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"""Handle extraction of final files from processing pipelines into storage.
"""
import datetime
import os
import six
import toolz as tz
from bcbio import log, utils
from bcbio.upload import shared, filesystem, galaxy, s3, irods
from bcbio.pipeline import run_info
from bcbio.variation import vcfutils
import bcbio.pipe... | vladsaveliev/bcbio-nextgen | bcbio/upload/__init__.py | Python | mit | 38,853 | [
"Galaxy"
] | 8b7d097679a1fa36f201526338cc22e79890d1dcec64757ae3a7d337460dc0fb |
# 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... | pkreissl/espresso | samples/rigid_body.py | Python | gpl-3.0 | 4,220 | [
"ESPResSo"
] | 9d3fb8dabe732042165f4e9ab7bb44eb958f3c38eea385588a7088d5ff3499af |
##% Demo 5: How to use plotting functions
#
# This demo will demostrate the options for plotting projection and images
# on TIGRE. The functions have been in previous demos, but in here an
# exaustive explanation and usage of them is given.
#
# --------------------------------------------------------------------------
... | CERN/TIGRE | Python/demos/d05_plottingFunctions.py | Python | bsd-3-clause | 4,161 | [
"Gaussian"
] | 8a3342b40549d9e01e5a15cbbb8aeb843323d847751f6b96f338905542b50f11 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | caio2k/RIDE | src/robotide/lib/robot/model/modifier.py | Python | apache-2.0 | 2,055 | [
"VisIt"
] | 0a6b4e295cf83fd8a3da3c7e74e6b64c7eb506e4893b583e633d1c405c38b290 |
# coding=utf-8
from splinter import Browser
import unittest
from google.appengine.ext import testbed
browser = Browser()
class StaticPagesTest(unittest.TestCase):
def setUp(self):
global browser
self.tb = testbed.Testbed()
self.tb.activate()
self.tb.init_memcache_stub()
def t... | iandouglas/flask-gae-skeleton | tests/integration/static/test_static_pages.py | Python | mit | 929 | [
"VisIt"
] | 43188aa6ebcfd4367eb9d296428d3d5407d7efb2f8842d40e1ba509b5056ec06 |
import argparse
import sys
import datetime
import os
from collections import OrderedDict
import json
import base64
import logging
from functools import partial
import pybedtools
import pysam
import vcf
import fasta_utils
mydir = os.path.dirname(os.path.realpath(__file__))
vcf_template = os.path.join(mydir, "resources... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/MetaSV-0.5-py2.7.egg/metasv/generate_final_vcf.py | Python | apache-2.0 | 25,501 | [
"pysam"
] | d237351bfdc47351b2162283edc54384218de21d0cfbab0f1a3c01953fe6c7bf |
import pytest
pytest_plugins = [
'clincoded.tests.features.browsersteps',
'clincoded.tests.features.customsteps',
]
@pytest.fixture(scope='session')
def app_settings(server_host_port, elasticsearch_server, postgresql_server):
from .. import test_indexing
return test_indexing.app_settings(server_host_... | ClinGen/clincoded | src/clincoded/tests/features/conftest.py | Python | mit | 3,148 | [
"VisIt"
] | ec544399eef062b2b350f010f10dc1e9c18b5c60d8d91e0b77203803b269403b |
# $HeadURL$
""" TopErrorMessagesReporter produces a list with the most common errors
injected in the SystemLoggingDB and sends a notification to a mailing
list and specific users.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.AgentMo... | calancha/DIRAC | FrameworkSystem/Agent/TopErrorMessagesReporter.py | Python | gpl-3.0 | 5,457 | [
"DIRAC"
] | 75b5dc572d105c53156dd655aad2dc313cdd41145cf9d2c092a0dcfab47a92c3 |
# coding=utf-8
# Copyright 2019 The Interval Bound Propagation 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 ... | deepmind/interval-bound-propagation | interval_bound_propagation/src/layer_utils.py | Python | apache-2.0 | 10,655 | [
"NEURON"
] | 21cc9e289503a4ce0646b50f61fc7872d2b8c59418eedd27cd9bd1f5af79a26e |
# monkey-batch the matplotlibrc for peri:
from peri.viz import base
from builtins import range
import matplotlib as mpl
import matplotlib.pylab as pl
from matplotlib import ticker
from matplotlib.gridspec import GridSpec
from matplotlib.offsetbox import AnchoredText
from mpl_toolkits.axes_grid1.inset_locator import ... | peri-source/peri | peri/viz/plots.py | Python | mit | 40,194 | [
"Gaussian"
] | 8fd2d218df19709d4a3a560e36b332e64ae2fb8652ba77faddef98a5cfe7a432 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# PMDA
# Copyright (c) 2019 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher ve... | MDAnalysis/pmda | pmda/hbond_analysis.py | Python | gpl-2.0 | 22,063 | [
"MDAnalysis"
] | e3047303e02cbf0fbd2c6e5ae157e3b35ada32675c496eb9618a19a9dec6438a |
import sys
import antlr
class Visitor(antlr.ASTVisitor):
def __init__(self,*args):
super(Visitor,self).__init__(*args)
self.level = 0
if not args:
self.cout = sys.stdout
return
if isinstance(args[0],file):
self.cout = args[0]
return
assert 0
... | bamboo/boo | lib/antlr-2.7.5/examples/python/IDL/idl.py | Python | bsd-3-clause | 1,732 | [
"VisIt"
] | 200cf64fe0c5ee832060d1003f032dafce5fcad11f432d2cdb8b03cee7682b77 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import rdkit
from rdkit.Chem import AllChem
from rdkit import DataStructs
__license__ = "X11"
METADATA = {
"id": "method_rdkit_fcfc4_tanimoto",
"representation": "fcfc4",
"similarity": "tanimoto"
}
def _compute_fingerprint(molecule):
return AllChem.GetM... | skodapetr/lbvs-environment | methods/fcfc/fcfc4_tanimoto.py | Python | mit | 1,383 | [
"RDKit"
] | 8af0e7fb6582978593ccf788c4d236bb7b495f313eff1e707e1285c90b369407 |
#import CV libraries
import numpy
import cv2
img=cv2.imread("/home/udayan/Downloads/Lena.png", 0) #read image, 0=read as grayscale, -1=read as color
#blurring
blur1=cv2.blur(img, (5, 5)) #averaging using a 5x5 kernel
blur2=cv2.GaussianBlur(img, (5, 5), 0) #Gaussian blurring using 5x5 kernel; effective again... | UdayanSinha/Code_Blocks | OpenCV/cv_blurring_sharpening.py | Python | mit | 1,081 | [
"Gaussian"
] | ee46405dedac8dfd4409e20f215722269be0e167fea789ed62d0fab4839fe0d2 |
import unittest
import numpy
import chainer
from chainer.backends import cuda
from chainer import functions
from chainer import gradient_check
from chainer import testing
from chainer.testing import attr
@testing.parameterize(*testing.product({
'shape': [(3, 2), ()],
}))
class TestGaussian(unittest.TestCase):
... | anaruse/chainer | tests/chainer_tests/functions_tests/noise_tests/test_gaussian.py | Python | mit | 4,241 | [
"Gaussian"
