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"""
The B{0install list-feeds} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _
from zeroinstall.cmd import UsageError
from zeroinstall.injector import model, reader
synta... | rammstein/0install | zeroinstall/cmd/list_feeds.py | Python | lgpl-2.1 | 653 | [
"VisIt"
] | 04b4ed3b814a47fbdd45786515a7def8d3f4edd56e215ad5fc061bd7fbc142b2 |
#! /usr/bin/env python
"""
Usage:
calc-blast-cover.py reference.fa query.x.reference.blastn minmatch query.fa
calc-blast-cover calculates the fraction of bases in 'reference.fa' that are
covered by BLAST matches from 'query.fa', for sequence in 'query.fa' that are
longer than 'minmatch'.
"""
import sys
import bla... | jrherr/bioinformatics_scripts | python_scripts/calc_blast_cover.py | Python | mit | 2,343 | [
"BLAST"
] | 30a8f802487b1a99da0eebe9d6c17e4b8962ae6f980d83a93bc15c711976e6fc |
import warnings
from datetime import datetime
from numbers import Number as NumberBase
from itertools import chain
from functools import partial
from . import controlled_vocabulary
from lxml import etree
def make_counter(start=1):
'''
Create a functor whose only internal piece of data is a mutable contain... | mobiusklein/mzidentml_writer | mzident_writer/components.py | Python | apache-2.0 | 32,651 | [
"Dalton"
] | eeb62b8e83cb58a49e8db97bea9a76ff6c9d026c3bf83e63e4334767496d26f0 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.metrics.pairwise` submodule implements utilities to evaluate
pairwise distances or affinity of sets of samples.
This module contains both distance metrics and kernels. A brief summary is
given on the two here.
Distance metrics are a function d(a, b) such that d(a, b) < d(... | johnowhitaker/bobibabber | sklearn/metrics/pairwise.py | Python | mit | 37,117 | [
"Gaussian"
] | dee422c9b516b4733ea08b1dabc447936bdd980c7f4a404e6b951cc03d63cc27 |
"""
This is the courseware context_processor module.
This is meant to simplify the process of sending user preferences (espec. time_zone and pref-lang)
to the templates without having to append every view file.
"""
import string
from django.utils.translation import get_language
from pytz import timezone
from pytz.ex... | eduNEXT/edx-platform | lms/djangoapps/courseware/context_processor.py | Python | agpl-3.0 | 3,856 | [
"VisIt"
] | 4b67a9bcfbcba485c14b774374739cbad3e89a839600dbb4bdb8e872a8d4f791 |
"""
Pyinvoke tasks.py file for automating releases and admin stuff.
Author: Shyue Ping Ong
"""
import datetime
import glob
import json
import os
import re
import subprocess
import webbrowser
import requests
from invoke import task
from monty.os import cd
from pymatgen.core import __version__ as CURRENT_VER
@task
d... | gmatteo/pymatgen | tasks.py | Python | mit | 9,817 | [
"pymatgen"
] | 49ad6a3caa085f9da5722886c232e2eb754ad5bee2f0382a36959e199f6711c3 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/coordinates/core.py | Python | gpl-2.0 | 4,610 | [
"Gromacs",
"MDAnalysis"
] | 48842b2af38246a8a02e71d3d1e8e785fa11eb1aa5bff062a51650b9b077a3e6 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | Eric89GXL/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 29,327 | [
"Brian"
] | b2cad71d982cbd929382a45eddc4dca3ba435ae2fe53ca039cf9f6d406a741d3 |
# -*- coding: utf-8 -*-
"""
Created on Mon Dec 16 11:02:59 2013
Author: Josef Perktold
"""
import numpy as np
from scipy import stats
import matplotlib.pyplot as plt
import statsmodels.nonparametric.api as npar
from statsmodels.sandbox.nonparametric import kernels
from statsmodels.distributions.mixture_rvs import mi... | bashtage/statsmodels | statsmodels/examples/ex_kde_confint.py | Python | bsd-3-clause | 1,941 | [
"Gaussian"
] | 77de82f590cbb90c07de86de3f088d5149abb9d6d5cc49f368520f96abf82a36 |
# electronics.py ---
#
# Filename: electronics.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Wed Feb 22 00:53:38 2012 (+0530)
# Version:
# Last-Updated: Tue Jul 10 10:28:40 2012 (+0530)
# By: subha
# Update #: 221
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
... | BhallaLab/moose | moose-examples/squid/electronics.py | Python | gpl-3.0 | 3,885 | [
"MOOSE"
] | 51af2b4cec81cf71251f59205b0c1ef005bf5e6ae6f3af8c44053f5de05026a3 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from contextlib import contextmanager
from datetime import datetime
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from ...pages.common.logout import LogoutPage
from ...pages.lms.account_settings import Acc... | ahmadiga/min_edx | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 34,284 | [
"VisIt"
] | 54df58916cae3e33fc93e4408383771300729b7d7863bd4429dfda0e852ed743 |
# 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 | src/python/espressomd/io/mpiio.py | Python | gpl-3.0 | 3,867 | [
"ESPResSo"
] | 33f6711c19f36a3ecf50fe73e6380208b1bdc5e05f0242db3a4a24aeeb1c3612 |
"""
A number of function that enhance IDLE on MacOSX when it used as a normal
GUI application (as opposed to an X11 application).
"""
import sys
import Tkinter
from os import path
_appbundle = None
def runningAsOSXApp():
"""
Returns True if Python is running from within an app on OSX.
