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import os
from pathlib import Path
import numpy as np
import pytest
from pysisyphus.helpers_pure import results_to_json, json_to_results
from pysisyphus.run import run_from_dict
from pysisyphus.testing import using
def test_results_to_json():
size = 12
results = {
"energy": -1000.0,
"forces"... | eljost/pysisyphus | tests/test_calculator/test_calculator.py | Python | gpl-3.0 | 1,247 | [
"PySCF"
] | 3b2aab8307ad2461ad0e1847840a67a4e6f4bb2647643464da6a8668468f6f8d |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, tddft, scf
from pyscf.nao import gw
from pyscf.data.nist import HARTREE2EV
class KnowValues(unittest.TestCase):
def test_0168_cn_rohf(self):
""" Interacting case """
spin = 1
mol=gto.M(verbose=0,atom='C 0... | gkc1000/pyscf | pyscf/nao/test/test_0169_cn_uks_b3lyp.py | Python | apache-2.0 | 634 | [
"PySCF"
] | 869ff7e9b52086ae8d4bfdc840258f708f6c7a4ba1adbc1fa83f854401281517 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2012, 2013 CERN.
##
## Invenio 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 ... | Panos512/invenio | modules/bibupload/lib/batchuploader_engine.py | Python | gpl-2.0 | 29,489 | [
"VisIt"
] | c3424430153d2769a834c82d095e835410d8335152a946f696676124bf81b669 |
# Shared and common functions (declustering redundant code)
import numpy as np, os
import random, cv2
import operator
def get(link, save_as=False):
import urllib
base_dir = './tmp'
assert type(link) == str, type(link)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
if save... | minyoungg/selfconsistency | lib/utils/util.py | Python | apache-2.0 | 5,391 | [
"Gaussian"
] | c94e89d7ce2f21aa5156094b9f6b4bca935a6261401601b364b98baa45147845 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | thomasaarholt/hyperspy | hyperspy/model.py | Python | gpl-3.0 | 82,634 | [
"Gaussian"
] | d6480f42ef71cc011905bc68561abb229202a77737e0f9dcfd3a92ad5a542107 |
"""A simple example of how to use IPython.config.application.Application.
This should serve as a simple example that shows how the IPython config
system works. The main classes are:
* IPython.config.configurable.Configurable
* IPython.config.configurable.SingletonConfigurable
* IPython.config.loader.Config
* IPython.... | cloud9ers/gurumate | environment/share/doc/ipython/examples/core/appconfig.py | Python | lgpl-3.0 | 3,307 | [
"Brian"
] | 6a642e5169de9166882b384776f67651b18de174c5fe80d0d9d04b5c0b106187 |
# -*- encoding: utf-8
from sqlalchemy.testing import eq_, engines
from sqlalchemy import *
from sqlalchemy import exc
from sqlalchemy.dialects.mssql import pyodbc, pymssql
from sqlalchemy.engine import url
from sqlalchemy.testing import fixtures
from sqlalchemy import testing
from sqlalchemy.testing import assert_raise... | wfxiang08/sqlalchemy | test/dialect/mssql/test_engine.py | Python | mit | 8,017 | [
"ASE"
] | 7a4d200f5d53c2a6be01bede1f296fcc5aa358eb779145e20958a77ce9bdba18 |
""" Test functions for stats module
WRITTEN BY LOUIS LUANGKESORN <lluang@yahoo.com> FOR THE STATS MODULE
BASED ON WILKINSON'S STATISTICS QUIZ
https://www.stanford.edu/~clint/bench/wilk.txt
Additional tests by a host of SciPy developers.
"""
from __future__ import division, print_function, absolute_imp... | gertingold/scipy | scipy/stats/tests/test_stats.py | Python | bsd-3-clause | 206,871 | [
"Gaussian"
] | d7790b0be7f5bef3c3c83e9de7742edce1627c397d4813ea63b1c7bbd7bf8bfc |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains the classes to build a ConversionElectrode.
"""
from typing import Iterable, Dict
from dataclasses import dataclass
from monty.dev import deprecated
from scipy.constants import N_A
from pymatgen.anal... | vorwerkc/pymatgen | pymatgen/apps/battery/conversion_battery.py | Python | mit | 18,974 | [
"pymatgen"
] | 30e067310e934ae1d0db32d6d3c187b71ac746bda3b93652ca755b0853104642 |
# This is a very simple implementation of the uct Monte Carlo SearchTree Search algorithm in Python 2.7.
# The function uct(root_state, __iter_max) is towards the bottom of the code.
# It aims to have the clearest and simplest possible code, and for the sake of clarity, the code
# is orders of magnitude less efficient ... | aijunbai/uct | common.py | Python | bsd-2-clause | 21,228 | [
"VisIt"
] | 25a0e276bc73f64c818ed3c50226e7d0bf8eeb499a9860dd6862c0095be0fda5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | CDSherrill/psi4 | psi4/share/psi4/databases/NHTBH.py | Python | lgpl-3.0 | 36,605 | [
"Psi4"
] | 7509a27b7042c25619a4c41cff7833bb5baabae4fcef6e31e47dac1a28e884d7 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParallel import R... | wgapl/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 41,159 | [
"MOOSE",
"VTK"
] | 9da32ac036503823d8a2790357dad00968361145de930e99e25f2142299b44be |
""" Analyze libraries in trees
Analyze library dependencies in paths and wheel files
"""
import logging
import os
import sys
import warnings
from os.path import basename, dirname
from os.path import join as pjoin
from os.path import realpath
from typing import (
Callable,
Dict,
Iterable,
Iterator,
... | matthew-brett/delocate | delocate/libsana.py | Python | bsd-2-clause | 26,935 | [
"VisIt"
] | b5c726d0ea51be93c7d117589a11f39f038a49c08b7eeca18b2eda56a02f1074 |
'''OAuth support functionality
'''
