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import subprocess
import os
import click
import yaml
from dgl import library_constants
from Bio import AlignIO
@click.group()
def cli():
pass
#@cli.command()
#@click.argument('embl_gtf')
def parse_gtf(embl_gtf):
"""
organise embl gtf into genes
output in yaml format
"""
with open(embl_gtf) as... | DeskGen/dgcli | library_design/dgl/genome_remap3.py | Python | gpl-2.0 | 24,336 | [
"BWA",
"Bowtie"
] | 024affc3702da5d631c840a58ea0d8d50c17b24eeaf3335b78770ae45dcbcf46 |
# Copyright 2010 The Closure Library Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by a... | isabela-angelo/scratch-tangible-blocks | scratch-blocks/node_modules/google-closure-library/closure/bin/build/jscompiler.py | Python | bsd-3-clause | 4,870 | [
"VisIt"
] | 7f0266e4755723336d6d12191dfba34bdfca5f2f123a4249de781ebfe21e0447 |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2018 by Tobias Houska
This file is part of Statistical Parameter Optimization Tool for Python(SPOTPY).
:author: Tobias Houska and Motjaba Sadegh
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ imp... | bees4ever/spotpy | spotpy/algorithms/dream.py | Python | mit | 16,847 | [
"Gaussian"
] | 7a351bfc001547e477496f846ebe70a0deca3f8d102b80b702f6ad4799d14574 |
# LIBTBX_SET_DISPATCHER_NAME dev.dials.ssx_index
"""
This program runs indexing on the spotfinding results from a
still sequence i.e. SSX data. This wraps a call to the regular
indexing code, and so all parameters from dials.index can be set.
If a unit cell is given, indexing of each image will be attempted with the
f... | dials/dials | command_line/ssx_index.py | Python | bsd-3-clause | 6,171 | [
"CRYSTAL"
] | 2b32dd22c152d69e951f0ec6713e1bde0aba3e0c5b381151f66d1afed65dac95 |
# -*- coding: utf-8 -*-
"""Vibrational modes."""
import pickle
from math import sin, pi, sqrt
from os import remove
from os.path import isfile
import sys
import numpy as np
import ase.units as units
from ase.io.trajectory import PickleTrajectory
from ase.parallel import rank, barrier, paropen
class Vibrations:
... | slabanja/ase | ase/vibrations.py | Python | gpl-2.0 | 13,163 | [
"ASE",
"Jmol"
] | 8e3dae8f0c4aa66f07f33741e2e2b7a2831364558a63b86b6fcc97c9a4aef260 |
# Generated by Django 3.1.8 on 2021-06-10 17:39
import TWLight.resources.models
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("resources", "0076_auto_20210607_1312"),
]
operations = [
migrations.AlterField(
model_name="lang... | WikipediaLibrary/TWLight | TWLight/resources/migrations/0077_auto_20210610_1739.py | Python | mit | 29,851 | [
"ASE",
"MOE"
] | 1fc1934e5a0a987a1c73eceb08a8d14e36c7da73200f5c1ac7d27387d2a778c1 |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2012 OpenStack 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-2.0
#
# Unless required by... | dencaval/swift | test/unit/proxy/test_server.py | Python | apache-2.0 | 415,761 | [
"MOOSE"
] | e5f8850c845e4490d6baadd549c8d645517d46c6a37e7e085931121c0b85cdf1 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | karllessard/tensorflow | tensorflow/python/keras/optimizer_v2/learning_rate_schedule.py | Python | apache-2.0 | 38,455 | [
"Gaussian"
] | 99fff8c8f1d9d41426f30edb197f7272edda42626493d5c79f193c7ddb25a549 |
import math
import cStringIO
import os
import copy as cp
from itertools import chain, ifilter, ifilterfalse
from functools import partial
import re
import operator as op
from string import Template as T
import logging
from lib.typecheck import *
import lib.const as C
from lib.enum import enum
import util
import sampl... | plum-umd/pasket | pasket/encoder.py | Python | mit | 48,157 | [
"VisIt"
] | 4a0c7b5c7407df98fdcd70c61857e78ff917e90094e401e2c385651e4dc5955d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import os
import re
import json
import warnings
from io import open
from enum import Enum
from pymatgen.core.units import Mass, Length, unitiz... | matk86/pymatgen | pymatgen/core/periodic_table.py | Python | mit | 38,356 | [
"CRYSTAL",
"pymatgen"
] | 5ce0a447ee4d8c8e6542cfd7e15dd8d0dc724810fa25d596f4785017b65310c1 |
#!/usr/bin/env python
'''
Script to convert .xsd file to VASP input files.
'''
import argparse
import os
import re
import sys
import logging
import numpy as np
from vaspy.matstudio import XsdFile
from vaspy.incar import InCar
from vaspy import PY2
if PY2:
import commands as subprocess
else:
import subpr... | PytLab/VASPy | scripts/create_inputs.py | Python | mit | 5,291 | [
"VASP"
] | 9180bc93e4886768ce6d5abbf1e7b34da58122cd564e8c3aeb982a7bd9e724b7 |
# ex01.py
#
# Functions and data useful in exercise 1 (bacterial GC content, etc.) of
# the BS32010 course at the University of Dundee
from Bio import SeqIO # For working with sequence data
from Bio.Graphics.ColorSpiral import get_color_dict # For defining colours
import matplotlib.pyplot as plt # For creating gra... | widdowquinn/Teaching-2015-03-17-UoD_compgenvis | workshop_1/bs32010/ex01.py | Python | mit | 4,059 | [
"Biopython"
] | 691c352180a197cb6e6d4dfe5ff03523175a900feb458c23b1ad1dc41c92dd81 |
from __future__ import absolute_import
from typing import Any, List, Set, Tuple, TypeVar, \
Union, Optional, Sequence, AbstractSet
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import QuerySet
from django.db.models import Manager
... | ahmadassaf/zulip | zerver/models.py | Python | apache-2.0 | 65,012 | [
"VisIt"
] | df45b0f642a61e4be7f3db82c73358e05fd47b7c131c41a4fc48196578d2bc42 |
from __future__ import print_function
import numpy as np
import pdb
from . import Utils
"""
This module contains definitions for basic proposal distribution
classes to be used by the MetropolisHastings sampler. Note that
these class definitions should contain pretune() methods, rather
than the MetropolisHastings clas... | tomevans/pyhm | pyhm/BuiltinProposals.py | Python | gpl-2.0 | 18,196 | [
"Gaussian"
] | bf6b52c8e06bcd29e1d01e53636dd065a8ba68d48a1e14f1411d58ef04f64e18 |
"""
This script tests the cisd module.
