text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""MGEScan-nonLTR: identifying non-ltr in genome sequences
Usage:
nonltr.py all <genome_dir> [--output=<data_dir>]
nonltr.py forward <genome_dir> [--output=<data_dir>]
nonltr.py backward <genome_dir> [--output=<data_dir>]
nonltr.py reverseq <genome_dir> [--output=<data_dir>]
nonltr.py qvalue <genom... | MGEScan/mgescan | mgescan/nonltr.py | Python | gpl-3.0 | 7,365 | [
"Biopython"
] | c00dd03b81e853f2eb351713baf3470e9605a3ae6919130fab01edb4f7dda8ef |
"""I produce the hourly analysis used by IEMRE."""
import datetime
import os
import sys
import pygrib
import numpy as np
import pandas as pd
from metpy.units import masked_array, units
from metpy.calc import wind_components
from metpy.interpolate import inverse_distance_to_grid
from scipy.interpolate import NearestNDI... | akrherz/iem | scripts/iemre/hourly_analysis.py | Python | mit | 7,939 | [
"NetCDF"
] | 6422e4fb1cdf12e91f87008d94935bd60b575bc4c0048e218d18df742fb63ddf |
# Copyright (c) 2015-2018 Cisco Systems, Inc.
#
# 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, merge... | metacloud/molecule | molecule/dependency/shell.py | Python | mit | 3,865 | [
"Galaxy"
] | be2c0e604f096d304fae1cd1cfd4816017dfd52e880a446440f2b969735f5376 |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC FileCatalog component representing a directory tree with
enumerated paths
"""
__RCSID__ = "$Id$"
import os
from types import ListType, StringTy... | Sbalbp/DIRAC | DataManagementSystem/DB/FileCatalogComponents/DirectoryLevelTree.py | Python | gpl-3.0 | 19,028 | [
"DIRAC"
] | 8a40b8765d7d3fd025fb3152f8f7d655ce243f249e0516f615532329e9b533cc |
# Copyright (C) 2010 by CAMd, DTU
# Please see the accompanying LICENSE file for further information.
# This file is taken (almost) verbatim from CMR with D. Landis agreement
FIELD_SEPARATOR="\\"
PARA_START="\n\n"
PARA_END="\\\\@"
names = ["", "", "Computer_system", "Type_of_run", "Method", "Basis_set", "Chemical_fo... | grhawk/ASE | tools/ase/io/gaussian_reader.py | Python | gpl-2.0 | 3,674 | [
"ASE"
] | 62e09ecf2fc0743a3b694d7292a145fff6ac5fc38550621dcc1bb0d66c9f044f |
#!/usr/bin/env python
"""
Implementation for `pmg potcar` CLI.
"""
import os
from pymatgen.io.vasp import Potcar
def proc_dir(dirname, procfilefunction):
"""
Process a directory.
Args:
dirname (str): Directory name.
procfilefunction (callable): Callable to execute on directory.
""... | vorwerkc/pymatgen | pymatgen/cli/pmg_potcar.py | Python | mit | 1,580 | [
"VASP",
"pymatgen"
] | 64e9a1ee3c8f07f5291eaa29f1b08788b57e86f10b73545ae34a395e036cb539 |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from datetime import datetime
from collections import defaultdict
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import setti... | beni55/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 56,361 | [
"VisIt"
] | e7ae041f568c85551f877047728339b909a7dde1d697d3bf109b3d3eed464590 |
import molecule
import qcjob
# create the molecule from xyz file
h2 = molecule.from_xyz('geometries/hydrogen.xyz')
# generate Q-Chem job
job = qcjob.QCjob(h2, rems={"gen_scfman": "true"})
job.run()
# if you wish to test the JMol viewer, uncomment to following line:
# h2.to_jmol()
| EhudTsivion/QCkit | examples/simple_job.py | Python | lgpl-3.0 | 285 | [
"Jmol",
"Q-Chem"
] | b8306693a514218dbf8c9840e4e272bb1f9968ecfeed76bba0948088fe2f298e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements plotter for DOS and band structure.
