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#!/usr/bin/env python
import argparse
import datetime
import numpy as np
import pandas as pd
import pysam
def calculate_variant_quality(variant):
try:
return int(min(100, round(-10 * np.log10(1 - (variant.contig_support / float(variant.contig_depth))) * np.log(variant.contig_depth), 0)))
except ZeroDi... | EichlerLab/pacbio_variant_caller | scripts/variants_bed_to_vcf.py | Python | mit | 7,070 | [
"pysam"
] | 29135a6a155f48b781b8ebb7ac64f0374b5998c579266f4671d8ed696cbb382c |
# 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_supercell.py | Python | apache-2.0 | 26,739 | [
"MOE",
"PySCF"
] | 5e4ef533c883c5a6ad2c4eb8e7d28441e8c144fa45e7492734c17cec42986ccd |
"""
cda_tools.py
Author: Dereck J. Padden
This module contains the functions necessary to perform Continuous Decomposition Analysis as described by
Benedek, M. & Kaernbach, C. (2010). "A Continuous Measure of Phasic Electrodermal Activity."
Journal of Neuroscience Methods, 190, 80-91.
"""
import scipy as sp
from sci... | plazadeloslagartos/PyCDA | cda_tools.py | Python | gpl-3.0 | 13,128 | [
"Gaussian"
] | 9420c05e602339035161d064a6bfd220e022624051d59235db1c2747c1d089a6 |
"""
Provides factory methods to assemble the Galaxy web application
"""
import logging, atexit
import os, os.path, sys
from inspect import isclass
from paste.request import parse_formvars
from paste.util import import_string
from paste import httpexceptions
from paste.deploy.converters import asbool
import flup.midd... | dbcls/dbcls-galaxy | lib/galaxy/webapps/reports/buildapp.py | Python | mit | 8,693 | [
"Galaxy"
] | 927a8c3cf63a78c8a86d32599dcb6639ad007afb75d164002e034fd031ce4973 |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2012 Nick Hall
# Copyright (C) 2012 Brian G. Matherly
# Copyright (C) 2012-2014 Paul Franklin
#
# 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
# t... | beernarrd/gramps | gramps/plugins/textreport/tableofcontents.py | Python | gpl-2.0 | 4,908 | [
"Brian"
] | b2689fd4d0a54e5e4d9e2d364569904261674352605f80e2353c29a0d4915e9c |
from __future__ import unicode_literals
"""
This package implements various VASP Jobs and Error Handlers.
"""
__author__ = "Shyue Ping Ong"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "ongsp@ucsd.edu"
__status__ = "Production"
__date__ = "2/4/13"
| specter119/custodian | custodian/vasp/__init__.py | Python | mit | 271 | [
"VASP"
] | f33dc4aa80eda86556ee0ce5ebce896354d1807fa1e5bd6bf2cc145bd0c482fa |
""" JobWrapper test
"""
import unittest
import os
import sys
from DIRAC import gLogger
from DIRAC.Resources.Computing.ComputingElementFactory import ComputingElementFactory
from DIRAC.WorkloadManagementSystem.Utilities.Utils import createJobWrapper
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
class JobWr... | andresailer/DIRAC | tests/Integration/WorkloadManagementSystem/Test_JobWrapper.py | Python | gpl-3.0 | 2,529 | [
"DIRAC"
] | 508ee0a747e9e6d5f7199c3c144c148058033e13e2f02e311d0d1148400daab3 |
## @package shesha.init.lgs_init
## @brief Initialization of a LGS in a Wfs object
## @author COMPASS Team <https://github.com/ANR-COMPASS>
## @version 5.2.1
## @date 2022/01/24
## @copyright GNU Lesser General Public License
#
# This file is part of COMPASS <https://anr-compass.github.io/compass/>
#
#... | ANR-COMPASS/shesha | shesha/init/lgs_init.py | Python | gpl-3.0 | 12,354 | [
"DIRAC",
"Gaussian"
] | 9d15253d7de08b5baeaea7e50b2cc1c86326e08788063356d7f003f93fe46fad |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/tdscf/__init__.py | Python | apache-2.0 | 3,413 | [
"PySCF"
] | 20bc45d241da5f10fa92a467cbc84fac352b5521bf930546989f8c4fe6b6eeee |
'''
Plotting modules
'''
import os
import h5py
import corner
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.ticker import MaxNLocator
# --- local ---
import util
import data as Data
from prior import PriorRan... | mjvakili/ccppabc | ccppabc/code/plotting.py | Python | mit | 15,241 | [
"TINKER"
] | b1df15e58b7bb21c4fb0384f47c063f2a062cf8574aa957eb3a7487035470cfc |
../../../../../../../share/pyshared/orca/scripts/apps/Instantbird/script_utilities.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Instantbird/script_utilities.py | Python | gpl-3.0 | 85 | [
"ORCA"
] | 21c15d3a634c62c3a0924062969dac4d553a7d424bda7efed96896bca5e2afa5 |
import numpy as np
def bin_data(x, y, yerr, npts):
"""
A function for binning your data.
Binning is sinning, of course, but if you want to get things
set up quickly this can be very helpful!
It takes your data: x, y, yerr
npts (int) is the number of points per bin.