"""
import os
import numpy as np
import time
from frankenstein import scf, ci
from frankenstein.tools.lat_utils import get_mol
def test_cisd_ch4():
nocc = 5
basis = "sto-3g"
if __name__ == "__main__":
xyz = "geom/ch4.zmat"
else:
xyz = os.path.di... | hongzhouye/frankenstein | tests/cisd_test.py | Python | bsd-3-clause | 2,057 | [
"PySCF"
] | c37ad5e59f404d08bdf964583ef47561589e6a454d2415971ae758a02d73a2c3 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | olitheolix/azrael | demos/ship_boostercube.py | Python | agpl-3.0 | 11,803 | [
"VisIt"
] | e8999e2d052af76ba89b10beaafe6502c5c0984c6df194136c58814361983073 |
#
# Copyright 2018 Analytics Zoo 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 applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/orca/learn/tf2/estimator.py | Python | apache-2.0 | 21,813 | [
"ORCA"
] | fceaef5c382112586489e03685a9d3df4e802e6e743afbc407818c3d1d08e018 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
======================
ELM Classifiers Comparison
======================
A comparison of a several ELMClassifiers with different types of hidden
layer activations.
ELMClassifier is a classifier based on the Extreme Learning Machine,
a single layer feedforward network with ... | chrinide/PyFV | pyfv/elm/plot_elm_comparison.py | Python | gpl-2.0 | 7,043 | [
"Gaussian"
] | 6d6629cc1ad1d1a8f0bb3290169eb841836422f2f3fe03c687ade309fe07d3fe |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module contains simple statistical algorithms that are
straightforwardly implemented as a single python function (or family of
functions).
This module should generally not be used directly. Everything in
`__all__` is imported into `astropy.stats... | mhvk/astropy | astropy/stats/funcs.py | Python | bsd-3-clause | 61,721 | [
"Gaussian"
] | f048daf3d1066e0664f7ed0e2394fa1863f385d1c4dd04151b1ca8efbded967a |
# -*- coding: UTF-8 -*-
import random
from neat import config
class NodeGene(object):
def __init__(self, id, nodetype, bias=0, response=4.924273, activation_type=None):
""" A node gene encodes the basic artificial neuron model.
nodetype should be "INPUT", "HIDDEN", or "OUTPUT"
"""
... | davidmfinol/py3NEAT | neat/genome.py | Python | gpl-3.0 | 7,772 | [
"NEURON"
] | 70b3ec03a6e03a6613854c5c015b96251aefb6d1dcc5071387f18a1aebfd6125 |
'''
--------------------------------------------------------
Authors:
- Brin Rosenthal (sbrosenthal@ucsd.edu)
- Julia Len (jlen@ucsd.edu)
- Mikayla Webster (13webstermj@gmail.com)
--------------------------------------------------------
'''
from __future__ import print_function
import json
import math
i... | ucsd-ccbb/visJS2jupyter | visJS2jupyter/visualizations.py | Python | mit | 33,209 | [
"Cytoscape"
] | acbcada08afdfad47b9b5d081e7562a46bfe8302022ce524a989b1fa44b4e38a |
#!/usr/bin/python
"""
# Created on Aug 12, 2016
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com) GitHub ID: grastogi23
#
# module_check: not supported
#
# 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 publ... | civisanalytics/ansible | lib/ansible/modules/network/avi/avi_api_session.py | Python | gpl-3.0 | 8,020 | [
"VisIt"
] | 5a07eaaa1aa37e56ace988fb6be6e05f02719a7b55234b929869602c5a21eb14 |
"""Get the error of a model. This tool supports multiple error measures."""
# Core Library modules
import csv
import itertools
import logging
import os
import subprocess
import sys
import tempfile
import time
from collections import Callable, OrderedDict
# Third party modules
import pkg_resources
import yaml
# First... | MartinThoma/hwrt | hwrt/test.py | Python | mit | 12,629 | [
"NEURON"
] | b2defa7ef11d501f681138e48a9b93a982b89a2830226b7f4e5b05dda75f2f93 |
# -*- coding: utf-8 -*-
import re
from numbers import Integral
from collections import namedtuple
__all__ = ["countries"]
try:
basestring
except NameError:
basestring = str
Country = namedtuple('Country',
'name alpha2 alpha3 numeric apolitical_name')
_records = [
Country(u"Afghanis... | schleichdi2/OpenNfr_E2_Gui-6.0 | lib/python/Plugins/Extensions/MediaPortal/resources/iso3166/__init__.py | Python | gpl-2.0 | 18,719 | [
"BWA"
] | d6cd65a9921d113b10a1e1edcaaaf36906206d1b7986f6e491cdafb5f08264c5 |
#
# @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
#... | psi4/psi4 | psi4/driver/driver_findif.py | Python | lgpl-3.0 | 38,143 | [
"Psi4"
] | 6ffb0b9b538f6f84241c277b4069a62129e93b0508d10638b21d4b02ed74faba |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Execute computations asynchronously using threads or processes."""
