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#
# The Python Imaging Library.
# $Id$
#
# the Image class wrapper
#
# partial release history:
# 1995-09-09 fl Created
# 1996-03-11 fl PIL release 0.0 (proof of concept)
# 1996-04-30 fl PIL release 0.1b1
# 1999-07-28 fl PIL release 1.0 final
# 2000-06-07 fl PIL release 1.1
# 2000-10-20 fl PIL release 1.1.1... | sauloal/cnidaria | scripts/venv/lib/python2.7/site-packages/PIL/Image.py | Python | mit | 80,659 | [
"Gaussian"
] | 3b50f1c0056aa03072a962bd30b1234e592304f7507cbae3e97fc6ca7a6aac57 |
import re
import sys
from ez_setup import use_setuptools
MIN_SETUPTOOLS_VERSION = "0.7"
use_setuptools(version=MIN_SETUPTOOLS_VERSION)
from setuptools import setup
# Following the recommendations of PEP 396 we parse the version number
# out of the module.
def parseVersion(moduleFile):
"""
Parses the version ... | jeromekelleher/server | setup.py | Python | apache-2.0 | 1,966 | [
"pysam"
] | 11a1e1bbd813adc6fd0aea813f5adfc03b4a170b26ccbd52ce4d0b80a556e749 |
# coding=UTF-8
#
# Copyright 2017 Google Inc. 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 ap... | googlei18n/glyphsLib | tests/builder/designspace_gen_test.py | Python | apache-2.0 | 11,549 | [
"VisIt"
] | b3bf2f72df50d7af317b472143c8d2529483e4c47e8e194627878d9f65cc0d6a |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Peek StdOut of the given DIRAC job
Example:
$ dirac-wms-job-peek 1
"""
import DIRAC
... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_peek.py | Python | gpl-3.0 | 1,043 | [
"DIRAC"
] | 305d33106b9c1a35a6293dbe8a6b35872d7ef4100d687edde777e97c63abe2c9 |
#
# Copyright (C) 2015-2021 University of Oxford
#
# This file is part of msprime.
#
# msprime 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... | jeromekelleher/msprime | tests/test_lowlevel.py | Python | gpl-3.0 | 111,628 | [
"DIRAC"
] | 9da5b7ab54a869249e7158ddc5fff92d6736486b54c5857a6e3a66d276137195 |
# Author: Tom Furnival
# License: GPLv3
import numpy as np
from ._pguresvt import pguresvt_d, pguresvt_f, pguresvt_u8, pguresvt_u16
def _is_power_of_two(n):
"""Checks if n is a power of 2"""
return (n & (n - 1) == 0) and n != 0
def mixed_noise_model(X, alpha=1.0, mu=0.0, sigma=0.0, random_state=None):
... | tjof2/pgure-svt | pguresvt/svt.py | Python | gpl-3.0 | 12,261 | [
"Gaussian"
] | fcd972e5aad99c2cc4d1d9616b33151bb4dc8ce39cf768ca058119d9d11b0b74 |
#!/usr/bin/env python
import gzip
import json
import optparse
import os
import os.path
import re
import shutil
import sys
import urllib
import zipfile
from pysam import ctabix
"""
# Install dbNSFP databases
# from DbNsfp site
# Download dbNSFP database
$ wget ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFPv... | yhoogstrate/tools-iuc | data_managers/data_manager_snpsift_dbnsfp/data_manager/data_manager_snpsift_dbnsfp.py | Python | mit | 7,885 | [
"pysam"
] | 9f90ef5b7f86a6a422e4b1c83523618760a8b58f59a01f7b4964d19f5f2235c2 |
# Copyright 2021, The TensorFlow 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | tensorflow/privacy | tensorflow_privacy/privacy/analysis/dp_event.py | Python | apache-2.0 | 8,487 | [
"Gaussian"
] | 80ee4bc93d196e6dc1b287fcc75c2a3fb19980ffa200fac17c2bbbf13ec684c4 |
"""
.. _tut_forward:
Head model and forward computation
==================================
The aim of this tutorial is to be a getting started for forward
computation.
For more extensive details and presentation of the general
concepts for forward modeling. See :ref:`ch_forward`.
"""
import mne
from mne.datasets i... | nicproulx/mne-python | tutorials/plot_forward.py | Python | bsd-3-clause | 7,399 | [
"Mayavi"
] | 1ae6238b8df5cf7d5eb954149351335b17cf81ac3e30588581fd00d202e31a35 |
"""
Module for the UngriddedData class
"""
import logging
from time import gmtime, strftime
import numpy
import six
from cis.data_io.netcdf import get_data as netcdf_get_data
from cis.data_io.hdf_vd import get_data as hdf_vd_get_data
from cis.data_io.hdf_sd import get_data as hdf_sd_get_data
from cis.data_io.commo... | zak-k/cis | cis/data_io/ungridded_data.py | Python | gpl-3.0 | 36,075 | [
"NetCDF"
] | 8dd46dbde6be455d2c16fbcc0690cf320c90f8d1fcceb328da73e467596c4675 |
from typing import Any, DefaultDict, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr, Callable, Iterable
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import QuerySet, F
from django... | mahim97/zulip | zerver/models.py | Python | apache-2.0 | 81,187 | [
"VisIt"
] | e754cf332c437530b29d8fce3f26bb41364d0d8f9ed17f60af680193a4bbf0db |
"""
Simulating Periodic Signals
===========================
Simulate periodic, or oscillatory, signals.
This tutorial covers the ``neurodsp.sim.periodic`` module.