"""
mod, nbins = len(... | RuthAngus/kalesalad | code/tools.py | Python | mit | 3,049 | [
"Gaussian"
] | 8cbf547965fda23761d5edcde08d517965fa51873f8a24b606fb8d7ce1aca9d2 |
# Copyright (C) 2018-2021 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU Affero General Public License version 3, or any later version
# See top-level LICENSE file for more information
from django.conf.urls import url
from django.core.paginator i... | SoftwareHeritage/swh-web-ui | swh/web/misc/origin_save.py | Python | agpl-3.0 | 3,435 | [
"VisIt"
] | 8ea148893949e669f62ea56285e3ac584e810bc887955f6b36f9a335eb6c4782 |
from __future__ import unicode_literals
import copy
from six.moves import xrange
from scrapi.base import XMLHarvester
from scrapi.base.schemas import DOESCHEMA
from scrapi.linter.document import RawDocument
from scrapi.base.helpers import updated_schema, build_properties, single_result
RAW_DOC = {
'doc': b'{}',... | mehanig/scrapi | tests/utils.py | Python | apache-2.0 | 8,179 | [
"Brian"
] | c606f3d838a1a3158d16bf7886a96f8997f1719b124013df0567d66c5ff539ef |
"""Mayavi/traits GUI for converting data from KIT systems"""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
import numpy as np
from scipy.linalg import inv
from threading import Thread
from ..externals.six.moves import queue
from ..io.meas_info import _read_dig_points... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/mne/gui/_kit2fiff_gui.py | Python | bsd-3-clause | 18,619 | [
"Mayavi"
] | d3d357a8c809f0e498771258fd3b77d798c7eba51db50be0a6560962e71302e4 |
# -*- coding: utf-8 -*-
from typing import Dict
from django.db import connection
from catmaid.error import ClientError
from catmaid.control.authentication import requires_user_role
from catmaid.models import UserRole
from rest_framework.decorators import api_view
from rest_framework.request import Request
from rest_... | tomka/CATMAID | django/applications/catmaid/control/transaction.py | Python | gpl-3.0 | 12,397 | [
"NEURON"
] | 8ccaac77d4ab3c896109ca877f03cad14e5e97d3ac346928689e7f0f1bfd87fe |
# This file is part of PyEMMA.
#
# Copyright (c) 2016, 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, eithe... | gph82/PyEMMA | pyemma/coordinates/data/util/frames_from_file.py | Python | lgpl-3.0 | 8,838 | [
"MDTraj"
] | d8553fb9010d72c28916c23ad3983fec2d5a9998b2b6bb0ff1f6330271aed974 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
TODO: Modify module doc.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "6/6/13"
import unittest
import os... | Dioptas/pymatgen | pymatgen/io/tests/test_nwchemio.py | Python | mit | 12,009 | [
"pymatgen"
] | 1e7f13d33099399739c5bd0e5bb26cb3bc7a4559c898c42e58be24c993151d8d |
#!/usr/bin/env python
""" compare how the elements behave
We create a folder ground truth that possess the same thing than the other
in a form of a dictionnary containing nparrays and other info.
the other files contains every test and the name is the date of the test
See Also
------------
Link
\image dev/kalfon/i... | agiovann/Constrained_NMF | caiman/tests/comparison/comparison.py | Python | gpl-2.0 | 24,550 | [
"NEURON"
] | 74ceed944c9669b037865e8bce4d0f3ac3018c4ecd39da8b0666c32b333e277e |
"""
http://code.activestate.com/recipes/578353-code-to-source-and-back/
"""
import ast
import inspect
import re
from types import CodeType as code, FunctionType as function
import inspect
from monadic.interop import map_list
from monadic.python_ver import PYTHON_VERSION, invalid_python_version
import __future__
PyCF... | andorp/monadic | monadic/decorator.py | Python | lgpl-3.0 | 11,846 | [
"VisIt"
] | 38f639a00aad5c641c56d7b0ad9f790da1c742c08aa7fbbd467cf3ae18e6d9f9 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLPUnstructuredGridReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkXMLPUnstructuredGridReader.py | Python | bsd-3-clause | 532 | [
"VTK"
] | 840e95336e39aa425bc42d8ebc8f398358247b32ce762d7daef6bd36bb2816fb |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | pmarques/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 17,696 | [
"Brian",
"Galaxy"
] | 582feadaf3dbc055100b359bf3a2e5d377358989f7a635c27ce76b14b12a47a2 |
# Lint as: python3
# Copyright 2020 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 ... | tensorflow/lingvo | lingvo/core/gshard_builder_test.py | Python | apache-2.0 | 32,873 | [
"MOE"
] | 14b418198e6bd1925221d449df22d057b77fba28c0b3636604a0e5f0774b23a3 |
#/###################/#
# Import modules
#
#ImportModules
import ShareYourSystem as SYS
#/###################/#
# Build the model
#
#Definition an instance
MyBrianer=SYS.BrianerClass(
).mapSet(
{
'-Populations':
{
'set':{
'#liarg:#lambda':{
'|#NeuronStr':{
'BrianingRecordSkipKeyStrsLis... | Ledoux/ShareYourSystem | Pythonlogy/build/lib/ShareYourSystem/Standards/Recorders/Brianer/05_ExampleCell.py | Python | mit | 2,054 | [
"Brian"
] | 0e967739cff299830f3edcc956849e3b844cb179e4a7249909e4815557dc10ea |
try:
from urllib.parse import urlparse
except ImportError: # Python 2
from urlparse import urlparse
from django.http import HttpResponse, HttpResponseRedirect
from django.shortcuts import render, get_object_or_404, resolve_url
from django.conf import settings
from django.contrib.auth import REDIRECT_FIELD_... | AtenDesignGroup/ohai-kit | ohai_kit/views.py | Python | agpl-3.0 | 15,287 | [
"VisIt"
] | 2631fa0b49c56dbd6823ef949d1d09e8ab252a2e25dce7ece4e201d9d9eee5f0 |
nouns = ["aardvark",
"abacus",
"abbey",
"abdomen",
"ability",
"abolishment",
"abroad",
"abuse",
"accelerant",
"accelerator",
"access",
"accident",
"accommodation",
"accompanist",
"accordion",
... | TreeFrogBandit/Project-Codenames | libraries/nouns.py | Python | gpl-3.0 | 89,759 | [
"Bowtie",
"CASINO",
"Elk",
"Jaguar",
"Octopus",
"VisIt"
] | a810ff42e39c701d8eddb0456aa0a9afb87364332f8bd9fa23db0fee057e9677 |
from tcga_encoder.utils.helpers import *
from tcga_encoder.data.data import *
from tcga_encoder.definitions.tcga import *
#from tcga_encoder.definitions.nn import *
from tcga_encoder.definitions.locations import *
#from tcga_encoder.algorithms import *
import seaborn as sns
from sklearn.manifold import TSNE, locally_li... | tedmeeds/tcga_encoder | tcga_encoder/analyses/old/kmeans_from_z_space_local.py | Python | mit | 14,719 | [
"Amber"
] | d1785f2126c7db3c7b35058f40e4ede4ed2cdc8a3d6a89e48dcccc442d35d4af |
import argparse
import os
import sys
def main():
"""
Main interface that reads the file and retrieve all useful geoms etc.
