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# -*- coding: utf-8 -*-
import itertools
import os
import re
import urllib
import logging
import datetime
import urlparse
from collections import OrderedDict
import warnings
import pytz
from flask import request
from django.core.urlresolvers import reverse
from modularodm import Q
from modularodm import fields
from m... | sbt9uc/osf.io | website/project/model.py | Python | apache-2.0 | 125,658 | [
"VisIt"
] | 64ac9fdfc07d6f607f5f804189d958df44fcd961475502ca3d6012d70eccbb67 |
#!/usr/bin/python -u
import os
import sys
import fnmatch
# do a basic check to see if pylint is even installed
try:
from pylint.__pkginfo__ import version as pylint_version
except ImportError:
print "Unable to import pylint, it may need to be installed"
sys.exit(1)
# Classes of errors we ignore on quiet ... | kylazhang/virt-test | tools/run_pylint.py | Python | gpl-2.0 | 4,357 | [
"VisIt"
] | bf32b0c7ec3dc5a6d7a7f7ebed7aeb43d0faf235184efca88e617dbb0007a64e |
"""Grow preprocessors."""
import json
from protorpc import protojson
from grow.preprocessors import blogger
from grow.preprocessors import google_drive
from grow.preprocessors import gulp
from grow.preprocessors import webpack
from grow.common import extensions
_preprocessor_kinds_to_classes = {}
_builtins = (
b... | grow/pygrow | grow/preprocessors/preprocessors.py | Python | mit | 1,620 | [
"GULP"
] | 475b7217ba2d68f3c4088876a1039ed3bca65ce350317a8410ff249ae8f83c2a |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 6 20:43:23 2017
@author: zqwu
"""
from __future__ import division
from __future__ import unicode_literals
import numpy as np
import tensorflow as tf
from deepchem.models.tensorgraph import activations
from deepchem.models.tensorgraph import initia... | Agent007/deepchem | deepchem/models/tensorgraph/symmetry_functions.py | Python | mit | 17,234 | [
"Gaussian"
] | a0402f850920b6f3fd768f5eecfcf5453e6e5de181abb1a16db421ec6deccea0 |
import random
import string
import unittest
from game import Game, Player
class TestUDontKnowMe(unittest.TestCase):
def setUp(self):
self.brian = Player("Brian")
self.billy = Player("Billy")
self.john = Player("John")
self.jordan = Player("Jordan")
self.rob = Player("Rob")... | udontknowmeapp/udontknowme | webapp/game/tests.py | Python | gpl-2.0 | 8,002 | [
"Brian"
] | a6aeeb04aacea54f463edb0199c4187a343c8309591cdca01ec3de8324ae8aa0 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/people/views/persons.py | Python | gpl-3.0 | 12,094 | [
"Brian"
] | 8054963ed7b279cd843e2273fc0714e557e13ad9c4e6c68b105cd27ffa2c528f |
#!/usr/bin/env python
"""
This file provides a more advanced example of vtkTable access and
manipulation methods.
"""
from __future__ import print_function
from vtk import *
#------------------------------------------------------------------------------
# Script Entry Point (i.e., main() )
#--------------------------... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Infovis/Python/tables4.py | Python | gpl-3.0 | 1,335 | [
"VTK"
] | f86181bc71442ae333865a4f0e3ede59a204d47d256efe4dce9b69b98787904e |
#!/usr/bin/env python
#Dan Blankenberg
"""
Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended.
"""
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.intervals.io
from bx.bitset import BitSet
from galaxy.tools.util import ma... | volpino/Yeps-EURAC | tools/maf/maf_stats.py | Python | mit | 4,889 | [
"Galaxy"
] | a92deb5f6f599237035645b598821594635ea44682d88d665ccc10eae352ad18 |
## This file is part of Invenio.
## Copyright (C) 2011, 2012, 2013 CERN.
##
## 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 (at your option) any later versio... | jmartinm/invenio | modules/webauthorlist/lib/authorlist_engine.py | Python | gpl-2.0 | 34,338 | [
"VisIt"
] | f7ddcaf85bdc50a3293cb8181168586f5514d622e7436eedc797b0fd1ac74c29 |
# -*- coding: utf-8 -*-
"""
:mod:`propagator` -- Tree level propagator.
====================================================
The tree level propagator is implemented here.
"""
import numpy as np
from dirac import Pp, Pm, gamma
# Fermion propagator helper functions
def hat(p):
return 2. * np.sin(0.5 * p);
def rin... | dhesse/tree-level-improve | propagator.py | Python | mit | 2,903 | [
"DIRAC"
] | ed75db4f5bbed7fb13d3aa36a6a4854a3ef0acefe9709cbc8f49f56ce7639d7c |
import img_scale
import pyfits as pyf
import pylab as pyl
from mpl_toolkits.axes_grid1 import axes_grid
import cPickle as pickle
import os
from scipy.stats import scoreatpercentile
def mk_image(galaxy):
base = './../../images_v5/GS_2.5as_matched/gs_all_'
i_img = pyf.getdata(base+str(galaxy)+'_I.fits')
j_i... | boada/ICD | sandbox/legacy_plot_code/plot_icd_sfr_montage.py | Python | mit | 3,857 | [
"Galaxy"
] | d0712edf30a198c9a50d9ebf675085ee2cd4a10316b79695815bc0b5ecd8251f |
# -*- coding: utf-8 -*-
from __future__ import print_function
from .dataObject import ObjectProperty, Alias
from .connection import Connection
from .neuron import Neuron
from .biology import BiologyType
from .worm_common import WORM_RDF_TYPE
class Network(BiologyType):
""" A network of neurons """
class_co... | gsarma/PyOpenWorm | PyOpenWorm/network.py | Python | mit | 3,251 | [
"NEURON"
] | 15799bdf9eaa2f39c3d03ffd2ca7ebb89a528bf46530c08b4a44447aaacdb969 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from __future__ import print_function
import re
import argparse
import os.path
import io
parser = argparse.ArgumentPar... | AGIsmail/open62541 | tools/amalgamate.py | Python | mpl-2.0 | 2,960 | [
"VisIt"
] | 6f20be4dfa22a2eb596d3a804ccfecabd7e6c10fa73bbf73ca476e19e349575b |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Provides classes for generating high-symmetry k-paths using different conventions.
