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#!/usr/bin/python
#
# Copyright 2012 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | jath03/projects | local/Google server test/authorized_api_web_server_calendar.py | Python | mit | 10,730 | [
"VisIt"
] | 8847e04fb5f6ef5bd8909a39eda7085980b8d176c80433ad79146e57bc241ed6 |
#!/usr/bin/env python
#Error Report Generator v1.0
#Copyright (c) 2014 by Brian Mikolajczyk, brianm12@gmail.com
#For generating error reports from 'drclog' files in copied directory
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | bmikolaj/direscraw | genreports.py | Python | gpl-3.0 | 3,399 | [
"Brian"
] | 023eaa8671ba52996f201af3deae17f860a06c0009ab1dc5c22535997b900c4a |
#!/usr/bin/env python3
import os
import sys
import logging
import runner
import collections
import tempfile
import shutil
import re
from fasta_clean_name import read_fasta_file_handle, format_seq
logger = logging.getLogger(__name__)
def index_ref(indexdb_bin_path, input_fasta_ref_path, output_basepath, max_mem, ver... | ppericard/matamog | scripts/compute_abundance.py | Python | agpl-3.0 | 6,189 | [
"BLAST"
] | e6bfdddf04bea6aa10289f01c14a2195905bebcec93a5495498bc6f83a3b0a14 |
#!/usr/bin/env python
"""
meta-sweeper - for performing parametric sweeps of simulated
metagenomic sequencing experiments.
Copyright (C) 2016 "Matthew Z DeMaere"
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 F... | cerebis/meta-sweeper | bin/readthru_parser.py | Python | gpl-3.0 | 16,212 | [
"BWA",
"pysam"
] | c15f7be08d90620c35ce289d90797dc0c697e6561fc950d9198398a01a73baa8 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_R16.py | Python | gpl-3.0 | 2,237 | [
"VTK"
] | 9704e462ed74d5cdf759cbccd2cb9c3b9827dc896efffa8cf68a3e10e5a55dea |
#!/usr/bin/env python
#
# Copyright 2012 Google Inc. All Rights Reserved.
"""Python script for interacting with BigQuery."""
import cmd
import codecs
import datetime
import httplib
import json
import os
import pdb
import pipes
import platform
import shlex
import sys
import time
import traceback
import types
impor... | harshilasu/GraphicMelon | y/google-cloud-sdk/platform/bq/bq.py | Python | gpl-3.0 | 81,521 | [
"VisIt"
] | c2a1569391a3271e2d5947800d95b21593002701ac44bf69afc16d9d3212614a |
"""
This module provides a number of algorithms that can be used with
the dataset classes defined in the dataset_adapter module.
See the documentation of the dataset_adapter for some examples.
These algorithms work in serial and in parallel as long as the
data is partitioned according to VTK data parallel execution
gui... | mspark93/VTK | Wrapping/Python/vtk/numpy_interface/algorithms.py | Python | bsd-3-clause | 43,328 | [
"VTK"
] | 1a88bcba13187b5479517b27e1fe3c8ca3af4a4100a4e242c82b39fa0faf571e |
"""
Maps: ComboMaps
===============
Invert synthetic magnetic data with variable background values
and a single block anomaly buried at depth. We will use the Sum Map
to invert for both the background values and an heterogeneous susceptibiilty
model.
.. code-block:: python
:linenos:
"""
import discretize
from S... | simpeg/simpeg | examples/01-maps/plot_sumMap.py | Python | mit | 6,018 | [
"Gaussian"
] | 21cd2db5159081034e54bceaf47cfa7c132299428c6210932d03d2c1d57b198a |
from PyQt5.QtWidgets import QDialog, QApplication
from GEMEditor import __projectpage__, __version__, __citation__
from GEMEditor.main.about.ui import Ui_AboutDialog
class AboutDialog(QDialog, Ui_AboutDialog):
def __init__(self, parent):
QDialog.__init__(self, parent)
self.setupUi(self)
ap... | JuBra/GEMEditor | GEMEditor/main/about/about.py | Python | gpl-3.0 | 2,728 | [
"VisIt"
] | e37cf0323d6940f8716c82693dd7dace87e5bf9854ee2193083ec72227f2e916 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
QE Type Conversions
######################
"""
lengths = {'alat': 'alat', 'bohr': 'au', 'crystal': 'crystal',
'angstrom': 'A', 'crystal_sg': 'crystal_sg'}
def to_qe_... | alexvmarch/atomic | exatomic/qe/types.py | Python | apache-2.0 | 1,774 | [
"CRYSTAL"
] | b39b3a7aa2b13a191d59f8adfbfc2c92dbeade5832dadafe625a84f6cc32c917 |
""" The JobDB class is a front-end to the main WMS database containing
job definitions and status information. It is used in most of the WMS
components
**Configuration Parameters**:
The following options can be set in ``Systems/WorkloadManagement/<Setup>/Databases/JobDB``
* *MaxRescheduling*: Set the ma... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/DB/JobDB.py | Python | gpl-3.0 | 78,777 | [
"DIRAC"
] | fb9d257da55630fbd064fa9878c2bb04aea8f462d37fb363fcc3d48e69d03eaa |
#!/usr/bin/env python
"""
Lammps potentital types.
