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"""
The :mod:`sklearn.lda` module implements Linear Discriminant Analysis (LDA).
"""
from __future__ import print_function
# Authors: Matthieu Perrot
# Mathieu Blondel
import warnings
import numpy as np
from scipy import linalg
from .base import BaseEstimator, ClassifierMixin, TransformerMixin
from .utils.e... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/sklearn/lda.py | Python | apache-2.0 | 9,614 | [
"Gaussian"
] | b1527a634672c5efbe18bf15ccab82bc79e6b418c5775965daf77ae339348177 |
import csv
import datetime
import dateutil.tz
import httpretty
import mixcloud
import io
import unittest
from mixcloud.mock import MockServer, parse_headers, parse_multipart
try:
from urllib.parse import parse_qs
from urllib.parse import urlsplit
from unittest import mock
except ImportError:
# Python 2... | emillon/mixcloud | tests.py | Python | bsd-2-clause | 9,400 | [
"CRYSTAL"
] | 4f65f250e48b3d6f92d194e9c634732049eb5a758e81d9e926c70517bc580778 |
########################################################################
# File : DiracSiteAgent.py
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Agent to manage a DIRAC site, it submits and monitors pilots to a local cluster
"""
__RCSID__ = "$Id$"
... | vmendez/DIRAC | WorkloadManagementSystem/Agent/DiracSiteAgent.py | Python | gpl-3.0 | 10,038 | [
"DIRAC"
] | 06cfb4aa5c61b3118dd50ea213f9c1ccf236550a62c7f41388b2a35bff63b6f1 |
#!/usr/bin/env python
import os
import random
import pysam
import argparse
'''
Tool for generating random sites for bamsurgeon input
'''
class Genome:
def __init__(self, gfn, bedfile=None):
''' gfn = genome file name '''
self.chrlen = {} # length of each chromosome
self.chrmap = [] # use... | adamewing/bamsurgeon | scripts/randomsites.py | Python | mit | 7,999 | [
"pysam"
] | b38c3618b2e5da4a40dd7ae5a84ed1bbe44720f6d88be571e0d158ff5e74b6de |
"""
All of the metadata related to MITgcm variables, grids, naming conventions, etc.
"""
# python 3 compatiblity
from __future__ import print_function, division
import numpy as np
from xarray.core.pycompat import OrderedDict
# We are trying to combine the following two things:
# - MITgcm grid
# http://mitgcm.org/se... | sambarluc/xmitgcm | xmitgcm/variables.py | Python | mit | 22,333 | [
"NetCDF"
] | aef7e83bd355b7a37776c0b36e8ac6a9a90cd8b3f12d515513ac1a14d16d6a8c |
from StringIO import StringIO
from common import *
from mock import *
import pysam
from bio_pieces import subsamplebam
class Base(BaseTester):
modulepath = 'bio_pieces.subsamplebam'
def setUp(self):
super(Base,self).setUp()
self.refname = 'Ref1'
self.reads = [
'ATG',
... | demis001/bio_pieces | tests.old/test_subsamplebam.py | Python | gpl-2.0 | 5,038 | [
"pysam"
] | 6439ea063ec9d5eabda8a7dfecb205f5349592285cd282f7b0a1b46cdfd6abd8 |
"""
The definition of different kinds of metadata that is put into the
mayavi registry
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import HasTraits, Str, Callable, Either, List, Instance
from mayavi.... | dmsurti/mayavi | mayavi/core/metadata.py | Python | bsd-3-clause | 4,458 | [
"Mayavi"
] | 419774e16df09528be3cfadfe6477c822eb2847718c6596142cbaa8282c0ce8a |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import os
import re
import cgi
import sys
import json
import codecs
import pprint
import string
import fnmatch
import time
PY3 = (sys.version_info[0] == 3)
if PY3:
unicode, string_types = str, (str, bytes)
else:
string_types = (str, unicode)
__... | natesilva/javascript-eslint.tmbundle | Support/ashes.py | Python | bsd-3-clause | 78,799 | [
"VisIt"
] | b95a46cc4a46b1f0afa1b8aea857ab215074cac0fadbaba79d19909d0f47781e |
# coding: utf-8
#
# Detection of extreme intervals in multivariate time-series
# Author: Erik Rodner (2015-) & Björn Barz (2016)
# Python implementation of several variants of the "Maximally Divergent Intervals (MDI)" algorithm.
# In the following, we will derive an algorithm based on Kullback-Leibler (KL) divergence... | cvjena/libmaxdiv | maxdiv/maxdiv_py.py | Python | lgpl-3.0 | 27,792 | [
"Gaussian"
] | c85d4bb8fee4298ffcb6ab68524f05d5700dbb6d397b304308ffd2eeeba5b562 |
###############################################################################
# Copyright 2016 - Climate Research Division
# Environment and Climate Change Canada
#
# This file is part of the "EC-CAS diags" package.
#
# "EC-CAS diags" is free software: you can redistribute it and/or modify
# it under... | neishm/EC-CAS-diags | eccas_diags/interfaces/cccma_nc.py | Python | lgpl-3.0 | 3,833 | [
"NetCDF"
] | 7185cb2dcbca3acf2b8242d83e0f9d0ab60ded8d82b8d5f6dca6727649ae7308 |
# Copyright 2018 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 law or agreed to in writing,... | google/differentiable-atomistic-potentials | dap/py/bpnn.py | Python | apache-2.0 | 2,823 | [
"Gaussian"
] | ed901aceef251f05bfb0420d5f35267eb73cee4b78df736d0db3d708e289f5a2 |
#!/usr/bin/env python
import os
import platform
import sys
try:
import yaml
except ImportError:
print('Please install pyyaml (try: pip install pyyaml)')
sys.exit(1)
import subprocess as sp
import shlex
import argparse
import tempfile
if sys.version_info.major == 3:
PY3 = True
from urllib.request i... | xguse/bioconda-recipes | simulate-travis.py | Python | mit | 15,882 | [
"Bioconda"
] | deef6a17b6a0b4ae3e05eea919528e5ef8c2372a435c3b07f0b3b676e34783a4 |
# Copyright 2017 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... | kevin-coder/tensorflow-fork | tensorflow/python/autograph/pyct/templates.py | Python | apache-2.0 | 9,413 | [
"VisIt"
] | d2ffa984c28c529f8ab6530e5b80351432e79b352c58d95598076606162a234c |
"""Virtual oscilloscope.