from __future__ import unicode_literals
# Try importing the Python 3 packages first
# falling back to 2.x packages when it fails.
try:
from http import server as http_server
except ImportError:
import BaseHTTPServer as http_server
try:
from urllib import parse as urllib_... | onitu/onitu | drivers/flickr/onitu_flickr/flickrapi/auth.py | Python | mit | 17,734 | [
"VisIt"
] | f2a1271e63ecae9da6fa6a10a7a01214d430f6f9bb799179b90ec37965aec972 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Utilities for manipulating coordinates or list of coordinates, under periodic
boundary conditions or otherwise. Many of these are heavily vectorized in
num... | sonium0/pymatgen | pymatgen/util/coord_utils.py | Python | mit | 12,786 | [
"pymatgen"
] | dc153a19497d56f28a920f80724adf64a68b2f5405584bb86312a50701add4c6 |
#
# if inflow == 'log':
# kappa = 0.4 # Kappa: von karman constant
# us = WS * kappa / np.log(WF.WT[0].H / z0) # friction velocity
# #eq inflow ws
# WS_inf = gaussN(WF.WT[0].R, Ua, [WF.WT[0].H,us,z0]).sum()
# elif inflow == 'pow':
# #eq inflow ws
# WS_inf = gaussN(WF.WT[0].R, Ua_shear, [WF.WT[0... | DTUWindEnergy/FUSED-Wake | fusedwake/wind_farm_flow.py | Python | mit | 14,757 | [
"Gaussian"
] | f255d2fd83d2e1c47df2843d4f4f8c681316bcc0fbdf6ac3dd2dc27989dac8d1 |
import numpy as np
from cs231n.layers import *
from cs231n.layer_utils import *
class TwoLayerNet(object):
"""
A two-layer fully-connected neural network with ReLU nonlinearity and
softmax loss that uses a modular layer design. We assume an input dimension
of D, a hidden dimension of H, and perform c... | vermouth1992/deep-learning-playground | analysis/cs231n/classifiers/fc_net.py | Python | apache-2.0 | 19,060 | [
"Gaussian"
] | a2c4f019449667f7e5f3bdd26049fe2cc1881cbd7aee413a0ad87859dd007c75 |
#############################
##
## The Sire python module
##
## This contains the parts of the main Sire program
## that are exposed to Python.
##
## (C) Christopher Woods
##
_module_to_package = {}
def _install_package(name, package_registry):
"""Internal function used to install the module
called 'name'... | chryswoods/Sire | wrapper/__init__.py | Python | gpl-2.0 | 10,800 | [
"MDTraj"
] | fc11d49977b841679e04d7f51a032a46e2d95d06b60cfdbe90a8964910919474 |
# Orca
#
# Copyright 2010-2011 The Orca Team
#
# 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 library... | GNOME/orca | src/orca/chat.py | Python | lgpl-2.1 | 34,518 | [
"ORCA"
] | 6259966fb721b4361281900d66e33954a885459be7eb976462c748039654be7a |
"""
"""
import os
from tempfile import tempdir
from pulsar.manager_factory import build_managers
from pulsar.cache import Cache
from pulsar.tools import ToolBox
from pulsar.tools.authorization import get_authorizer
from pulsar import messaging
from galaxy.objectstore import build_object_store_from_config
from galaxy.t... | ssorgatem/pulsar | pulsar/core.py | Python | apache-2.0 | 5,506 | [
"Galaxy"
] | 1e4857506e41c8bfcdc20c569890ef9d9a66a4c7a2e2e5e387572532b0d36edd |
# (C) British Crown Copyright 2013 - 2014, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | Jozhogg/iris | lib/iris/tests/unit/fileformats/netcdf/__init__.py | Python | lgpl-3.0 | 850 | [
"NetCDF"
] | 1a8a7828d2ee90251e3f424ec38207f8390434653e3f68a1ad13fcf1184498ef |
#!/usr/bin/env python
"""
PolyGA - version 1.2b - Last modified: 30-DEC-2013
Usage:
python polyga.py -h
python polyga.py -a feature -c <filename> -i <filename> -g <filename> -s <filename> -o <file prefix>
python polyga.py -a feature -c <filename> -d <HDF5 filename> -o <file prefix>
Copyright (C) 2013 Michael Mo... | mooneymi/polyga | polyga.py | Python | gpl-3.0 | 6,315 | [
"Cytoscape"
] | 756e016b46744f91fa22cf1ca7905d2322f956b24bd82fa2542d2d0eb98e781e |
#############################################################################
# Code for managing and training a variational Iterative Refinement Model. #
#############################################################################
# basic python
import numpy as np
import numpy.random as npr
from collections import ... | capybaralet/Sequential-Generation | MultiStageModel.py | Python | mit | 24,500 | [
"Gaussian"
] | ba4997c85036fe4886246d9acd70aeb8686746a176b712e184e0e5f658b931b8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# jobschedule - Save schedule for a waiting or running job
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU Ge... | heromod/migrid | mig/cgi-bin/jobschedule.py | Python | gpl-2.0 | 1,097 | [
"Brian"
] | 600e40f10804725c7020324c03304926cf2805632b207ef7f081e74f81ecc47a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Contribution 2009 by Brad Crittenden <brad [AT] bradcrittenden.net>
# Copyright (C) 2008 Benny Malengier
# Copyright (C) 2010 Jakim Friant
#
# This program is free... | pmghalvorsen/gramps_branch | gramps/gui/plug/export/_exportassistant.py | Python | gpl-2.0 | 24,859 | [
"Brian"
] | c76363ab541dff98fe431196804b7c1819b07e062889084ba4d0fe285354da35 |
#!/usr/bin/env python
from numpy.distutils.core import setup
from numpy.distutils.core import Extension
setup(name='py-bgo',
version='0.2',
descreption='Bayesian gloabl optimization',
author='Ilias Bilionis',
author_email='ibilion@purdue.edu',
keywords=['Bayesian global optimization', '... | PredictiveScienceLab/py-bgo | setup.py | Python | mit | 384 | [
"Gaussian"