"""
import logging
from collections import OrderedDict, namedtuple
import numpy as np
import scipy.constants as const
from monty.json import jsan... | gmatteo/pymatgen | pymatgen/phonon/plotter.py | Python | mit | 31,427 | [
"Gaussian",
"pymatgen"
] | 737185e5a991a35c9a864148212fdf21ae4c10735425cb4d13f1561cec8daa48 |
import numpy as np
import tensorflow as tf
import tensorflow.contrib.slim as slim
from tensorflow.contrib.layers.python import layers as tf_layers
from models.conv_lstm import basic_conv_lstm_cell
# Amount to use when lower bounding tensors
RELU_SHIFT = 1e-12
FC_LAYER_SIZE = 256
FC_LSTM_LAYER_SIZE = 128
# kernel siz... | jonasrothfuss/DeepEpisodicMemory | models/model_zoo/model_conv5_fc_lstm_128.py | Python | mit | 9,768 | [
"Gaussian"
] | d0554cf4b1a847dfa621da8d6263bf99dd5a7420047e1dc17735be9494d5eca8 |
"""Dynamical matrix classes."""
# Copyright (C) 2011 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must ret... | atztogo/phonopy | phonopy/harmonic/dynamical_matrix.py | Python | bsd-3-clause | 35,625 | [
"phonopy"
] | 51cc9a20e2281de17b055c8d21155a50957b0c77a3798ce56c145d076fa98f11 |
import numpy as np
from itertools import count
from ase import Atom, Atoms
from ase.data import atomic_numbers
from ase.calculators.calculator import Calculator
from ase import units
COUL_COEF = 14.399651725922272
def _tup2str(tup):
""" Convert tuple of atomic symbols to string
i.e. ('Ce','O') ->... | lavakyan/ase-bimetall | calculators/buck.py | Python | gpl-2.0 | 3,849 | [
"ASE"
] | 505e08f858c04dd8ec69928d29dd6752ac4a8fc3d47b7d640ec7c2316b08d75d |
# tests 10341 weighted paths of TNFalpha pathway
plRead = open("TNFalpha-weighted-paths-pathlinker.txt", "r")
csRead = open("TNFalpha-weighted-paths-cytoscape.txt", "r")
# dict that stores path: weight
pl = {}
epsilon = 0.0001
def sameFloat(a, b):
return abs(a - b) <= epsilon
for line in plRead:
words = line.spl... | tmmurali/PathLinker | data/TNFalpha/test-files/TNFalpha-NLT-weighted-paths-comparison.py | Python | gpl-3.0 | 673 | [
"Cytoscape"
] | 581afd6ee7e1bad7575320d4c77b5cf3b4a21411ac36e80dc9df27b28d954f96 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/core/files/storage.py | Python | gpl-2.0 | 10,189 | [
"VisIt"
] | 93977b246d1447430ff08bc08231f093106ed89fd60f1de59be1f5930bd0987f |
"""
=================================
Gaussian Mixture Model Ellipsoids
=================================
Plot the confidence ellipsoids of a mixture of two Gaussians with EM
and variational Dirichlet process.
Both models have access to five components with which to fit the
data. Note that the EM model will necessari... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/mixture/plot_gmm.py | Python | bsd-3-clause | 2,817 | [
"Gaussian"
] | dce93cc6481c7fb2c742c65a0128b2c0cb14aa9a0ba81974ff87be9e73fef75f |
import pysam
import sys
import re
import subprocess
import os
from collections import defaultdict
from Bio import AlignIO
# reverse complement a sequence
complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
def revcomp(seq):
reverse_complement = "".join(complement.get(base, base) for base in reversed(seq))
re... | jts/nanocorrect | nanocorrect.py | Python | mit | 6,748 | [
"pysam"
] | 871120fd1c6a1ea1c50d4e837c203b7bcb11b82334c4b5c4d63338b9592dd66f |
"""Unrolls neighbor loops and InputElementZeroOffset nodes in a StencilModel.
The second stage in stencil kernel processing, after
stencil_python_front_end and before stencil_convert. This stage is
done once per call because the dimensions of the input are needed.