"""
class BondPotential(object):
"""
Class to hold bond styles that are implemented in lammps
Purpose is to store info that the user wants to use to overwrite standard UFF output of lammps_interface
"""
class Class2(object):
"""Potential ... | peteboyd/lammps_interface | lammps_interface/lammps_potentials.py | Python | mit | 45,269 | [
"CHARMM",
"LAMMPS"
] | 22342b240df9f0bee18de2b6fc7fd369ec86fa3f69212dab8dceb7b7c1a5564b |
#!/usr/bin/env python
"check test farm build examples"
#
# Copyright (C) 2010-2021 ABINIT Group (Yann Pouillon)
#
# This file is part of the ABINIT software package. For license information,
# please see the COPYING file in the top-level directory of the ABINIT source
# distribution.
#
# FIXME: detect duplicate definit... | abinit/abinit | abichecks/scripts/check-build-examples.py | Python | gpl-3.0 | 6,826 | [
"ABINIT"
] | fdf60b3c9efffc38ae22c8714014356f2c3fa77ffd37a2dbf8221083a78b845b |
from read_spec import *
from read_spec import Inst
from calcspec import redshift
# https://www.eso.org/sci/facilities/paranal/instruments/espresso/ESPRESSO_User_Manual_P105_v1.0.pdf
# ftp://ftp.eso.org/pub/dfs/pipelines/instruments/espresso/espdr-reflex-tutorial-1.3.2.pdf
name = inst = __name__[5:]
drs = 2 if name.en... | mzechmeister/serval | src/inst_ESPRESSO.py | Python | mit | 5,174 | [
"ESPResSo"
] | baf9ce671b703d2867e38830873a608a17c64dd2fa8664df78faac6e97b083e3 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/sequence/_genetic_code.py | Python | bsd-3-clause | 19,374 | [
"scikit-bio"
] | d721ba919aa6a0dad7d204b0d1839ed8883d9c75b1c151c2a135a7bbfef72bfc |
import sys
import os.path
#sys.path.insert(0, '/home/andy/theano/tool_examples/theano-lstm-0.0.15')
from theano_lstm import Embedding, LSTM, RNN, StackedCells, Layer, create_optimization_updates, masked_loss
from utilities import *
import dill
import argparse
#import cPickle
import pickle
import numpy
from collections... | darongliu/Lstm_Turing_LM | lstm-neural-turing-machines-lm/v3/lm_v4.py | Python | mit | 25,577 | [
"NEURON"
] | 7a08134ea515d2148e3f18a83c3b7ca823b7c3d7df7111e277e047a6c7446546 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | lach76/scancode-toolkit | tests/cluecode/test_copyrights.py | Python | apache-2.0 | 183,412 | [
"Brian",
"VisIt"
] | e6a7e0703d0f5a286f821f7311713db2da7e0d3ffcf32e77220dea1257488fed |
# -*- coding: utf-8 -*-
# Copyright 2016 Christoph Reiter
#
# 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.
"""Check fo... | elbeardmorez/quodlibet | quodlibet/quodlibet/update.py | Python | gpl-2.0 | 5,034 | [
"VisIt"
] | 58b19f1118daf2f648ea4c96215d4f53ea4f1d53c21347b70d6dfc0c3fdafa59 |
r"""
This module contains methods for solving
.. math:: m_t^i + \nabla \cdot (f^i - \sum_k a^{ik} \nabla \phi^k) + H^i(\nabla u) + r^i = 0 \quad i=0,\ldots,nc-1
The solution is the vector of components :math:`u=u_0,\ldots,u_{nc-1}`, and
the nonlinear coefficients are :math:`m^i,f^i,a^{ik},\phi^k, H^i` and :math:`r^i... | erdc/proteus | proteus/Transport.py | Python | mit | 493,821 | [
"VTK"
] | 23f01ee3edf9e94864617caf6c77d7fb28e702850f621596d55038ba022e3e26 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-attributes
# Author : Stuart Paterson
########################################################################
"""
Retrieve attributes associated with the given DIRAC job
Example:
$ dirac-wms-job... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_attributes.py | Python | gpl-3.0 | 2,144 | [
"DIRAC"
] | 97f4198112eb50479fe32d06b8e21a0e694a579f4abd1a29044d409e9b5292c8 |
"""
Contains an abstract base class that supports chemically aware data splits.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import tempfile
i... | joegomes/deepchem | deepchem/splits/task_splitter.py | Python | mit | 3,939 | [
"RDKit"
] | d1da47f03ac9b37b47c0c500439997fccb3577d0e6a1e3ce55a8a9e45925ca9b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/analysis/align.py | Python | gpl-2.0 | 54,145 | [
"Biopython",
"MDAnalysis"
] | 5e941f7e3bd4888a09dc587b2abe2c229c13431f3db618fff57e42bb2f058abe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pytest
from netCDF4 import Dataset
from compliance_checker.cf import util
# get current std names table version (it changes)
std_names = util.StandardNameTable()
# The meat and potatoes of most integration tests lies here
# To add a new integration test, simply... | ioos/compliance-checker | compliance_checker/tests/test_cf_integration.py | Python | apache-2.0 | 22,048 | [
"NetCDF"
] | a3fcef67225c7438985fee676bd5b669003c971786873feabda3d4e6c12b7b66 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import six
import ruamel.yaml as yaml
import os
import json
"""
This module provides classes to perform analyses of
the local environments (e.g., finding near... | czhengsci/pymatgen | pymatgen/analysis/local_env.py | Python | mit | 90,716 | [
"Gaussian",
"Jmol",
"pymatgen"
] | 58899579fd9c87b86e75048834ef67de123045417bb8cb3a1f7e83d8a197f144 |
# Author : Kevin Murphy(@murphyk), Aleyna Kara(@karalleyna)
import matplotlib.pyplot as plt
from functools import partial
import numpy as np
import jax
import jax.numpy as jnp
from jax import jit, tree_leaves, tree_map, vmap
from jax.random import split, PRNGKey, permutation
from jax.nn import one_hot, log_softmax
fr... | probml/pyprobml | old/subspace_sample_mlp_mnist_fixed_dim.py | Python | mit | 4,273 | [
"Gaussian"
] | e394552d1718efa6e0ee7bca8f4d965e24bf3a03d809290cfdb6b6234b2b51f2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# rfestimationLib.py
#
# Copyright 2014 Carlos "casep" Sepulveda <casep@alumnos.inf.utfsm.cl>
#
# 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 Found... | creyesp/RF_Estimation | LIB/rfestimationLib.py | Python | gpl-2.0 | 7,042 | [
"Gaussian"
] | 10e4f8ce9abbeeb6976a7b5bb698a6ce875b61546b8e22bd5a5a33ceef453461 |
#!/usr/bin/env python
########################################################################
# File : dirac-dms-get-file
# Author : Stuart Paterson
########################################################################
"""
Retrieve a single file or list of files from Grid storage to the current directory.