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
from ._base import (FIRST_COMPLETED,
FIRST_EXCEPTION,
... | blopker/PCLite | pclite/lib/concurrent/futures/__init__.py | Python | mit | 706 | [
"Brian"
] | f7f443694b0580da0fb97d0fc249f550e635fbc7e7acf238233bbad126c77dab |
"""Source code analyzer for chalice app.
The main point of this module is to analyze your source code
and track which AWS API calls you make.
We can then use this information to create IAM policies
automatically for you.
How it Works
============
This is basically a simplified abstract interpreter.
The type inferen... | awslabs/chalice | chalice/analyzer.py | Python | apache-2.0 | 26,421 | [
"VisIt"
] | 704b8ea01d384c4eb5a13fec2884e1e1a3f529b74ee616c848edeb2195985b79 |
#!/usr/bin/env python
import roslib; roslib.load_manifest('viconToGps')
import rospy
import conversion as c
from sensor_msgs.msg import NavSatFix
from sensor_msgs.msg import NavSatStatus
from geometry_msgs.msg import TransformStamped
latestViconMsg = TransformStamped()
latestViconMsg.transform.translation.x = 30
pa... | kdhansen/roburoc4 | viconToGps/nodes/talker.py | Python | gpl-3.0 | 2,492 | [
"Gaussian"
] | ff345c284f9e464b0d6a650615588ce5aba1cd00b3154191e010057e09a3844d |
"""Tests for parse.py"""
import unittest
from qcl import parse
import numpy as np
class ParseTest(unittest.TestCase):
"""Tests for parse.py"""
def test_xyzfile(self):
"""Test for parse.xyzfile()"""
ccdata = parse.xyzfile('../data/xyz/water.xyz')
self.assertEqual(ccdata.charge, 0)
... | ben-albrecht/qcl | test/test_parse.py | Python | mit | 4,238 | [
"cclib"
] | c1c088990de63f002ee1dda5652fff60d4e11cdef139d78ff3644f73a38e69f2 |
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2019 Manas.Tech
# License granted by Canonical Limited
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation.
#
# ... | snapcore/snapcraft | snapcraft/plugins/v1/crystal.py | Python | gpl-3.0 | 4,670 | [
"CRYSTAL"
] | ef1f163ff1226da6e333b5d42f5cf095806a881a658711cffe9c3b13799bf296 |
"""
Image Pyramids
functions: cv2.pyrUp(), cv2.pyrDown()
sometimes, need to work with images of different resolution of the same image
create images with different resolution, search for object in all the images
image pyramid = {images of different resolution}
pyramid types
Gaussian pyramid
Laplacian pyram... | SSG-DRD-IOT/commercial-iot-security-system | opencv/tutorials/imageProcessing/pyramids/pyramids.py | Python | mit | 2,980 | [
"Gaussian"
] | 6d60eb5fefdf19af5ddcb50fedef735dd547a6a39489c1a4c7a77d6751209f11 |
# -*- coding: utf-8 -*-
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | sasha-gitg/python-aiplatform | tests/unit/gapic/aiplatform_v1beta1/test_endpoint_service.py | Python | apache-2.0 | 110,793 | [
"Octopus"
] | ba8e1c944ddce0685d631ef5aa6dbc0428e53668695e69218407e656aadcdb8c |
import glob
import hashlib
import sys
import math
import time
# 'nwchem.py' is an intrinsic module
import nwchem
#______________________________________________________
#
#________________ PHYSICAL CONSTANTS _________________
#______________________________________________________
kCalPerHartree = 627.509451
Boltz... | mattbernst/composite-thermochemistry-nwchem | Gn.py | Python | mit | 56,608 | [
"Avogadro",
"GAMESS",
"Gaussian",
"NWChem"
] | 56e1e834dd8669b19b2caed4ed252d064d9a9ae998ec257a068abdd3c5dfe549 |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck ... | kashif/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 45,532 | [
"Gaussian"
] | e0473eda66378cb1852459324d0138c683d4ec1620cb1db3a6021c677e26dbc1 |
"""
Upload class
"""
from galaxy import jobs, util, datatypes, web
import common
import logging, urllib
log = logging.getLogger( __name__ )
class ASync(common.Root):
@web.expose
def default(self, trans, tool_id=None, data_id=None, **kwd):
"""Catches the tool id and redirects as needed"""
re... | jmchilton/galaxy-central | galaxy/interfaces/async.py | Python | mit | 4,565 | [
"Galaxy"
] | f78dee9bb475264fefda1af82b2854d6c2face9bce5ce0cb3d4881b996ae59a1 |
import os
import time
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
import mdtraj.reporters
import sys
code = "3DMV"
ff_name = "amber99sbnmr"
water_name = 'tip3p-fb'
which_forcefield = "%s.xml" % ff_name
which_water = '%s.xml' % water_name
platform_name = "CUDA"
timestep = 2.0 *... | kyleabeauchamp/fah-projects | old/equilibrate_boxes2.py | Python | gpl-2.0 | 1,762 | [
"MDTraj",
"OpenMM"
] | 87524127cea5df88e9bfd17238deb88ffb0d8fb8ace8fb3128c98cc0a7fdb90f |
# -*- coding: utf-8 -*-
"""
pysteps.nowcasts.anvil
======================
Implementation of the autoregressive nowcasting using VIL (ANVIL) nowcasting
method developed in :cite:`PCLH2020`. Compared to S-PROG, the main improvements
are using an autoregressive integrated (ARI) model and the option to use
vertically inte... | pySTEPS/pysteps | pysteps/nowcasts/anvil.py | Python | bsd-3-clause | 19,462 | [
"Gaussian"
] | 7dffccaace853f549e7b650be51e60583a4d55203d6b1de3ecbb501915632e03 |
from edc_navbar import Navbar, NavbarItem, site_navbars
visit_schedule = Navbar(name='edc_visit_schedule')
visit_schedule.append_item(
NavbarItem(name='visit_schedule',
title='Visit Schedule',
label='Visit Schedule',
fa_icon='fa-calendar',
url_name='edc... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/navbars.py | Python | gpl-2.0 | 717 | [
"VisIt"
] | 81e54165875523aaf3f694f5f3d7d7dd9f42bf5fae95856987eeca953b0fa7a4 |
"""Module defining ``Eigensolver`` classes."""