Then rewrite geometries in a usable formatter_class
Prep all NBO computations
Run ADF on each computation
"""
# Retrieve command line values
args =... | chemistry-scripts/computations-scripts | ASM_extract_NBO_from_t21.py | Python | mit | 4,590 | [
"ADF"
] | 3e2f1a7b02089157093a4f3a947edc5d2bf75be4a86ade47e8644d1c52432361 |
from __future__ import (absolute_import, division, print_function)
import unittest
from mantid.simpleapi import LRPeakSelection, CreateSampleWorkspace, DeleteWorkspace
import logging
class LRPeakSelectionTest(unittest.TestCase):
def setUp(self):
self.ws = None
def tearDown(self):
if self.ws i... | ScreamingUdder/mantid | Framework/PythonInterface/test/python/plugins/algorithms/LRPeakSelectionTest.py | Python | gpl-3.0 | 2,620 | [
"Gaussian"
] | 6e50076ef990525246dc295c683c211e20d7906d8926332967deb5f4564dabe9 |
# Copyright 2013-2020 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 P4est(AutotoolsPackage):
"""Dynamic management of a collection (a forest) of adaptive octr... | iulian787/spack | var/spack/repos/builtin/packages/p4est/package.py | Python | lgpl-2.1 | 2,699 | [
"VTK"
] | d89ba7b4ff408a3a52d0eccafbd2d6b27ddc0a6a1085dcf1f276d13b2f1fb764 |
import bpy
import os
from .util import *
from .transform import *
from .image import *
from .renderbuffer import *
from .submesh import *
from .data import *
from .object import *
from .group import *
from .scene import *
from .material import ExportMaterials
from io_scene_cs.utilities import B2CS
def Write(fi):
... | baoboa/Crystal-Space | scripts/blender/io_scene_cs/io/__init__.py | Python | lgpl-2.1 | 6,624 | [
"CRYSTAL"
] | 92ee49dd8f1fcd16585ad7e5b1b1a6181a5d1576734bd252ed88442f618e9b12 |
import arrow
from dateutil.relativedelta import relativedelta
from django.apps import apps as django_apps
from django.core.exceptions import ValidationError
from edc_base.model_validators.date import datetime_not_future
from edc_protocol.validators import datetime_not_before_study_start
class CrfReportDateAllowanceE... | botswana-harvard/edc-visit-tracking | edc_visit_tracking/crf_date_validator.py | Python | gpl-2.0 | 3,615 | [
"VisIt"
] | 0253e44a15f47e1951ae7318cdf1d7b2d483ee592d25029a8c0abb02f5f4a83a |
# Version: 0.12
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
[]... | t2abdulg/SALib | versioneer.py | Python | mit | 36,531 | [
"Brian"
] | 46632d1bdc8fc4653c534c2ce0c7bf4b20a67a3ebb41c1ba0079c72db6fb4976 |
"""
Cross Compilation and RPC
=========================
**Author**: `Ziheng Jiang <https://github.com/ZihengJiang/>`_
This tutorial introduces cross compilation and remote device
execution with RPC in TVM.
With cross compilation and RPC, you can **compile program on your
local machine then run it on remote device**. ... | phisiart/tvm | tutorials/deployment/cross_compilation_and_rpc.py | Python | apache-2.0 | 10,961 | [
"Firefly"
] | 408a423e57d16d9128c1f25f952f1f242b77220c57cc8f29bc261a27a64d6a04 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your... | Forage/Gramps | gramps/gen/proxy/living.py | Python | gpl-2.0 | 11,673 | [
"Brian"
] | db52aa07641bfe4940de0b66ac66c8080673dde0318fe1d1a2bd932bad4f320e |
'''
Output query and subject sequences to be fed into blastx. The
complementary strand of the query should align to two separate domains in the
subject AA seq.
In an earlier version, running BLAST locally produced no results, while running
it via NCBI blastx (i.e., feeding the queries into the web interface) worked.
T... | jwintersinger/kablammo | test-cases/blastx-test/blastx-test.py | Python | mit | 1,429 | [
"BLAST"
] | 5927a777c279022ce6de53a9befb872acb41b51581ac6a3665f6344f1636e954 |
# -*- coding: utf-8 -*-
"""
A rhythmbox plugin for playing music from baidu music.
