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from itertools import takewhile
import re
from StringIO import StringIO
import shutil
import tempfile
import time
from unittest import skipUnless
from urllib import urlencode
import django
from django.conf import settings
from django.core.files.uploadedfile import SimpleUploadedFile
from django.core.urlresolvers impor... | ellak-monades-aristeias/enhydris | enhydris/hcore/tests/test_views.py | Python | agpl-3.0 | 53,671 | [
"VisIt"
] | 0a02ae6686a7450bf79b5c7e3a73302b235f0d000cf219c309c56465f4c67e53 |
from django.db import models
from django.apps import apps
from django.core.exceptions import ValidationError
from edc_base.model.validators import (date_not_before_study_start, date_not_future,
datetime_not_future, datetime_not_before_study_start)
from edc_constants.choices impor... | botswana-harvard/tshilo-dikotla | td_maternal/models/enrollment_mixin.py | Python | gpl-2.0 | 7,736 | [
"VisIt"
] | f18d146d5472c68f9c3608365fda6d5da2befa8e659f5d5220068b9d83f8a5ca |
"""
Restricted open-shell Kohn-Sham
"""
import numpy as np
from frankenstein.sgscf import rks, rhf, rohf
from pyscf.dft import uks as pyuks
def get_E(mf):
h1e = mf.h1e
dmm = mf.rdm1m
dmt = mf.rdm1t
vhfm = mf.vhfm
vhft = mf.vhft
e1m = sum([np.trace(h1e@dmm[s]) for s in [0,1]])
em_scf = ... | hongzhouye/frankenstein | sgscf/roks.py | Python | bsd-3-clause | 6,266 | [
"PyMOL",
"PySCF"
] | ae4fba801ee47e08215fb838f5fa53e458a6f2dbcc0ff1c68b8ab3e5f11bef32 |
# python3
# pylint: disable=g-bad-file-header
# Copyright 2021 DeepMind Technologies Limited. 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... | deepmind/enn | enn/networks/gaussian_enn.py | Python | apache-2.0 | 3,742 | [
"Gaussian"
] | 3d242c509f6ad7f6c43a500fb4a453264015745060cd6c1a6423e165fb5dc37e |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Foundati... | tiagocardosos/stoq | stoqlib/gui/test/test_baseeditor.py | Python | gpl-2.0 | 5,747 | [
"VisIt"
] | 1de7e2e59546099b88665d2b16f8da0a4cc35758f5ec609a8bd38a96b03e0de0 |
#!/usr/bin/env python
# Copyright (c) 2012 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.
import glob
import logging
import os
import pyauto_functional # Must be imported before pyauto
import pyauto
class ThemesTest(p... | keishi/chromium | chrome/test/functional/themes.py | Python | bsd-3-clause | 5,976 | [
"VisIt"
] | 439c49b303493391fd3bf726850e572d3fd559ccb14114e933911b3216baa840 |
#!/usr/bin/env python
#
# This code was copied from the data generation program of Tencent Alchemy
# project (https://github.com/tencent-alchemy).
#
#
# Copyright 2019 Tencent America LLC. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in com... | sunqm/pyscf | pyscf/df/grad/uks.py | Python | apache-2.0 | 5,117 | [
"PySCF"
] | 62c8da9330baefb65ed3b9ecaeb9da06080c28a2d7204a37fe99ba4a536b01ab |
from django.contrib.auth.models import User
from django.core.mail import send_mail
from django.core.mail.message import EmailMessage
from django.db import models
from what_apps.people.models import Group, Role, RoleInGroup, RoleHierarchy
class BlastMessage(models.Model):
'''
This is the model whose fields wil... | SlashRoot/WHAT | what_apps/email_blast/models.py | Python | mit | 1,927 | [
"BLAST"
] | 82c06f2ce05ed97aa6b07389d0b4426ae894c9ac121e35430adf1842a1c233ba |
import unittest
import json
import os
import igraph as ig
import networkx as nx
from py2cytoscape import util
import scipy as sp
import tempfile
# Utilities
def compare_edge_sets(nx_edges, cy_edges):
edge_set = set()
for cyedge in cy_edges:
source = cyedge['data']['source']
target = cyedge[... | scholer/py2cytoscape | tests/test_util.py | Python | mit | 11,636 | [
"Cytoscape"
] | a0968c7facdd43694c089820f30cb73b143b251d3de3a9c4151432404d10fa19 |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | ghislainp/iris | lib/iris/util.py | Python | gpl-3.0 | 53,476 | [
"NetCDF"
] | ff5fbf9b0a338e0f7cd77ab71718e81c4b39a99d6fe075b19e9af9855f018ce9 |
#!/usr/bin/env python
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl... | harterj/moose | tutorials/tutorial02_multiapps/app/doc/moosedocs.py | Python | lgpl-2.1 | 1,016 | [
"MOOSE"
] | 754e13f227d9428952646d7ccaef8ba95c6c7faed1d521a594c56b27805b7f1f |
"""
This program takes a set of documents (all streamed from stdin at once) and formats them in a way suitable for
use with the NIST-distributed mteval script. The output is in UTF-8.
