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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects for extracting timing data from the ABINIT output files
It also provides tools to analye and to visualize the parallel efficiency.
"""
import collections
import logging
import o... | richardtran415/pymatgen | pymatgen/io/abinit/abitimer.py | Python | mit | 31,371 | [
"ABINIT",
"pymatgen"
] | 6bf745e8d683fa1886654d99d315d04588049be8e9c74e3a0a025c28f0b87828 |
import numpy
from chainer import cuda
from chainer import function
from chainer.utils import type_check
class Gaussian(function.Function):
"""Gaussian sampling function.
In forward calculation, this funciton takes mean and logarithm of variance
as inputs, and draw a sample from a gaussian distribution.... | woodshop/chainer | chainer/functions/gaussian.py | Python | mit | 2,174 | [
"Gaussian"
] | 73b56bcbdbb0d6d51633cd05579cc0453aa142243dcb6a2e21b3eb289309d528 |
# -*- coding: utf-8 -*-
"""
Update a database with point observation netcdf files
"""
import netcdfio
####
# Inputs
create = False
dbfile = 'C:/Projects/GOMGalveston/DATA/GalvestonObs.db'
#ncfiles = ['C:/Projects/GOMGalveston/DATA/Ocean/USIOOS_OceanObs_20102011.nc',\
# 'C:/Projects/GOMGalveston/DAT... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/DataIO/updateDataBase.py | Python | mit | 804 | [
"NetCDF"
] | 0de3678fa24601fd311fc67efc5e63230cc69be10ff8c200ea5d4f85909773ab |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2016, 2017, 2018 Guenter Bartsch
#
# 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.... | gooofy/voxforge | zamiaai/skills/bio/bio.py | Python | lgpl-3.0 | 53,436 | [
"ESPResSo",
"Firefly",
"Jaguar",
"MOOSE"
] | 6b349204ced5d4d320710a55efbe369772353dd4067f9e2e64674ad2f8b7f8fa |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import functools
import io
import json
import random
import shutil
import tempfile
import ddt
from boto.exception import BotoServerError
from django.conf import settings
from django.contrib.auth.models import User
from django.core i... | hastexo/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 226,673 | [
"VisIt"
] | efc275110e019c09db9df667781571a92c2693bd08c6e49ad1c9360d56ecb067 |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | pbrady/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 172,183 | [
"Gaussian"
] | 7f925f70ce97a528bc919c6fbb01bd67b85ba5fad5599f1300c3b3b6950b9b29 |
"""
Module for managing the installation of DIRAC components:
MySQL, DB's, NoSQL DBs, Services, Agents, Executors and Consumers
It only makes use of defaults in LocalInstallation Section in dirac.cfg
The Following Options are used::
/DIRAC/Setup: Setup to be used for any operation
/LocalInstallation/... | arrabito/DIRAC | FrameworkSystem/Client/ComponentInstaller.py | Python | gpl-3.0 | 105,625 | [
"DIRAC"
] | 0892e805363188e9f5ce8baafd9c1354259ecdfefa2ca6906875c54fc34af6c2 |
""" Functions related to convolution."""
# py2.6+ compatibility
from __future__ import division, print_function, unicode_literals
import numpy as np
from .utilities import nan2num
from .sed import make_constant_dv_wa_scale
def convolve_psf(a, fwhm, edge='invert', replace_nan=True, debug=False):
""" Convolve an ... | nhmc/Barak | barak/convolve.py | Python | bsd-3-clause | 6,017 | [
"Gaussian"
] | 9efafa493acbccfed86482f5c27d523accb15036a90adb918ff590f5d739b6a5 |
import os.path as op
from sfepy.base.base import *
import sfepy.base.ioutils as io
from sfepy.fem import ProblemDefinition
from sfepy.solvers.generic import solve_direct
from application import Application
class SimpleApp( Application ):
def process_options( options ):
"""Application options setup. Sets ... | certik/sfepy | sfepy/applications/simple_app.py | Python | bsd-3-clause | 3,192 | [
"VTK"