Copyright (C) 2013 pandasunny <pandasunny@gmail.com>
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 Found... | pandasunny/rhythmbox-baidu-music | client.py | Python | gpl-3.0 | 29,460 | [
"VisIt"
] | c571fdc6f253cad200ee9ac9a21873416840c703dc1e868c7c8ddd2f281ce719 |
import unittest
import numpy as np
import pysal
#import pysal.spreg as EC
from scipy import sparse
from pysal.contrib.handler import Model
from functools import partial
OLS = partial(Model, mtype='OLS')
BaseOLS = partial(Model, mtype='BaseOLS')
PEGP = pysal.examples.get_path
class TestBaseOLS(unittest.TestCase):
... | schmidtc/pysal | pysal/contrib/handler/tests/test_ols_sparse.py | Python | bsd-3-clause | 5,274 | [
"COLUMBUS"
] | 0a6d5f91e624188296e2531512c30bab6ab210177b70dd9aeef4de577fb8f671 |
# $HeadURL$
__RCSID__ = "$Id$"
"""
SystemLoggingReportHandler allows a remote system to access the contest
of the SystemLoggingDB
The following methods are available in the Service interface
getTopErrors()
getGroups()
getSites()
getSystems()
getSubSystems()
getFixedTextStrings()
getCou... | sposs/DIRAC | FrameworkSystem/Service/SystemLoggingReportHandler.py | Python | gpl-3.0 | 8,697 | [
"DIRAC"
] | 6e8fd8f9849cd7d9236697cb503f80f350c50b9a64b7e1ee52b0ea93571a6362 |
# -*- coding: utf-8 -*-
"""
Monte Carlo Tree Search in AlphaGo Zero style, which uses a policy-value
network to guide the tree search and evaluate the leaf nodes
@author: Junxiao Song
"""
import numpy as np
import copy
def softmax(x):
probs = np.exp(x - np.max(x))
probs /= np.sum(probs)
return probs
c... | Dryeck/17-18-Reinforcement | AlphaZero/mcts_alphaZero.py | Python | mit | 7,844 | [
"VisIt"
] | 42aad1b83276205494e56677ad7a655349c7d84cb9f1c5ece9ded71f0db1f4f6 |
#!/usr/bin/env python
'''
CREATED:2014-01-17 16:30:07 by Brian McFee <brm2132@columbia.edu>
Compute hierarchical segmentation evaluation metrics
Usage:
./segment_hier_eval.py -r TRUTH_LEVEL1.TXT [TRUTH_LEVEL2.TXT ...] \
-e PREDICTION_LEVEL1.TXT [PREDICTION_LEVEL2.TXT ...] \
... | urinieto/mir_eval | evaluators/segment_hier_eval.py | Python | mit | 3,022 | [
"Brian"
] | 4a83e1ebfe02d8d86c75f8c23af0f0ed2d61a973c774e2e399f5fa7141aecd9e |
"""
========================================
Ammonia inversion transition TROT fitter
========================================
Ammonia inversion transition TROT fitter translated from Erik Rosolowsky's
https://github.com/low-sky/nh3fit
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
Module API
^^^^^^^^^^... | low-sky/pyspeckit | pyspeckit/spectrum/models/ammonia.py | Python | mit | 54,171 | [
"Gaussian"
] | 2d83c07318bb8d3e93d00d99fdba211c2f8c5c4900aa02f8f97948f4748cf620 |
stations = {'acheng': 'ACB',
'aershan': 'ART',
'aershanbei': 'ARX',
'aihe': 'AHP',
'aijiacun': 'AJJ',
'ajin': 'AJD',
'akesu': 'ASR',
'aketao': 'AER',
'alashankou': 'AKR',
'alihe': 'AHX',
'alongshan': 'ASX',
'amuer': 'JTX',
'ananzhuang': 'AZM',
'anda': 'ADX',
'ande... | YangTe1/site_at_will | site_at_will/train_tickets/stations.py | Python | gpl-3.0 | 58,257 | [
"ADF",
"ASE",
"VTK"
] | 61158eabbb6381ebab1a4b0c3855c79b303f9408c88502dcfca3dcef5d1b38a8 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_compiled_0004.py | Python | gpl-3.0 | 3,912 | [
"Brian"
] | 55989c868d454403cc2a6f8b824e23c8ee9bcc594e03f3a6c43b98e8a331fdc4 |
# -*- coding: utf-8 -*-
# Copyright (C) 2017 Oscar Gerardo Lazo Arjona
# mailto: oscar.lazoarjona@physics.ox.ac.uk
r"""This is a template."""
import numpy as np
from scipy.optimize import curve_fit
import pandas as pd
from matplotlib import pyplot as plt
from scipy.constants import physical_constants
from tabulate imp... | oscarlazoarjona/quantum_memories | examples/hyperfine_orca/doppler_dephasing/plot_data_rb.py | Python | gpl-3.0 | 14,036 | [
"Gaussian"
] | f1255ca1f1179004d42099f85dcfec47fa8107e8b35098d038d9f06fcb36a1e0 |
#!/usr/bin/env python
#-*- coding: utf-8 -*-
"""
rtsim.py
This is a simulation of a broadband electromagnetic pulse propagating through a structure.
The structure is loaded from a module. After the simulation, its s-parameters are calculated and saved.
About this script:
* Written in 2012-2013 by Filip Dominec (domi... | FilipDominec/python-meep-utils | wedge_refraction.py | Python | gpl-2.0 | 12,212 | [
"Gaussian",
"exciting"
] | 739a477d8c1652be3daab16ac8e66e409c8e99104f5c7337e305a9c5903cb179 |
#
# Copyright 2010, Kay Hayen, mailto:kayhayen@gmx.de
#
# Part of "Nuitka", an attempt of building an optimizing Python compiler
# that is compatible and integrates with CPython, but also works on its
# own.
#
# If you submit Kay Hayen patches to this software in either form, you
# automatically... | pombredanne/nuitka-old-no-longer-maintained | src/templates/CodeTemplatesCompiledGeneratorType.py | Python | gpl-3.0 | 12,702 | [
"VisIt"
] | 7bd11fdd314fe89ec01ad8fb584c02f5db94d8bc737c62fe104481974b0573f4 |
# Orca
#
# Copyright 2005-2010 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/yelp/yelp_v2/__init__.py | Python | gpl-3.0 | 1,008 | [
"ORCA"
] | e9c7fd436a29e58c7aa820bb759640cc48191717295b739d89ee4524d4a08e6a |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
from datetime import datetime, timedelta
import uuid
import pytz
from odoo import fields, models, api, _
from odoo.addons.base.models.res_partner import _tz_get
from odoo.exceptions import UserError
from odoo.tools.misc... | jeremiahyan/odoo | addons/website/models/website_visitor.py | Python | gpl-3.0 | 16,352 | [
"VisIt"
] | 0ce4bbf4792a53274135f9dfdf395c7721949c2578bc1fa36a82271b6d68c9f6 |
import numpy as np
from astropy.coordinates import SkyCoord
from astropy import units as u
from astropy.table import Table
from matplotlib import pyplot as plt
import pdb
from frb.surveys import des
import sys,os
import progressbar as pb #pip install progressbar2
from matplotlib import pyplot as plt
import seaborn as s... | FRBs/DM | frb/scripts/random_assoc.py | Python | bsd-3-clause | 4,628 | [
"Galaxy"
] | c42eae9f02b6fc50251017eaab6da31f46650939cde0c376332c40cd783684f5 |
import sys
ZIP_LIBRARIES = ['library/babel.zip', 'library/pyhaml_jinja.zip',
'library/pytz.zip', 'library/stripe.zip',
'library/webapp2.zip', 'library/wtforms.zip', 'library/']
# Zipimport configuration:
def configure_libraries():
sys.path.extend(ZIP_LIBRARIES)
# Ensure no dup... | nardorb/OneStop | config.py | Python | gpl-2.0 | 2,442 | [
"BLAST"
] | cdbf9cf38cf3f8a4950dd6c6eab9cae380ae32938f8dfc33e5ab5addbeb3f74b |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/custom/forms/editcustomform.py | Python | gpl-2.0 | 11,025 | [
"Brian"
] | b251c8b0db7e2a9edb51dd14a2f9d7a2b518dca18a0d56c8d02d3dc28b39e3f9 |
""" StratusLabImage
Class used by DIRAC to control virtual machine instances on StratusLab
cloud infrastructures. This provides just the core interface methods for
DIRAC, the real work is done within the StratusLabClient class.
