text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""
==========================================================================
Using the free water elimination model to remove free water contamination
==========================================================================
As shown previously (see :ref:`example_reconst_dti`), the diffusion tensor
model is a simpl... | villalonreina/dipy | doc/examples/reconst_fwdti.py | Python | bsd-3-clause | 8,467 | [
"Gaussian"
] | 969baf1229f9a6cf40275e95c1cb097d22087427c4ec4f5cbfc7151bce7d523e |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | zasdfgbnm/tensorflow | tensorflow/contrib/py2tf/converters/list_comprehension.py | Python | apache-2.0 | 2,616 | [
"VisIt"
] | cf99566ab6c60e61980408a173d36cc315decc6f2d25c428bfbc6de745f27190 |
from dgw.data.parsers import bam as bam_parser
__author__ = 'saulius'
import unittest
from numpy.testing import *
import numpy as np
# -- Stub classes to simulate pysam behaviour ---
class StubAlignedRead(object):
def __init__(self, pos, alen, is_reverse):
self.pos = pos
self.alen = alen
s... | lukauskas/dgw | dgw/tests/data/parsers/test_bam.py | Python | gpl-3.0 | 7,992 | [
"pysam"
] | b2ca609eda392d28cd023cf39e1dad2686f8c4c5e048032e0d3a9a7ed48aa69d |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | willemneal/Docky | lib/pylint/checkers/classes.py | Python | mit | 42,351 | [
"VisIt"
] | fd90461c1c5779568714fc8521c5f686faed2d723d8b58bba6a5f97c92d9142a |
"""End-To-End Memory Networks.
The implementation is based on http://arxiv.org/abs/1503.08895 [1]
"""
from __future__ import absolute_import
from __future__ import division
import inspect
import tensorflow as tf
import numpy as np
from six.moves import range
from tensorflow.python.ops import rnn, rnn_cell
def posit... | tianlongwang/memn2n | memn2n/mc_memn2n.py | Python | mit | 16,941 | [
"Gaussian"
] | 276884f183cc54222b9ea807ed30b5496ed069edbb451acd24f424c162bde5ca |
"""
elite_mapping.py
Setup for the Elite control mapping.
Copyright (C) 2016 Bob Helander
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your optio... | bobhelander/launchpad_mapper | elite_mapping.py | Python | gpl-3.0 | 13,679 | [
"Galaxy"
] | 386cc8e94214ec5369f926cdf39bfffd61b3eb908edb21c9ecb2a6cde0dc8ead |
# Authors: Veeresh Taranalli <veeresht@gmail.com>
# License: BSD 3-Clause
"""
============================================
Pulse Shaping Filters (:mod:`commpy.filters`)
============================================
.. autosummary::
:toctree: generated/
rcosfilter -- Raised Cosine (RC) Filter.
rrcos... | tarunlnmiit/CommPy | commpy/filters.py | Python | bsd-3-clause | 4,729 | [
"Gaussian"
] | ce846408715a2f1cac3a7020316df1dc0b946486abbf9fcba80c5503bbcb3df0 |
#!/usr/bin/env python
'''
@name: probEstimate.py
@author: Juan C. Castro <jccastrog at gatech dot edu> & William T. Harvey <wharvey31@gatech.edu>
@update: 21-Jun-2017
@version: 1.0.8
@license: GNU General Public License v3.0.
please type "./protEstimate.py -h" for usage help
'''
'''1.0 Import modules, define function... | jccastrog/imGLAD | probEstimate.py | Python | gpl-3.0 | 4,852 | [
"BLAST"
] | 95da3310550d2bbd97d55e642c3abb4d36062a953f09d01d35fc408235628478 |
#!/usr/bin/env python
from pyscf import gto
from pyscf import scf
from pyscf import mrpt
from pyscf.dmrgscf import DMRGSCF
#
# NEVPT2 calculation requires about 200 GB memory in total
#
b = 1.5
mol = gto.Mole()
mol.verbose = 5
mol.output = 'cr2-%3.2f.out' % b
mol.atom = [
['Cr',( 0.000000, 0.000000, -b/2)],
... | gkc1000/pyscf | examples/dmrg/30-dmrg_casscf_nevpt2_for_Cr2.py | Python | apache-2.0 | 1,289 | [
"PySCF"
] | 6ed856cecd3299d57482a1804b628c87fa958bdaed4f612b984e13ab2b0dd4f5 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ghchinoy/tensorflow | tensorflow/python/data/experimental/benchmarks/rejection_resample_benchmark.py | Python | apache-2.0 | 2,654 | [
"DIRAC"
] | 583aa760b1ce3df2e521b8116ad71afd45ce3ac980921e9b3dcadb04f471535b |
#
# (c) 2015 Brian Ccoa, <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, either version 3 of the License, or
# (at your option) any later versio... | xpac1985/ansible | lib/ansible/module_utils/api.py | Python | gpl-3.0 | 3,198 | [
"Brian"
] | 27850f7e69a04045ae26e0209869e1b33efa0cf828a150ce8c1806c12ff287bd |
# -*- coding: utf-8 -*-
"""Test parsing variants."""