] | 17861af70232c6f0833d4f33e4505339d094b804f4169115aa0bc13e7a39670b |
#
# FRETBursts - A single-molecule FRET burst analysis toolkit.
#
# Copyright (C) 2014-2016 Antonino Ingargiola <tritemio@gmail.com>
#
"""
This module provides functions to fit gaussian distributions and gaussian
distribution mixtures (2 components). These functions can be used directly,
or more often, in a typical FRE... | chungjjang80/FRETBursts | fretbursts/fit/gaussian_fitting.py | Python | gpl-2.0 | 31,065 | [
"Gaussian"
] | 3ce80be751d23ce2e8defa1055824ffaf5607fddda49bf82558d6c6fc6f095c9 |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/lib/scipy_helper.py | Python | apache-2.0 | 3,604 | [
"PySCF"
] | bd3f73ad672a1f780dfdf4d445d9a309b6c2d2b5922329f943e9c84adbadb99a |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | tutorials/darcy_thermo_mech/step07_adaptivity/problems/step7d.py | Python | lgpl-2.1 | 2,298 | [
"MOOSE",
"VTK"
] | e487fcd737e7ea714bf7e2a936e722e1ca0427f8431da474a1e5eb1cc7dfcc99 |
import os
import re
import logging
log = logging.getLogger(__name__)
import elements
def get_language(tag):
"""
Helper function for extracting code highlight language from tag attributes.
"""
# Map from lower case hljs name to latex listings name
languages = {'c++':'C++', 'python':'Python'}
lang = ''
... | paulthulstrup/moose | python/MooseDocs/html2latex/moose_elements.py | Python | lgpl-2.1 | 10,005 | [
"MOOSE"
] | 7739e8c0386490b587b88cad3e4ec2c794f3b25795c03bed1a0079ece7285fbf |
#!/usr/bin/env python
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at you... | loriab/qcdb | bin/imake-DB.py | Python | lgpl-3.0 | 10,650 | [
"Molpro",
"NWChem",
"Psi4"
] | f1dc975e5c53ec3a34b7bdb0b3872af84f29585d00491ddba43475ce55fe3004 |
#!/usr/bin/python
import pysam
import string
import argparse
# The MIT License (MIT)
# Copyright (c) [2014] [Peter Hickey (peter.hickey@gmail.com)]
# 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 S... | PeteHaitch/Lister2BAM | Python/Lister_style_6_to_bam.py | Python | mit | 14,247 | [
"pysam"
] | 2a7eea413006638e028a988fe06898ca316a446a848c33abe2bc25d7db44bb61 |
from os.path import basename
from os.path import join
from os.path import dirname
from os import sep
from ..util import PathHelper
COMMAND_VERSION_FILENAME = "COMMAND_VERSION"
class ClientJobDescription(object):
""" A description of how client views job - command_line, inputs, etc..
**Parameters**
com... | jmchilton/lwr | lwr/lwr_client/staging/__init__.py | Python | apache-2.0 | 6,647 | [
"Galaxy"
] | 83ecfa38c71a55b7ab27924186e71abf9e3c9f65b51933088c2ee8af3fe1c482 |
# This test calculates spherical harmonic expansion of all-electron kohn-sham potential of helium atom
# using nucleus.calculate_all_electron_potential method
from gpaw import *
from ase import *
from gpaw.atom.all_electron import AllElectron
# Calculate Helium atom using 3D-code
he = Atoms(positions=[(0,0,0)], symbo... | qsnake/gpaw | oldtest/he_ae.py | Python | gpl-3.0 | 1,030 | [
"ASE",
"GPAW"
] | 8cf735432ebfb67b1e53b0aabfd46a27f0f434b76f48598e628f21ef293ff215 |
#!/usr/bin/env python
###########################################################################
## ##
## Language Technologies Institute ##
## Carnegie Mellon University ... | leahrnh/ticktock_text_api | galbackend_conversation.py | Python | gpl-2.0 | 20,084 | [
"Galaxy"
] | 01c599d66ee9343ae03423c3223e58413294a39abb45f72c6b3dac429835dad4 |
from functools import partial
import numpy as np
from numpy.testing import assert_allclose
import scipy.sparse as sps
from scipy.optimize import approx_fprime
from sklearn.datasets import make_regression
from sklearn.preprocessing import StandardScaler
from sklearn.cross_validation import KFold
from sklearn.model_se... | the872/pyglmnet | tests/test_pyglmnet.py | Python | mit | 9,602 | [
"Gaussian"
] | d2f934f7cf554f4f5e48cb7bef1a9b7633e2c53c6d24258a456fda289b97d0e8 |
import numpy as np
import os
import cv2
import sys
#sys.setrecursionlimit(1000000)
import Config
def init_parts(bkg_path,em_it = 1):
emit_parts_root = Config.parts_root_folder%em_it
if not os.path.exists(emit_parts_root):
os.mkdir(emit_parts_root)
for cam in Config.cameras_list:
if not os... | pierrebaque/EM | EM_funcs.py | Python | gpl-3.0 | 910 | [
"Gaussian"
] | 31552f2a3b3668950b3962179da346f0926cbb9e32e85ae10625a9ff40ee6992 |
# pylint: disable=bad-continuation
"""
Certificate HTML webview.