] | c7af56ed4c82477339f337621298a868091bf3c3dec224b1cebe2c9d9fc0fceb |
# Copyright 1999-2000 by Jeffrey Chang. All rights reserved.
# Copyright 2008 by Michiel de Hoon. 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.
"""Provides code to access NCB... | bryback/quickseq | genescript/Bio/Entrez/__init__.py | Python | mit | 17,259 | [
"Biopython"
] | 3a5603392247bcdb17eaa3deafc0aa8d9376dd589cb92e7f73c5b847c4d52361 |
import logging
from logging.config import fileConfig
import os
import re
import sys
import click
import bripipetools
config_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)),
'config'
)
fileConfig(os.path.join(config_path, 'logging_config.ini'),
disable_existing_loggers=False)
logg... | jaeddy/bripipetools | bripipetools/__main__.py | Python | mit | 22,056 | [
"Galaxy"
] | 191aeb98250737bf1eb78573716852bd7829d6e0058e983fca186c9c931675c1 |
# Copyright (c) 2013-2015 Unidata.
# Distributed under the terms of the MIT License.
# SPDX-License-Identifier: MIT
from datetime import datetime
from contextlib import contextmanager
import numpy as np
import siphon.testing
from siphon.ncss import NCSS, NCSSQuery, ResponseRegistry
from nose.tools import eq_
recor... | MoonRaker/siphon | siphon/tests/test_ncss.py | Python | mit | 5,448 | [
"NetCDF"
] | 2525824cfa09c4ddff17e8ddc737a5157afcd0f2e64e24ee10940583feb79e2d |
from functools import wraps
from typing import Any, Callable, Dict, List, Optional, Set, Tuple
from django.utils.timezone import now as timezone_now
from zerver.lib.actions import do_add_reaction, do_add_realm_filter, update_user_presence
from zerver.lib.events import do_events_register
from zerver.lib.test_classes i... | synicalsyntax/zulip | zerver/openapi/curl_param_value_generators.py | Python | apache-2.0 | 8,178 | [
"Octopus"
] | ac2fd821069ee77c4da532cecdf1152a7b281e78e884a50d049d36dcd18ef160 |
# Import the old tracking id from the RCM file for period 19660101-19701231,
# as it is the first used file to create historical indices:
# (e.g. tasmin_EUR-44_IPSL-IPSL-CM5A-MR_historical_r1i1p1_SMHI-RCA4_v1_day_19660101-19701231.nc)
#track_GCM_indice=$(
import netCDF4
from netCDF4 import Dataset
import ctypes
im... | igryski/Indices_icclim_ClipC | src/get_put_invar_tracking_id_python_TMAX.py | Python | gpl-3.0 | 11,728 | [
"NetCDF"
] | fcfd61d179eb2937157f7d1d137735a79e581dd79be1e4bb91f0c0741df6cd62 |
#!/usr/bin/python
import numpy as np
import os
import sys
import math
import matplotlib
matplotlib.use('Pdf')
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.font_manager as fm
## 6-1-15
## Simple code to e... | plazas/wfirst-detectors-vnl | code/bias_nonlinearity_vs_beta.py | Python | mit | 22,964 | [
"Gaussian"
] | c062ef679bdcdadbfb1eac6a10c608422119f00a6a6de842b0159714c399b776 |
# -*- coding: utf-8 -*-
# Generated by Django 1.10 on 2016-11-09 07:34
from __future__ import unicode_literals
import datetime
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('accounts', '0016_auto_20161012_1826'),
]
operations = [
migra... | fenglb/mysite | accounts/migrations/0017_auto_20161109_1534.py | Python | cc0-1.0 | 1,029 | [
"VisIt"
] | b369585a896b0e90b18c4d71f12cb479c618903298faf015d20243a10275a8cb |
# -*- coding: utf-8 -*-
"""
Created on Sun Jul 19 11:42:52 2015
Test Processing Chain with Synthetic Data
@author: ckirst
"""
##############################################################################
# Test Resampling / Make Reference
###########################################################################... | ChristophKirst/ClearMap | ClearMap/Test/test_chain_synthetic.py | Python | gpl-3.0 | 19,680 | [
"Gaussian",
"VTK"
] | 3fb45bcdf22f20181dd14403504316911738e115366cc1065906d5692b22332e |
import tensorflow as tf
import numpy as np
class ReceptiveField2D:
""" Single layer of neurons working as receptie fields (each neuron is connected only to a small part of input)
"""
def __init__(self, field_height, field_width, in_channels, out_channels, strides=None, padding='SAME',
fl... | KarolAntczak/DeepModel | deepmodel/ReceptiveField2D.py | Python | apache-2.0 | 1,866 | [
"NEURON"
] | d4cc94ab8041af8cdaf2b8d15fb769b047937a0e000e3785c45309ac329bb0cd |
#!/usr/bin/env python
import click
import os
import requests
import sys
import leagueids
import teamnames
from soccer.exceptions import IncorrectParametersException
from writers import get_writer
BASE_URL = 'http://api.football-data.org/alpha/'
LIVE_URL = 'http://soccer-cli.appspot.com/'
LEAGUE_IDS = leagueids.LEA... | ueg1990/soccer-cli | soccer/main.py | Python | mit | 6,269 | [
"VisIt"
] | 6455f48e6f95a07e6e7dec1b0dccd9a82d66fc8df25f6fc11771b04eaceb949f |
import logging
import os
from igraph import Graph, plot