] | 46bf2a785aa80b01544d35ed776a88131b1f9d4e737bcfd227e4e87df9f85027 |
# -*- coding: utf-8 -*-
# Copyright (c) 2006-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2009 Mads Kiilerich <mads@kiilerich.com>
# Copyright (c) 2010 Daniel Harding <dharding@gmail.com>
# Copyright (c) 2011-2014, 2017 Google, Inc.
# Copyright (c) 2012 FELD Boris <lothiraldan@gmail.com>
# Cop... | AtomLinter/linter-pylama | bin/deps/pylint/checkers/variables.py | Python | mit | 61,565 | [
"VisIt"
] | ad22c5bbb68ae8f4735f5f8e07631aac426128f4efdd568b67524732c2c3defa |
import inspect
import logging
import os
from Firefly import error_codes
from Firefly.const import COMMAND_NOTIFY, SERVICE_NOTIFICATION
from logging.handlers import RotatingFileHandler
LOG_PATH = '/opt/firefly_system/logs/new_firefly_log.log'
FORMAT = '%(asctime)s\t%(levelname)s:\t%(message)s'
LOGGING_LEVEL = {
'd... | Firefly-Automation/Firefly | Firefly/helpers/logging.py | Python | apache-2.0 | 4,004 | [
"Firefly"
] | 3d305c2b5d0cebf170c8cb634b4edea69b6483154601a4782b05c14c3f96dc10 |
"""Configuration Tests"""
from os.path import join
import ckanapi
import pytest
from hdx.utilities.loader import LoadError
from hdx.utilities.useragent import UserAgentError
from hdx.api import __version__
from hdx.api.configuration import Configuration, ConfigurationError
class TestConfiguration:
@pytest.fixtu... | OCHA-DAP/hdx-python-api | tests/hdx/api/test_configuration.py | Python | mit | 34,873 | [
"MOE"
] | 28d4aad33dfc8205e07a6d60a22d485bb8da29fff093b532ca8a99211cc44fd1 |
##########################################################################################
############################## IMPORTING USEFUL DEFINITIONS ############################
# standard libraries imports
import os, sys
# external libraries imports
import numpy as np
# fullrmc library imports
from full... | bachiraoun/fullrmc | Examples/dihedralConstraint/run.py | Python | agpl-3.0 | 10,235 | [
"VMD"
] | 75f4be86f844423702427289aaf185291404c4a1e1f2f50ed26224b8912b75ed |
""" Module that holds the ReportsClient Client class
"""
import tempfile
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.Core.Tornado.Client.ClientSelector import TransferClientSelector as TransferClient
from DIRAC.Core.Utilities.Plotting.FileCoding import codeRequest... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/Client/ReportsClient.py | Python | gpl-3.0 | 3,637 | [
"DIRAC"
] | 85b2b9b04f455274d999f310101d9ee0cb2aa2959a62528553b6a8e83765472d |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
Calibration module:
This module contains the classes for
1. Calibrate: Base class for specifying the parameters for
calibration a... | henniggroup/MPInterfaces | mpinterfaces/calibrate.py | Python | mit | 50,223 | [
"VASP",
"pymatgen"
] | 05941a0e3798124f7d64e7875bf79a9850371d847960ec226828bf7ad5999d2a |
import numpy as np
import simtk.openmm as mm
import simtk.openmm.app as app
import simtk.unit as u
eu = u.kilocalories_per_mole
temperature = 288 * u.kelvin
friction = 1.0 / u.picosecond
pdb = app.PDBFile('resi-1-15.pdb')
forcefield = app.ForceField('amber99sb.xml',"tip3p.xml")
system = forcefield.createSystem(pdb.... | kyleabeauchamp/AlphaSynuclein | python/production.py | Python | apache-2.0 | 718 | [
"OpenMM"
] | cf2fcf5de9f78f6ef31df3576691f7db9eafa2c456f2b74f782b900f8cc58402 |
import datetime
import json
import re
import sys
from dataclasses import dataclass as vanilla_dataclass
from decimal import Decimal
from enum import Enum
from ipaddress import IPv4Address, IPv4Interface, IPv4Network, IPv6Address, IPv6Interface, IPv6Network
from pathlib import Path
from typing import List, Optional
from... | samuelcolvin/pydantic | tests/test_json.py | Python | mit | 11,293 | [
"Galaxy"
] | 356523a52dcc0a0156c74bf8ae20b5259bc81a2d57343aa6cc63ad51c0dec095 |
# Copyright 2008-2009 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of django-facebookconnect.
#
# django-facebookconnect is free software: you can redistribute it and/or modify
# it under the te... | ryszard/django-facebookconnect | facebookconnect/views.py | Python | gpl-3.0 | 3,567 | [
"Brian"
] | d06fff6be9d731cc92c4eec88bcc4cd076d152b604140dd717b467deae97a1c8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# __author__ = "leisurem"
class stock():
def __init__(self):
pass
@staticmethod
def getsina(sinjs):
'''
resolve info from wangyi
example input:
http://hq.sinajs.cn/list=sz150019
var hq_str_sz15001... | leisurem/somecode | etf/shareprice.py | Python | mit | 1,821 | [
"ADF"
] | 2637303a6113abf58838038dd19f04964f50dd0e195b9d6538c366b51b5f54cb |
"""
This module contains classes that can learn the weights.
"""
import numpy as np
class STDP:
"""
Spike Timing Dependent Plasticity
"""
def __init__(self, eta, w_in, w_out, tau, window_size, verbose=False, tau2=None):
"""
:param eta: learning rate
:param w_in:
:par... | johannesmik/neurons | neurons/learning.py | Python | bsd-2-clause | 6,346 | [
"NEURON"
] | 6e891ba3b674235e61bd575a184c11a713ed77e1bc2dbfb1813363459a8d6f23 |
import matplotlib
matplotlib.use('Agg')
import numpy as np
import netCDF4
from datetime import datetime
import pyroms
import pyroms_toolbox
import sys
def create_HYCOM_file(name, time, lon, lat, z, var):
print 'Write with file %s' %name
#create netCDF file
nc = netCDF4.Dataset(name, 'w', format='NETCD... | dcherian/pyroms | examples/Arctic_HYCOM/get_hycom_GLBa0.08_v_2014.py | Python | bsd-3-clause | 4,733 | [
"NetCDF"
] | 652f5e62e426634d04b38f67b4cc2062cd853c2d0a2eea5877b9e557d7f81036 |
################################################################################
# Copyright (C) 2013-2015 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Unit tests for `gaussian` module.
"""
import numpy as np
fr... | jluttine/bayespy | bayespy/inference/vmp/nodes/tests/test_gaussian.py | Python | mit | 50,883 | [
"Gaussian"
] | e356d8ce8ff0547a3af65d8996100ad051aa521133e382f7f8d1a17b421c06fd |
import os
import unittest
from pheme.util.config import Config, configure_logging
from pheme.util.pg_access import db_connection, db_params
from pheme.longitudinal.generate_daily_essence_report import GenerateReport
from pheme.longitudinal.generate_daily_essence_report import ReportCriteria
from pheme.longitudinal.sta... | pbugni/pheme.longitudinal | pheme/longitudinal/tests/test_region_report.py | Python | bsd-3-clause | 3,908 | [
"VisIt"
] | 6d2eb40b3203060a870e0a1936e705b5fe30ae9e5a8955cd2a840304b6eedcaf |
#!/usr/bin/env python
"""
Start DIRAC component using runsvctrl utility
"""
from DIRAC.Core.Base.Script import Script
@Script()
def main():
Script.disableCS()
# Registering arguments will automatically add their description to the help menu
Script.registerArgument(
" System: Name of the system fo... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_start_component.py | Python | gpl-3.0 | 1,289 | [
"DIRAC"
] | 9e50924e31bfc39eede16daf955ff6dbfb2d05ad8765f2174ce89c4b37d85e0d |
from __future__ import unicode_literals
from django.test import TestCase
from django.utils import six
from .models import (
A, B, Building, C, Chick, Child, Class, Client, ClientStatus, Connection,
Country, Device, Enrollment, Hen, Item, Organizer, Person, Port,
SpecialClient, State, Student, TUser,
)
c... | koniiiik/django | tests/select_related_regress/tests.py | Python | bsd-3-clause | 9,498 | [
"Brian"
] | e62745d76443149c9c8fed2c7f74131a9b9435a0cb44f5f9005f9cf4b9c8f897 |
import os
if __file__ in [f for f in os.listdir('.') if os.path.isfile(f)]:
# This is executed when the script is loaded by the labradnode.
SCRIPT_PATH = os.path.dirname(os.getcwd())
else:
# This is executed if the script is started by clicking or
# from a command line.
SCRIPT_PATH = os.path.dirname... | McDermott-Group/LabRAD | LabRAD/TestScripts/fpgaTest/conf.py | Python | gpl-2.0 | 1,676 | [
"Gaussian"
] | 3aaaa75dacbd2a05de40bf1858039a5aa7dfa27defe2f4907e6daff59c9c0a09 |
########################################################################
# $HeadURL $
# File: RequestDB.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/12/04 08:06:30
########################################################################
""" :mod: RequestDB
=======================
.. module: Request... | calancha/DIRAC | RequestManagementSystem/DB/RequestDB.py | Python | gpl-3.0 | 32,051 | [
"DIRAC"
] | 7cc060e3f2d4927300a7feec7c8edafbc726d9527396419932b316b6724f39ea |
from __future__ import annotations
import logging
logger = logging.getLogger(__name__)
from libtbx.phil import parse
from scitbx.array_family import flex
from dials.algorithms.refinement import DialsRefineConfigError
phil_str = """
min_nref_per_parameter = 5
.help = "the smallest number of reflection... | dials/dials | algorithms/refinement/parameterisation/autoreduce.py | Python | bsd-3-clause | 10,175 | [
"CRYSTAL"
] | 73ed0546f2f68369957b3a7ce80f4fcdf1d02b7ccff971250943d00c617457c5 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/analysis/test_gnm.py | Python | gpl-2.0 | 8,061 | [
"MDAnalysis"
] | 96dd9ba4dda331da3251edf5af634d56d6f74dbdd12711e2190095d24b03c95c |
# -*- coding: utf-8 -*-
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD 3 clause
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_rand... | chrsrds/scikit-learn | sklearn/cluster/spectral.py | Python | bsd-3-clause | 21,118 | [
"Brian",
"Gaussian"
] | 71801d203bcbb693294730625daa74684aabc1187924c98e12a44e9b4692a6c7 |
from __future__ import unicode_literals
from frappe import _
def get_data():
return {
'fieldname': 'sales_order',
'non_standard_fieldnames': {
'Delivery Note': 'against_sales_order',
'Journal Entry': 'reference_name',
'Payment Entry': 'reference_name',
'Payment Request': 'reference_name',
'Auto Rep... | saurabh6790/erpnext | erpnext/selling/doctype/sales_order/sales_order_dashboard.py | Python | gpl-3.0 | 1,033 | [
"VisIt"
] | 5cf9ef7f7880e0c816cee3e6f115b872dcd15b4077cd256649e73d6ca3656216 |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | hkupty/python-mode | pymode/libs/pylama/lint/pylama_pylint/pylint/checkers/classes.py | Python | lgpl-3.0 | 34,392 | [
"VisIt"
] | 06a643503f5264821f09a655ea62f84d2ee84133184f159ed270f781f50edf6f |
#!/usr/bin/env python
import os
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This example demonstrates the reading of a field and conversion to PolyData
# The output should be the same as polyEx.tcl.
# Create a reader and write out the field
reade... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Core/Testing/Python/fieldToPolyData.py | Python | gpl-3.0 | 2,400 | [
"VTK"
] | a192e8a6d7956f1aa8d492a94bbe5ed229bd9cedc266683d966d14b74fa51414 |
#
#
# Tutorial Yambo School. Lausanne, 24-28 April 2017
# Convergence GW on hexagonal BN
# Alejandro Molina-Sanchez & Henrique P. C. Miranda
#
#
from __future__ import print_function
import sys
from yambopy import *
from qepy import *
from schedulerpy import *
import argparse
yambo = 'yambo'
p2y = 'p2y'
pre... | alexmoratalla/yambo-py | tutorial/bn/gw_conv_bn.py | Python | bsd-3-clause | 10,517 | [
"Yambo"
] | 29c4b7069a535ee47a3d3e4aba7b087e8e1cd5300430b3aee85ffa94740bc1e1 |
#-------------------------- LICENCE BEGIN ---------------------------
# This file is part of DaleyMenard93.
#
# DaleyMenard93 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... | martndj/DaleyMenard1993 | DM93/__init__.py | Python | gpl-3.0 | 1,173 | [
"Gaussian"
] | 58205ff2a8ef3a1575b8254be4a4199cae9201f2cf331bf4451b2aa6a2ef9b53 |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | meshes/c4080ang/Generate4080Centreline_60.py | Python | gpl-2.0 | 1,015 | [
"VTK"
] | 230a3da8a93073403acc1895f10de5d0903ed4b8b6833ab71f81f8e0e28b1893 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
from setuptools import setup
import sys
from os.path import exists
def parse_version(fpath):
"""
Statically parse the version number from a python file
"""
import ast
if not exists(fpath)... | Erotemic/dtool | setup.py | Python | apache-2.0 | 7,107 | [
"VisIt"
] | 9f1a310a2f8592149f65ad22c5e180a94ff0b9e895fa39056a9954010ffbad2d |
import json
import math
import os
from statistics import mean
import numpy
from django.conf import settings
from django.contrib.gis.geos import Polygon
from django.core.management import BaseCommand, CommandError
from django.db.models import Avg
from ncdjango.models import Service, SERVICE_DATA_ROOT, Variable
from net... | consbio/seedsource-core | seedsource_core/django/seedsource/management/commands/calculate_zone_transfers.py | Python | bsd-3-clause | 14,279 | [
"NetCDF"
] | 8c2a9326205fc1c50538bb45db7cbab679594d405faeba64aa7788c70888571a |
# -*- coding: utf-8 -*-
"""Implementation of execution-related magic functions.