"""
import logging
import urllib
from datetime import datetime
from uuid import uuid4
import pytz
from django.conf import settings
from django.contrib.auth.models import User
from django.http import Http404, HttpResponse
from django.template import Reque... | philanthropy-u/edx-platform | lms/djangoapps/certificates/views/webview.py | Python | agpl-3.0 | 32,149 | [
"VisIt"
] | 3c3a88e600a8321d2adf2acc1310a3d7d48c06fe8f3514cdf26b3cc58efb97b2 |
import pysam
import argparse
import sys
import logging
import os
import re
from asyncore import read
def write_reads(fout, refmap, reads, counts):
hostReads = []
feedReads = []
hasSecondary = False
for read in reads:
if read.is_secondary:
hasSecondary = True
continue
if refmap[read.referenc... | shengqh/ngsperl | lib/Alignment/filterMixBam.py | Python | apache-2.0 | 3,954 | [
"pysam"
] | 4cd901994a880cd51f7732cfd8a40ac8adfe1ec62f5b111089648b03889183bc |
#! /usr/bin/env python
# This file comes originally from: https://github.com/Kentzo/git-archive-all
#
# coding=utf-8
#
# The MIT License (MIT)
#
# Copyright (c) 2010 Ilya Kulakov
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "... | jorisv/Tasks | cmake/git-archive-all.py | Python | lgpl-3.0 | 19,609 | [
"ParaView"
] | 08f802926083c5d3bd3a82477596bf76d627199f0e106a9b5ef6783ba56d5e35 |
"""Integrate stochastic master equations in vectorized form.
.. py:module:: integrate.py
:synopsis: Integrate stochastic master equations in vectorized form.
.. moduleauthor:: Jonathan Gross <jarthurgross@gmail.com>
"""
from functools import partial
import itertools as it
import numpy as np
from scipy... | CQuIC/pysme | src/pysme/integrate.py | Python | mit | 62,208 | [
"Gaussian"
] | 078969c5af5f72b74f6b69d48ce07687d9bf7f8806257d6b6c71bb5d72459731 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
DOCUMENTATION = '''
---
module: svc
author: Brian Coca
version_added:
short_description: Manage daemontools services.
description:
- Controls daemontools services on remote hosts using the svc utility.
options:
name:
required: true
description:
... | ravello/ansible-modules-extras | system/svc.py | Python | gpl-3.0 | 8,918 | [
"Brian"
] | 53b5ad0a95022e4d7bd2c9a79d0c427721d77fe0a541c89ae5a356432f4bc869 |
import chemistry
from openmoltools import cirpy
import mdtraj as md
import pymbar
import os
import pandas as pd
import glob
import dipole_errorbars
from density_simulation_parameters import DATA_PATH
num_bootstrap = 100
fixed_block_length = 20 # 200 ps blocks for dielectric error bar block averaging.
prmtop_filename... | choderalab/LiquidBenchmark | src/munge_output_amber.py | Python | gpl-2.0 | 2,349 | [
"MDTraj"
] | 8a865290296c56867207dba16af4610a4af9903d5acb2f523673220906988352 |
#!/usr/bin/env python
"""
=================
dMRI: Camino, DTI
=================
Introduction
============
This script, camino_dti_tutorial.py, demonstrates the ability to perform basic diffusion analysis
in a Nipype pipeline.
python dmri_camino_dti.py
We perform this analysis using the FSL course data, which ca... | rameshvs/nipype | examples/dmri_camino_dti.py | Python | bsd-3-clause | 11,489 | [
"ParaView",
"VTK"
] | 6845237fa0e42981febf08eb82271db5b16eb04c71c1f705c5132cf592ffa293 |
import datetime
import faker
import re
import threading
import sqlalchemy
import sqlalchemy.orm
from sqlalchemy import or_, and_
from sqlalchemy.sql import expression
from typing import Collection
# Note: leaving for future use if we go back to using a relationship to PatientStatus table.
# from sqlalchemy.orm impor... | all-of-us/raw-data-repository | rdr_service/dao/participant_summary_dao.py | Python | bsd-3-clause | 57,595 | [
"VisIt"
] | e537a77da8089c045073a0a521272cfdd3c0f229bb768eea1e93a645d285b3cf |
# -*- coding: utf-8 -*-
# Copyright (C) Brian Moe (2013-2014), Duncan Macleod (2014-)
#
# This file is part of LIGO CIS Core.
#
# LIGO CIS Core 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 ... | lscsoft/cis.server | cisserver/models.py | Python | gpl-3.0 | 14,782 | [
"Brian",
"MOE"
] | 77b5321d970ffb678c010ff708f6d1381be953b0fb64318459fb9b58bf94ee86 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on 29/03/17 at 11:40 AM
@author: neil
Program description here
Version 0.0.0
"""
import numpy as np
from astropy.io import fits
from astropy.table import Table
import matplotlib.pyplot as plt
import sys
import os
import mpmath
from tqdm import tqdm as wrap
... | njcuk9999/neil_superwasp_periodogram | LCA_test_ernst.py | Python | mit | 33,394 | [
"Gaussian"
] | 7dfb8bdcfdc48c694c3fdc230a63e891d860cb447d88f12d45fbb325e67f28c2 |
__author__ = "waroquiers"
import numpy as np
from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
from pymatgen.analysis.chemenv.utils.graph_utils import (
MultiGraphCycle,
SimpleGraphCycle,
get_delta,
)
from pymatgen.util.testing import PymatgenTest
class FakeNode:
d... | vorwerkc/pymatgen | pymatgen/analysis/chemenv/utils/tests/test_graph_utils.py | Python | mit | 29,166 | [
"pymatgen"
] | 8b6e90c30a22bf7864e4e2e4501a2bf129d0142ceba591599e93f63ff99fa5fb |
from gpaw.utilities import unpack
import numpy as np
from gpaw.mpi import world, rank
from gpaw.utilities.blas import gemm
from gpaw.utilities.timing import Timer
from gpaw.utilities.lapack import inverse_general
from gpaw.transport.tools import get_matrix_index, collect_lead_mat, dot
import copy
import _gpaw
class Ba... | ajylee/gpaw-rtxs | gpaw/transport/sparse_matrix.py | Python | gpl-3.0 | 35,877 | [
"GPAW"
] | f6c036bc67f1bd933f785e72a7254bfe9b1cdb741e6d69b688b5e840f0852872 |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2012 - 2013 Daniel Reis
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free S... | raycarnes/project | project_issue_task/__openerp__.py | Python | agpl-3.0 | 2,070 | [
"VisIt"
] | 0b4060307639e9589767809cdee46244058a3c9d0cff50feec4f24235d202fa3 |
compliments = [
"You have very smooth hair.",
"You deserve a promotion.",
"Good effort!",
"What a fine sweater!",
"I appreciate all of your opinions.",
"I like your style.",
"Your T-shirt smells fresh.",
"I love what you've done with the place.",
"You are like a spring flower; beauti... | nerdzeu/NERDZCrush | mediacrush/mcmanage/compliments.py | Python | mit | 11,200 | [
"VisIt"
] | 50800828cac3f7a26b9860241715cc87a70c75d789bd5637b537eb20541659cd |
"""Utilities to lazily create and visit candidates found.