If ran as a script, connects to a NIDAQserver and serves as a virtual oscilloscope.
If imported as a module, exports the various components of the oscilloscope as classes.
"""
__author__ = "Karim Liman-Tinguiri <klt@mit.edu>"
__version__ = "0.1"
__date__ = "25 June 2007"
import wx
import num... | Cynary/distro6.01 | arch/6.01Soft/lib601-F13-4/soar/v_oscillo.py | Python | mit | 17,403 | [
"Gaussian"
] | 17e7a0dff8a19b46a6a686d378633dcc491bf17d15c3bfcf6444ee2f3bc47bec |
""" This integration test runs the RMS test scenari using
the MySQL DB
"""
# pylint: disable=invalid-name,wrong-import-position
import DIRAC
DIRAC.initialize() # Initialize configuration
from pytest import fixture
from DIRAC.RequestManagementSystem.DB.RequestDB import RequestDB
from DIRAC.RequestManagementSystem.D... | DIRACGrid/DIRAC | tests/Integration/RequestManagementSystem/Test_ReqDB.py | Python | gpl-3.0 | 552 | [
"DIRAC"
] | 8fb1264c1431a92cd398e0c4dd694d712482e6ce38218817ebba8146d6883e29 |
# Copyright 2020 The LUCI Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0
# that can be found in the LICENSE file.
"""Validation of realms.cfg config files."""
from components import auth
from components.config import validation
from proto import realms_confi... | luci/luci-py | appengine/auth_service/realms/validation.py | Python | apache-2.0 | 10,447 | [
"VisIt"
] | 72129db58037e8edb2cac8198c9cef8139b92f3f6ab61f7d78b11659490da5d7 |
#
# Copyright (C) 2013,2014 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 l... | sehrhardt/espresso | samples/H5MD/h5md_WriteFile.py | Python | gpl-3.0 | 6,722 | [
"ESPResSo",
"VMD"
] | 87b44a39a7b8d3a1d4a0d27f6e4fb4faee26f998a76ddb6bfd36ea49b6f201c4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/simulation/neuron/objects/__init__.py | Python | bsd-2-clause | 1,784 | [
"NEURON"
] | 7c69a9fd8e46abc194f699cf53aa5e681549e4e1db0a2ee5439f57f4ded5fd88 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/tree/_majority_rule.py | Python | bsd-3-clause | 11,189 | [
"scikit-bio"
] | dc1ab283bcf4a917a605e4128d55d8cf15169e5d275d7f5ac32d95176d5aff25 |
# test_nmda.py ---
#
# Filename: test_nmda.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Mon Mar 22 16:58:57 2010 (+0530)
# Version:
# Last-Updated: Fri May 27 11:09:34 2011 (+0530)
# By: Subhasis Ray
# Update #: 163
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
... | BhallaLab/moose-thalamocortical | pymoose/tests/regression/test_nmda.py | Python | lgpl-2.1 | 3,491 | [
"MOOSE",
"NEURON"
] | c466fea91c977e98f26f15500e0aceac5747a95907ca3cb8fecccee5b9b531f8 |
import socket
import webbrowser
import httplib2
import oauth2client.clientsecrets as clientsecrets
from apiclient.discovery import build
from functools import wraps
from oauth2client.client import FlowExchangeError
from oauth2client.client import AccessTokenRefreshError
from oauth2client.client import OAuth2WebServerF... | guillaume-chs/Drive-in-Line | gdrive/pydrive/auth.py | Python | gpl-3.0 | 14,844 | [
"VisIt"
] | 5df5ed604f425b259dcca8401eeed436fbc30911584cabbd510d77e02bc683c2 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read a MAF from standard input and determine the mean length of ungapped pieces
in each block.
usage: %prog < maf > out
"""
from __future__ import division
import sys
import bx.align.maf
def main():
for m in bx.align.maf.Reader( sys.stdin ):
unga... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_mean_length_ungapped_piece.py | Python | bsd-3-clause | 759 | [
"Galaxy"
] | 2c8002069833ab095bd9b9b459d71fb31e76b81bcfbaae3ded2073b725b341ef |
'''
MetaFunctions is a function composition and data pipelining library.
For more information, please visit the `project on github <https://github.com/ForeverWintr/metafunctions>`_.
'''
import os
import sys
import contextlib
import pathlib
import shutil
from setuptools import setup, find_packages, Command
import met... | ForeverWintr/metafunctions | setup.py | Python | mit | 2,488 | [
"VisIt"
] | b891c4b2272eca10615707a4ed966bfb5e77ccd815d5d8370fa6dad6ea8fbd6b |
#!/usr/bin/env python
# Copyright (c) 2012, 2014 ARM Limited
# All rights reserved
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implemen... | SanchayanMaity/gem5 | util/streamline/m5stats2streamline.py | Python | bsd-3-clause | 42,052 | [
"VisIt"
] | 04349a638cffc36c631fc8449bca23e509f4a3709b4ecbc87f2f728c23435cef |
# coding=utf-8
# Copyright 2021 DeepMind Technologies Limited.
#
# 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 applic... | deepmind/jax_verify | jax_verify/extensions/functional_lagrangian/verify_utils.py | Python | apache-2.0 | 4,339 | [
"Gaussian"
] | c74237810be3d0e7b44531d2040d40294b5da5b79f973801eee44d82f9b56969 |
# ## Copyright (c) 2013, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
import itertools, logging
from ..kern import Kern
from ..core.parameterization.variational import NormalPosterior, NormalPrior
from ..core.parameterization import Param, Parameterized... | jameshensman/GPy | GPy/models/mrd.py | Python | bsd-3-clause | 14,617 | [
"Gaussian"
] | c8ecc1aee08a13a9f1f71a6a2d01341def624d93dce49fef1739fab1fbaf5b64 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is used to estimate the cost of various compounds. Costs are taken
from the a CostDB instance, for example a CSV file via CostDBCSV.