"""
###################################################################################################
# sphinx_gallery_thumbnail_number = 1
# Import s... | voytekresearch/neurodsp | tutorials/sim/plot_SimulatePeriodic.py | Python | apache-2.0 | 6,799 | [
"Gaussian"
] | a875d0cacf0c0c9d2024a9690f4d6eac14a07dba0035ebea311ebb1291844fb7 |
#!/usr/bin/env python
"""Script to run all the tests.
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008-2015, Prabhu Ramachandran
# License: BSD Style.
import sys
import os
from os.path import splitext
import glob
from common import TestCase
def get_tests():
"""Get all th... | dmsurti/mayavi | integrationtests/mayavi/run.py | Python | bsd-3-clause | 2,512 | [
"Mayavi"
] | 0fb99800ce7bed7075fd643ac6ad0bb5b3645b111682c9ccb607bd82a6dc3db8 |
# ----------------------------------------------------------------------------
# Copyright 2014 Nervana Systems Inc. All rights reserved.
# ----------------------------------------------------------------------------
import os
import ctypes as ct
import ctypes.util
from ctypes import pythonapi
import numpy as np
MAX... | NervanaSystems/cuda-convnet2 | cudanet/cudanet.py | Python | apache-2.0 | 69,815 | [
"Gaussian"
] | 27cb7b5f1322e007f49731f62ac8128ae15d16ef258a03b14a6ae32b1ecfd027 |
'''getting started with diffusions, continuous time stochastic processes
Author: josef-pktd
License: BSD
References
----------
An Algorithmic Introduction to Numerical Simulation of Stochastic Differential
Equations
Author(s): Desmond J. Higham
Source: SIAM Review, Vol. 43, No. 3 (Sep., 2001), pp. 525-546
Published... | bashtage/statsmodels | statsmodels/sandbox/tsa/diffusion.py | Python | bsd-3-clause | 18,750 | [
"Desmond"
] | 17b38afccef78690f5b62779c239a8aa6ec6966feb993567b3cd3d13766244b5 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/MooseDocs/test/common/test_project_find.py | Python | lgpl-2.1 | 1,007 | [
"MOOSE"
] | 0bf636f2b48e2811ae7ffbe3dd747e32904c70b7b7a0149b1e5c22f3c1101dce |
import functools
from itertools import product
import numpy as np
from scipy.stats import norm as ndist
from scipy.optimize import bisect
from regreg.affine import power_L
import regreg.api as rr
from .selective_MLE_utils import solve_barrier_affine as solve_barrier_affine_C
from ..distributions.api import discrete... | selective-inference/selective-inference | selectinf/randomized/query.py | Python | bsd-3-clause | 59,267 | [
"Gaussian"
] | b7b0da8eedd4b20a87f64a298a01e8a6438132e0cbf427f1173a2c385448f1ab |
# Copyright 2018 Google Inc. 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 applicable law or a... | tensorflow/transform | tensorflow_transform/nodes.py | Python | apache-2.0 | 12,912 | [
"VisIt"
] | 548b2c5442025c39a788a09805a735a2c8fa7dc18dd6917168ea7f87d909211f |
#
# @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 ... | andysim/psi4 | psi4/driver/p4util/exceptions.py | Python | gpl-2.0 | 5,625 | [
"Psi4"
] | 8cb61c91c45280c16ba7238a4d0a4c807506ea70d7ef561835d4a3e52f8850eb |
'''This package controls the views generated for the proteins app'''
from urllib import urlencode
from urllib2 import urlopen
import json
from django.shortcuts import render_to_response, get_object_or_404
from django.http import HttpResponse, Http404
from reagents.models import Antibody, Construct, Primer
from djang... | davebridges/ExperimentDB | proteins/views.py | Python | bsd-3-clause | 5,418 | [
"Biopython"
] | c220a2c62cf11ebf5b4a587051fdb828f77e77f9d84b8f951fecb3e14325ffdc |
from __future__ import annotations
import logging
from libtbx.phil import parse
from dials.util import show_mail_handle_errors
logger = logging.getLogger("dials.command_line.create_profile_model")
help_message = """
This program computes the profile model from the input reflections. It then
saves a modified model... | dials/dials | command_line/create_profile_model.py | Python | bsd-3-clause | 8,173 | [
"CRYSTAL"
] | ddcd9da293fc4179b2a92a95171aa843013ea09643b82306580ca2a53397a72d |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-2010 Tiny SPRL (<http://tiny.be>).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU... | inovtec-solutions/OpenERP | openerp/addons/account/wizard/__init__.py | Python | agpl-3.0 | 2,311 | [
"MOE"
] | a43a2c98961ca2f0fbdbe770cc91184776582687c4916ca3c2baf3deea763c45 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5.... | nuclear-wizard/moose | python/peacock/PeacockApp.py | Python | lgpl-2.1 | 4,352 | [
"MOOSE"
] | d8d1d1a35d2c4b48053ea4a9f5976db3435f88705f17cb43be2a80208b693216 |
"""Developed using https://github.com/hachepunto/adj2cytoscape and http://stackoverflow.com/questions/17099458/python-convert-a-matrix-to-edge-list-long-form """
"""The matrix must be in a csv and the first row and collumn must include: null, (including the comma). """
"""To run it in the console. $python matrix2map.... | jmsiqueiros/data_tools | matrix2map.py | Python | gpl-3.0 | 901 | [
"Cytoscape"