Exam... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_dms_get_file.py | Python | gpl-3.0 | 1,393 | [
"DIRAC"
] | 83a3536f2f6e5468ed91b9e320f120eeabafc7aa17167c9a9b867f51c38fd924 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | shepdelacreme/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 41,092 | [
"VisIt"
] | da99158db1441eb16d921a80dcf3c7b23790a3575ea1ef43c5696f7867bb546b |
# -*- coding: utf-8 -*-
"""
Models used to implement SAML SSO support in third_party_auth
(inlcuding Shibboleth support)
"""
import json
import logging
import re
from config_models.models import ConfigurationModel, cache
from django.conf import settings
from django.contrib.sites.models import Site
from django.core.e... | edx-solutions/edx-platform | common/djangoapps/third_party_auth/models.py | Python | agpl-3.0 | 36,966 | [
"VisIt"
] | 98da1626abe55fb0f4ac77010523c636a3b6e75314c767f3f85ae7a77e59c49d |
# test_synchan.py ---
#
# Filename: test_synchan.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Tue Dec 29 14:32:23 2009 (+0530)
# Version:
# Last-Updated: Tue Dec 29 17:12:21 2009 (+0530)
# By: subhasis ray
# Update #: 43
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:... | BhallaLab/moose-thalamocortical | TESTS/pymoose/test_synchan.py | Python | lgpl-2.1 | 2,518 | [
"MOOSE"
] | 2cc010112ed66788bdeac0e13d1748de97cb81fbf3f5f1e660e073cb87f60903 |
# $Id$
#
# Copyright (C) 2007 greg Landrum
#
# @@ 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.
#
from __future__ import print_function
import doctest... | rvianello/rdkit | rdkit/VLib/UnitTestVLib.py | Python | bsd-3-clause | 4,576 | [
"RDKit"
] | 9673fe76eb7709858bcfad85b44fae93ba0748ed6df88ca876d8b1beb2456634 |
# -*- coding: utf-8 -*-
#
# fortpy documentation build configuration file, created by
# sphinx-quickstart on Thu Jul 7 11:13:05 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | rosenbrockc/fortpy | docs/conf.py | Python | mit | 10,105 | [
"ASE"
] | ca517fdf67f5398472bc02bc4a67efb942390dd2814b0fb12c9ed09db684a0fc |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_client_details.py | Python | gpl-2.0 | 6,128 | [
"VisIt"
] | 9343ddceeb3d773be1334e4c8b62a9071e51995f35d609ae94bfa4842e34a683 |
#!/usr/bin/python
# (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# most of it copied from AWX's scan_packages module
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': ... | tersmitten/ansible | lib/ansible/modules/packaging/os/package_facts.py | Python | gpl-3.0 | 10,698 | [
"Brian"
] | 0d98dfbcd618aa63108ea24383b717f3b4bb94d681463a0582b552b714e2f424 |
# coding: utf-8
"""Mixin for mapping set/getattr to self.set/get"""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# th... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/sugar/attrsettr.py | Python | lgpl-3.0 | 2,254 | [
"Brian"
] | 4a12fb8ace40ee9989d042ceccaefd04a9e32c1e1e4f33c508377c2a6cb857f1 |
# Copyright (c) 2013 Paul Tagliamonte <paultag@debian.org>
#
# 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, modif... | rwaldron/hy | hy/core/mangles.py | Python | mit | 2,980 | [
"VisIt"
] | 0408fb506742d64e573e2d063affc985448fda7d36a140fd3e49766dc03f77db |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
import tempfile
import shutil
from pymatgen.util.testing import PymatgenTest
from monty.functools import lazy_property
from pymatgen... | migueldiascosta/pymatgen | pymatgen/io/abinit/tests/test_flows.py | Python | mit | 10,732 | [
"ABINIT",
"pymatgen"
] | 974806f094ec498a0ed4abbb368f3951c37204cc844d9be32ca60702578f3a99 |
"""
Implementation of Regression on Order Statistics for imputing left-
censored (non-detect data)
Method described in *Nondetects and Data Analysis* by Dennis R.
Helsel (John Wiley, 2005) to estimate the left-censored (non-detect)
values of a dataset.
Author: Paul M. Hobson
Company: Geosyntec Consultants (Portland, ... | bashtage/statsmodels | statsmodels/imputation/ros.py | Python | bsd-3-clause | 18,862 | [
"Gaussian"
] | 0a124022b2afada26f924ca31a9c3643dcd302d024a2ceac3b5d360a198f931c |
#!/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/Openwebif | plugin/controllers/views/web/mediaplayerlist.py | Python | gpl-2.0 | 5,819 | [
"VisIt"
] | 048c97572fbc093e765e62609cdbca599cbb516e5bbcba09c0120e2ebd6fe735 |
""" Class that contains client access to the transformation DB handler. """
__RCSID__ = "$Id$"
from DIRAC import S_OK, gLogger
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.Core.Utilities.List import break... | chaen/DIRAC | TransformationSystem/Client/TransformationClient.py | Python | gpl-3.0 | 20,036 | [
"DIRAC"
] | 160aa1dba78df8b07f0afe71e1fdc237361ab2a3482201bb1467abfce5bffeee |
"""
API operations on the contents of a library folder.