If so, assume that ... | bussiere/pypyjs | website/demo/home/rfk/repos/pypy/lib-python/2.7/idlelib/macosxSupport.py | Python | mit | 6,028 | [
"VisIt"
] | d7f97d85bfe48bad1fa4baa9e6c817922f09288efb5b229bd3da7e86cb482640 |
#Ignore this sed code echo "126,55,55,71INTER,Cameron" | sed 's/\([0-9].*,[0-9].*,[0-9].*\)/\1/'
#\1 is the reference to the first stored pattern.
import csv
import os
import pickle
d={}#declare a dictionary
dl=[]#A list to store the dictionary in.
fn = open('neocortex_region.txt')
neocortex = [line.strip() for line... | russelljjarvis/neurogateway | atlas_reader3.py | Python | gpl-3.0 | 5,865 | [
"NEURON"
] | 77d50e34539fd0102d70a260e68fbaee666d5e057fbb3c8343ef8ad59871d7aa |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | testsuite/python/interactions_non-bonded.py | Python | gpl-3.0 | 27,497 | [
"ESPResSo",
"Gaussian"
] | d9709b4fad87e242fb638cf7444962d8d802f38b4f9f526651e70358ec52fce2 |
import sys, os, re, types, HTMLParser, urllib2
import parser, db, data, constants
def _rune_cost(generator, filter_data, record, *args):
cost = 0
for rune_type in xrange(0, 4):
for i in xrange(0, getattr(record, 'rune_cost_%d' % (rune_type + 1))):
cost |= 1 << (rune_type * 2 + i)
retu... | utecht/simcraft_shaman | dbc_extract/dbc/generator.py | Python | gpl-3.0 | 171,229 | [
"BLAST",
"CRYSTAL"
] | 0dfc23cf6cb9e09fd01c39cedd7a3158cd54cc6d4cb9a4beafebbae4f0b2eed9 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later ver... | spring01/libPSI | lib/databases/BAKERJCC96.py | Python | gpl-2.0 | 16,029 | [
"Psi4"
] | e2b0549613eff50c4878c1d2a317da7a84e451ad9a150188a4e36aa030be9f0c |
# from django.db.models import get_model
from edc_appointment.models import Appointment
from edc_meta_data.models import CrfMetaDataMixin
# from edc_base.audit_trail import AuditTrail
from edc_base.model.models import BaseUuidModel
from edc_constants.constants import (
UNSCHEDULED, SCHEDULED, COMPLETED_PROTOCOL_VI... | TshepangRas/tshilo-dikotla | td_infant/models/infant_visit.py | Python | gpl-2.0 | 5,263 | [
"VisIt"
] | 685c5c68abf0439f8a68b1f65687bd2c7be8bb172eeab88ae25cb96d600f2d80 |
"""
Tests which scan for certain occurrences in the code, they may not find
all of these occurrences but should catch almost all.
"""
from __future__ import division, absolute_import, print_function
import sys
import pytest
if sys.version_info >= (3, 4):
from pathlib import Path
import ast
import tokenize... | kubaszostak/gdal-dragndrop | osgeo/apps/Python27/Lib/site-packages/numpy/tests/test_warnings.py | Python | mit | 2,594 | [
"VisIt"
] | c9ee130469ceb8f019caee5b4b9243c5857984b82551041f292acc5b063fa612 |
from .layer import Layer
from ..activation import Activation
from ..potential import Potential
import numpy as np
class ParticleVectorNLocalConvolutionInput(object):
def __init__(self, output_size, nr=3, nv=3, sr=1.0, sv=1.0):
self.output_size = output_size
self.nv = nv
self.nr = nr
... | awlange/brainsparks | src/calrissian/layers/particle_vector_n_local_conv.py | Python | mit | 8,208 | [
"Gaussian"
] | 47f3f4b6257f122a5a1b3ed7ab23432862be99e101f5c8df311929fd8424a86f |
# Dual Annealing implementation.
# Copyright (c) 2018 Sylvain Gubian <sylvain.gubian@pmi.com>,
# Yang Xiang <yang.xiang@pmi.com>
# Author: Sylvain Gubian, Yang Xiang, PMP S.A.
"""
A Dual Annealing global optimization algorithm
"""
import numpy as np
from scipy.optimize import OptimizeResult
from scipy.optimize import... | anntzer/scipy | scipy/optimize/_dual_annealing.py | Python | bsd-3-clause | 29,863 | [
"VisIt"
] | 0bb2dc4eb8a4cf2ed5dd88b559029a183488299211ce58ff368aaee580997144 |
# -*- coding: utf-8 -*-
"""
__author__ = "Konstantin Klementiev", "Roman Chernikov"
__date__ = "2017-02-01"
Created with xrtQook
"""
import numpy as np
import sys
import os, sys; sys.path.append(os.path.join('..', '..')) # analysis:ignore
import xrt.backends.raycing.sources as rsources
import xrt.backends.raycing.sc... | kklmn/xrt | tests/raycing/test_laue_bent.py | Python | mit | 8,473 | [
"CRYSTAL"
] | e9e1322cf1d4bef8005d0f7740ef40653feb413d31674492e550525ac34e4e8b |
from __future__ import with_statement
from copy import deepcopy
import os
from galaxy.util import parse_xml
def load_tool(path):
"""
Loads tool from file system and preprocesses tool macros.
"""
tree = raw_tool_xml_tree(path)
root = tree.getroot()
_import_macros(root, path)
# Expand xm... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/loader.py | Python | gpl-3.0 | 6,724 | [
"Galaxy"
] | c8baba74929cf680c56af62963491140ae67dbf1bd7a7ef58b12a03772ed7609 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
import os
import numpy as np
from rmgpy import getPath
from rmgpy.qm.main import QMCalculator
from rmgpy.molecule import Molecule
from rmgpy.qm.gaussian import GaussianMolPM3, GaussianMolPM6
gaussEnv = os.getenv('GAUSS_EXEDIR') or os.getenv('g09root') or os... | enochd/RMG-Py | rmgpy/qm/gaussianTest.py | Python | mit | 5,807 | [
"Gaussian"
] | 157ba42bdf1d9ebbfde53920d9a79f009c93b0c349eb96963adebe4f4529506d |
"""This module provides common utility functions.