] | c942d92090ecfbc53f77b4c0564020b8e37d55c04f9dd3cda1cf24219e6fe345 |
# Kevin van Rensburg 11/10/2021
# Copyright 2001
# Testing Startup Script version 0.17
# kstart1.py
# Working on Kvep8.
# added def's ALL(), ALI(), COMCODE(), core(), cipl() and AnotherCode().
# fixed and added scipt to Kvep8 and relevant def's
import sys
import os
import random
from time import sleep
#import Kendy11... | kurg/KendyVerse | kstart17.py | Python | gpl-3.0 | 80,896 | [
"BLAST"
] | ac778c775e4bedde16c29c8ac681a6e72a9b87c54db1e0cfecdbd2749ac413ef |
#####################################################################
# #
# Remodel NCS copies of protein to a template model #
# and average map #
# ... | mifit/miexpert | mi_ncsmodeler.py | Python | gpl-3.0 | 49,028 | [
"CRYSTAL"
] | f10efbe6c69369666ae2ff9e209cc48a590e5a6d4bef60f26072db26298f585d |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | alexlo03/ansible | lib/ansible/modules/network/avi/avi_autoscalelaunchconfig.py | Python | gpl-3.0 | 4,476 | [
"VisIt"
] | 04408734bec9bf99fdd2db87371471721ca592da4142f0e47bc6d70645e38d73 |
#!/bin/env python3
# AUTHORS:
# Hakan Ozadam
#
# Moore Laboratory
# UMASS Medical School / HHMI
# RNA Therapeutics Institute
# Albert Sherman Center, ASC4-1009
# 368 Plantation Street
# Worcester, MA 01605
# USA
#
#################################################... | hakanozadam/bal | bal/bin/scripts/filter_general_from_sam.py | Python | gpl-2.0 | 4,574 | [
"pysam"
] | 5b032c368928ecb648d84a6af130734ddbfa02929ed457e2fa667d124487de68 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python 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)
# ... | crs4/blast-python | BlastPython/fasta_stream.py | Python | gpl-3.0 | 917 | [
"BLAST"
] | ada35dd35c3da1f17ee781a8e1606bb7cb7b1d4c67338f634c9d20e0b881cb38 |
import moose
print(( 'Using moose form %s' % moose.__file__ ))
def main():
solver = "gssa"
moose.Neutral('/model')
moose.CubeMesh('/model/kinetics')
moose.Pool('/model/kinetics/A')
#delete if exists
if ( moose.exists( 'model/kinetics/stoich' ) ):
moose.delete( '/model/kinetics/st... | subhacom/moose-core | tests/issues/issue_124.py | Python | gpl-3.0 | 866 | [
"MOOSE"
] | 5ba681ab19534fdcbcecf55342b787d13aef0b783fab23a46418b3de8b55d3ec |
#
# 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 ... | intel-analytics/BigDL | python/orca/example/tfpark/estimator/estimator_inception.py | Python | apache-2.0 | 5,334 | [
"ORCA"
] | df673406889b7e0249b75fce8b587933a318390be569f17f4b828db1d45b8c5f |
#!/usr/bin/env python3
# Utility for detecting and fixing whitespace issues in LAMMPS
#
# Written by Richard Berger (Temple University)
import os
import sys
import glob
import re
import yaml
import argparse
import shutil
DEFAULT_CONFIG = """
recursive: true
include:
- cmake/**
- doc
- doc/src/**
- pyth... | rbberger/lammps | tools/coding_standard/whitespace.py | Python | gpl-2.0 | 4,098 | [
"LAMMPS"
] | 45ddcd1e7e0aee18b8807b3e7466e7723dac1cb98760db3979c18b4ac5134ada |
from behave import *
from django.db.models import Q
use_step_matcher('parse')
@given('Exist a bet created by "{username}"')
def step_impl(context, username):
from sportsBetting.models import Bet
from sportsBetting.models import Event
from django.contrib.auth.models import User
for row in context.tab... | Marcelpv96/SITWprac2017 | sportsBetting/features/steps/register_bets.py | Python | gpl-3.0 | 1,224 | [
"VisIt"
] | bc80fd53fdb42650812c645d0a7b5c8109f66595db3bafd97d3a36dab815ef5a |
""" NotificationDB class is a front-end to the Notifications database
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import time
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.Mail import Mail
from DIRAC... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/DB/NotificationDB.py | Python | gpl-3.0 | 33,070 | [
"DIRAC"
] | d2591175a81b27840ecab9fff4f2da9e7711092aa6c7e066f1724f0d071edb83 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 Google Inc.
#
# 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 ... | riannucci/rietveldv2 | upload.py | Python | apache-2.0 | 99,595 | [
"VisIt"
] | f8efdb33aa998f4e2f6ff95365c262b35f6399417ad7fdd3dfb4b35d0a69163a |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'NeuronEphysSummary'
db.create_table('neuroelectro_neuronephyssummary', (
... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0031_auto__add_neuronephyssummary__add_field_ephyspropsummary_value_mean_ne.py | Python | gpl-2.0 | 22,878 | [
"NEURON"
] | d96cac02328fff37e1e8da865ee6c01d022fd6cb2e649bfdc1cae28927245852 |
# MIT License
#
# Copyright (c) 2017, Stefan Webb. All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to us... | stefanwebb/tensorflow-models | tensorflow_models/models/vae_beta_obs.py | Python | mit | 5,548 | [
"Gaussian"
] | 8f2996f338c2d098cec8f715405d3dd7a7d8e221eac2b4c674675419d3fa9084 |
#pylint: disable=C0111
#pylint: disable=W0621
from lettuce import world
import time
import platform
from urllib import quote_plus
from selenium.common.exceptions import WebDriverException, StaleElementReferenceException
from selenium.webdriver.support import expected_conditions as EC
from selenium.webdriver.common.by ... | wwj718/edx-video | common/djangoapps/terrain/ui_helpers.py | Python | agpl-3.0 | 8,213 | [
"VisIt"
] | 7ea62ca9ad523a08a2021998b6329b226e2e0e4c39b1318173a470cfe65bd0d0 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/images/lib/mediaitem.py | Python | gpl-2.0 | 34,551 | [
"Brian"
] | 1279ae42b01820fe4b746c99aebb8fb9a0a0bc045896dcfe1cc2028060bf4cd1 |
import argparse
parser = argparse.ArgumentParser(description="e.g. python kinect_drive_and_reach.py green_table cd --interactive")
parser.add_argument("scene_name")
parser.add_argument("geom_type", choices=["mesh","cd","spheres", "boxes"])
parser.add_argument("--interactive", action="store_true")
args = parser.parse_ar... | DeadSocks/trajopt | python_examples/kinect_drive_and_reach.py | Python | bsd-2-clause | 5,777 | [
"VTK"
] | 9137283d2937c0935e40be9bdd01f7755ff01d776d3bdbb7a5ef209688627a70 |
#!/usr/bin/env python
"""
Copyright (c) 2006-2016 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
class PRIORITY:
LOWEST = -100
LOWER = -50
LOW = -10
NORMAL = 0
HIGH = 10
HIGHER = 50
HIGHEST = 100
class SORT_ORDER:
FIRST = 0
SECOND = 1
... | glaudsonml/kurgan-ai | tools/sqlmap/lib/core/enums.py | Python | apache-2.0 | 9,630 | [
"Galaxy"
] | ea81e426758aa5a93494675b2de26867177ef4fe9a758403bd8de41db337c264 |
"""STIX 2.0 Common Data Types and Properties."""