import logging
import re
import unittest
from pybel.constants import (
CONCEPT,
FRAGMENT,
FRAGMENT_DESCRIPTION,
FRAGMENT_MISSING,
FRAGMENT_START,
FRAGMENT_STOP,
FUSION_MISSING,
FUSION_REFERENCE,
FUSION_START,
FUSION_STOP,
... | pybel/pybel | tests/test_parse/test_parse_bel_variants.py | Python | mit | 16,938 | [
"Pybel"
] | 967fc4b34ffa56ce6eabefaee0584ea4738b7264a7f56db5e97f8fd11829dea1 |
#
# Copyright 2021 Jack Grigg
#
# This file is part of the Translate Toolkit.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later v... | miurahr/translate | translate/storage/fluent.py | Python | gpl-2.0 | 6,515 | [
"VisIt"
] | 402c17243b45ed14f7d2d35714492eea97e113216e63ba06a0c7664e0b29bfea |
#!/usr/local/sci/bin/python
# PYTHON3.6.1
#
# Author: Kate Willett
# Created: 18 Jul 2018
# Last update: 15 Apr 2019
# Location: /data/local/hadkw/HADCRUH2/UPDATE2017/PROGS/PYTHON/
# GitHub: https://github.com/Kate-Willett/HadISDH_Build
# -----------------------
# CODE PURPOSE AND OUTPUT
# ----------------------... | Kate-Willett/Climate_Explorer | PYTHON/ExtractMergeRegridERA_JUL2018.py | Python | cc0-1.0 | 44,486 | [
"NetCDF"
] | 8ced00da3ac75b08ccecd8cb2ae3720b00985fcf978da0b9e5d8effe57f9aaa9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, absolute_import
import os
import unittest
import mock
import nikola
import nikola.plugins.command.import_wordpress
from .base import BaseTestCase
class BasicCommandImportWordpress(BaseTestCase):
def setUp(self):
self.module = nikola.plugi... | x1101/nikola | tests/test_command_import_wordpress.py | Python | mit | 22,546 | [
"VisIt"
] | 1646948462bc1b7566692684c0e28d0c55669be586c890d1503fa574369e09bb |
"""Needed a way to go through the evaluation VCF from VCF benchmarking and spit out the FP and FN
calls into separate VCFs and then extract reads from those regions into a BAM.
vcffilter can mark the FP and FNs but leaves all the other records in. Would need to chain with vcftools
and at this point things are complica... | sbg/Mitty | mitty/benchmarking/filterevalvcf.py | Python | apache-2.0 | 1,782 | [
"pysam"
] | 88afa5b540a179455ff04833761446b251e86b4cc7e41cd2467ad7af4545e816 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/libcerf/package.py | Python | lgpl-2.1 | 2,049 | [
"Gaussian"
] | 7a0a33e04f4a406ce5aad1306b292df8ab3a2a2e7c6989dee51ceb29cacf839e |
#!/usr/bin/env python
#
# 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
# A... | zozo123/buildbot | slave/setup.py | Python | gpl-3.0 | 4,830 | [
"Brian"
] | 526e61913a1b671d7e9c44a975b8919461e1846f413acd6bf1e9b596ff93606d |
# proxy module
from __future__ import absolute_import
from mayavi.modules.surface import *
| enthought/etsproxy | enthought/mayavi/modules/surface.py | Python | bsd-3-clause | 91 | [
"Mayavi"
] | c07d5755cb9124654ff447a5926466cb1573a0a9c3f311a85c51c54fc3eb45e6 |
#!/usr/bin/env python
# Install.py tool to do automate build of Colvars
from __future__ import print_function
import sys,os,subprocess
# help message
help = """
Syntax from src dir: make lib-colvars args="-m machine -e suffix"
Syntax from lib/colvars dir: python Install.py -m machine -e suffix
specify -m and optio... | ovilab/lammps | lib/colvars/Install.py | Python | gpl-2.0 | 4,039 | [
"LAMMPS"
] | f58958e2992f10f065b571a57fa7d10fe4f5274390d6756c2827b3a2ba2e16ec |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual 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 L... | iwm911/plaso | plaso/parsers/plist_plugins/safari_test.py | Python | apache-2.0 | 2,306 | [
"VisIt"
] | 7a70ff35644223ec95c1fb07f31b7513cdcc0fed47293cfa4adee29d4fdd93fb |
########################################################################
# File: ReplicateAndRegister.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/13 18:49:12
########################################################################
""" :mod: ReplicateAndRegister
==========================
.. mo... | petricm/DIRAC | DataManagementSystem/Agent/RequestOperations/ReplicateAndRegister.py | Python | gpl-3.0 | 23,812 | [
"DIRAC"
] | 08a1b0c9eead2537406a2cb80fcb63d7d07da762db8aee801d91ef8427c2fd50 |
# Copyright (c) 2020, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | BlueBrain/NeuroM | neurom/features/morphology.py | Python | bsd-3-clause | 22,328 | [
"NEURON"
] | ea0c375a08c27951fca7da4e27f02a1e5d2261766aa176966ca57eab8b2088e8 |
from common import Modules, load_yara_rules, PEParseModule, ModuleMetadata
from pefile import PE, RESOURCE_TYPE
from string import printable
class CyberGate(PEParseModule):
first_value_table = None
precomputed_list = None
def __init__(self):
md = ModuleMetadata(
module_name="cybergate... | bwall/bamfdetect | BAMF_Detect/modules/cybergate.py | Python | mit | 6,827 | [
"Brian"
] | dcea76e32f7bf2aef53019dc31a208446b04a3485ddb56e7de19dbf96f9a98b5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import numpy as np
import warnings
import xml.etree.cElementTree as ET
from pymatgen.core.periodic_table import Element... | nisse3000/pymatgen | pymatgen/io/vasp/tests/test_outputs.py | Python | mit | 57,196 | [
"VASP",
"pymatgen"
] | aa393d21ab010551783e40c7a15d7f3f4ddc6683c2c8571890a98fcc1195dcaf |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Utilities for generating nicer plots.