Creating and visiting a candidate is a *very* costly operation. It involves
fetching, extracting, potentially building modules from source, and verifying
distribution metadata. It is therefore crucial for performance to keep
everything here lazy all the way dow... | pantsbuild/pex | pex/vendor/_vendored/pip/pip/_internal/resolution/resolvelib/found_candidates.py | Python | apache-2.0 | 3,773 | [
"VisIt"
] | fe8f650a291e70cffad64825e7108a001caffe169110596b735a91a32541f6db |
#!/usr/bin/env python
import sys
import os
import pdb
# Locate MOOSE directory
MOOSE_DIR = os.getenv('MOOSE_DIR', os.path.join(os.getcwd(), '..', 'moose'))
if not os.path.exists(MOOSE_DIR):
MOOSE_DIR = os.path.join(os.getenv('HOME'), 'projects', 'moose')
if not os.path.exists(MOOSE_DIR):
raise Exception('Failed to... | paulthulstrup/moose | docs/moosedocs.py | Python | lgpl-2.1 | 651 | [
"MOOSE"
] | cc85b1743eeca04120c844f1f75b3d71de47dafa8787c4506de7248b2ab6a33f |
'''==============================
Long non-coding RNA pipeline
==============================
Overview
========
The pipeline_rnaseqLncRNA.py pipeline aims to predict lncRNAs from an ab initio
assembly of transcripts.
It requires that raw reads have been mapped to a reference
transcriptome and assembled into transcr... | CGATOxford/CGATPipelines | obsolete/pipeline_rnaseqlncrna.py | Python | mit | 43,524 | [
"BLAST"
] | 89abb2291e6c901c13c69a5c745cfd6f5f829c738ae07d2adaed2139078cbefa |
# (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... | benjixx/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 29,173 | [
"VisIt"
] | 8768e7e75160153bb1aa4e545f9f899de5e8369b4193c44b2c6c8d67241eb556 |
#!/usr/bin/python
"""Test to verify bug #469367 is still fixed.
Orca StarOffice script not properly announcing (potential) indentation
in OOo Writer.
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
######################################################################
# 1. Start oo... | h4ck3rm1k3/orca-sonar | test/keystrokes/oowriter/bug_469367.py | Python | lgpl-2.1 | 3,573 | [
"ORCA"
] | 8d7093244b18a4cf810c201cf3f1baa1fc442fb6ce291db5fa5cb6eb8902e649 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/gw/ugw_ac.py | Python | apache-2.0 | 18,653 | [
"PySCF"
] | b10f2e5064b25ae5b9b507e2b075a6a0146f2af2f5688f63976e43f1a8da5e21 |
# 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/Scaled_Features/results/4_categories/test10_cross_validate_categories_1200ms_scaled_method_i.py | Python | mit | 4,665 | [
"Mayavi"
] | 048ccb7ef4fd5bd568d19ec8efff212ae57a564d80c371441607bc9a7c4d78f7 |
# Adaptive Comfort Calculator
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Ladybug is free software; you can redistribute it and/or modify
# it under the te... | boris-p/ladybug | src/Ladybug_Adaptive Comfort Calculator.py | Python | gpl-3.0 | 31,814 | [
"EPW"
] | 10db9c92ab0e46e93daf45740bd57146353c978c6c6441dc18f44c87c0a9b4ff |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""usage: blobtools create -i FASTA [-y FASTATYPE] [-o PREFIX] [--title TITLE]
[-b BAM...] [-C] [-a CAS...] [-c COV...]