Usage: cat [MTC_DIR_FOR_SYSTEM] | python convert-mtc.systems.py [doctype-string {'source', 'target', 'ref'} (default='target')] | [NEW_... | DanielCoutoVale/openccg | ccgbank/bin/convert-mtc-systems.py | Python | lgpl-2.1 | 4,455 | [
"Jaguar"
] | 0d66b88e77f0ddf1250cfe189ad0ee66b03f76520aab17449ae1f507d1f99f75 |
from ev3.ev3dev import LED
import unittest
import time
from util import get_input
class TestLED(unittest.TestCase):
def test_led(self):
get_input('Test LED')
led = LED()
get_input('Test left red')
led.left.color=LED.COLOR.RED
get_input('Test left green')
led.left.c... | topikachu/python-ev3 | test/test_ev3_led.py | Python | apache-2.0 | 824 | [
"Amber"
] | 05bcd44273b69d43d46d1fa1260df2c3491c5ab57f41ec13a65bcc80869c3304 |
# -*- coding: utf-8 -*-
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General ... | upibhalla/moose-core | tests/python/testXreacs4a.py | Python | gpl-3.0 | 3,950 | [
"MOOSE"
] | 9c62a2780276eb5c2533fe56f75019d064df8a954b0bad78f6abacc68cd78b4d |
import param
import numpy as np
from ..core import Dimension, Dataset, NdOverlay
from ..core.operation import Operation
from ..core.util import basestring, cartesian_product, isfinite
from ..element import (Curve, Area, Image, Distribution, Bivariate,
Contours, Polygons)
from .element import co... | basnijholt/holoviews | holoviews/operation/stats.py | Python | bsd-3-clause | 9,824 | [
"Gaussian"
] | 14aa62c0dab2716e1fcef021dbe2a36453cd203c8a2e8ee58525383cf45d21c3 |
import os
import operator
import subprocess
import multiprocessing
from .. utils import *
from .. process import *
from .. task import *
from .. package import *
__all__ = ["Index", "Align"]
class Index(Process):
Command = "bwa"
Arguments = [
ProcessArgument(name="bwa_module", type=str, default="inde... | vishnubob/bones | bones/tools/bwa.py | Python | mit | 6,980 | [
"BWA"
] | 12ec4d25dde0eebf4bd960538c6d05792f6cd7076a2c676eacb0b05d897c5274 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/integrator/unittest/PTestVelocityVerlet.py | Python | gpl-3.0 | 4,246 | [
"ESPResSo"
] | 970644ec21ad13ae0c1eea0372717bbc5d632b2e4ebd8c24042e1c1bf88ac975 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/gui/widgets/fieldgrid.py | Python | gpl-2.0 | 17,791 | [
"VisIt"
] | 80cd08b8ea1aa5d543471f0f46eab93b31cd5387945cf00b57b6ff0f4df93ad9 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You s... | Clyde-fare/cclib | src/cclib/bridge/cclib2biopython.py | Python | lgpl-2.1 | 1,441 | [
"Biopython",
"cclib"
] | 7958eda2a39d359aa9e7562505aa9c40b1c91afe40b2db0994d0982dae733098 |
#
# Adrian Soto
# 22-12-2014
# Stony Brook University
#
################################################
# Plot band structure and DOS from the
# output of the bands.x program in the
# Quantum Espresso package.
#
# Features:
# 1) Allows for scissor correction (band shift)
# 2)
#
###################################... | adrian-soto/QEdark_repo | tools/bandsndos/bandsndos_TlBr.py | Python | gpl-2.0 | 20,254 | [
"Quantum ESPRESSO"
] | b761697578032650a21ffe64d4d1a166b18eae82fc4d864d11b477fa6b826364 |
import pandas as pd
from . import cytoscapejs as cyjs
def from_dataframe(df, source_col='source', target_col='target', interaction_col='interaction',
name='From DataFrame', edge_attr_cols=[]):
"""
Utility to convert Pandas DataFrame object into Cytoscape.js JSON
:param df:
:param s... | scholer/py2cytoscape | py2cytoscape/util/dataframe.py | Python | mit | 2,033 | [
"Cytoscape"
] | 02951c6f7687776a2bc796f7686b411501ce371cf28a7d6dc8fd27e3962661de |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.2 on 2016-04-08 11:15
from __future__ import unicode_literals
import django_rdkit.models.fields
from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
('compound_db', '0002_auto_20160314_2022'),
]
operations = [... | martin-sicho/MI_ADM | MI_ADM_website/compound_db/migrations/0003_compound_mol.py | Python | gpl-3.0 | 599 | [
"RDKit"
] | ff233bbe75ccf2f2b809fdb8be611f92246aa9b00f1b4edf5b9831e9cb698db8 |
# Write the benchmarking functions here.
# See "Writing benchmarks" in the asv docs for more information.
import os
import py_entitymatching as em
from py_entitymatching.utils.generic_helper import get_install_path
import sys
if sys.version[0] == '2':
reload(sys)
sys.... | anhaidgroup/py_entitymatching | benchmarks/benchmark_down_sample_sampler.py | Python | bsd-3-clause | 12,585 | [
"VisIt"
] | 41a66fc2d65cedd6510fcb00caad256d0267555616f9790d4d2f87422b11c3ed |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to interface with the Materials Project REST
API v2 to enable the creation of data structures and pymatgen objects using
Materials Project data.
To make use of the Materials AP... | davidwaroquiers/pymatgen | pymatgen/ext/matproj.py | Python | mit | 66,579 | [
"ABINIT",
"VASP",
"pymatgen"
] | 5717ad124890fa137a52d1e08664ddac35c664fc314337b264bc9cca1e7bee25 |
"""
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(datadir)
"""
import os
import glob
from nipype.interfaces.base import (... | dmordom/nipype | nipype/interfaces/camino/convert.py | Python | bsd-3-clause | 31,722 | [
"VTK"
] | 2789997682af30eaf341108d68dead7a9723877fed10fd21c6881f059e00faa0 |
"""
CGI Script handling github webhooks
this script mainly takes care of in- and output
and hands off most of the actual work to the build module
"""
import sys
import json
import logging
import os
import io
from . import github, build, config
import traceback
from lesson_builder import misc
from .misc import Maybe
... | fsr/lesson-builder | lesson_builder/webhook_receiver_proxy.py | Python | mit | 9,568 | [
"VisIt"
] | b160411407d4bb3cfebfd8422426b59efd0aadd064b21c5c9386e937a5dfabad |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Checks that RamanFiber propagates properly the spectral information. In this way, also the RamanSolver and the NliSolver
are tested.