Copyright 2021--2022 Michael Hayes, UCECE
"""
import sympy as sym
def factor_const(expr, var):
"""Extract constant factor from expression and return tuple
of constant and the rest of the expression.
For example `a * r(var)` returns `a, r(var)`.
If h... | mph-/lcapy | lcapy/utils.py | Python | lgpl-2.1 | 8,995 | [
"VisIt"
] | 06389a092ae60a94b5a5fdbc7ccc4de20228e06a359bf18a8ff3966f2cab924f |
# -*- coding: utf-8 -*-
import os
import wave
import json
import requests
import pyaudio
from settings import HTTP_PROXY, HTTPS_PROXY
TTS_URL = "https://try-api.recaius.jp/tts/v1/"
class RecaiusTTS(object):
"""Speech Synthesizer by RECAIUS-dev API"""
speaker2info = {
'itaru': ('ja_JP', 'ja_JP-M0001-H0... | aidiary/python-recaius | recaius/tts.py | Python | mit | 6,847 | [
"MOE"
] | 187cbd8e3eab5fcf95026cb6253797f424949b924341d2d378c8c05b6e620acf |
# -*- coding: utf-8 -*-
# Copyright (C) 2015-16 Red Hat, Inc.
# This file is part of the Infinity Note Compiler.
#
# The Infinity Note Compiler 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 ... | gbenson/i8c | src/i8c/compiler/visitors.py | Python | lgpl-2.1 | 2,062 | [
"VisIt"
] | 9c51595cae0839056d166f1e25cdadc37bfb63eb382fab0a1f09e7120a8d41f2 |
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/sound-separation | models/train/data_meeting_io.py | Python | apache-2.0 | 23,738 | [
"Gaussian"
] | d1b8a627651bb6c0f3d2b36e72c496cf3ef04518095b011e9c8dc27c30bc97e5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import collections
import numbers
import string
from itertools import combinations_with_replacement, product
import os
import re
from collections import defaultdict
from monty.serialization import loadfn
... | blondegeek/pymatgen | pymatgen/core/composition.py | Python | mit | 49,756 | [
"pymatgen"
] | b04866790d9bbb7f21fdec978da0d5ae2bfe7c55287303952480da76472477ce |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | majidaldo/ansible | v2/ansible/plugins/cache/memcached.py | Python | gpl-3.0 | 5,987 | [
"Brian"
] | 62fba83cc21ce9f4ab954235d638870da8edaf6befc05c6667410a9f127789ec |
# -*- 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 General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoqlib/test/tests_runner.py | Python | gpl-2.0 | 10,136 | [
"VisIt"
] | 6b4dc73d64cb4e3724029754a70cb19592769acbe3769aa910af69ec70f84e3e |
# $HeadURL$
__RCSID__ = "$Id$"
"""This Backend sends the Log Messages to a Log Server
It will only report to the server ERROR, EXCEPTION, FATAL
and ALWAYS messages.
"""
import threading
import Queue
from DIRAC.Core.Utilities import Time, Network
from DIRAC.FrameworkSystem.private.logging.backends.BaseBackend import Bas... | avedaee/DIRAC | FrameworkSystem/private/logging/backends/RemoteBackend.py | Python | gpl-3.0 | 2,903 | [
"DIRAC"
] | 5f1da7aa092689618507cf59b51908104204547ce352643dc4c6c8be93cf95da |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the BorgQueen class, which manages drones to assimilate
data using Python's multiprocessing.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
... | dongsenfo/pymatgen | pymatgen/apps/borg/queen.py | Python | mit | 4,940 | [
"pymatgen"
] | 817df79eaed5c31096b1f46c7185a024a0d48f85155effbad8289bb2bb556c5a |
# coding: utf-8
from vale import ValeCodegen
from vale import ValeParser
from vale import construct_model
from sympy import S
from sympy.core.sympify import sympify
import numpy as np
# ...
def run(filename):
# ...
from caid.cad_geometry import cube
geometry = cube()
from clapp.spl.mapping import M... | ratnania/vale | tests/test_laplace_3d.py | Python | mit | 3,147 | [
"ParaView",
"VTK",
"VisIt"
] | fb590ec6b0b554bbaf72f13dab717f303449f305d79436e595ecb6422d7f3b20 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/core2/PyscesCore2Modules.py | Python | bsd-3-clause | 25,783 | [
"PySCeS"
] | c1907ea193a2fef143c4b61fea93b6a57fbf03a70d11710766e3645b839fe9e2 |
#!/usr/bin/env python
# Copyright JS Foundation and other contributors, http://js.foundation
#
# 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.... | zherczeg/jerryscript | targets/mbedos5/tools/generate_pins.py | Python | apache-2.0 | 6,927 | [
"VisIt"
] | e5a8f0598943629996173a35697582c4e9a24a3663aacef7535aa9940b66604f |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import matplotlib as mpl
from pymatgen.analysis.diffraction.neutron import NDCalculator
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.util.testing impor... | vorwerkc/pymatgen | pymatgen/analysis/diffraction/tests/test_neutron.py | Python | mit | 3,130 | [
"pymatgen"
] | 919753020b480cf530635610dbbc113584f8a5694b5fb1f04bcf3bb1a5fbf29c |
from ase import *
from ase.lattice import bulk
from ase.dft.kpoints import monkhorst_pack
from gpaw import *
from gpaw.mpi import serial_comm
from gpaw.test import equal
from gpaw.xc.rpa import RPACorrelation
import numpy as np
a0 = 5.43
cell = bulk('Si', 'fcc', a=a0).get_cell()
Si = Atoms('Si2', cell=cell, pbc=True,
... | robwarm/gpaw-symm | gpaw/test/rpa_energy_Si.py | Python | gpl-3.0 | 948 | [
"ASE",
"GPAW"