from pynsett.auxiliary.rule_utils import repeat_db_rules_n_times
from pynsett.nl import SpacyParser as Parser
from parvusdb import GraphDatabase, create_graph_from_string, convert_graph_to_string
_path = os.path.dirname(__file__)
_logger = logging.getLogger(__f... | fractalego/pynsett | pynsett/drt/drs.py | Python | mit | 3,605 | [
"VisIt"
] | b83c1cdd9148a64f223d48bb93ec6a8564c50c5dc195b2acbf569490687bb60f |
#!/usr/bin/env python
import argparse
import sys
import subprocess
import os
import glob
import shutil
import fileinput
# This script blasts the entries of a fasta file,
# provided they're over the length threshold
# It also concatenates the results and does some minor filtering
humantaxid = '9606'
# --------------... | RabadanLab/Pandora | scripts/blast_wrapper.py | Python | mit | 11,197 | [
"BLAST"
] | bed9314276477e0160c16dd676a293d3ad50f538688dace8ef3bd0f8d414a212 |
#!/usr/bin/env python2.5
#
# Copyright 2008 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | robertobarreda/django-safe-browsing | safebrowsing/vendors/google/client.py | Python | bsd-3-clause | 14,701 | [
"VisIt"
] | 74d1310f79046f0cb05dcd2fe0cdca4bb04e22a9b6704f350aa2a91f0041e861 |
import os, sys, getopt
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
except ImportError:
raise ImportError("Cannot load either PyQt or PySide")
import vtk
import time
... | amburan/moose | gui/vtk/ExodusResult.py | Python | lgpl-2.1 | 5,503 | [
"VTK"
] | 1bf4c670daa8a83e4ccd84b748199ae4e233383a4856ae351ba7a35815c4f598 |
from django.core.urlresolvers import resolve
from nose.tools import assert_raises
from django.conf.urls import url
from django.conf.urls import include
from nose.tools import eq_
from nose.tools import ok_
from rest_framework.reverse import reverse
from rest_framework.routers import SimpleRouter
from drf_nested_resour... | pombredanne/drf-nested-resources | tests/test_routers.py | Python | bsd-3-clause | 17,072 | [
"VisIt"
] | 49bce5a1a746459e17297a5e4e78c19816ec1ccba87bd31de11021159927fb5f |
#!/usr/bin/env python
# coding: utf-8
"""
Implementation for `pmg potcar` CLI.
"""
import os
from pymatgen.io.vasp import Potcar
def proc_dir(dirname, procfilefunction):
"""
Process a directory.
Args:
dirname (str): Directory name.
procfilefunction (callable): Callable to execute on d... | mbkumar/pymatgen | pymatgen/cli/pmg_potcar.py | Python | mit | 1,616 | [
"VASP",
"pymatgen"
] | caf95d2f8569997729fee555711c14bf6f87575cda4405fa008c95a59271d309 |
#!/usr/bin/python
bowtie_build = "/mnt/home/grcuser/GRC_projects/GRC_miseq-quality_UI/Phi-X"
fasta_file = "/mnt/home/grcuser/GRC_projects/GRC_miseq-quality_UI/Phi-X.fa"
def directory_crawler(pathname):
import sys
import os
lst_R1_R2= []
i = 0
if pathname[-1] != '/':
pathname += '/'
if os.path.isdir(pathn... | ibest/APER | scripts/dir_crawler.py | Python | apache-2.0 | 3,342 | [
"BWA"
] | 800b8d8017919df6b840313785b4943809bef9b9ce4b2861b119d06f9deaac6b |
# Licensed to the .NET Foundation under one or more agreements.
# The .NET Foundation licenses this file to you under the MIT license.
# See the LICENSE file in the project root for more information.
import sys
import os
if __name__ == '__main__':
#Dynamically append current script path to PYTHONPATH
sys.path... | schellap/corert | src/Common/src/Internal/Metadata/NativeFormat/Script/CsWriterGen2.py | Python | mit | 18,268 | [
"VisIt"
] | c60ddd6bfbfeeba699fc6d635b7f3029d9c440ffa7409dfeee49206ea39a32f1 |
# -*- coding:utf-8; python-indent:2; indent-tabs-mode:nil -*-
# Copyright 2013 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/... | pombredanne/pytype | pytype/pytd/parse/parser.py | Python | apache-2.0 | 28,627 | [
"VisIt"
] | 3a5b62a564277970856a2095fdb32a1a47921811c1e5ec41d9c09837c9cbc2e0 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | casawa/mdtraj | mdtraj/tests/test_trr.py | Python | lgpl-2.1 | 5,603 | [
"MDTraj"
] | 729c247ac5fcd352a7f60cac08b6d66490f6eaf031edbc10bf79405c9ab1dcf9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative sampling [1]_ [2]_.
The train... | largelymfs/paragraph2vec | gensim/models/word2vec.py | Python | gpl-3.0 | 42,762 | [
"VisIt"
] | c0571ee66a11197b3f8576d8272a7ed226584f684b1d0f906151947b911bb44d |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Intel-Corporation/tensorflow | tensorflow/python/ops/image_ops_test.py | Python | apache-2.0 | 245,283 | [
"Gaussian"
] | 2985b8defd3d89042f4a69310f17e7b2a47ccff198f08f79f813253ed7155572 |
__all__ = ["printAtomsXYZ", "PrintEvent"]
def printAtomsXYZ(fout, coords, line2="", atom_type=["LA"]):
"""
print atomic coordinate in vmd xyz format:
natoms
line2 ...could be anything, e.g. box lengths...
atom_type x[0] y[0] z[0]
atom_type x[1] y[1] z[1]
atom_type x[2] y[2] z[2]
...