"""
from galaxy import web
from galaxy import util
from galaxy import exceptions
from galaxy.managers import folders
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
from sqlalchemy... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/folder_contents.py | Python | gpl-3.0 | 15,764 | [
"Galaxy"
] | c4d6ecbd1b7e4412006aa43a89603b611ba738c1f0f535b343c86efddde3fd27 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | samples/lj_liquid_distribution.py | Python | gpl-3.0 | 5,946 | [
"ESPResSo"
] | 893af716d9bd8883a22d57408b979ec3de722b02b53a7e513a054b307122b0b2 |
# -*- coding: utf-8 -*-
from django.core.management import setup_environ
import forms.form_models.bfsql as bfsql
import forms.form_models.bform as bforms
from forms.form_models.bfbdb import *
bf = bforms.BerkeleyForm()
bf.baseFont='palatino'
bf.theme=('demos',)
"""
Don't just write documents, create an information ... | cbears/octoform | test/forms/studentaid.py | Python | gpl-3.0 | 4,935 | [
"VisIt"
] | 49fc58b8f4d9fd36455f3be2a17bcbb7f4df389745bd37fcfc4954c981496e2e |
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provid... | jjdmol/LOFAR | LTA/LTAIngest/SOAPpy-0.12.0/SOAPpy/Types.py | Python | gpl-3.0 | 51,785 | [
"Brian"
] | 3c90ad71e36e5335493c4eefb785591d8a568ad6e74c873620ccdee7baac4952 |
#!/usr/bin/env python
#
# Copyright 2014 Brian Quinlan
# See "LICENSE" file for details.
"""Tests for the Brainfuck executable."""
from __future__ import absolute_import
import functools
import os
import os.path
import random
import subprocess
import tempfile
import time
import unittest
EXECUTABLE_PATH = os.path.jo... | brianquinlan/brainfuck-jit | test_runner.py | Python | mit | 13,387 | [
"Brian"
] | 0171abcaa91257419d3f64e4ff591b8816ad2c84c83f486c6a7e02f34995bbe3 |
"""
The Job Agent class instantiates a CE that acts as a client to a
compute resource and also to the WMS.
The Job Agent constructs a classAd based on the local resource description in the CS
and the current resource status that is used for matching.
"""
__RCSID__ = "$Id$"
from DIRAC ... | fibbo/DIRAC | WorkloadManagementSystem/Agent/JobAgent.py | Python | gpl-3.0 | 28,075 | [
"DIRAC"
] | 4eb5f00543159f13936d1a4c856030b1f831ab813f392564c048ff94600cfa64 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
worker_thread.py -- FsDriftWorkload class used in each workload thread
Licensed under the Apache License at http://www.apache.org/licenses/LICENSE-2.0
See Appendix on this page for instructions pertaining to license.
'''
# allow for multi-thread tests
# allow threads... | bengland2/fsstress | worker_thread.py | Python | apache-2.0 | 20,128 | [
"Gaussian"
] | 48a6028ee215214d2074dda9e58732b5a35666553bc7a99debb29c5ff29f2adf |
# -*- mode: python; tab-width: 2; coding: utf8 -*-
#
# Copyright (C) 2015 Niklas Rosenstein
#
# 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
#
# ... | NiklasRosenstein/git-auth | git_auth/__init__.py | Python | apache-2.0 | 5,935 | [
"VisIt"
] | 27c7caffc251eff13d46f8ea49edbb0e54caa659bbdde99cdf4f0796139a3e5b |
#!/opt/local/bin/python
import subprocess
import os
import sys
import argparse
# sander The main engine used for running molecular simulations with Amber.Originally acronym standing for
# Simulated Annealing with Nmr-Derived Energy Restraints.
# The key thing that this file needs to be abel to do is take different DYNA... | marcvanderkamp/enlighten | dynam/sphere/dynam.py | Python | gpl-2.0 | 6,439 | [
"Amber",
"PyMOL"
] | fbb29dd36287bbada9dcb504a913d4505f4168b7842cb6a24726208af42d994d |
import argparse
import sys
import ovh
import providers
def main():
# configure options parsing
parser=argparse.ArgumentParser(description='Python CGI script to manage my domain zones.', epilog='No epilog yet')
parser.add_argument('-f', '--force', action='store_true')
parser.add_argument('action')
#parser.a... | flowgunso/server_manager | server_manager/__main__.py | Python | mit | 1,918 | [
"VisIt"
] | 4f69ee6aa8df9b1353783372593e1be5f550edda6eb35fc69d1590bff117092b |
# functions for loading, manipulating and creating phylogenetic trees
from Bio import Phylo
import sys, os, glob, subprocess, shutil
from multiprocessing import Pool
from xenoGI import xenoGI, blast, scores, parameters, fasta, genomes
#### General tree related functions
def bioPhyloToTupleTree(bpTree):
'''Convert... | ecbush/xtrans | xenoGI/trees.py | Python | gpl-3.0 | 19,889 | [
"BLAST",
"Biopython"
] | d68919ae4e7361215187a7eb9334c0621c6351b3a91398e67362f43a02c86d49 |
#pythran export _Aij(float[:,:], int, int)
#pythran export _Aij(int[:,:], int, int)
def _Aij(A, i, j):
"""Sum of upper-left and lower right blocks of contingency table."""