"""
from pathlib import Path
from pandas import read_csv
from numpy.testing import assert_allclose
import pytest
from gnpy.core.info ... | Telecominfraproject/gnpy | tests/test_science_utils.py | Python | bsd-3-clause | 1,839 | [
"ASE"
] | 5e3c42979714d19fcdb02854049ae839454ab10252200fc2ca20bef44b7cfac6 |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (http://w... | geimer/easybuild-easyblocks | easybuild/easyblocks/b/bowtie.py | Python | gpl-2.0 | 2,601 | [
"Bowtie"
] | fb2ef3198d6c210721db3eb76793e6e2d9a108b94741a664a7bfdc3821827c24 |
########################################################################
#
# B a r a K u d a
#
# Ploting functions and utilities
#
## Authors:
# --------
# 2010-2015: Laurent Brodeau (original primitive code)
# 2016: Saeed Falahat (update to fancy grown-up coding!) :D
#
#####################################... | plesager/barakuda | python/modules/barakuda_plot.py | Python | gpl-2.0 | 69,785 | [
"ORCA"
] | 15a9d42db950ea2e47fce80c5b8969cc525b8d390ba86773e6dc6e270570a3dd |
# Copyright (c) 2014, The MITRE Corporation. All rights reserved.
# See LICENSE.txt for complete terms.
import os
from collections import defaultdict
from lxml import etree
class XmlSchemaValidator(object):
NS_XML_SCHEMA_INSTANCE = "http://www.w3.org/2001/XMLSchema-instance"
NS_XML_SCHEMA = "http://www.w3.or... | bschmoker/stix-validator | validators/xml_schema.py | Python | bsd-3-clause | 7,809 | [
"VisIt"
] | 4553c1d25bbcd9f002a6882029cf8abb37fc1f05fc885706882723d3f1d66ba2 |
# 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/templatetags/karaage_tags.py | Python | gpl-3.0 | 7,686 | [
"Brian"
] | dd88956d8e36ea1e4c5dde1e5a5af680ab98ee6a7b0c4b2b56646f301346d79f |
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 20 18:23:08 2015
@author: Eric Dodds
"""
import numpy as np
# try/except block gets around an issue on the cluster
try:
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
except ImportError:
print("Plotting unavailable.")
c... | emdodds/DictLearner | StimSet.py | Python | mit | 16,335 | [
"Gaussian"
] | 54c43b7a0ccae919d07d77d2400e593358823611792e91eca97686f85bf7bf05 |
'''
NAME
NetCDF with Python
PURPOSE
To demonstrate how to read and write data with NetCDF files using
a NetCDF file from the NCEP/NCAR Reanalysis.
Plotting using Matplotlib and Basemap is also shown.
PROGRAMMER(S)
Chris Slocum
REVISION HISTORY
20140320 -- Initial version created and posted onlin... | CopyChat/Plotting | Python/PythonNetCDF.py | Python | gpl-3.0 | 10,821 | [
"NetCDF"
] | 207fb05507aa130abd18ac8b821ba0b9a94deb48dd5b2ffe18bee9508ee304d7 |
#!/usr/bin/env python
# mirto_code_main.py
import numpy as np
from scipy.linalg import lu , solve
import cProfile, pstats
import mirto_code_configuration
import mirto_code_compute_F
import sys
import ctypes
# Empty class to store result
class mirto_state:
pass
class mirto_residuals:
pass
class mirto_history:
d... | graziano-giuliani/pythoncode | mirto/mirto_code_main.py | Python | mit | 8,009 | [
"Gaussian"
] | 9bfcafce94f9def02a7614b1823f77afa57085bb9dc750c233e421d0614f798c |
import sklearn.cross_validation as cv
import sklearn.dummy as dummy
from sklearn.mixture import GMM
from sklearn.hmm import GMMHMM
from sklearn import linear_model, naive_bayes
import collections
import itertools
import pandas as pd
from testResults import TestResults
from counters import *
import utils as utils
cla... | phihes/sds-models | sdsModels/models.py | Python | mit | 12,892 | [
"Gaussian"
] | 814db040e8acba233fe1cb7ef74b8f4772dd28a9069c609cbdd1ed3e80567afc |
# Copyright: (c) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2018, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os.path
import re
import sh... | mikewiebe-ansible/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 59,804 | [
"Galaxy"
] | ad8a1327e37019a57247342d3906938e70f974a941ff1460e1cc57801bb5eb54 |
# -*- coding: utf-8 -*-
from __future__ import division, print_function, absolute_import
import gzip
from warnings import warn
import numpy as np
from scipy import ndimage
from copy import copy
from nibabel.tmpdirs import InTemporaryDirectory
from nibabel.py3k import asbytes
try:
import Tkinter as tkinter
h... | nilgoyyou/dipy | dipy/viz/window.py | Python | bsd-3-clause | 29,276 | [
"VTK"
] | f905daccb5a426fd8996c509fa54a1092a1c056a434ed68d96856b18866bdd2a |
#
# Copyright (C) 2000 greg Landrum
#
""" unit testing code for trees and decision trees (not learning/xvalidation) """
from __future__ import print_function
import copy
import os
import unittest
from rdkit import RDConfig
from rdkit.ML.DecTree import Tree
from rdkit.TestRunner import redirect_stdout
from rdkit.six... | rvianello/rdkit | rdkit/ML/DecTree/UnitTestTree.py | Python | bsd-3-clause | 4,480 | [
"RDKit"
] | 21b0c9143d33564fc3764b2e05c92e8b96f8037040c6db8ae69a1ffd67c172d9 |
import os
import random
import pytest
from datetime import datetime
from unittest import mock
from unittest.mock import MagicMock, Mock
from urllib.error import HTTPError
from pytube import request, Stream
@mock.patch("pytube.streams.request")
def test_stream_to_buffer(mock_request, cipher_signature):
# Given
... | pytube/pytube | tests/test_streams.py | Python | unlicense | 13,366 | [
"VisIt"