... | js850/PyGMIN | pygmin/printing/print_atoms_xyz.py | Python | gpl-3.0 | 1,394 | [
"VMD"
] | f047b5efcb91d2159ab43917bc0d4970a4dc179e6630c6b80942552e784e5f08 |
# HsolveInstability.py ---
# Commentary:
#
# A toy compartmental neuronal + chemical model in just a cubic volume
#
# 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, or
# (at yo... | BhallaLab/moose-examples | snippets/cubeMeshSigNeur.py | Python | gpl-2.0 | 11,984 | [
"MOOSE"
] | d968380248b7615e6197ffaadc8b4bf6c2446dfd0577443acd8d6b3d792cc4d9 |
from lettuce import step,before,world
from django.contrib.auth.models import User
from lettuce.django import django_url
@step("When I click the login link")
def when_i_click_the_login_link(step):
world.browser.click_link_by_text("Log in")
@step('Given there is a username "([^"]*)" with password "([^"]*)"')
def ma... | lkundrak/scraperwiki | web/frontend/features/sign_in_steps.py | Python | agpl-3.0 | 1,736 | [
"VisIt"
] | 80ab3c26f3e83b1c230b73cd7341f1081d5b622965f29bb7a8d83905c60857d0 |
# -*- coding: utf-8 -*-
"""Magic functions for InteractiveShell.
"""
#*****************************************************************************
# Copyright (C) 2001 Janko Hauser <jhauser@zscout.de> and
# Copyright (C) 2001-2006 Fernando Perez <fperez@colorado.edu>
#
# Distributed under the terms of th... | toomoresuch/pysonengine | eggs/ipython-0.10.1-py2.6.egg/IPython/Magic.py | Python | mit | 136,466 | [
"VisIt"
] | f18c1b736336559b30b8bcd8cbd77b3b0cffad83b9137a8843ef1a86770aab0c |
from django.conf import settings
from django.contrib.auth.models import AnonymousUser
from django.contrib.contenttypes.fields import (GenericForeignKey,
GenericRelation)
from django.contrib.contenttypes.models import ContentType
from django.contrib.sites.models import Sit... | mozilla/django-tidings | tidings/models.py | Python | bsd-3-clause | 5,421 | [
"VisIt"
] | 1b214d9a0f314fd802bde4cae2a5011edd9b5e0b5fb6621c26814ae31b3a0b01 |
# -*- coding: utf-8 -*-
"""QGIS Unit tests for edit widgets.
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
"""
__au... | carolinux/QGIS | tests/src/python/test_qgsrelationeditwidget.py | Python | gpl-2.0 | 10,901 | [
"Galaxy"
] | edaf799ac4228905f7e8cb6ecb00ad635100de3345d498053bb5ac2fc250bdf2 |
# MIT License
#
# Copyright (c) 2017 Anders Steen Christensen
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, mo... | qmlcode/qml | tests/test_energy_krr_atomic_cmat.py | Python | mit | 7,468 | [
"Gaussian"
] | d40cc92724a7e511d4b21828f27f1a6391f98ab0f4023bc53b12aa8d30f261d8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains the main object used to identify the coordination environments in a given structure.
"""
__author__ = "David Waroquiers"
__copyright_... | matk86/pymatgen | pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py | Python | mit | 75,875 | [
"pymatgen"
] | c210bdb37529c0400eb5d6e5e9ab49943ba172c83ca916023cbf1206537b6d09 |
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2015-11-17 14:24:57
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-18 22:34:28
import aces.config as config
import aces.tools as tl
from aces.runners import Runner
from aces.lammpsdata import lammpsdata
class runner(Runner):
def get_structu... | vanceeasleaf/aces | aces/runners/strain.py | Python | gpl-2.0 | 8,026 | [
"Gaussian",
"LAMMPS"
] | c23df517b8e7185eaab5e4e089b81ccbfd541ff639a12178c33bd78c0c3e037c |
import logging
import abc_code.global_var as g
import numpy as np
import scipy as sp
import scipy.stats
from numpy.fft import fftfreq, fftn, ifftn
from time import time
from abc_code.sobol_seq import i4_sobol_generate
from fast_histogram import histogram1d
import abc_code.distance as dist
import itertools
def timer(... | olgadoronina/LES_ABC | abc_code/utils.py | Python | gpl-3.0 | 8,359 | [
"Gaussian"
] | 59c1d7cc94661486381e99970735a8f5c53bf173dcbc6093414e51ac9d1cc850 |
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright (C) 2014 Dave Hocker
#
# 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, version 3 of the License.
... | dhocker/athomepowerlineserver | helpers/__init__.py | Python | gpl-3.0 | 365 | [
"xTB"
] | eaf46d927e038b6464f591c69b9b7df22cb90e904692d9a0e9732db88e4b949c |
"""Test PubChem JSON format using the OpenBabel Python bindings
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pybindtest -VV
You could also "chdir" into build/tes... | baoilleach/openbabel | test/testpcjsonformat.py | Python | gpl-2.0 | 10,277 | [
"Pybel"
] | 32d84e806fbf75b0270606b398ee3b9f92c310e04e8f75c4f827b627780420d8 |
# coding=utf-8
'''Define Schema'''
from __future__ import absolute_import
import hashlib
from datetime import datetime
from flask import url_for, current_app
from mongoengine import fields, DENY
from werkzeug import security
from flask_babel import gettext as _
from flask_mail import Message
from flask_login import lo... | matrixorz/firefly | firefly/models/user.py | Python | mit | 7,670 | [
"Firefly"
] | f48bbdc07c10516ccd769b270dda7105089727df8ddcdd6d789400b5c4cb1a56 |
import binascii
import string
import sys
def xor(*t):
from functools import reduce
from operator import xor
return [reduce(xor, x, 0) for x in zip(*t)]
def xor_string(t1, t2):
t1 = map(ord, t1)
t2 = map(ord, t2)
return "".join(map(chr, xor(t1, t2)))
with open('output.txt', 'r') as f:
ct... | Qwaz/solved-hacking-problem | ConfidenceCTF/2019/count_me_in/solver.py | Python | gpl-2.0 | 1,923 | [
"exciting"
] | 05276dd2fe298c9bbdfc8c152ed895102bc5606036b5db8f3e3a6b917b993b24 |
# coding=utf-8
"""This module, sk_missing_image_utilities.py, is a utility script to find missing images.
