cidPYPp1smwe-JVdDNwR9B_DOrsyoJ8gNYeCKKmXurVQ:EDkk66_ZRFYJl3g5VgXzUUkLoyZrZ3wwLaya3NsIU1rnjBIKZIeB... | wmles/scholarium.at | Grundgeruest/paypal.py | Python | mit | 3,108 | [
"Brian"
] | be5b8d65f8277e14664c4031744135c68e86895892d88f347fa43b7069018e1d |
# -*- coding: utf-8 -*-
""" GIS Module
@requires: U{B{I{gluon}} <http://web2py.com>}
@requires: U{B{I{shapely}} <http://trac.gispython.org/lab/wiki/Shapely>}
@copyright: (c) 2010-2014 Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaini... | gnarula/eden_deployment | modules/s3/s3gis.py | Python | mit | 376,655 | [
"Amber"
] | 967229bd089d84b270bf223cecbe6b76d9fe75fa820eee017b992d9142355b2c |
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | ychen820/microblog | y/google-cloud-sdk/platform/gsutil/third_party/oauth2client/oauth2client/tools.py | Python | bsd-3-clause | 8,468 | [
"VisIt"
] | 5b76134660c5c5c4bed81918e9a1fe9cfb874b757d0da4b1dadef430d30e66be |
#
# This file is part of the CCP1 Graphical User Interface (ccp1gui)
#
# (C) 2002-2005 CCLRC Daresbury Laboratory
#
# 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 ... | alexei-matveev/ccp1gui | interfaces/tools.py | Python | gpl-2.0 | 35,557 | [
"Dalton"
] | 5ec1356ee9bc503eb28b27b1e3432f75e425204d98b240d659c4e8921156c40d |
from __future__ import absolute_import, division, print_function
import numpy as np
# returns a list of augmented audio data, stereo or mono
def augment_audio(y,
sr,
n_augment=0,
allow_speedandpitch=True,
allow_pitch=True,
all... | imito/odin | odin/preprocessing/audio/audio.py | Python | mit | 5,392 | [
"Gaussian"
] | d4e07c12d719859e007699ddfe2e48ea36b82717ee5bc0e3569475a380b0b8cd |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.uk/wiki... | acsis-project/emissions | emissions/python/timeslice/regrid_aircNO_n96e_greg_1year.py | Python | gpl-3.0 | 6,625 | [
"NetCDF"
] | 4cec8bfd71f371e513030f242542bb5bbcc4a9434ab98903e1bc38a3a2752bd4 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'GenericFeedback.display_on_summary'
db.add_column(u'clini... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0044_auto__add_field_genericfeedback_display_on_summary__add_field_genericf.py | Python | bsd-2-clause | 13,740 | [
"VisIt"
] | 9bf890463bcbaec7e11df639e338973a43773ced53717b8bb0a8e6f8ff31fcaf |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import ast
import six
from . import cpp
from . import hook
from . import transformer
BOOLOP_MAP = {
ast.And: "&&",
ast.Or: "||",
}
OPERATOR_MAP = {
ast.Add: "+",
ast.Sub: "-",
ast.Mult: "*",
ast.Div: "/",
ast.Mod: "%",
... | mugwort-rc/py2cpp | py2cpp/converter.py | Python | gpl-3.0 | 8,572 | [
"VisIt"
] | a3abf4f5701cf55a949ad12e8a48dc92cd22862f1a144426ba2bbb323d0e6399 |
##
## Draw gene structure from a GFF file
##
import os, sys, operator, subprocess
import math
import pysam
import glob
from pylab import *
from matplotlib.patches import PathPatch
from matplotlib.path import Path
import misopy
import misopy.gff_utils as gff_utils
import misopy.sam_utils as sam_utils
from misopy.sash... | wyleung/rnaveer | misopy_modifications/sashimi_plot/plot_utils/plot_gene.py | Python | mit | 28,085 | [
"pysam"
] | a12f04b2b4157a63ae38443a3a7866344f08cab888e05d5f4989b2819593cfbf |
import numpy as np
from pymatgen.core.operations import SymmOp
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from mpinterfaces import get_struct_from_mp
from mpinterfaces.interface import Interface
# initial bulk structure to start with
def get_grain_boundary_interface(structure=None,
... | henniggroup/MPInterfaces | dev_scripts/grain_boundary.py | Python | mit | 3,953 | [
"VASP",
"pymatgen"
] | 7f40f416d6889b2651aa3987d939459ddaa644ede56f7c7ddf150132469450bb |
from __future__ import division
from builtins import range
import numpy as np
np.seterr(invalid='raise')
from matplotlib import pyplot as plt
import copy
import pybasicbayes
from pybasicbayes import models, distributions
from pybasicbayes.util.text import progprint_xrange
# EM is really terrible! Here's a demo of how... | mattjj/pybasicbayes | examples/EM_demo.py | Python | mit | 1,978 | [
"Gaussian"
] | bbe89f0a86b822dd0cc8a80f1186440373874afa2775d1dd392581d323a08111 |
class Coffee(object):
def __init__(self, name: str, price: float):
self.name = name
self.price = price
COFFEES = [Coffee('Americano', 1.50),
Coffee('Cappuccino', 2.00),
Coffee('Espresso', 1.30),
# Coffee('Latte Macchiato', 2.20),
Coffee('Moccaccino', 2.3... | swiesend/barista | barista/coffee.py | Python | mit | 1,299 | [
"ESPResSo"
] | 8d46f0d69e4907a7889363a3fe59342690a0c0b0b1868d4a6b0fc36a6ca021d5 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/util/_misc.py | Python | bsd-3-clause | 11,303 | [
"scikit-bio"