For compounds with no cost listed, a Phase Diagram style conv... | matk86/pymatgen | pymatgen/analysis/cost/cost.py | Python | mit | 5,949 | [
"pymatgen"
] | 842a490b9b595841c15b9d29ee9c16af06e6b14cfbff7db34089ec226aacd3ac |
# Copyright (C) 2020 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# noti... | atztogo/phono3py | phono3py/version.py | Python | bsd-3-clause | 1,606 | [
"phonopy"
] | f5283efb701330eedbf208723ee697de7f6033fad1e304ad1b89d85084afee66 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | config/patch_ordered_dict.py | Python | gpl-3.0 | 11,072 | [
"CRYSTAL",
"VASP"
] | 965c6430cc9965ad61c99b4c8a519e2c94d2e5e6bbe472af929c6f19f605022d |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements plotter for DOS and band structure.
"""
import logging
from collections import OrderedDict, namedtuple
import numpy as np
import scipy.constants as const
from monty.json import jsanitize
from pyma... | vorwerkc/pymatgen | pymatgen/phonon/plotter.py | Python | mit | 31,299 | [
"Gaussian",
"pymatgen"
] | cee5c04772864695ac46d3dfc20e31244b11f4269e054a36e92724a87b805e32 |
from __future__ import absolute_import
from __future__ import print_function
from __future__ import division
import unittest
from pymatgen.analysis.elasticity.elastic import *
from pymatgen.analysis.elasticity.strain import Strain, Deformation
from pymatgen.analysis.elasticity.stress import Stress
from pymatgen.util.... | nisse3000/pymatgen | pymatgen/analysis/elasticity/tests/test_elastic.py | Python | mit | 22,025 | [
"pymatgen"
] | 6856dbc1904a8e0a2dc4215c0d34f9d02d1c65c4b2078826c73c1788137902f5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Logging Facility
"""
import logging
import datetime
def print_msg(msg):
curtime = datetime.datetime.now()
mytime = "%s/%s/%s:%s.%s.%s" % \
(str(curtime.month), str(curtime.day), str(curtime.year),
str(curtime.hour), str(curtime.minute), str(c... | Symantec/py-statsd | pystatsd/pystats_log.py | Python | apache-2.0 | 2,670 | [
"Brian"
] | 2e1f21dc3f04b332528a38a7d1054ea2d1c7add9660b0af668729c181c016ada |
#
# Copyright (c) 2008--2012 Red Hat, Inc.
#
# This software is licensed to you under the GNU General Public License,
# version 2 (GPLv2). There is NO WARRANTY for this software, express or
# implied, including the implied warranties of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. You should have received a c... | dmacvicar/spacewalk | backend/server/rhnServer/server_class.py | Python | gpl-2.0 | 32,164 | [
"CDK"
] | d6824e30f0ee4d394f29bba49cad2f2c08393abaf2503fc98c2dd42adc8b3631 |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... | GoogleCloudPlatform/python-docs-samples | composer/airflow_1_samples/kubernetes_pod_operator.py | Python | apache-2.0 | 12,258 | [
"VisIt"
] | 0fd1a1c5a29d937fbdcb2841ba1b97808f7a75676ec08e131fcbcfbcfdb82b4f |
#!/usr/bin/env python
import os
import time
import re
import numpy
from pyscf import lib
from pyscf import gto, scf, dft, mcscf, mp, cc, lo
def sort_mo(casscf, idx, mo_coeff):
mol = casscf.mol
corth = lo.orth.orth_ao(mol)
casorb = corth[:,idx]
nmo = mo_coeff.shape[1]
ncore = casscf.ncore
ncas ... | gkc1000/pyscf | examples/2-benchmark/n2.py | Python | apache-2.0 | 2,085 | [
"PySCF"