"""
import abc
import itertools
import operator
from math import ceil, cos, e, pi, sin, tan
from warnings import warn
import networkx as ... | materialsproject/pymatgen | pymatgen/symmetry/kpath.py | Python | mit | 94,572 | [
"CRYSTAL",
"pymatgen"
] | 0e487d62ebcf7d5dd011d60ce0323e6185852499e2ce660e6cc3994f8e5b877d |
# Copyright 2014 Uri Laserson
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | churchlab/vdj | __init__.py | Python | apache-2.0 | 16,592 | [
"Biopython"
] | 7d97935d4275b3b275cb116bee59876825b3d5ef604815c490473e8cd38b0322 |
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... | bskinn/sphobjinv | doc/source/conf.py | Python | mit | 8,510 | [
"Brian"
] | 3a652817732101ef62e31b5e46dd9b24b678f60b99f338203a5ae2f4aa72a61d |
"""
C++ Export
----------
This module provides all necessary functionality specify an ODE model and
generate executable C++ simulation code. The user generally won't have to
directly call any function from this module as this will be done by
:py:func:`amici.pysb_import.pysb2amici`,
:py:func:`amici.sbml_import.SbmlImpor... | AMICI-developer/AMICI | python/amici/ode_export.py | Python | bsd-2-clause | 137,457 | [
"DIRAC",
"Gaussian"
] | 9917cdac720147844cdae9c1b93a48cf99cd6f3fc13e7dd32f978c81d7b41bf0 |
#!/usr/bin/env python
# File: plot_icd_vs_colorgrad.py
# Created on: Tue 08 May 2012 11:03:26 AM CDT
# Last Change: Sun 21 Oct 2012 02:43:33 PM CDT
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import pylab as pyl
from mk_galaxy_struc import mk_galaxy_struc
galaxies = mk_galaxy_struc()
f1 = pyl.figure(1,fig... | boada/ICD | sandbox/legacy_plot_code/plot_icd_vs_colorgrad_vs_sersic.py | Python | mit | 1,979 | [
"Galaxy"
] | fdf1d3038e1c570d16c378f57982aabcce3a3bae09b4181904922eca6bb9ef45 |
""" Test case for DIRAC.Core.Utilities.Network module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pytest
from DIRAC.Core.Utilities.Network import discoverInterfaces, getFQDN, getIPsForHostName, checkHostsMatch
def test_discoverInterfaces():... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/test/Test_Network.py | Python | gpl-3.0 | 1,386 | [
"DIRAC"
] | 1a6d97fdda84ab2b288ff877c758c087e90abec1460a8d24681928ea4984cecc |
#!/usr/bin/env python
from nac.workflows.input_validation import process_input
from nac.workflows import (
workflow_derivative_couplings, workflow_single_points, workflow_stddft)
import argparse
import os
import yaml
msg = "namd.py -i input"
parser = argparse.ArgumentParser(description=msg)
parser.add_argument(... | felipeZ/nonAdiabaticCoupling | scripts/cli/run_workflow.py | Python | mit | 1,377 | [
"NAMD"
] | d995dbf3c929a15ac660448bcd60b8fd9dfcb5d3aba343c87fd238043bf91930 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/util/__init__.py | Python | lgpl-3.0 | 913 | [
"Psi4"
] | 103b56a78d94d0fd9bfd46dfe3772e3566801ca77263e709151c72c2a7694207 |
#!/usr/bin/env python
###########################################################################
# #
# This Python script may be used to simulate a monatomic LJ fluid in the #
# NVE or NVT ensemble. The starting configuration may be taken from ... | acfogarty/espressopp | bench/lennard_jones/espressopp/espressopp_lennard_jones.py | Python | gpl-3.0 | 5,196 | [
"LAMMPS"
] | 09963eb09c773b6e1f41c5df47d908e13db930f175572d1f1e34e0fd4b325490 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, with_statement
import os
import pyqtgraph.multiprocess as mp
from acq4.devices.AxoPatch200 import CancelException
from acq4.devices.DAQGeneric import DAQGeneric, DAQGenericTask, DAQGenericTaskGui
from acq4.devices.PatchClamp import P... | acq4/acq4 | acq4/devices/MockClamp/MockClamp.py | Python | mit | 15,237 | [
"NEURON"
] | fe9d81b49531830fadcd64c7b660b0673e901579abf7c39f3cce21d34d71ff52 |
"""
Acceptance tests for Home Page (My Courses / My Libraries).
