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from __future__ import print_function, absolute_import
import os
import sys
import imp
import json
import string
import shutil
import subprocess
import tempfile
from distutils.dep_util import newer_group
from distutils.core import Extension
from distutils.errors import DistutilsExecError
from distutils.ccompiler import... | rmcgibbo/msmbuilder | basesetup.py | Python | lgpl-2.1 | 12,526 | [
"MDTraj"
] | 7a3af12143de53acd15cbdbd9791ad8fb73386d6423e9fb94753c2c4214bb940 |
# coding: utf-8
from __future__ import unicode_literals
"""
Created on Nov 14, 2012
"""
__author__ = "Anubhav Jain"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Anubhav Jain"
__email__ = "ajain@lbl.gov"
__date__ = "Nov 14, 2012"
import unittest
import os
from pymat... | yanikou19/pymatgen | pymatgen/util/tests/test_io_utils.py | Python | mit | 555 | [
"pymatgen"
] | 1465133a51676606c2ee983b0b3e4196ee1ba63a198b6d4181e7fb9d26ec877e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/auxiliary/test_core.py | Python | gpl-2.0 | 1,662 | [
"MDAnalysis"
] | c4b1535cd479cf10a3499b3c1b7dd6ae15fade88ae98e73136b7099e85417299 |
import itertools
import random
from ..core import Basic, Expr, Integer, Symbol, count_ops
from ..core.compatibility import as_int, is_sequence
from ..core.decorators import call_highest_priority
from ..core.sympify import sympify
from ..functions import cos, sin, sqrt
from ..logic import true
from ..simplify import si... | diofant/diofant | diofant/matrices/dense.py | Python | bsd-3-clause | 41,640 | [
"DIRAC"
] | 167cb31ef409e72b330354b3e69cd80d8bde7deb14862ee7cbbe68aebedb87bb |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
db.rename_column('profiles_indicatordata', 'feature_id', 'record_id')
def backwards(self, orm):
db.rename_co... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0006_change_feature_field_to_record.py | Python | mit | 10,006 | [
"MOE"
] | b43a0a6cd50d026802c82118fab976726f09c52f608f59eb82cb51cd2468083c |
"""
Die Main-Methode, die das 'Sonnensystem' startet.
Inspiriert von den Panda3D Samples.
Setzt alles zusammen und startet die Applikation.
"""
__author__ = 'Thomas Taschner, Michael Weinberger'
__date__ = 20151209
__version__ = 1.0
import direct.directbase.DirectStart
from direct.showbase import DirectObject
from pa... | mweinberger-tgm/VenusAndMars | src/VenusAndMars.py | Python | apache-2.0 | 2,334 | [
"Galaxy"
] | bb24069bb0dff1009c49fa317104fe49ce598bfce5d40189f6b002131c67c4b3 |
# Version: 0.15+dev
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* [![Latest Version]
(https... | fusionapp/methanal | versioneer.py | Python | mit | 65,723 | [
"Brian"
] | 56a4733c478d008e1261d1f8f8b9650dd7f4ebfb79e2b0e7d0b8c1aed55b9b17 |
#!/usr/bin/env python3
import os
import sys
import argparse
import traceback
# Add the pulsar path
thispath = os.path.dirname(os.path.realpath(__file__))
psrpath = os.path.join(os.path.dirname(thispath), "modules")
sys.path.insert(0, psrpath)
import pulsar as psr
def Run():
try:
out = psr.output.GetG... | pulsar-chem/Pulsar-Core | test/old/Old2/old/BasisSet.py | Python | bsd-3-clause | 2,286 | [
"Gaussian"
] | c671652d79ebb0a7aa600180f9606c1037a67b1037ff54a9d839be6d6cfb93a4 |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following d... | pizzathief/scipy | scipy/ndimage/fourier.py | Python | bsd-3-clause | 11,239 | [
"Gaussian"
] | 37d44664cce2c56929d4ec7ceb0659dca85de6e07b90bd5443e5a7e930457331 |
#!/usr/bin/env python
# Copyright 2014-2018 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... | gkc1000/pyscf | pyscf/tools/rhf_newtonraphson.py | Python | apache-2.0 | 9,935 | [
"PySCF"
] | 8d2a7b5503b1ff083938248d3c59cb0ac40e4b5d7b731271e754325148ae6a6b |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/vasp/test_runepidoc.py | Python | gpl-3.0 | 2,135 | [
"CRYSTAL",
"VASP"
] | 469ca8b5ab2720a9f85275bd99bd20440d515722f3906da79b22e7a9220b1f1f |
# -*- coding: utf-8 -*-
"""
@author: adosch <adam@wisehippy.com>
@author: SodaPhish <sodaphish@protonmail.ch>
"""
import sys,os,logging.config
from logging import handlers
try:
from sp.base import Exceptions
except:
print"must have splib installed in sys.path()"
sys.exit(1)
class LoggerConfig(object):
... | sodaphish/break | sp/base/Logging.py | Python | mit | 7,145 | [
"VisIt"
] | 044df0b753cf55b922178d71bb1d1b90aab0282b31ad2298830bcf94c87814a0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes to create phase diagrams.