"""
import math
import numpy as np
from pymatgen.core.periodic_table import Element
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Proje... | gVallverdu/pymatgen | pymatgen/util/plotting.py | Python | mit | 21,622 | [
"pymatgen"
] | 6af3af57b2322a6578dbe71fce76581d16e0be11dd4bc397eb5c1de43dae458d |
#
# Copyright (C) 2013,2014 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... | rbardak/espresso | testsuite/python/magnetostaticInteractions.py | Python | gpl-3.0 | 4,400 | [
"ESPResSo"
] | 2b5857c56117ecffc2e93f671c40ea40fcc2a91921a8f27e5f5b8d48b94bb958 |
# Copyright 2014 Open Connectome Project (http://openconnecto.me)
#
# 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... | neurodata/ndgrutedb | MR-OCP/mrcap/lcc.py | Python | apache-2.0 | 11,171 | [
"Mayavi"
] | ff287064e4e680749d0c583a3650bccff4d7777dd311762945ac16c2572f7480 |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris 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, or
# (at your option) any l... | ghislainp/iris | lib/iris/tests/test_grib_load.py | Python | gpl-3.0 | 28,650 | [
"Gaussian"
] | c8de41bcaea929c269010c78f44927ff5c4c4db4b573bb88b16cad48e5ccbf32 |
# Copyright (c) 2006, 2008, 2010, 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014 Brett Cannon <brett@python.org>
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2015-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015 Ionel Cristian Maries <contact@ionelm... | lucidmotifs/auto-aoc | .venv/lib/python3.5/site-packages/pylint/pyreverse/utils.py | Python | mit | 6,195 | [
"VisIt"
] | 972fd777b2fd8390909cb7d48834aec24ba943f6a900d38cd11e89beea71aa15 |
"""
Test the about xblock
"""
import datetime
import ddt
import mock
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.urls import reverse
from django.test.utils import override_settings
from milestones.tests.utils import MilestonesTestCaseMixin
from mock import patch
from... | jolyonb/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 28,229 | [
"VisIt"
] | fb1d46a9a42e8e944eea21bdc48b68a78f3f9479feb5fa836de9db3cfdc4e70f |
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from numpy import array
from numpy.testing import (assert_array_almost_equal, assert_array_equal,
run_module_suite, assert_raises, assert_allclose)
from scipy import signal
window_funcs = [
... | FRidh/scipy | scipy/signal/tests/test_windows.py | Python | bsd-3-clause | 9,372 | [
"Gaussian"
] | dc0289879474ba6c4fa753691ece68c4a9cc0b3cc50f37c4075a8be6060e0cf3 |
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 CERN.
##
## CDS Invenio 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 (... | lbjay/cds-invenio | modules/miscutil/lib/dbquery.py | Python | gpl-2.0 | 17,539 | [
"BLAST"
] | e017ea33cdfd08630ebc671c0b5fa0260db3fa72fc33d0f39e8080560c603653 |
# Copyright (C) 2020 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 versio... | espressomd/espresso | testsuite/scripts/samples/test_reaction_ensemble_complex_reaction.py | Python | gpl-3.0 | 1,700 | [
"ESPResSo"
] | e61b69abaa36da95816d34f2954ca33073523b4da6900f0aa57c671310b901b5 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import os
from os import path as op
import sys
from struct import pack
from glob import glob
import numpy as... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/mne/surface.py | Python | bsd-3-clause | 41,230 | [
"Mayavi"
] | cda162b96195424efbc0641dfed6cc15cc5c7ffc18669a61823cad578a5fa03b |
# Orca
# Copyright (C) 2016 UrbanSim Inc.
# See full license in LICENSE.
from __future__ import print_function
try:
from inspect import getfullargspec as getargspec
except ImportError:
from inspect import getargspec
import logging
import time
import warnings
from collections import namedtuple
try:
from co... | synthicity/orca | orca/orca.py | Python | bsd-3-clause | 60,782 | [
"ORCA"
] | 23006be0b6dfb43fc5e3af670282c57b61a18e797c575d21fa5eb91a93399e83 |
import json
from django.http import HttpResponse
from django.shortcuts import get_object_or_404
from django.db import connection
from django.contrib.auth.models import User
from catmaid.control.authentication import requires_user_role, \
can_edit_class_instance_or_fail, can_edit_all_or_fail
from catmaid.contr... | htem/CATMAID | django/applications/catmaid/control/neuron.py | Python | agpl-3.0 | 8,383 | [
"NEURON"
] | a1eb45dfcbccf5c075d498ae91cad2dcbe733bf87dbe7386b4f95bd7632d2e26 |
"""
@name: Modules/Core/Mqtt/_test/test_protocol.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Jun 3, 2015
@Summary:
Passed all 4 tests - DBK- 2019-08-15
"""
from Modules.Core.Config.config_tools impor... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Mqtt/_test/test_mqtt_protocol.py | Python | mit | 2,548 | [
"Brian"
] | 0eaf781adc32b9cff531ed94dff1dd8d481e86798bf3b22b12ae9e10d4c91060 |
"""
Append data to an existing CTD Profile dataset
==============================================
Use the TAMOC ambient module to append data to a CTD Profile object that has
already been created as in the other examples in this ./bin director. This
file demonstrates working with the data from the R/V Brooks McCall at... | socolofs/tamoc | bin/ambient/np_profile_append.py | Python | mit | 5,445 | [
"NetCDF"
] | 6d547451d5683b09f46698948d40249fca5624b6217e663335a7a06159670264 |
# Copyright 2015 Adriana Supady & Mateusz Marianski
#
# This file is part of fafoom.
#
# Fafoom 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, or
# (at yo... | FHIBioGroup/fafoom-dev | fafoom/measure.py | Python | gpl-3.0 | 15,433 | [
"RDKit"
] | 09e8f5cade117646140d3a499e49b424ec05c1f0eb6a69cbf30f3900fd807819 |
#!/usr/bin/env python
'''
Script to read data from DEIMOS EK60 instrument at MARS and write out NetCDF.