"""
# Needed for making simplified HTTP requests.
import requests
# Needed for getting more verbose information on the HTTP calls made with requests.
import logging
# Needed for grabbing the stderr.
import sys
# N... | utarsuno/urbtek | quality_assurance/web_utilities/sk_missing_image_utilities.py | Python | apache-2.0 | 2,186 | [
"VisIt"
] | 5689f8b5f1e7e23593aea8a0a19b0c74b6802e2958c05a94fe0b71a400ce5ab3 |
# 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... | govarguz/espressopp | testsuite/unittest/__init__.py | Python | gpl-3.0 | 2,714 | [
"ESPResSo"
] | d6c745f67433b40cdb030c2e05e29d385436870290eb927ae96488865b7f7c37 |
"""The code has been developed by Dr.Vidhya Balasubramanian as part of the CSE230 Data Structures Course, ASE Coimbatore.
The code is being constantly improved, so please bring to notice any bugs to dsdaa.amrita@gmail.com
"""
class MyQueue():
def __init__(self):
# this is the queue contai... | ksooraj2610/Get_the_Sum | queue.py | Python | mit | 2,333 | [
"ASE"
] | 0dc95004c54e35456d341e261847aec6e6fafdc22f7623c5ec12007a6ebd59b8 |
'''
_______
| \ \ / @@@;
| \ \ / `#....@
| | \ / ,;@.....;,;
| | \ / @..@........@` PyWeather Setup
| | \ / .............@ version 0.6.3 beta
| / \ / .............@ ... | ModoUnreal/PyWeather | setup.py | Python | gpl-3.0 | 99,122 | [
"VisIt"
] | 55c4f44b5ae46e9e06147f4ef5ae5ce35cad0c43a861dc2329c3ae8d5647114a |
""" Test class for agents
"""
# imports
import unittest, importlib, datetime
from mock import MagicMock
from DIRAC import gLogger
#sut
from DIRAC.TransformationSystem.Agent.TaskManagerAgentBase import TaskManagerAgentBase
from DIRAC.TransformationSystem.Agent.TransformationAgent import TransformationAgent
class Ag... | marcelovilaca/DIRAC | TransformationSystem/Agent/test/Test_Agent.py | Python | gpl-3.0 | 18,116 | [
"DIRAC"
] | 55e11f4fce502f201363795dadbfaac36aa7392afc611ced78ddcda91768a5fb |
#!/usr/bin/env python
'''
CREATED:2013-02-11 18:37:30 by Brian McFee <brm2132@columbia.edu>
Track beat events in an audio file
Usage: ./beat_tracker.py [-h] input_file.mp3 output_beats.csv
'''
from __future__ import print_function
import argparse
import sys
import numpy as np
import librosa
def beat_track(inp... | carlthome/librosa | examples/beat_tracker.py | Python | isc | 1,954 | [
"Brian"
] | 8f68c8fbac6a6c68f58dfb37d91dc50c97ccb3b29e5dc53ea526e76368bb0853 |
#
# $Id$
# ---------------------------------------------------------------------------
"""
Introduction
============
The ``pyutmp`` module provides a Python-oriented interface to the *utmp*
file on Unix-like operating systems. To paraphrase the *Linux Programmer's
Manual* page *utmp*\ (5), the *utmp* file allows one ... | bmc/pyutmp | pyutmp/__init__.py | Python | bsd-3-clause | 11,983 | [
"Brian"
] | 586a0799ae08dec016f6d8838f255ec6982d83c2bde1201a812d54f4770f0d50 |
from __future__ import print_function
from six import iteritems
from six.moves import range
import os
from numpy import arange, mean, amax, amin, array
import vtk
from vtk import vtkHexahedron, vtkQuad, vtkTriangle, vtkTetra
from pyNastran.converters.dev.avus.avus_grid import AvusGrid
from pyNastran.gui.gui_objects.... | saullocastro/pyNastran | pyNastran/converters/dev/avus/avus_io.py | Python | lgpl-3.0 | 9,955 | [
"VTK"
] | 536fa21c8a7dbcc6b42b63bb2f55abd7456b889253a26282734a25e5d4952997 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Atomic Position Data
############################
This module provides a collection of dataframes supporting nuclear positions,
forces, velocities, symbols, etc. (all data associ... | exa-analytics/atomic | exatomic/core/atom.py | Python | apache-2.0 | 22,735 | [
"Gaussian"
] | 20407e194b6c9dc1d8d8cc6e2be32adb7cd62faf25f64d3266c2f9f13322203b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements equivalents of the basic ComputedEntry objects, which
is the basic entity that can be used to perform many analyses. ComputedEntries
contain calculated information, typically from VAS... | davidwaroquiers/pymatgen | pymatgen/entries/computed_entries.py | Python | mit | 34,708 | [
"VASP",
"pymatgen"
] | a2d6343a9f3857a9c60ef0300a51f335f01a643c36da7777689b3786126007c1 |
#!/usr/bin/env python
# Created: Thu Feb 15 14:22:12 2001
# Last changed: Time-stamp: <01/02/18 11:16:42 thomas>
# Copyright 2000 by Thomas Sicheritz-Ponten. 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... | updownlife/multipleK | dependencies/biopython-1.65/Scripts/xbbtools/nextorf.py | Python | gpl-2.0 | 9,811 | [
"Biopython"
] | 0f9cfd3484d906c545c25d0365907b5ba368205426346222f08103199e2d3a8f |
# $HeadURL$
""" Resources helper class gives access to various computing resources descriptions
The following naming conventions are used:
Site names as input arguments can be specified in a full form, e.g. LCG.CERN.ch, or
a short form, e.g. CERN. Site names in the output are given in the short form... | miloszz/DIRAC | ConfigurationSystem/Client/Helpers/Resources.py | Python | gpl-3.0 | 31,545 | [
"DIRAC"
] | 71bc2d929cf7c781b4a8dd3438c6548829db23d87e1880dffd53e952597a8595 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import gzip
from Bio.Blast import NCBIXML
import multiprocessing
import argparse
def func_os_GetAllFilesPathAndNameWithExtensionInFolder (FolderAddress, FileExtension, ProcessSubFoldersAlso = True):