] | 61d1006612e83569cd74305bd7c0dc42ca8d9a4212cc06cd3bccc6830333b1cc |
# Inside of a python script.
# Call this function with "" or "__main__"
# in Crystal Clear.
print ("Hello, World!") | MatthewKaes/CrystalClear | Test/python/script.py | Python | lgpl-3.0 | 115 | [
"CRYSTAL"
] | 7ba5a5b9821a38775d0d9271a6a67baef494c9a2e9f4d7da22d24b5894b17e14 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/analysis/test_base.py | Python | gpl-2.0 | 5,601 | [
"MDAnalysis"
] | 083a5502be9cd2fb3d1a262d34aa78768d578b122ddc9b04d3a63a2bdea05d98 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | mol_dqn/chemgraph/optimize_logp.py | Python | apache-2.0 | 2,611 | [
"RDKit"
] | ae3f6dc49ded8efcc76aa3d758b6eb8c9de6ff14d04e86a5103b9e62e7ba92ec |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/analysis/encore/bootstrap.py | Python | gpl-2.0 | 4,872 | [
"MDAnalysis"
] | bb2ef36127490f4c518f953367bf5abd8e89c7666b781981b53e827e74a54372 |
# -*- coding: utf-8 -*-
import unittest
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
from .context import cdk
class BasicTestSuite(unittest.TestCase):
"""Unit tests go here!"""
def test_inserting_custom_css(self):
"""Custom css means opening the pro... | twitter/cdk | tests/test_basic.py | Python | apache-2.0 | 930 | [
"CDK"
] | aa2a30b04f27e6eb2ed513fadf809508f82228beea42c73488c186d3d0ad6f00 |
# 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/interaction/VSpherePair.py | Python | gpl-3.0 | 3,343 | [
"ESPResSo"
] | 9f36f8032e630fbd816bac3d27055c5e48f8bda351081342b8cf8aa883a8cdd2 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.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... | Azulinho/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 14,965 | [
"Brian",
"Galaxy"
] | c52ce13f53acce947b385b8b334c811491262ee0abdf3870bba9f48bf4f98831 |
from unittest import TestCase
from nose.tools import assert_equals
from rdkit import Chem
import deepchem as dc
class TestOneHotFeaturizer(TestCase):
def test_featurize(self):
smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O", "CC(=O)N1CN(C(C)=O)C(O)C1O"]
mols = [Chem.MolFromSmiles(smile) for smile in smiles]
f... | Agent007/deepchem | deepchem/feat/test_one_hot.py | Python | mit | 626 | [
"RDKit"
] | 8aec73a44ede9304a5b2577c33e9e6767a2a3c91867fa7f446c271517ade41c4 |
#!/usr/bin python
# -*- coding: utf-8 -*-
from __future__ import (print_function)
import os
import sys
import warnings
import argparse
import numpy as np
path = os.path.normpath(os.path.join(os.path.dirname(sys.argv[0]), '..'))
sys.path.insert(0, path)
from uvmod import stats
from uvmod import models
from uvmod import... | ipashchenko/uvmod | bin/fit_amp.py | Python | mit | 12,539 | [
"Gaussian"
] | b08b0e0612e9316d00987efa15a0d5f16b7e038071424aa425ac78e0cc004dac |
from sage.matrix.constructor import *
def Riordan_matrix_latex_code(
array, order=10, handlers_tuple=None, handle_triangular_region_only=True):
"""
Produces a chunk of infinite lower matrix denoted by functions *d* and *h*
Enhancement:
1. Add optional arguments that request to return a s... | massimo-nocentini/master-thesis | sympy/riordan_visiting.py | Python | mit | 2,884 | [
"VisIt"
] | 52dfff2903a63d739108a53ac245fc549ba7bf6e2ca23403c3c66b382aedc1ec |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('update_dataset')
@click.argument("history_id", type=str)
@click.argument("dataset_id", type=str)
@click.option(
"--annotation",
help="Replace history dataset annotation with... | galaxy-iuc/parsec | parsec/commands/histories/update_dataset.py | Python | apache-2.0 | 1,687 | [
"Galaxy"
] | bef8cf0067bccd82d9e9e82031569171324ba6b612f0faa11ce86856b148f784 |
In [57]: from sklearn.grid_search import RandomizedSearchCV
In [58]: from h2o.cross_validation import H2OKFold
In [59]: from h2o.model.regression import h2o_r2_score
In [60]: from sklearn.metrics.scorer import make_scorer
In [61]: from sklearn.metrics.scorer import make_scorer
# Parameters to test
In [62]: params ... | jangorecki/h2o-3 | h2o-docs/src/booklets/v2_2015/source/python/python_randomized_grid_search.py | Python | apache-2.0 | 5,102 | [
"Gaussian"
] | 8701bb33f50bbe2e99a57a59ce50cc3c48d2b5bef439c79a11447967f2debd05 |
# encoding: utf8
import re
from random import *
from collections import Counter
from pprint import pprint
# http://blog.echen.me/2011/08/22/introduction-to-latent-dirichlet-allocation/
# -> https://tedunderwood.com/2012/04/07/topic-modeling-made-just-simple-enough/
documents = [
# space
"Watching a bubble float effor... | mobarski/sandbox | topic/lda/lda3.py | Python | mit | 3,747 | [
"COLUMBUS"
] | 275763bc4472d6061acec0eff83fade39b90a0c4545777e53b64e7f20c9e2dea |
from BrowserManager import Browser
from DataAggregator import DataAggregator, LevelDBAggregator