# See `somersd` References [2] bottom of page 309
return A[:i, :j].sum() + A[i+1:, j+1:].sum()
#pythran export _Dij(float[:,:], int, in... | pombredanne/pythran | pythran/tests/scipy/_hypotests.py | Python | bsd-3-clause | 1,660 | [
"ASE"
] | 0122050fbcdbd3597eca1c59cfb9ab2bad6ccc1fbd051ffb6b38b00f7282367a |
#!/usr/bin/env python
#coding:utf-8
import os
from distutils.core import setup
from ImportDependence import *
from CustomClass import *
here = os.path.abspath(os.path.dirname(__file__))
try:
README = open(os.path.join(here, 'README.md')).read()
except:
README = 'https://github.com/GeoPyTool/GeoPyTool/blob/m... | chinageology/GeoPython | geopytool/old_setup.py | Python | gpl-3.0 | 1,591 | [
"VisIt"
] | a43ede014c8b15db9215bbc74631ba9e4d0dcec80664cb556e3af604aa5888e6 |
"""
Code for grouping 3 orthogonal Profiles into a single Block object.
"""
from __future__ import print_function, division, absolute_import
import pynams.styles as styles
from pynams.diffusion import models
from pynams import Spectrum
import numpy as np
import matplotlib.pyplot as plt
import lmfit
class Block():
... | EFerriss/pynams | pynams/blocks.py | Python | mit | 41,991 | [
"Gaussian"
] | 467a7122b3610becd53c45af1a53ece6924dfa9a1db416583310d73caea59e46 |
#!/usr/bin/python
import numpy as np
from numpy.random import randn,dirichlet
from scipy.linalg import det, inv
from scipy.cluster import vq
from scipy.special import psi,gammaln
from core import normalize
try:
from _vbgmm1d import _evaluateHiddenState_C, _lnPD_C
ext_imported = True
except:
ext_imported = False
... | lucidfrontier45/PyVB | pyvb/old_ver/vbgmm1d.py | Python | bsd-3-clause | 7,659 | [
"Gaussian"
] | 20fbba441c4be807e00d2089eff0802ea6654a9ab090f972f8060d922db1dc8b |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/analysis/OrderParameter.py | Python | gpl-3.0 | 1,961 | [
"ESPResSo"
] | 4500fe1d4bb7f01daf1df3327c7abddd761d5838b8b5a93cc6889eb3405caee6 |
#!/usr/bin/env python
# PythonJS to Dart Translator
# by Brett Hartshorn - copyright 2013
# License: "New BSD"
import sys
import ast
import pythonjs
class TransformSuperCalls( ast.NodeVisitor ):
def __init__(self, node, class_names):
self._class_names = class_names
self.visit(node)
def visit_Call(self, node):
... | kustomzone/Rusthon | pythonjs/pythonjs_to_dart.py | Python | bsd-3-clause | 16,191 | [
"VisIt"
] | c23338eccae800197ab91c216e2f2880573c97450c8db3f08a1d3b130545a442 |
__author__="peterman"
__date__ ="$Jan 10, 2009 11:23:18 PM$"
import _tech_table
def planet_size(size):
return ["Tiny", "Small", "Medium", "Large", "Huge"][size]
def planet_terrain(terrain):
return ["Toxic", "Radiated", "Baren", "Desert", "Tundra", "Ocean", "Swamp", "Arid", "Terran", "Gaia", "k", "l"][terrai... | mimi1vx/openmoo2 | oldmess/dictionary.py | Python | gpl-2.0 | 5,734 | [
"CRYSTAL"
] | 03336c6694c8cd54fec39083d168a9cebff822effdd42c6857ffcde69c67cb41 |
#!/bin/bash
# Authors: Yan Kai, Jeffery Hsu
# GRCh38
import sys,re,os
from optparse import OptionParser
import pandas as pd
import HTSeq
def inner_outer_pref(line, suffix):
'''
Preferences outer + suffix -> suffix -> inner + suffix
'''
prefix = ['inner_', '', 'outer_']
test = [i + suffix for i in... | NCBI-Hackathons/Structural_Variant_Comparison | py/make_gvf_and_bedgraph.py | Python | cc0-1.0 | 4,465 | [
"HTSeq"
] | 6679891f83efd01f0d4f58f5a3d1fc9501512fb790aa8cd6d9d306a73fc5f741 |
#!/usr/bin/env python3
# Note that the script gives different precision results for python2 and python3.
# The current archived ingrid_T*_unstructured.txt files have been produced with a
# miniconda3 environment active (see https://github.com/EC-Earth/ece2cmor3/issues/633).
# Call the script like:
# ./create_cdo_ing... | goord/ece2cmor3 | ece2cmor3/resources/lpjg-grid-content/create_cdo_ingrid_for_lpjgout.py | Python | apache-2.0 | 4,573 | [
"Gaussian",
"NetCDF"
] | 04a2eec2c722c411ec767585d1716c7e40472bfbaf0b06b5c0a0030e0a35d50a |
#!/usr/bin/env python3
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## 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 Softwa... | graik/biskit | scripts/amber_ensembleMD.py | Python | gpl-3.0 | 12,061 | [
"Amber"
] | bb07657f7049c2d1a319cda8f6956cf8a790cc5ac0c7d4b86f5499e26ee7c20b |
from ResoFit.calibration import Calibration
from ResoFit.fitresonance import FitResonance
from ResoFit.experiment import Experiment
import matplotlib.pyplot as plt
import numpy as np
import pprint
from ResoFit._utilities import get_foil_density_gcm3
from ResoFit._utilities import Layer
import lmfit
# Global parameters... | ornlneutronimaging/ResoFit | ResoFit/data/IPTS_20784/ipts_20784_AgI.py | Python | bsd-3-clause | 6,114 | [
"Gaussian"
] | ac412639838350490ae5a05da8af3c9934c34863f418057d688f56be95d1b86d |
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# 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 copyright
# ... | adalke/rdkit | Contrib/mmpa/rfrag.py | Python | bsd-3-clause | 8,578 | [
"RDKit"
] | 00efd5f5f024685d1b771f365bd56345717fe9e3a787f8b6f379b840f5b5e566 |
# -*- coding: utf-8 -*-
# Copyright 2019 The GraphicsFuzz Project 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | google/graphicsfuzz | gfauto/gfauto/gfauto_interestingness_test.py | Python | apache-2.0 | 9,025 | [
"Amber"
] | 286a6090e2f1dfcaf9c49abaf6f7dc4c0b9f4bf1c66459af595d013a1f287d50 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHOULD H... | mkalewski/sim2net | sim2net/speed/normal.py | Python | mit | 2,688 | [
"Gaussian",
"VisIt"
] | c08108899cf82c498186753fa18b8713e091c5e4bc8bb02334f0861002c2c3a2 |
'''
Depth First Search Algorithm to find shortest path.
