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# Orca
#
# Copyright 2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This libr... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/gnome-screensaver-dialog/__init__.py | Python | gpl-3.0 | 854 | [
"ORCA"
] | 46c676609fb3c72d486a6db2ebbe2f54c5a276d885006aefcaa790fdf6131ca1 |
#!/usr/bin/env python
import sys
import math
from simtk.openmm.app import Element
import simtk.unit as unit
import subprocess
import datetime
from six.moves import cStringIO
import mdtraj as md
import logging
logger = logging.getLogger(__name__)
def fix(atomClass):
if atomClass == 'X':
return ''
retur... | choderalab/openmoltools | openmoltools/amber_parser.py | Python | mit | 40,943 | [
"Amber",
"MDTraj",
"OpenMM"
] | 46bdda48242aebca7863269fe045bc5d315a8465e7bd445f3899a36fe08dac83 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | psi-rking/psi4 | psi4/driver/molutil.py | Python | lgpl-3.0 | 9,830 | [
"Psi4"
] | 1adbddd434f2d3cfe4444e29bf4cc888f2817ff8fedf50799a4c1fc18e1bb67e |
import tables
import glob
import os
import mdtraj as md
import mdtraj.utils.fah
n_runs = 1
n_clones = 500 # To do: look this up via glob
project = 10468
codename = {10466:"T4", 10467:"src", 10468:"abl", 10469:"EGFR"}[project]
input_data_path = "/data/choderalab/fah/analysis/%d/concatenated_trajectories/" % project
... | kyleabeauchamp/fah-projects | code/analysis/delete_bad_trajectories.py | Python | gpl-2.0 | 550 | [
"MDTraj"
] | 3b2e0fd3b89b4f9413ea83a101b1f8a52af61046218c0a571d124b4aa5341426 |
"""
======================================
Sparse inverse covariance estimation
======================================
Using the GraphLasso estimator to learn a covariance and sparse precision
from a small number of samples.
To estimate a probabilistic model (e.g. a Gaussian model), estimating the
precision matrix, t... | jaidevd/scikit-learn | examples/covariance/plot_sparse_cov.py | Python | bsd-3-clause | 5,079 | [
"Gaussian"
] | 6fef3fb0a6d887d8549d085b8975ccbe4aad5d9e175b59ccc7cdb9fd58cb0556 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, absolute_import, print_function
import os
import re
import sys
import uuid
import codecs
from setuptools import setup, find_packages
from setuptools.command.test import test as TestCommand
from pip.req import parse_requirements
class Tox(TestCommand):
... | jthi3rry/uniauth | setup.py | Python | mit | 2,280 | [
"VisIt"
] | 34bfd2d9d80fdc3ad627bbc3e88fe8b6886f4060e8c0ce9a83da3d4f6f114613 |
# -*- coding: utf-8 -*-
import hashlib
from .sailthru_http import sailthru_http_request
try:
import simplejson as json
except ImportError:
import json
def extract_params(params):
"""
Extracts the values of a set of parameters, recursing into nested dictionaries.
"""
values = []
if isinsta... | sailthru/sailthru-python-client | sailthru/sailthru_client.py | Python | mit | 28,899 | [
"BLAST"
] | efc10c43d3b4092959bb9f41384e8927b12d11cc1d2495df8ed95221fdaa3224 |
""" :mod: DataManager
=======================
.. module: DataManager
:synopsis: DataManager links the functionalities of StorageElement and FileCatalog.
This module consists DataManager and related classes.
"""
# # RSCID
__RCSID__ = "$Id$"
# # imports
from datetime import datetime, timedelta
import... | avedaee/DIRAC | DataManagementSystem/Client/DataManager.py | Python | gpl-3.0 | 87,813 | [
"DIRAC"
] | 5e4ea5ddf96c095df2a945092e1f25f6cb147938261d38b80ead1ee499e8ff39 |
## \package GONode Both node and term type vertice classes
# \author Brian Muller <mullerb@musc.edu>
from GOError import GOError
class GONode:
TERM_TYPE = "term_type"
PROTEIN_TYPE = "protein_type"
## Constructor
def __init__ (self, nodetype, dbid, storage=None, name=None, description=None):
... | aswarren/GOGranny | GOGranny/GONode.py | Python | gpl-2.0 | 4,304 | [
"Brian"
] | 2a693f965e14dfdd06d29256c0736dac4db5b6f3645fa162619f457a42395738 |
# 2D channel example
# ==================
#
# .. highlight:: python
#
# This example demonstrates a depth-averaged 2D simulation in a closed
# rectangular domain, where the flow is forced by an initial pertubation in the
# water elevation field.
#
# We begin by importing Thetis and creating a rectangular mesh with :... | tkarna/cofs | demos/demo_2d_channel.py | Python | mit | 3,870 | [
"Gaussian"
] | f2b9bb59222f78d0df5b489adcae99a8f188756e0eae2691d012ca61f3b9b206 |
from ase import Atoms
from ase.calculators.test import numeric_force
from gpaw import GPAW, FermiDirac, PoissonSolver
from gpaw.test import equal
a = 5.404
bulk = Atoms(symbols='Si8',
positions=[(0, 0, 0.1 / a),
(0, 0.5, 0.5),
(0.5, 0, 0.5),
... | robwarm/gpaw-symm | gpaw/test/8Si.py | Python | gpl-3.0 | 1,380 | [
"ASE",
"GPAW"
] | 53ad9534c42ee8f73a4122b25bb80519fd7c538f1a18b6bfad5020a3c2380f08 |
"""
=====================================================================
The Johnson-Lindenstrauss bound for embedding with random projections
=====================================================================
The `Johnson-Lindenstrauss lemma`_ states that any high dimensional
dataset can be randomly projected in... | 3manuek/scikit-learn | examples/plot_johnson_lindenstrauss_bound.py | Python | bsd-3-clause | 7,452 | [
"Gaussian"
] | 404a8f2b1b55a010b794e2851d69c4628ffb11844e99129d40813ea36791402a |
# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
Scrapers for embedding images
=============================
Collect images that have been produced by code blocks.