[--nodes <NODES>] [--names <NAMES>] [--db <NODESDB>]
[-t H... | DRL/blobtools | lib/create.py | Python | gpl-3.0 | 6,174 | [
"BLAST"
] | 89a3c38eb64c739ad9d45bf0c210986461e1944a2e16c1e66ae0a3a11dac9356 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RRsamtools(RPackage):
"""Binary alignment (BAM), FASTA, variant call (BCF), and tabix file... | LLNL/spack | var/spack/repos/builtin/packages/r-rsamtools/package.py | Python | lgpl-2.1 | 2,555 | [
"Bioconductor"
] | a8c44785429c638a084c161e480bef4a0c970f2df9fc3419dd4cf65cf354701d |
import sys, Image
from numpy import *
import scipy.ndimage
def score_from_autocorr(img0, img1, corres):
# Code by Philippe Weinzaepfel
# Compute autocorrelation
# parameters
sigma_image = 0.8 # for the gaussian filter applied to images before computing derivatives
sigma_matrix = 3.0 # for the integration gau... | CansenJIANG/deepMatchingGUI | src/rescore.py | Python | mit | 4,539 | [
"Gaussian"
] | da80fd4c1f37e6e8b7066364cbf86a780292b4c8e935cedb0a910a3945e68774 |
# coding: utf-8
__author__ = 'czhou <czhou@ilegendsoft.com>'
mime_types = {
"ai": "application/postscript",
"aif": "audio/x-aiff",
"aifc": "audio/x-aiff",
"aiff": "audio/x-aiff",
"asc": "text/plain",
"atom": "application/atom+xml",
"au": "audio/basic",
"avi": "video/x-msvideo",
"bc... | MaxLeap/SDK-CloudCode-Python | ML/mime_type.py | Python | cc0-1.0 | 6,931 | [
"NetCDF"
] | 06df4a44cfae3e3afad6789ac19e5295eb4cf4158c0803a7a460fa7b99118d2e |
# coding=utf-8
import json
import logging
import os
import datetime
from collections import OrderedDict
import pytz
import shutil
from PyQt4.QtCore import QObject, QFileInfo, QUrl, Qt
from PyQt4.QtXml import QDomDocument
from qgis.core import (
QgsProject,
QgsCoordinateReferenceSystem,
QgsMapLayerRegistr... | Samweli/inasafe | realtime/ash/ash_event.py | Python | gpl-3.0 | 30,298 | [
"VisIt"
] | 64a9ba178e5dfe2c312b840d536ce0fc83e3ff1aa38be2770057ec7254ef6e79 |
#import pdb # pause code for debugging at pdb.set_trace()
import numpy as np
import toolbox as tool
import slab_functions as sf
from pysac.plot.mayavi_seed_streamlines import SeedStreamline
import matplotlib.pyplot as plt
from mayavi import mlab
import gc
#import move_seed_points as msp
import mayavi_plotting_function... | SP2RC-Coding-Club/Codes | 13_07_2017/3D_slab_modes.py | Python | mit | 35,096 | [
"Mayavi"
] | b64507ac6de475e036aee59f2a628b3140248f3a159d6b0d641b0a8fe9c4ba16 |
from __future__ import division, print_function
import numpy as np
from bct.utils import BCTParamError, binarize
from bct.utils import pick_four_unique_nodes_quickly
from .clustering import number_of_components
def latmio_dir_connected(R, itr, D=None):
'''
This function "latticizes" a directed network, while ... | boomsbloom/dtm-fmri | DTM/for_gensim/lib/python2.7/site-packages/bct/algorithms/reference.py | Python | mit | 53,864 | [
"Gaussian"
] | 32d6bb764e4ad46676386fc3767bdda7400eba449b99fd45ba374cb9fea8bb08 |
from collections import defaultdict
import matplotlib.pyplot as plt
import re
import scipy.stats
import subprocess
import os
import cPickle
import tps_utils
import numpy as np
from collections import Counter
import pysam
import bzUtils
class TPS_Lib:
def __init__(self, experiment_settings, lib_settings):
... | borisz264/toeprint_seq | tps_lib.py | Python | mit | 8,362 | [
"pysam"
] | ef11ee84102b5d823fadd6cffa7381997c9b9c393068d835d0e745c9cff9f8c3 |
import collections
import itertools as it
import mrf
import ve
from operator import mul
from operator import add
import numpy as np
def tree_sum_product(tree_network, root):
'''
Perform sum-product belief propagation for trees computing the marginal
distribution of each variable using two passes.
Para... | blr246/mrf | mrf/belief_propagation.py | Python | mit | 9,461 | [
"VisIt"
] | 15f2e79308a3fcfb51e584edd5c778296d5dd0319704ca4b775d623ae654b721 |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'castep'
tab.settings['Output file name'] = 'phonon.castep'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 5
tab.settings['Mass definition... | JohnKendrick/PDielec | Examples/Mie/MgO_lognormal/script.py | Python | mit | 2,598 | [
"CASTEP"
] | 5856af81fb58a6778eabe0ce6a17ece9bd5d1d1859ea8bedd06baca68a3d0f75 |
from __future__ import print_function
import os, string, tempfile, shutil
from subprocess import Popen
from ase.io import write
from ase.units import Bohr
class Bader:
'''class for running bader analysis and extracting data from it.
The class runs bader, extracts the charge density and outputs it
to a cu... | suttond/MODOI | ase/calculators/jacapo/utils/bader.py | Python | lgpl-3.0 | 6,745 | [
"ASE"
] | 2e2de13fe07a47f907ae3140d8cecca93a9c3008d653b6980ca9f53b7bad402c |
#!/usr/bin/env python
import gd_util
import sys
from Population import Population
################################################################################
def convert_percent(string_value):
if string_value.endswith('%'):
val = convert_non_negative_int(string_value[:-1])
if val > 100:
... | gigascience/galaxy-genome-diversity | tools/filter_gd_snp/filter_gd_snp.py | Python | gpl-3.0 | 2,636 | [
"Galaxy"
] | 2c10698d2c11297ca4c0f6202643cac6f105a4096c6de1afdff4bc1a04032834 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2005-2018 (ita)
"""
Runner.py: Task scheduling and execution
"""
import heapq, traceback
try:
from queue import Queue, PriorityQueue
except ImportError:
from Queue import Queue
try:
from Queue import PriorityQueue
except ImportError:
class PriorityQueue(Q... | jackaudio/jack2 | waflib/Runner.py | Python | gpl-2.0 | 16,146 | [
"VisIt"
] | 8ed650123a345e09f2445cd8e89a664c3b69bf53d87dd2d714542e34cad80bc4 |
import numpy as np
import os
import theano
import theano.tensor as T
from deepmonster.adlf.activations import Rectifier
from deepmonster.adlf.initializations import Initialization, Gaussian, Orthogonal
from deepmonster.adlf.network import Feedforward, find_nets, find_attributes
from deepmonster.adlf.rnn import ConvLST... | olimastro/DeepMonster | deepmonster/testing/conlstm_bn.py | Python | mit | 2,248 | [
"Gaussian"
] | fcf8868eed7b35d08f180434a62417ad7905218d13b4795d37923af3b8a5eef2 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Peter G. LAndgren
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | gramps-project/gramps | gramps/plugins/rel/rel_sv.py | Python | gpl-2.0 | 23,593 | [
"Brian"
] | 6c5bf91959b18d99845124e7ab03d61f25914fed03e852b47ffd9899948de3cd |
from __future__ import absolute_import
import sys, os, yaml, glob
import subprocess
import pandas as pd
import argparse
import re
import string
import shutil
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot as plt
from nougat import common
from nougat import pdf
from nougat.pdf.theme import colors,... | senthil10/NouGAT | sciLifeLab_utils/run_assembly_report.py | Python | mit | 28,372 | [
"BWA",
"Gaussian"
] | 8584bab1c7fc973c741df03fb469373efcb1e2e7e0d3cc76e11a1748bb9af220 |
from io import BytesIO
import numpy as np
import warnings
from .. import Variable
from ..conventions import cf_encoder
from ..core.pycompat import iteritems, basestring, unicode_type, OrderedDict
from ..core.utils import Frozen, FrozenOrderedDict
from ..core.indexing import NumpyIndexingAdapter
from .common import A... | clarkfitzg/xray | xray/backends/scipy_.py | Python | apache-2.0 | 5,480 | [
"NetCDF"
] | 3de8897a47d65015dff01927affa2fe6b27f0ea130f5e14a1f0a292206dd8909 |
#
# Copyright 2010 - 2012 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 ... | dursobr/Pythics | pythics/instruments/SRS_DS345.py | Python | gpl-3.0 | 1,805 | [
"Brian"
] | 7520ca86ad2b11c4247ced769ca0adc264d1ed17ced7e0644a1bb5f790d9122c |
"""Fast PSF modelling and centroiding in python
Calculates an accurate one-dimensional undersampled Gaussian profile by
integrating the profile over each pixel analytically.