"""
from six.moves import filter
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, Th... | sonium0/pymatgen | pymatgen/phasediagram/pdmaker.py | Python | mit | 18,442 | [
"pymatgen"
] | ad94c8d31568f7b54f8d76891850912b23ff08c735cc3d3be033f8feca0e031c |
from __future__ import annotations
import importlib
import types
from typing import (
TYPE_CHECKING,
Sequence,
)
from pandas._config import get_option
from pandas._typing import IndexLabel
from pandas.util._decorators import (
Appender,
Substitution,
)
from pandas.core.dtypes.common import (
is_... | gfyoung/pandas | pandas/plotting/_core.py | Python | bsd-3-clause | 61,841 | [
"Gaussian"
] | e85704e89256685fd50c89d95938ead3b84b2475413872b23f3c0fd48e6d68a8 |
"""
Created on 6/05/2013
@author: thom
"""
from evaluator import Evaluator
from molecule import Molecule
from molecular_population import MolecularPopulation
import logging
import os
from rdkit.Chem import Draw
from rdkit.Chem import AllChem as Chem
class DrawMolecules(Evaluator):
"""Draw to a file the longes... | th0mmeke/toyworld | evaluators/draw_molecules.py | Python | gpl-3.0 | 1,244 | [
"RDKit"
] | 025e90a07061b6516d800b9af1471bb040b91aec0be2738013caf1a188c4edf9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0009_auto_20150429_0450'),
]
operations = [
migrations.CreateModel(
name='Location',
fields... | koebbe/homeworks | visit/migrations/0010_auto_20150429_1453.py | Python | mit | 803 | [
"VisIt"
] | a84f12a687eec561e1fc485fc2d1fd42715b06dad72ee9011146f2515e19bebc |
""" Functions to run full experiment """
import contour_utils as cc
import experiment_utils as eu
import mv_gaussian as mv
import clf_utils as cu
import generate_melody as gm
import pandas as pd
import numpy as np
import random
import json
import os
from contour_utils import getFeatureInfo
from sklearn.externals im... | georgid/SourceFilterContoursMelody | src/contour_classification/run_experiments.py | Python | gpl-3.0 | 16,043 | [
"Gaussian"
] | 2f9edbc854b75f3635cab64657f78d9402ae43d6672da98e6c16ac57621180a9 |
from robot import Robot
from math import copysign
class TheRobot(Robot):
'''Strategy:
Stay near the middle of the field,
Move if being attacked.
'''
def initialize(self):
self.health = 100
self._flee = 15
self._goto = 0
self._moveto_choices = [7, 7, -7,... | jav/pybotwar | robots/examples/robot07.py | Python | gpl-3.0 | 2,223 | [
"BLAST"
] | c1df1cd634d324e6c311c79c25e651aaa9aa0129a5dd2d99509f2430530ba60e |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
DEBUG = True
# count of edges not cells
W=20+1
def d(args):
global DEBUG
if DEBUG:
print(args)
def printBoard(b):
cell = 0
for i in b:
print(i," \t", end='')
cell = cell + 1
if (cell == W):
print ('')
cell = 0
def xmain():
... | anomen-s/programming-challenges | projecteuler.net/0015-Lattice_paths/solve.py | Python | gpl-2.0 | 1,347 | [
"VisIt"
] | 10706785b87b2cc827911cb853013376d7bdeb727d4e4c96876b42652543e88f |
"""Dirac notation for states."""
from __future__ import print_function, division
from sympy import (cacheit, conjugate, Expr, Function, integrate, oo, sqrt,
Tuple)
from sympy.core.compatibility import range
from sympy.printing.pretty.stringpict import stringPict
from sympy.physics.quantum.qexpr imp... | kaushik94/sympy | sympy/physics/quantum/state.py | Python | bsd-3-clause | 29,163 | [
"DIRAC"
] | 399ea47599be53c4a7dcaba058c2ec4c8b16af77a1a78edfdd6e4df40871ad31 |
#!/usr/bin/python
"""Image smoothing filter."""
# build-in modules
# third-party modules
import numpy
from scipy.ndimage.filters import gaussian_filter
# path changes
# own modules
# information
__author__ = "Oskar Maier and others (see below)"
__version__ = "r0.3, 2013-08-23"
__email__ = "oskar.maier@googlemail.... | kleinfeld/medpy | medpy/filter/smoothing.py | Python | gpl-3.0 | 5,384 | [
"Gaussian"
] | 11270f0101e07b33c317ac97d082b6c2b915113f532b95e575e7fb013236a1f2 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | samples/lj_liquid_distribution.py | Python | gpl-3.0 | 5,841 | [
"ESPResSo"
] | 42ff0ed3d64f153f2103e605f5c684048ca79d1e511bfe4dd4c3ae994ca215e9 |
# encoding: utf-8
"""nanoparticle.py - Window for setting up crystalline nanoparticles.
"""
import gtk
from gettext import gettext as _
from copy import copy
from ase.gui.widgets import pack, cancel_apply_ok, oops, help
from ase.gui.setupwindow import SetupWindow
from ase.gui.pybutton import PyButton
import ase
import... | grhawk/ASE | tools/ase/gui/nanoparticle.py | Python | gpl-2.0 | 25,943 | [
"ASE",
"CRYSTAL"
] | 6507914c5490a71c5600f7c3d0ae8273188ff7d0ce6da93e19a128a93985396e |
"""
local path implementation.
"""
from __future__ import with_statement
from contextlib import contextmanager
import sys, os, re, atexit, io
import py
from py._path import common
from py._path.common import iswin32
from stat import S_ISLNK, S_ISDIR, S_ISREG
from os.path import abspath, normpath, isabs, exists, isdir... | jessekl/flixr | venv/lib/python2.7/site-packages/py/_path/local.py | Python | mit | 31,843 | [
"VisIt"
] | adc9852207fb520b6f9f1e2aefd6299aced993639231c4dfe2a4c4031916ec8f |
"""
This module contains code for adding queries from a file. It should take a filepath
and type, a reference to an open database, and some other basic information in order
to parse the file correctly and then add the resulting queries to the database.