] | b7577e89552b587adf42a8ac9cdc58e5335baca30a92150ba6bc158f3e87770d |
# this script starts a new AIMS calculation. Ethylene, SA2-CASSCF(2/2).
import numpy as np
import pyspawn
import pyspawn.general
# terachemserver port
port = 54322
# random number seed
seed=87061
# Velocity Verlet classical propagator
clas_prop = "vv"
# adapative 2nd-order Runge-Kutta quantum propagator
q... | blevine37/pySpawn17 | examples/ethylene_fomocasci/start_c2h4.py | Python | mit | 3,778 | [
"Gaussian",
"TeraChem"
] | 58f781f192ddb8d99f87449bdb257d7cf0d718fb01c3a6f29cb240cdfae5f075 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXYZMolReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | chrisidefix/devide | modules/vtk_basic/vtkXYZMolReader.py | Python | bsd-3-clause | 476 | [
"VTK"
] | d0662bc5a751109b90968060f25f15c49f37f0028aaaca42db1cc05f36516ab5 |
"""
Unit page in Studio
"""
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise, Promise
from . import BASE_URL
from .container import ContainerPage
class UnitPage(PageObject):
"""
Unit page in Studio
"""
NAME_SELECTOR = '#unit-display-name-input'
def __init__... | carsongee/edx-platform | common/test/acceptance/pages/studio/unit.py | Python | agpl-3.0 | 5,826 | [
"VisIt"
] | 34e826354453e415a64983d3bf978a0f2f4171bae83761b2fd6c51c75c7062e6 |
__author__ = 'abel'
import montemodes.functions.calculate as calc
method_function = {
1: calc.get_energy_from_tinker,
2: calc.get_energy_from_gaussian
}
class gaussian:
def __init__(self,
methodology='pm3',
internal=False,
memory=None,
... | abelcarreras/MonteModes | montemodes/functions/methods.py | Python | mit | 1,986 | [
"Gaussian",
"TINKER"
] | a86795783b4bc545ba5072d92ba597a4488fd7d9dc01d3c62c5c2c53eba079f2 |
from django.test import SimpleTestCase
from unittest.mock import patch
from corehq.apps.app_manager.const import (
AUTO_SELECT_USERCASE,
WORKFLOW_CASE_LIST,
WORKFLOW_MODULE,
)
from corehq.apps.app_manager.models import (
AdvancedModule,
AdvancedOpenCaseAction,
Application,
AutoSelectCase,
... | dimagi/commcare-hq | corehq/apps/app_manager/tests/test_case_list_form.py | Python | bsd-3-clause | 25,183 | [
"VisIt"
] | 3c1c0ba460c998faafa5432a781942bf5abde86dfbc47bf6ceeceeee81654ade |
#!/usr/bin/env python
# ---------------------------------------------------------------------------
# Licensing Information: You are free to use or extend these projects for
# education or reserach purposes provided that (1) you retain this notice
# and (2) you provide clear attribution to UC Berkeley, including a lin... | BARCproject/barc | workspace/src/labs/src/lab8/observer.py | Python | mit | 10,153 | [
"Gaussian"
] | 9b4bcffc396031887296c5b8fba78752f499f721208418df26b8016f47486dff |
#!python
# ----------------------------------------
# scikit-ribo
# ----------------------------------------
# pre-processing module
# ----------------------------------------
# author: Han Fang
# contact: hanfang.cshl@gmail.com
# website: hanfang.github.io
# date: 3/28/2017
# ----------------------------------------
... | hanfang/scikit-ribo | build/scripts-3.4/scikit-ribo-build.py | Python | gpl-2.0 | 5,237 | [
"pysam"
] | 031db0d76b32b41812b12f9d0d5cbd6be269af1ddd7d5e9fb42a07969cf225cc |
from __future__ import unicode_literals
import json
import logging
import numbers
import phonenumbers
import pytz
import regex
import time
import urllib2
import xlwt
import re
from collections import OrderedDict, defaultdict
from datetime import timedelta
from decimal import Decimal
from django.conf import settings
f... | ewheeler/rapidpro | temba/flows/models.py | Python | agpl-3.0 | 232,241 | [
"VisIt"
] | 520bdb148589d308407fceedaaffd50275dfb0328489693f874bb4adb57e434f |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test coupled cluster logfiles"""
import os
import unittest
import numpy
__filedir__ = os.path.realpath(os.path.dirn... | gaursagar/cclib | test/data/testCC.py | Python | bsd-3-clause | 815 | [
"cclib"
] | 25d6ef43c35db808b60f2201c3ad445eb3bb56e7477e83c56d684d9f5f7cecab |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | h4ck3rm1k3/orca-sonar | src/orca/scripts/apps/soffice/formatting.py | Python | lgpl-2.1 | 5,309 | [
"ORCA"