Contains
--------
gaussian1d - 1D Gaussian profile
gaussian1dmt - 1D Gaussian profile (multithreaded)
gaussians1d ... | hpparvi/psf-centroid | src/__init__.py | Python | gpl-3.0 | 3,362 | [
"Gaussian"
] | 5a0e11e31ff8fd62ea81ecb8106d436e446bd9e878aea5dd3e6ea9972cffd180 |
# Copyright 2016 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... | xodus7/tensorflow | tensorflow/contrib/distributions/python/ops/mvn_diag_plus_low_rank.py | Python | apache-2.0 | 10,134 | [
"Gaussian"
] | 59060ac3957493e8813e5ce9bb7b259d7381372b58c07e12d341fa5465d34081 |
# $Id$
#
# Copyright (C) 2004-2012 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" uses pymol to inter... | adalke/rdkit | rdkit/Chem/PyMol.py | Python | bsd-3-clause | 8,287 | [
"PyMOL",
"RDKit"
] | 8525123d1d7b2b934408046a201f8fd7440a131270ae9d5c1bf627b7baf2661d |
"""
DIRAC.Core.Utilities package
"""
| DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/__init__.py | Python | gpl-3.0 | 40 | [
"DIRAC"
] | 3b4067e7a42b22e239c04583aca7006609a6f105b01c5e9ff480403096d10943 |
"""
A simple script to analyse ground/lab flat fields.
This script has been written to analyse the wavelength dependency of the PRNU.
:author: Sami-Matias Niemi
:version: 0.4
"""
import matplotlib
#matplotlib.use('pdf')
matplotlib.rc('text', usetex=True)
matplotlib.rcParams['font.size'] = 17
matplotlib.rc('xtick', la... | sniemi/EuclidVisibleInstrument | analysis/analyseGroundFlatsLambda.py | Python | bsd-2-clause | 53,358 | [
"Gaussian"
] | 4da4f908ef9fd935d834144def1bdc16618e6d53c933c897b67b25f31c14329c |
#! /usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
"""
Change file owner's group
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_func... | DIRACGrid/COMDIRAC | src/COMDIRAC/Interfaces/scripts/dchgrp.py | Python | gpl-3.0 | 2,531 | [
"DIRAC"
] | e53552435ac1444cda68b4489399d04bc0d6fed85989832b823e7a264767d335 |
# -*- coding: utf-8 -*-
# Copyright 2011 Viewfinder Inc. All Rights Reserved.
"""Tests DB indexing and querying.
"""
__author__ = 'spencer@emailscrubbed.com (Spencer Kimball)'
import logging
import platform
import random
import time
import unittest
from functools import partial
from tornado import escape
from viewf... | treejames/viewfinder | backend/db/test/indexing_test.py | Python | apache-2.0 | 24,773 | [
"Brian"
] | aeb7f1dcb293279a075c370d6ed939a529ad850f10e232c3c207a5e96efe2261 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/__init__.py | Python | bsd-3-clause | 2,376 | [
"scikit-bio"
] | 632ad6142f79447369a1c3a27511a686656b17a1a702be6c1e2352970edbd7de |
"""Flowline modelling: bed shapes and model numerics.
"""
# Builtins
import logging
import copy
from collections import OrderedDict
from functools import partial
from time import gmtime, strftime
import os
import shutil
import warnings
# External libs
import numpy as np
import shapely.geometry as shpg
import xarray ... | TimoRoth/oggm | oggm/core/flowline.py | Python | bsd-3-clause | 198,026 | [
"Gaussian",
"NetCDF"
] | aeb6f8da5f46087c31b932e2bfb5f66cc3c5cbcf3d2ad869ba417e798b788a90 |
#-------------------------------------------------------------------------------
# Name: module1
# Purpose:
#
# Author: Eli
#
# Created: 06/04/2014
# Copyright: (c) Eli 2014
# Licence: <your licence>
#-------------------------------------------------------------------------------
def m... | ejspina/Gene_expression_tools | Python/FilterByID_dict_parse.py | Python | gpl-2.0 | 7,098 | [
"BLAST"
] | 0696a8289bd7351a6287ebf0ebd57dce2d39cd89751e25205b09e16da50547bc |
# Copyright 2002 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Hetero, Crystal and Chain exist to represent the NDB Atlas structure. Atlas is a mini... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Crystal/__init__.py | Python | apache-2.0 | 8,604 | [
"Biopython",
"CRYSTAL"
] | 1323d12d06882d94ffcb1dea0b6361bcc4fe391cab46f84fd3e5acbb4d80e03e |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either vers... | flavioamieiro/pypln.web | pypln/web/indexing/urls.py | Python | gpl-3.0 | 1,206 | [
"NAMD"
] | c39d614c9e1c745f2230f28bc57280e88468e8d2d0444b0b241d70b22adbae49 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | imaculate/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 68,961 | [
"Gaussian"
] | 752a0c0df84c0407da7bbe4d45fdacad4fb1f77441b1cb176f8e8bd309468f8b |
"""This is a simple simulation code for GHOST or Veloce, with a class ARM that simulates
a single arm of the instrument. The key default parameters are hardwired for each named
configuration in the __init__ function of ARM.