import numpy as np
from gpaw.utilities.blas import axpy
from gpaw.eigensolvers.eigensolver import Eigensolver
from gpaw.utilities import unpack
from gpaw.mpi import run
class RMM_DIIS(Eigensolver):
"""RMM-DIIS eigensolver
It is expected that the trial wave fu... | ajylee/gpaw-rtxs | gpaw/eigensolvers/rmm_diis.py | Python | gpl-3.0 | 4,437 | [
"GPAW"
] | 2048340e691b44fa12a4c4b1b02a552f8a20f9458801633e8fa4bf6e36cc840a |
#!/usr/bin/env python
'''CREATED:2013-12-08 14:28:34 by Brian McFee <brm2132@columbia.edu>
Demonstration of phase vocoder time stretching.
'''
from __future__ import print_function
import argparse
import sys
import librosa
def stretch_demo(input_file, output_file, speed):
'''Phase-vocoder time stretch demo func... | ebattenberg/librosa | examples/time_stretch.py | Python | isc | 1,908 | [
"Brian"
] | e77b07cb1efd64318e8ace9215f590b670d2b2101cd4b77b761a1c9b74533e46 |
""" Algorithms for locating an embryo in the image
"""
# Author: Ilya Patrushev ilya.patrushev@gmail.com
# License: GPL v2.0
import sys
import numpy as np
import scipy as sp
import scipy.linalg as la
import scipy.sparse as spr
import scipy.stats as st
from scipy.signal import fftconvolve
from sklearn import linear_mo... | ilyapatrushev/isimage | isimage/find_embryo.py | Python | gpl-2.0 | 25,100 | [
"Gaussian"
] | 1129d723cc27680ac29263fbe54d5315b5c852c52ec8e4e1434dad545d23424b |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | milking_cowmask/masking/cow_mask.py | Python | apache-2.0 | 3,750 | [
"Gaussian"
] | 448bc9465e85f406adb8cab27f517654b9daf405bd68fc9c8c00e034daa83d71 |
# -*- coding: utf-8 -*-
#
# testiaf.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, or
# (... | terhorstd/nest-simulator | pynest/examples/testiaf.py | Python | gpl-2.0 | 4,728 | [
"NEURON"
] | a5899ac5181be4205aff41f7ccb2e3933ccf6e503f4ca1ef3bf9965b4c9e4d81 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | jmehnle/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 30,286 | [
"Galaxy",
"MOOSE"
] | bb836d84177ed0f25e694bc7849fd730b4918fc281937faab904fe97134fe594 |
# -*- coding: utf-8 -*-
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2018 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU General Public ... | upibhalla/moose-core | tests/python/testXreacs6.py | Python | gpl-3.0 | 4,205 | [
"MOOSE"
] | 4dd61812004a5b846a456da88d4fe1f198fc0a1ee8e243ec6afa72bdfb88f007 |
import unittest
from iSDM.environment import ClimateLayer
from iSDM.environment import RasterEnvironmentalLayer
from iSDM.environment import Source
import geopandas as gp
from shapely.geometry import Polygon
from rasterio.transform import Affine
import numpy as np
class TestEnvironment(unittest.TestCase):
def se... | remenska/iSDM | tests/test_environment.py | Python | apache-2.0 | 5,831 | [
"ADF"
] | 7ee6a2d299ef9a9b52b54f1110b28592ae23abd9bae3c665802cf62611786504 |
from IPython.display import HTML, display
devs = [
('Fernando Perez', 'fperez.jpg'),
('Brian Granger', 'ellisonbg.jpg'),
('Min Ragan-Kelley', 'minrk.jpg'),
('Thomas Kluyver', 'takluyver.jpg'),
('Jonathan Frederic', 'jdfreder.jpg'),
('Paul Ivanov', 'ivanov.jpg'),
('Matthias Bussonnier', 'mat... | sccolbert/talk-2015 | ipythonproject.py | Python | mit | 1,192 | [
"Brian"
] | a468c7cd455de2cb454157dbc0aea412c1057fe4f2047761e599ec0537a705fc |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
import logging
log = logging.getLogger( __name__ )
repository_name = 'filtering_0310'
repository_description = "Galaxy's filtering tool for test 0310"
repository_long_description = "Long description of Galaxy's filtering tool for test 0310"
cat... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_0310_hg_push_from_api.py | Python | gpl-3.0 | 8,930 | [
"Galaxy"
] | 6d8f3ee716e5830a75f95b0967503f5665c8ba7916da84302dcbadf731f7827d |
## \example atom/charmm_forcefield.py
# In this example, a PDB file is read in and scored using the CHARMM
# forcefield. For more control over the setup of the forcefield, see
# the 'charmm_forcefield_verbose.py' example.
from __future__ import print_function
import IMP.atom
import IMP.container
import sys
IMP.setup_... | shanot/imp | modules/atom/examples/charmm_forcefield.py | Python | gpl-3.0 | 3,076 | [
"CHARMM"
] | 4eab1b2263c4d19344ae7c9ba468d0cc73b0d334b75b5fb1cb149a91b0795591 |
"""
================================
Time-related feature engineering
================================
This notebook introduces different strategies to leverage time-related features
for a bike sharing demand regression task that is highly dependent on business
cycles (days, weeks, months) and yearly season cycles.