The only scrapers we support are Matplotlib and Mayavi, others should
live in modules that will support them (e.g., PyVista, Plo... | Eric89GXL/sphinx-gallery | sphinx_gallery/scrapers.py | Python | bsd-3-clause | 15,061 | [
"Mayavi"
] | bd966265ab697fd600422d8df5abcca919e5bc1130bc352ce78a1fc41f8f55b1 |
import unittest, time, sys, os, re
sys.path.extend(['.','..','../..','py'])
import h2o, h2o_cmd, h2o_import as h2i, h2o_exec
import h2o_glm, h2o_gbm, h2o_rf
class ModelManagementTestCase(unittest.TestCase):
tear_down_cloud = True
# tear_down_cloud = False
def tearDown(self):
h2o.check_sandbox_for_... | rowhit/h2o-2 | py/testdir_multi_jvm/test_model_management.py | Python | apache-2.0 | 67,229 | [
"Gaussian"
] | a42633ba1a3320d5aad1204da0f3b4732190aec90e3992f62ca4c04a66571bcd |
# encoding: utf-8
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import datetime
import numpy as np
storm_num = 1
# Landfall for storm choosen
if storm_num == 1:
# Storm 1
... | mandli/surge-examples | mumbai/setrun.py | Python | mit | 17,576 | [
"NetCDF"
] | aa656d1e88eac56d346b8c1795d44ca3277a1334e0c94373b91011ff7e112060 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jH0ward/psi4 | psi4/share/psi4/databases/ACENES.py | Python | lgpl-3.0 | 162,818 | [
"Psi4"
] | 5b7269bd93e8fa764c93598fc2fa10caf99f159b6491fe78819c4a861fc7ab14 |
#### import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
def display_reader(reader, renderView) :
# show data in view
Display = Show(reader, renderView)
# trace defaults for the display properties.
D... | jeanfeydy/lddmm-ot | LDDMM_Python/demo/Notebooks/Feb2017_paper/render.py | Python | mit | 7,282 | [
"ParaView",
"VTK"
] | 8d67e846a0b39234cfae0421715fb856bbabe7fef04a8376972093af9aa99a16 |
# coding: utf-8
# # Test out standardized ADCIRC, SELFE and FVCOM datasets with pyugrid, IRIS and Cartopy
# The datasets being accessed here are NetCDF files from ADCIRC, SELFE and FVCOM, with attributes added or modified virtually using NcML to meet the [UGRID conevntions standard for unstructured grid models](htt... | rsignell-usgs/notebook | pyugrid_test.py | Python | mit | 2,987 | [
"NetCDF"
] | 553f53830daa78019a1ebe88816409962eae662b98dd2a897f3c89aa3f8eb74a |
from __future__ import division, print_function
import numpy as np, models as m, sql_utils as sql, pandas as pd,\
multiprocessing as mp, gus_utils as gu
from scipy.interpolate import InterpolatedUnivariateSpline
from scipy.integrate import fixed_quad
from functools import partial
from scipy.special import gam... | anguswilliams91/OnTheRun | code/fits.py | Python | mit | 12,759 | [
"Gaussian"
] | d3142d2ae5c9d641428f094de59b17a834db5267a6765f9885f66dd418fdae0b |
import os
import pytest
from numpy.testing import (assert_almost_equal,
assert_array_equal,
assert_array_almost_equal)
import numpy as np
import oddt
from oddt.spatial import (angle,
dihedral,
rmsd,
... | oddt/oddt | tests/test_spatial.py | Python | bsd-3-clause | 7,062 | [
"RDKit"
] | 3f3a0dd70cf841a0dd4ffaea640450399a1eb20e2925afc9e377162a2cf34cb8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import os
import re
import json
import warnings
import numpy as np
from io import open
from enum import Enum
from pymatgen.core.units import M... | gpetretto/pymatgen | pymatgen/core/periodic_table.py | Python | mit | 46,496 | [
"CRYSTAL",
"pymatgen"
] | 06ddbb0ac8bf8c9e887b5bcba670e729018d58da137dd2ec1bb30c2ad884ca36 |
# -*- coding: utf-8 -*-
#
#Created on Fri Apr 14 13:37:08 2017
#
#author: Elina Thibeau-Sutre
#
from .initializations import initialize_log_assignements,initialize_mcw
from .base import _log_B,_log_C
from .base import BaseMixture
from .base import _log_normal_matrix
from .base import _full_covariance_matrices,_spheric... | 14thibea/megamix | megamix/batch/VBGMM.py | Python | apache-2.0 | 20,615 | [
"Gaussian"
] | b5403282a3130e0fb8901f6147fa2669b25d40adf6bd2d1b3750d52dc4cb861b |
#!/usr/bin/env python
# a bar plot with errorbars
import numpy as np
import matplotlib.pyplot as plt
N = 6
scale = 100.0
ppr = np.array([[0.389, 0.486531845513, 0.563139309706, 0.525082089958, 0.956529670642, 0.584492],
[0.0888, 0.201719007817, 0.0650382409885, 0.28306446735, 0.893289636035, 0.337310]]... | CG-F16-24-Rutgers/steersuite-rutgers | steerstats/tools/plotting/plotMetricDataBar.py | Python | gpl-3.0 | 1,790 | [
"ORCA"
] | 1745246b6083ab1b86162e831a6f79674afa35e1d0b26fd5b40345ac76493878 |
__all__ = ["run_tli"]
import numpy as np
from scipy.signal import fftconvolve as convolve
import utils
def pad_image_and_weight(image, weight, final_shape, offset=None):
final_image = np.zeros(final_shape, dtype=float)
final_weight = np.zeros(final_shape, dtype=float)
shape = image.shape
rng = (0.... | davidwhogg/TheThresher | thresher/tli.py | Python | gpl-2.0 | 6,238 | [
"Gaussian"
] | b32913175337717e5a803e5afc22e51fbf1ea6b3dfb5b49620cbb1b21694555a |
""" Module for ginga routines. Mainly for debugging
"""
try:
basestring
except NameError:
basestring = str
import os
import numpy as np
import time
# A note from ejeschke on how to use the canvas add command in ginga: https://github.com/ejeschke/ginga/issues/720
# c
# The add() command can add any of the sha... | PYPIT/PYPIT | pypeit/ginga.py | Python | gpl-3.0 | 17,725 | [
"Gaussian"