] | c8a1ec6ffc2caf10c78f17cdeb8ffe3329953bc09595b9560ad083ff8d186645 |
# Copyright 2009-2013 Eucalyptus Systems, Inc.
#
# 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.
#
# This program is distributed in the hope that it will be useful,
# b... | eucalyptus/euca-python-lib | eucalib/log_util.py | Python | bsd-2-clause | 1,966 | [
"VisIt"
] | f13e556460161a9c4e18ea1a56656a6da82ca135283ffabe6490e5a7fd6df154 |
#!/usr/bin/env python
# This script generates pvd files for time series in paraview
import vtktools as vtk
import glob
import re
import sys
def generate_pvd(pvdfilename, list_vtu_filenames, list_time):
""" This function writes a simple xml pvd file that can be
loaded in paraview to display time series co... | rjferrier/fluidity | tools/genpvd.py | Python | lgpl-2.1 | 3,433 | [
"ParaView",
"VTK"
] | 2b9b85f5b3c1a8db8f2980fd4cd539571cc2810a14e532264015d797e41252e6 |
#!/usr/bin/env python
#
# $File: output.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute it ... | BoPeng/simuPOP | docs/output.py | Python | gpl-2.0 | 1,867 | [
"VisIt"
] | 201fd39ef992834f4babb086273ffc8e6592c95a813813d7c2364511ff21fb88 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | tronlogistics/micro | venv/lib/python2.7/site-packages/setuptools/command/easy_install.py | Python | bsd-3-clause | 82,743 | [
"VisIt"
] | 2e2deb9a1a4d658df72755a0d330613f5d623f9522564125dcfce4eb1c144b31 |
"""MSMBuilder: Statistical models for Biomolecular Dynamics
"""
from __future__ import print_function, absolute_import
DOCLINES = __doc__.split("\n")
import os
import sys
import glob
import traceback
import numpy as np
from os.path import join as pjoin
from setuptools import setup, Extension, find_packages
try:
... | rmcgibbo/msmbuilder | setup.py | Python | lgpl-2.1 | 6,936 | [
"Gaussian",
"MDTraj"
] | 9ad051e072120e3c6bdfec3a6308522e00f7378fa016f380435972e559e7c5c9 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/experimenting.py | Python | gpl-2.0 | 6,644 | [
"ChemPy",
"PyMOL",
"TINKER"
] | 81ee8818f6f90d750ef013b0cf5a1bd1e960ff454c8271628b1bb4083cb269c9 |
from net.canarymod.api.inventory import ItemType
#for full list of ItemTypes visit CanaryMod documention
#http://docs.visualillusionsent.net/CanaryLib/1.2.0/net/canarymod/api/inventory/ItemType.html
IRON_SHOVEL = ItemType.IronSpade
IRON_PICKAXE = ItemType.IronPickaxe
IRON_AXE = ItemType.IronAxe
FLINT_AND_STEEL = ... | gamestartdev/mponline | server/python/items.py | Python | gpl-2.0 | 343 | [
"VisIt"
] | af67f6efdd7e07f1f8d3a0a4870f5e86fc84e89368b3e8709578295be559d1f0 |
"""
User policy settings
"""
from askbot.conf.settings_wrapper import settings
from askbot.conf.super_groups import LOGIN_USERS_COMMUNICATION
from askbot.deps import livesettings
from django.conf import settings as django_settings
from askbot.skins import utils as skin_utils
from django.utils.translation import ugettex... | afdelgado/askbot | askbot/conf/user_settings.py | Python | gpl-3.0 | 3,305 | [
"VisIt"
] | a6b1b4cc136e1c314940c5b338dfc3f393ba97f46a77f8f9ebecd688408cb099 |
# Copyright (C) 2014-2019 The BET Development Team
r"""
This module contains unittests for :mod:`~bet.sampling.adaptiveSampling`
"""
import unittest
import os
import glob
import numpy.testing as nptest
import numpy as np
import bet.sampling.adaptiveSampling as asam
import scipy.io as sio
from bet.Comm import comm
im... | smattis/BET-1 | test/test_sampling/test_adaptiveSampling.py | Python | gpl-3.0 | 36,587 | [
"MOOSE"
] | 42533c96290444f3404657e9f12bc0720288a32a6ca897b80727014bee94c21f |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
QAD Quantum Aided Design plugin
classe per gestire il map tool di richiesta di un punto
-------------------
begin : 2013-05-22
copyright ... | gam17/QAD | qad_getpoint.py | Python | gpl-3.0 | 69,743 | [
"CASINO"
] | b7155e5eced6c86bf4a2331f22218acc43d7a72f840d002ada4d21f3e019d5d8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
author: Martin Alexandre
last edited: May 2013
"""
import sys,os,commands,time
import string, math
from numpy import array,sqrt,zeros,conjugate,arange,linspace,exp,log,sin,dot,degrees,arccos
from numpy.fft import rfft,fft, ifft
from num... | SamKChang/abinit-7.10.5_multipole | scripts/post_processing/appa/utility/analysis.py | Python | gpl-3.0 | 33,580 | [
"ABINIT",
"ADF",
"Gaussian",
"NetCDF"
] | d1a2eac2d1e959f1e7cada0e3e1e9e88b220ff4ad34aaf9ab769956107c5fea1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is intended to be used to compute Pourbaix diagrams
of arbitrary compositions and formation energies. If you use
this module in your work, please consider citing the following:
General formalis... | gmatteo/pymatgen | pymatgen/analysis/pourbaix_diagram.py | Python | mit | 42,106 | [
"pymatgen"
] | 8535347464d4e8c7734baf5348600f46d8d8c059b393a993aebdc37743c79f1a |
country_mappings = {
'Afghani': 'AFG',
'Albanian': 'ALB',
'Antarctic': 'ATA',
'Algerian': 'DZA',
'Samoan': 'ASM',
'Andorran': 'AND',
'Angolan': 'AGO',
'Antiguan': 'ATG',
'Azerbaijani': 'AZE',
'Argentine': 'ARG',
'Australian': 'AUS',
'Austrian': 'AUT',
'Bahameese': 'BHS',
'Bahrainian': 'BHR',
'Banglade... | darenr/MOMA-Art | geotagger/nationality-to-countrycode.py | Python | mit | 5,004 | [
"BWA"
] | 8765dd1daedd250d8f8d9eca67bf15b8342a506b532a33d0cf911b2e5d3c3a73 |
"""Timeseries plotting functions."""