] | 1f1ee9e4d8b19a71f25360062c5ff8216eddc33ccc7cf6427a757d1531c01de7 |
# Eigenvalues of Orientation Tensor by Local Polynomial Approximation using Numba JIT Acceleration
#
# Calculates the eigenvalues of an orientation tensor derived from the coefficients of a local polynomial
# approximation (3D 2nd order polynomial using gaussian weighted least squares) as proposed by Farneback.
#
# Th... | waynegm/OpendTect-Plugins | bin/python/wmpy/Experimental/LocalPolynomialApproximation/ex_lpa_eigenvals.py | Python | gpl-3.0 | 2,624 | [
"Gaussian"
] | 08e4547f163acb4366d1b13d0dd103955c4f65b80e22135159693cea62998d38 |
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup ------------------------------------------------------------... | dimonaks/siman | docs/source/conf.py | Python | gpl-2.0 | 5,558 | [
"ASE",
"pymatgen"
] | e54e0985c3860d5bb3bb3345aa5bd6461ee99dd985c49776591866f01c197590 |
#!/usr/bin/env python
''' script for filtering insertions vs. the human reference GRCh37/hg19 '''
''' may be useful as a template for extension to other species '''
import pysam
import sys
import os
def usage():
return 'usage: %s </path/to/TEBreak directory> <tabular output from resolve.py>' % sys.arg... | ValentinaPeona/tebreak | scripts/filter_hg19.py | Python | mit | 3,719 | [
"pysam"
] | c046554ecb2272b76f31e7b30f5be12115821b26e912e4ecc0d3aad67ec4012f |
filedict = 'c10.dic'
fileweights = 'fig7.weight.dat'
try:
import custom_params
custom_params.filename='fig7'
except:
print 'You can\'t import the params file'
from colors import palette
from misc import Spherical
from math import sqrt, sin, cos, pi
def ConvertDirection(phi, theta, phir, thetar, transf):
... | JustasB/MitralSuite | Models/Migliore2014/mayasyn.py | Python | mit | 12,745 | [
"Mayavi",
"VTK"
] | 6514647a3f0ae50666e26da9a755da71cc8ef7b3e9b996bdd960f2b290a1a993 |
# pylint: disable=missing-docstring
from lettuce import world, step
from selenium.webdriver.common.keys import Keys
from xmodule.modulestore.django import modulestore
VIDEO_BUTTONS = {
'CC': '.hide-subtitles',
'volume': '.volume',
'play': '.video_control.play',
'pause': '.video_control.pause',
'ha... | olexiim/edx-platform | cms/djangoapps/contentstore/features/video.py | Python | agpl-3.0 | 8,674 | [
"VisIt"
] | af4ddda2106e7a5dea7642fa67512ed2c9e535610b1d652260aa4303b58de0c7 |
## NIFTY (Numerical Information Field Theory) has been developed at the
## Max-Planck-Institute for Astrophysics.
##
## Copyright (C) 2014 Max-Planck-Society
##
## Author: Maksim Greiner, Marco Selig
## Project homepage: <http://www.mpa-garching.mpg.de/ift/nifty/>
##
## This program is free software: you can redistribu... | ultimanet/nifty | lm/nifty_power_conversion_lm.py | Python | gpl-3.0 | 5,320 | [
"Gaussian"
] | 745bcf6caf828e8f9af242e5bd48da62014d7dcf955f95cd48d77c6f6b3ee05e |
from __future__ import print_function
import logging
import numpy
import pywt
import SimpleITK as sitk
import six
from six.moves import range
logger = logging.getLogger(__name__)
def getMask(mask, **kwargs):
"""
Function to get the correct mask. Includes enforcing a correct pixel data type (UInt32).
Also su... | Radiomics/pyradiomics | radiomics/imageoperations.py | Python | bsd-3-clause | 54,849 | [
"Gaussian"
] | 3cfa92549925878c7f2a0940f9dfdcc26b5095e2a6bfa81aaa00228904669b24 |
import re
class Compiler(object):
RE_INTERPOLATE = re.compile(r'(\\)?([#!]){(.*?)}')
doctypes = {
'5': '<!DOCTYPE html>'
, 'xml': '<?xml version="1.0" encoding="utf-8" ?>'
, 'default': '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-tr... | xlk521/cloudguantou | pyjade/compiler.py | Python | bsd-3-clause | 10,790 | [
"VisIt"
] | 8206bf1b9f969d691ca4f0dfe8b66521f956949bb077f394160ae9c9383c5343 |
#!/bin/env python
"""
Script to call the DataRecoveryAgent functionality by hand.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK, gLogger
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
__RCSID__ = "$Id$"
cla... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/scripts/dirac_transformation_recover_data.py | Python | gpl-3.0 | 2,021 | [
"DIRAC"
] | c53877cf1eed8b7f7fe7e1f7b09fba8c1014c45574ca904a7545174313f6c58b |
"""hiPhive force constants calculator interface."""
# Copyright (C) 2018 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of s... | atztogo/phonopy | phonopy/interface/hiphive_interface.py | Python | bsd-3-clause | 7,020 | [
"ASE",
"phonopy"
] | d8ff69c8e3da13fbc6211acc6e5c9447f0362c65f3ae71a4d4c7efbb2530bff8 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageImport(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vt... | nagyistoce/devide | modules/vtk_basic/vtkImageImport.py | Python | bsd-3-clause | 470 | [
"VTK"
] | 43627b7d0558cfa77e3c2ccebc86298052af3e8e896688a753905f9b46dd4e1e |
__author__ = 'tylin'
__version__ = '1.0.1'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that
# assists in loading, parsing and visualizing the annotations in COCO.
# Ple... | CivilNet/Gemfield | dockerfiles/py-faster-rcnn/files/gemfield/py-faster-rcnn/lib/pycocotools/coco.py | Python | gpl-3.0 | 14,891 | [
"VisIt"
] | 6ee13da76ab022a328af1d1d1e61fe634e63627088bc9b77f7e80dcf9861604b |
import sys
import unittest
sys.path.append("..")
from NeuralNet import *
class NeuronTest(unittest.TestCase):
def testWeights(self):
_weights = 10
Neuron = neuron(_weights)
self.assertEqual(len(Neuron.weights),_weights+1)
self.assertEqual(Neuron.numinputs,_weights+1)
self.assertNotEqual(Neuron.weights,Non... | washt/NeuralNetPy | tests/nnetTest.py | Python | mit | 1,445 | [
"NEURON"
] | f4fb1bf000eb1a7c35371e71e15207e495fe3cf548e6e571eac55c43c714dc1f |
# Copyright (C) 2015-2022: The University of Edinburgh
# Authors: Craig Warren and Antonis Giannopoulos
#
# This file is part of gprMax.
#
# gprMax 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 Foundatio... | gprMax/gprMax | gprMax/optimisation_taguchi.py | Python | gpl-3.0 | 20,476 | [
"Gaussian"
] | 90bd868a111fdbd358d393eeee665ed24de583b3aa8d94b59365a334e869ab15 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/pbc/tools/test/test_k2gamma.py | Python | apache-2.0 | 1,797 | [
"PySCF"
] | da030a092e00136fed42aaf512f1f97c388259ebcfc8a17bb82a1f74c2fe2561 |
# -*- coding: UTF-8 -*-
import numpy as np
from numpy.fft import fft
class fgn( object ) :
"""A class to generate fractional Gaussian process of fixed length using
a circulant matrix method suggested by Dietrich and Newsam (1997). For the
best performance N-1 should be a power of two."""