Use the conventions for timeSeriesProfile feature type and write as much metadata as possible.
This script is meant to preserve the data identically as it is reported in the orignal files.
Mike McCann
MBARI 10 Jun... | stoqs/stoqs | stoqs/loaders/CANON/toNetCDF/deimosCSVToNetCDF.py | Python | gpl-3.0 | 10,997 | [
"NetCDF"
] | 3cb9eb9b26114a813ceee237437a092c94fd3d9051f462c5f7bf69aa214fb3a4 |
"""Support for package tracking sensors from 17track.net."""
from datetime import timedelta
import logging
from py17track import Client as SeventeenTrackClient
from py17track.errors import SeventeenTrackError
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA
from homeassistant.const... | postlund/home-assistant | homeassistant/components/seventeentrack/sensor.py | Python | apache-2.0 | 10,853 | [
"VisIt"
] | 95ca4440f70942bd10a169347a04b1b2e70c9e0380a039a74f559686c5894c61 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = '''
module: systemd
author:
- Ansible C... | privateip/ansible | lib/ansible/modules/systemd.py | Python | gpl-3.0 | 23,358 | [
"Brian"
] | 94293668e0a78651055536cbbbde3c902c9762e94c48338795aa339d12c86dc6 |
#### Convenience Functions to be moved to kerneltools ####
import numpy as np
def forrt(X,m=None):
"""
RFFT with order like Munro (1976) FORTT routine.
"""
if m is None:
m = len(X)
y = np.fft.rfft(X,m)/m
return np.r_[y.real,y[1:-1].imag]
def revrt(X,m=None):
"""
Inverse of forr... | pprett/statsmodels | statsmodels/nonparametric/kdetools.py | Python | bsd-3-clause | 1,766 | [
"Gaussian"
] | 75553c9fbf2b54dc6d8d89b964e5d952b7897ea8899d517e6003a968e89c5226 |
from __future__ import division
import numpy as np
na = np.newaxis
import operator
import parallel
def kde(sigma,locs,vals=None):
'''
returns a density function p defined by
p(x) = \sum_{xbar \in locs} vals[xbar] * rbf(xbar,x; sigma)
rbf(xbar,x; sigma) is the value of a normalized isotropic gaussi... | mattjj/dirichlet-truncated-multinomial | density.py | Python | mit | 1,623 | [
"Gaussian"
] | 482e0eb98934d275ee4aefe65730dd7cf36f76be3abac683d99c3bdbad3a8a45 |
# Version: 0.14+dev
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* [![Latest Version]
(https://pypip.in/version/versioneer/badge.svg?style=flat)
... | jshiv/turntable | versioneer.py | Python | mit | 57,307 | [
"Brian"
] | c42f23e30a70b8cae136749eefde20b0fed8b7811751862576acee2e1d11163d |
"""
@name: PyHouse_Install/src/uninstall.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2016 by D. Brian Kimmel
@license: MIT License
@note: Created Jan 12, 2016
@Summary:
"""
import subprocess
def cleanup():
# sudo deluser pyhouse
subprocess.call('sudo'... | DBrianKimmel/PyHouse_Install | uninstall.py | Python | mit | 640 | [
"Brian"
] | f7f1e7d72e9543c3cb5e682cd8ecc6ef772c39e07c330a57343104968e6147eb |
Dict = {"10guy": "10+Guy",
"chucknorris": "3g3xw",
"anditsgone": "Aaaaand+Its+Gone",
"advicemallard": "Actual+Advice+Mallard",
"aintnobodygottimeforthat": "Aint+Nobody+Got+Time+For+That",
"amitheonlyone": "Am+I+The+Only+One+Around+Here",
"ancientaliens": "Ancient+Aliens",... | adisuciu/AeB-Telegram-Bot | meme.py | Python | gpl-2.0 | 4,143 | [
"Brian"
] | ec2ee3470d3dc52ef8b81e681e5e6ec9ca36acb25df587f6f8dff8f179cb0724 |
#
# Copyright 2001 - 2016 Ludek Smid [http://www.ospace.net/]
#
# This file is part of Outer Space.
#
# Outer Space 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
# (... | ospaceteam/outerspace | server/lib/ige/ospace/Scanner.py | Python | gpl-2.0 | 5,575 | [
"Galaxy"
] | 050caf3d17813b0277c89f07067e344378a397e453f9e7c7e34067d79cd6824d |
# -*- coding: utf-8 -*-
# This file is part of periscope3.
# Copyright (c) 2013 Roman Hudec <black3r@klikni.cz>
#
# This file contains parts of code from periscope.
# Copyright (c) 2008-2011 Patrick Dessalle <patrick@dessalle.be>
#
# periscope is free software; you can redistribute it and/or modify
# ... | black3r/periscope3 | periscope/plugins/TvSubtitles.py | Python | gpl-2.0 | 10,030 | [
"Firefly"
] | fcbbab762bb0b45e25937e6f8c14c72541e65f9c937961a41e0796b998e3269b |
######################################################################
# Copyright (C) 2013-2014 Jaakko Luttinen
#
# This file is licensed under Version 3.0 of the GNU General Public
# License. See LICENSE for a text of the license.
######################################################################
###############... | nipunbatra/bayespy | bayespy/demos/lssm.py | Python | gpl-3.0 | 11,413 | [
"Gaussian"
] | 4565e9c26e3a837d2cfb4d044bc9f87fedd0d3cabca9a74a999d694d4671156e |
#!/usr/bin/env python
# Copyright (C) 2004 Rune Linding & Lars Juhl Jensen - EMBL
# The DisEMBL is licensed under the GPL license
# (http://www.opensource.org/licenses/gpl-license.php)
# DisEMBL pipeline
# Modified to work with current versions of Biopython (1.7+)
# by Shyam Saladi (saladi1@illinois.edu), Janauary 20... | jurnho/DisEMBL-1.4-fix | DisEMBL-1.4/DisEMBL.py | Python | gpl-2.0 | 6,498 | [
"Biopython"
] | d0655f00ed8137358586cbfc79c15888f39272d352e6ec2923901bd8f0b44262 |
"""
This class is used to define the plot using the plot attributes.