Author: Charles Loomis
"""
#DIRAC
from DIRAC import gLogger, S_ERROR
# VMD... | myco/VMDIRAC | WorkloadManagementSystem/Client/StratusLabImage.py | Python | gpl-3.0 | 5,479 | [
"DIRAC"
] | 23acc54a61907d78fe93bd09bfbd0eccb8126a4fb975477830d3f092e0723f5a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
#... | alvaroaleman/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 13,382 | [
"Brian"
] | 23ac7babf265d38112990e1fec8e8e2ef77c83fe1903287c10bf140a065f0d3a |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: 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... | bearstech/ansible | lib/ansible/modules/network/avi/avi_microservicegroup.py | Python | gpl-3.0 | 3,741 | [
"VisIt"
] | 9d4a7d66bd710dc8d60d9a11a27a922dd02d160a8ad2d50d9d5192628e144fcc |
from contextlib import closing
import logging
from traits.api import ListStr, Instance, Bool, TraitError, HasTraits
from traitsui.api import View, Group, Item, VGroup
from apptools.persistence.file_path import FilePath
from apptools.persistence.state_pickler import set_state
from mayavi.core.common import handle_child... | simphony/simphony-mayavi | simphony_mayavi/sources/cuds_file_source.py | Python | bsd-2-clause | 4,942 | [
"Mayavi"
] | ed113c35fd617d23bb5dfa3b4f0d4bf96415285d7a443931d756eb2b72fedc14 |
# -*- coding: utf-8 -*-
"""Tests for gam.AdditiveModel and GAM with Polynomials compared to OLS and GLM
Created on Sat Nov 05 14:16:07 2011
Author: Josef Perktold
License: BSD
Notes
-----
TODO: TestGAMGamma: has test failure (GLM looks good),
adding log-link didn't help
resolved: gamma doesn't fai... | yarikoptic/pystatsmodels | statsmodels/sandbox/tests/test_gam.py | Python | bsd-3-clause | 9,762 | [
"Gaussian"
] | 50423d4221d92630b0646911e7ba7a12a2d09667ac2f01e602f282c6834a76fd |
# -*- coding: UTF-8 -*-
# Genro
# Copyright (c) 2004 Softwell sas - Milano see LICENSE for details
# Author Giovanni Porcari, Francesco Cavazzana, Saverio Porcari, Francesco Porcari
import unittest
import datetime
import os
from gnr.core.gnrbag import Bag
class TestBasicBag(unittest.TestCase):
def setUp(self):
... | poppogbr/genropy | gnrpy/tests/zz_test/core/bag/testbag.py | Python | lgpl-2.1 | 10,310 | [
"Desmond"
] | 7381099eb28ad25c4f6660b26e5d78443cdc82f972a7f7082cb26a479735af64 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Rietveld."""
from distutils.vers... | fracting/depot_tools | git_cl.py | Python | bsd-3-clause | 130,012 | [
"VisIt"
] | bec58575a94a831d7f7586d520573dbe7b338d1293b68b4a5186a76b2f7c7fd3 |
"""
KeepNote
HTML reader/writer for RichText
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@mit.edu>
#
# 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 Softwa... | reshadh/Keepnote-LaTeX | keepnote/gui/richtext/richtext_html.py | Python | gpl-2.0 | 40,999 | [
"VisIt"
] | 230e98348bccedccfe6d76f03be9953f398a3c3f8a8f530a46638093a717e324 |
#!/usr/bin/python
import os, sys # low level handling, such as command line stuff
import string # string methods available
import re # regular expressions
import getopt # comand line argument handling
from low import * # custom functions, written by myself
# =================================================... | lotharwissler/bioinformatics | python/blast/homology_blast.py | Python | mit | 6,193 | [
"BLAST"
] | 37607683075c71b7172b862509e82fa20edd1ba575852651574cdaaa1955e3e7 |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | nuclear-wizard/moose | python/chigger/annotations/ImageAnnotationSource.py | Python | lgpl-2.1 | 2,197 | [
"MOOSE",
"VTK"
] | a08bde36fb69902572b003ea5705b3488bac265043522bdd82890a44d685b2df |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/decorations/fccsets.py | Python | gpl-3.0 | 481,440 | [
"CRYSTAL",
"VASP"
] | aa66ce490d6197ed69c50cfceb16e410166cdf9c089e8ae00810fc298bb5e7f8 |
import os
import sys
import numpy as np
import mdtraj as md
import tables
from IPython.utils.traitlets import Unicode, Int, Enum, Instance
from msmbuilder3.config.app import MSMBuilderApp
from msmbuilder3.base import TransformerMixin
from msmbuilder3 import (PositionVectorizer, DistanceVectorizer,
... | rmcgibbo/msmbuilder3 | msmbuilder3/command/vectorapp.py | Python | gpl-3.0 | 4,185 | [
"MDTraj"
] | 1750814096a5f02f2341711ebd75bdbac45d9957f2177273792707e4917f47a3 |
import unittest, random, sys, time