## For better performance N... | ivannz/study_notes | year_14_15/course_project/release/processes/fgn_numpy.py | Python | mit | 4,560 | [
"Gaussian"
] | 192c7419e52a8e9218bb86012fc9363415663253a94e7832840c4a3c1efdfcbe |
# $Id$
#
# Copyright (C) 2004-2006 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.
#
""" unit testing code for MOE-type des... | bp-kelley/rdkit | rdkit/Chem/EState/UnitTestVSA.py | Python | bsd-3-clause | 1,529 | [
"MOE",
"RDKit"
] | 174e5271a22811e5e9f02075bc9733561e4b03867fdedd898eb2f69737786d7c |
#!/usr/bin/env python
"""Copyright 2008 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.4'
__date__ = 'May 02 2008'
#Basi... | jantman/tuxostat | fs_backup/home/tuxostat/devel/Python/LED-simple.py | Python | gpl-3.0 | 2,952 | [
"VisIt"
] | c6a5cb35fcf9a829a85d3b79571e514fcb764fe42ef5ff0374745b727f4b3de2 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import with_statement
import errno
import filecmp
import os.path
import re
import tempfile
import sys
# A minimal memoizing decorator. It'll blo... | lianliuwei/gyp | pylib/gyp/common.py | Python | bsd-3-clause | 15,816 | [
"VisIt"
] | 757cf8bdd0ba5156fb28d49f06961e189de692f7afc9f27b41ccd39abdbbdc0e |
#!/usr/bin/env python
'A model of the earth and its magnetic field, with earth center as origin.'
from __future__ import division # avoid integer division
import numpy as np
import mayavi
from mayavi.mlab import *
def makeRcoordinates(x,y,z):
'''Makes r length and r^hat from coordinates'''
r = np.sqrt(x**2 + ... | arve0/TFY4240-Semester-project | src/mag_field_flow.py | Python | mit | 3,215 | [
"Mayavi"
] | 7b832762db67e19503a8114f591a51f29eaa2791df12a0732dfb408f38bd55b2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2017 GIG Technology NV
#
# 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 requ... | rogerthat-platform/rogerthat-backend | src-test/rogerthat_tests/sourcechecks/test_sourcetest.py | Python | apache-2.0 | 4,576 | [
"VisIt"
] | fb896d70be887c2c0d4e7be19965f5fb466e6670218f35fe5ca7fc2ffc2e2afb |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/exodus/test_ExodusReader.py | Python | lgpl-2.1 | 6,862 | [
"MOOSE"
] | 70bd3260a5edc942d966e17cdf2980d3d8a6116fddaa2b64415d03da29ba65fe |
from schema_transformer.helpers import compose, single_result
TEST_XML_DOC = b'''
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcq="http://purl.org/dc/terms/">
<records count="97" morepages="true" start="1" end="10">
<record... | fabianvf/schema-transformer | tests/utils.py | Python | apache-2.0 | 3,811 | [
"Brian"
] | 95ac82709477c5a99d490cb7e0eeab78d37ad92b8aeba36bd9a8f1749461bc4c |
# sybase/base.py
# Copyright (C) 2010-2019 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is par... | wujuguang/sqlalchemy | lib/sqlalchemy/dialects/sybase/base.py | Python | mit | 31,953 | [
"ASE"
] | 3c19f96897b9a548d08eb11bbf2758bca1ea975f7418d8039992178ada3a942a |
# -*- coding: utf-8 -*-
"""
Lower exception-related instructions.
"""
from pykit import types
from pykit.ir import visit, FunctionPass
class LowerExceptionChecksCostful(FunctionPass):
"""
Lower exception checks (check_error) using C-like checks:
if (result == bad)
goto error;
"""
... | ContinuumIO/pykit | pykit/lower/lower_errcheck.py | Python | bsd-3-clause | 758 | [
"VisIt"
] | 225407bf25893ac90903beae995d72da51da847efd29b619ca4d60e2950e977e |
"""Support for package tracking sensors from 17track.net."""