I... | shyamalschandra/scikit-learn | examples/applications/plot_cyclical_feature_engineering.py | Python | bsd-3-clause | 31,010 | [
"Gaussian"
] | e2f06d5ca56ed3f7fffd316e65b8947786a599d466f110c44be333eb985e8ca0 |
# Copyright 2009-2012 Ram Rachum.
# This program is distributed under the MIT license.
'''
This module defines number-selecting scripts.
See their documentation for more information.
'''
from __future__ import with_statement
import re
import _ast
import os.path, sys
sys.path += [
os.path.dirname(__file__),
... | cool-RR/cute-wing-stuff | scripts/selecting_numbers.py | Python | mit | 3,069 | [
"VisIt"
] | 5caf89b15c88a3bb589470229e2489a652f8d29484aa84c9993ae2e8c2b791c9 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | michaelrup/scancode-toolkit | tests/extractcode/test_archive.py | Python | apache-2.0 | 121,251 | [
"VisIt"
] | 3ff63d7c199d56d7eb017bb8e81072e65fc9f67946a82b5382204287c1005915 |
from sympy import E as e
from sympy import (Symbol, Abs, exp, expint, S, pi, simplify, Interval, erf, erfc, Ne,
EulerGamma, Eq, log, lowergamma, uppergamma, symbols, sqrt, And,
gamma, beta, Piecewise, Integral, sin, cos, tan, sinh, cosh,
besseli, floor, expand_fu... | kaushik94/sympy | sympy/stats/tests/test_continuous_rv.py | Python | bsd-3-clause | 44,661 | [
"Gaussian"
] | a41750543a74e9ab8d69f34a2e09732de279e36626d3665e1c7e494a3c3737fb |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | daviddesancho/mdtraj | mdtraj/utils/unitcell.py | Python | lgpl-2.1 | 6,899 | [
"MDTraj"
] | ac811877bbb1ea56d6e74445503c9de4a469818174ec0e410cf7a1bd997b38a3 |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.anovaglm import H2OANOVAGLMEstimator
# Simple test to check correct frame transformation
def testFrameTransform():
train = h2o.import_file(path=pyunit_utils.locate("smalldata/anovaGlm/Moore.csv"))
answer = h2o.i... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/anovaglm/pyunit_PUBDEV_8088_transformFrame.py | Python | apache-2.0 | 1,305 | [
"Gaussian"
] | cf0ff3db2bdce4f21d7bc00baa3ed7ac41613519d6312db8bdd8aa8d56d98f54 |
# Copyright 2005 by Jonathan Taylor.
# 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.
import sys
# Add path to Bio
sys.path.append('../..')
"""This module deals with CAPS marke... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/CAPS/__init__.py | Python | gpl-2.0 | 3,889 | [
"Biopython"
] | 7134bd38305c64fcd2aae98d181c61b2122d9d4ae19548a54b02949de0e56477 |
"""Dynamic Imaging of Coherent Sources (DICS)."""
# Authors: Marijn van Vliet <w.m.vanvliet@gmail.com>
# Britta Westner <britta.wstnr@gmail.com>
# Susanna Aro <susanna.aro@aalto.fi>
# Roman Goj <roman.goj@gmail.com>
#
# License: BSD (3-clause)
import numpy as np
from ..utils import (logger,... | adykstra/mne-python | mne/beamformer/_dics.py | Python | bsd-3-clause | 34,894 | [
"NEURON"
] | 0820cf4b7b66b18511edca7dc682400cf764090a61c08778819b16bfcccd7cf5 |
# Copyright (C) 2010 CAMd
# Copyright (C) 2010 Argonne National Laboratory
# Please see the accompanying LICENSE file for further information.
"""Module for high-level BLACS interface.
Usage
=====
A BLACS grid is a logical grid of processors. To use BLACS, first
create a BLACS grid. If comm contains 8 or more ra... | qsnake/gpaw | gpaw/blacs.py | Python | gpl-3.0 | 20,358 | [
"GPAW"
] | e1aca2a1fd4c46738df4fd6c557040a3f4d4537bdd2bd9fcd049dc07f023f8d5 |
#!/usr/bin/python
# http://mcsp.wartburg.edu/zelle/python/graphics.py
# https://mcsp.wartburg.edu/zelle/python/graphics/graphics/index.html
import math
from graphics import *
XSCALE = 2550
YSCALE = 1310
XCENTER = XSCALE / 2
YCENTER = YSCALE / 2
# https://en.wikipedia.org/wiki/Incircle_and_excircles_of_a_triangle#... | jtraver/dev | python/graphics/circles7.py | Python | mit | 24,324 | [
"Amber"
] | df41fff1a3210666eddb11c9333a49305b5c6c2443e8f8d9242345299e2ca3c3 |
# 03.10.2007, c
filename_mesh = 'database/phono/mesh_circ21.mesh'
# Whole domain $Y$.
region_1000 = {
'name' : 'Y',
'select' : 'all',
}
# Domain $Y_1$.
region_1 = {
'name' : 'Y1',
'select' : 'elements of group 1',
}
# Domain $Y_2$.
region_2 = {
'name' : 'Y2',
'select' : 'elements of group 2',... | certik/sfepy | tests/test_lcbc_2d.py | Python | bsd-3-clause | 2,482 | [
"VTK"