For now, start with just FASTA files, but eventually should accomm... | chris-klinger/Goat | queries/query_file.py | Python | gpl-3.0 | 2,895 | [
"Biopython"
] | bf32c4d85baf67b17669abf96c0e9492009150f85d4d408e26f0a6ab7734722a |
from .test_base import TestBase
from werkzeug.exceptions import NotFound, Forbidden
from app.exceptions import ConflictError, ValidationError
class TestBucketlistItems(TestBase):
""" Test users' Bucketlist items """
def test_add_bucketlist_item(self):
""" Test for new item creation """
res, j... | andela-akhenda/maisha-goals | tests/test_bucketlist_items.py | Python | mit | 5,947 | [
"VisIt"
] | 1dbedf9732726fb09cb8d489a067e73ebf92383dc84c9cf7d959a5ee9661ed6a |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.7 on 2016-07-07 02:14
from __future__ import unicode_literals
from django.db import migrations, models
import django.utils.timezone
class Migration(migrations.Migration):
initial = True
dependencies = [
]
operations = [
migrations.CreateMod... | iannesbitt/iannesbitt.org | blinker/migrations/0001_initial.py | Python | mpl-2.0 | 607 | [
"VisIt"
] | ffaad4bd751275b24bfd36891a88a958d8ec1aa40976670c27e0e51bacd1b2f9 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import sys
sys.path.append('/home/will/PySeqUtils/')
from GeneralSeqTools import fasta_reader, fasta_writer
import os
os.chdir('/home/will/PySeqUtils/TransToolStuff/')
# <codecell>
from itertools import islice
start = 806
stop = -1
path = 'HIV1_ALL_201... | JudoWill/ResearchNotebooks | Untitled1.py | Python | mit | 3,297 | [
"BLAST"
] | 0edcfc18ba989aa81adc5010e188a407e832ff2555012d327e20df654d36cc0b |
from neat import (NetworkSpec, GeneSpec,
NumericParamSpec as PS, NominalParamSpec as NPS,
Mutator, NEAT, neuron, connection)
#### CONFIG #### #### #### #### #### #### #### #### #### #### #### #### #### #### #### #### #### #### ####
neuron_sigma = 0.25 # mutation sigma f... | egdman/neat-lite | examples/init_example.py | Python | mit | 2,364 | [
"NEURON"
] | ee99dede93efa88e926de1e29c198b02eed295de7decc925cc6c25effd059427 |
from ase import *
from ase.constraints import StrainFilter
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0,b,b),(b,0,b),(b,b,0)], pbc=1) * (6, 6, 6)
try:
import Asap
except ImportError:
pass
else:
cu.set_calculator(ASAP())
f = StrainFilter(cu, [1, 1, 1, 0, 0, 0])
opt = MDMin(f, dt=0.01)
t = PickleTr... | freephys/python_ase | ase/test/strain.py | Python | gpl-3.0 | 737 | [
"ASE"
] | 21566fd2e7cdb9e597ea253c8b18ae369c297b830524a952c8ca0affae85f5c5 |
# coding: utf-8
#
# Copyright 2015 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 version 3 o... | fccoelho/pypln.backend | pypln/backend/workers/gridfs_data_retriever.py | Python | gpl-3.0 | 1,547 | [
"NAMD"
] | e8e2074a4af4671280c8ea4a361ab8a77b3c8c7a4ad823032b79282ef1cf9463 |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2017, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | maxvonhippel/q2-diversity | q2_diversity/_alpha/_method.py | Python | bsd-3-clause | 2,667 | [
"scikit-bio"
] | 2236537edcb3075c22184187b6bb6d310987aaeac10793a707a38755b3cd271a |
#!/usr/bin/env python
# @package vfnow
# \author Ed Bueler and Constantine Khroulev, University of Alaska Fairbanks, USA
# \brief A script for verification of numerical schemes in PISM.
# \details It specifies a refinement path for each of Tests ABCDEFGIJKL and runs
# pismv accordingly.
# Copyright (C) 2007--2013 Ed B... | talbrecht/pism_pik07 | test/vfnow.py | Python | gpl-3.0 | 13,396 | [
"NetCDF"
] | 7ab58d5db6a27164a1d12e1110aa7051669cfb10a8969acebe54e810218e0a5c |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jturney/psi4 | psi4/driver/procrouting/empirical_dispersion.py | Python | lgpl-3.0 | 15,011 | [
"Psi4"
] | d4f6bbafd682b5fde527a91263e0d313ba6e54322d69f63f7bdb06d8ca7141dc |
import lan
import copy
import stringstream
import exchange
import collect_device as cd
import collect_gen as cg
import collect_id as ci
import collect_array as ca
import cgen
def print_dict_sorted(mydict):
keys = sorted(mydict)
entries = ""
for key in keys:
value = mydict[key]
entries += ... | dikujepsen/OpenTran | v2.0/framework/Matmul/snippetgen.py | Python | mit | 4,161 | [
"VisIt"
] | b3ceac8ff4ddce02c2dea47b520431607246db8ecffaa075a145342cfed2ae7a |
#!/usr/bin/env python
"""
Module for various statistics utilities.
"""
import copy
from collections import OrderedDict as odict
import numpy as np
import numpy.lib.recfunctions as recfuncs
import scipy.special
import scipy.stats
# These should probably live in this file
from ugali.utils.bayesian_efficiency import ba... | DarkEnergySurvey/ugali | ugali/utils/stats.py | Python | mit | 13,490 | [
"Gaussian"
] | c4f3f2ec70fe7f621b063d4498cf88ba59e99379e04b1f8e8d4eb83649ae40a0 |
"""
General-purpose functions that map R -> [0,1].