from collections import OrderedDict
import copy
from ..custom import _custom_marking_builder
from ..markings import _MarkingsMixin
from ..markings.utils import check_tlp_marking
from ..properties import (
HashesProperty, IDProperty, ListProperty, Property, Referenc... | oasis-open/cti-python-stix2 | stix2/v20/common.py | Python | bsd-3-clause | 7,894 | [
"Amber"
] | bc0f44c27fca22e6677c426e42e6f0fe0f67003527843f3303be65a324788fe0 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import numpy as np
import os
import os.path as op
from scipy import sparse, linalg
from copy import deepcopy
from .io.constants import FIFF
from .io.tree import dir... | lorenzo-desantis/mne-python | mne/source_space.py | Python | bsd-3-clause | 92,126 | [
"Mayavi"
] | 1d237fb2d5d86a39d80d6b786443107fbda9adc936a4df1d5fab5c7ad85c5d8f |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
# Set the background color.
colors.SetColor("BkgColor", [51, 77, 102, 255])
sphere = vtk.vtkSphere()
# Sample the function
sample = vtk.vtkSampleFunction()
sample.SetSampleDimensions(50,50,50)
sample.SetImpl... | lorensen/VTKExamples | src/Python/ImplicitFunctions/ImplicitSphere.py | Python | apache-2.0 | 1,399 | [
"VTK"
] | cb4faeec3cf751c1a1fd2834a51a91a40ded5464e4b21c728f97dbc16c4eccaa |
"""
A couple of auxiliary functions
"""
import numpy as np
def sidekick(w1, w2, dt, T, A=1):
"""
This function crates the sidekick time series provided
the two mixing frequencies w1, w2, the time resolution dt
and the total time T.
returns the expresion A * (cos(w1 * t) + cos(w2 * t))
where t... | h-mayorquin/time_series_basic | signals/aux_functions.py | Python | bsd-3-clause | 2,499 | [
"Gaussian"
] | 9ddb2928f41d9cea2e8104cefe53792936009a03c8d9f9fe09e0e9a3c438f04f |
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/df/test/test_df_jk.py | Python | apache-2.0 | 6,888 | [
"PySCF"
] | 20396da8cadca0bc53d694f677bf5c00a6dc2c0d38682e2486ead61d06600b00 |
# coding: utf-8
import sys
sys.path.append("D:\\projects\\visual\\")
from mmdlab.datareader import readfile_metgas_boxes
from mmdlab.utils import init_mlab_scene
import glob
from mayavi import mlab
from tvtk.api import tvtk
init_mlab_scene((200,768))
fc = 1500
rot_per_frame = 20
files = glob.glob(s... | detorto/mdvis | src/temperature_volume.py | Python | mit | 3,362 | [
"Mayavi"
] | c070fdb5f45507e87c3834494fad1b4f9fea8ed2b0dee3134bd9f4b820603baf |
# encoding: utf-8
# 2009 © Václav Šmilauer <eudoxos@arcig.cz>
"""
Module for 2d postprocessing, containing classes to project points from 3d to 2d in various ways,
providing basic but flexible framework for extracting arbitrary scalar values from particles/contacts
and plotting the results. There are 2 basic components... | woodem/woo | py/post2d.py | Python | gpl-2.0 | 18,056 | [
"Gaussian"
] | cf0fe162b6e667a8fdabf9f78e93619accffb61cf678047062e495d07f4af461 |
"""
samfiles_to_sqlite.py
by Fred Ross, <madhadron@gmail.com>
Load a list of SAM/BAM files into an SQLite database as a group,
calculating their leftsite depth on each transcript and the
multiplicities. The resulting database is ready to be handed to
find_subproblems.py and to inference.py, both of which will treat i... | madhadron/rnaseq | bin/samfiles_to_sqlite.py | Python | gpl-3.0 | 4,053 | [
"pysam"
] | 22055685db854a5f46dc28390353c395acd2adb55b6bdfc4edd304474c2998eb |
import time
import datetime
from pymouse import PyMouse
from pykeyboard import PyKeyboard
m = PyMouse()
k = PyKeyboard()
#POSITION DEFINITIONS
pagetop = (679, 40)
chromecast_button = (1314, 75)
stop_button = (1182, 216)
chromecasts = [(1150, 142), (1150, 182), (1130, 230)]
print("================= Welcome to Club Hu... | imsa-clubhub/imsa-clubhub.github.io | present/meta/clubhubassure.py | Python | lgpl-3.0 | 2,415 | [
"MOE"
] | d52be40861ef9ca8758194e54fc5f5242e59fa7c329063b31f5341135ee77a5d |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
ExtractorError,
unsmuggle_url,
)
from ..compat import (
compat_parse_qs,
compat_urlparse,
)
class SenateISVPIE(InfoExtractor):
_COMM_MAP = [
['ag', '76440', 'http://ag... | daeseokyoun/youtube-dl | youtube_dl/extractor/senateisvp.py | Python | unlicense | 6,267 | [
"EPW"
] | 8229648e1370907da8ed272efc0d76cc3c77f1c2cff75b571235948e240dc683 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Perform fragmentation of molecules.