"""
from DIRAC import S_OK
from DIRAC.MonitoringSystem.Client.Types.PilotMonitoring import PilotMonitoring
from DIRAC.MonitoringSystem.private.Plotters.BasePlotter import BasePlotter
class WMSHistoryPlotter(BasePlotter):
"""
.. class:: Pi... | ic-hep/DIRAC | src/DIRAC/MonitoringSystem/private/Plotters/PilotMonitoringPlotter.py | Python | gpl-3.0 | 4,264 | [
"DIRAC"
] | 29bcdd632d7f1109382d78afed534f3a148709e6b622825c86b1d1d773ba137e |
import unittest
from test import support
from itertools import *
from weakref import proxy
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def lzip(*args):
... | mancoast/CPythonPyc_test | fail/314_test_itertools.py | Python | gpl-3.0 | 67,570 | [
"GULP"
] | 123ec438a1a121480c404818f540d1dadad6acc9258f6db00d4cf9cf1bf2591d |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http:/... | stuart-knock/tvb-framework | tvb/interfaces/web/controllers/spatial/base_spatio_temporal_controller.py | Python | gpl-2.0 | 16,353 | [
"Gaussian"
] | f694dff6b1153c0f8c955ca42f597017642715536ab23cdec399483766369345 |
"""Functionality to query and extract information from aligned BAM files.
"""
import collections
import contextlib
import os
import itertools
import subprocess
import numpy
import pysam
import toolz as tz
from bcbio import utils
from bcbio.bam import ref
from bcbio.distributed import objectstore
from bcbio.distribute... | guillermo-carrasco/bcbio-nextgen | bcbio/bam/__init__.py | Python | mit | 18,753 | [
"pysam"
] | c8550e49b637874db8c1c5a365f9726f78e116b203688fc68e2876c338385429 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Module to test fitting routines
"""
# pylint: disable=invalid-name
import os.path
import warnings
from unittest import mock
from importlib.metadata import EntryPoint
import pytest
import numpy as np
import unittest.mock as mk
from numpy import linalg
... | pllim/astropy | astropy/modeling/tests/test_fitters.py | Python | bsd-3-clause | 49,705 | [
"Gaussian"
] | fd857ada0fd26e96966ed5171cf85e8a2ca5c1dc8976c3d3a924bf6a15deedb0 |
#pylint: disable=no-init
from __future__ import (absolute_import, division, print_function)
import stresstesting
from mantid.simpleapi import *
#----------------------------------------------------------------------
class ConvertToMDworkflow(stresstesting.MantidStressTest):
"""
"""
tolerance = 1e-5
... | dymkowsk/mantid | Testing/SystemTests/tests/analysis/ConvertToMDworkflow.py | Python | gpl-3.0 | 3,907 | [
"CRYSTAL"
] | f17b94b1eff55bb53082d6972a2911e8ffcc2c85a1a10c6ccbc594d45a0e7237 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-documentai | tests/unit/gapic/documentai_v1beta2/test_document_understanding_service.py | Python | apache-2.0 | 65,523 | [
"Octopus"
] | b41ba4f573291292a29a96a867f3693197d722750d8fe10139083cc34b0dc5d8 |
# -*- coding: utf-8 -*-
"""
Created on Tue Nov 1 18:45:15 2016
@author:
"""
# LECTURA Y GRAFICADO RADAR (Formato binario GVAR-SMN)
import numpy as np
import matplotlib as plt
import datetime as dt
import binary_io as bio
import bred_vector_functions as bvf
import os
basedir='/data9/jruiz/EXPERIMENTS/'
expname = ... | gustfrontar/LETKF_WRF | wrf/verification/python/plot_letkfpert_growthrate.py | Python | gpl-3.0 | 8,806 | [
"Gaussian"
] | 39887852ddbc798261a5f47fdada88c72855a785a14feecd618b7381da35edfa |
#!/usr/bin/env python
#
# License: BSD
# https://raw.githubusercontent.com/stonier/py_trees/devel/LICENSE
#
##############################################################################
# Documentation
##############################################################################
"""
Visitors are entities that can ... | stonier/py_trees_suite | py_trees/visitors.py | Python | bsd-3-clause | 4,739 | [
"VisIt"
] | 44fb90368276ae227796cbe97a84397849b438019bb97cef4653f41da88f467b |
# Copyright (C) 2004-2008 Paul Cochrane
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distribut... | paultcochrane/pyvisi | examples/ellipsoidPlot.py | Python | gpl-2.0 | 1,977 | [
"VTK"
] | 64511d60c811412d35469f1ef932b49ad063ffc0e78b3fdc6612e9aca3ae9784 |
# -*- coding: utf-8 -*-
"""
Spike Triggered Average calculator
Input:
stimulus (t)
spike spikeTimes (t)
if no spiketimes, generate randoms
Given stim and spiketimes, grabs the spike windows, and calcs the spike triggered average.
output:
spike triggered average
Created on Wed Feb 11 21:20:00 2015
@author: Rich... | isomerase/MyPyGLM | calc_STA.py | Python | mit | 2,653 | [
"Gaussian"
] | b11445f9a05e63adcaa2c85208d2d3932f8d386b103ca476e0a41752c7661eed |
"""System test for multivariate TE using the discrete JIDT estimator."""