#IMPORTANT ... Extenstion should be like : "tx... | TurkuNLP/CAFA3 | sequence_features/new_BLAST_results_FeatureGenerator.py | Python | lgpl-3.0 | 5,873 | [
"BLAST"
] | d7158996242bb28783388056205d07e7956b8240180adb340af4f1a209a95213 |
# $Id$
#
# Copyright (C) 2002-2006 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 ... | rdkit/rdkit | rdkit/Dbase/UnitTestDbUtils.py | Python | bsd-3-clause | 7,337 | [
"RDKit"
] | 2b1ed66409f874fbf06f72995a000d583ec861132dec7bdd545b150f47c0c9f1 |
"""
CloudEndpoint is a base class for the clients used to connect to different
cloud providers
"""
import os
from DIRAC import S_ERROR, S_OK
from DIRAC.Resources.Cloud.Utilities import createUserDataScript, createPilotDataScript, createCloudInitScript
class Endpoint(object):
"""Endpoint base class"""
... | DIRACGrid/DIRAC | src/DIRAC/Resources/Cloud/Endpoint.py | Python | gpl-3.0 | 1,781 | [
"DIRAC"
] | 5d52ffa90cabaa93dddfa1f58ac152c63ce35c0dd044f23ca32c5828acd224a8 |
def _dcgpann_visualize(self, show_connections = True, fill_color = 'w', active_connection_alpha = 0.1, inactive_connection_alpha = 0.01, legend = True, axes = None, show_inactive = False, show_nonlinearities = False):
"""visualize(show_connections = True, fill_color = 'w', show_nonlinearities = False, active_connec... | darioizzo/d-CGP | dcgpy/_visualize.py | Python | gpl-3.0 | 10,680 | [
"NEURON"
] | 0384f5d9d22d9917ebd89b2933bd3a2fc82ef1385ad784d423de368a7876b9b7 |
#!/usr/bin/pvpython
from paraview.simple import *
#position camera
view = GetActiveView()
if not view:
view = CreateRenderView()
#draw the object
Show()
dp = GetDisplayProperties()
#set point color
dp.AmbientColor = [1, 0, 0] #red
#set surface color
dp.DiffuseColor = [0, 1, 0] #blue
#set point size
dp.Point... | wegatron/SSCCE | python/paraview_pc_red.py | Python | gpl-3.0 | 388 | [
"ParaView"
] | 1459f92b00be8ad7819855648144a6c28dfaf09a3e8fb4f1446162ee2089c07c |
"""
Dashboard view and supporting methods
"""
import datetime
import logging
from collections import defaultdict
from django.conf import settings
from django.contrib import messages
from django.contrib.auth.decorators import login_required
from django.shortcuts import redirect
from django.urls import reverse
from dj... | msegado/edx-platform | common/djangoapps/student/views/dashboard.py | Python | agpl-3.0 | 35,400 | [
"VisIt"
] | 9bfc9ebe6a785f7d29dff0f5cd95b6ee768acc9d11c42b43972a40f8e235ae95 |
# -*- coding: utf-8 -*-
"""module defines utility methods for MPContribs core.io library"""
from __future__ import unicode_literals
from decimal import Decimal, DecimalException, InvalidOperation
import six
from mpcontribs.io.core import mp_id_pattern
try:
from StringIO import StringIO
except ImportError:
from... | materialsproject/MPContribs | mpcontribs-io/mpcontribs/io/core/utils.py | Python | mit | 5,005 | [
"pymatgen"
] | 57fbdd7a50a090caf521f8532284d771ed3d8cfb4456dfb601cedea5217ddb1a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
# Create the polydata where we will store all the geometric data
linesPolyData = vtk.vtkPolyData()
# Create three points
origin = [0.0, 0.0, 0.0]
p0 = [1.0, 0.0, 0.0]
p1 = [0.0, 1.0, 0.0]
# Create a vtkPoints container... | lorensen/VTKExamples | src/Python/GeometricObjects/ColoredLines.py | Python | apache-2.0 | 3,060 | [
"VTK"
] | dcd12db350fb2e9b0532a14a32ad8e6c4513a7d6a0de6cb8f0bc4a949835e7cb |
from typing import List
from .. import Provider as AddressProvider
def getcities(fulldict):
cities = []
for cap in fulldict:
for c in fulldict[cap]:
cities.append(c[0]) if c[0] not in cities else cities
return cities
class Provider(AddressProvider):
# Converted from: https://dow... | joke2k/faker | faker/providers/address/it_IT/__init__.py | Python | mit | 666,991 | [
"CASINO",
"RASPA"
] | 4f51112bcea674d1bd047d4134796a6383c54384bca2f7022f66e4cd164b43b8 |
# Copyright (c) 2012, Cloudscaling
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | shakamunyi/nova | nova/hacking/checks.py | Python | apache-2.0 | 20,103 | [
"VisIt"
] | 20fb60929042253588b3978e17a428186c7de0f34defeb51fea4744ae076cc9d |
# -*- coding: utf-8 -*-
"""Convert the Yelp Dataset Challenge dataset from json format to csv.
For more information on the Yelp Dataset Challenge please visit http://yelp.com/dataset_challenge
"""
import argparse
import collections
import csv
import simplejson as json
def read_and_write_file(json_file_path, csv_file_... | JoshuaEbenezer/SNLP-reviews | SNLP/src/json_to_csv.py | Python | gpl-3.0 | 3,662 | [
"VisIt"
] | c8486dc0891506dcfb53bf0c3574737c750999eef4e58d47d0ef47ac9886e47b |
# -*- coding: utf-8 -*-
"""
==================
plotft
==================
*PlotTF --> will plot a time frequency distribution of your choice
Created on Mon Aug 19 16:24:29 2013
@author: jpeacock
"""
#=================================================================
import numpy as np
import matplotlib.pyplot a... | MTgeophysics/mtpy | mtpy/imaging/plotspectrogram.py | Python | gpl-3.0 | 22,267 | [
"Gaussian"
] | cc2388d4a36c6bf4529bc41d81c10c10f4a7a71377d22ad24f8db6a0a0c286c0 |
"""
=========================================
Image denoising using dictionary learning
=========================================
An example comparing the effect of reconstructing noisy fragments
of a raccoon face image using firstly online :ref:`DictionaryLearning` and
various transform methods.