"""
#-----------------------------------------------------------------------------
# Copyright (c) 2012 The IPython Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYIN... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/core/magics/execution.py | Python | apache-2.0 | 47,540 | [
"VisIt"
] | 2b1ec7597ec58df770c898f069e78336aa7126998c8bb88bd4b97a8941263d42 |
"""
Sample problems on which to test algorithms.
XXX: get some standard optimization problems from literature
"""
import numpy as np
import base
from pyll import as_apply
from pyll import scope
from pyll_utils import hp_choice, hp_randint, hp_pchoice
from pyll_utils import hp_uniform, hp_loguniform, hp_quniform, hp... | CVML/hyperopt | hyperopt/bandits.py | Python | bsd-3-clause | 4,259 | [
"Gaussian"
] | 82ce1f18a90baed1fa82b991548bcf4f7f1585eaf6ff202c3e908dd2830f0787 |
r"""
Bending of a long thin cantilever beam computed using the
:class:`dw_shell10x <sfepy.terms.terms_shells.Shell10XTerm>` term.
Find displacements of the central plane :math:`\ul{u}`, and rotations
:math:`\ul{\alpha}` such that:
.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}, \ul{\beta})
e_{kl}(\ul{u}, \ul... | rc/sfepy | examples/linear_elasticity/shell10x_cantilever.py | Python | bsd-3-clause | 3,878 | [
"VTK"
] | 5877dc38aec80d43f06747ec89463ad59ca36432324ae7de56a3bc0cc1661554 |
""" This module includes radio channel models and routines to create a sum of
sinusoids or a sum of cisoids. """
# sum of sinusoids
from spec2sos import spec2sos
# sum of cisoids
from spec2soc import spec2soc
# Gaussian random procss
from gauss_rand_proc_c import gauss_rand_proc_c
# radio channel models, e.g. COST 207
... | no-net/gr-winelo | python/channel/__init__.py | Python | gpl-3.0 | 334 | [
"Gaussian"
] | 155c3f19976b0967c298b5ceab7c6d3b57440e30069313330f441195328a6f1e |
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/adc/test/test_P_uadc_ip.py | Python | apache-2.0 | 3,131 | [
"PySCF"
] | fa30a54353349794fe13dc7b973998eec96f18c9fdaa9edc2ca2d46be51cba24 |
### Fetch Genomics Sequence Using Coordinates In Biopython
from Bio import Entrez, SeqIO
Entrez.email = "A.N.Other@example.com" # Always tell NCBI who you are
handle = Entrez.efetch(db="nucleotide",
id="307603377",
rettype="fasta",
strand=1, ... | minesh1291/Sequence-Utilities | Online/FetchNCBIseq.py | Python | apache-2.0 | 671 | [
"Biopython"
] | e355ef24b120951edfc598e245e9ce22efd769813f32b9d9713445d49678aeb1 |
# Copyright 2011 by Wibowo Arindrarto (w.arindrarto@gmail.com)
# Revisions copyright 2011, 2014 by Peter Cock.
# 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.
"""Bio.SeqIO parser for the ABI format.
... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/SeqIO/AbiIO.py | Python | apache-2.0 | 24,878 | [
"Biopython",
"VisIt"
] | 4f452c8d3a85761f2d78f258aaedf7d138d339f80f6c12e6b6a1d17a4003bc37 |
"""
Create and put Requests to move files.
List of operations:
#. ReplicateAndRegister LFNs
#. Check for Migration
#. Remove all other replicas for these files
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import DIRAC
from DIRAC import gL... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_create_moving_request.py | Python | gpl-3.0 | 11,650 | [
"DIRAC"
] | 91b0df005c86b9dda07d2f0cf968eb135f04485754c2609943166b50533c574b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from rdkit.Chem.AtomPairs import Pairs
from rdkit import DataStructs
__license__ = "X11"
METADATA = {
"id": "method_rdkit_ap_tanimoto",
"representation": "ap",
"similarity": "tanimoto"
}
def _compute_fingerprint(molecule):
return Pairs.GetAtomPairFinger... | skodapetr/lbvs-environment | methods/ap/ap_tanimoto.py | Python | mit | 1,351 | [
"RDKit"
] | 7eceb64eef850a8bb43ead72b666ade519f75927206bc0c69d6ef2329912bf0f |
from aces.materials import Material
from ase import Atoms,Atom
from math import pi,sqrt
from ase.dft.kpoints import ibz_points
from ase.lattice import bulk
from aces import config
class structure(Material):
def set_parameters(self):
self.enforceThick=False
self.latx=1
self.laty=1
self.latz=1
self.timestep=s... | vanceeasleaf/aces | aces/materials/diamond.py | Python | gpl-2.0 | 903 | [
"ASE"
] | b84e62f93eafe8067940ca064076d7bf547530800083c3e2a2bfb2c98df90f49 |
# -*- coding: utf-8 -*-
TOILET_CHOICES = (
('F', 'Flush'),
('PT', 'Pit toilet'),
('TPT', 'Traditional Pit toilet'),
('L', 'Latrine'),
('BF', 'Bush /Field'),
('R', 'River'),
('O', 'Others'),
)
COOKING_FACILITIES = (
('Electricity', 'Electricity'),
('Gas'... | aazhbd/medical_info01 | irpmemr/const.py | Python | bsd-3-clause | 4,357 | [
"VisIt"
] | 1b0d430bcab021d90a5fb6f9ec24d92735a218b8b00e54b1c1fdc6d2d8d22ca8 |
# Copyright (c) 2015-2016 Cisco Systems
#
# 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, modify, merge, publ... | rjfellman/molecule | test/unit/test_ansible_galaxy.py | Python | mit | 2,825 | [
"Galaxy"
] | 946e7d2013a827e148f17b8824ad2228a2359a4346ee8db195039b3ef4408b76 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
from __future__ import division
import os, os.path
from pandas import *
import numpy as np
import csv
from itertools import groupby
from collections import defaultdict
from copy import deepcopy
from types import TupleType
import matplotlib.pyplot as plt
... | JudoWill/ResearchNotebooks | MissingHIVDs.py | Python | mit | 2,212 | [
"VisIt"
] | cf519408157a8c1e4a441936470be8a7c8f1105b51257826134309d808d3a6a5 |
"""
Implements basic GraphModels.