from datetime import timedelta
import logging
from py17track import Client as SeventeenTrackClient
from py17track.errors import SeventeenTrackError
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA
from homeassistant.const... | turbokongen/home-assistant | homeassistant/components/seventeentrack/sensor.py | Python | apache-2.0 | 11,106 | [
"VisIt"
] | 0246c8541bb285badebf9ccc862e2965f4d279f7db19eebb38138374e2d8f858 |
"""
Contains the user interface in the Universe class
"""
from galaxy.web.base.controller import *
from galaxy.model.orm import *
from galaxy import util
import logging, os, string
from random import choice
log = logging.getLogger( __name__ )
require_login_template = """
<h1>Welcome to Galaxy</h1>
<p>
This insta... | dbcls/dbcls-galaxy | lib/galaxy/web/controllers/user.py | Python | mit | 12,689 | [
"Galaxy"
] | fba44d875f365511507cfbcdd004a22c2bca4e16af8a80b6b663b773a12a4a35 |
import matplotlib.pyplot as plt
import os
from astropy.table import Table
import numpy as np
# setup information sources
degas = Table.read(os.path.join(os.environ['SCRIPTDIR'],'degas_base.fits'))
stack = Table.read('/lustre/cv/users/akepley/degas/stack_test/stack_IR6p0_mom1.fits')
plotDir = os.path.join(os.environ['... | low-sky/degas | scripts/plot_SFEdense_vs_mstar_combined.py | Python | gpl-3.0 | 2,351 | [
"Galaxy"
] | 091d46d64788bcc059eda2c29cfcb684dccf9c3b22c76a002e901e270db5b485 |
"""
Linear Discriminant Analysis and Quadratic Discriminant Analysis
"""
# Authors: Clemens Brunner
# Martin Billinger
# Matthieu Perrot
# Mathieu Blondel
# License: BSD 3-Clause
from __future__ import print_function
import warnings
import numpy as np
from scipy import linalg
from .extern... | beepee14/scikit-learn | sklearn/discriminant_analysis.py | Python | bsd-3-clause | 27,308 | [
"Gaussian"
] | bf199c3a631741a07394cfe909160e81badad2ebd7bfee5ff15f23c95f3b3b03 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/pbc/mpicc/__init__.py | Python | apache-2.0 | 862 | [
"PySCF"
] | ef18ca9bbf3f240124b9dc3e451a81e52d241279d40851647c08ad0707fe0688 |
import re
import discord
import Data
import deco
import utilities
import misc
import undecorated
import MemeMachine
import re
import owner
client = discord.Client()
@client.event
async def on_ready():
print('Logged in !')
print('------------')
@client.event
async def on_message(message):
if message.aut... | zenAndroid/zenBot | zenBot.py | Python | mit | 1,864 | [
"VisIt"
] | db4d37cc31c3b65fc7d0d264cbdaff1f4559dfcc5e029aa6646e72353a0f7977 |
#!/usr/bin/env python
#
# Data manager for reference data for the 'humann2' Galaxy tools
import datetime
import json
import optparse
import os
import shutil
import subprocess
import sys
HUMANN2_REFERENCE_DATA = {
"full": "Full",
"DEMO": "Demo",
"uniref50_diamond": "Full UniRef50",
"uniref50_ec_filtere... | blankclemens/tools-iuc | data_managers/data_manager_humann2_database_downloader/data_manager/data_manager_humann2_download.py | Python | mit | 5,238 | [
"Galaxy"
] | 5d09d487e50fd27a6e03f2eeb0aaa1d3b5b0de740a5acb7f9b1e7cde59ca03aa |
# -*- python -*-
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2007 Donald N. Allingham, Martin Hawlisch
# Copyright (C) 2009 Yevgeny Zegzda <ezegjda@ya.ru>
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2013 Pat Lefebre
#
# This program is free soft... | sam-m888/addons-source | HtreePedigreeView/HtreePedigreeView.py | Python | gpl-2.0 | 83,738 | [
"FLEUR"
] | e65e8b509ecdd7005d8943c835f5ac07c8cfa10d245c7698a70a899633739631 |
################################################################################
# The Neural Network (NN) based Speech Synthesis System
# https://svn.ecdf.ed.ac.uk/repo/inf/dnn_tts/
#
# Centre for Speech Technology Research
# ... | ronanki/merlin | src/layers/mdn_layers.py | Python | apache-2.0 | 16,415 | [
"Gaussian"
] | 205a848cc8d428b56b857cb3b6ff393a89ac92c0539d85ad04ee4f3cf6661bcd |
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from asap3.testtools import ReportTest
print "Making atoms"
atoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size=(25,25,25), symbol="Cu")
memory_usage(atoms)
print "Attaching EMT potential"
atoms.set_calculat... | auag92/n2dm | Asap-3.8.4/Test/PrintMemory.py | Python | mit | 439 | [
"ASE"
] | adbf8c95505453d4a813213e189104350a5e328d4f1ea039c3bac2be7835c100 |
# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | google-research/language | language/serene/model.py | Python | apache-2.0 | 12,697 | [
"Gaussian"
] | 857ecc093abd5c516d05e212239610341121e381dd459149fe53d22449001db6 |
#!/usr/bin/env python3
try:
import http.client as httplib
except ImportError:
import httplib
import httplib2
import os
import sys
import errno
from time import sleep
from decimal import Decimal
from . import consts
from google_auth_oauthlib.flow import InstalledAppFlow
from googleapiclient.discovery import ... | NikhilNarayana/FRC-CLI-Youtube-Uploader | frcuploader/youtube.py | Python | gpl-3.0 | 7,809 | [
"VisIt"
] | fd99a76a6e8957c27579855ff41ec115a944f87563d6e7a5bbd69c32b9c8d231 |
import pygame as pg
from .fastfont import Fastfont
black = (0, 0, 0)
white = (255,255,255)
darkgrey = (25, 25, 48)
grey = (84, 84, 114)
darkblue = (25, 25, 64, 100)
white = (255, 255, 255)
green = (0, 255, 0)
blue = (0, 0, 255)
red = (255, 0, 0)
lightgreyblue = (130, 150, 190) # waypoint symbol color
lightgreygree... | ProfHoekstra/bluesky | bluesky/ui/pygame/console.py | Python | gpl-3.0 | 5,866 | [
"Amber"
] | 7c965ff2245f13e7c284ec31befbf00a3585aab9a9575747d87f0f5a5c0136ff |
from . import core, utils
import cgt
import ctypes, os.path as osp, hashlib, numpy as np, sys, subprocess, string, os, time, traceback, cPickle
from collections import defaultdict, namedtuple
from StringIO import StringIO
import logging
def function(inputs, outputs, dbg=None, updates=None, givens=None):
assert isi... | jameshensman/cgt | cgt/compilation.py | Python | mit | 35,903 | [
"VisIt"