"""
import copy
import logging
from monty.json import MSONable
from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError
from pymatgen.analysis.local_env ... | gmatteo/pymatgen | pymatgen/analysis/fragmenter.py | Python | mit | 17,596 | [
"pymatgen"
] | 74184733cc45d877bc0d2aa6fe75d203731a1b7d610b2c493e9548d81005e4b2 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | omwomotieno/tunza_v2 | config/urls.py | Python | mit | 1,796 | [
"VisIt"
] | d49475bd54b47c78dd951b4a9d51fb9c8ea64cb973fc0b477eb3de0408e3a88b |
import numpy as np
from . import _algorithm
from spotpy.parameter import ParameterSet
class DDSGenerator:
"""
This class is used by the DDS algorithm to generate a new sample of parameters based on the current one.
Current parameter are exchanged in `ParameterSet` objects.
"""
def __init_... | bees4ever/spotpy | spotpy/algorithms/dds.py | Python | mit | 19,835 | [
"Gaussian"
] | 7389fe4ae18faed1b6d4e4d66623144a457026108adbb26f58df806285eef30c |
"""
Testing the FileCatalog logic
"""
import sys
import unittest
import mock
import DIRAC
from DIRAC.Resources.Catalog.FileCatalog import FileCatalog
from DIRAC import S_OK, S_ERROR
__RCSID__ = "$Id $"
current_module = sys.modules[__name__]
class GenericCatalog( object ):
""" Dummy catalog """
def __init_... | andresailer/DIRAC | Resources/Catalog/test/Test_FileCatalog.py | Python | gpl-3.0 | 16,054 | [
"DIRAC"
] | 19a0def53283b91fc52bc34e03bd0b517382bdd56d011cf59855045b1fc745da |
#!/usr/bin/env python
import os
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
... | timkrentz/SunTracker | IMU/VTK-6.2.0/Filters/Core/Testing/Python/fieldToSGrid.py | Python | mit | 4,290 | [
"VTK"
] | a511a1723a51d601a86133bb7401f91d16b50c5f5bf31aca03a3b44e6382e413 |
"""
This module provides classes to declare, play and plot auditory scene populated by elements in the (time, frequency) domain
The scene is organized as a tree with Leaves as atom elements of the scene.
The tree offers a way to group atoms, and make group of groups etc...
This is useful:
- to declare structured... | vincentadam87/time_freq_auditory_scene | TimeFreqAuditoryScene.py | Python | bsd-3-clause | 37,100 | [
"Gaussian"
] | e325166369780e3a431f21d59c22f5f0c2f1e3ab2d28e178be409919bf0aa358 |
# coding: utf-8
from __future__ import unicode_literals, division
import time
"""
This module implements error handlers for QChem runs. Currently tested only
for B3LYP DFT jobs.
"""
import copy
import glob
import json
import logging
import os
import re
import tarfile
from pymatgen.core.structure import Molecule
from... | davidwaroquiers/custodian | custodian/qchem/handlers.py | Python | mit | 24,105 | [
"pymatgen"
] | 68afc28dbe1b8952981adf2f261c336203a98cca80690c642dd88c86ef7e081f |
# ======================================================================
# USER-GFMD - Elastic half-space methods for LAMMPS
# https://github.com/Atomistica/user-gfmd
#
# Copyright (2011-2016,2021)
# Lars Pastewka <lars.pastewka@imtek.uni-freiburg>,
# Tristan A. Sharp and others.
# See the AUTHORS file in the top... | Atomistica/user-gfmd | tests/TEST_Hertz_nonperiodic_64x64/eval.py | Python | gpl-2.0 | 2,244 | [
"LAMMPS"
] | e21ebffeeeb172b1dd95a9b3ed66f4992f98964b9e5681dd8dcdb960786597db |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham, A. Roitman
# Copyright (C) 2007-2009 B. Malengier
# Copyright (C) 2008 Lukasz Rymarczyk
# Copyright (C) 2008 Raphael Ackermann
# Copyright (C) 2008 Brian G. Matherly
# Copyright... | SNoiraud/gramps | gramps/cli/argparser.py | Python | gpl-2.0 | 23,180 | [
"Brian"
] | 75541299f9fe24221ec806616cfa8cb54fd1046d3b4db16497e87cac32f4c32d |
#!/usr/bin/env python
import os
import sys
import pysam
def usage():
return 'usage: %s </path/to/TEBreak directory> <tabular output from resolve.py>' % sys.argv[0]
def avgmap(maptabix, chrom, start, end):
''' return average mappability across chrom:start-end region; maptabix = pysam.Tabixfile'''
scores... | ValentinaPeona/tebreak | scripts/filter_refgene.py | Python | mit | 3,307 | [
"pysam"