"""
from bok_choy.web_app_test import WebAppTest
from opaque_keys.edx.locator import LibraryLocator
from ...fixtures import PROGRAMS_STUB_URL
from ...fixtures.config import ConfigModelFixture
from ...fixtures.programs import ProgramsFixture
from ...pages.... | antoviaque/edx-platform | common/test/acceptance/tests/studio/test_studio_home.py | Python | agpl-3.0 | 7,445 | [
"VisIt"
] | d3e3febf188cf6ae53acdc99c0b3b452bd9800b7b143a0276c11adc0bd41fca5 |
# 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/polymer_diamond.py | Python | gpl-3.0 | 5,649 | [
"ESPResSo"
] | f39de00919a7756ff8d4a5860c067e89d013fd20c27197e84c6d0369071b26b9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# MIT License
#
# Copyright (c) 2018 Miha Purg <miha.purg@gmail.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, ... | mpurg/qtools | packages/Qpyl/qmakefep.py | Python | mit | 34,438 | [
"Amber"
] | 2206f2f9f4e3cb80ad1382ce3370c0fc89313dbd457a1f7cd22c22c3b04344db |
import moogli
import moose
# class MooseSpineHead(moogli.core.Frustum):
# pass
# class MooseSpineShaft(moogli.core.Frustum):
# pass
# class MooseSoma(moogli.core.Sphere):
# pass
# class MooseDendrite(moogli.core.Frustum):
# def __init__(self, moose_element):
# self.parent = pass
# class Moo... | dilawar/moogli | moogli/extensions/moose/network.py | Python | gpl-2.0 | 5,203 | [
"MOOSE",
"NEURON"
] | 371d325d3f513893f80c6e24a0c1c53f0a6c4e853fdf6d12a9edcdd91c2caf8d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import re
import abc
import six
from abc import ABCMeta, abstractmethod
"""
Error handlers for errors originating from the Submission systems.... | setten/pymatgen | pymatgen/io/abinit/scheduler_error_parsers.py | Python | mit | 14,025 | [
"pymatgen"
] | 688d15bc0f1da69c60d9a857781034dba2bccfe94171a03bfbe2f851cfdaae04 |
""" X509Chain is a class for managing X509 chains with their Pkeys
"""
__RCSID__ = "$Id$"
import os
import stat
import tempfile
import hashlib
import random
import binascii
from GSI import crypto
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.X509Certificate import X... | arrabito/DIRAC | Core/Security/X509Chain.py | Python | gpl-3.0 | 22,583 | [
"DIRAC"
] | 59b1fe2375541218d255bc237d02008aa349b10ca3a60078b49e8ba1e73b53f1 |
# 2017 DeepCrystal Technologies - Patrick Hop
#
# Data loading a splitting file
#
# MIT License - have fun!!
# ===========================================================
import os
import random
from collections import OrderedDict
import deepchem as dc
from deepchem.utils import ScaffoldGenerator
from deepchem.utils.... | deepchem/deepchem | contrib/mpnn/donkey.py | Python | mit | 3,029 | [
"RDKit"
] | 59be2ed99af07d0df581ba38c05320eb2b1c47e4ccbc33cb6e7fbefb8ad68cd9 |
"""
Experiment on real text data.
"""
from __future__ import print_function
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
from builtins import str
from builtins import range
import freqopttest.data as data
import freqopttest.tst as tst
import freqopttest.... | wittawatj/interpretable-test | freqopttest/ex/ex4_text.py | Python | mit | 16,542 | [
"Gaussian"
] | 4473f195e7b836a03df0c4e2d1485b13eaeda6285e9ae25f4c8a7c5e53b0816e |
"""
Solve Helmholtz equation on a sphere
Using spherical coordinates
"""
import os
from shenfun import *
from shenfun.la import SolverGeneric1ND
import sympy as sp
by_parts = False
# Define spherical coordinates
r = 1
theta, phi = psi = sp.symbols('x,y', real=True, positive=True)
rv = (r*sp.sin(theta)*sp.cos(phi), ... | spectralDNS/shenfun | demo/sphere_helmholtz.py | Python | bsd-2-clause | 2,342 | [
"Mayavi"
] | e17437cd0b0e64663042f005480001571ca1e3ef8caeaa54ec429654a2042156 |
#
# AUTHORS:
# Hakan Ozadam
# Rachel Brown
#
# Moore Laboratory
# UMASS Medical School / HHMI
# RNA Therapeutics Institute
# Albert Sherman Center, ASC4-1009
# 368 Plantation Street
# Worcester, MA 01605
# USA
#
#############################################... | hakanozadam/bal | bal/lasso/lasso.py | Python | gpl-2.0 | 9,229 | [
"pysam"
] | d027d6c4901c1d82bc013bede48b3b6c7670a827786ca7bcf42f92c7d7d74750 |
import sys
import os
import numpy as np
import h5py
import multiprocessing
import cPickle
import ephem
import matplotlib.pyplot as plt
import types
from sklearn.gaussian_process import GaussianProcess
from sklearn.cross_validation import train_test_split
from sklearn import metrics, linear_model, tree, ensemble
# NOTE... | acbecker/solar | regress6submit.py | Python | mit | 9,650 | [
"Gaussian"
] | 97ea74b07aca4fb09453b283da2ff9405c0d28a50e535a92cb42d408c455bdad |
# -*- coding: utf-8 -*-
# ---
# jupyter:
# jupytext:
# formats: ipynb,.pct.py:percent
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.6.0
# kernelspec:
# display_name: Python 3
# language: python
# name: python3... | GPflow/GPflow | doc/source/notebooks/advanced/variational_fourier_features.pct.py | Python | apache-2.0 | 19,554 | [
"Gaussian"
] | c5024673046fe30cf72c948dc4fe3ed74d0cd56961e1712f683a7faea64f92b7 |
import logging
from flask import current_app
from flask.ext.sqlalchemy import BaseQuery
from sqlalchemy import ForeignKey
from sqlalchemy.sql import desc, text
from sqlalchemy.sql.expression import func
from sqlalchemy.ext.hybrid import hybrid_property
from sqlalchemy.ext.mutable import MutableDict
from sqlalchemy.orm ... | arsgeografica/kinderstadt-registry | registry/models.py | Python | gpl-3.0 | 7,534 | [
"VisIt"
] | 3c2ebfa6f63e5c13a94b06c8cacd3d93b9d78347485a13859e68ec6107860385 |
#!/usr/bin/python
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
try:
import traceback
from optparse import make_option
from os import makedirs, path, listdir, remove, rename,... | kishori82/MetaPathways_Python.3.0 | libs/python_modules/pipeline/metapathways.py | Python | mit | 26,328 | [
"BLAST"
] | f867fc8d96ddb0f77cdda04e1990a9077c7ef8571cd7be5b94c22f6b9c4fe607 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