Note that in this simulation code, the 'x' and 'y' directions are the along-slit and
dispers... | mikeireland/pyghost | pyghost/ghostsim.py | Python | mit | 25,668 | [
"Gaussian"
] | 7f59381d3c5d79f269a35fc534ed65fa93d199a77c3c0182a5b22ee4cf5052f1 |
from __future__ import division
import os
from skimage import io
from skimage.util import random_noise
from skimage.filters import scharr
from scipy import ndimage
import matplotlib.pyplot as plt
import numpy as np
import cv2
import phasepack
def input_data(path, filename):
img_path = os.path.join(path, file... | charparr/tundra-snow | fsim.py | Python | mit | 2,813 | [
"Gaussian"
] | 6813694f779ce42cca6e73e0257a75cfdccb661cf29c4225a3a3ff8976f20da7 |
# Python Version: 3.x
import pathlib
import re
import sys
import time
import webbrowser
from typing import *
import onlinejudge_command.download_history
import onlinejudge_command.logging as log
import onlinejudge_command.utils as utils
import onlinejudge
from onlinejudge.type import *
if TYPE_CHECKING:
import a... | kmyk/online-judge-tools | onlinejudge_command/subcommand/submit.py | Python | mit | 17,077 | [
"CRYSTAL"
] | d21d48015da328d1fb4117093a37bf93a83a5f81d077a25ed9b808c2f2ea8a3d |
# -*- coding:utf-8 -*-
# Copyright (c) 2015, Galaxy Authors. All Rights Reserved
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
# Author: wangtaize@baidu.com
# Date: 2015-03-30
import logging
from common import http
from galaxy import wrapper
from bootstrap impor... | leoYY/galaxy | console/backend/src/console/taskgroup/views.py | Python | bsd-3-clause | 2,835 | [
"Galaxy"
] | eb65b2f71eb924000ed07712ced789cc94956eb43a28297c6ca30ec66167bc02 |
#!/usr/bin/env python
"""This example demonstrates the flow for retrieving a refresh token.
This tool can be used to conveniently create refresh tokens for later use with your web
application OAuth2 credentials.
To create a Reddit application visit the following link while logged into the account
you want to create ... | praw-dev/praw | docs/examples/obtain_refresh_token.py | Python | bsd-2-clause | 2,728 | [
"VisIt"
] | a506bd9ddf25af6464f93da94d14a6a1b06104ab23e829db0b0acbbfd2f6bce1 |
"""
The reader for Gaussian input files
===================================
A primitive reader for Gaussian ``.gjf`` input files is defined here. Note that
basically it just read the atomic coordinate and the connectivity if possible.
And the atomic coordinate has to be in Cartesian format.
"""
import itertools
imp... | tschijnmo/ccpoviz | ccpoviz/gjfreader.py | Python | mit | 3,826 | [
"Gaussian"
] | 452bd31b0ea9d10e9ae7e26f5cf0c76f26ac9412dfc1f064a29747ed1a15a32c |
"""
Assesment of Generalized Estimating Equations using simulation.
Only Gaussian models are currently checked.
See the generated file "gee_simulation_check.txt" for results.
"""
from statsmodels.compat.python import lrange
import scipy
import numpy as np
from itertools import product
from statsmodels.genmod.families... | bashtage/statsmodels | statsmodels/genmod/tests/gee_simulation_check.py | Python | bsd-3-clause | 9,433 | [
"Gaussian"
] | 89800b5891776c9b253d9e3499a300b84c469d0531d25964348f60660c3852d1 |
"""
A collection of utility functions and classes. Originally, many
(but not all) were from the Python Cookbook -- hence the name cbook.
This module is safe to import from anywhere within matplotlib;
it imports matplotlib only at runtime.
"""
from __future__ import (absolute_import, division, print_function,
... | andyraib/data-storage | python_scripts/env/lib/python3.6/site-packages/matplotlib/cbook.py | Python | apache-2.0 | 83,371 | [
"Gaussian"
] | 00f6c922beb07699ef8cd317587fcde7b448d93771d3cfb14ee96b8cda155279 |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import gw as gw_c
class KnowValues(unittest.TestCase):
def test_gw(self):
""" This is GW """
mol = gto.M( verbose = 0, atom = '''H 0.0 0.0 -0.3707; H 0.0 0.0 0.3707''', basis = 'cc-pvdz', ... | gkc1000/pyscf | pyscf/nao/test/test_0060_gw_h2_ae.py | Python | apache-2.0 | 687 | [
"PySCF"
] | 76cb3f3666594db83f97c1d1c8411d17bbd264a159986b6614b14adf3a029c4c |
"""
SystemLoggingHandler is the implementation of the Logging service
in the DISET framework.
The following methods are available in the Service interface::
addMessages()
"""
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.DISET.RequestHandler ... | Andrew-McNab-UK/DIRAC | FrameworkSystem/Service/SystemLoggingHandler.py | Python | gpl-3.0 | 2,278 | [
"DIRAC"
] | eb8abca3f81452429690730d9ef6131193177828a414e33e931951aa226fe6e6 |
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