from SocketInterface import clientsocket
from Errors import CommandExecutionError
from utilities.platform_utils import get_version, get_configuration_string
import CommandSequence
import MPLogger
from multiprocess import Pr... | tommybananas/OpenWPM | automation/TaskManager.py | Python | gpl-3.0 | 25,684 | [
"VisIt"
] | 60b5942b08b0132c91283417bdcd71a41c6661ceac3ef42dd289e6fa6ce6f6d0 |
#!/usr/bin/env python
# fig 3b preprocess files for allele sensitive ATAC analysis
# description: code to "unfix" bams (ie in the appropriate situations,
# remove the 1bp position shift to realign base pairs and position)
# this is necessary to correctly pull the base pair from the correct position
# data: /mnt/lab_da... | vervacity/ggr-project | figs/fig_2.modelling/fig_3-b.0.preprocess.py | Python | mit | 6,429 | [
"pysam"
] | ff5150a9b850bd837bb9d35c6ad79386e13c95391be03993a444f3707ab41dc1 |
from __future__ import print_function, division
import copy
from collections import defaultdict
from sympy.core.containers import Dict
from sympy.core.expr import Expr
from sympy.core.compatibility import is_sequence, as_int, range
from sympy.core.logic import fuzzy_and
from sympy.core.singleton import S
from sympy.f... | antepsis/anteplahmacun | sympy/matrices/sparse.py | Python | bsd-3-clause | 45,694 | [
"DIRAC"
] | bb946c554f14d655a61eaeb6b0f607b7998796c259e817bc644f4fe99f99325c |
import pkg_resources
# can't find it in the frozen library.zip...
# pkg_resources.require("pysam>=0.8.1")
import pysam
NEEDED_VERSION = "0.15.4"
assert pkg_resources.parse_version(pysam.version.__version__) >= pkg_resources.parse_version(NEEDED_VERSION), "PySam version at least %s required"%(NEEDED_VERSION,)
| HorvathLab/NGS | common/src/pysamimport.py | Python | mit | 310 | [
"pysam"
] | 1dd22a2c1ca56bb9a1ddfeb8cbc8007079770d9140d693e512293305d1e71005 |
from sdssgaussfitter import gaussfit
import numpy as np
from util import utils
import matplotlib.pyplot as plt
import sys
### this is used to view a single frame from display stack or psffit npz. Into the command type "python sdssview_frameBlue.py 3" to view image number 3.
def aperture(startpx,startpy,radius=3):
... | bmazin/ARCONS-pipeline | examples/Pal2012-sdss/sdssview_frameBlue.py | Python | gpl-2.0 | 1,595 | [
"Gaussian"
] | bd571c08d0a8705dafc07605f6afb5084147f3d179bd4c29ca4534117477708d |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, John D. Cho... | kyleabeauchamp/mdtraj | mdtraj/formats/mol2.py | Python | lgpl-2.1 | 7,419 | [
"MDTraj",
"OpenMM"
] | 934d7a3238b464d443855d4a072f54b395fb80928aeee5e607f5bd581468cad7 |
import logging
import re
import os
import signal
from avocado.utils import path
from avocado.utils import process
from avocado.utils import linux_modules
from .compat_52lts import results_stdout_52lts
from .versionable_class import VersionableClass, Manager, factory
from . import utils_misc
# Register to class mana... | lmr/avocado-vt | virttest/openvswitch.py | Python | gpl-2.0 | 17,049 | [
"ASE"
] | 18fca03a35e4af6bfabd154da2b244ea3f3769a159491bb4ea2abe46cde89b71 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/mcscf/umc1step.py | Python | apache-2.0 | 38,605 | [
"PySCF"
] | 55fd2be609245c8cf472f091ca9b20f276328d811f82ddc056f178d4769ba0f6 |
# vim:set et sts=4 sw=4:
#
# ibus-xkb - IBus XKB
#
# Copyright(c) 2012 Takao Fujiwara <takao.fujiwara1@gmail.com>
# Copyright(c) 2007-2010 Peng Huang <shawn.p.huang@gmail.com>
# Copyright(c) 2007-2012 Red Hat, Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU ... | fujiwarat/ibus-xkb | ui/gtk2/handle.py | Python | lgpl-2.1 | 4,191 | [
"FLEUR"
] | 416d5f8a7bc4f812d9f64cc15f1ce9e6ac2b2b6ec82d458cd2ef3f4ec7cb7c8e |
"""
This file is part of pyS5p
https://github.com/rmvanhees/pys5p.git
The class LV2io provides read access to S5p Tropomi S5P_OFFL_L2 products
Copyright (c) 2018-2021 SRON - Netherlands Institute for Space Research
All Rights Reserved
License: BSD-3-Clause
"""
from datetime import datetime, timedelta
from pathl... | rmvanhees/pys5p | src/pys5p/lv2_io.py | Python | bsd-3-clause | 19,043 | [
"NetCDF"
] | 1ca07f930d576e2455fd06a2ab07ff156d566afe548e197768363b6651887167 |
import collections
import copy
from ..core import Dict, Expr, Integer
from ..core.compatibility import as_int, is_sequence
from ..core.logic import fuzzy_and
from ..functions import sqrt
from ..logic import true
from ..utilities.iterables import uniq
from .matrices import MatrixBase, ShapeError, a2idx
class SparseMa... | skirpichev/omg | diofant/matrices/sparse.py | Python | bsd-3-clause | 42,378 | [
"DIRAC"
] | 08cc63327c66c680f726dbe38d19c6056fbb3e097f7798b316845ad8449ed0eb |
#!/usr/bin/env python
"""
galaxy-fuse.py will mount Galaxy datasets for direct read access using FUSE.