"""
from stencil_model import *
from stencil_grid imp... | pbirsinger/aspNew | tools/debugger/stencil/stencil_unroll_neighbor_iter.py | Python | bsd-3-clause | 3,792 | [
"VisIt"
] | 1919c0f576916a6111684344935a064e93cceb2b9c2dcf78c3e1f0eecc793644 |
# -*- coding: utf-8 -*-
"""
Created on Tue May 17 13:17:30 2016
@author: nn31
"""
import pandas as pd
import pickle
#read in cmmi data
#import our data based on the file 'DataDictionary for QDACT on V
cmmi = pd.read_csv("/Volumes/DCCRP_projects/CMMI-Pro62342/data/QDACT 05-03-2016.csv",
parse_date... | benneely/qdact-basic-analysis | notebooks/python_scripts/03_follow-up_viz.py | Python | gpl-3.0 | 3,939 | [
"VisIt"
] | 257e4c4ff5cde7280b9e10b038a031b9dec3c093489d397e48a8597c0c2024e4 |
import random
import hashlib
from django.conf import settings
NAMES = [u'3_d_man',
u'alars',
u'aardwolf',
u'abdul_alhazred',
u'abe_brown',
u'abigail_brand',
u'abner_jenkins',
u'abner_little',
u'abominable_snowman',
u'abomination',
u'abominatrix',
u'abraham_cornelius',
u'abraxas',
u'absalom',
u'absorbing_man',
u'abyss... | LilithWittmann/froide | froide/helper/name_generator.py | Python | mit | 41,989 | [
"CRYSTAL",
"Jaguar"
] | 9c40aa93d2bcc9923fc9f48e459c246ba6fad1bbc46163ab6ffc9f381e9b2f81 |
#
# 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... | chgm1006/spark-app | src/main/python/ml/gaussian_mixture_example.py | Python | apache-2.0 | 1,570 | [
"Gaussian"
] | e2fc6cf695a2ddd723196a65213cdb651337112a6d8df8c729a4318b26945189 |
# -*- coding: utf-8 -*-
import os
import random
import pygame.display
import core
import engine
import platformsbuilder
class Level0(core.BaseLevel):
BACKGROUND_PATH = engine.background_path("wall.png")
def create_ennemies(self):
self.create_slow_fantom(250, 150)
def create_platforms(self):
... | sblondon/jumpjump | src/levels/progress.py | Python | gpl-3.0 | 3,624 | [
"Octopus"
] | 1efb721b2bdcba2de27102edbad472598224117585d22b132972cd6a1de9cb02 |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
import torch.autograd as autograd
import torch.optim as optim
from torch.distributions import transform_to
import pyro.contrib.gp as gp
import pyro.optim
from pyro.infer import TraceEnum_ELBO
class GPBayesOptimizer(... | uber/pyro | examples/contrib/oed/gp_bayes_opt.py | Python | apache-2.0 | 5,456 | [
"Gaussian"
] | 75c2d6eb5c224b219bb67a5ef25d8eb6c084232d66968541b841a9c36f75056b |
import os, sys
import numpy as np
from ase.units import Hartree, Bohr
import inspect
class ORCA:
"""class for performing ORCA calculations, without inclusion of the
ORCA python wrapper"""
def __init__(self,label='orca',**kwargs):
"""input file hack will be put in here right now"""
self.la... | PHOTOX/fuase | ase/ase/calculators/old-orca.py | Python | gpl-2.0 | 8,101 | [
"ASE",
"NWChem",
"ORCA"
] | 9792412fc7d6c2a64f1695553e97254e8c7110a10976511b6cffcf4cb3d3e17d |
from math import exp
import torch
import torch.nn.functional as F
from torch.autograd import Variable
def gaussian(window_size, sigma):
gauss = torch.Tensor([exp(-(x - window_size // 2) ** 2 / float(2 * sigma ** 2)) for x in range(window_size)])
return gauss / gauss.sum()
def create_window(window_size, sig... | ECP-CANDLE/Benchmarks | examples/image-vae/utils.py | Python | mit | 3,249 | [
"Gaussian"
] | 9698c3426e2db69570903752b22415194c598992b3aa547fe1f087411672c2e4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2010 Prof. William H. Green (whgreen@mit.edu) and the
# RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of c... | nyee/RMG-Py | rmgpy/data/base.py | Python | mit | 56,343 | [
"RDKit"
] | e241019addd624a3d69ddbe1ff1fb2e318017a41aba3732fcdb3ce10bb88c42c |
#
# Generates random data for SYNTH dataset in paper
# N dimensions, 1 group-by dim (5 outlier, 5 normal groups), 1 value attr
# Normal points draw value from N(u_h, s_h) -- gaussian, u_h mean, s_h std
# Outlier points draw value from N(u_o, s_o)
# Outlier points fall in a 10% (variable) volume box in k<=N dimensions
#... | sirrice/scorpion | scorpion/misc/gensinglecluster.py | Python | mit | 4,523 | [
"Gaussian"
] | fcfd132e145c35c487bec64de5ec340f98e8a947b576b26cec3d9242f53035c4 |
"""
Script to plot the autocorrelation and fit for previously found optimal parameters
"""
from mjhmc.search.objective import obj_func_helper
from mjhmc.figures.ac_fig import load_params
from mjhmc.samplers.markov_jump_hmc import ControlHMC, MarkovJumpHMC
from mjhmc.misc.distributions import RoughWell, Gaussian, Multi... | rueberger/MJHMC | mjhmc/search/validation.py | Python | gpl-2.0 | 2,780 | [
"Gaussian"
] | b61b2b2373b181bbf351dfb14309725cdef6694a1b027464d97a06281817e9fa |
"""Main entry point for dvc CLI."""