import os
import numpy as np
from idtxl.multivariate_te import MultivariateTE
from idtxl.data import Data
from test_estimators_jidt import _get_gauss_data
from idtxl.idtxl_utils import calculate_mi
def test_multivariate_te_corr_gaussian(estimato... | pwollstadt/trentoolxl | test/systemtest_multivariate_te_discrete.py | Python | gpl-3.0 | 13,241 | [
"Gaussian"
] | f68503f15accb1b55948c9f1d45af06e5700b3d04ae9a0332af85840af5012e4 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse
import sys
import fnmatch
import os
import dma_resolver
import shlex
import pickle
import re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directo... | Pedals2Paddles/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 68,886 | [
"CRYSTAL"
] | d6b04cbf554a67b7bff65906bfa4be80b34990ac09950c5d1ff01db2bbc2e63a |
import POVME.packages.binana.peel as peel
#import packages.pymolecule.pymolecule as pymolecule
#import numpy
my_params = peel.defaultParams
#my_protein = pymolecule.Molecule()
ligand = peel.PDB()
ligand.LoadPDB('3CZ_reduced.pdb')
#my_protein.fileio.load_pdb_into('3CZ_reduced.pdb', bonds_by_distance=True, serial_reinde... | POVME/POVME | POVME/packages/binana/tests/peel_lig_basic/ligTest.py | Python | mit | 1,325 | [
"VMD"
] | 24232f2be14a71318492c1cca0f9cc5dd690093c6251351fca403fdd2606deb2 |
from astn import AstToGAst, GAstToAst
import ast
import gast
class Ast2ToGAst(AstToGAst):
# mod
def visit_Module(self, node):
new_node = gast.Module(
self._visit(node.body),
[] # type_ignores
)
return new_node
# stmt
def visit_FunctionDef(self, node):... | iproduct/course-social-robotics | 11-dnn-keras/venv/Lib/site-packages/gast/ast2.py | Python | gpl-2.0 | 12,391 | [
"VisIt"
] | 9d6d491f33f788e3127725d21ed310273b1d7f1847b1c4a05ce2b0b17bf38e2e |
"""
Plotting functions.
(c) Oscar Branson : https://github.com/oscarbranson
"""
import itertools, re, warnings
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
from scipy.stats import gaussian_kde
from scipy.optimize import curve_fit
# from IPython import display
from pandas import IndexSli... | oscarbranson/latools | latools/helpers/plot.py | Python | mit | 44,377 | [
"Gaussian"
] | 5e67a86c00d07a6d9c7a89b2ac329ed4ca397a511b37ebc9a4d857c5f84d0cf7 |
import sys;
sys.path.append("/Users/roger/Dropbox/pyglm-master/pyglm/")
sys.path.append("/Users/roger/Dropbox/pyglm-master/pyglm/utils/")
import numpy as np
import pickle
np.random.seed(150)
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_style("white")
sns.set_context("paper")
plt.ion()
from pybasic... | sheqi/TVpgGLM | demo/syn_LDM_weight_demo1.py | Python | mit | 5,247 | [
"NEURON"
] | 5dd8029d5fa7c69cda1904a5df5ea44d5e089417446d91f4c299c75be0870fd4 |
../../../../../../../share/pyshared/orca/scripts/apps/gnome-panel/speech_generator.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/gnome-panel/speech_generator.py | Python | gpl-3.0 | 85 | [
"ORCA"
] | a1465958cd28f83c1d0d89555efbdbd3a590b575fb7a0b1e0df1a18be0fca0c5 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements input and output processing from PWSCF.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Virtual Lab"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "ongsp@ucsd.edu"
__date_... | rousseab/pymatgen | pymatgen/io/pwscf.py | Python | mit | 7,309 | [
"CRYSTAL"
] | 6627dbb8ac07ab7d11b090c79b0dcd0fb9826def8da9efcdfee5b5369828f5a1 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
__author__ = '7sDream'
import os
import shutil
from datetime import datetime
from zhihu import ZhihuClient, ActType, CollectActType, ANONYMOUS
def test_question():
url = 'http://www.zhihu.com/question/24825703'
question = client.question(url)
# 获取该问题的详细描述... | 7sDream/zhihu-py3 | test/zhihu-test.py | Python | mit | 26,626 | [
"VisIt"
] | 5bd4c4fb51e45f019c00f5251dfd7d84b98a7663474489438a5dfe5f51a9d856 |
# -*- coding: utf-8 -*-
"""
sphinx.writers.texinfo
~~~~~~~~~~~~~~~~~~~~~~
Custom docutils writer for Texinfo.
:copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
import string
import textwrap
from os import path
from docutils imp... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sphinx/writers/texinfo.py | Python | agpl-3.0 | 44,646 | [
"VisIt"
] | 8821ff1ada157035858ef7e3e1368627a7647b3335089eb2dd04307ce33e150e |
# -*- coding: utf-8 -*-
#
# brunel_alpha_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licen... | hakonsbm/nest-simulator | pynest/examples/brunel_alpha_nest.py | Python | gpl-2.0 | 14,167 | [
"NEURON"
] | 217ff3a4251e7b07dd264ea3972cbf126ba94889290f1078de48347bd1a33597 |
import os
import sys
import numpy as np
from flare.otf_parser import OtfAnalysis
from flare.env import AtomicEnvironment
from flare.predict import predict_on_structure
from ase.io import read
def test_parse_header():
os.system("cp test_files/sample_slab_otf.out .")
header_dict = OtfAnalysis("sample_slab_otf... | mir-group/flare | tests/test_parse_otf.py | Python | mit | 3,817 | [
"ASE"
] | 979f02f3e94f3133f6e4ad1b781744ddbc4a5db8569c7b1a3032e04cd4194918 |
from functools import total_ordering
from dark.score import HigherIsBetterScore, LowerIsBetterScore
@total_ordering
class _Base(object):
"""
Holds information about a matching region from a read alignment.