from __future__ import division
import numpy as np
import pandas as pd
from scipy import stats, interpolate
import matplotlib as mpl
import matplotlib.pyplot as plt
import warnings
from .external.six import string_types
from . import utils
from . import algorithms as algo
from .p... | phobson/seaborn | seaborn/timeseries.py | Python | bsd-3-clause | 16,051 | [
"NEURON"
] | fb0a381b38ac4475cbfa8f0f9a4e6a90b721357565a1fb8f447237c1dbd6bde2 |
"""HeatMap of restaurants on map"""
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from scipy.cluster.vq import vq, kmeans, whiten
from scipy.spatial.distance import cdist
from MapUtils import Coordinate, Position, Rectangle, create_n_unique_colors
from Map import Map
from DataImporter import ge... | harinisuresh/yelp-district-clustering | LDAHeatMap.py | Python | mit | 5,654 | [
"Gaussian"
] | feef32bd4b9c4c809d78d3c5dd1b5d70eb30bace861721e422ace517f4ec2e74 |
#import importlib
#import collections
import StringIO
import numpy
import json
import pyscf
from pyscf import gto
from pyscf import dft
def json2pyscf(jstr):
jdic = json2pydict(jstr)
mol = load_jdict_mol(jdic)
driver = jdic['driver']
rawinp = to_pyscf_rawinput(jdic, mol)
exec rawinp
output =... | PyQC/json_schema | pyscf/from_json.py | Python | apache-2.0 | 5,076 | [
"Psi4",
"PySCF"
] | 93b1b3af1fdc7f1e17ac8202355f2d8d00af0fc974634a693225b284a1f5060b |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/mobile/eventview.py | Python | gpl-2.0 | 9,982 | [
"VisIt"
] | 3cc8c41b92d1eb5b5c045164d8a1782dd6eb429eb64139369c72428c99ffc54d |
import os
from matplotlib import pyplot as plt
base = 92
path = "/fslhome/holiver2/vasp/alloydatabase/"
dirs = sorted([d for d in os.listdir(newpath) if os.path.isdir(os.path.join(newpath,d))])
EATOM = []
PSCENC = []
TOTEN = []
TEWEN = []
EBANDS = []
SIGMA0 = []
nENTRO = []
CPUTIME = []
IRRKPTS = []
KPTORDER = []
w... | hallover/alloy-database | code/plotdata.py | Python | mit | 3,510 | [
"VASP"
] | 430d35e04c1605f7162f9e9c03fdaccfcc0f918f97c4a1daa8b30af61121ac9d |
# Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
import functools
import logging
import operator
import re
import warnings
from abc import ABC, abstractmethod
from collections import OrderedDict
from contextlib import ExitStack, contextmanager
from functools import reduce
from timeit... | uber/pyro | pyro/contrib/epidemiology/compartmental.py | Python | apache-2.0 | 49,843 | [
"Gaussian"
] | 487c82cb64a2a414504dd13ce78c45b28a398efb2b2154eab40b17541c25e85a |
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 9 17:52:23 2015
@author: Villanueva
"""
import os
import time
import logging
from typing import Dict, List, Tuple, Union
import warnings
from collections import Counter
import numpy as np
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import h... | pedvide/simetuc | simetuc/lattice.py | Python | mit | 24,784 | [
"ASE",
"CRYSTAL"
] | c41938f3ff5933606795240c1ebce178d49e7c621e8e785cf3c3dde9d737e6a9 |
"""Acceptance tests for LMS-hosted Programs pages"""
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.catalog import CatalogFixture, CatalogIntegrationMixin
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.fixtures.programs import ProgramsConfigMixin... | Stanford-Online/edx-platform | common/test/acceptance/tests/lms/test_programs.py | Python | agpl-3.0 | 5,324 | [
"VisIt"
] | f4569da76953a987ed9ec9205bec97b93a0cf46019afcc0e9fc5dbee4267cd92 |
import random
import sys
import uuid
from datetime import datetime, timedelta
from django.conf import settings
from django.contrib.auth.models import User
from django.contrib.flatpages.models import FlatPage
from django.contrib.sites.models import Site
from django.core.management.base import BaseCommand
from chipy_or... | chicagopython/chipy.org | chipy_org/dev_utils/management/commands/makedevdata.py | Python | mit | 6,636 | [
"Galaxy"
] | d2d94ae9d98908d7b3def7dac86a9d82149ff9277ce502f92ad7ebda84edae8f |
"""
Linear dynamical system model for the AP text dataset.
Each document is modeled as a draw from an LDS with
categorical observations.
"""
import os
import gzip
import time
import pickle
import collections
import numpy as np
from scipy.misc import logsumexp
from sklearn.feature_extraction.text import CountVectorizer... | HIPS/pgmult | experiments/alice_lds.py | Python | mit | 20,359 | [
"Gaussian"
] | 47c3cea34e3b5ee544dc4f83f25322ec72b8125377d49b4e4ab334a147feea09 |
import os
from lutris.runners.runner import Runner
from lutris.util.display import get_current_resolution
class fsuae(Runner):
human_name = "FS-UAE"
description = "Amiga emulator"
platforms = [
"Amiga 500",
"Amiga 500+",
"Amiga 600",
"Amiga 1000",
"Amiga 1200",
... | daniel-j/lutris | lutris/runners/fsuae.py | Python | gpl-3.0 | 10,290 | [
"ADF"
] | 8049d76f7a0506a03c853545a87b49d31bf28874d4ecd8938ee2e0ce824cdd69 |
from collections import OrderedDict
from django.utils.translation import ugettext_lazy as _
from django.utils.translation import ungettext_lazy
from privacyscore.evaluation.description import describe_locations
from privacyscore.evaluation.rating import Rating
# Checks are ordered in groups.
# Each check defines a s... | PrivacyScore/PrivacyScore | privacyscore/evaluation/default_checks.py | Python | gpl-3.0 | 122,823 | [
"VisIt"
] | 51b1b83b1ad8e8b84448f6d08de8f16a5bd0eb8c77197ae4e7861fb609662dd4 |
from __future__ import division, print_function, absolute_import
import os
import sys
if sys.version_info[0] < 3:
from urllib2 import urlopen
else:
from urllib.request import urlopen
from os.path import join as pjoin
from hashlib import md5
import numpy as np
import nibabel as nib
from dipy.core.gradients ... | maurozucchelli/dipy | dipy/data/fetcher.py | Python | bsd-3-clause | 11,104 | [
"VisIt"
] | 91ba2c6e5e2df1e1a9de94ac8c07b32e3d0f081a647f3959dbe8fd81f6543d7a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
E-I network connected with NEST topology
----------------------------------------
Simulation of a network consisting of an excitatory and an inhibitory
neuron population with distance-dependent connectivity.