These functions work as closures.
The inner function uses the variables of the outer function.
These functions work in two steps: prime and call.
In the first step the function is constructed, initialized and
constants pre-evaluated. In the second step the actual v... | amogorkon/fuzzy | src/fuzzylogic/functions.py | Python | mit | 12,953 | [
"Gaussian"
] | 8c25ece14e30c55f047d9abcba82c9e014166de7c372d637a0bec4cf39f0460f |
#!/usr/bin/env python
####################################################################################################
# @file command.py
# @package
# @author
# @date 2009/01/12
# @version 0.1
#
# @mainpage
#
#################################################################################################... | mikrosimage/OpenRenderManagement | src/octopus/worker/model/command.py | Python | bsd-3-clause | 1,873 | [
"Octopus"
] | 1a98658fd2155ea124380bc6e18ada9924e43a439a19d5c3da584b865ff7c9fc |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
from sympy import init_printing
init_printing()
import numpy as np
import sympy as sy
import matplotlib.pyplot as plt
... | zerothi/sisl | developments/distributions.py | Python | mpl-2.0 | 4,701 | [
"Gaussian"
] | 9d7a4867516e1484ff885966560f8d9adb193dbee37e801eed59af57d0d64117 |
'''Screen
======
This module changes some environment and configuration variables
to match the density / dpi / screensize of a specific device.
To see a list of the available screenid's, just run::
python main.py -m screen
To simulate a medium-density screen such as the Motorola Droid 2::
python main.py -m... | darkopevec/kivy | kivy/modules/screen.py | Python | mit | 6,792 | [
"Galaxy"
] | 6005884c70399ac6c2553d4e826f60d6ede0c3d489f5288bc103a3c04c938cda |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 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
# it u... | psi4/psi4 | psi4/driver/ipi_broker.py | Python | lgpl-3.0 | 5,014 | [
"Psi4"
] | da024fbf5485df37ac2530b0f44975e49bffc235999ebabdd8c5c894b847d473 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'PresentMedicalHistory.others'
db.delete_column(u'patient_presentmedicalhistory', 'others')... | aazhbd/medical_info01 | patient/migrations/0012_auto__del_field_presentmedicalhistory_others__del_field_pastmedicalhis.py | Python | bsd-3-clause | 30,034 | [
"VisIt"
] | 52b8f659f6fde7c2047f27ac39bdbe7c3d93aafb708d55462cac9eff76389a6c |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | juanchopanza/NeuroM | neurom/view/_dendrogram.py | Python | bsd-3-clause | 10,982 | [
"NEURON"
] | cb0eb96cfcc2d16c5415883537017b6a9917ae0d126dff69d3215eacdf8d30cc |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The main routine of this package that aims at performing the
extraction of ROIs from multisubject dataset using the localization
and activation strength of extracted regions.
This has been published in... | alexis-roche/nipy | nipy/labs/spatial_models/bayesian_structural_analysis.py | Python | bsd-3-clause | 14,865 | [
"Gaussian"
] | b7cc2b54c8db62dc2b47f31297ee976e3d1007016c32887263b808f783fa874d |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Numpy2Vtk documentation build configuration file, created by
# sphinx-quickstart on Sat Jun 20 19:11:32 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# ... | selaux/numpy2vtk | docs/conf.py | Python | lgpl-3.0 | 9,252 | [
"VTK"
] | 231f88041769c58e1d99e22aeb81512f17efe0afff74f636f0a47c13604341b3 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Enumerator with the libxc identifiers.
This is a low level object, client code should not interact with LibxcFunc directly
but use the API provided by the Xcfunc object defined in core.xcfunc.py.
Part of this module is auto... | vorwerkc/pymatgen | pymatgen/core/libxcfunc.py | Python | mit | 13,095 | [
"pymatgen"
] | 7d37b556700b8b26611c6691b430247342eeeae2b3bc1e4ab2532f5e7d5044fa |
# -*- coding:utf-8 -*-
#
# Copyright © 2011-2012 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""
IPython v0.13+ client's widget
"""
# Fix for Issue 1356
from __future__ import absolute_import
# Stdlib imports
import os
import os.path as osp
from string import... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/spyderlib/widgets/ipython.py | Python | gpl-3.0 | 29,448 | [
"Mayavi"
] | b438106f6770393d7bfa191880d4d71584508110f01f980bbf1f48cff72eab85 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import numpy as np
import warnings
from ..utils.exceptions import AstropyUserWarning
from ..extern.six.moves import range
__all__ = ['SigmaClip'... | kelle/astropy | astropy/stats/sigma_clipping.py | Python | bsd-3-clause | 18,281 | [
"Gaussian"
] | b095710938489da3723ef449d8d720abdcd5caeddcf376c363290dd90e4839d3 |
# $Id$
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
import wx
class metaImageRDR(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._reader = vtk.... | nagyistoce/devide | modules/readers/metaImageRDR.py | Python | bsd-3-clause | 2,082 | [
"VTK"
] | 694758cc5f414af50b21250c196396504a82243e7bd51dae7757dded1527b870 |
import unittest
from pyml.linear_models import LinearRegression, LogisticRegression
from pyml.linear_models.base import LinearBase
from pyml.datasets import regression, gaussian
from pyml.preprocessing import train_test_split
class LinearRegressionGradientDescentTest(unittest.TestCase):
@classmethod
def setU... | gf712/PyML | tests/regression_tests.py | Python | mit | 17,822 | [
"Gaussian"
] | c3cf9a4eebd4cd4f0f1e39baa8e334005eed076a27dd83a5dc65a2fa342d32ed |
"""Support library for the IEM Reanalysis code
.. data:: SOUTH
Latitude of the southern edge of the IEM Reanalysis.