The dictionary is fi... | huzq/scikit-learn | examples/decomposition/plot_image_denoising.py | Python | bsd-3-clause | 5,879 | [
"Gaussian"
] | 197b65622869b7e33dcd9f6f46dccf368f35bae66aad860a97996567b3156e49 |
#!/usr/bin/env python
"""
Various utility code that gets used throughout the command-line tools.
Recent changes
- Moved scipy and numpy imports into relevant functions so that
other python builds (e.g. PyMOL) can easily use this.
"""
import os,sys,bz2
from copy import copy
from optparse import Option, Option... | LernerLabs/PyPAT | pypat/tool_utils.py | Python | apache-2.0 | 11,979 | [
"PyMOL"
] | 9600016ec580a16d70683889bc8ce355e7707f1243054cd02c56ef197798a061 |
# Copyright 2013, SIL International
# All rights reserved.
#
# This library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version 2.1 of License, or
# (at your option) any lat... | silnrsi/graide | lib/graide/findmatch.py | Python | lgpl-2.1 | 38,189 | [
"VisIt"
] | 9657b5808da55112aa6bf0c68e5af1520eed53f51e0753323ad6e13645a537e2 |
import os
import shutil
import logging
import mdtraj.utils
from distutils.spawn import find_executable
import parmed
from openmoltools.utils import getoutput
logger = logging.getLogger(__name__)
logging.basicConfig(level=logging.DEBUG, format="LOG: %(message)s")
GROMACS_PATH = find_executable('gmx')
def stripcomme... | jchodera/openmoltools | openmoltools/gromacs.py | Python | gpl-2.0 | 17,215 | [
"Gromacs",
"MDTraj"
] | 322dafa5ad00b37ffc75616de4bca05c86d1a4972ddfc870ef6adff2a96643dc |
"""
========================
Random Number Generation
========================
Use ``default_rng()`` to create a `Generator` and call its methods.
=============== =========================================================
Generator
--------------- ---------------------------------------------------------
Generator ... | jorisvandenbossche/numpy | numpy/random/__init__.py | Python | bsd-3-clause | 7,527 | [
"Gaussian"
] | c97f52dc4a461140274a2c2806b71cc4566782be692e66c4c7a7602cf1f5af9b |
from __future__ import division, print_function, absolute_import
import math
import warnings
import numpy as np
# trapz is a public function for scipy.integrate,
# even though it's actually a numpy function.
from numpy import trapz
from scipy.special import roots_legendre
from scipy.special import gammaln
from scipy... | DailyActie/Surrogate-Model | 01-codes/scipy-master/scipy/integrate/quadrature.py | Python | mit | 28,488 | [
"Gaussian"
] | 6c6586a29035fd78a9d2a77a83923e2af0368ab90b000c9dc591a2d0554a8626 |
"""
Acceptance tests for Studio.
"""
from unittest import skip
from bok_choy.web_app_test import WebAppTest
from ...pages.studio.asset_index import AssetIndexPage
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.course_info import CourseUpdatesPage
from ...pages.studio.edit_tabs import PagesPag... | wwj718/edx-platform | common/test/acceptance/tests/studio/test_studio_general.py | Python | agpl-3.0 | 5,599 | [
"VisIt"
] | 540e2522a211d13e4c7aef98035515dbd36660cda0a1bcadea08021555fdb661 |
#!/usr/bin/env python
# Copyright 2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless... | sunqm/pyscf | pyscf/tdscf/test/test_tdrhf.py | Python | apache-2.0 | 1,957 | [
"PySCF"
] | 5ec7ebd04f35ee2222f4504a2f61bc338d153c9add461573e313bd808d8ef486 |
import os
import sys
import numpy
import pyprind
# settings
SCORES_TXT = '../data/test/list_scores.txt'
PHOTOS_LOCATION = '/media/p307k07/ssd/opt/msc/data/test/'
PHOTOS_LIST_FILE = PHOTOS_LOCATION + 'list.txt'
MODEL_WEIGHTS_LOCATION = '../experiments/results/alexnet_model_iter_450000.caffemodel'
MODEL_DEFINITION_LOCAT... | mc-suchecki/MSc | scripts/score_photos.py | Python | gpl-3.0 | 2,505 | [
"NEURON"
] | c951acd8eb5a524377bb3c520330a9695b0885c32741995c5a46988e828a6249 |
from setuptools import setup
def main():
install_list = ['pysb>=1.3.0', 'objectpath', 'rdflib==4.2.1',
'requests>=2.11', 'lxml', 'ipython', 'future',
'networkx>=2', 'pandas', 'ndex2==2.0.1', 'jinja2',
'protmapper>=0.0.6']
extras_require = {
... | pvtodorov/indra | setup.py | Python | bsd-2-clause | 4,867 | [
"Pybel"
] | 82a7316255d2c8237476f29ffae1804d786c69b1cc49ca0d1998b33dad7f4365 |
# 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 | milking_cowmask/main_semisup.py | Python | apache-2.0 | 10,838 | [
"Gaussian"
] | 81cdc3fe06f71f8c502efadf2f35f6846c1f146c586c33112ad25c1620195a38 |
# -*- coding: utf-8 -*-
from datetime import datetime, timedelta
from unittest import mock
from actstream.models import Action, Follow
from django.core.management import call_command
from django.db.models import Q
from nose.tools import eq_, ok_, raises
from taggit.models import Tag
import kitsune.sumo.models
from ki... | mozilla/kitsune | kitsune/questions/tests/test_models.py | Python | bsd-3-clause | 22,191 | [
"VisIt"
] | 6e0d875c09a984c9a524dfd7774e16daaf0fee4877075e88356fc05448a00235 |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE-A... | jeremiahyan/lammps | python/lammps/data.py | Python | gpl-2.0 | 3,151 | [
"LAMMPS"
] | ce8096f52791a0cbd1476144198caa8fa5b131a409b141a1d8fa01714dcd1ce5 |
# 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.
#
"""Deal with Affymetrix related data such as cel files.