import numpy as np
#### Utility functions for conversion to vtkUnstructuredGrid.
def _get_cell_faces(G, cell_idx):
# MRST equivalent: G.cells.faces(facePos(i) : facePos(i+1)-1, :)
return G.... | roessland/PRST | prst/plotting.py | Python | gpl-3.0 | 7,321 | [
"Mayavi",
"VTK"
] | 8fed2bba2b91160548253fb1219605d98b0ec62c40760423949a58867e3b7a67 |
from os import path, mkdir,curdir
from ..external import Structure
from ..core import Workflow,IOTask
from numpy import int as np_int
from numpy import array as np_array
from numpy import linalg as np_linalg
from numpy import ones as np_ones
__all__ = ['KKflow']
class KKflow(Workflow,IOTask):
def __init__(self,... | trangel/OPTpy | OPTpy/utils/kk.py | Python | gpl-3.0 | 5,948 | [
"ABINIT",
"pymatgen"
] | 7a99d1516340fc6df76ef51f7bef82d80c54f9b605e039d6f6cb49bcc7f80568 |
"""Module containing CMSAF CLAAS v2 FileHandler."""
import datetime
import pyresample.geometry
from .netcdf_utils import NetCDF4FileHandler
class CLAAS2(NetCDF4FileHandler):
"""Handle CMSAF CLAAS-2 files."""
def __init__(self, *args, **kwargs):
"""Initialise class."""
super().__init__(*arg... | pytroll/satpy | satpy/readers/cmsaf_claas2.py | Python | gpl-3.0 | 2,965 | [
"NetCDF"
] | e63fec3ba3d878e5dba22a82b13983a0e11ea3cd121a0d6bdad4b1c96d74fe90 |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | src/formattedcode/format.py | Python | apache-2.0 | 7,852 | [
"VisIt"
] | b5bf9265a07087b8963edc7806fb5fc010c4d936d90bab0ebe6c6921fbc69c9a |
"""
Plot the first two TICS with ensembler models.
"""
#Note ensembler models are still after implicit refine.
import matplotlib
matplotlib.use('Agg')
from msmbuilder import example_datasets, cluster, msm, featurizer, lumping, utils, dataset, decomposition
from sklearn.pipeline import make_pipeline
import numpy as np
... | hainm/MSMs | initial_ipynbs/do_gmm_4src_n_abl/make_ensembler_fig.py | Python | gpl-2.0 | 1,294 | [
"MDTraj"
] | c21afdb722113e42eaea62778082d20e6399e9da3efa4c7cb2f8edbe60ff9f71 |
# Copyright (c) 2015, 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 ... | liesbethvanherpe/NeuroM | neurom/core/tests/test_population.py | Python | bsd-3-clause | 3,010 | [
"NEURON"
] | ec62896fa1a8c96eee1f2dc38299cb2f4bee09f5bfbe1a349fe344e51f7a2c9b |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/tfpark/test_tfnet.py | Python | apache-2.0 | 4,335 | [
"ORCA"
] | 00a700b304552515873f9289376925a8e6f51aee2b5aa09379a590c0e4778f35 |
from collections import OrderedDict
from datetime import datetime, timedelta
from itertools import product
import warnings
from warnings import catch_warnings
import numpy as np
from numpy.random import randn
import pytest
from pandas.compat import range, zip
from pandas.errors import UnsupportedFunctionCall
import p... | GuessWhoSamFoo/pandas | pandas/tests/test_window.py | Python | bsd-3-clause | 156,476 | [
"Gaussian"
] | aa4276ef037855c8259de625956981a4973923bac5f1577571514dfcf2433e89 |
#
# Transmission Line Simulator
#
# Author(s): Jiacong Xu
# Created: Jul-14-2017
#
from popupeditor import PopupEditor
from kivy.properties import *
from materialbutton import MaterialButton
from util.constants import *
from kivy.animation import Animation
from models.powersource import *
from kivy.metrics import *
i... | flyingbanana1024102/transmission-line-simulator | src/views/sourceeditor.py | Python | mit | 5,620 | [
"Gaussian"
] | 0776d0689f2bffce3f53d25aed21cf5c7a21feca44c1183c9cc48d4c96363535 |
import numpy as np
from numpy.testing import assert_equal, assert_almost_equal, assert_array_less
from numpy.testing import assert_raises
from skimage.measure import LineModelND, CircleModel, EllipseModel, ransac
from skimage.transform import AffineTransform
from skimage.measure.fit import _dynamic_max_trials
from skim... | paalge/scikit-image | skimage/measure/tests/test_fit.py | Python | bsd-3-clause | 12,580 | [
"Gaussian"
] | 2e68e20f662ccc17522aa04b513b21905626f5473a1b9fcbbebabf4872d218e5 |
# lint as python3
# Copyright 2019 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | google-research/neural-structural-optimization | neural_structural_optimization/autograd_lib.py | Python | apache-2.0 | 7,407 | [
"Gaussian"
] | 91d5e199e51de53204762ddecbe4c544bf433a882ef31930e093d6c4c31ca5b8 |
import datetime as dt
import os
import sys
import re
import pytest
from click.testing import CliRunner
from freezegun import freeze_time
from khal.cli import main_ikhal, main_khal
from .utils import _get_ics_filepath, _get_text
class CustomCliRunner(CliRunner):
def __init__(self, config_file, db=None, calendars... | pdav/khal | tests/cli_test.py | Python | mit | 29,696 | [
"VisIt"