You should not use this class directly. Use one of its subclasses,
either HSP or LSP, dependin... | terrycojones/dark-matter | dark/hsp.py | Python | mit | 7,156 | [
"BLAST"
] | f8b348b24edea16c9058dd4a8117c74d5ccee269ce74c7803ed2c5401d11ee4d |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-dataflow-client | tests/unit/gapic/dataflow_v1beta3/test_flex_templates_service.py | Python | apache-2.0 | 52,176 | [
"Octopus"
] | 164a83dd17b34eb58c7cb92875e0d6650f39989e623d9225d83ad95a8be77b38 |
#!/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/dft/test/test_grids.py | Python | apache-2.0 | 5,058 | [
"PySCF"
] | e4af4153bdbbef39de92ebbd6b875534f67c72468388e0d67008d33a25a6ebd3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License,... | sparkslabs/kamaelia_ | Sketches/MPS/Old/Compose/Compose/GUI/BuilderControlsGUI.py | Python | apache-2.0 | 9,668 | [
"DIRAC"
] | 62c3e720719c1c2c8eecbe507847ed5deaae41205d398ee486cb286a0f0862e1 |
# -*- coding: latin-1 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# 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 ... | FedoraScientific/salome-hexablock | doc/test_doc/make_transformation/make_translation.py | Python | lgpl-2.1 | 1,307 | [
"VTK"
] | 9270315e61a577b33019ebd4993d55e33bb1fc0861b14dcf88a61e3aac5f0095 |
# coding=utf-8
# coding=utf-8
import time
import os
import subprocess
import sys
from sys import argv
from subprocess import call
import glob
import shutil
from argparse import (ArgumentParser, FileType)
import logging
import yaml
import re
import thread
import threading
from threading import Thread
global pipeline_pa... | wholeGenomeSequencingAnalysisPipeline/BacPipe | Pipeline_cmd.py | Python | gpl-3.0 | 52,132 | [
"BLAST"
] | dacf3b1c3be4f8a6b4a58be867025cd946fbc5b2e1435cd8aae0feb5985bbe51 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011-2012 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | jralls/gramps | gramps/gui/plug/report/_reportdialog.py | Python | gpl-2.0 | 30,880 | [
"Brian"
] | 3ff9d5086b802791783c115c79a30af6000d446358b11fbf5f0630a8c8c0c143 |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2017 IBM Corporation
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 agre... | open-power-sdk/migration-advisor | ma/visitor.py | Python | apache-2.0 | 3,748 | [
"VisIt"
] | 6c38fab94d6c59ee75d6eb309fef97f1b63a31d65f3e6a5a4383721a1fd44712 |
#!/usr/bin/python
# -*- coding: latin-1 -*-
## This is a class I pulled off of stackoverflow--- may be useful for reference
import calendar
import Bio
from Bio import Entrez
def format_ddate(ddate):
"""Turn a date dictionary into an ISO-type string (YYYY-MM-DD)."""
year = ddate['Year']
month = ddate['Mon... | dgutman/ADRC_Analytics | src/PubmedPulled_ExampleClass.py | Python | apache-2.0 | 7,022 | [
"Biopython"
] | fac713d71d068b183815bf90d2aa1949208371cf16f6c9abed3947b9b8f7817e |
from __future__ import unicode_literals
import unittest
from django.utils import html
class TestUtilsHtml(unittest.TestCase):
def check_output(self, function, value, output=None):
"""
Check that function(value) equals output. If output is None,
check that function(value) equals value.
... | cobalys/django | tests/regressiontests/utils/html.py | Python | bsd-3-clause | 5,490 | [
"ADF"
] | e8699a659f4cd893789cd41ddf34c89ad1a4a2d0abbc6fced69d5c42d98e28aa |
#!/usr/bin/env python
# Copyright 2015(c) The Ontario Institute for Cancer Reserach. All rights reserved.
#
# This program and the accompanying materials are made available under the
# terms of the GNU Public License v3.0.
#
# You should have received a copy of the GNU General Public License along with
# this program... | oicr-ibc/cssscl | setup.py | Python | gpl-3.0 | 2,016 | [
"Biopython"
] | 1bfe24c5296a66ccf5bf360f3fcdbfca2fb997b33b035f24e0de3aff1fb434f2 |
# $HeadURL$
# $Id$
__version__ = "0.10-svn"
__license__ = """
Mirage, a fast GTK+ Image Viewer
Copyright 2007 Scott Horowitz <stonecrest@gmail.com>
This file is part of Mirage.