"""
import os
from typing import Dict, List, Union
from warnings import warn
import numpy as np
from monty.serialization import dumpfn, loadfn
from pymatgen.core import Structure
from tensorflow.keras.backend import int_shape
from tensorflow.keras.callbacks import Callback
from tenso... | materialsvirtuallab/megnet | megnet/models/base.py | Python | bsd-3-clause | 15,694 | [
"CRYSTAL",
"pymatgen"
] | cb183e2f855b4fff6cbdaa9256cffb7794ac0498cdd7c35907bb047c19fe13f3 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2015-2016 Hans Hoogenboom, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any ... | docwhite/appleseed | scripts/oslextractmeta.py | Python | mit | 16,465 | [
"VisIt"
] | 1d990cd2ed0247923a3aa554e8c21a9e341bcfdbed4c77285c75015c8459df3f |
#!/usr/bin/env python2
from ase import Atoms
from ase.optimize import QuasiNewton
from obcalc import OBForceField
atoms = Atoms('OCO', [[0.0, 0.0, 0.0],
[3.0, 0.0, 0.0],
[6.0, 0.0, 0.0]])
calc = OBForceField()
atoms.set_calculator(calc)
relax = QuasiNewton(atoms)
relax.run(... | tkjacobsen/obcalc | examples/CO2-relax.py | Python | gpl-2.0 | 684 | [
"ASE"
] | 59a0cf441a4fb62e7dc053b9713ecc256f3a8f34b4aae2edf141b315c5bc7a6b |
import glob
import sys
import os
from setuptools import setup, find_packages, Extension
from Cython.Distutils import build_ext
import pysam
test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1]
test_module_name = "PysamTestModule_{}".format(test_module_suffix)
pysam_libraries = pysam.get... | kyleabeauchamp/pysam | linker_tests/link_without_rpath/setup.py | Python | mit | 954 | [
"pysam"
] | 6fe9f33b95e98485e1eda4f350f5226b2d380651bfca5b275851b35daa720933 |
#! /usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-bdii-site
# Author : Adria Casajus
########################################################################
"""
Check info on BDII for Site
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Base ... | avedaee/DIRAC | Core/scripts/dirac-admin-bdii-site.py | Python | gpl-3.0 | 1,478 | [
"DIRAC"
] | 2a5a54b2df0acc7e0a2dc615fa2aadc095e4725a9c01c7c88c72ffc36b70ced6 |
#!/usr/bin/python
"""
Copyright 2010 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/logout.py | Python | gpl-3.0 | 1,892 | [
"Galaxy"
] | 8132cdb6e896d4d92d4b32d62d4aa3523f52472a900fe827f23412d20c615363 |
"""Delay Stage
===============
"""
import random
from pymoa.stage import MoaStage
import trio
__all__ = ('Delay', 'UniformRandomDelay', 'GaussianRandomDelay')
class Delay(MoaStage):
"""A stage that delays for :attr:`delay` seconds before the stage
is automatically completed.
"""
_config_props_ = ('... | matham/moa | pymoa/stage/delay.py | Python | mit | 1,486 | [
"Gaussian"
] | 8236d94b3d19c0efcef7bf61064d784cdc8abdec6978bbdca4652c91362bed6f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Wrapper for netCDF readers."""
from __future__ import unicode_literals, division, print_function
import os.path
from monty.dev import requires, deprecated
from monty.collections import AttrDict
from monty.f... | aykol/pymatgen | pymatgen/io/abinit/netcdf.py | Python | mit | 10,119 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | a5ab9066081fc954dfb96478a8331c0e789c130ba2c6a33405ef3e0cd3c849b8 |
# -*- coding: utf-8 -*-
import math
import random
# The transfer function of neurons, g(x)
def log_func(x):
return 1.0 / (1.0 + math.exp(-x))
# The derivative of the transfer function, g'(x)
def log_func_derivative(x):
return math.exp(-x) / pow(math.exp(-x) + 1.0, 2)
# Initializes a matri... | myth/trashcan | tdt4171/ex05/nnet.py | Python | gpl-2.0 | 8,099 | [
"NEURON"
] | 9b6c821ee1e97ce9a88543172dd77fdd3289463daa0fbe4d9931e3fa939e80c8 |
import reflowrestclient.utils as Rest
import flowio
import json
import csv
import sys
import os
import re
import hashlib
import getpass
if not len(sys.argv) == 2:
sys.exit("Provide an input file")
input_file = sys.argv[1]
host = raw_input('Host: ')
username = raw_input('Username: ')
password = getpass.getpass('P... | whitews/ReFlowRESTClient | examples/batch_upload.py | Python | bsd-3-clause | 8,279 | [
"VisIt"
] | cbc86f86da703dacbb9ef40d8ba00a005765dfc4e1dbae63e226d43a0466fc35 |
# 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... | gunan/tensorflow | tensorflow/python/autograph/converters/lists.py | Python | apache-2.0 | 8,234 | [
"VisIt"
] | 4c13c47ca064df3cfa78d7a05a21b6bd634a6c6fabff9c786b4f9492c944719b |
# $Id$
#
# Copyright (C) 2004-2008 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.
#
from rdkit import Geome... | greglandrum/rdkit | rdkit/Chem/Features/FeatDirUtilsRD.py | Python | bsd-3-clause | 12,296 | [
"RDKit"
] | f9710bcea0d65ea45ca89182bff6bbb66719f9b9942207e5ba2ddc6573a09185 |
#!/usr/bin/env python
"""
Usage: python vtk_reindent_code.py [--test] <file1> [<file2> ...]