@author Fernando Felix do Nascimento Junior
@links
https://code.google.com/p/tspuib/source/browse/trunk/TravelingSalesMan/src/travelingsalesman/DepthFirstSearch.java?r=13
'''
from datetime import datetime
from graph import Graph
class DepthFirstSearch:
... | fernandojunior/searching-techniques | src/dfs.py | Python | mit | 2,250 | [
"VisIt"
] | 0dcf57d756e2c23aa6b2204f510eb18afee09ebe8daafebbfe695953ceddd24b |
#
# :.
# :: Exploit/Writeup for BFS Labs's Ekoparty Challenge
# ::
# :: URL: https://labs.bluefrostsecurity.de/blog/2017/08/02/bfs-ekoparty-exploitation-challenge/
# :.--------------------------------------------------------------------------------------------- :
# :.. By Asger Friis-Vigh of Rota Galaxy, August 2017 ..... | asgerfv/ctf-writeup_2017__bfs-ekoparty-challenge | src/ctf-writeup_2017__bfs-ekoparty-challenge__exploit.py | Python | mit | 12,396 | [
"Galaxy"
] | 82b1a2472d1eb6cabb01479b5002ba175d994e325da71ac335597be6a06fd5f3 |
# Authors: Nicolas Goix <nicolas.goix@telecom-paristech.fr>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# License: BSD 3 clause
import numbers
import numpy as np
from scipy.sparse import issparse
from warnings import warn
from ..tree import ExtraTreeRegressor
from ..utils import (
chec... | sergeyf/scikit-learn | sklearn/ensemble/_iforest.py | Python | bsd-3-clause | 19,109 | [
"Gaussian"
] | 94ae9dad0dbb7e89c99241ff60cde058d767916e91574ef3338f22e649a68198 |
# -*- coding: utf-8 -*-
"""Utility functions for downloading, caching, and importing."""
import sys
import os.path
import tempfile
from importlib import import_module
from urllib.request import urlretrieve
import numpy as np
import pygimli as pg
from pygimli.meshtools import (readFenicsHDF5Mesh, readGmsh, readPLC, r... | gimli-org/gimli | pygimli/core/load.py | Python | apache-2.0 | 7,735 | [
"VTK"
] | ccb279d9fb90a41fdde925e983977e47a1f298f2ddd8028e190350fa77dcce44 |
"""
Export
======
On this page, we demonstrate how to quickly share a 3D rendering of your
ParaView visualizations with anyone who has access to the internet so that that
can explore the whole scene in a dynamic manner.
Motivation
----------
In order to effectively communicate our geoscientific findings, we often nee... | banesullivan/ParaViewGeophysics | pvmacros/export/__init__.py | Python | bsd-3-clause | 6,786 | [
"ParaView",
"VTK"
] | 5257e6e09f48c49ac1bfbc9fe2f2b30d72c1d1f1c1ca616dd8b27855331f2f50 |
import random
import string
from django.db import transaction
from django.shortcuts import render, redirect
import haikunator
from .models import Room
def about(request):
return render(request, "chat/about.html")
def new_room(request):
"""
Randomly create a new room, and redirect to it.
"""
new_ro... | davidkjtoh/GlorgoChat | chat/views.py | Python | bsd-3-clause | 1,279 | [
"VisIt"
] | c12eb98866730b8c4c2eb478b8fbefa3a620a377b7476176fc484df40ea7e30e |
# coding=utf-8
# Copyright 2019 The Google AI Language Team 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 ... | google-research/tapas | tapas/models/bert/modeling.py | Python | apache-2.0 | 46,732 | [
"Gaussian"
] | da0864a6e9e6898f0547874a44634119ecd1901cd8570436eb0608388b6e762c |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/analysis/Temperature.py | Python | gpl-3.0 | 1,694 | [
"ESPResSo"
] | a07c5b93f48dfdf269177e00cb03d878dd34eee89added95921cee8939386e2c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2017, Brian Coca <bcoca@ansible.com>
# (c) 2017, Adam Miller <admiller@redhat.com>
# (c) 2017 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__m... | thaim/ansible | lib/ansible/modules/system/sysvinit.py | Python | mit | 13,409 | [
"Brian"
] | b291a9784dd86993bde3975444232fe7b55fbfa63675a184dd9afbcaae1094e4 |
import collections
import Read
import jellyfish
import bs4
class Base:
def __init__(self):
self._A = 0
self._T = 0
self._G = 0
self._C = 0
self._N = 0
self._INDEL = 0
self.count = 0
self.coordinate = None
self.chromosome = None
def __iadd... | ResearchDx/HardSearch | scripts/Break.py | Python | mit | 21,280 | [
"BLAST"
] | 472eafcb87aee06b05c8f018f87781bcdd03dca49823a76d2640abbc7870d3fe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 24 10:38:55 2015
@author: landman
This class sets up and LTB model and find the observables on the PLC0
"""
from numpy import linspace,sqrt,sinh,arccosh,zeros,cosh,flipud,squeeze,pi,array,savez,argwhere,loadtxt,exp, tanh, isnan
from scipy.optimize... | landmanbester/Copernicus | genLTB.py | Python | gpl-3.0 | 17,035 | [
"ADF"
] | 7e04a0abe62487574527b50f341cddd9d82c94e1d9ff7cefcedf6d3389f6b266 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Code to support unit and validation tests.