"""
import string
import random
from datetime import timezone, datetime
from affine import Affine
import numpy as np
import xarray as xr
from pyiem.util import get_dbconn
# 1/8 degree grid, grid... | akrherz/pyIEM | src/pyiem/iemre.py | Python | mit | 7,932 | [
"NetCDF"
] | 1ca415e6604a7d9b40494be44384655a7ea67a7a06442e0db4d081c5c5f726e3 |
import ast
import itertools
import multiprocessing
import logging
from enum import Enum
log = logging.getLogger(__name__)
class SymbolKind(Enum):
"""SymbolKind corresponds to the SymbolKind enum type found in the LSP
spec."""
File = 1
Module = 2
Namespace = 3
Package = 4
Class = 5
M... | sourcegraph/python-langserver | langserver/symbols.py | Python | mit | 6,135 | [
"VisIt"
] | 558218d73035f38f8f04a2f5fec9cb28b35419143229ac4fd10ca6a903e41e36 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | galsim/real.py | Python | gpl-3.0 | 31,286 | [
"Galaxy"
] | d115c5f5dbac00df43468cf35acebe96f18d199394ee8985a9bfeb307640c96b |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | testsuite/python/array_properties.py | Python | gpl-3.0 | 11,121 | [
"ESPResSo"
] | 1c6e3eac854945da240be89bfaf666d2c986cdcb4fc2e660097a4bbfd6d359c0 |
#!/usr/bin/python
# Copyright (c) 2009, Purdue University
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyright notice, this
# list of... | stephenlienharrell/roster-dns-management | test/pylint_test.py | Python | bsd-3-clause | 4,788 | [
"VisIt"
] | 333c27468e0ee428febc44faa7dacad18471b75513d551dbafbc47295a3b9017 |
# -*- coding: utf-8 -*-
#
# BrodyHopfield.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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, ... | kristoforcarlson/nest-simulator-fork | pynest/examples/BrodyHopfield.py | Python | gpl-2.0 | 3,825 | [
"Gaussian",
"NEURON"
] | b32e96353feae6df498b1c7ce4b7f965eba640bc2bc41a919e9bcee72483ae89 |
import py, re, os, signal, time, commands, sys
from subprocess import Popen, PIPE
mod_re = (r"\bmodule\s+(", r")\s*\(\s*")
func_re = (r"\bfunction\s+(", r")\s*\(")
def extract_definitions(fpath, name_re=r"\w+", def_re=""):
regex = name_re.join(def_re)
matcher = re.compile(regex)
return (m.group(1) for m i... | Obijuan/tutorial-openscad | temporada-2/T16-estudiando-codigo-de-otros/04-cyclone/smooth_rod_fix/MCAD/openscad_utils.py | Python | gpl-2.0 | 2,036 | [
"VisIt"
] | 9e5019e1d52bc14d7178cd796aabe5addc6e948a42f9d2ca960798191b71f54d |
# BEGIN_COPYRIGHT
# END_COPYRIGHT
"""
Parse a `SAM <http://samtools.sourceforge.net/>`_ file and output
alignment info in one of the following formats:
* tabular, suitable for processing by the marker alignment importer
* tabular, suitable for processing by the `Galaxy
<http://galaxyproject.org/>`_ DNA extractor
E... | crs4/omero.biobank | bl/vl/app/snp_manager/convert_sam.py | Python | gpl-2.0 | 5,388 | [
"BWA",
"Galaxy"
] | be5a4d0fedd61a686bf82ff6b5aa322abbc11c59e35d0177b988627dff0d79d0 |
import numpy as np
import numpy.random as rng
import pylab as pl
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.mlab as mp
import copy, sys
import math
import optparse
import scipy.signal
import scipy.special.basic as sp
def make_dirichlet_bins(data,num_bins,strategy,num_dirs=50,alpha=10.... | garibaldu/radioblobs | code/code_1d/old_and_extra/score_grad_ascent.py | Python | gpl-2.0 | 13,040 | [
"Gaussian"
] | b0f25c22578ebbe827620f6b69b21a5a2d4a2129a96f5dbcd681d1fe3237824d |
# -*- coding: utf-8 -*-
"""
Methods that generate or adjusted energy related timeseries based on given assumptions/input
"""
from __future__ import absolute_import, division, print_function
import numpy as np
import pandas as pd
import scipy.interpolate
import scipy.linalg
import scipy.stats
from .utils import make_t... | kavvkon/enlopy | enlopy/generate.py | Python | bsd-3-clause | 21,354 | [
"Gaussian"
] | 0530705b37449ff1ab6102798bb42f8e6fa64859cdf2c922e4f7f9fd31635232 |
#
# Copyright 2015 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful, but WITHOUT ANY WARRANTY expressed... | dashea/anaconda | tests/dracut_tests/parse-kickstart_test.py | Python | gpl-2.0 | 15,355 | [
"Brian"
] | 916e54a94ca2419cdeb45b5ac3f45bcd7161e9e99c659fd73dc654f439e37690 |
""" @package antlr3.tree
@brief ANTLR3 runtime package, tree module
This module contains all support classes for AST construction and tree parsers.