] | 2f12048791c4902b42cdab8e01c9102c8b280d34bcb2c2a87222bcbb5ad00a2c |
#coding=utf8
# I don't know about this author. LEE said.
# @status Thanks God AC
# write-only
def start():
def has(lst,ele):
return lst.count(ele)>0
n,m=map(int,raw_input().split(' '))
mlist=[
map(int,raw_input().split(' '))
for i in xrange(m)
]
group=[[] for i in xrange(n+10)]
# desire-satisfy
# write-o... | SnowOnion/CodeForcesLee | thisAndThat/300b.py | Python | mit | 2,765 | [
"VisIt"
] | 0eaa093f55e05e595e6681bff742e33f919ee46c0e877119ba314288a50e9a8a |
# ##WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING #
# Under development #
# ##WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING#... | avedaee/DIRAC | Workflow/Modules/UploadOutputs.py | Python | gpl-3.0 | 3,453 | [
"DIRAC"
] | 799893ba316d24e183357ad63b73aad7b21472d54fd828b014aa9da497e8c6a0 |
#!/usr/bin/env python
#
# Copyright 2016 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... | googlei18n/nototools | nototools/noto_cmap_reqs.py | Python | apache-2.0 | 103,028 | [
"FEFF",
"FLEUR"
] | e36613ecde965b86e978a2602e37218d31e7e284af4bcb49b6d9b0bb060b8b4c |
#!/usr/bin/env python
"""
File I/O class
A wrapper around various NetCDF libraries, used by
BOUT++ routines. Creates a consistent interface
across machines
NOTE: NetCDF includes unlimited dimensions,
but this library is just for very simple
I/O operations. Educated guesses are made
for the dimensions.
Supported libr... | erikgrinaker/BOUT-dev | tools/pylib/boututils/datafile.py | Python | gpl-3.0 | 19,217 | [
"NetCDF",
"VisIt"
] | 35de7213d4a5ce5a03be38bbe9073d35d3ce4f0955ec737bbdccc3be1fb04256 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is intended to be used to compute Pourbaix diagrams
of arbitrary compositions and formation energies. If you use
this module in your work, please consider citing the following:
General formalis... | davidwaroquiers/pymatgen | pymatgen/analysis/pourbaix_diagram.py | Python | mit | 40,558 | [
"pymatgen"
] | 06c480645de6a84ba5883ea9e02d408fa1654dfc267849f863ab82f737fc4f2a |
# Copyright (c) 2018 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
=================================
MetPy Declarative Syntax Tutorial
=================================
The declarative syntax that is a part of the MetPy packaged is designed to ... | Unidata/MetPy | tutorials/declarative_tutorial.py | Python | bsd-3-clause | 21,805 | [
"NetCDF"
] | 3e911a1e1a4e152d7e09f4390aafd48e3849e0367e2d37401daced7f869b916d |
"""
LLVM pass that converts intrinsic into other math calls
"""
from __future__ import print_function, absolute_import
import llvmlite.llvmpy.core as lc
from llvmlite import ir
class _DivmodFixer(ir.Visitor):
def visit_Instruction(self, instr):
if instr.type == ir.IntType(64):
if instr.opname ... | ssarangi/numba | numba/targets/intrinsics.py | Python | bsd-2-clause | 3,712 | [
"VisIt"
] | 57c314620b009da828a27e68b563d755d6d6f6f50b7b91ee2e25201d15eaf86b |
import numpy as np
import shutil
import os
import mdtraj as md
from mdtraj.utils import enter_temp_directory
import tempfile
from distutils.spawn import find_executable
PACKMOL_PATH = find_executable("packmol")
HEADER_TEMPLATE = """
# Mixture
tolerance %f
filetype pdb
output %s
add_amber_ter
"""
BOX_TEMPLATE = ""... | kyleabeauchamp/openmoltools | openmoltools/packmol.py | Python | gpl-2.0 | 5,446 | [
"MDTraj",
"OpenMM"
] | bb451c7a01968c4a8033d62f349df6fce128a017d1ddc0f6b47cc0c876f8d9c1 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 ... | nuclear-wizard/moose | python/peacock/base/PreferenceWidget.py | Python | lgpl-2.1 | 2,015 | [
"MOOSE"
] | 4da46760217085074dca530eb05caa55cb41250d81e1f3210f43c0e025f1ff48 |
# -*- 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/DeviceAllLightsOff.py | Python | gpl-3.0 | 1,451 | [
"xTB"
] | 2aafcd297a76c38cc6d74eafb0b233377165cab24d917dd4a1ca632a812a3883 |
"""
@created_at 2014-06-09
@author Exequiel Fuentes <efulet@gmail.com>
@author Brian Keith <briankeithn@gmail.com>
"""
# Se recomienda seguir los siguientes estandares:
# 1. Para codificacion: PEP 8 - Style Guide for Python Code (http://legacy.python.org/dev/peps/pep-0008/)
# 2. Para documentacion: PEP 257 - Docst... | efulet/laberinto | laberinto/main.py | Python | mit | 2,429 | [
"Brian"
] | 9b1387a880c479497d2203cc2423a08f41621bde0a9a1fb2e3674ca367b7c4f5 |
#!/bin/python
"""
Test how sex reproduction evolve to 50% male children and 50% female children
Whatever the starting configuration, if there is no extinction,
the equilibrium look like a gaussian curbe:
[0, 0, 0, 0, 0, 8, 55, 148, 298, 433, 448, 338, 197, 59, 16, 0, 0, 0, 0, 0, ]
"""
from generation_manager import G... | dionisos2/evolve | sex_equilibrium.py | Python | gpl-2.0 | 629 | [
"Gaussian"
] | 777b0b69a1325d31b4a6ed2e2801ebc1201940dc1ee89a5ace60d5abfe924858 |
"""
Basic tool parameters.