sys.path.extend(['.','..','../..','py'])
import h2o, h2o_cmd, h2o_browse as h2b, h2o_import as h2i, h2o_glm, h2o_util, h2o_jobs, h2o_gbm, h2o_exec as h2e
DO_BUG = False
DO_HDFS = False
DO_ALL_DIGITS = False
print "Uses numpy to create dataset..I guess we have to deal with jenkins no... | rowhit/h2o-2 | py/testdir_single_jvm/test_GLM2_syn_corr.py | Python | apache-2.0 | 6,473 | [
"Gaussian"
] | a4a06a1bbc5f5bb8036b782f30aa27fb78cc118b4d535fb39492d75b114a327b |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from unittest import skipUnless
from urllib import urlencode
import json
import mock
import ddt
from django.test import TestCase
from django.conf import settings
from django.core.urlresolvers import reverse
from django.core import mail
from dj... | peterm-itr/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 23,924 | [
"VisIt"
] | ca5e03515626d07b67124e1192ada04e3753ffae1f780c04f0eefdbd9b1f6f28 |
{
'name': 'Export data in Excel',
'summary' : 'Manage export list with custom domain,export them to Excel & email it',
'version': '1.0',
'category': 'Extra Tools',
'author': 'Emipro Technologies Pvt. Ltd.',
'website': 'www.emiprotechnologies.com',
'maintainer': 'Emipro Technologies Pvt. Ltd.... | MarcosCommunity/odoo | comunity_modules/ir_export_extended_ept/__openerp__.py | Python | agpl-3.0 | 1,622 | [
"VisIt"
] | 82fd57cb1657839ceb024c248f24da6095374624736aec8448900e0285c1c681 |
"""Unit tests for the VTK io library"""
# Copyright (C) 2011 Garth N. Wells
#
# 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 Public License as published by
# the Free Software Foundation, either version 3 of the License, ... | maciekswat/dolfin_1.3.0 | test/unit/io/python/vtk.py | Python | gpl-3.0 | 6,821 | [
"VTK"
] | 7deaab412716413f67bbbe4fe5cea8af4be06f3622ef7a2835cdb444bdc3514c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# uploadprogress - [insert a few words of module description on this line]
# Copyright (C) 2003-2012 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the ter... | heromod/migrid | mig/cgi-bin/uploadprogress.py | Python | gpl-2.0 | 1,116 | [
"Brian"
] | 5a884bdaef0e4f56af80bacdce923fa3667de617599a2c73e403e845cc46c89d |
import os
import pandas as pd
import numpy as np
from sklearn.cluster import KMeans
from scipy.stats import kendalltau
LOG_SMALL = -10 # log(x) when x is a very small positive real number
LOG_ZERO = -1000 # log(0)
BIN_CLUSTER = 5 # discritization parameter
LOG_TRANSITION = False
"""
POI Features given query (s... | cdawei/digbeta | dchen/tour/src/shared.py | Python | gpl-3.0 | 23,828 | [
"VisIt"
] | b2cf80610509353d95cd88c03ae7249f48262f7a169359ab076d62051cbb6693 |
# -*- coding: utf-8 -*-
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright © 2014, 2019 Dave Hocker
#
# 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 Fou... | dhocker/athomepowerlineserver | commands/SetTime.py | Python | gpl-3.0 | 1,077 | [
"xTB"
] | 36538cb955641d25a4dfc2291088bdeeb06901de818155f15e60af903a57e0cc |
"""Benchmarking module for AlignmentFile functionality"""
import os
import subprocess
import pysam
from TestUtils import BAM_DATADIR
def count_number_lines_with_samtools(fn):
os.system("samtools view {} | wc -l > /dev/null".format(fn))
return 3270
def count_number_lines_with_samtoolspipe(fn):
with sub... | kyleabeauchamp/pysam | tests/AlignmentFile_bench.py | Python | mit | 1,921 | [
"pysam"
] | db7c9aafe312e85a306b0de1177dedfa194c2bfef58bc8558f0fc1b37fb85c40 |
import os
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
#warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)
import cmr
from ase.calculators.emt import EMT
from ase.struct... | grhawk/ASE | tools/ase/test/cmr/cmr_rw.py | Python | gpl-2.0 | 793 | [
"ASE"
] | fa949733c505aba8ec0f24e2374a0511c1315050ab6949ab0fbebf3eff6f5390 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
ren1.SetBackground(0,0,0)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.SetSize(300,300)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRende... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/Geometry/Testing/Python/TestXYZMol.py | Python | gpl-3.0 | 2,599 | [
"VTK"
] | 47a92c33858572c9acd2c496cce36846f73d4df1b22f5a6bfa456434125d74b2 |
# -*- coding: utf-8 -*-
"""Tests for obfuscation utilities."""