] | 412e2709048076eb728e742072c8158ab2aa062881ccf04b50d549b6ea48f731 |
#!/usr/bin/python
# Python conterpart of rsync written by Vivian De Smedt
# Send any comment or bug report to vivian@vdesmedt.com.
# I would like to thanks William Tan for its support in tuning rsync.py to support unicode path.
# I would like to thanks Luc Saffre for its bug reports and fixes.
#from __future__ import... | quanticio/backupstore | backupstore/src/core/common/rsync.py | Python | gpl-2.0 | 19,060 | [
"VisIt"
] | 8d4dc939fd3e2a73f744dae98d2ab69144991b8857df604873e2e39d140a48dd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012-2014 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHO... | mkalewski/sim2net | sim2net/__init__.py | Python | mit | 981 | [
"VisIt"
] | 68c90201602a7133a3285bc9a36c2e04e7a789969fee4b3dad3218a70709def8 |
import pytest
from ispyb.cli import last_data_collections_on
_header = "------Date------ Beamline --DCID-- ---Visit---\n"
def test_basic(capsys, testconfig):
last_data_collections_on.main(["i03", f"--credentials={testconfig}"])
captured = capsys.readouterr()
assert not captured.err
assert captured.o... | DiamondLightSource/ispyb-api | tests/cli/test_last_data_collections_on.py | Python | apache-2.0 | 2,229 | [
"VisIt"
] | 1db1f9386a948ed278ca45c473c76a81c760ac160630383759f36ab4fa6a68c0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | arunkgupta/gramps | gramps/gen/filters/rules/person/_hasassociation.py | Python | gpl-2.0 | 2,577 | [
"Brian"
] | 5d9a930bf603ccd50b42dfde2f3030cc02b236ffb371fd69be33b891623de0cb |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_shortcutseditor.py | Python | gpl-2.0 | 1,162 | [
"VisIt"
] | 544096cdb9675820ee2368c9230a735178241aa2b23c8738c9f1fa59c86f781c |
# setBonusGuristas
#
# Used by:
# Implants named like: grade Crystal (18 of 18)
runTime = "early"
type = "passive"
def handler(fit, implant, context):
fit.appliedImplants.filteredItemMultiply(lambda mod: mod.item.group.name == "Cyberimplant",
"shieldBoostMultiplier", i... | Ebag333/Pyfa | eos/effects/setbonusguristas.py | Python | gpl-3.0 | 370 | [
"CRYSTAL"
] | 2dfb09382598b3f1e0c1eda0ffac2e733031f41c90beb427b072ba37842803eb |
#!/usr/bin/python2
# coding=UTF-8
#
# Samsung-Tools
#
# Part of the 'Linux On My Samsung' project - <http://loms.voria.org>
#
# Copyleft (C) 2010 by
# Fortunato Ventre - <vorione@gmail.com> - <http://www.voria.org>
#
# 'Samsung-Tools' is free software; you can redistribute it and/or modify
# it under the terms of the G... | voria/samsung-tools | samsung-tools.py | Python | gpl-3.0 | 28,993 | [
"VisIt"
] | 83b7d49c55b793cc9381b4ba86a1d65605bff6484e33deaef4d247e75bb8e343 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
res = 6
plane = vtk.vtkPlaneSource()
plane.SetResolution(res,res)
colors = vtk.vtkElevationFilter()
colors.SetInputConnection(plane.GetOutputPort())
colors.SetLowPoint(-0.2... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Programmable/Testing/Python/progGlyphsBySource.py | Python | bsd-3-clause | 2,931 | [
"VTK"
] | 63eefaeb56879efffe889f5c463b1091600b7879d2d76985e125c70493253365 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-gostats/package.py | Python | lgpl-2.1 | 2,181 | [
"Bioconductor"
] | af76ca9b4add81b37edc2028665da41dcfb9a861ab316ad33dcfff5f944c24e4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2016-2017, Konstantin Shalygin <k0ste@k0ste.ru>
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING... | indrajitr/ansible | lib/ansible/modules/find.py | Python | gpl-3.0 | 16,313 | [
"Brian"
] | 0ccef32e9fa6c1c6a7acd02f792f51b37090a21aabf6910a4cffd8e4071d1d09 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, sum, around, unique, asarray,
... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/scipy/stats/morestats.py | Python | gpl-2.0 | 82,400 | [
"Gaussian"
] | e6523048d1035ffcfe6c439996cf2a076f8ae64eb40d554cb8ba1b1c51d45478 |
import sys
sys.path.append('/usr/local/lib/python2.7/dist-packages')
from flask import Flask, jsonify, render_template, request, abort
import nest
import lib.helpers as hh
app = Flask(__name__)
trusted_proxies = ('127.0.0.1','132.230.177.59')
@app.before_request
def limit_remote_addr():
if request.remote_addr ... | babsey/nest-webapp | iaf_neuron.py | Python | mit | 1,747 | [
"NEURON"
] | b1be39f1d22f2c7e21b1dc8454ff84b0d8a936aed5ec0d0de0a4461d806c45c1 |
from aloe import step, world
from aloe_webdriver.util import find_any_field, find_field_by_value
from aloe_webdriver import TEXT_FIELDS
from selenium.common.exceptions import NoSuchElementException
from user.models import UserProfile, CATEGORY, ENGINEERING, Settings
from booking.models import Booking, Place, BookTime, ... | fga-gpp-mds/2016.2-SAS_FGA | sas/sas/steps/steps.py | Python | gpl-3.0 | 8,231 | [
"VisIt"
] | 4bae468d41546aa09a2c53d056b678189bb656bc20f5a29307ead79fd55e635f |
""" Contains unit tests of NetworkAgent module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import sys
import DIRAC.AccountingSystem.Agent.NetworkAgent as module
from mock.mock import MagicMock
__RCSID__ = "$Id$"
MQURI1 = "mq.dirac.... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/Agent/test/Test_NetworkAgent.py | Python | gpl-3.0 | 3,928 | [
"DIRAC"
] | 9237d38d7961ca8ebd894bcf4eaa4d8fa1cfe5a1ed21100a80b414a006be2969 |
#
# Copyright 2016 The BigDL 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 applicable law or agreed to in ... | wzhongyuan/BigDL | pyspark/bigdl/nn/criterion.py | Python | apache-2.0 | 35,190 | [
"Gaussian"
] | d56097baa3540cb854babfafa36c584662e21f20c4696ecb9ea6269e8ef98087 |
""" The CS! (Configuration Service)
"""
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.private.ServiceInterface import ServiceInterface
from DIRAC.Core.DISET.RequestHandler import RequestHandler, getServiceOption
from DIRAC.WorkloadManagementSystem.Utilities.PilotCStoJSONSyn... | hgiemza/DIRAC | ConfigurationSystem/Service/ConfigurationHandler.py | Python | gpl-3.0 | 4,258 | [
"DIRAC"
] | 9e3378d9878787ebf85e15279a6c96131deaa1ef06d6be0fc668752e8df6faad |
from BoloMass.Arnett82 import tau_0, Lambda, A82LC_full, A82LC_gp
from RetroSpect.Plotting import color_ramp
import sys
import numpy as np
import matplotlib.pyplot as pypl
def test_A82_Lambda():
"""Test plots for Lambda"""
y = np.arange(0.7, 1.41, 0.1)
c = color_ramp(len(y))
for yi, ci in zip(y, c):
... | rscalzo/pyBoloSN | Tests/test_A82.py | Python | mit | 3,804 | [
"Gaussian"
] | 650d2aa508c7ae014e5e3d42214f5f401e6445268e69ca1fecea80d2a3b241c9 |
import os
from setuptools import setup, find_packages
import distutils.command.build_py
from ece2cmor3 import __version__
name = "ece2cmor3"