"""
import logging, string, sys, os, os.path
from elementtree.ElementTree import XML, Element
from galaxy import config, datatypes, util
from galaxy.web import form_builder
from galaxy.util.bunch import Bunch
from galaxy.util import string_as_bool, sanitize_param
from sanitize import ToolPar... | volpino/Yeps-EURAC | lib/galaxy/tools/parameters/basic.py | Python | mit | 62,561 | [
"Galaxy"
] | 7b30e2ac493c2c8ae72e9c784d790c66828f0d831cd366b877dcaf040eebbc9a |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/io/tests/test_phylip.py | Python | bsd-3-clause | 3,973 | [
"scikit-bio"
] | b076609f49c324cb4ab4164664f8242a163f5aebc3d5ff4162793289c408f5d7 |
# coding: utf-8
# Copyright 2013 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | wavemind/mlgcb | tests/functional/test_classes.py | Python | apache-2.0 | 177,291 | [
"VisIt"
] | 85f68f29f0708c7e4de0b6dc19d829e8bbe37e08182a95d134c86ad7d5e00e03 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | robertwb/incubator-beam | sdks/python/apache_beam/runners/dataflow/dataflow_runner.py | Python | apache-2.0 | 71,425 | [
"VisIt"
] | f67394a8127bb9e337df6b74263f51c3a960961406f41488406d0274ae01193d |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/learn/pytorch/torch_runner.py | Python | apache-2.0 | 18,769 | [
"ORCA"
] | 14453a58039eb110d91f08f1e364489f7f12f112851d62588654f48508e6b175 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects describing the basic parameters of the
pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..
"""
from __future__ import unicode_literals, divisio... | matk86/pymatgen | pymatgen/io/abinit/pseudos.py | Python | mit | 63,625 | [
"ABINIT",
"pymatgen"
] | 0d7f6db916fc196315e88fa7a0b955fb3f99f4849569e2ad30910b913251006e |
"""
authors: Xi Chen, Eric García de Ceca, Jaime Mendizábal Roche
This module is an advanced version of our MLP using tensorflow.
In this module, we have optimization's methods, like "SDG",
"momentum", "adagrad","RMS_prop", "adadelta", "nesterov" and "adam".
"""
from __future__ import print_function, division
import s... | daxadal/Computational-Geometry | Practica_4/net_constructor_documented.py | Python | apache-2.0 | 21,096 | [
"NEURON"
] | d6e34011dc8b9a67288f326a22d0bb362340147df5dd777eabfe453e1ea0409d |
class InvalidIntervalException(Exception):
def __init__(self, l, u):
self.l = l
self.u = u
def __str__(self):
return "Invalid interval [" + str(l) + ", " + str(u) + "]"
class ArithmeticException(Exception):
def __init__(self, msg):
self.msg = msg
def __str__(self):
return self.msg
def lt(x... | vhscampos/range-analysis | prototype/PythonRangeAnalysis/bck/DS1.py | Python | gpl-2.0 | 11,116 | [
"VisIt"
] | c7204696ec29b5def20f1441fa6c35aa496e9f7f31d94ec71e26efba8b2364cc |
"""
This file contains Python code illustrating the creation and manipulation of
vtkTable objects.
"""
from vtk import *
#------------------------------------------------------------------------------
# Script Entry Point (i.e., main() )
#------------------------------------------------------------------------------
... | berendkleinhaneveld/VTK | Examples/Infovis/Python/tables1.py | Python | bsd-3-clause | 1,422 | [
"VTK"
] | 9c30b52102788b9e68141197f9081fd31b3f46460b4a285b2dec2b99dff7084c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""transforms.py -- This module contains parameter transformations that may be
useful to transform from parameters that are easier to _sample_ in to the
parameters required for building SED models.
They can be used as ``"depends_on"`` entries in parameter specifications.
... | bd-j/prospector | prospect/models/transforms.py | Python | mit | 16,746 | [
"Galaxy"
] | 83747e5d29fec6dc5cd934a1056d672aefa6f58370d8f50e1639d970f4d0ca15 |
# Copyright (C) 2017 Martin Nilsson
# This file is part of the Memtran compiler.
#
# The Memtran compiler is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | LJMNilsson/memtran | src/ast.py | Python | gpl-3.0 | 106,488 | [
"VisIt"
] | 12d4436c5b29ded605c7af7783211e61196bc5364176b7142b66fad05fd9470a |
#! /usr/bin/env python
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
plipcmd - Main script for PLIP command line execution.
Copyright 2014-2015 Sebastian Salentin
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except... | lituan/tools | plip/plip_phos_local.py | Python | cc0-1.0 | 8,562 | [
"PyMOL"
] | 247c2d9bdeb99c6d5398678d2f64c126708b6425c0d88e86c35caf4740e29d79 |
"""
Signal handling functions for use with external commerce service.