The code bases on the script
brunel_alpha_nest.py
which... | jhnnsnk/VIOLA | test_data/topo_brunel_alpha_nest.py | Python | gpl-2.0 | 39,361 | [
"Gaussian",
"NEURON"
] | b063386d0b218e00ef4fc0c24363a82b2e15e3fab1fe7bb99e435079254ba134 |
# (c) 2015, Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | emersonsoftware/ansiblefork | lib/ansible/plugins/action/patch.py | Python | gpl-3.0 | 2,631 | [
"Brian"
] | a50647ba78ca23cc77d7e86c042a10e8cde50ec9e1610c41b12444f0b752b203 |
#
# Copyright (C) 2010,2012,2013,2014,2015,2016 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of th... | KonradBreitsprecher/espresso | doc/tutorials/02-charged_system/scripts/nacl.py | Python | gpl-3.0 | 6,525 | [
"ESPResSo"
] | a7b68e7017b88599e46009ffcc8fd684b8f1a6ec98be3ab917299af780e3ae3e |
#!/usr/bin/env python
# Convenience script - extracts Plexus import file and slice images from NetCDF
#
# (c)2013 ANUSF
if __name__ == "__main__":
import sys, os, os.path, time, re
import optparse
from logger import *
from file_cache import FileCache
from history import History, as_json
from m... | odf/PlexusIngest | extract.py | Python | mit | 1,355 | [
"NetCDF"
] | 4a388d68e0c836dc72e771671f1b4898d5947b58cdace29658a3ecb1dbef837b |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
import yaml
import unittest
from collections import OrderedDict
from monty.collections import AttrDict
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinitio.tasks import ParalConf
from pymatgen.io.abinitio.qadapters i... | rousseab/pymatgen | pymatgen/io/abinitio/tests/test_qadapters.py | Python | mit | 12,021 | [
"pymatgen"
] | fbdbc6b51a09cc8e356245a8d845da70ba123a61aced140b745361a272359d64 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Time_Window/test10_cross_validate_categories_800ms.py | Python | mit | 4,370 | [
"Mayavi"
] | ca7e259758bec6880cfbdd5a8aaec60001640d242c691c7afd0b54a6fc64fa2c |
#!/usr/bin/env python
#/**********************************************************************
#** This program is part of 'MOOSE', the
#** Messaging Object Oriented Simulation Environment.
#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
#** It is made available under the terms of the
#** GNU Lesser G... | dilawar/moose-full | moose-examples/snippets/HigginsGraupnerBrunel2014_LifetimeCaPlasticity.py | Python | gpl-2.0 | 6,074 | [
"MOOSE"
] | d1d551be383b43e5938c6ee6ab4819cb7751890fd09058236b11869f596db4db |
try:
from django.urls import reverse
except ImportError:
from django.core.urlresolvers import reverse
from tastypie import authorization
from tastypie.authentication import MultiAuthentication
from crits.backdoors.backdoor import Backdoor
from crits.backdoors.handlers import add_new_backdoor
from crits.core.ap... | Magicked/crits | crits/backdoors/api.py | Python | mit | 3,830 | [
"Amber"
] | 3710d5004a73cdeb93a433194fc1fadffb0a64dd706bece6a65623123148d615 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | Nick-Hall/gramps | gramps/plugins/webreport/media.py | Python | gpl-2.0 | 32,089 | [
"Brian"
] | 28ae63af059605994385128d531c17d05bf4ae772d921fa8d5df982ce1481626 |
#!/usr/bin/env python2
# Make.py tool for managing packages and their auxiliary libs,
# auto-editing machine Makefiles, and building LAMMPS
# Syntax: Make.py -h (for help)
# Notes: needs python 2.7 (not Python 3)
import sys,os,commands,re,copy,subprocess
# switch abbrevs
# switch classes = created class for each s... | zimmermant/dlvo_lammps | src/Make.py | Python | gpl-2.0 | 82,243 | [
"LAMMPS"
] | 8d1aa19311d7d48f8ca9b6f97145e5e1746561a3b06f28b924094d3b8a094943 |
# encoding: utf-8
"""sys.excepthook for IPython itself, leaves a detailed report on disk.
Authors:
* Fernando Perez
* Brian E. Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2001-2007 Fernando Perez. <fperez@colorado.edu>
# Copyright (C) 2008-2011 The IP... | Vvucinic/Wander | venv_2_7/lib/python2.7/site-packages/IPython/core/crashhandler.py | Python | artistic-2.0 | 7,635 | [
"Brian"
] | e8a68228c73964c4e537601cd382817c8856223ee76e75d113c39f4ef78d0421 |
"""
Acceptance tests for Library Content in LMS
"""
import textwrap
import ddt
import six
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.studio.library import StudioLibraryContainerXBlockWrapper, StudioLibraryContentEditor
from common.test.accep... | cpennington/edx-platform | common/test/acceptance/tests/studio/test_studio_library_container.py | Python | agpl-3.0 | 7,531 | [
"VisIt"
] | f62e9db357bb452125de2adc7037f58a0be756d693c692a740278602531b52d1 |
#!/usr/bin/env python
#
# $File: iterator.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute i... | BoPeng/simuPOP | docs/iterator.py | Python | gpl-2.0 | 1,311 | [
"VisIt"
] | 018f005bb09d729360a5254c140251e165fa0446ed7a7aa15d9d61eaf05f7276 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#
# GitHub to Kibana
#
# Copyright (C) 2016 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 your o... | sanacl/GrimoireELK | utils/gh2arthur.py | Python | gpl-3.0 | 9,899 | [
"Elk"
] | 22158d46f3a9929ff115fbdd8ed2b735aedf09190b7ea0f2f62c13a5516051f2 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-ape/package.py | Python | lgpl-2.1 | 2,835 | [
"Bioconductor"
] | 4acb240b7c265398c64a3fdca4e397136dcce99795b348a8cfde59f019a0e3b3 |
# -*- coding: utf-8 -*-
"""
Test model update steps.