] | c4acbbe350122e684be68c4541accef877b65b0d71a1574a1886bfa56a5051b3 |
# Copyright (c) 2012 - N.P. de Klein
#
# This file is part of Python Mass Spec Analyzer (PyMSA).
#
# Python Mass Spec Analyzer (PyMSA) 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 ver... | davidmam/pyMSA | example_scripts/filling_database_mysql.py | Python | gpl-3.0 | 9,237 | [
"OpenMS"
] | 17f4645143a140690d87193e3277677e4f859717167b943aa83ecccfde1253b2 |
# -*- 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/download/RepEntry.py | Python | gpl-3.0 | 6,086 | [
"ORCA"
] | 903243b2483b64aefaf06a794ca08677959dbf3a077571ca27376aaa190b5e3c |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyPipits(PythonPackage):
"""Automated pipeline for analyses of fungal ITS from the Illumin... | LLNL/spack | var/spack/repos/builtin/packages/py-pipits/package.py | Python | lgpl-2.1 | 3,013 | [
"Bioconda"
] | d52fbcef9cbf5901d466409c22d3f36e8a0ca5ddce9d081043c63f98472b0f9c |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
From a set of regions and two sets of intervals inside those regions
compute (for each region separately) the overlap between the two sets
of intervals and the overlap in `nsamples` random coverings of the
regions with intervals having the same lengths. Prints the z-score ... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/bed_rand_intersect.py | Python | bsd-3-clause | 5,896 | [
"Galaxy"
] | c23a601c5de4b9194558b788cab2feb517d486587e56742c7527aab1a438000d |
#!/usr/bin/env python
""" Get a proxy from the proxy manager
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import os
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
Script.setUsageMessage(
"\n".join(
[
__doc_... | ic-hep/DIRAC | tests/Jenkins/dirac-proxy-download.py | Python | gpl-3.0 | 1,202 | [
"DIRAC"
] | 2dac0a526fb6ae591dc3a272aff81cb0052c7feb36a7c328d4d94a7709711e03 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# SpectralClustering.py
#
# Copyright 2014 Carlos "casep" Sepulveda <casep@alumnos.inf.utfsm.cl>
#
# 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 Fo... | creyesp/RF_Estimation | Clustering/clustering/gmm.py | Python | gpl-2.0 | 6,063 | [
"Gaussian"
] | b2ec9a78002fa7349b77c32482452b1b230346e5ee284466d420a837031ef3a8 |
#!/usr/bin/env python
import os
# WE RELY ON THESE BEING SET !!!
# set default verbose level
# verbose = os.environ.get('RADICAL_PILOT_VERBOSE', 'REPORT')
# os.environ['RADICAL_PILOT_VERBOSE'] = verbose
# set default URL to IMP Mongo DB
# path_to_db = os.environ.get(
# 'RADICAL_PILOT_DBURL', "mongodb://ensemble... | jrossyra/adaptivemd | examples/tutorial/test_setconda.py | Python | lgpl-2.1 | 2,664 | [
"OpenMM"
] | e201325a9f751f71e839125c7b346f6a07252d5581efcf1395391819ee395c1e |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_v1p0.py | Python | gpl-3.0 | 2,428 | [
"VTK"
] | c0eb30b11037fcc980e11163135cad203b6d0a68e810063a41db005747b04681 |
"""
A script to calculate the projection of 3D world coordinates to
2D display coordinates (pixel coordinates) for a given scene.
The 2D pixel locations of objects in the image plane are related to their
3D world coordinates by a series of linear transformations. The specific
transformations fall under the group known... | liulion/mayavi | docs/source/mayavi/auto/mlab_3D_to_2D.py | Python | bsd-3-clause | 11,050 | [
"Mayavi",
"VTK"
] | 4439c46a6855c5b60682be01ca46e937238b48323269690a636d3e69f51714ee |
# $HeadURL$
"""
DIRAC - Distributed Infrastructure with Remote Agent Control
The LHCb distributed data production and analysis system.
DIRAC is a software framework for distributed computing which
allows to integrate various computing resources in a single
system. At the same time it integrates all kin... | calancha/DIRAC | __init__.py | Python | gpl-3.0 | 4,852 | [
"DIRAC"
] | c3748f9e71a96e16765bdc19a8e023c51ee9243f82f2154bdbf4ca4fbefe7a8e |
#!/usr/bin/env python
#
# $File: demoFunc1.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute ... | BoPeng/simuPOP | docs/demoFunc1.py | Python | gpl-2.0 | 1,469 | [
"VisIt"
] | fe562d135f9e6b96aaa83252b27a80e26b8fdb1a5bc9e05247f391bc1a88c65d |
'''
Created on Aug 11, 2014
@author: luamct
Some later empirical experiments showed that this metric performs
poorly to more general cases to assess the rule of thirds.
We are currently working on improvements.
'''
import numpy as np
import utils.image
import pyublas # @UnusedImport
from sharpness... | luamct/WebSci14 | features/composition/thirds.py | Python | gpl-3.0 | 1,784 | [
"Gaussian"
] | a0fe83ac893b769a125577d365b3906bb610dd98b670b970bf93c402e101eef5 |
from __future__ import print_function
import numpy as np
import cv2
import tensorflow as tf
import sys
import os
sys.path.append('./agent')
sys.path.append('./deep_feedback_learning')
from agent.doom_simulator import DoomSimulator
from agent.agent import Agent
import deep_feedback_learning
from deep_feedback_learning i... | nlholdem/icodoom | ICO1/run_agentDFL.py | Python | gpl-3.0 | 19,681 | [
"NEURON"