] | 4b821138de2e9cfda25e0072e00c7695ca677d6f3477709fed6ee97924d94284 |
#
# Copyright (c) 2008--2016 Red Hat, Inc.
#
# This software is licensed to you under the GNU General Public License,
# version 2 (GPLv2). There is NO WARRANTY for this software, express or
# implied, including the implied warranties of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. You should have received a c... | wraiden/spacewalk | backend/server/rhnChannel.py | Python | gpl-2.0 | 70,207 | [
"VisIt"
] | 0882c0edfbe25bd2982c0ded0b96954da88495bf21ef552a1c70827cba0c6ed8 |
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 20 17:40:07 2015
@author: casimp
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import h5py
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpol... | Simclass/EDXD_Analysis | pyxe/plotting.py | Python | mit | 14,755 | [
"Gaussian"
] | 270019aff841d35c1b7002c6e7eb619e986e9c3f9385e43c922cb9f8e93f495a |
# search.py
# ---------
# Licensing Information: Please do not distribute or publish solutions to this
# project. You are free to use and extend these projects for educational
# purposes. The Pacman AI projects were developed at UC Berkeley, primarily by
# John DeNero (denero@cs.berkeley.edu) and Dan Klein (klein@cs.be... | evilzone/Artificial-Intelligence | search.py | Python | gpl-2.0 | 7,805 | [
"VisIt"
] | ee7d7207666b8c85928aed7847fb76c6003a5e2c508af684a0e76c2ba9f523c4 |
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License Version
# 1.1 (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.mozilla.org/MPL/
#
# Softwa... | centrumholdings/buildbot | buildbot/changes/manager.py | Python | gpl-2.0 | 5,753 | [
"Brian"
] | b2af8e5b962bd0dec77102af9614f9d4ab6ec44ae92e66f0211995eeb6496bad |
# Copyright 2021 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... | annarev/tensorflow | tensorflow/python/util/nest.py | Python | apache-2.0 | 64,128 | [
"VisIt"
] | 5be7a352a4f5416f2b932e2ee254aad8b66b26b1c0918965b27555a701da2ec8 |
"""This module contains the main classes for handling geophysical (climate)
variables and dimensions. It also reads and writes NetCDF files.
The :mod:`~geodat.nc.Dimension` and :mod:`~geodat.nc.Variable` classes in this
module act as containers of :py:mod:`~numpy` arrays which can be easily
accessed.
"""
from __futur... | kitchoi/geodat | geodat/nc.py | Python | mit | 88,536 | [
"Gaussian",
"NetCDF"
] | 5294cb27ce1ecd7c22f4e55620cd21c4b5680e9b1a28487c15cd6fe5f45f4060 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe import _
from erpnext.utilities.transaction_base import TransactionBase
class MaintenanceVisit(TransactionBase):
def get_fe... | gsnbng/erpnext | erpnext/maintenance/doctype/maintenance_visit/maintenance_visit.py | Python | agpl-3.0 | 3,120 | [
"VisIt"
] | ac45b1f2c39ac89fab7f260028d9d36f8550049299e835a96f17d0a7773c8f83 |
# -*- coding: utf-8 -*-
import datetime
import json
import os
from django.conf import settings
from django.core.urlresolvers import reverse
import mock
from nose.tools import eq_, ok_
from pyquery import PyQuery as pq
import mkt
from mkt.constants.applications import DEVICE_TYPES
from mkt.files.tests.test_models imp... | jasonthomas/zamboni | mkt/submit/tests/test_views.py | Python | bsd-3-clause | 38,479 | [
"exciting"
] | 79ece097434dc55c37486444f3e2b99a88503c6c18c10300179ca320a7a128cb |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_, PY2
from scipy._lib._util import getargspec_no_self as _getargspec
import sys
import keyword
import r... | jamestwebber/scipy | scipy/stats/_distn_infrastructure.py | Python | bsd-3-clause | 126,866 | [
"Gaussian"
] | 8f00a046b4b32660b37f3d4f38d43a6fc2ba59225fce53e2e5919a10ee17d3c0 |
"""som - Self-organising-map"""
from typing import Optional, Tuple
import numpy as np
from sklearn.decomposition import PCA
class SOM:
"""
SOM - Self-Organising-Map.
A 2D neural network that clusters high-dimensional data iteratively.
Parameters
----------
nx : Number of neurons on x-axis.
... | tlhr/plumology | plumology/learn/som.py | Python | mit | 12,304 | [
"Gaussian"
] | 881a4b09aad02924a63e9705bfbedd20617070e8b0954a8a8f7e2e99a92d304a |
# 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... | psci2195/espresso-ffans | src/python/espressomd/drude_helpers.py | Python | gpl-3.0 | 10,686 | [
"ESPResSo"
] | 06a459e7ee2f6635416dee33ba034db43c249320da8d899ca96e61c08a884d1f |
import unittest
import pysal
import numpy as np
from pysal.spreg import error_sp_hom_regimes as SP
from pysal.spreg.error_sp_hom import GM_Error_Hom, GM_Endog_Error_Hom, GM_Combo_Hom
class TestGM_Error_Hom_Regimes(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r... | darribas/pysal | pysal/spreg/tests/test_error_sp_hom_regimes.py | Python | bsd-3-clause | 14,805 | [
"COLUMBUS"
] | f6d2138055b54f5d05f155053507c970c4e8bf44f4616c5d671fff3414ec894f |
import numpy as np
from . import _marching_cubes_cy
def marching_cubes(volume, level, spacing=(1., 1., 1.)):
"""
Marching cubes algorithm to find iso-valued surfaces in 3d volumetric data
Parameters
----------
volume : (M, N, P) array of doubles
Input data volume to find isosurfaces. Will... | almarklein/scikit-image | skimage/measure/_marching_cubes.py | Python | bsd-3-clause | 6,374 | [
"Mayavi"
] | 2801d604f7ddb23e66941d55bf057b6079852d605efebac8e0bbc40c295b8f0e |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Google Chrome History database plugin."""