"""
# begin[licence]
#
# [The "BSD licence"]
# Copyright (c) 2005-2012 Terence Parr
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or... | openstack/congress | thirdparty/antlr3-antlr-3.5/runtime/Python3/antlr3/tree.py | Python | apache-2.0 | 81,112 | [
"VisIt"
] | ad35412ebdd766e380aa9f8602ba3909daa759983ed5651ae8325a938bb3da24 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@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... | opoplawski/ansible | lib/ansible/galaxy/__init__.py | Python | gpl-3.0 | 2,460 | [
"Brian",
"Galaxy"
] | 5fffc52ca3491f5ffcb27ad583ceaec658c7ed7b54a01d983332e94b6d9615e6 |
"""
test MNW2 package
"""
import sys
sys.path.insert(0, '..')
import os
import flopy
import numpy as np
from flopy.utils.flopy_io import line_parse
cpth = os.path.join('temp', 't027')
# make the directory if it does not exist
if not os.path.isdir(cpth):
os.makedirs(cpth)
mf2005pth = os.path.join('..', 'examples',... | bdestombe/flopy-1 | autotest/t027_test.py | Python | bsd-3-clause | 7,694 | [
"NetCDF"
] | 6d731c06059e4467b52cc3fb4f2684d3b248d3206d07de85fa44dc2e2e9dc2be |
# Copyright (c) 2016 GeoSpark
#
# Released under the MIT License (MIT)
# See the LICENSE file, or visit http://opensource.org/licenses/MIT
# Inspired by: https://thoughtsbyclayg.blogspot.co.uk/2008/10/parsing-list-of-numbers-in-python.html
# return a set of selected values when a string in the form:
# 1-4,6
# would r... | GeoSpark/ILI9341-font-packer | src/range_parser.py | Python | mit | 992 | [
"VisIt"
] | ad7e4134f9ebe96312f7006dc4cfccda7b65923efac8df4fda990b8dfc5fbf2e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import warnings
from pymatgen.analysis.ewald import EwaldSummation, EwaldMinimizer
from pymatgen.io.vasp.inputs import Poscar
import numpy as np
test_dir = os.path.join(os.path.dirn... | gVallverdu/pymatgen | pymatgen/analysis/tests/test_ewald.py | Python | mit | 4,740 | [
"LAMMPS",
"VASP",
"pymatgen"
] | 6b8d58e0407317e24ca7b8e7e1d1e64084fa216d33af5c76a3ec8a0b9473d382 |
## Copyright 2015-2017 Tom Brown (FIAS), Jonas Hoersch (FIAS)
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 3 of the
## License, or (at your option) any later version.
## T... | FRESNA/PyPSA | pypsa/io.py | Python | gpl-3.0 | 41,766 | [
"NetCDF"
] | decafa6df53d4e17735ba4deedd115afcd42cf355862b5c05c815e13a9669f78 |
#------------------------------------------------------------------------------
# pycparser: c-to-c.py
#
# Example of using pycparser.c_generator, serving as a simplistic translator
# from C to AST and back to C.
#
# Eli Bendersky [http://eli.thegreenplace.net]
# License: BSD
#------------------------------------------... | CtheSky/pycparser | examples/c-to-c.py | Python | bsd-3-clause | 1,584 | [
"VisIt"
] | d511d1068e1c1d4edbb43b6368e80ed57ff9b1d6f78dbeff8b3f5204964a8398 |
# Copyright (C) 2006-2011, University of Maryland
#
# 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,... | reflectometry/direfl | direfl/gui/about.py | Python | mit | 8,853 | [
"VisIt"
] | a415abf87a26b23028b001f5ec4865d52b16c2a2c059ceeceb7a945187b516a8 |
# Copyright 2008-2014 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2008-2015 by Peter Cock. 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.
"""Parser for XML r... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/Entrez/Parser.py | Python | apache-2.0 | 24,770 | [
"Biopython"
] | d7632667570d67099604fe34bfab448ca930c7aab748ec8f26ee10c4d26f9e37 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/images/lib/mediaitem.py | Python | gpl-2.0 | 11,415 | [
"Brian"
] | 5744683bf0ada2f92e877116fafffd989bfb2ad5a286f15c2501807b051c4767 |
# Package OpenMM serialized systems in Folding@Home project directory structure.
#
# John D. Chodera <choderaj@mskcc.org> - 16 Mar 2013
# PARAMETERS
import sys
from ast import literal_eval
# Process only these targets, if specified.
# e.g. -targets '["SRC_HUMAN_PK0_P12931", "ABL1_HUMAN_PK0_P00519"]'
try:
process... | choderalab/Ensembler2 | scripts/attic/package-for-fah-openmm.py | Python | gpl-2.0 | 11,059 | [
"OpenMM"
] | e2e33e6c00459a78fcbfaa9b339810878cad487496bdf589bdafe9e26f5a9659 |
import theano
import theano.tensor as T
# from theano.tensor.shared_randomstreams import RandomStreams
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams # veel sneller
import numpy as np
numpy_rng = np.random.RandomState(123)
theano_rng = RandomStreams(numpy_rng.randint(2**30))
## samplers
def b... | gupta-abhay/morb-theano | samplers.py | Python | unlicense | 6,056 | [
"Gaussian"
] | 088d605e08905200462883a15cc13748dacfc221cb71051d2f15a0c79c3e82a8 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import pytest
from ansible import context
... | amenonsen/ansible | test/units/galaxy/test_api.py | Python | gpl-3.0 | 1,934 | [
"Galaxy"
] | 4065f149ad36517e56a06361e48474b9b2aa089cba16a878359e127eb022d393 |
import pysam
"""
This script is for filtering out soft-clipped reads that are speciously mapped.