This script takes old-style "Whitesmiths" indented VTK source files as
input, and re-indents the braces according to the new VTK style.
Only the brace indentation is modified.
If called with the --test option, then it will pri... | keithroe/vtkoptix | Utilities/Maintenance/vtk_reindent_code.py | Python | bsd-3-clause | 16,384 | [
"VTK"
] | b8bf40960e7a0842430607e831811846d0185be19504f62fbbfe8f7f5aa823ec |
animal_adjectives = [
'agile',
'bashful',
'clever',
'clumsy',
'drowsy',
'fearful',
'graceful',
'hungry',
'lonely',
'morose',
'placid',
'ruthless',
'silent',
'thoughtful',
'vapid',
'weary'
]
animal_colours = [
'beige',
'black',
'blue',
'bri... | Drakekin/hipku | hipku/dictionaries.py | Python | mit | 12,392 | [
"Elk",
"GULP"
] | ba48cc3cec59f82a79ce4b520faa979397bb25d0e57445902fe0ce3a4ac9b162 |
# TO-DO: to be moved to tests directory
from __future__ import print_function
import cmd
import sys
import os.path
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.AbstractFileSystem import UnixLikeFileSystem
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.DirectoryCompletion import DirectoryCompletion... | chaen/DIRAC | DataManagementSystem/Client/test/new_dir_completion.py | Python | gpl-3.0 | 1,144 | [
"DIRAC"
] | 8c9c672688987a1939d61c35297179a9e346e08f2d90568ebc5f4b966975fc00 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import time
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.create_mode import ModeCreationPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.lms.courseware import Courseware... | wwj718/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware.py | Python | agpl-3.0 | 18,897 | [
"VisIt"
] | b5db115235e595e12dd9fc179f5cf0d4ad6418b1427480bc1b005b50bb54cda1 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (t... | apache/incubator-allura | Allura/allura/tests/functional/test_auth.py | Python | apache-2.0 | 45,336 | [
"VisIt"
] | b9bb5d436b34e18c3f5856b6be75bffe464cb4fc59b2571c30f49a7206b67100 |
"""
Tiger.
Copyright (c) 2011 Brian Browning, David Bern
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, modify, merge, ... | facelessuser/Rummage | rummage/lib/gui/actions/checksum/tiger.py | Python | mit | 33,392 | [
"Brian"
] | 6fbbd343b9dbca8a28881d079fdc1910c23d1c4dae831ca7bfedc177dd6fbb3a |
# transform passes used to encode / decode cards
import re
import random
# These could probably use a little love... They tend to hardcode in lots
# of things very specific to the mtgjson format.
import utils
cardsep = utils.cardsep
fieldsep = utils.fieldsep
bsidesep = utils.bsidesep
newline = utils.newline
dash_mar... | billzorn/mtgencode | lib/transforms.py | Python | mit | 23,368 | [
"CRYSTAL"
] | f0a7e91299f8f0c7766990a55a783177531b4ed4721f487b007d1874edbafd83 |
# (C) British Crown Copyright 2014 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | andrewcbennett/iris | lib/iris/tests/integration/test_grib2.py | Python | gpl-3.0 | 12,226 | [
"Gaussian",
"NetCDF"
] | f5399e4a86a614a7056b99772fa16a271c874f7068cb33289ad2961dd2c72792 |
from twisted.trial import unittest
import inspect, glob, os
from os import path
from twisted.python import reflect
import twisted
def errorInFile(f, line=17, name=''):
"""Return a filename formatted so emacs will recognize it as an error point
@param line: Line number in file. Defaults to 17 because that's... | waseem18/oh-mainline | vendor/packages/twisted/twisted/test/test_doc.py | Python | agpl-3.0 | 3,683 | [
"VisIt"
] | 77d4825f0b0a93c30aa18441fe927970d9f27ab8da0e2db82f72a594d21788fa |
# 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... | renyi533/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 170,477 | [
"Gaussian"
] | 6b47450f36a2417f40a28a78326c053c31d0821cfe318adf12c916b0c8d208e0 |
""" This is a test of the chain
ReqClient -> ReqManagerHandler -> ReqDB
It supposes that the DB is present, and that the service is running
"""
# pylint: disable=invalid-name,wrong-import-position
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
im... | ic-hep/DIRAC | tests/Integration/RequestManagementSystem/Test_Client_Req.py | Python | gpl-3.0 | 7,946 | [
"DIRAC"
] | e8e9b8bece3e9dc59933e4e1a5c9639771c685836508a3666aecfb993f2e101e |
""" Story views for editorial app.
editorial/views/storyviews.py
"""
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import json
from actstream import action
from braces.views import LoginRequiredMixin, FormMessagesMixin
from django.core.exceptions import PermissionDenied
from djang... | ProjectFacet/facet | project/editorial/views/story.py | Python | mit | 12,385 | [
"VisIt"
] | a1d64a2b1c17c787d8768eb7ba7349068a91e3599db56bd3dc7eb3dfcc97fe8c |
from pype.ast import *
from pype.error import *
class PrettyPrint(ASTVisitor):
'''
Vistor sublcass to visit an AST.