import unittest
from plaso.lib import definitions
from plaso.parsers.sqlite_plugins import chrome_history
from tests.parsers.sqlite_plugins import test_lib
class GoogleChrome8HistoryPluginTest(test_lib.SQLiteP... | joachimmetz/plaso | tests/parsers/sqlite_plugins/chrome_history.py | Python | apache-2.0 | 10,175 | [
"VisIt"
] | fd2dc191267eaa1ddb29730d42dcad28c4dcacf0087410800e5a1038b723ee81 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_comp_dm.py | Python | apache-2.0 | 1,074 | [
"PySCF"
] | 234d4a5113c323d59be6f7285ef4eef8b2865739ee8be25bcc0083476a3c9381 |
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 31 17:09:57 2015
This script converts output from WrapDbihar code to the format expected by the
legacy Coupled Cells code.
The code reorders cells and produces the required files in TXT format.
VTK files are written out for visual verification.
This code assumes there a... | BlueFern/DBiharMesher | util/DumpMeshToLegacyFormat.py | Python | gpl-2.0 | 30,826 | [
"VTK"
] | 882210a3b79ce8eb9b6e5e64dffd95e162cf35458279d607ba7bd2e382f306c7 |
import numpy as np
import pytest
from pysisyphus.calculators import XTB
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.helpers import geom_loader
from pysisyphus.optimizers.hessian_updates import (
bfgs_update,
damped_bfgs_update,
double_damp,
sr1_update,
psb_update,
flowchart_u... | eljost/pysisyphus | tests/test_hessian_updates/test_hessian_updates.py | Python | gpl-3.0 | 2,385 | [
"PySCF",
"xTB"
] | 0b1a1dae2f971f9cc12ed91bfe031a53064be6f0c5f351be587663256dc466cf |
########################################################################
# This example demonstrates synaptic triggering of a wave of calcium
# release (CICR) from the endoplasmic reticulum. The wave is confined to
# a subset of a dendrite where there is elevated IP3 present.
#
# Copyright (C) Upinder S. Bhalla NCBS ... | BhallaLab/moose | moose-examples/tutorials/Rdesigneur/ex8.1_synTrigCICR.py | Python | gpl-3.0 | 1,889 | [
"MOOSE"
] | 7d9a7cf15ab3f1ab0d840ee2c42da31a73de9baa6a0ac6f6f9c3401b32d168ed |
#!/usr/local/sci/bin/python
#***************************************
# 7 March 2018 KMW - v2
# Plots global time series from ASCII
# Can plot against other datasets
# Requires uncertainty values for HadISDH
#************************************************************************
# STAR... | Kate-Willett/Climate_Explorer | PYTHON/PlotGlobalTimeSeries_MAR2018.py | Python | cc0-1.0 | 14,911 | [
"NetCDF"
] | 77d5bc2662517d5898630334bce7e35060621d2911c44a0715b78562a59de4f3 |
########################
# File to analyze the data produced by the networks
# Ramon Martinez February / 2014
########################
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from visualization_functions import *
from time import localtime
import h5py
# Analysis ... | h-mayorquin/Neural_Pattern_Doursat | analyze_01.py | Python | gpl-2.0 | 2,827 | [
"NEURON"
] | 1b49456af66f87ab93093c47c5afef74fed439932ad147cba9b2b94bb25bb43a |
#!/usr/bin/env python
class VTK_XML_Serial_Unstructured:
"""
USAGE:
vtk_writer = VTK_XML_Serial_Unstructured()
vtk_writer.snapshot("filename.vtu", (x,y,z), optional arguments...)
vtk_writer.writePVD("filename.pvd")
"""
def __init__(self):
self.fileNames = []
def snapshot(self, f... | ansobolev/shs | shs/vtkxml/xml_write.py | Python | mit | 8,152 | [
"ParaView",
"VTK"
] | cc2bb39cd863c3d2e9316f340330cf80c9fc9853ee646c4cb2d3c2c3730e923e |
# -*- coding: utf-8 -*-
import numpy as np
import parabem
from parabem.vtk_export import VtkWriter
from parabem import PanelVector2, Vector2, Panel2
from parabem.airfoil import Airfoil
from parabem.pan2d import NeumannSource0Case2 as Case
from parabem.utils import check_path
airfoil = Airfoil.joukowsky(m=-0.1 +0.1j)
... | booya-at/paraBEM | examples/vtk/vtk_airfoil_neumann_source.py | Python | gpl-3.0 | 1,600 | [
"VTK"
] | 64b4960d7b7f5d6c1454559b3347029853cc5175e5c9df607f9a0f0d410655b5 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'DataFile'
db.create_table(u'profiles_datafile', (
(u'id', self.gf('django.db.m... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0004_auto__add_datafile.py | Python | mit | 27,394 | [
"MOE"
] | 75a9ecc9f426961b49be6879d10defa5330aa2fc790838fe62fea3a1cb6016d1 |
#!/usr/bin/env python
import os
import sys
import subprocess as sp
import argparse
if sys.version_info.major == 3:
PY3 = True
from urllib.request import urlretrieve
else:
PY3 = True
from urllib import urlretrieve
usage = """
The easy way to test recipes is by using `circleci build`. However this doe... | dmaticzka/bioconda-recipes | bootstrap.py | Python | mit | 3,844 | [
"Bioconda"
] | c891dd359bae1cda382eb521e38da7ef2ee25d9a6d4b6c751e25da38629747da |
""" core implementation of testing process: init, session, runtest loop. """
import functools
import os
import sys
import _pytest
import _pytest._code
import py
import pytest
try:
from collections import MutableMapping as MappingMixin
except ImportError:
from UserDict import DictMixin as MappingMixin
from _py... | razvanc-r/godot-python | tests/bindings/lib/_pytest/main.py | Python | mit | 27,330 | [
"VisIt"
] | 91d243848189dda41cf851fb0d06311c96fac3117759542e31bad8afa5e2d7f8 |
#!/usr/bin/env python
""" Patch utility to apply unified diffs