Mirage is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fre... | xiongchiamiov/Mirage | mirage.py | Python | gpl-3.0 | 222,023 | [
"FLEUR"
] | 335d441952d99b8f448de634fd312dbb9c0745b0cfd57bd4266d506ad3b6d269 |
## serpent.py - pure Python implementation of the Serpent algorithm.
## Bjorn Edstrom <be@bjrn.se> 13 december 2007.
##
## Copyrights
## ==========
##
## This code is a derived from an implementation by Dr Brian Gladman
## (gladman@seven77.demon.co.uk) which is subject to the following license.
## This Python ... | geheimnis/core-commands | cryptoalgo/symmetric/serpent.py | Python | gpl-3.0 | 70,557 | [
"Brian"
] | 5ffb70769584db678f222cf90dfdde19d7659e4b0bf2d7dbe5fa70bd633ebaa0 |
from setuptools import setup
VERSION = '0.0.1'
QUALIFIER = ''
DISTNAME = 'fixnc'
LICENSE = 'MIT'
AUTHOR = 'Nikolay Koldunov'
AUTHOR_EMAIL = 'koldunovn@gmail.com'
URL = 'https://github.com/koldunovn/fixnc/'
CLASSIFIERS = [
'Development Status :: 3 - Alpha',
'License :: OSI Approved :: MIT License',
'Opera... | koldunovn/fixnc | setup.py | Python | mit | 1,661 | [
"NetCDF"
] | 0bae51c5d911b807c8eb76de7d5e801193ebbd1d7bd4b31b00d8bf006cfc5f6b |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/gto/test/test_mole.py | Python | apache-2.0 | 39,894 | [
"Gaussian",
"NWChem",
"PySCF"
] | d6171d7913bca4a33b725889b7e518f44e77d763f59cc35465ff91c3c43fb6e1 |
"""Base class for mixture models."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
from __future__ import print_function
import warnings
from abc import ABCMeta, abstractmethod
from time import time
import numpy as np
from .. impor... | Titan-C/scikit-learn | sklearn/mixture/base.py | Python | bsd-3-clause | 16,655 | [
"Gaussian"
] | bbf310a1c16a67e1f2a8f832e9ddc9cf4fc713781bcd40da2f0e837c8a88cc0c |
from dateutil.relativedelta import relativedelta
from edc_visit_schedule import VisitSchedule, Schedule, Visit, Panel
from edc_visit_schedule import FormsCollection, Crf, Requisition
crfs = FormsCollection(
Crf(show_order=1, model='edc_metadata.crfone', required=True),
Crf(show_order=2, model='edc_metadata.cr... | botswana-harvard/edc-visit-tracking | edc_visit_tracking/tests/visit_schedule.py | Python | gpl-2.0 | 3,492 | [
"VisIt"
] | 1c73867f12fd3b0ef0c4fcdfa22f6c00c22a32c6f76a5c37567aaeb7bc92bdfd |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | eagle/connection.py | Python | agpl-3.0 | 4,327 | [
"Galaxy"
] | 480c72b0ee7939c3b14ae77def111ba5abc07f24319454f3d763b6ec0c2a541d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Hybrid LFP scheme example script, applying the methodology with the model of:
Potjans, T. and Diesmann, M. "The Cell-Type Specific Cortical Microcircuit:
Relating Structure and Activity in a Full-Scale Spiking Network Model".
Cereb. Cortex (2014) 24 (3): 785-806.
doi: ... | INM-6/hybridLFPy | examples/Hagen_et_al_2016_cercor/cellsim16pops_modified_ac_inh.py | Python | gpl-3.0 | 6,659 | [
"NEURON"
] | d71fd09544b0615db18620d2587630fc93ecdb6ec01dd7fcab9bbbf699962281 |
import os
import numpy as np
import sys
import itertools
import multiprocessing as mp
import getopt
try:
opts, args = getopt.getopt(sys.argv[1:],"r:n:",["ref-transcriptome=","njobs="])
except getopt.GetoptError:
print ("getopterrror")
print ('usage is : \n python process_xprs.py [-n number-of-processes-to... | govinda-kamath/clustering_on_transcript_compatibility_counts | Zeisel_pipeline/process_xprs.py | Python | mit | 1,102 | [
"Bowtie"
] | 35429ceb465383a3efb7f5cc34a8d32c2dba48a57c63dab919c1b7b049752ba8 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2017 Francois Beaune, The appleseedhq Organizatio... | Aakash1312/appleseed | scripts/rendermanager.py | Python | mit | 21,721 | [
"VisIt"
] | 6a0f16f6b0a241854c4ed164711d534ddaa1c0008d9f70746de4dce8e15816f3 |
def run_singlepoint(parameters):
""" Drive the calculation, based on passed parameters
Args:
parameters (dict): dictionary describing this run (see
https://github.com/Autodesk/molecular-design-toolkit/wiki/Generic-parameter-names )
"""
mol =
class PySCFCalculator(object):
... | molecular-toolkit/chemistry-docker-images | makefiles/buildfiles/pyscf/run.py | Python | apache-2.0 | 1,558 | [
"PySCF"
] | a03aaebf483c501e2304103fdd04655bf9d72ee8ae22b3187fab7213bf39c1c1 |
"""Minimal Python 2 & 3 shim around all Qt bindings
DOCUMENTATION
Qt.py was born in the film and visual effects industry to address
the growing need for the development of software capable of running
with more than one flavour of the Qt bindings for Python - PySide,
PySide2, PyQt4 and PyQt5.
1. Bu... | krathjen/studiolibrary | src/studiovendor/Qt.py | Python | lgpl-3.0 | 56,512 | [
"VisIt"
] | cb0adba3f07913a5333a8aead5e7d8ae2a3a20652a049a84e12b97c6baa27306 |
# -*- coding: utf-8 -*-
# python-holidays
# ---------------
# A fast, efficient Python library for generating country, province and state
# specific sets of holidays on the fly. It aims to make determining whether a
# specific date is a holiday as fast and flexible as possible.
#
# Author: ryanss <ryanssdev@icl... | ryanss/python-holidays | tests.py | Python | mit | 274,276 | [
"COLUMBUS"
] | 80ca879fbac2322e8903c48868036217b407c02923e1a95d3ee0e076befbae5b |
#!/usr/bin/env python
# Copyright 2014-2021 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/kuhf.py | Python | apache-2.0 | 13,207 | [
"PySCF"
] | 8ab7789056265950013e2aa533f92e0c94234451554f727915eed5571c006d40 |
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