To do this you will need your Galaxy API key, found by logging into Galaxy and
selecting the menu option User -> API Keys. You can mount your Galaxy datasets
using a command like
python galaxy-fuse.py <api-key>... | gvlproject/gvl_commandline_utilities | roles/gvl.commandline-utilities/files/galaxy-fuse.py | Python | mit | 12,065 | [
"Galaxy"
] | 5dd8ed2cb5b15b96fb089d2b3794d4b276e5924f5b8eca51df496dca6922757d |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | DSLituiev/scikit-learn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 32,070 | [
"Gaussian"
] | 48753ca6dabfda6881f2a2c161eb31d5f419d7676c09d1c55efca0f2a5fba825 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkRendererSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | chrisidefix/devide | modules/vtk_basic/vtkRendererSource.py | Python | bsd-3-clause | 476 | [
"VTK"
] | 33a35a70e80bdff79256d88095758b0cb8d78f1e5a7989f8e42dbbf329cad0c5 |
# coding: utf-8
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import os.path
import pathlib
import yam... | azaghal/ansible | hacking/build_library/build_ansible/command_plugins/collection_meta.py | Python | gpl-3.0 | 3,270 | [
"Galaxy"
] | 86c6bb67d451097490beaeecc9af80d7dcb10b090132e33f71dd42f2a7888905 |
#
# This file is part of Plinth.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distribute... | freedomboxtwh/Plinth | plinth/modules/owncloud/__init__.py | Python | agpl-3.0 | 3,888 | [
"VisIt"
] | bcd65f8ce33ec9e67274069bdbf1f1276ddf47bbc5763ade30e2765fbd1859c2 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | liuwenf/moose | python/MooseDocs/common/__init__.py | Python | lgpl-2.1 | 1,905 | [
"MOOSE"
] | 01b84146cbeb7601d47401e98550b70b9f4f8b5e6898bdc9f8f1e936a2cf4461 |
'''
Created on Jun 2, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3... | genome-vendor/chimerascan | chimerascan/lib/sam.py | Python | gpl-3.0 | 6,694 | [
"pysam"
] | 3b80738b8ba3a505b9447bd6a1e52e50861ce7328ffc33e2b24717a7b6705898 |
#!/usr/bin/env python
# B a r a K u d a
#
# Generate global plots related to wind
# wind stress, its curl, wind speed, etc
# Use climatology fields built with 'build_clim.sh'
#
# L. Brodeau, 2017
import sys
from os import path
import numpy as nmp
from netCDF4 import Dataset
import barakuda_to... | brodeau/barakuda | python/exec/wind.py | Python | gpl-2.0 | 8,877 | [
"ORCA"
] | 4e6b6f97e398ebc790873c50b5901ab0eb311e50b5e2d8812f3764fb2198019a |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later ver... | spring01/libPSI | lib/python/pubchem.py | Python | gpl-2.0 | 7,182 | [
"Psi4"
] | 7eff2ccb48476380246c3b8b783ec70c6d9407adf191d94f2bab15d7ffb0a5fb |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# from https://github.com/jameslz/benchmark
import sys
if len(sys.argv) != 4:
print "\nUsage: %s <alignment> <evalue> <bit_score>\n" % sys.argv[0]
sys.exit(1)
blast = sys.argv[1]
max_evalue = float(sys.argv[2])
min_bit_score = float(sys.argv[3])
with o... | shenwei356/bio_scripts | blast/blast_best_hit_outfmt6.py | Python | mit | 726 | [
"BLAST"
] | 083cda7c372e1726721298c377ac465bcb353f9cd73a83a21578b422bed02d80 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | mol_dqn/experimental/multi_obj_gen.py | Python | apache-2.0 | 4,724 | [
"RDKit"
] | dd19a4c3ef79a052027ebdaa6eda8dff8026e2755a1f7cbb5521ca31f35843a6 |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.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 ... | jimi-c/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 33,077 | [
"Galaxy"
] | 1e6693d707e0efbd25fccfac63ec81ec8727f3d394180c50fd48601d083db1e1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#################################################################################
# LAYMAN ACTIONS
#################################################################################