import logging
from dvc._debug import debugtools
from dvc.cli import parse_args
from dvc.config import ConfigError
from dvc.exceptions import DvcException, DvcParserError, NotDvcRepoError
from dvc.logger import FOOTER, disable_other_loggers
# Workaround for CPython bug. See [1] and... | efiop/dvc | dvc/main.py | Python | apache-2.0 | 3,133 | [
"VisIt"
] | baee61d0767b4050893d75fe59128cfb9cabd714ab41bb3c0f541bf4cbf6cda7 |
# coarse graining in MDAnalysis
# Copyright (c) 2015, 2019 Richard J Gowers
# Released under the GNU Lesser General Public License, version 2 or later.
from numpy.testing import assert_allclose
import MDAnalysis as mda
from cguniverse import CGUniverse
import pytest
@pytest.fixture
def water_at_universe():
ret... | richardjgowers/MDAnalysis-coarsegraining | test_cguniverse.py | Python | gpl-2.0 | 1,314 | [
"MDAnalysis"
] | 3a54c06b45119fc84f3233e8a6d16c5aa9ea5abd4437db346a41eed725d1c7d3 |
# -*- coding: utf-8 -*-
#
# helpers.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (... | sdiazpier/nest-simulator | pynest/examples/Potjans_2014/helpers.py | Python | gpl-2.0 | 13,631 | [
"NEURON"
] | abef0bb526fbf651ccaa7a99cd9b52f783aabd8d599a83b626a532344ea0a152 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree.py
lttree.py is an extension of the generic ttree.py pr... | ganzenmg/lammps_current | tools/moltemplate/src/lttree.py | Python | gpl-2.0 | 35,180 | [
"LAMMPS"
] | c870f6feeef543b7d5e893a9f46674176bd0800aaccdee1ac6e81f077f691fe1 |
# $Id$
##
## This file is part of pyFormex 0.8.9 (Fri Nov 9 10:49:51 CET 2012)
## pyFormex is a tool for generating, manipulating and transforming 3D
## geometrical models by sequences of mathematical operations.
## Home page: http://pyformex.org
## Project page: http://savannah.nongnu.org/projects/pyformex/
##... | dladd/pyFormex | pyformex/utils.py | Python | gpl-3.0 | 47,793 | [
"VTK"
] | 64405fa32360722dacde0a7c807f20909307a0bf17369c30cc412d551b33362f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Define miscellaneous utilities.