] | 89472612a945c998641818e8a7fb636428f3cb52451ca9e66efb05f7aa18dac9 |
#!/usr/bin/env python
#
# Copyright (c) 2010-2012 Appcelerator, Inc. All Rights Reserved.
# Licensed under the Apache Public License (version 2)
#
# parse out Titanium API documentation templates into a
# format that can be used by other documentation generators
# such as PDF, etc.
import os, sys, traceback
import re,... | hieupham007/Titanium_Mobile | apidoc/docgen.py | Python | apache-2.0 | 23,340 | [
"VisIt"
] | c591dc9493aecbe65a8f07e2df5f7b37f59a12a8cabc9ba8c5f921b9857120f3 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
"... | zwChan/VATEC | ~/eb-virt/Lib/site-packages/setuptools/command/easy_install.py | Python | apache-2.0 | 85,945 | [
"VisIt"
] | a922a0e8867e5d1737f585fe040b7dc646a7d84e491df3144595859d3e5b014a |
# disable missing docstring
# pylint: disable=missing-docstring
import json
from lettuce import step, world
from nose.tools import assert_equal, assert_true
from advanced_settings import ADVANCED_MODULES_KEY, change_value
from common import open_new_course, type_in_codemirror
from course_import import import_file
D... | Stanford-Online/edx-platform | cms/djangoapps/contentstore/features/problem-editor.py | Python | agpl-3.0 | 12,940 | [
"VisIt"
] | 0a7beea51bc287e9fd2ce4bde85b929db7648fe935f02532fb9848c53e80f14c |
from db import session
import model
def to_json(thread, user_id=None, unread_cnt=None, posts_cnt=None):
if posts_cnt is None:
posts_cnt = session.query(model.Post).\
filter(model.Post.thread == thread.id).count()
if unread_cnt is None:
if user_id is None:
unread_cnt = p... | fi-ksi/web-backend | util/thread.py | Python | mit | 1,869 | [
"VisIt"
] | 5bd67ef23ae0c6e92e0fcdec65a8b64d65f9072eccf1b7814585486615e339da |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2014-2016, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This p... | EricSB/nupic | src/nupic/algorithms/anomaly_likelihood.py | Python | agpl-3.0 | 28,156 | [
"Gaussian"
] | 5c9cb40e291807a208b7c9c6f321111a1cc02972eb74cb716ad810467f6f9eba |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from g... | adminq80/Interactive_estimation | config/urls.py | Python | mit | 1,987 | [
"VisIt"
] | 6f9a94c169489109ee29be287b71875e055151d1ff24323e5fa4d5ea13552a3f |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor 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... | rsepassi/tensor2tensor | tensor2tensor/data_generators/translate_enzh.py | Python | apache-2.0 | 10,261 | [
"VisIt"
] | 11ab007424cf181753cf1bc864ac277b6ba860d2f6e046b202f3a8a4194c9616 |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | denny820909/builder | lib/python2.7/site-packages/buildbot-0.8.8-py2.7.egg/buildbot/test/unit/test_steps_shell.py | Python | mit | 34,816 | [
"exciting"
] | b14573b2c798927c92a05a14f3d1562f0e212fe0fbeeb52451cca922a297828c |
"""
fitpack --- curve and surface fitting with splines
fitpack is based on a collection of Fortran routines DIERCKX
by P. Dierckx (see http://www.netlib.org/dierckx/) transformed
to double routines by Pearu Peterson.
"""
# Created by Pearu Peterson, June,August 2003
from __future__ import division, print_function, abs... | kmspriyatham/symath | scipy/scipy/interpolate/fitpack2.py | Python | apache-2.0 | 52,059 | [
"Gaussian"
] | f17325a4b5b3470d5cf51aaf268b067de028e56de6fab856d2fd808eafb8b400 |
# Generic parser schema
# with the default values
# Author: Evgeny Blokhin
import os, sys
import re
import time
import math
import random
from numpy import array
import hashlib
import base64
from tilde.core.settings import settings
from ase.data import chemical_symbols
HASH_LENGTH = 47
class Output:
def __in... | ansobolev/tilde | tilde/parsers/__init__.py | Python | mit | 6,624 | [
"ASE",
"CRYSTAL"
] | 3399b9ff709d9c457013c13a30b2ab80bbeded60b30875a6488a96b9ddb80fba |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2012-2013 Daniel Reis
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Sof... | syci/odoo-project-service | service_desk/__openerp__.py | Python | agpl-3.0 | 2,160 | [
"CRYSTAL"
] | 0be8c00ddd0d665486292d91b912780de0202486d37d7044fcdf3060369cfa91 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Demonstrate extracellular electric stimulation of a LFPy.Network instance,
using the LFPy.Network.enable_extracellular_stimulation() method.
Here a simple model of neuron ball-and-stick is used to populate two
morphologies with active HH channels inserted in the somas a... | LFPy/LFPy | examples/example_network/example_network_stim.py | Python | gpl-3.0 | 17,165 | [
"NEURON"
] | 970a9663f59af5325cebd637bb954be655d98be026678159c8b64fd5fb0d07b9 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2012 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 Lesser General Public License as published by
## the Free Softw... | tiagocardosos/stoq | stoqlib/gui/editors/crediteditor.py | Python | gpl-2.0 | 3,820 | [
"VisIt"
] | baa02d63ca3206e8b75b0376b365e695dd9590dbb1a0e4557c705d27cd2ba841 |
import PythonQt
from PythonQt import QtCore, QtGui, QtUiTools
import director.applogic as app
import director.objectmodel as om
from director.timercallback import TimerCallback
from director import robotstate
from director import visualization as vis
from director import transformUtils
from director import ikconstraint... | RobotLocomotion/director | src/python/director/teleoppanel.py | Python | bsd-3-clause | 59,794 | [
"VTK"
] | e2ce4787fca0d69389ef037075c95006b21afada2a91c21583716cbb005bb882 |
"""Tests for pytest-splinter plugin."""
import os.path
import time
import socket
import pytest
from splinter.driver import DriverAPI
from pytest_splinter.plugin import get_args
@pytest.fixture
def simple_page_content():
"""Simple page content."""