# Utility function to read the README file.
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
# Utility function to get the git hash, po... | goord/ece2cmor3 | setup.py | Python | apache-2.0 | 3,554 | [
"ORCA"
] | 462478c5e541dbbeaeebe1476aea9c279271ddc449a66828a1caab513786d760 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from monty.json import MSONable
from enum import Enum, unique
import numpy as np
"""
This module provides core classes needed by all define electronic structure,
such as the Spin, Orbital, etc.
"""
__author__... | dongsenfo/pymatgen | pymatgen/electronic_structure/core.py | Python | mit | 15,795 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | af14e8e0a0701d8aad7105357aef96012c86487ab8f86c1a10dfd7ff9fa1bce5 |
# coding: utf-8
from __future__ import unicode_literals
import unittest
import os
import json
from io import open
from pymatgen.electronic_structure.bandstructure import Kpoint
from pymatgen import Lattice
from pymatgen.electronic_structure.core import Spin, Orbital
from pymatgen.electronic_structure.bandstructure i... | Dioptas/pymatgen | pymatgen/electronic_structure/tests/test_bandstructure.py | Python | mit | 8,363 | [
"pymatgen"
] | 597b27e6e3e1bd2eb8f97cb2aab5d017ee1cf704610cba60a8fed3160654d713 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from scipy.constants import N_A
from pymatgen.core.periodic_table import Element
from pymatgen.core.units import Charge, Time
from pymatgen.analysis.reaction_calculator import BalancedReaction
from pymatgen.c... | dongsenfo/pymatgen | pymatgen/apps/battery/conversion_battery.py | Python | mit | 20,849 | [
"pymatgen"
] | 0ab9e2c615798ae5eab05cdd1bc7969042670803252556f2df9045b71d58f8e5 |
import gdb
def exit_handler(event):
"""Quit GDB as soon as the program exited. """
# print("Program exited with exit code: %d" % event.exit_code)
# gdb.execute('quit')
gdb.events.exited.connect(exit_handler)
gdb.execute('set pagination off')
gdb.execute('file gzip')
gdb.execute('set args ' + '-cdk test.... | timtian090/Playground | GDB/Experiments/gzip/get_variables.py | Python | mit | 2,482 | [
"CDK"
] | 4cb61f63a66563a53cc49d13334384d2f946f07a79a903af530568bf87141b16 |
# 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/rt/tdscf.py | Python | apache-2.0 | 22,845 | [
"PySCF"
] | b8b13a294a3f1d0baff6078d36bef6b60908147e8ca58fc4e529e4fa5ae8050e |
"""This demo program solves the incompressible Navier-Stokes equations
on an L-shaped domain using Chorin's splitting method."""
# Copyright (C) 2010-2011 Anders Logg
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Publi... | mathstuf/ParaViewCatalystExampleCode | PythonDolfinExample/simulation-catalyst-step6.py | Python | bsd-3-clause | 8,110 | [
"ParaView",
"VTK"
] | c750f04f53ceeae9bb81c55fcdd5a51562e393a5cb89ffa29199078345f5e484 |
import sys
class Node(object):
def children(self):
""" A sequence of all children that are Nodes
"""
pass
def show(self, buf=sys.stdout, offset=0, _my_node_name=None):
""" Pretty print the Node and all its attributes and
children (recursively) to a buffer.
... | dikujepsen/OpenTran | src/framework/lan/lan_ast.py | Python | mit | 17,449 | [
"VisIt"
] | c3a6736c3bc6a23afe18341e50cdaf1a335a3e79f27c04e79a0aa4190ade979d |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_chainreader.py | Python | gpl-2.0 | 6,872 | [
"MDAnalysis"