"""
from __future__ import absolute_import
from debtcollector import removals
from collections import Iterable, OrderedDict
from itertools import tee
import os
import sys
import subprocess
import six
from six.moves import range, ... | Autoplectic/dit | dit/utils/misc.py | Python | bsd-3-clause | 16,425 | [
"VisIt"
] | c2009d045db21f80a4b664d3bf4615d71ffcabe2629fd6d5fd11f1106af8ebc9 |
# This module implements trajetories and trajectory generators.
#
# Written by Konrad Hinsen
# last revision: 2002-5-10
#
import Collection, Units, Universe, Utility, ParticleProperties, Visualization
from Scientific.Geometry import Vector
import Numeric, copy, os, string, sys, types
# Report error if the netCDF modu... | fxia22/ASM_xf | PythonD/site_python/MMTK/Trajectory.py | Python | gpl-2.0 | 49,365 | [
"NetCDF"
] | ff075317aeb1e0d7fd940fabed3a109b60ef95fcc01ba23e8129737e8d3c8211 |
# Copyright 2018 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Recipe which runs the SKQP apk using docker and an Android Emulator
DEPS = [
'checkout',
'infra',
'recipe_engine/file',
'recipe_engine/path',
'r... | endlessm/chromium-browser | third_party/skia/infra/bots/recipes/test_skqp_emulator.py | Python | bsd-3-clause | 3,021 | [
"Galaxy"
] | e87c3f031a3cf7aade28e069c239eadb6d19865116d278fe323d756f4abb54d7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import numpy as np
from pymatgen.core import PeriodicSite
from pymatgen.io.vasp import Vasprun, Poscar, Outcar
from pymatgen.analysis.defects.core import Vacancy, Interstitial, Defe... | gVallverdu/pymatgen | pymatgen/analysis/defects/tests/test_defect_compatibility.py | Python | mit | 19,040 | [
"VASP",
"pymatgen"
] | 8854055dbcde70da112e088665244ddac7674a752a53b8a66a6320d66b8190bc |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | kkreis/espressopp | src/tools/io_extended.py | Python | gpl-3.0 | 8,986 | [
"ESPResSo",
"LAMMPS"
] | cff8c25b9118886bd9dbb0928182d424005bed843bdbfba3ae2425d230477e30 |
#!/usr/bin/env python
description = ">> New automated psf version"
usage = "%prog image [options] "
# ###############################################################
# EC 2012 Feb 20
# modified by SV for lsc
################################################################
import os, sys, shutil, subprocess
import t... | svalenti/agnkey | trunk/bin/agnpsf2.py | Python | mit | 17,133 | [
"Gaussian"
] | ed1c1bf7bf7a3b4fa903aa7149487f70158d1ca98783b082c89c78e3679fcf7e |
"""
Regression test for refinement of beam, detector and crystal orientation
parameters using generated reflection positions from ideal geometry.
"""
from __future__ import annotations
def test():
# Python and cctbx imports
from math import pi
from cctbx.sgtbx import space_group, space_group_symbols
... | dials/dials | tests/algorithms/refinement/test_refinement_regression.py | Python | bsd-3-clause | 10,585 | [
"CRYSTAL"
] | fb784ad678f6066b5f22ac54ed4cc474fdb25299d73937ce4ab188275090cfd4 |
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Kenneth Hoste
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Geor... | hajgato/easybuild-easyblocks | easybuild/easyblocks/b/bwa.py | Python | gpl-2.0 | 2,458 | [
"BWA"
] | af5dd994f65024f2716643070af5686743dc4790e7449de2000716ae24cb71da |
from prisoner.gateway.ServiceGateway import ServiceGateway, WrappedResponse
import prisoner.SocialObjects as SocialObjects
import datetime # Used for creating standardised date / time objects from Facebook's attribute values.
import json # Used for parsing responses from Facebook.
import md5 # Used for generating uni... | uoscompsci/PRISONER | prisoner/gateway/FacebookGateway.py | Python | bsd-3-clause | 65,871 | [
"VisIt"
] | 59fd35e2483a18433f7243b02872eeb855653a0fe0d352f0bd74bc650b1a5746 |
import re
import collections
from enum import Enum
from ydk._core._dm_meta_info import _MetaInfoClassMember, _MetaInfoClass, _MetaInfoEnum
from ydk.types import Empty, YList, YLeafList, DELETE, Decimal64, FixedBitsDict
from ydk._core._dm_meta_info import ATTRIBUTE, REFERENCE_CLASS, REFERENCE_LIST, REFERENCE_LEAFLI... | 111pontes/ydk-py | cisco-ios-xe/ydk/models/cisco_ios_xe/_meta/_CISCO_FLASH_MIB.py | Python | apache-2.0 | 120,346 | [
"VisIt"
] | 1476d424703121827cee9b48a92c97f719fd462b18ecfbb0d1b26079391b03cf |
"""ovf2vtk -- data conversion from OOMMF's ovf/ovf file format to VTK.