# File: cli.py
#
# Handles layman actions via the command line interface.
#
# C... | jmesmon/layman | layman/cli.py | Python | gpl-2.0 | 11,815 | [
"Brian"
] | 6b88d821284e89415f22eb205d1316912887d29df7cd58ac6c0db54ab88b9a07 |
# ---
# jupyter:
# jupytext:
# formats: ipynb,.pct.py:percent
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.3.3
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
# %% [markdown]
... | GPflow/GPflow | doc/source/notebooks/advanced/multiclass_classification.pct.py | Python | apache-2.0 | 4,736 | [
"Gaussian"
] | 1529f08db013fbfba6a1b78931334ece4cb5abc233b039a6698792b95add76ab |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from loguru import logger
# import funkcí z jiného adresáře
import os.path
import os.path as op
# import copy
import unittest
import pytest
# sample_data_path = os.path.dirname(os.path.abspath(__file__))
# sample_data_path
# sys.path.append(os.path.join(path_to_scrip... | mjirik/io3d | tests/qt_test.py | Python | mit | 5,887 | [
"VTK"
] | 86d4a2472a3956ac9b685f1ed8307406eb7bd2099ddc9dd36fd71904062baef7 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#
# Grimoire general utils
#
# Copyright (C) 2015 Bitergia
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at ... | sanacl/GrimoireELK | grimoire/utils.py | Python | gpl-3.0 | 11,497 | [
"Elk"
] | 031fe87597416ed420607032a9fc90cd9fe11ce65814799c93ee031a5e82e6e0 |
#!/usr/bin/env python
# encoding: utf-8
from gi.repository import Moose
from gi.repository import GLib
import sys
import logging
LOGGER = logging.getLogger('zeroconf')
def print_server(browser):
LOGGER.info('-- SERVER LIST --')
for server in browser:
for attr, value in server:
LOGGER.in... | studentkittens/snobaer | snobaer/zeroconf.py | Python | lgpl-3.0 | 1,748 | [
"MOOSE"
] | da62313ea5ac84e21c34bf8e676ae9d91a7d1bc72c938f00e088fadc585b7ed1 |
from django.db import models
from django.db.models import Q
from django.utils.dateformat import format as django_format
from stages.models import Corporation, CorpContact, Teacher
GENDER_CHOICES = (
('M', 'Masculin'),
('F', 'Féminin'),
('I', 'Inconnu')
)
SECTION_CHOICES = (
('ASA', 'Aide en soin et a... | epcoullery/epcstages | candidats/models.py | Python | agpl-3.0 | 8,114 | [
"ASE"
] | 36fb4928881e8dff022b5f7ee0b6de9b800ca686e00f048db7b9a350c63c2312 |
# ---------------- User Configuration Settings for speed-track.py ---------------------------------
# Set display and log settings
verbose = True # display basic status information on console
display_fps = False # show average frame count every 100 loops
log_data_to_file = True # save comma delimited file... | xadnem/motion-track | speed-track/speed_settings.py | Python | mit | 2,582 | [
"Gaussian"
] | 5fe32247b2631ff7b78ffe04232e22c78457a592b14bbd6787cd94c3940552cf |
# $HeadURL: $
''' TransferCommand module
'''
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
from DIRAC.... | vmendez/DIRAC | ResourceStatusSystem/Command/TransferCommand.py | Python | gpl-3.0 | 8,006 | [
"DIRAC"
] | 3099ad87e139dddc585663562ea30e1ec5a468147078a60f7b39bbfc72e0baf2 |
__all__ = [
'WriteRectilinearGridToUBC',
'WriteImageDataToUBC',
]
__displayname__ = 'Writers'
import os
import numpy as np
from .. import interface
from ..base import WriterBase
class ubcTensorMeshWriterBase(WriterBase):
"""A base class to assist in writing data bjects to the UBC Tensor Mesh
forma... | banesullivan/ParaViewGeophysics | PVGeo/ubc/write.py | Python | bsd-3-clause | 5,502 | [
"VTK"
] | 1ff6756b9123da13044db9002ca9eb5bf8b4b3b7e34bcadee7cce426dc3f5146 |
# -*- coding: utf-8 -*-
#
# test_import_lobbyists.py - Test lobbyist importing.
# Copyright (C) 2008 by Drew Hess <dhess@bothan.net>
#
# 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 vers... | dhess/lobbyists | lobbyists/tests/test_import_lobbyists.py | Python | gpl-3.0 | 14,553 | [
"Brian"
] | 80dfb154d0797ccb8f176cd9e512bb173f34abd177660225b8fc88bd2db943c2 |
import ast
from collections import deque
import sys
import pytest
class FuncCallVisitor(ast.NodeVisitor):
def __init__(self):
self._name = deque()
@property
def name(self):
return '.'.join(self._name)
@name.deleter
def name(self):
self._name.clear()
def visit_Name(sel... | frc1418/2017-robot | tests/test_print.py | Python | mit | 1,132 | [
"VisIt"
] | ab126fd9d416fe024d2179677b48d718e79cbbed940e784da39b5587634246c3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Wrapper for netCDF readers."""
from __future__ import unicode_literals, division, print_function
import os.path
import warnings
import numpy as np
from collections import OrderedDict
from monty.dev import r... | setten/pymatgen | pymatgen/io/abinit/netcdf.py | Python | mit | 17,296 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | 178c4875be43e0eaf31cdccf98325b99b9e2d708cf24ee4c6a0fc5e76463b95f |
# -*- coding: utf-8 -*-
"""
Functions related to fetching and manipulating skeletons.