It is of particular concern especially if no attempt has been made to filter
reads during mapping for duplicate regions such as are found between chloroplast
and mitochondrial regions. Even if filtering i... | NDHall/pysam_tools | cigar_filter/pysam_cigar_filter.py | Python | mit | 9,273 | [
"pysam"
] | 9152173b3a40c51f4820333a537f51bfe2fb9bd4f6a30a94214723344ad7784a |
# nmda.py ---
#
# Filename: nmda.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Wed Mar 17 14:07:20 2010 (+0530)
# Version:
# Last-Updated: Sat Oct 15 19:08:44 2011 (+0530)
# By: subha
# Update #: 292
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Chang... | BhallaLab/moose-thalamocortical | TESTS/pymoose/test_nmda.py | Python | lgpl-2.1 | 6,693 | [
"MOOSE",
"NEURON"
] | a1e1fd37f53f5e5eb107d2c658e98ace5f639314f275c0d0f3b399c4c908b629 |
#!/usr/bin/env python
# Copyright 2017.
# Michael A. DeJesus, Chaitra Ambadipudi, and Thomas R. Ioerger.
#
#
# This file is part of TRANSIT.
#
# TRANSIT 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 Foun... | mad-lab/transit | src/pytpp/tpp_gui.py | Python | gpl-3.0 | 25,744 | [
"BWA"
] | 290f8f3b9a28535a2abfb24b39c4f5de2b7f3bb60a1c90b52d17f6be4efced49 |
#!/usr/bin/env python
"""
This script demonstrates how one can script the Mayavi application by
subclassing the application, create a new scene and create a few
simple modules.
This should be run as::
$ python test.py
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2007, Enthought, ... | dmsurti/mayavi | examples/mayavi/interactive/subclassing_mayavi_application.py | Python | bsd-3-clause | 2,818 | [
"Mayavi",
"VTK"
] | c7b6697b83adc1b442806d4d2573bce9461ed097f8c78277680f26da6087a700 |
#!/usr/bin/env python
"""
==============================
orcaPose.py - Orca Pose Client
==============================
Reads Vicon pose data via Orca
"""
import sys, time, struct
import array as pyarray # So as not to conflict with numpy's array
from socket import *
from numpy import *
class poseHandler:
def __... | jadecastro/LTLMoP | src/lib/handlers/pose/_orcaPose.py | Python | gpl-3.0 | 2,767 | [
"ORCA"
] | e9e733c186a94da42d6f7952a5895c83cc411d01075504897bc5bbd0ad7bdff2 |
#!/usr/bin/env python
# This code is licensed under the New BSD License
# 2009, Alexander Artemenko <svetlyak.40wt@gmail.com>
# For other contacts, visit http://aartemenko.com
import unittest
from task_tests import *
if __name__ == '__main__':
unittest.main()
| svetlyak40wt/gtdzen | tests/testsuite.py | Python | bsd-3-clause | 267 | [
"VisIt"
] | bc17b0eef164c363424b8a2f6af1d1db12ecd2c91c4365632ee2220dfe50f180 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGenericDataObjectWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkGenericDataObjectWriter.py | Python | bsd-3-clause | 520 | [
"VTK"
] | 46f8fab86bbcec048605128328ec7ccbc0a949f57d9ae017c1562eac51fbc513 |
from __future__ import (
unicode_literals,
absolute_import,
print_function,
division,
)
str = type('')
import sys
import pytest
from time import sleep
from gpiozero.pins.mock import MockPin, MockPWMPin
from gpiozero import *
def setup_function(function):
import gpiozero.devices
# dirty,... | lurch/python-gpiozero | tests/test_boards.py | Python | bsd-3-clause | 25,935 | [
"Amber"
] | 048f173fc0d38692bcab02f98d155b42a53286315622bf1559a54a3dad3bdade |
from direct.directnotify import DirectNotifyGlobal
from direct.fsm import StateData
import CogHQLoader, MintInterior
from toontown.toonbase import ToontownGlobals
from direct.gui import DirectGui
from toontown.toonbase import TTLocalizer
from toontown.toon import Toon
from direct.fsm import State
import CashbotHQExteri... | silly-wacky-3-town-toon/SOURCE-COD | toontown/coghq/CashbotCogHQLoader.py | Python | apache-2.0 | 3,390 | [
"VisIt"
] | a426b9156942c3e4ea6a6e11b68a5e7e58395ea2892718aaa14460417a9bec9d |
import collections
from pycparser import CParser
from pycparser import c_ast
def extractTypeAndName(n, defaultName=None):
if isinstance(n, c_ast.EllipsisParam):
return ('int', 0, 'vararg')
t = n.type
d = 0
while isinstance(t, c_ast.PtrDecl) or isinstance(t, c_ast.ArrayDecl):
d += 1
... | pwndbg/pwndbg | pwndbg/funcparser.py | Python | mit | 2,371 | [
"VisIt"
] | ee69a0d714616f8f0387015510540ba8bbda920574712074298010426572c44a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
import pickle
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.periodic_table import Element, Specie
from pymatgen.core.si... | matk86/pymatgen | pymatgen/core/tests/test_sites.py | Python | mit | 10,437 | [
"pymatgen"
] | d40e6bc11c330a4e2fb371ac966da052d599e729bc2d9b0a348bbac2f0297396 |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014, 2015, 2016 CERN.