This module contains submodules
omfread -- reading of ovf files
analysis -- some post processing.
There is an executable (usually of name ovf2vtk) which imports these modules
and can be used to convert ovf files to vtk from the command promp... | fangohr/ovf2vtk | ovf2vtk/Lib/__init__.py | Python | bsd-2-clause | 413 | [
"VTK"
] | 6bb9b711fa1cf55294eb5c192cf2d0b602a02ebe05d6efe4a04416f5816e215d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from phoenix.dashboard.views import DashboardView
from django.views.generic import RedirectView
from pho... | savioabuga/phoenix | config/urls.py | Python | bsd-3-clause | 1,821 | [
"VisIt"
] | 328e09aa6132204bcd0589809a544609df6c3b7af6ac7023cb9ec9de770dbf65 |
# -*- coding: utf-8 -*-
import numpy as np
from dipy.reconst.cache import Cache
from dipy.core.geometry import cart2sphere
from dipy.reconst.multi_voxel import multi_voxel_fit
from scipy.special import genlaguerre, gamma
from dipy.core.gradients import gradient_table_from_gradient_strength_bvecs
from scipy import speci... | FrancoisRheaultUS/dipy | dipy/reconst/qtdmri.py | Python | bsd-3-clause | 84,043 | [
"Gaussian"
] | 56078a25f3145bef060ab0a24c7784832b2d346fdbb0f736d5ca67aba94ae216 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
## GNU GENERAL PUBLIC LICENSE
## Version 2, June 1991
## Copyright (C) 1989, 1991 Free Software Foundation, Inc.
## 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
## Everyone is permitted to copy and distribute verbatim copies
... | CuonDeveloper/cuon | cuon_client/cuon_newclient/bin/Cuon.py | Python | gpl-3.0 | 37,879 | [
"VTK"
] | af475cc88cd3499403aaa4b704d6be3d17a730e5a93a9ea2eef165890a796401 |
'''
Compiler classes for Cheetah:
ModuleCompiler aka 'Compiler'
ClassCompiler
MethodCompiler
If you are trying to grok this code start with ModuleCompiler.__init__,
ModuleCompiler.compile, and ModuleCompiler.__getattr__.
'''
import sys
import os
import os.path
from os.path import getmtime, exi... | binhex/moviegrabber | lib/site-packages/Cheetah/Compiler.py | Python | gpl-3.0 | 80,397 | [
"VisIt"
] | fd3bf440ae43ce0e13ead4fab3fc194144ad657dbf54270c2055ccf9d933c92c |
# 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 u... | apache/climate | examples/podaac_integration_example.py | Python | apache-2.0 | 4,033 | [
"NetCDF"