``conftest`` is not part of HOOMD-blue's public API.
"""
import logging
import pickle
import pytest
import hoomd
... | joaander/hoomd-blue | hoomd/conftest.py | Python | bsd-3-clause | 17,997 | [
"HOOMD-blue"
] | 6df2c092aa7f578dacde68b8b538db098120b70a36cf7ba2cb549e4a32e6baa3 |
# 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 | graph_sampler/enumerate_stoichiometries.py | Python | apache-2.0 | 2,547 | [
"RDKit"
] | 36312c85e4e6f65e591f933b0b6402577d10a95993a28437efffd946bfbe73a3 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/presentations/__init__.py | Python | gpl-2.0 | 2,263 | [
"Brian"
] | 8b0d5129dba8137ea63249f852ad83ee6296b826bf27e06edf497fb327931cfa |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This pr... | pmghalvorsen/gramps_branch | gramps/gen/plug/docgen/graphdoc.py | Python | gpl-2.0 | 40,092 | [
"Brian"
] | 16689066e4b31492ca3bf7532d5dad2a4d3565633f6f07e860f3a0b9ecb8edb5 |
# -*- coding: utf-8 -*-
try:
import BaseHTTPServer as server
except ImportError:
import http.server as server
try:
from urlparse impor... | Haynie-Research-and-Development/jarvis | deps/lib/python3.4/site-packages/pyfttt/server.py | Python | gpl-2.0 | 4,646 | [
"Brian"
] | c6f494c9c5f83684af38fdd470d98d066889114608ccac4767b230c3066e2f6b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Analysis classes for batteries
"""
import math
from collections import defaultdict
import scipy.constants as const
from pymatgen.core.periodic_table import Element, Species
from pymatgen.core.structure i... | gmatteo/pymatgen | pymatgen/apps/battery/analyzer.py | Python | mit | 9,104 | [
"pymatgen"
] | 9f193773a1e7aac642750672bd624e04353caae1758e2b2e2c7a266cba6fb245 |
# Authors: John Dennis <jdennis@redhat.com>
#
# Copyright (C) 2011 Red Hat
# see file 'COPYING' for use and warranty information
#
# 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... | realsobek/freeipa | ipapython/log_manager.py | Python | gpl-3.0 | 62,632 | [
"VisIt"
] | d222d385ed378e9dbf44f24593e9b01fa1b5343948f2c8f8d6ee41b94dd081ea |
import os
from lutris import settings
from lutris.runners.runner import Runner
from lutris.util.display import get_current_resolution
class fsuae(Runner):
"""Run Amiga games with FS-UAE"""
human_name = "FS-UAE"
executable = 'fs-uae'
platform = "Amiga"
tarballs = {
'i386': "fs-uae-i386.tar... | GoeGaming/lutris | lutris/runners/fsuae.py | Python | gpl-3.0 | 4,825 | [
"ADF"
] | a5c5aca2e6c465d971f8ccba4dc692cde4e28ae2124b95b8e0a6858e4a015d10 |
"""
MOSEXTRACT
extract galaxy spectra from MOS image
"""
import os, sys, glob, shutil
import numpy as np
from astropy.io import fits
from scipy.ndimage.filters import median_filter
from astropy import modeling as md
import pylab as pl
#from pyraf import iraf
#from iraf import pysalt
#from specsky import skysub... | dmnielsen/zSALT | zsalt/mosextract.py | Python | bsd-3-clause | 6,028 | [
"Galaxy"
] | 2694252c69c7a5f07d8665206833ed3e2836147d82e7524679e07fc2f41b62f2 |
#!/usr/bin/env python
#
#
# ex_toy4
#
# Building on toy3 example, this adds drift distance
# information to the pixel color. It also adds a
# random z-vertex position in addition to the phi
# angle.
#
# The network is defined with 2 branches to calculate
# the phi and z. They share a common input layer and
# initial ... | BDannowitz/polymath-progression-blog | jlab-hackathon/loadCode.py | Python | gpl-2.0 | 3,811 | [
"NEURON"
] | eba5396106ec893d6b499212a328c9acc6db22c4c54b9af642e6635921ac39e7 |
#!/usr/bin/env python3
# Copyright (c) 2018 The DigiByte Core developers
# Distributed under the MIT software license, see the accompanying
# file COPYING or http://www.opensource.org/licenses/mit-license.php.
"""Verify commits against a trusted keys list."""