import textwrap
from unittest import TestCase
from ddt import data, ddt, unpack
from mock import MagicMock, patch
import edx.analytics.tasks.util.obfuscate_util as obfuscate_util
from edx.analytics.tasks.util.tests.target import FakeTask
@ddt
class Bac... | Stanford-Online/edx-analytics-pipeline | edx/analytics/tasks/util/tests/test_obfuscate_util.py | Python | agpl-3.0 | 26,191 | [
"VisIt"
] | 0f448e6ccfaa88669df7eb75c1fd7b146f0a905c068754e7d9cfa2324dd5c0fc |
#############################################################################
# Copyright Kitware 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/licen... | DigitalSlideArchive/large_image | sources/gdal/large_image_source_gdal/__init__.py | Python | apache-2.0 | 44,615 | [
"NetCDF"
] | d6f36864856b372037bc10526b65d9b088dd1bf091e79f8593508dfd9df12afd |
#! /usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2010 (ita)
"""
This file is provided to enable compatibility with waf 1.5
It was enabled by default in waf 1.6, but it is not used in waf 1.7
"""
import sys
from waflib import ConfigSet, Logs, Options, Scripting, Task, Build, Configure, Node, Runner, TaskGen, Ut... | hmgaudecker/econ-project-templates | {{cookiecutter.project_slug}}/.mywaflib/waflib/extras/compat15.py | Python | bsd-3-clause | 11,813 | [
"VisIt"
] | 2b07fa37010a70d985f2b1ebca3603a3fba7f5582ec3736eeaefcb0729aeff61 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import sys
import os
import ast
sys.path.append(os.path.dirname(os.path.dirname(__file__)))
from py2cpp.converter import Converter
from py2cpp import cpp
def main(argv):
parser = argparse.ArgumentParser()
parser.add_argument("input", type=arg... | mugwort-rc/py2cpp | tools/cpp_dump.py | Python | gpl-3.0 | 580 | [
"VisIt"
] | a02e7feb12aa9c0ed2d66b695799349ca8305b7db963378c1c5392b10f437713 |
# Test version of wflow Delft-FEWS adapter
#
# Wflow is Free software, see below:
#
# Copyright (c) J. Schellekens 2005-2011
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... | openstreams/wflow | wflow/wflow_adapt.py | Python | gpl-3.0 | 23,531 | [
"NetCDF"
] | 385b5712fefcf1305d163792f73833eb68f52db1e5b45a6a9a1c4b4e5cccd906 |
#!/usr/bin/env python
import numpy as np
import pylab
from scipy.stats.distributions import gamma,norm as norm_dist
import Infer
from MyFuncs import Transit_aRs
#light curve parameters
lc_pars = [.0,2.5,11.,.1,0.6,0.2,0.3,1.,0.]
gp = [.0003,2.5,10.,.104,0.6,0.2,0.3,1.,0.]
hp = [0.0004,0.1,0.0001]
#create the data s... | nealegibson/Infer | examples/InferMGP_test1.py | Python | gpl-3.0 | 2,950 | [
"Gaussian"
] | f41ada0250f1efd5ac85541dd09431f935001add1f53148c3ab195952d97d28f |
from ploting import *
from neuron import *
from numpy import *
from fixedpoints import *
from stimulus import *
#import matplotlib.animation as animation
#################################
#structure of the network
N=3 #number of neurons
struct=ones(N) # excitatory or inhibitory neurons
##############################... | ulisespereira/LearningSequences | Plasticity/popModel/experiment.py | Python | gpl-2.0 | 3,963 | [
"NEURON"
] | c258c79f1b7b9b14eb71eae31477d961b983dec4d5b4033ea60836070900cba1 |
from __future__ import print_function, absolute_import
import os
import sys
import imp
import json
import string
import shutil
import subprocess
import tempfile
from distutils.dep_util import newer_group
from distutils.core import Extension
from distutils.errors import DistutilsExecError
from distutils.ccompiler import... | msultan/msmbuilder | basesetup.py | Python | lgpl-2.1 | 12,523 | [
"MDTraj"
] | 87cae4733b326e0790f84a6c8b2a55bb3aeabb3c14bcc9b27bbe649f308113ac |
# encoding: utf-8
# Copyright (C) 2015 John Törnblom
class Node(object):
'''
Tree node which may be walked a walker, and visited by a visitor.
'''
def __str__(self):
return self.__class__.__name__
class Visitor(object):
'''
A visitor may be used to visit tree nodes walked by a wa... | perojonsson/pyxtuml | xtuml/tools.py | Python | gpl-3.0 | 1,741 | [
"VisIt"
] | 4160e47f28614a75427ae49af16102030e6931cf9fbf6e021d6f865816eaef83 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/lb_electrohydrodynamics.py | Python | gpl-3.0 | 2,444 | [
"ESPResSo"
] | c19cfc86bf012b6aaa94147e0ee9a8dbaceb524470a17916b4e5cfb683d9d748 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
#from __future__ import print_function
import numpy as np
class Neuron(object):
def __init__(self, n_inputs):
self.w = np.random.random(size=n_inputs)
self.bias = np.random.random()
self.output_val = None
self.err =... | alliemacleay/MachineLearning_CS6140 | utils/NNet_5.py | Python | mit | 3,657 | [
"NEURON"
] | d9271f0afbbb6de57a495909b0e53c08a2422006ba35bd1300479c2c59ebd662 |
# Copyright 2016-2017 Capital One Services, 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 agreed ... | kapilt/cloud-custodian | tests/test_resolver.py | Python | apache-2.0 | 6,813 | [
"Galaxy",
"MOOSE"
] | fbd66bc6a0c5e88054355886cb2dabb2e474126ac7fd6b18a0b2be1f39719c5e |
from nose.plugins.attrib import attr
from splinter import Browser
from time import sleep
from selenium.common.exceptions import ElementNotVisibleException
from settings import settings
from lib import db
from lib import assets_helper
import unittest
from datetime import datetime, timedelta
asset_x = {
'mimetype': ... | wireload/screenly-ose | tests/splinter_test.py | Python | gpl-2.0 | 11,206 | [
"VisIt"
] | 2ea203b5158bc9b2fec692c87430ea53fbffecc4333e99a2f22d0c7d723ddb19 |
#!/usr/bin/python
import numpy as np, matplotlib.pyplot as plt, subprocess as sp, argparse
parser=argparse.ArgumentParser()
parser.add_argument('--option_tag',nargs='*')
parser.add_argument('--path',nargs='*')
args=parser.parse_args()
option_tag=''.join(args.option_tag)
path_current=''.join(args.path)
def add_in_di... | JXing-Lab/ME-SCAN-SVA | modules/JW_template_inheritance_calculation_for_latest_data_with_TPM-UR_filters.py | Python | gpl-3.0 | 10,639 | [
"BLAST"
] | f6186a7c3b6a105e28c467c55ee4c22c5afab888d893d4922a5f4a4db0101201 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides conversion between the Atomic Simulation Environment
Atoms object and pymatgen Structure objects.
"""
__author__ = "Shyue Ping Ong, Andrew S. Rosen"
__copyright__ = "Copyright 2012, The Materials Proj... | vorwerkc/pymatgen | pymatgen/io/ase.py | Python | mit | 7,493 | [
"ASE",
"pymatgen"
] | d5ab75abb6a297dec1e285378da4b6e393e4b14722c562bbd0f69ac8de437d58 |
"""Convenience functions for running common Picard utilities.