"""
from io import StringIO
from itertools import combinations
from collections import namedtuple
import numpy as np
import pandas as pd
import networkx as nx
from scipy.spatial import cKDTree
from .client import inject_client
@in... | connectome-neuprint/neuprint-python | neuprint/skeleton.py | Python | bsd-3-clause | 13,578 | [
"NEURON"
] | 231095b57c39446493ac2aa531c827757c128c9f13537c5da80b779fbdf8c2bd |
import random, unittest, cPickle, collections
from copy import deepcopy, copy
from pylpsolve import LP, LPException
from numpy import array as ar, ones, eye, float64, uint, int, ones
class TestErrorCatch(unittest.TestCase):
# test constraint adding by (wrong typed index array, value array)
def test01_constrain... | hoytak/pylpsolve | tests/test_errorcatch.py | Python | lgpl-2.1 | 33,500 | [
"ADF"
] | 3a4797cb98f28ecddbe2e502deb160d27c088aaeae632c1ea3c0a517e3a2d35b |
from django.contrib.contenttypes import generic
from django.contrib.contenttypes.models import ContentType
from django.db import models
from django.utils.translation import ugettext_lazy as _
class Visit(models.Model):
when = models.DateTimeField(_('when'), auto_now_add=True)
# Who visited
visitor_c... | SpreadBand/django-visitors | visitors/models.py | Python | gpl-3.0 | 911 | [
"VisIt"
] | a830e2578f3937638160ce2debdb79ae1a8621037103a409f8a9f23d6c809edc |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/images/forms/addgroupdialog.py | Python | gpl-2.0 | 3,966 | [
"Brian"
] | aca30d70477a822ef6777493c796f4aa18b8448efbd95d5939adbd4f85389155 |
from Sire.IO import *
from Sire.MM import *
from Sire.Maths import *
from Sire.Mol import *
(mols,space) = Amber().readCrdTop("../io/waterbox.crd", "../io/waterbox.top")
cljboxes = CLJBoxes()
idxs = []
natoms = 0
for i in range(0,mols.nMolecules()):
idxs.append( cljboxes.add( CLJAtoms(mols[MolIdx(i)]) ) )
... | chryswoods/SireTests | unittests/SireMM/test_cljdelta.py | Python | gpl-2.0 | 3,003 | [
"Amber"
] | 5fb98dd07d875549458e96e62fc7bef6f4d23963d1acc753fdb83f1b83e351d9 |
from django.utils import timezone
from dateutil.relativedelta import relativedelta
from edc_constants.constants import SCREENED
from edc_registration.models import RegisteredSubject
from edc_identifier.models import SubjectIdentifier
from edc_constants.constants import FAILED_ELIGIBILITY, OFF_STUDY, SCHEDULED, POS, YES... | botswana-harvard/tshilo-dikotla | td_maternal/tests/test_maternal_lab_del.py | Python | gpl-2.0 | 6,380 | [
"VisIt"
] | 5eb1f23d4d670280b371b28695a2a78fe2f52b6b9383a55b370c56a949f4f6a2 |
import numpy as np
from gpaw.blacs import BlacsGrid, parallelprint
from gpaw.mpi import world, rank, size
from gpaw.utilities.lapack import diagonalize
from gpaw.utilities.scalapack import scalapack_diagonalize_dc
from gpaw.blacs import Redistributor
def scal_diagonalize(A, nodes='master'):
# Diagonalize matrix A... | robwarm/gpaw-symm | gpaw/test/parallel/scalapack_diag.py | Python | gpl-3.0 | 2,279 | [
"GPAW"
] | d83a8dee63824214f4b1454a12091e85a82ae05a92ae7564be6c89f945c630b8 |
import numpy as np
import orca
import pandas as pd
from activitysim import activitysim as asim
from activitysim.util import reindex
@orca.table(cache=True)
def households(set_random_seed, store, settings):
if "households_sample_size" in settings:
return asim.random_rows(store["households"],
... | bhargavasana/activitysim | activitysim/defaults/tables/households.py | Python | agpl-3.0 | 4,771 | [
"ORCA"
] | 1e1e35ae7500e98f47601cfcf96450f1c9cd024af4e68a133c528a1c7a81f0ba |
import sys
import gzip
import threading
from glob import glob
from io import BytesIO
from .. import backends, conventions
from .common import ArrayWriter
from ..core.combine import auto_combine
from ..core.utils import close_on_error, is_remote_uri
from ..core.pycompat import basestring, OrderedDict, range
def _get_... | markelg/xray | xray/backends/api.py | Python | apache-2.0 | 15,889 | [
"NetCDF"
] | 931585b6e4af3d6a8ef9983e224d9a96e908f90d8871583a21307fa3ca80a2ed |
#!/usr/bin/python
"""
Copyright 2010 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/getMemberList.py | Python | gpl-3.0 | 1,927 | [
"Galaxy"
] | 2a8cbb60c4b59a271c8091a6b2bfdb4fa79afab16eaf50c6070bccf8317e9453 |
"""
Routines for running a Columbus computation.
"""
import sys
import os
import shutil
import subprocess
import numpy as np
import nomad.math.constants as constants
import nomad.core.glbl as glbl
import nomad.core.atom_lib as atom_lib
import nomad.core.trajectory as trajectory
import nomad.core.surface as surface
impo... | mschuurman/FMSpy | nomad/interfaces/columbus.py | Python | lgpl-3.0 | 44,712 | [
"COLUMBUS",
"Dalton"
] | fa6b931e252c7882334e3fd778676a88fc06dbe43cbf8ba7f2f4527cf1e532ed |
# find the people from the same town
# use python 3.5 as default
"""
How to find the people from the same home town?
Xiao Ming is a new colleage student, he wants to know who is from the
same town as him. But many people just tell him that he or she is from the
same town with another student.
... | smileboywtu/Code-Interview | find-people-from-same-town.py | Python | gpl-2.0 | 3,443 | [
"VisIt"
] | f751c1c70f4aa43216b00a1ebbd14d86db04d2cf1570983359dcf0f9919db2d6 |
"""Tests for the ArraySource data source for MayaVi.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from StringIO import StringIO
import copy
import numpy
# Enthought library imports.
from t... | liulion/mayavi | integrationtests/mayavi/test_array_source.py | Python | bsd-3-clause | 6,964 | [
"Mayavi"
] | a2dabc0d0e1e1c924c95aca9da7c9971910c7c0bc607c93fbe9e0c0d001c19a6 |
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