import argparse
import hashlib
import logging
import os
impo... | aurarad/auroracoin | contrib/verify-commits/verify-commits.py | Python | mit | 8,234 | [
"Octopus"
] | 6f14c50707e887890db27b920a46b541c0208c006a22c1bdbf0ddb1b94f39a97 |
from pandac.PandaModules import *
from toontown.toonbase.ToonBaseGlobal import *
from direct.directnotify import DirectNotifyGlobal
from direct.fsm import StateData
from direct.fsm import ClassicFSM, State
from direct.fsm import State
from direct.task.Task import Task
from ToontownMsgTypes import *
from toontown.toonba... | Spiderlover/Toontown | toontown/distributed/PlayGame.py | Python | mit | 22,267 | [
"VisIt"
] | 980c381161b8f4e3a1577238c9d8a31c1cb5f0e1dfff7ad2df540ecb7399f75f |
import peakutils
from scipy.optimize import curve_fit
from uncertainties import ufloat, unumpy
import numpy as np
def find_peaks(xdata, ydata, thres=0.3, min_dist=1):
# Finds the peak intensities in ydata, and returns the
# corresponding frequencies
indexes = peakutils.indexes(ydata, thres=thres)
peak... | laserkelvin/FTSpecViewer | python/fittingroutines.py | Python | gpl-3.0 | 4,727 | [
"Gaussian"
] | 3fb5716d67cbcc491eb0dd7a080f741c5832fa4ed23ef1a33dac159ec78ee05d |
from __future__ import print_function, division
import collections
from sympy.core.add import Add
from sympy.core.basic import Basic, Atom
from sympy.core.expr import Expr
from sympy.core.function import count_ops
from sympy.core.logic import fuzzy_and
from sympy.core.power import Pow
from sympy.core.symbol import Sym... | jerli/sympy | sympy/matrices/matrices.py | Python | bsd-3-clause | 134,228 | [
"DIRAC",
"Gaussian"
] | 8be04e54277371acfa46dceaa4894315dcab57697232d1f594151b4c4818ade7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides various representations of transformed structures. A
TransformedStructure is a structure that has been modified by undergoing a
series of transformations.
"""
import datetime
import js... | richardtran415/pymatgen | pymatgen/alchemy/materials.py | Python | mit | 13,928 | [
"VASP",
"pymatgen"
] | b8c393c49c4236ca21c2375fd9e562a52f5602697c872bd4aac68912227bbbdd |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/scipy/optimize/optimize.py | Python | gpl-2.0 | 95,952 | [
"Gaussian"
] | 3553a7e8dba0ce78a207f54d8d75f0d8c44cb02762880772da5217f7cdd62096 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/share/psi4/databases/BAKERJCC96.py | Python | lgpl-3.0 | 16,142 | [
"Psi4"
] | 0e73ba52d9eaacef0f22d38b4d7a816dc5f289a64fb0f856fadb3ec2422763cd |
# UrbanFootprint v1.5
# Copyright (C) 2017 Calthorpe Analytics
#
# This file is part of UrbanFootprint version 1.5
#
# UrbanFootprint is distributed under the terms of the GNU General
# Public License version 3, as published by the Free Software Foundation. This
# code is distributed WITHOUT ANY WARRANTY, without impl... | CalthorpeAnalytics/urbanfootprint | footprint/client/configuration/default/built_form/old_placetypes.py | Python | gpl-3.0 | 71,803 | [
"Elk"
] | a718461d65282be77bf59099f166e201ec99e1ce4fd8df6656f3c8497fe0d172 |
import traceback
import os
import argparse
import multiprocessing
import subprocess
import hashlib
from functools import partial
import json
import base64
import pysam
import pybedtools
from spades_contig import SpadesContig
from tigra_contig import TigraContig
from svregion import SVRegion
from age_parser import *
f... | chapmanb/metasv | metasv/run_age.py | Python | bsd-2-clause | 16,882 | [
"pysam"
] | 3b69ba911064ad36066917b2d5b178461b32b2aa9e498a59d326163a552654b8 |
# 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... | 7Puentes/Amazon | amazon.py | Python | apache-2.0 | 11,815 | [
"Gaussian"
] | 92bbe87fe4847fd46d8ec826ff75f9e14d44b27e0ba35a236c4164c9691c2e6b |
from math import sqrt
import optparse
import numpy as np
from ase.atoms import Atoms, string2symbols
from ase.structure import molecule
from ase.tasks.task import OptimizeTask
from ase.data import covalent_radii, atomic_numbers
from ase.data import ground_state_magnetic_moments
from ase.utils.eos import EquationOfSta... | grhawk/ASE | tools/ase/tasks/molecule.py | Python | gpl-2.0 | 9,273 | [
"ASE"
] | 2ea4543ba533e29902db0af1b1f9618ca1f82c8eed522e6416cf17e66124bb72 |
# -*- coding: utf-8 -*-
import os
import subprocess
import vim
from orgmode._vim import ORGMODE, echoe, echo, echom
from orgmode.menu import Submenu, ActionEntry
from orgmode.keybinding import Keybinding, Plug, Command
from orgmode import settings
class Export(object):
u"""
Export a orgmode file using emacs orgmo... | j-a-m-l/.dot | vim/bundle/vim-orgmode/ftplugin/orgmode/plugins/Export.py | Python | mit | 3,647 | [
"VisIt"
] | d2ec3f5158502dc73376f95a605b2daf79d7a39e1e168da812680234ef1d405c |
#!/usr/bin/env python
import numpy as np
import lib.env as env
from lib.env import runs_dir, cases_dir, spikes_dir
import bayesopt
from bayesopt import ContinuousGaussModel
import os
from os.path import join as pj
from lib.bo_validation import create_model
from lib.bo_validation import get_validation_params
import ... | vvoZokk/dnn | scripts/opt.py | Python | mit | 2,120 | [
"Gaussian"
] | 9abf974553497181c6c6593a1d408d0e506637622191a034bfd6ba657591374f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Midautumn
# Copyright 2011 Ron Huang
# See LICENSE for details.
from google.appengine.dist import use_library
use_library('django', '1.2')
import os
import logging
import time
from datetime import date, timedelta
from google.appengine.runtime import DeadlineExceededErr... | ronhuang/adieu | backend/midautumn/achievement.py | Python | mit | 13,480 | [
"VisIt"
] | eea7a31bdcc94c5106c268ea45dd5e78e3668d0bb0d9e7be4188afa5bc797c79 |
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