] | da7f20f6d94d11d02266f0a564ef036b818588b9aba828a2159df8d0e17535d9 |
#------------------------------------------------------------------------------
#
# This file is part of the SternheimerGW code.
#
# Copyright (C) 2010 - 2018
# Henry Lambert, Martin Schlipf, and Feliciano Giustino
#
# SternheimerGW is free software: you can redistribute it and/or modify
# it under the terms of the GNU... | mmdg-oxford/SternheimerGW | install/generate_library.py | Python | gpl-3.0 | 2,232 | [
"ESPResSo"
] | 63d20e44cbfdb02f75c6d1bc6245ac54df318925bfbec5af6745aa9fa43edd07 |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Fri May 8 15:56:32 2015
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
... | SamWitte/Codds_DarkMatter | src/Data/CDMSSiArtif.py | Python | gpl-2.0 | 3,319 | [
"Gaussian"
] | 85a14272692c8b36c80547f2e806f85743c8b3e6bbd18197a196d562ba963616 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0032_exc.py | Python | apache-2.0 | 1,202 | [
"PySCF"
] | d43fe519337c7cfa4e2a9a7de0732e2c0ab40591d0a84f3292425b620dd43ac1 |
import operator
from functools import partial
import numpy as np
from .. import Variable
from ..conventions import pop_to, cf_encoder
from ..core import indexing
from ..core.utils import (FrozenOrderedDict, NDArrayMixin,
close_on_error, is_remote_uri)
from ..core.pycompat import iteritems, b... | clarkfitzg/xray | xray/backends/netCDF4_.py | Python | apache-2.0 | 9,252 | [
"NetCDF"
] | 8d121b86de3a5e2836197dbdd2f06361d7353afc53d690d19747189122786140 |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max-Planck-Institute of Neurobiology, Munich, Germany
# Authors: Philipp Schubert
import time
from multiprocessing import Queue, Process
from typing import Optional
import networkx as nx
import numpy as np
from ... | StructuralNeurobiologyLab/SyConn | syconn/exec/exec_render.py | Python | gpl-2.0 | 14,228 | [
"NEURON"
] | ef194b6568a5709fb7dab8fafab9668ddc9b93288c8350198dd8fd423d6a7f73 |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# vizplotgui_pymol.py
# Purpose: viz running LAMMPS simulation via PyMol with plot and GUI
# Syntax: vizplotgui_pymol.py in.lammps Nfreq compute-ID
# in.lammps = LAMMPS input script
# Nfreq = plot data point and v... | ganzenmg/lammps_current | python/examples/vizplotgui_pymol.py | Python | gpl-2.0 | 4,404 | [
"LAMMPS",
"PyMOL"
] | 3bca16212357ba35ecc3d0b0d3c71ee167a66a52084a578fe14e114ebb1c239c |
#!/usr/bin/env python
#
# -----------------------------------------------------------------------------
# Copyright (C) 2016 Daniel Standage <daniel.standage@gmail.com>
#
# This file is part of tag (http://github.com/standage/tag) and is licensed
# under the BSD 3-clause license: see LICENSE.
# ------------------------... | standage/tag | tag/tests/test_cli.py | Python | bsd-3-clause | 4,767 | [
"ABINIT"
] | 6bd7b363e1a6885f55a03df24871024fc5b443e7ee4665d33ce7cfd753cdec71 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/cov_radii.py | Python | gpl-2.0 | 5,363 | [
"Psi4"
] | e82efd4b62d3737bf17af0a5952c10a228308ad5bb1e70a6c1dc97ab9e478229 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
""" Ban one or more Storage Elements for usage
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base im... | coberger/DIRAC | DataManagementSystem/scripts/dirac-admin-ban-se.py | Python | gpl-3.0 | 8,432 | [
"DIRAC"
] | 56548845b47d4b93307cf2db7f8e5a2470c9e033fc24561323fef4e566a452ec |
"""
Use these tags and filter when you're rolling your own search results.
This is intended to be a whole templatetags module. I keep it in my apps
as templatetags/search.py. These should not be used to perform search
queries, but rather render the results.
Basics
-------
There are three functions, each has both a ... | Alir3z4/django-kewl | django_kewl/templatetags/search.py | Python | bsd-3-clause | 11,201 | [
"Brian"
] | 3236f18ae7210a603d42e0e567c39e1fc6b6f4cbda13f012f7567cffa602b84f |
# Copyright 2011 Luc Saffre
# License: BSD (see file COPYING for details)
"""
This is for writing fixtures that import data from an MS-Access
database (:xfile:`.mdb`) into Lino.
Usage examples see
:mod:`lino.projects.pcsw.fixtures.pp2lino`
and
:mod:`lino.projects.crl.fixtures.hs2lino`.
It uses `mdb-export` to extr... | khchine5/lino | lino/utils/mdbtools.py | Python | bsd-2-clause | 5,749 | [
"Brian"
] | ac32260d9256d4fca5a047179dccbde432614d546ec66c92caf95305b07eb09b |
import numpy as np
import pytest
import logging
import skimage
import tempfile
import nibabel
from spinalcordtoolbox.scripts import sct_compute_snr
logger = logging.getLogger(__name__)
# Declare the signal intensity in the object created in the dummy_*() functions. This object will be used to compute
# the SNR usin... | neuropoly/spinalcordtoolbox | testing/cli/test_cli_sct_compute_snr.py | Python | mit | 12,233 | [
"Gaussian"
] | b4bcac46acce297b08837d7efa3b89ad9f8d18e23be24e44822554c253efffe1 |
# (c) 2012, Michael DeHaan, <michael.dehaan@gmail.com>
# (c) 2017 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
DOCUMENTATION = '''
... | valentin-krasontovitsch/ansible | lib/ansible/plugins/callback/osx_say.py | Python | gpl-3.0 | 2,870 | [
"exciting"
] | 083f199462bf1e7ee919db16203363c063ca0a38757da3656493c780aea51fa4 |
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