Brute-force line-by-line non-recursive parsing
Copyright (c) 2008-2012 anatoly techtonik
Available under the terms of MIT license
Project home: http://code.google.com/p/python-patch/
$Id: patch.py 181 2012-11-23 16:03:05Z techtonik... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/doc/patch.py | Python | gpl-3.0 | 34,815 | [
"Galaxy"
] | 8e0df9aa3a996f0a6ecc8ac56e476da5626385a8571385fbbaaac81181b89cca |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkBlankStructuredGrid(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkBlankStructuredGrid.py | Python | bsd-3-clause | 511 | [
"VTK"
] | 8ffa2166548caebb2e90200eabdfc03a3290d269f5f8dd1f2433e1a6f6c90402 |
import serial
import inspect
import time
import itertools
from util import two_byte_iter_to_str, to_two_bytes
# Message command bytes - straight from Firmata.h
DIGITAL_MESSAGE = 0x90 # send data for a digital pin
ANALOG_MESSAGE = 0xE0 # send data for an analog pin (or PWM)
DIGITAL_PULSE = 0x91 # SysE... | nvazquez/Turtlebots | plugins/rodi/pyfirmata/pyfirmata.py | Python | mit | 18,699 | [
"CRYSTAL"
] | 1581b7244b16fddfd7c8d34702a5f9bf0d43aa877a9ac6c4cecf4360b5ab5172 |
#!/usr/bin/python
# -*- coding: utf-8
# Copyright (C) 2010 - 2012, A. Murat Eren
#
# 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 lat... | meren/oligotyping | Oligotyping/lib/oligotyping.py | Python | gpl-2.0 | 70,869 | [
"BLAST"
] | cdba9d5a7174880627f3492525ed0c991385ad083a94c85041301d013532c182 |
########################################################################
# $HeadURL $
# File: LcgFileCatalogProxyClient.py
########################################################################
""" File catalog client for LCG File Catalog proxy service """
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Client ... | Sbalbp/DIRAC | Resources/Catalog/LcgFileCatalogProxyClient.py | Python | gpl-3.0 | 2,536 | [
"DIRAC"
] | 8fac93c30a59784a483743a3344fd490bf903d97f4ab1b44f9784634c5a312dd |
import logging
from typing import List
import numpy as np
from deepchem.utils.typing import RDKitMol
from deepchem.utils.molecule_feature_utils import one_hot_encode
from deepchem.feat.base_classes import MolecularFeaturizer
logger = logging.getLogger(__name__)
ZINC_CHARSET = [
'#', ')', '(', '+', '-', '/', '1'... | lilleswing/deepchem | deepchem/feat/molecule_featurizers/one_hot_featurizer.py | Python | mit | 3,091 | [
"RDKit"
] | f90125e55956a05086304e529475997f360aec07001e0dd1297e8f92480e9977 |
"""MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
MDTraj is a python library that allows users to manipulate molecular dynamics
(MD) trajectories and perform a variety of analyses, including fast RMSD,
solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj
is ... | ctk3b/mdtraj | setup.py | Python | lgpl-2.1 | 12,594 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF",
"TINKER"
] | e93693a59c5cc7e0e6b38496c23774d5166bff906b61036ef8adda4141362ced |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/share/psi4/databases/RGC10.py | Python | gpl-2.0 | 81,975 | [
"Psi4"
] | 87919b9911912253c6a65080cb3c5651c68460b6ceda252e4a96c892ea9d6d59 |
# -*- coding: utf-8 -*-
# Tested on Markdown 2.3.1
#
# Copyright (c) 2014, Esteban Castro Borsani
# Copyright (c) 2014, Jesús Espino García
# The MIT License (MIT)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to... | xdevelsistemas/taiga-back-community | taiga/mdrender/extensions/emojify.py | Python | agpl-3.0 | 14,160 | [
"Bowtie",
"Octopus"
] | e90676b9fed64350889808bbb5729447d5712bafd0b6cc44bc71ce31bdecdfc3 |
'''
Arthur Glowacki
APS ANL
10/17/2014
'''
from Model import Model
import numpy as np
import math, time, sys
import h5py
from PyQt4 import QtCore
from vtk import *
import Optics
class Scanner(QtCore.QThread):
notifyProgress = QtCore.pyqtSignal(int)
notifyFinish = QtCore.pyqtSignal()
def __init__(self):
QtCore.Q... | aglowacki/ScanSimulator | Scanner.py | Python | gpl-2.0 | 4,299 | [
"VTK"
] | 72fa1fed3040cb2d0b51533ac4282c456629fca1d87ca3faf8c72d2b09b256df |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | poem/core/loss_utils.py | Python | apache-2.0 | 28,809 | [
"Gaussian"
] | a3187fa6bcabe8b26070453305585c491d732e643d015650bd6fdaff2b32cd18 |
# 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 libraries:
... | boutproject/BOUT-2.0 | tools/pylib/boututils/datafile.py | Python | gpl-3.0 | 11,686 | [
"NetCDF"
] | fe83268cef1797743c60048e2a839d238b10523c257aac29815e2ec0631a8f44 |
# coding=utf-8
from pkg_resources import resource_filename
from compliance_checker.suite import CheckSuite
from compliance_checker.base import Result, BaseCheck, GenericFile
import numpy as np
import unittest
import os
static_files = {
'2dim' : resource_filename('compliance_checker', 'tests/data/2dim-grid.... | lukecampbell/compliance-checker | compliance_checker/tests/test_suite.py | Python | apache-2.0 | 9,873 | [
"BWA",
"NetCDF"
] | 4254152a7df83faefdefd326873828de1dab7ffd66b14ecb9e392e0e4e660a07 |
"""cdbifunc.py
Developer: Noelle Todd
Last Updated: August 30, 2014
This module holds all functions that will be called directly by the user
interface. This module uses several functions in cdbfunctions.py; the two
modules have been split to make designing the user interface as simple as
simple as possible.