'''
def __init__(self):
pass
def visit(self, astnode):
if astnode.children is not None:
for child in astnode.children:
self.visit(child)... | Mynti207/cs207project | pype/semantic_analysis.py | Python | mit | 2,806 | [
"VisIt"
] | 42cde5be7185992fffd0bc83c8322c0b3fed2f670509439240750fa128511066 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | kvar/ansible | lib/ansible/modules/network/avi/avi_snmptrapprofile.py | Python | gpl-3.0 | 3,563 | [
"VisIt"
] | 72d7e31a8cc92296c15e76814dcd339db4c35996ef763ea1c5e7a187eebd649d |
# Copyright 2002 by Andrew Dalke. All rights reserved.
# Revisions 2007-2009 copyright by Peter Cock. All rights reserved.
# Revisions 2008 copyright by Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have be... | zhenghaiyong/BioInfo_CAHEC-VRL-ISM | scripts/biopython/BioSQL/Loader.py | Python | gpl-2.0 | 51,248 | [
"BioJava",
"BioPerl",
"Biopython"
] | 8cf93323aa2bf0e1ca8687925297d3b0a33a803085ba065ca14d758bb7485a75 |
#!/usr/bin/env python
# B a r a K u d a
#
# Generate zonal (and maybe one day global) plots related to
# air-sea fluxes
# Use climatology fields built with 'build_clim.sh'
#
# L. Brodeau, 2017
import sys
from os import path
import numpy as nmp
from netCDF4 import Dataset
import barakuda_tool ... | brodeau/barakuda | python/exec/sfluxes.py | Python | gpl-2.0 | 4,389 | [
"ORCA"
] | 0924875717370ad9aa5e423001ec0e233dbc0a708bd83e36807105642ff01d4c |
from octopus.runtime import *
v = variable(0, "variable", "variable")
run(
sequence( #23
once(v > 4, log("v > 4")), #2 #1
wait("2s"), #3
loop_while(v < 2, #7
sequence( #6
increment(v), #4
wait("1 s"), #5
)
),
parallel( #15
loop_until(v > 5... | rasata/octopus | examples/variables1.py | Python | mit | 666 | [
"Octopus"
] | 106f9120258a7b0a53f8cd64e14ee156bb8e9ae5d7aa8e10cf81fc72a7343fc0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | migueldiascosta/pymatgen | pymatgen/io/cssrio.py | Python | mit | 577 | [
"pymatgen"
] | e4b7b3e8da794460e152ec6026f4e4dbfc370acd3a2932da0fb5ab0e5e53b85d |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from ..common.utils import click_css, confirm_prompt
from .course_page import ... | nttks/edx-platform | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 29,396 | [
"VisIt"
] | d4b19e814a79671a05df9b9d9151cbdae0573a83714433ed9a98eba6b6c374b6 |
#!/usr/bin/env python
#
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law ... | Aloomaio/googleads-python-lib | examples/adwords/v201806/basic_operations/add_responsive_search_ad.py | Python | apache-2.0 | 3,443 | [
"VisIt"
] | b97a01c3bdf8c1d212d2113db2e0eda80c5e0b134aac6adfdd02e877fa477a51 |
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use ... | apache/libcloud | libcloud/common/digitalocean.py | Python | apache-2.0 | 6,993 | [
"VisIt"
] | b793ad983896209cbf577808553843a1f139f6290c55a0858c758e24c5a2ab0e |
# This code was modified from the tss plot code, that it can plot any other ChIP-seq signal
# at other genomic positions. In this case, it is the HRE. HIF1a ChIP-seq data
# is available, peaks were called by MACS in Galaxy, generated a bed file. the middle point
# of each peak is used as the center of the plot. all HRE... | crazyhottommy/some-unorganized-old-scripts | python_scripts/metaPlot_three_groups.py | Python | mit | 4,281 | [
"Galaxy",
"HTSeq"
] | 4d244d0b34e16a673df52e0f4002804d2ad4076b8f8987cf77dd62a717b08a49 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001 David R. Hampton
# Copyright (C) 2001-2006 Donald N. Allingham
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of... | Forage/Gramps | gramps/gen/plug/report/__init__.py | Python | gpl-2.0 | 1,239 | [
"Brian"
] | 00351fc9cd213fdc4f68c0c4925e09cb67009c4c36ce31a47ee8a1ee80ba43cd |
import os
import vtk, qt, slicer
import logging
from SegmentEditorEffects import *
class SegmentEditorEffect(AbstractScriptedSegmentEditorEffect):
"""This effect uses markup fiducials to segment the input volume"""
def __init__(self, scriptedEffect):
scriptedEffect.name = 'Draw tube'
scriptedEffect.perSeg... | lassoan/SlicerSegmentEditorExtraEffects | SegmentEditorDrawTube/SegmentEditorDrawTubeLib/SegmentEditorEffect.py | Python | bsd-3-clause | 28,323 | [
"VTK"
] | 846bf7989d5e75b5236e7e1429b532fdb5da3634aef3e162f8ebce43e199099b |
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.cm
from scipy.signal.windows import gaussian
import sklearn.metrics
from DataSet import createDataSetFromFile
from Utils import getProjectPath
from Evaluation import getSpecificCol... | ravenshooter/BA_Analysis | Figures.py | Python | mit | 10,091 | [
"Gaussian"
] | ca6e1c8a3648aaca676da4620d53532faa19a61e6d3ab8901ad7b9e38fadde82 |
# -*- coding: utf-8 -*-
"""
Module for dealing with constants `Henry's law
<https://en.wikipedia.org/wiki/Henry's_law>`_.