] | 61b75731a66a12edca907d66e3819da093f04793972071924e448e10edc0d2e2 |
#
# tsne.py
#
# Implementation of t-SNE in Python. The implementation was tested on Python 2.7.10, and it requires a working
# installation of NumPy. The implementation comes with an example on the MNIST dataset. In order to plot the
# results of this example, a working installation of matplotlib is required.
#
# The ... | dedert/Brand2Vec | tsne.py | Python | mit | 5,216 | [
"Gaussian"
] | f8bf19e0bc13a86762d5513b57c04216baab594a4d9d43f4466b79d1ebf77cd3 |
# Author: Artem Pulkin
"""
This and other `proxy` modules implement the time-dependent mean-field procedure using the existing pyscf
implementations as a black box. The main purpose of these modules is to overcome the existing limitations in pyscf
(i.e. real-only orbitals, davidson diagonalizer, incomplete Bloch space... | gkc1000/pyscf | pyscf/pbc/tdscf/kproxy.py | Python | apache-2.0 | 7,386 | [
"PySCF"
] | aaa19fc95b214cb7ca682445a7c3bdc67ec148dd4f7ad24e73fdd87ddbb45b60 |
import os
import pickle
import pylab as pl
from operator import itemgetter
import netcdf
import numpy as np
import sys
from operator import mul
from ncdftools import nccopydimension
from Scientific.IO import NetCDF
from array import array
import struct
def nctypecode(dtype):
# purose: netcdf-typecode from array... | hendrikwout/pynacolada | trash/pynacolada-20131101-2.py | Python | gpl-3.0 | 36,260 | [
"NetCDF"
] | 2fdc7774f88fd76856e728a9cde4037f230690b2fe03f819c8baecbb2b1cbe7f |
#! /usr/bin/env python
import sys, os, re, subprocess
from . import anno_formatter
from . import vcf_formatter
from .fisher_info import FisherInfo
def read_hotspot_file(hotspot_file):
tmp_list = []
hIN = open(hotspot_file, 'r')
for line in hIN:
F = line.rstrip('\n').split('\t')
if len(F[3])... | ken0-1n/GenomonHotspotCall | hotspot_call/process_mutation.py | Python | gpl-3.0 | 5,933 | [
"ADF"
] | 125cf3e1287515409cc7b1b65f1122ebf1af484d18d09ddd0bff5aad76113be3 |
# NeHe Tutorial Lesson: 41 - Volumetric Fog
#
# Ported to PyOpenGL 2.0 by Brian Leair 18 Jan 2004
#
# This code was created by Jeff Molofee 2000
#
# The port was based on the PyOpenGL tutorials and from
# PyOpenGLContext (tests/glprint.py)
#
# If you've found this code useful, feel free to let me know
# at (Brian Lea... | mgood7123/UPM | Sources/PyOpenGL-Demo-3.0.1b1/PyOpenGL-Demo/NeHe/lesson41.py | Python | gpl-3.0 | 13,490 | [
"Brian"
] | a8390ee9211f6d427c7fbce7c09083c33de1200db8a22a77e995716557205c2f |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/ui/InputKeyboard.py | Python | gpl-3.0 | 5,771 | [
"ORCA"
] | f3fc40867f88611625b07936ac1f1d5339d9682342ed24b33970ae2bc2dddafa |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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... | shiwalimohan/RLInfiniteMario | system/codecs/Python/examples/mines-sarsa-example/sample_sarsa_agent.py | Python | gpl-2.0 | 7,076 | [
"Brian"
] | b93b7ce768c8e1632bb38f10cba7674c626a9882f9a4c5f57926c9a2bef59653 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | riverma/climate | ocw/data_source/local.py | Python | apache-2.0 | 13,561 | [
"NetCDF"
] | abbb8da465a2fe18ce9323b392cc314706dde340af8a53e422943832e57a59de |
# (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.
... | Tatsh-ansible/ansible | lib/ansible/plugins/cache/jsonfile.py | Python | gpl-3.0 | 1,679 | [
"Brian"
] | 0cc021b587a4c3e9a4bd52bd2399c3bd152bcc225cfceb63e764a20e512dd7e6 |
# Version: 0.16+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, 3.3, 3.4, 3.5, and pypy
* [![Latest Version]
(https... | geometalab/geoconverter | versioneer.py | Python | mit | 65,737 | [
"Brian"
] | b3862395fff704ef5428fb454ecbbc8b02bfa24468d6ce4260712d20e85cea4e |
# Demonstrates pseudo-likelihood estimation
# for a large system of continuous variables
from plmrf import *
import numpy as np
import scipy
import time
# Generating a big ring by sampling variables independently,
# then sampling based on each configuration's 'true' potential
nvars = 1000
nsamp = 1000
print("Gene... | dgarant/pl-markov-network | examples/large_non_gaussian.py | Python | mit | 2,076 | [
"Gaussian"
] | d423aa2c9ce9279e2589bcea713e68da7daf0b5048833642a233f20e12eab264 |
#===============================================================================
# LICENSE Bartsidee Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported L... | bartsidee/bartsidee-boxee | sources/podcast/libs/ba.py | Python | gpl-3.0 | 4,003 | [
"VisIt"
] | 558d4fe6a41aa5d4b4edd5119d4dafef93d4ed89b6cb151f360a1bee646e791c |
'''module to provide git integration with jasp.
The intent is to provide a hook function that puts a vasp directory
under version control and commits changes to the repository
things to do:
1. figure out how to specify the git repository you want, or have the
CWD as the default directory.
2. figure out how to get ... | jkitchin/jasp | jasp/vc/vgit.py | Python | gpl-2.0 | 1,195 | [
"VASP"
] | 226a3902e460f030a9df67c70199934d892b28286bd03d702f36086ffa936aa1 |
import enum
import inspect
import pydoc
import unittest
from collections import OrderedDict
from enum import Enum, IntEnum, EnumMeta, unique
from io import StringIO
from pickle import dumps, loads, PicklingError, HIGHEST_PROTOCOL
# for pickle tests
try:
class Stooges(Enum):
LARRY = 1
CURLY = 2
... | michalliu/OpenWrt-Firefly-Libraries | staging_dir/target-mipsel_1004kc+dsp_uClibc-0.9.33.2/usr/lib/python3.4/test/test_enum.py | Python | gpl-2.0 | 57,132 | [
"MOE"
] | 70731b0fc8928da4cebe93461f8a8984a68290846c669d58dcd4057e647454d5 |
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