"""
impo... | ChristinaHammer/Client_Database | cdbifunc.py | Python | mit | 12,536 | [
"VisIt"
] | 2c8f7aacdac3b80d0868bff523e25a2dd454bc7d45e5c88e2cbda1411a251cda |
import unittest, random, sys, time
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_hosts, h2o_browse as h2b, h2o_import as h2i, h2o_glm, h2o_util, h2o_jobs, h2o_gbm, h2o_exec as h2e
DO_BUG = False
DO_HDFS = False
DO_ALL_DIGITS = False
print "Uses numpy to create dataset..I guess we have to deal with jenkins... | janezhango/BigDataMachineLearning | py/testdir_single_jvm/test_GLM2_syn_corr.py | Python | apache-2.0 | 6,766 | [
"Gaussian"
] | d55552e05ac5ed291dbb844626d29df514940237ec7a00305fb11a52a44236c4 |
"""Probe image with mesh. Use VTK 5.10 which comes with Anaconda: Created by Arjan Geers, Modified by Noel Conlisk"""
import os
import vtk
def read_image(path):
"""Read VTK ImageData"""
filename, extension = os.path.splitext(path)
if extension == '.vtk':
reader = vtk.vtkStructuredPointsRe... | nconlisk/python | VTK/probe_mesh_combined.py | Python | gpl-3.0 | 1,502 | [
"VTK"
] | fa5d5ae68cec61ce5e84783082eb9167a949a93c076fdd733d2250436b2c6ee0 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#======================================================================
#
# ccport.py - cclib port
#
# ³õʼ»¯·þÎñ
#
#======================================================================
import sys, time, struct, os
import ctypes
from ctypes import c_uint, c_i... | skywind3000/cannon | cannon/lib/cport.py | Python | apache-2.0 | 11,083 | [
"cclib"
] | 8703f14c3b10ff849fa0c5282513433858fde459e62d061594cae515e49f34b3 |
"""
Class for management of Stomp MQ connections, e.g. RabbitMQ
"""
import json
import random
import os
import socket
import ssl
import time
import stomp
from DIRAC.Resources.MessageQueue.MQConnector import MQConnector
from DIRAC.Core.Security import Locations
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.U... | DIRACGrid/DIRAC | src/DIRAC/Resources/MessageQueue/StompMQConnector.py | Python | gpl-3.0 | 12,925 | [
"DIRAC"
] | 387060d2c2cbe6a3d09418b28689755aa7f05bdf637b574019cf9e52f6a03c56 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# __init__ - [insert a few words of module description on this line]
# 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 ... | heromod/migrid | mig/shared/__init__.py | Python | gpl-2.0 | 1,270 | [
"Brian"
] | a5f89bd6ed360c27a17d3d7d605effff0da338bf55ec91eaa252d6afc57e7c63 |
# -*- coding: utf-8 -*-
"""Define pRF finding parameters here."""
# Part of py_pRF_motion library
# Copyright (C) 2016 Marian Schneider, Ingo Marquardt
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Fo... | MSchnei/py_pRF_motion | pyprf_feature/simulation/configs/pRF_sim_config_square2.py | Python | gpl-3.0 | 4,233 | [
"Gaussian"
] | 61e34086108f19738ca9c5bbbfe595b5d71837a2ddea104cb56c37afac0a3076 |
#!/usr/bin/env python
"""
python script/module that uses pyamg to calculat and plot fiedler vectors of a graph
using pyamg,numpy and scipy.
Input:
A sif file or any three column white space deliminated file with the first and
third column repesenting node names and each row repesenting an edge.
Comand line Usage:
p... | ryanbressler/GraphSpectrometer | fiedler.py | Python | bsd-3-clause | 20,913 | [
"Gaussian"
] | a964eab4799a5ce823f9b558cdb0f863537322ed728715354e6d581ef9167a0f |
#!/usr/bin/env python
'''
Convert back and forth between the molecule (open boundary) and the 0D PBC
system.
'''
import numpy
from pyscf import gto, scf
from pyscf.pbc import gto as pbcgto
from pyscf.pbc import scf as pbcscf
from pyscf.pbc import df
cell = pbcgto.Cell()
cell.atom = 'N 0 0 0; N 0 0 1.2'
cell.basis = ... | sunqm/pyscf | examples/pbc/31-pbc_0D_as_mol.py | Python | apache-2.0 | 1,848 | [
"PySCF"
] | 2636673c03e1329ebb50616bb2e1d961cf93e4a86e32dbf516f03d4e80306c32 |
#!/usr/bin/env python
"""Create rst files for documentation of DIRAC source code."""
import sys
from diracdoctools.cmd.codeReference import run, CLParser
sys.exit(run(**(CLParser().optionDict())))
| DIRACGrid/DIRAC | docs/diracdoctools/scripts/dirac-docs-build-code.py | Python | gpl-3.0 | 199 | [
"DIRAC"
] | daad506257d57a4e06452992a1d44b360556fa6812a9c4eef5b1a8bd0512dc27 |
"""
The MIT License (MIT)
Copyright (c) 2015 <Satyajit Sarangi>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, ... | ssarangi/spiderjit | src/optimizer/const_propagation.py | Python | mit | 4,120 | [
"VisIt"
] | 2640cbe5ef7006d73b6e98102ca3142c2b28fa5a24b2e5647b42771fa67c3367 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# vim:set ts=2 sw=2 et:
#
# -----------------------------------------------------------------------
#
# Go2C is based on the c-to-c.py example from pycparser by Eli Bendersky,
# and uses pycparser extensively.
#
# Alexander Rødseth <rodseth@gmail.com>
# License: BSD
#
# -... | xyproto/c2go | c2go.py | Python | bsd-3-clause | 43,202 | [
"VisIt"
] | 12f4da4bf0a3e8eb3e006aaf36c5edb5045b40f57a13d7be701fe3c284cd2c0b |
'''
The MIT License (MIT)
(c) Juergen Simon 2014 (juergen.simon@uni-bonn.de)
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, c... | meteo-ubonn/meanie3D | python/meanie3D/visualisation/tracks.py | Python | mit | 3,744 | [
"VTK",
"VisIt"
] | f9a8dfc8865da159a3f596861bc8a9b167aa8c43449993bb06929ab9fee78cc2 |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | 0xkag/tornado | tornado/websocket.py | Python | apache-2.0 | 38,343 | [
"VisIt"
] | cd5ac097ba18e3d94db443aa581cd561843f92786af9bca3bedeeb0f49f4085c |
# JN 2016-03-02
"""
show resposes in css-gui
"""
from __future__ import print_function, division, absolute_import
import os
import numpy as np
import scipy.signal as signal
from .sort_widgets import MplCanvas
from matplotlib.pyplot import imread
from matplotlib.offsetbox import OffsetImage, AnnotationBbox
HGAP = VGA... | jniediek/combinato | combinato/guisort/raster_figure.py | Python | mit | 7,173 | [
"Gaussian"
] | 33cb0d766a03e6295045a4017654784096089b5ad07a5796b807322aca44ad2b |
#!/usr/bin/python
########################################################################
# 2 September 2014
# Patrick Lombard, Centre for Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import os, re, ... | pdl30/pyngsplot | pyngsplot/tools/custom_heatmaps.py | Python | mit | 2,543 | [
"HTSeq"
] | f432ffb79619d2b3a1358c516c6b58049d16f3d54dbf378775c801d8305dc8d5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
readme = open('README.rst').read()
history = open('HISTORY.rst').read().replace('.. :changelog:', '')
requirements = [
# TODO: put package requirements here
]
test_requi... | petrilli/jana | setup.py | Python | bsd-3-clause | 1,410 | [
"Amber"
] | 3efeef94247d1f25e73bccd61b9cc4680d324d7fdbfa639f29148429c82eebcc |
import superimport
import pyprobml_utils as pml
import numpy as np
from scipy.stats import uniform, laplace, norm
import matplotlib.pyplot as plt
n = 2000
x = np.arange(-4, 4, 0.01)
y1 = norm.pdf(x, 0, 1)
y2 = uniform.pdf(x, -2, 4)
y3 = laplace.pdf(x, 0, 1)
plt.plot(x, y1, color='blue')
plt.plot(x, y2, color='green'... | probml/pyprobml | scripts/sub_super_gauss_plot.py | Python | mit | 1,270 | [
"Gaussian"
] | 63d5705c88dea18e594b420974d5547efe7beaa8adecb89bd1fd54b57c965476 |
# 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.
"""Asynchronous execution of Fdist and spliting of loads.
FDistAsync All... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/PopGen/FDist/Async.py | Python | gpl-2.0 | 6,761 | [
"Biopython"
] | 9c64de7613f0fea194aefd155e5ccd69f226adc13e6af0b5f9da79559be1e52e |
from cifsdk.format.cifbind import Bind
import re
def test_format_bind():
data = [
{
'observable': "example.com",
'provider': "me.com",
'tlp': "amber",
'confidence': "85",
'reporttime': '2015-01-01T00:00:00Z',
'otype': 'fqdn'
... | aeppert/py-cifsdk | test/test_bind.py | Python | lgpl-3.0 | 1,121 | [
"Amber"
] | 792847584aa86e4915b1aca7a337eed2aca22b63dc46d4d92b9bd965c2e6a195 |
"""Test that set_momenta behaves as expected when constraints are
involved."""
import numpy as np
from ase import Atoms, Atom
from ase.constraints import Hookean, FixAtoms
# FixAtoms check
atoms = Atoms([Atom('H', (0., 0., 0.)),
Atom('H', (2., 0., 0.))])
atoms.set_constraint(FixAtoms(indices=[0]))
ato... | suttond/MODOI | ase/test/set_momenta.py | Python | lgpl-3.0 | 805 | [
"ASE"
] | 74c5c6209d1628f487a4ad834a134f570e398d19b1cb3e5a5446708d9b17f8c3 |
#! /usr/bin/env python
# coding:utf-8
# Author: bingwang
# Email: toaya.kase@gmail.com
# Copylight 2012-2012 Bing Wang
# LICENCES: GPL v3.0
__docformat__ = "epytext en"
#1. get scer 1:1 seub
#2. get scer 1:1 suva 1:1 anc
#3. map scer:suva:seub use 1:1:1
#4. insert suva specific genes, check seub gene use anc and blas... | BingW/yeast_anno_pipe | src/make_seub_pillar.py | Python | gpl-3.0 | 2,349 | [
"BLAST"
] | b147eb16518fff8a402476a1fade9644566cb5361cbef35df3a4184c2945e612 |
import time, sys, os
import numpy as np
np.errstate(invalid='ignore')
from prospect.models import model_setup
from prospect.io import write_results
from prospect import fitting
from prospect.likelihood import lnlike_spec, lnlike_phot, write_log
from dynesty.dynamicsampler import stopping_function, weight_function, _kl... | bd-j/bsfh | scripts/prospector_dynesty.py | Python | gpl-2.0 | 5,286 | [
"Gaussian"
] | 11236bf87ce1c9e67352e0ab3ca9f655a3d4bf2084b77d98a13b3880df245bdc |
# 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... | oostende/openblachole | lib/python/Components/Converter/PliExtraInfo.py | Python | gpl-2.0 | 25,721 | [
"Galaxy"
] | e7c14b4c26fe52110c505d8a0442ad250d64f7ffbed9acd937ef68fc981c2246 |
#!/usr/bin/env python2.7
import os
import httplib2
import oauth2client
import apiclient
import flask
from uuid import uuid4
from flask import Flask, render_template, request, g
from models import users_model, index_model, teachers_model, students_model, \
courses_model, model
from google.cloud import datasto... | keirl/coms4156_jumpstart | imhere/imhere.py | Python | apache-2.0 | 11,312 | [
"VisIt"
] | 8c181ad0911bb645fb9c33be0eef033132f8e4a45d1e6998b20dcfa2bfb88425 |
#!/usr/bin/env python
# Imports
try: import argparse
except: error('This version of python is not new enough. python 2.7 or newer is required.')