"""
from nose.tools import ( # pylint:disable=no-name-in-module
assert_equals,
assert_in,
assert_not_equals,
)
from tests.util import in_directory, run_scenario
@in_directory(__file__, 'django', 'dill')
def test_model_creation():
'Models are crea... | koterpillar/aloe_django | tests/integration/test_model_steps.py | Python | gpl-3.0 | 3,522 | [
"Octopus"
] | 7c296a74a86a599041a1b46d14378f8ec6360bdf35adf8d7a8a68fab00b5eb39 |
'''
This is a Brian script implementing a benchmark described
in the following review paper:
Simulation of networks of spiking neurons: A review of tools and strategies
(2007). Brette, Rudolph, Carnevale, Hines, Beeman, Bower, Diesmann, Goodman,
Harris, Zirpe, Natschlager, Pecevski, Ermentrout, Djurfeldt, Lansner, Roc... | brian-team/brian2cuda | examples/cuba.py | Python | gpl-2.0 | 4,237 | [
"Brian",
"NEURON"
] | a8609dc618894aecd2a2734e5d8a62c831f4a82e10740850a3c48ff9cffbed55 |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
from pyclaw import data
#------------------------------
def setrun(claw_pkg='classic'):
#------------------------------
... | clawpack/clawpack-4.x | doc/sphinx/example-acoustics-1d/setrun.py | Python | bsd-3-clause | 5,699 | [
"Gaussian"
] | b5b16908b5276a0f8801d3bff5abc0d9dd6aff5d35e3e0070dfed3af055c51bd |
"""
Acceptance tests for Home Page (My Courses / My Libraries).
"""
from bok_choy.web_app_test import WebAppTest
from flaky import flaky
from opaque_keys.edx.locator import LibraryLocator
from uuid import uuid4
from ...fixtures import PROGRAMS_STUB_URL
from ...fixtures.config import ConfigModelFixture
from ...fixtures... | solashirai/edx-platform | common/test/acceptance/tests/studio/test_studio_home.py | Python | agpl-3.0 | 7,610 | [
"VisIt"
] | 50093649a576e3a900597fbd051a83e942aef5c09413f3ed9139f3c9adb32af2 |
#!/usr/bin/python
# -*- coding: cp1252 -*-
#
#dxf2gcode_b02_geoent_spline
#Programmers: Christian Kohl�ffel
# Vinzenz Schulz
#
#Distributed under the terms of the GPL (GNU Public License)
#
#dxf2gcode is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public L... | workflo/dxf2gcode | source/DxfImport/GeoentSpline.py | Python | gpl-3.0 | 7,495 | [
"Gaussian"
] | ee80ea047535e7a047ebffd293993c5913f68a6fb72a3aa743934c00553f0492 |
from abc import abstractmethod
from kameleon_mcmc.distribution.Gaussian import Gaussian
from kameleon_mcmc.mcmc.samplers.MCMCSampler import MCMCSampler
from numpy import eye
from numpy.ma.core import sqrt, exp, log, shape, reshape, outer, ones
class AdaptiveMetropolis(MCMCSampler):
'''
Plain Adaptive Metropoli... | karlnapf/kameleon-mcmc | kameleon_mcmc/mcmc/samplers/AdaptiveMetropolis.py | Python | bsd-2-clause | 3,227 | [
"Gaussian"
] | 033b8f05ca406535abf3a6c28d8814264b1ab23ffb463883cc550119d22deab3 |
#!/usr/bin/env python
import numpy as np
from matplotlib import pyplot
from scipy import constants
import csv
cdata = []
with open('../xray_attenuation/coeffs.csv', 'rb') as coeffs_file:
creader = csv.DictReader(coeffs_file, skipinitialspace = True)
for row in creader:
cdata.append(row)
gdata = []
w... | darkstar007/xseeker | data/atmosphere/atmospheric_atten.py | Python | gpl-3.0 | 3,163 | [
"Avogadro"
] | 7a52ba6ddc0327f736f2efef3c377aa0bc1f16ffc0c7f27012f2949fc7723320 |
# This work is licensed under the GNU Public License (GPL).
# To view a copy of this license, visit http://www.gnu.org/copyleft/gpl.html
# Written by Abd Allah Diab (mpcabd)
# Email: mpcabd ^at^ gmail ^dot^ com
# Website: http://mpcabd.igeex.biz
# Ported and tweaked from Java to Python, from Better Arabic
# Reshaper ... | edx/edx-certificates | arabic_reshaper.py | Python | agpl-3.0 | 15,013 | [
"VisIt"
] | a627f2bcd8965d4065983aedb901a52c6b1732c251f02d2807590fbb7d757c12 |
# $HeadURL $
''' DIRAC.ResourceStatusSystem.PolicySystem.Actions package
'''
__RCSID__ = '$Id: $'
################################################################################
#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF | Sbalbp/DIRAC | ResourceStatusSystem/PolicySystem/Actions/__init__.py | Python | gpl-3.0 | 264 | [
"DIRAC"
] | 3e7da3410de49eb0ea44ff58973ac8e5e7b16acda26d2690343ce81d6ab8c42a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Pierre Legrand
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyrig... | jsburg/xdsme | XOalign/XOalign.py | Python | bsd-3-clause | 35,674 | [
"CRYSTAL"
] | 7eff1d03d87c9caf4b7fececda01a62527cec6daf10837b43342239f6af7cee4 |
##
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Copyright:: Copyright 2013-2019 CaSToRC, The Cyprus Institute
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>
# License:: MIT/GPL
# $Id$
#
##
"""
Easybuild support for building NAMD, implemented as an easyblock
@autho... | hpcuantwerpen/easybuild-easyblocks | easybuild/easyblocks/n/namd.py | Python | gpl-2.0 | 11,125 | [
"NAMD"
] | 5007430833369682b27bb34c7593188b9a9851c2d949bf7e7090693b4b0e89f5 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import logging
logger = logging.getLogger(__name__)
# import funkcí z jiného adresáře
import os.path
import os.path as op
# import copy
import unittest
from nose.plugins.attrib import attr
# sample_data_path = os.path.dirname(os.path.abspath(__file__))
# sample_data_pat... | kunesj/io3d | tests/qt_test.py | Python | mit | 4,009 | [
"VTK"
] | bd1960db0db2e363e435bd4972b39e1999808a559c8dbd2dab89cbf685c32a76 |
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, ... | CMUSV-VisTrails/WorkflowRecommendation | scripts/gen_vtk_examples/vtk_to_vt.py | Python | bsd-3-clause | 55,789 | [
"VTK"
] | b4b116bcf0b41d84b3bb6f1a3364d39e828f076bb3d5dd0a611d377123f7f431 |
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit import DataStructs
from rdkit.Chem import MACCSkeys
from rdkit.Chem import FragmentCatalog
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import os
# This is James Sungjin Kim's library
import j3.jutil... | jskDr/jamespy | j3/jchem.py | Python | mit | 50,029 | [
"RDKit"
] | b8fb7c64770eb95aed282e26bef7d46cefbca7daea885deb34b82f398de710f6 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/gtk-window-decorator/__init__.py | Python | gpl-3.0 | 857 | [
"ORCA"
] | be5c2fbb3f1b2edcb7d75c7750359f2f5e3e8b5cc6280f0e2989d8d7fc009721 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/cgo.py | Python | gpl-2.0 | 13,712 | [
"ChemPy",
"PyMOL"