"""
import os
import collections
from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
def picard_rnaseq_metrics(picard, align_bam, ref, ribo="null", out_file=None):
""" Collect RNASeq metrics for a ... | a113n/bcbio-nextgen | bcbio/broad/picardrun.py | Python | mit | 13,620 | [
"pysam"
] | 321f7b28782277804f8aae89a1f7255ff4d4d2abf439a3f0b5430e09fac419f8 |
from pycparser import c_generator, c_ast
class CGenerator(c_generator.CGenerator):
def visit_FileAST(self, n):
"""
Slightly different than pycparser's version. Top level ids are #directives, no ;
"""
s = ''
for ext in n.ext:
if isinstance(ext, c_ast.FuncDef):
... | jamie-pate/jstruct | parse/jstruct_generator.py | Python | mit | 882 | [
"VisIt"
] | 89b6548bafec407807a3ea834438de163db633fb5dae0d2452a7543e5e1c0f67 |
"""
@name: Modules/House/Lighting/Controllers/__init__.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2020-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Feb 8, 2020
"""
__updated__ = '2020-02-18'
__version_info__ = (20, 2, 8)
__version__ = '.'.join(ma... | DBrianKimmel/PyHouse | Project/src/Modules/House/Lighting/Controllers/__init__.py | Python | mit | 927 | [
"Brian"
] | 17fec740a1ef87c1c0f9ad277d7df5f44a61f4a70e383cfdaecf7ef8322d4b86 |
"""
[10/10/2014] Challenge #183 [Hard] Dimensionality Reduction
https://www.reddit.com/r/dailyprogrammer/comments/2iy7xl/10102014_challenge_183_hard_dimensionality/
# [](#HardIcon) _(Hard)_: Dimensionality Reduction
I have submitted in such a long time so i though i give a hard challenge! This week's and next week's ... | DayGitH/Python-Challenges | DailyProgrammer/DP20141010C.py | Python | mit | 3,151 | [
"VisIt"
] | 7efa337d7dbfe3f9fab7ccb5117be3c865d4d95960b56b0ec5d3cd4cd7cc8816 |
""" Transition methods to allow to move from DEncode to JEncode
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
from DIRAC.Core.Utilities import DEncode, JEncode
__RCSID__ = "$Id$"
def encode(inData):
"""Encode the input data
:para... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/MixedEncode.py | Python | gpl-3.0 | 1,259 | [
"DIRAC"
] | 1183965a180d19475da01a467ca7e5a60fcd2e267411da9aac5ca06255e066e1 |
# coding: utf-8
from __future__ import unicode_literals
import re
import xml.etree.ElementTree
from .common import InfoExtractor
from ..utils import (
ExtractorError,
float_or_none,
int_or_none,
parse_duration,
parse_iso8601,
)
from ..compat import compat_HTTPError
class BBCCoUkIE(InfoExtractor)... | preparationh67/youtube-dl | youtube_dl/extractor/bbc.py | Python | unlicense | 34,127 | [
"VisIt"
] | 51611c57f206ba2df22cafdbc0495a1436ec43f6d805bc04265ff21c289bb994 |
from eventlet import hubs
from eventlet.support import greenlets as greenlet
__all__ = ['Event']
class NOT_USED:
def __repr__(self):
return 'NOT_USED'
NOT_USED = NOT_USED()
class Event(object):
"""An abstraction where an arbitrary number of coroutines
can wait for one event from another.
Ev... | Cue/eventlet | eventlet/event.py | Python | mit | 7,066 | [
"VisIt"
] | c24f207bc5172e25fcdcad01c6460d9cdca4a970469dcc74c00cae9acf2bc240 |
""" User Interface bits and widgets """
import collections
import tcod
from game import events, utils
class Widget(object):
"""
A widget is something that knows how to render itself. All things that know
how to render themselves are widgets.
Widgets may have child widgets; when a widget is told to re... | narc0tiq/NP-Complete | game/widgets.py | Python | mit | 15,829 | [
"Amber"
] | d9a258026196141cd6ae2c3da7a4e74e57f8030b17d1db41b0b46a0925904199 |
#!/usr/bin/env python3
import numpy as np
import typing as T
from mayavi import mlab
"""
trivial demo of Mayavi VTK visualization
using ionosphere-like space
Michael Hirsch
"""
def gsim(
z0: float = 200,
h0: float = 50,
n0: float = 1e12,
zlim: T.Sequence[float] = (100, 500),
dz: float = 2,
x... | scienceopen/mayavi-examples-python | volumetrans.py | Python | mit | 2,733 | [
"Mayavi",
"VTK"
] | 94f7a4ff03d68f013f666376ce8eda24e3dc1ee3e3920e8d1011f7eea902e2c3 |
"""Test TorsionFitModel"""
from torsionfit.tests.utils import get_fun
import torsionfit.database.qmdatabase as qmdb
from torsionfit.model_omm import TorsionFitModel as TorsionFitModelOMM
from torsionfit.model import TorsionFitModel
from torsionfit.backends import sqlite_plus
import torsionfit.parameters as par
from p... | ChayaSt/Torsions | torsionfit/tests/test_torsionFitModel.py | Python | gpl-2.0 | 7,569 | [
"CHARMM",
"OpenMM"
] | 8b5462b5033f2040b9590593598b5eb7b6c281a60edd259c02848365bed1c845 |
import sys
import os.path
#sys.path.insert(0, '/home/andy/theano/tool_examples/theano-lstm-0.0.15')
from theano_lstm import Embedding, LSTM, RNN, StackedCells, Layer, create_optimization_updates, masked_loss
from utilities import *
import dill
import argparse
#import cPickle
import pickle
import numpy
from collections... | darongliu/Lstm_Turing_LM | lstm-neural-turing-machines-lm/v2-adadelta/lm_v4.py | Python | mit | 25,420 | [
"NEURON"
] | a7e22fa8bd95a3798ed64b3f2c1d1f1b2ca39ae1a6d7d9c9638dd90eeef89fd2 |
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