try: from netCDF4 import Dataset
except: error('Unable to import netCDF4 module. Check your PYTHONPATH.\n'
+'Perhaps try:\n module load python_netcdf4')
try: impo... | nicjhan/MOM6-examples | ice_ocean_SIS2/OM4_025/preprocessing/extract_edits.py | Python | gpl-3.0 | 2,926 | [
"NetCDF"
] | 392f9eff8d5908af27b679935a651c61a9ec6b0ed582638d9507109f733678ed |
# coding=utf-8
"""Login in the application feature tests."""
import pytest
from django.contrib.auth.models import User
from model_mommy import mommy
from pytest_bdd import (
given,
scenario,
then,
when,
)
from quiz.models import Unity, Lesson
@pytest.mark.django_db
@scenario('features/signin.feature'... | jesuejunior/golingo | quiz/tests/functional/test_signin.py | Python | bsd-3-clause | 2,071 | [
"VisIt"
] | e2ea9f9fa823f24534361e2e01888dae702081800b5e1f5480c65990b2b13a74 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'PreviousObstetricHistory.problems'
db.delete_column(u'patient_previousobstetrichistory', '... | aazhbd/medical_info01 | patient/migrations/0026_auto__del_field_previousobstetrichistory_problems__add_field_previouso.py | Python | bsd-3-clause | 30,623 | [
"VisIt"
] | 48e681658e693b6ed7271e78d251ded95514de58c13e47b9c77c3873728cf7f0 |
# $Id$
#
# Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" unit testing code for composite models
"""
import unittest
import io
import pickle
from rdkit.ML.Composite import Composite
from rdkit.ML.DecTree.DecTree import DecTreeNode as Node
from rdkit import RDConfig
c... | bp-kelley/rdkit | rdkit/ML/Composite/UnitTestComposite.py | Python | bsd-3-clause | 7,222 | [
"RDKit"
] | 3bdfa92a82ce6b490a640ba112adeb8ec086febdd57dcd221d70dc925b38d764 |
########################################################################
# File : JobWrapper.py
# Author : Stuart Paterson
########################################################################
""" The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts ... | miloszz/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 62,516 | [
"DIRAC"
] | cfb840e02aa279a1d63740c82187299f56a339d3a10b3a2861ebbd470f5954ae |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Takes a list of maf filenames on the command line and prints a comma separated
list of the species that occur in all of the mafs.
usage %prog maf1 maf2 ...
"""
import operator
import sys
import bx.align.maf
files = sys.argv[1:]
sets = []
for file in files:
sys.stde... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_species_in_all_files.py | Python | bsd-3-clause | 572 | [
"Galaxy"
] | a5e8efb4071366af727f2ac6549dec82e45efd4db5024c68862f3c0346fbddda |
# -*- coding: utf-8 -*-
import math
import zope.event
from bika.lims.utils import formatDecimalMark
from Products.Archetypes.event import ObjectInitializedEvent
from Products.CMFCore.WorkflowCore import WorkflowException
from Products.CMFPlone.utils import _createObjectByType
def create_analysis(context, service, ke... | DeBortoliWines/Bika-LIMS | bika/lims/utils/analysis.py | Python | agpl-3.0 | 11,236 | [
"VisIt"
] | c157fda1de9fe1896ec291ecaa050bca54f8b54e9c316adbc5a46a993cde1930 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) Philipp Wagner. All rights reserved.
# Licensed under the BSD license. See LICENSE file in the project root for full license information.
import os
import sys
import numpy as np
from scipy import ndimage
sys.path.append("../..")
# try to import the PIL ... | bytefish/facerec | py/apps/scripts/lpq_experiment.py | Python | bsd-3-clause | 10,585 | [
"Gaussian"
] | 96bb617f1d02e49e70b5c633e2a629ec8e22e2c5f579289e847a47cdc1e2499e |
# Copyright (c) 2018 PaddlePaddle 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 appli... | PaddlePaddle/Paddle | python/paddle/fluid/dygraph/nn.py | Python | apache-2.0 | 138,442 | [
"NEURON"
] | 7a8da982dda86889a647db91edadbd55e578aa6fb86b8b9ff3b620c8993d2733 |
#!/usr/bin/env python3
#
# blist2xmlgo.py
#
# Copyright (C) 2013, Jian-Long Huang
# Licensed under The MIT License
# http://opensource.org/licenses/MIT
#
# Author: Jian-Long Huang (jianlong@ntu.edu.tw)
# Version: 0.1.0
# Created: 2013.1.6
#
# Usage: blist2xmlgo.py <blast_list> <map_ids> <output>
#
# Columns:
# 0 aln_ra... | jlhg/bdorpy | bdorpy/blist2xmlgo.py | Python | mit | 4,234 | [
"BLAST"
] | 93738fdba39d44899ef65b656fce9fc8dca4d854a6e8b3a15f3eeaee1fcee774 |
#!/usr/bin/env python
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# 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.
#
"""Restriction Digest Enzymes.
Example:
... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Restriction/__init__.py | Python | gpl-2.0 | 8,705 | [
"Biopython"
] | c7216be886c9882e3ed7b65c95d14341f2031206c203a217b1be67f64b767249 |
# 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.
"""Code for calling ClustalW and parsing its output (DEPRECATED).
This module has been superseded by the Bio.AlignIO framework for
alignment parsing, a... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Clustalw/__init__.py | Python | gpl-2.0 | 21,060 | [
"Biopython"
] | 97b89ef08413148073edd4af4de7a4e6a1d4f7ba0422ce817111f41fd0aacbcd |
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