] | 4a272d65147aa282f57ebda39d0adcf829527c5884aea70c821131b8b7abe8ac |
# MicroPython python3
# vim: set sw=2 ai expandtab
#
# Released under the Apache 2.0 license.
# http://www.apache.org/licenses/
import os
import sys
import time
import apa102
from apa102 import DISC_RINGS, NUM_DISC_LEDS, NUM_RINGS, DISC_RING_OFFSETS
orig = [apa102.cyan, apa102.blue, apa102.indigo, apa102.violet,
... | gpshead/life_circle | life.py | Python | apache-2.0 | 13,039 | [
"Amber"
] | eb9c3aab886ca97d7b3faf59bb5cba1f2bc4d1228e9234af0852eb5d373291d1 |
import os
import subprocess
from gpaw.test.big.agts import Cluster
class NiflheimCluster(Cluster):
def __init__(self, asepath='', setuppath='$GPAW_SETUP_PATH'):
self.asepath = asepath
self.setuppath = setuppath
def submit(self, job):
dir = os.getcwd()
os.chdir(job.dir... | robwarm/gpaw-symm | gpaw/test/big/niflheim.py | Python | gpl-3.0 | 3,853 | [
"ABINIT",
"ASE",
"GPAW",
"NWChem"
] | d70e7e2d8b4c1ab96807ff7008e460ad005540b71835b992785f172826f9feec |
import unittest
from test import test_support
from itertools import *
from weakref import proxy
import sys
import operator
import random
maxsize = test_support.MAX_Py_ssize_t
minsize = -maxsize-1
def onearg(x):
'Test function of one argument'
return 2*x
def errfunc(*args):
'Test function that raises an er... | mancoast/CPythonPyc_test | cpython/252_test_itertools.py | Python | gpl-3.0 | 34,195 | [
"GULP"
] | 560e78bd99b4bc1ee80301a1cc4c0092967a7bcef2355203afacbe1b3a8e5320 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
NeuroKit plugin for MOOSE.
"""
__author__ = "Aviral Goel"
__credits__ = ["Upi Lab"]
__license__ = "GPL3"
__version__ = "1.0.0"
__maintainer__ = "Aviral Goel"
__email__ = "goel.aviral@gmail.com"
__status__ = "Development"
# i... | dilawar/moose-full | moose-gui/plugins/NeuroKit.py | Python | gpl-2.0 | 2,145 | [
"MOOSE"
] | b15db6390a8deff4a0cd5e891c8f154e65ec0d4ed838fe32aa193ad89a41bd88 |
from __future__ import print_function, division, unicode_literals
import os
from pymatgen.core.structure import Structure
from pymatgen.io.vasp.inputs import Kpoints, Incar
from mpinterfaces import VASP_STD_BIN, VASP_TWOD_BIN, VDW_KERNEL, QUEUE_SYSTEM
import mpinterfaces.utils as utl
__author__ = "Michael Ashton"
_... | henniggroup/MPInterfaces | mpinterfaces/mat2d/stability/startup.py | Python | mit | 3,141 | [
"VASP",
"pymatgen"
] | c2d681f05dd4e368a2005e5d309b24751c9da5eba5d8af74b78364db0d47700c |
# Illustrative GUI driving a small subset of PyAbel methods
# tkinter code adapted from
# http://matplotlib.org/examples/user_interfaces/embedding_in_tk.html
import numpy as np
import abel
from scipy.ndimage import shift
import matplotlib; matplotlib.use('TkAgg') # avoids crash on OSX
from matplotlib.backends.ba... | PyAbel/PyAbel | examples/example_simple_GUI.py | Python | mit | 7,949 | [
"Gaussian"
] | 02d170b109b15c2b504f86ee24777e0ce84597d8bf97824f27cfc27ac0e7f958 |
"""Command line options, ini-file and conftest.py processing."""
import argparse
import collections.abc
import copy
import enum
import inspect
import os
import re
import shlex
import sys
import types
import warnings
from functools import lru_cache
from pathlib import Path
from textwrap import dedent
from types import T... | pytest-dev/pytest | src/_pytest/config/__init__.py | Python | mit | 59,523 | [
"VisIt"
] | d19816ec2339222cd23845e5b9aadaf6e47265fad203d0e35af13aad7c6cbbbd |
# pylint: disable=invalid-name
#
# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MAPS - Execute this
#
# Here we run the calibration of a selected part of MAPS
from __future__ import absolute_import, division, print_function
import tube
from tube_calib_fit_params import TubeCalibFitParams
import mantid.simpleapi as mant... | dymkowsk/mantid | scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py | Python | gpl-3.0 | 2,774 | [
"Gaussian"
] | edec02cc35595ca11c478892dff2508c30507384030e59dd4aeab5aa740eb814 |
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