return """<html xmlns="http://www.w3.org/1999/xhtml"><head></... | miohtama/pytest-splinter | tests/test_plugin.py | Python | mit | 6,299 | [
"VisIt"
] | 4d39bc865a6088cd760f1afe82fea6bc159eff5dfcd932b24f4a045f789437cf |
#!/usr/bin/env python3
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# To use a consistent encoding
import codecs
import os
import re
import sys
# RPMs generated for fedora/rhel/centos need to have a different name
# (debia... | ocket8888/slackbot | setup.py | Python | gpl-3.0 | 7,071 | [
"VisIt"
] | 05b375a933939f17e351f504a8c27d420fcc67c269478e7b06a571a6da71ae22 |
from copy import copy, deepcopy
from collections import deque
try:
from collections import OrderedDict
except:
from ordereddict import OrderedDict
class DAGValidationError(Exception):
pass
# Added by the MOOSE group
class DAGEdgeDepError(Exception):
pass
# Added by the MOOSE group
class DAGEdgeIndE... | liuwenf/moose | python/contrib/dag/__init__.py | Python | lgpl-2.1 | 7,748 | [
"MOOSE"
] | be0f1c8798e436dbfb5d068f1b843d59a004f14ace91bd568f47068dcfe5e520 |
import csv
import numpy as np
import gzip
from sklearn.metrics import roc_auc_score, f1_score, precision_score, recall_score
from collections import defaultdict
def evaluate(labels, predicted, examples, terms=None, averageOnly=False, average="micro", noAUC=False):
print "Evaluating the predictions"
results = {... | TurkuNLP/CAFA3 | learning/evaluation.py | Python | lgpl-3.0 | 11,852 | [
"BLAST"
] | ee495efa7926e55b702a253eb1893a0bd0e331d303c5bdc3f8d85fcd8d2cca28 |
# Copyright (c) 2015-2018 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
=========
Smoothing
=========
Using MetPy's smoothing functions.
This example demonstrates the various ways that MetPy's smoothing function
can be utilized. While this exa... | Unidata/MetPy | examples/calculations/Smoothing.py | Python | bsd-3-clause | 2,428 | [
"Gaussian"
] | b3c50cd0edbbe7447a960bb992d41ff381b4cc76de806ce15aa6df317668313e |
import numpy as np
import os
from copy import deepcopy
import logging
import parser
from settings import Settings
grid_logger = logging.getLogger('grid')
WORKDIR = os.path.dirname(__file__)
def ortho_axis(plane):
for i in [0, 1, 2]:
if not i in plane: return i
def ortho_plane(axis):
if axis==0: retu... | maxivanoff/fftoolbox-app | q/fftoolbox/grid.py | Python | gpl-2.0 | 11,541 | [
"Gaussian"
] | bac6c8b38e35a563a2d127746508ced98caad309b97da3398d9704471dede1ef |
from trees.construction import Node
def predecessor(x): # predecessor is a bijective function
c = x.left
assert c is not None
while c.right is not None and c.right is not x: # ignore back pointer
c = c.right
return c
def in_order(root):
"""
Morris in-order traversal: Traverses a tree... | liboyin/algo-prac | trees/morris_traversal.py | Python | gpl-3.0 | 3,332 | [
"VisIt"
] | d3bc9c394ac206cfde9e09bc5a38c9c09f3bb8676dc33fce70ea75aa677908ac |
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 25 15:50:57 2016
@author: Gaspar Pandy
"""
from build.management.commands.base_build import Command as BaseBuild
from django.db.models import Q
from protein.models import Protein, ProteinConformation, ProteinSequenceType, ProteinSource, ProteinState
from residue.models i... | cmunk/protwis | structure/management/commands/new_xtals.py | Python | apache-2.0 | 21,773 | [
"CRYSTAL"
] | b8f9c20e80e4be1df36e0d0501e18d1ad36c2f82a322a5923caae7e660ad3f58 |
import argparse
import pysam
import sys
from Bio import SeqIO
from Bio.Seq import Seq
def _gen_seqs(bam):
"""Yield SeqIO records of the reference sequence each query is aligned to."""
for read in bam:
ref_seq = read.get_reference_sequence().upper()
name = '{}_{}'.format(read.reference_name, re... | nanoporetech/pomoxis | pomoxis/ref_seqs_from_bam.py | Python | mpl-2.0 | 888 | [
"pysam"
] | c7edca68f8a50e3d6896d716edc4e2a2843d26eed43dddb59607056cc9ad4cb9 |
# -*- coding: utf-8 -*-
"""
Optimized images (gif, jpeg & png)
Assumes that Gifsicle, ImageMagick's convert and pngquant are isntalled on path
http://www.lcdf.org/gifsicle/
http://www.imagemagick.org/
http://pngquant.org/
Copyright (c) 2014 Marc Alexandre (http://www.malexandre.fr)
"""
import os
import re
import shut... | malexandre/pelican-image-optimizer | pelican_image_optimizer.py | Python | mit | 3,100 | [
"Gaussian"
] | a480b1aa97408bc162934c61971498e94922606120b7de4e93562fc0f492112b |
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is... | quang-ha/lammps | python/examples/pizza/vmd.py | Python | gpl-2.0 | 8,836 | [
"VMD"
] | e18b8c91d4b117f68f381837a65550f588122c125e81ca0a9d034331abef5a00 |
# encoding: utf-8
"""A simple configuration system."""
# Copyright (c) IPython Development Team.
# Distributed under the terms of the Modified BSD License.
import argparse
import copy
import logging
import os
import re
import sys
import json
from ast import literal_eval
from ipython_genutils.path import filefind
fro... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/traitlets/config/loader.py | Python | bsd-2-clause | 28,772 | [
"Brian"
] | 34a50549a86491d712218f07834c50555a610a25bfeeb6fc2075922b823722b7 |
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