"""
from ._util import get_backend
from .util.pyutil import defaultnamedtuple, deprecated
from .units import default_units
def Henry_H_at_T(T, H, Tderiv, T0=None, units=None, backend=None):
"... | bjodah/chempy | chempy/henry.py | Python | bsd-2-clause | 3,595 | [
"ChemPy"
] | 4ba48bff07b2644d951fda0a0420b0e33714e7c3561363c9a2a8fb1a138ac3a5 |
#!/usr/bin/env python
"""Toy Parser Generator is a lexical and syntactic parser generator
for Python. This generator was born from a simple statement: YACC
is too complex to use in simple cases (calculators, configuration
files, small programming languages, ...).
TPG can very simply write parsers that are usefull for... | barnone/EigenD | pi/logic/tpg.py | Python | gpl-3.0 | 77,757 | [
"VisIt"
] | 4cf24fd69ef81db5cec28dd5fe89015994dfdc6d7f72196f46f2d470d86f8b1e |
import unittest
import os
import tempfile
import io
from oplus import simulate, CONF, Epm
from tests.util import iter_eplus_versions
class SimulateTest(unittest.TestCase):
"""
we test everything in one simulation, for performance reasons
"""
def test_simulate(self):
for eplus_version in iter_... | Openergy/oplus | tests/test_simulate.py | Python | mpl-2.0 | 2,138 | [
"EPW"
] | 209e5048dfeece6c4c8e0a0179ab1f4df2e2781b57ab67fe4449e79d9c262262 |
# -*- coding: utf-8 -*-
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "L... | ioana-delaney/spark | python/pyspark/ml/tests.py | Python | apache-2.0 | 106,975 | [
"Gaussian"
] | 12af118def2d2c9b001231562224c9c2201b50779fbebed4591092216119448f |
"""Convert MERAXES output to TAO.
A control script to be used with `taoconvert` to convert SAGE output
binary data into HDF5 input for TAO.
"""
import re
import os
import numpy as np
import tao
from collections import OrderedDict
from tqdm import tqdm, trange
import h5py
class MERAXESConverter(tao.Converter):
""... | CAS-eResearch/TAOImport | examples/meraxes.py | Python | gpl-3.0 | 60,989 | [
"Galaxy"
] | 3f8b50fe092da3182828ce720a51e9a329eeb5fde014d9f4a73e5e756d396be2 |
# -*- encoding: utf-8 -*-
"""
Gaussian optics.
The module implements:
- Ray transfer matrices for geometrical and gaussian optics.
See RayTransferMatrix, GeometricRay and BeamParameter
- Conjugation relations for geometrical and gaussian optics.
See geometric_conj*, gauss_conj and conjugate_gauss_beams
The co... | grevutiu-gabriel/sympy | sympy/physics/optics/gaussopt.py | Python | bsd-3-clause | 19,995 | [
"Gaussian"
] | 54da2317667062e59ede74d821e4a5db9167dc24bb09fabae0106d4e39f4e29c |
"""This module defines an ASE interface to NWchem
http://www.nwchem-sw.org/
"""
import os
import sys
import numpy as np
from ase.units import Hartree, Bohr
from ase.io.nwchem import write_nwchem
from ase.calculators.general import Calculator
class KPoint:
def __init__(self, s):
self.s = s
self.e... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/calculators/nwchem.py | Python | gpl-2.0 | 13,398 | [
"ASE",
"NWChem"
] | 1d122ca1a0d9fec9a606c108069ac6f312644908d84d67ba32413c12b61e7af4 |
"""
Script to make insertion track
@author: Alicia Schep
"""
##### IMPORT MODULES #####
# import necessary for python
import os
import multiprocessing as mp
import itertools
import numpy as np
import pysam
import traceback
import pyximport; pyximport.install(setup_args={"include_dirs":np.get_include()})
from pyatac.t... | GreenleafLab/NucleoATAC | pyatac/get_ins.py | Python | mit | 3,485 | [
"Gaussian",
"pysam"
] | e2fc37493ace24fbdf9f4b57ecefa0c896355bbaf13f8d80162c5015c5651b0c |
#!/usr/bin/env python
import code
import cpp
import cpp_file_parser
import file_parser
import parser_addition
import to_string
import util
import os
def add_aliases(data, scope, detail_namespace):
if data.small_buffer_optimization:
buffer = 'using Buffer = std :: array < char , ' + data.buffer + ' > ;'
... | lubkoll/friendly-type-erasure | type_erasure/table_interface_generator.py | Python | mit | 18,035 | [
"VisIt"
] | 6c86a491d6f8382520b14d2546b50fe1b9603349ca8d301d5815aa286453da14 |
#!/usr/bin/env python
#
# test_moderna_superimposer.py
#
# unit tests for ModernaStructure.ModernaSuperimposer
#
# http://iimcb.genesilico.pl/moderna/
#
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "G... | lenarother/moderna | tests/test_moderna_superimposer.py | Python | gpl-3.0 | 2,885 | [
"PyMOL"
] | 2c8fbd32e55f787f7384b7a95e3bdc76ea766ad456f77ea36fd5a46bcc402f0d |
# Take model refined in OpenMM, make Gromacs topology, and run a brief energy minimzation and MD equilibration
#
# Daniel L. Parton <partond@mskcc.org> - 13 Mar 2013
#
# PREREQUISITES
#
# TODO Change to amber99sb-ildn-star?
#
# =============================
# IMPORTS
# =============================
import sys,re,os,co... | choderalab/Ensembler2 | scripts/attic/gmx-simulate-explicit.py | Python | gpl-2.0 | 22,316 | [
"Gromacs",
"OpenMM"
] | a1290e5a91feccf4ee155ee6e683ec6adc50858cca60295dea1e36ac51604466 |
# Copyright (C) 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 versio... | KaiSzuttor/espresso | testsuite/scripts/samples/test_visualization_lbboundaries.py | Python | gpl-3.0 | 1,265 | [
"ESPResSo"
] | 6d74073476d86037875d6b3bf3eaaf03abc577c756cb6cf864af25a00b965ef5 |
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