"""
from __future__ import unicode_literals
import json
import logging
from urlparse import urljoin
import requests
from django.conf import settings
from django.contrib.auth import get_user_model
from django.contrib.auth.models import AnonymousUser... | pepeportela/edx-platform | lms/djangoapps/commerce/signals.py | Python | agpl-3.0 | 9,151 | [
"VisIt"
] | ef16f93a5b4809fea36a66d2a12f063c5e502944c48c0ed69d95b6cc6302fd2c |
import os, re
import subprocess
from multiprocessing import Pool
import Config.ADNI_RecurserConfig as arc
import Config.StudyConfig as sc
from Recursor.ScanSession import ScanSession
from Utils.PipelineLogger import PipelineLogger
class DIANRecursor:
def __init__(self, study, recurse_folder):
self.study ... | sulantha2006/Processing_Pipeline | Recursor/DIAN/DIANRecursor.py | Python | apache-2.0 | 8,040 | [
"VisIt"
] | 49dede003ed6618f83f9659d5ae339435f09b3ec7a18502425fdc345af468ca1 |
# Code from Chapter 6 of Machine Learning: An Algorithmic Perspective (2nd Edition)
# by Stephen Marsland (http://stephenmonika.net)
# You are free to use, change, or redistribute the code in any way you wish for
# non-commercial purposes, but please maintain the name of the original author.
# This code comes with no... | Anderson-Lab/anderson-lab.github.io | csc_466_2021_spring/MLCode/Ch6/kpcademo.py | Python | mit | 1,531 | [
"Gaussian"
] | 6e6bdac58ce429f5fd570d7a2c8e29745b77101c86b77a3b8ad6f707b2e1f533 |
# shamelessly copied from pliExpertInfo (Vali, Mirakels, Littlesat)
from os import path
from enigma import iServiceInformation, iPlayableService
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHumanRe... | TwolDE2/enigma2 | lib/python/Components/Converter/PliExtraInfo.py | Python | gpl-2.0 | 28,072 | [
"Galaxy"
] | 1e9f9d5b5dacdd41c4a27cbb50db096bfbbc4e5a0e998d15723b7b9d305288da |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/prop/nmr/uhf.py | Python | apache-2.0 | 10,174 | [
"Gaussian",
"PySCF"
] | 2a75d21f70b8c343f10fcfd375a35bb9a4007fad071066ca2a7758e9645ff694 |
#!/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/dft/krkspu.py | Python | apache-2.0 | 10,564 | [
"PySCF"
] | 87cc6a163d8e1813fc563fc8e49a2bfa1ef7f57b178913aef3b673dbf6a6c411 |
"""The core Python FlickrAPI module.
This module contains most of the FlickrAPI code. It is well tested and
documented.
"""
from __future__ import print_function
import logging
import six
import functools
from . import tokencache, auth
from flickrapi.xmlnode import XMLNode
from flickrapi.exceptions import *
from f... | search5/nanumlectures | lib/flickrapi/core.py | Python | apache-2.0 | 29,860 | [
"VisIt"
] | 08ad0c07cd8fc5d63dd845c716dbb847b14d415bd75591b2881d95d8fba127dc |
#!/usr/bin/env python
##nex2phy.py
##written 6/26/14 by Groves Dixon
Description = '''
Description:
Uses biopython to convert an alignment in nexus format to phylip format
'''
AdditionalProgramInfo = '''
Additional Program Information:
'''
##Import Modules
import argparse
from sys import argv
from sys import exit
... | grovesdixon/metaTranscriptomes | scripts/nex2phy.py | Python | mit | 2,840 | [
"Biopython"
] | 819f81b03c71f79ef72c933b4232e4b61b71338357108ccec38f3194821382d3 |
""" The FileCatalogClient is a class representing the client of the DIRAC File Catalog
"""
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.DISET.TransferClient import TransferClient
from DIRAC.Core.Security.ProxyInfo import getVOfromProxyGroup
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import g... | petricm/DIRAC | Resources/Catalog/FileCatalogClient.py | Python | gpl-3.0 | 23,994 | [
"DIRAC"
] | 877aa6233097adb48957eb4e2525dd8e878356fadb73e75d03bb66a57b042417 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex, pickle, re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'--bootloade... | tatsuy/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 44,294 | [
"CRYSTAL"
] | e438c968353742c9fd40fb90665a68998321b4614640a5c34a49327f8a8bcada |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import warnings
from operator import itemgetter
from tabulate import tabulate
import numpy as np
from monty.io import zopen
from monty.json import MSONable
from pymatgen import Structure, Lattice... | blondegeek/pymatgen | pymatgen/io/feff/inputs.py | Python | mit | 32,854 | [
"FEFF",
"pymatgen"