] | fdd5031d7c54369047af6ef12986fa5e90a592864db3c86a825e6ea51d4f2ebd |
# Copyright 2006-2010 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.
#
#Nice link:
# http://www.ebi.ac.uk/help/formats_frame.html
"""Sequence input/output as Seq... | bryback/quickseq | genescript/Bio/SeqIO/__init__.py | Python | mit | 39,267 | [
"BioPerl",
"Biopython"
] | 9e0a27c25ee6fb8416f4eb412480f206f208153fedddfa22fa2e1aef701f7912 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | Karaage-Cluster/python-tldap | tldap/backend/__init__.py | Python | gpl-3.0 | 2,141 | [
"Brian"
] | 446f453c958ee2068c625c744ef8c6b95abaf267a46fe87220748122240a7dca |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/removelocation.py | Python | gpl-2.0 | 5,260 | [
"VisIt"
] | 56d8682f8574a6112ac0f1641a683738634db191755831c35825fef27fea3b3d |
# -*- coding: utf-8 -*-
"""Influence and Outlier Measures
Created on Sun Jan 29 11:16:09 2012
Author: Josef Perktold
License: BSD-3
"""
from collections import defaultdict
import numpy as np
from statsmodels.compat.python import lzip
from statsmodels.compat.pandas import Appender
from statsmodels.graphics._regressi... | jseabold/statsmodels | statsmodels/stats/outliers_influence.py | Python | bsd-3-clause | 49,574 | [
"Gaussian"
] | 2b00efb2a443b86ab4d1e60c38025d715379c5538e4f00cf1d4adfe9c7b35254 |
#!/usr/bin/env python
# Standard packages
import sys
import argparse
# Third-party packages
from toil.job import Job
# Package methods
from ddb import configuration
from ddb_ngsflow import gatk
from ddb_ngsflow import annotation
from ddb_ngsflow import pipeline
from ddb_ngsflow.align import bwa
from ddb_ngsflow.vari... | GastonLab/ddb-scripts | defunct/workflow-haplotypecaller-annotate.py | Python | mit | 3,213 | [
"BWA"
] | d24e5a1c7d5adbaa21be41af4df76946ab947623dc470c31a2269bf058cacdc0 |
""" StorageManagerHandler is the implementation of the StorageManagementDB in the DISET framework """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
from DIRAC import gLogger, S_OK
from DIRAC.Core.DISET.RequestHandler import... | yujikato/DIRAC | src/DIRAC/StorageManagementSystem/Service/StorageManagerHandler.py | Python | gpl-3.0 | 15,132 | [
"DIRAC"
] | ed2cef32d51e1a934f2aa63907c94f749a88b3e72ee8f682f58af216a9fdcf60 |
# DistTarBuilder: tool to generate tar files using SCons
# Copyright (C) 2005, 2006 Matthew A. Nicholson
# Copyright (C) 2006-2010 John Pye
#
# This file is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License version 2.1 as published by the Free Software... | cloudkick/cast | site_scons/site_tools/disttar.py | Python | apache-2.0 | 5,443 | [
"VisIt"
] | a4120256abb098465e2e8e347ef068ac3cb6cc1f348c6fb84a9ba1d5f499193c |
# This file is part of Copernicus
# http://www.copernicus-computing.org/
#
# Copyright (C) 2011-2014, Sander Pronk, Iman Pouya, Magnus Lundborg,
# Erik Lindahl, and others.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as publis... | soellman/copernicus | cpc/lib/gromacs/mdrun.py | Python | gpl-2.0 | 24,506 | [
"Gromacs"
] | 408a2819a57db3651c05826f74203af3e081ffa70bc1e81bd28aafef0bf3322e |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.