#
# INSPIRE 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 optio... | jacenkow/inspire-next | tests/unit/references/test_processors.py | Python | gpl-2.0 | 5,167 | [
"Brian"
] | db44cb85fa824e9703a72fff3e3b72507bebce7f126e554f6d970d3eac29e25b |
"""
This package contains the XML handlers to read the NineML files and related
functions/classes, the NineML base meta-class (a meta-class is a factory that
generates classes) to generate a class for each NineML cell description (eg.
a 'Purkinje' class for an NineML containing a declaration of a Purkinje
ce... | tclose/PyPe9 | pype9/simulate/common/cells/base.py | Python | mit | 24,986 | [
"NEURON"
] | 532298413a4673e9007bf5183e1101acfa6a2fefd9bf92d83af0e85911126464 |
#!/usr/bin/python
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# 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, or (at your option)
# any later version.
#
# Thi... | RTS2/rts2 | scripts/rts2saf/rts2saf/log.py | Python | lgpl-3.0 | 3,360 | [
"VisIt"
] | ed188c6ddddbb5aaeb177dfba6297de331a842f5cc32bef1702a62ef58b762da |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2014 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/dialogs/tilldetails.py | Python | gpl-2.0 | 1,624 | [
"VisIt"
] | c33d8df536549d8524e535f30464fe141a5ba65a1045e94e5c31251d0d7abd3a |
"""Test all components for instatiation issues."""
# pylint: disable=unused-argument,redefined-outer-name
from inspect import isclass
import pytest
from bowtie import App
from bowtie import control, visual, html
from bowtie._component import COMPONENT_REGISTRY
from bowtie.tests.utils import reset_uuid, server_check
... | jwkvam/bowtie | bowtie/tests/test_components.py | Python | mit | 2,786 | [
"Bowtie"
] | 61a818aacc3296bd7386d9d381c1c407b282fb1be6125a43919ad20c6c414d1c |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
import logging, time
log = logging.getLogger(__name__)
repository_name = 'filtering_1410'
repository_description = "Galaxy's filtering tool"
repository_long_description = "Long description of Galaxy's filtering repository"
category_name = 'Test ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1410_update_manager.py | Python | gpl-3.0 | 7,266 | [
"Galaxy"
] | 2a04fa7ce3e931f23020981f9833f064e72ebf71fba3d10f7a7d7fdbfa415491 |
from __future__ import unicode_literals, print_function, division
import argparse
import ast
import functools
import heapq
import importlib
import inspect
import json
import logging
from contextlib import contextmanager
from collections import defaultdict
import operator
import os
import sys
import textwrap
from . imp... | east825/green-type | greentype/core.py | Python | mit | 56,441 | [
"VisIt"
] | 4df68976cf77fe3feed7790a5bda22b7cb2106b8a4033082c8350b797cd135e1 |
# Django settings for hth project.
ADMINS = (
('Brian Rutledge', 'bhrutledge@gmail.com'),
)
MANAGERS = ADMINS
EMAIL_SUBJECT_PREFIX = '[HtH] '
SERVER_EMAIL = 'django@hallelujahthehills.com'
# Local time zone for this installation. Choices can be found here:
# http://en.wikipedia.org/wiki/List_of_tz_zones_by_name... | bhrutledge/hallelujahthehills.com | hth/settings/__init__.py | Python | mit | 4,282 | [
"Brian"
] | 7c5d1a8826aaad76fae42a3120d4cf0a1e2c5581a717364095ae2354acf3a738 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/diversity/beta/_unifrac.py | Python | bsd-3-clause | 23,175 | [
"scikit-bio"
] | 7a0c0117d721561b92494d3a95f59a4473cd0238ba4ae2d3950214b2bf916237 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0091_auto_20150830_0950'),
]
operations = [
migrations.RemoveField(
model_name='visit',
nam... | koebbe/homeworks | visit/migrations/0092_remove_visit_improvementissues.py | Python | mit | 360 | [
"VisIt"
] | 307674de9ae307138e8e9dcfd19a8e659090369979440fa645d1133637145f74 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 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... | vidartf/hyperspy | hyperspy/_signals/eels.py | Python | gpl-3.0 | 52,216 | [
"Gaussian"
] | 25593f2a8b2703b005b043d915fbb332754bbeef3e73e3d35d1e4b61bbb05709 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | susilehtola/psi4 | psi4/driver/molutil.py | Python | lgpl-3.0 | 9,874 | [
"Psi4"
] | 700d52926611a222d6541bd59a6b0ee1f3dc6ce9a30667fa0f9ce4339b66c191 |
# -*- coding: utf-8 -*-
"""
Part of the astor library for Python AST manipulation.
License: 3-clause BSD
Copyright (c) 2008 Armin Ronacher
Copyright (c) 2012-2017 Patrick Maupin
Copyright (c) 2013-2017 Berker Peksag
This module converts an AST into Python source code.
Before being version-controlled as part of... | ryfeus/lambda-packs | Keras_tensorflow_nightly/source2.7/astor/code_gen.py | Python | mit | 27,485 | [
"VisIt"
] | 533c7fb86faef7df17bc2f297320524551fceed8a93c50a4ae4053247e5ea78f |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
__RCSID__ = "$Id$"
from DIRAC import exit as DIRACExit
from DIRAC.Core.Base import Script
Script.setUsageMessage( """
Remove the ... | sposs/DIRAC | DataManagementSystem/scripts/dirac-dms-remove-replicas.py | Python | gpl-3.0 | 1,637 | [
"DIRAC"
] | 6937475fa3ef71c18c590a65a75dd47857fd1ddc6012ffe12860c7cf89862779 |
r"""XML-RPC Servers.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to handle XML-RPC requests in a CGI
environment using CGIXMLRPCRequestHandler.
The Doc* classes can b... | xyuanmu/XX-Net | python3.8.2/Lib/xmlrpc/server.py | Python | bsd-2-clause | 36,665 | [
"Brian"
] | ae2017eb9eb0403bf04a51f3ccf17c73aa4ec47d120779f80e2f6c2beba3268b |
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