] | 5a8d4568af0090bd12920331d8bd4f20e0c9d4587a4a23d84cf769f6d544026b |
################################################################################
# Copyright (C) 2013-2015 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Unit tests for `gaussian` module.
"""
import numpy as np
fr... | dungvtdev/upsbayescpm | bayespy/inference/vmp/nodes/tests/test_gaussian.py | Python | mit | 46,041 | [
"Gaussian"
] | 6b544421586c95bf55c5090db488f866cf690f8586c6965e1098e54c0066f332 |
#!/usr/bin/env python
import re
import argparse
import sys
def create_field_dict(line):
field_dict = dict()
for field in line.rstrip().split('\t'):
if not field.startswith('@'):
key, value = field.split(':', 1)
field_dict[key] = value
return field_dict
def create_field_se... | ernfrid/oneoffs | ccdg_synch/validate_header.py | Python | mit | 4,856 | [
"BWA"
] | eb2036c3e97ff133ef779fe7f3e4826e58540d1583d3b20503e32fe14cdfd235 |
from __future__ import print_function, division
inp = """
#File names and Format
#Directory to save output files
direc 'Al1000'
stem 'Al1000'
make_image 0
output '.gve' '.flt' '.par' '.ubi'
# Structural parameters
structure_phase_0 'Al.cif'
# Crystal/grains parameters
no_grains 1000
# Total number of grains summed o... | jonwright/ImageD11 | test/simul_1000_grains/make_u_t.py | Python | gpl-2.0 | 2,397 | [
"CRYSTAL"
] | 4abe66a9ef61b1ae3042e4c8ae4139585b2f5ac4a2413db7cc28c3d311f68056 |
# -*- coding: utf-8 -*-
__author__ = 'xuanwo'
a = 100
print('''
a
ad
adf
a
sgds
afg
asdf
as
d
''')
| Xuanwo/chineseregion | chineseregion/learn.py | Python | mit | 100 | [
"ADF"
] | f2f0e962e017349bc1515b7083745b6c98647b2c73906a2f6a5fc1fe5bf29265 |
from ase.lattice.spacegroup import crystal
a = 4.6
c = 2.95
rutile =crystal(['Ti', 'O'], basis=[(0, 0, 0), (0.3, 0.3, 0.0)],
spacegroup=136, cellpar=[a, a, c, 90, 90, 90])
| grhawk/ASE | tools/doc/tutorials/spacegroup/spacegroup-rutile.py | Python | gpl-2.0 | 189 | [
"ASE",
"CRYSTAL"
] | 89d28b9139ac2ce62260b420d337595729cbe18d3ef9c30646d021e2d7219fd8 |
#!/usr/bin/python
# ORF prediction for the sequences without homologs
from Bio import SeqIO
from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate
from Bio.Alphabet import IUPAC
import getopt, sys
import string
# getopt reads in my input file
input_file = ""
#print "All arguments: ", sys.arg... | lotharwissler/bioinformatics | python/openreadingframe/orf_prediction_part2.py | Python | mit | 3,626 | [
"exciting"
] | f7a3f72b7e2c12e4a8b0977b3eb991c7c97674b506e8f5a3168f964763b14aa4 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""eprimer3.py
Code to conduct primer prediction with ePrimer3
(c) The James Hutton Institute 2016-2019
Author: Leighton Pritchard
Contact:
leighton.pritchard@hutton.ac.uk
Leighton Pritchard,
Information and Computing Sciences,
James Hutton Institute,
Errol Road,
Inve... | widdowquinn/find_differential_primers | diagnostic_primers/eprimer3.py | Python | mit | 3,730 | [
"Biopython"
] | 9b531fe2cd5442dfc1fb91ff17ac4f8ff4b794f5487055c58fc9c4e8ef802ca3 |
# -*- coding: utf-8 -*-
# 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 Florian Bruhin... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/pyreverse/diadefslib.py | Python | apache-2.0 | 8,344 | [
"VisIt"
] | b808821a73b81cc21c6907cb52d6770c978c0a51fe7b4ee33b9e613bc1227eb7 |
from __future__ import unicode_literals, division, absolute_import
import logging
import re
from datetime import datetime, timedelta
from dateutil.parser import parse as dateutil_parse
from sqlalchemy import Table, Column, Integer, String, Unicode, Boolean, Date, DateTime, Time, or_, func
from sqlalchemy.orm import re... | lildadou/Flexget | flexget/plugins/api_trakt.py | Python | mit | 36,575 | [
"VisIt"
] | d5994f86fba028b7e2f63667ec174601d43d8ca28b9bbab3a189762108695c39 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/common/test_load_extensions.py | Python | lgpl-2.1 | 2,108 | [
"MOOSE"
] | 8e3c417375483b7887d03e57c4284224f160a1132e122aa7ca70895753e66215 |
# Copyright (c) 2015 OpenStack Foundation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to ... | openstack/swift | swift/container/sharder.py | Python | apache-2.0 | 101,527 | [
"VisIt"
] | b4a2748a777acbc5c758089af1b5e9b2f04b4c93caa22ce45391e259e7ac93d7 |
"""
Caffe network visualization: draw the NetParameter protobuffer.
.. note::
This requires pydot>=1.0.2, which is not included in requirements.txt since
it requires graphviz and other prerequisites outside the scope of the
Caffe.
"""
from caffe.proto import caffe_pb2
"""
pydot is not supported under p... | KellyChan/python-examples | cpp/deeplearning/caffe/python/caffe/draw.py | Python | mit | 8,974 | [
"NEURON"
] | 0cf6364da5e31b02383f1a92542e3ccbcbb5114024ea255a7bb25ba5055d6d14 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os
from Bio.PopGen import GenePop
from Bio.PopGen.GenePop import ... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PopGen/FDist/Utils.py | Python | gpl-2.0 | 6,997 | [
"Biopython"
] | 3b4c98eaedd377fd710da086828ba14240006b674d3fbe23d3705e8e840c8f6e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# stopstore - Back end to stop one or more resource store units
# Copyright (C) 2003-2009 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 terms of the G... | heromod/migrid | mig/shared/functionality/stopstore.py | Python | gpl-2.0 | 4,455 | [
"Brian"
] | 9adde452000f4c281c1c3de89f95cb1feb8bb2751bcfb77a182683f648073bce |
'''
Created on 2013-06-05
@author: brian
'''
class Item(object):
def __init__(self):
pass
def load(self, data):
pass
def save(self):
data = {}
data['type'] = self.__class__.__name__
return data
| Greymerk/python-rpg | src/items/item.py | Python | gpl-3.0 | 279 | [
"Brian"
] | dec5b0c13fa6974b8af286ebe8098061147260a1c612b1cbf5c3f8db24405755 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 18 17:48:12 2016
@author: antlaplante
"""
import argparse
import pandas as pd
from Bio import SeqIO
def get_aln(header):
(name, _, chrom, pos, qual) = header
return {'name' : name, \
'chrm' : chrom, \
'pos' : int(pos)... | antrec/spectrassembler | tools/extract_pos_from_sam.py | Python | mit | 3,127 | [
"BWA"
] | 91445ba46439f529e9fb75b460274666e39d9a96cf9da68139e22ee71b1ae010 |
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