"""
| zjuchenyuan/BioWeb | Lib/Bio/Affy/__init__.py | Python | mit | 231 | [
"Biopython"
] | be0a53cefa45ccaf7d1dcb86cc54481676060f03e604493122586f56ff7195c6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# copyright Julien TREBOSC 2012-2013
# check that variable PYTHONPATH points to the right folder for brukerIO.py library
from __future__ import division
Descript="""
OK so what is this program doing exactly ?
Not much : it reads 2D SER file. Turn it into Hypercomplex data and... | jtrebosc/JTutils | CpyBin/apod2DEAE_.py | Python | bsd-3-clause | 8,138 | [
"Gaussian"
] | fbb83a2b2a6f677454b2204f64c05282966d222f93683d96b8ee5870a690dde9 |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 12 15:11:17 2018
@author: tih
"""
def main(input_nc, output_nc, input_JRC, Inflow_Text_Files, include_reservoirs = 1):
import time
import wa.General.raster_conversions as RC
import wa.General.data_conversions as DC
import numpy as np
import netCDF4
... | wateraccounting/wa | Models/SurfWAT/Run_SurfWAT.py | Python | apache-2.0 | 10,974 | [
"NetCDF"
] | 790e232b369e6dbc95cc138ddde374216bc49b2aa5e11f6638279e220a35d4fd |
#!/usr/bin/env python
desc="""Produce contact matrix from SAM/BAM.
"""
epilog="""Author: l.p.pryszcz+git@gmail.com
Bratislava, 19/10/2016
"""
import gzip, os, resource, sys
import commands, os, subprocess, sys
from datetime import datetime
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
f... | lpryszcz/HiCembler | fastq2array.py | Python | gpl-3.0 | 12,794 | [
"BWA"
] | aafff029a2eb2dcd811be6dc105ab4ae5ded247b550871057d817d25181472a5 |
# ABANDONWARE ### ABANDONWARE ### ABANDONWARE ### ABANDONWARE ### ABANDONWARE ### ABANDONWARE ###
# ABANDONWARE ### ABANDONWARE ### ABANDONWARE ### ABANDONWARE ### ABANDONWARE ### ABANDONWARE ###
#
# At the moment no one is writing a "integrity" Requests.
# It can be resurrected once we'll write those requests again.... | avedaee/DIRAC | DataManagementSystem/Agent/SEvsLFCAgent.py | Python | gpl-3.0 | 14,229 | [
"DIRAC"
] | 6028690c6e3e797d18fb1ea0815385fb0ea748a328f54dc0c86c2547765aa106 |
# -*- coding: utf-8 -*-
# ###
# Copyright (c) 2013, Rice University
# This software is subject to the provisions of the GNU Affero General
# Public License version 3 (AGPLv3).
# See LICENCE.txt for details.
# ###
import io
import re
import datetime
import json
import logging
try:
import urllib2 # python2
except Im... | Connexions/cnx-authoring | cnxauthoring/utils.py | Python | agpl-3.0 | 26,464 | [
"VisIt"
] | c32aa499d6745fd9afa7b4e76d419ae1301134606fa482aa940e4a3286a0a677 |
# Copyright (C) 2008 CSC - Scientific Computing Ltd.
"""This module defines an ASE interface to VASP.
Developed on the basis of modules by Jussi Enkovaara and John
Kitchin. The path of the directory containing the pseudopotential
directories (potpaw,potpaw_GGA, potpaw_PBE, ...) should be set
by the environmental flag... | askhl/ase | ase/calculators/vasp.py | Python | gpl-2.0 | 75,118 | [
"ASE",
"VASP",
"Wannier90"
] | e02b073dc4f5b5c465ad6a55e7357a1d950946b2c2abbf0e43c6af67329ac573 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Author: Chinmaya Pancholi <chinmayapancholi13@gmail.com>
# Copyright (C) 2017 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""Scikit learn interface for :class:`~gensim.models.ldaseqmodel.LdaSeqModel`... | midnightradio/gensim | gensim/sklearn_api/ldaseqmodel.py | Python | gpl-3.0 | 6,828 | [
"Gaussian"
] | b12dfbb60b4bc115c0cec752c555e90b56fd65616e2b17389561d8226d4ba333 |
#!/usr/bin/env python
"""
Benchmark various integrators provided in openmmtools on some test systems.
"""
try:
import openmm
from openmm import unit
from openmm import app
except ImportError: # OpenMM < 7.6
from simtk import openmm
from simtk import unit
from simtk.openmm import app
from open... | choderalab/openmmtools | examples/integrator-benchmarks/integrator-benchmarks.py | Python | mit | 2,727 | [
"OpenMM"
] | 7b9e0394106396c066d3de85a8e7fe8626a6245f9f9b12c39599f763540e8c0d |
# -*- coding: utf-8 -*-
"""
Created on Thu May 26 22:25:14 2016
@author: casim
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from itertools import product
import matplotlib.pyplot as plt
import copy
from nose.to... | casimp/edi12 | pyxe/test/test_energy.py | Python | mit | 10,792 | [
"Gaussian"
] | a91e2f58b21c67da90374212d01a8b6f4030318761e7a03f8e8611f70bdbf49a |
import numpy
from orbkit.qcinfo import QCinfo
from orbkit.orbitals import AOClass, MOClass
from orbkit.units import aa_to_a0, ev_to_ha
from orbkit.display import display
from orbkit.tools import l_deg, lquant, get_atom_symbol
from importlib import import_module
def read_with_cclib(filename, cclib_parser=None, all_mo=... | orbkit/orbkit | orbkit/read/cclib_parser.py | Python | lgpl-3.0 | 7,730 | [
"GAMESS",
"Gaussian",
"Molpro",
"ORCA",
"cclib"
] | 380e784bbf030348bfdc0a48cfb8564d6ffb155f33114154b22cd56980cc456b |
import re
from copy import deepcopy
from xml.dom import minidom, getDOMImplementation
from intermine.util import openAnything, ReadableException
from intermine.pathfeatures import PathDescription, Join, SortOrder, SortOrderList
from intermine.model import Column, Class, Model, Reference, ConstraintNode
import intermi... | alexkalderimis/intermine-ws-client.py | intermine/query.py | Python | lgpl-3.0 | 72,478 | [
"TINKER"
] | 7eb95ee693f20332845f38081ff124c5fe7019a2fdf41938d76fd2d37d821700 |
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