] | f4d3887e409a5d7ce687924e9ce3c74d6070611c074022b6279846607f213b88 |
# Dual Annealing implementation.
# Copyright (c) 2018 Sylvain Gubian <sylvain.gubian@pmi.com>,
# Yang Xiang <yang.xiang@pmi.com>
# Author: Sylvain Gubian, Yang Xiang, PMP S.A.
"""
A Dual Annealing global optimization algorithm
"""
from __future__ import division, print_function, absolute_import
import numpy as np
fr... | arokem/scipy | scipy/optimize/_dual_annealing.py | Python | bsd-3-clause | 29,770 | [
"VisIt"
] | 7a3590a1cefe9c726e400667846c302935c540ec9ab9f12ca9c237344e6c2cee |
# creates: a1.png a2.png a3.png cnt1.png cnt2.png gnr1.png gnr2.png
from ase.io import write
from ase.structure import bulk, nanotube, graphene_nanoribbon
import numpy as np
for i, a in enumerate([
bulk('Cu', 'fcc', a=3.6),
bulk('Cu', 'fcc', a=3.6, orthorhombic=True),
bulk('Cu', 'fcc', a=3.6, cubic=True)])... | slabanja/ase | doc/ase/structure.py | Python | gpl-2.0 | 1,259 | [
"ASE"
] | 3cc511ecc82db12af7fbfecc61051ac4e11423aa9938ec4e27e190b9853c638c |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
from copy import copy
import re
from unittest import skipUnless
from urllib import urlencode
import mock
import ddt
from django.conf import settings
from django.core import mail
from django.core.files.uploadedfile import SimpleUploadedFile
from django.c... | JioEducation/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 27,185 | [
"VisIt"
] | 54426bdb47ffb72122cda4a810c7535f7410d0da90718f98908154048f585e03 |
import numpy as np
import time
import logging
import math
# Dimensions of the playing field
WORLD_X = 3000
WORLD_Y = 2000
BEAC_R = 40
BORDER = 15
BEACONS = np.array([[WORLD_X+BEAC_R+BORDER, WORLD_Y / 2.],
[-BEAC_R-BORDER, WORLD_Y + BEAC_R+BORDER],
[- BEAC_R-BORDER, - BEAC_R - BORDER... | SkRobo/Eurobot-2017 | NewCommunication/npParticle.py | Python | mit | 12,287 | [
"Gaussian"
] | 5aa6de848f3aaae4856b137ea8533478a8374d8eea7213f31163688b1cc19081 |
import pytest # noqa
import os
import utilities
from ..automation import CommandSequence
from ..automation import TaskManager
expected_lso_content_a = [
1, # visit id
u'localtest.me',
u'FlashCookie.sol',
u'localtest.me/FlashCookie.sol',
u'test_... | tommybananas/OpenWPM | test/test_storage_vectors.py | Python | gpl-3.0 | 5,581 | [
"VisIt"
] | 95fa96cece78a84b1c6e0a17e295e85a7bcdc6e20e39872398a7bf0a8708a279 |
import numpy as np
import scipy.special as sps
from numpy.testing import (run_module_suite,
assert_,
assert_equal,
assert_raises,
assert_array_almost_equal)
from dipy.denoise.localpca import (localpca, mppca, gen... | FrancoisRheaultUS/dipy | dipy/denoise/tests/test_lpca.py | Python | bsd-3-clause | 12,484 | [
"Gaussian"
] | b104383447ca689cf376a4cf184d6e89a5734f6ba2c30544378f1ae103e7db9d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <briancoca+ansible@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = r'''
---
module... | nitzmahone/ansible | lib/ansible/modules/debconf.py | Python | gpl-3.0 | 6,261 | [
"Brian"
] | 45a85af6c869cd06de2701a4e11233f35a88912bd7cb3b3dc638d039ed936779 |
import os
import sys
import subprocess
import threading
import errno
import unittest
from pysam import AlignmentFile
from TestUtils import BAM_DATADIR
IS_PYTHON2 = sys.version_info[0] == 2
def alignmentfile_writer_thread(infile, outfile):
def _writer_thread(infile, outfile):
"""read from infile and write... | kyleabeauchamp/pysam | tests/StreamFiledescriptors_test.py | Python | mit | 3,024 | [
"pysam"
] | 916a4300fb52f9d51d1b63c36c9b290b880f6bf90909b724cbf9cf70ccc9efa5 |
#!/usr/bin/env python
# Copyright 2014-2020 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/scf/test/test_dhf.py | Python | apache-2.0 | 11,076 | [
"PySCF"
] | f35f52617ab9ea6f53ce532d7b752f36d4ae3f7ea65b6cf7e24dfacc67dc7417 |
import logging, re, json, commands, os, copy
from datetime import datetime, timedelta
import time
import json
import copy
import itertools, random
import string as strm
import math
from urllib import urlencode
from urlparse import urlparse, urlunparse, parse_qs
from django.http import HttpResponse
from django.http im... | tkorchug/panda-bigmon-core | core/views.py | Python | apache-2.0 | 340,870 | [
"VisIt"
] | df51f7258c046fa48374ecc2faf90461f15d8ce88ba773ee5323d5a9765b7dd3 |
import numpy
import mlpy
import time
import scipy
import os
import audioFeatureExtraction as aF
import audioTrainTest as aT
import audioBasicIO
import matplotlib.pyplot as plt
from scipy.spatial import distance
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from sklearn.lda import LDA
import csv
import os.p... | DynaLite/DynaLite_1.0 | Sources/SpeechProcessing/pyAudioAnalysis/myAudioSegmentation.py | Python | mit | 43,897 | [
"Gaussian"
] | 9c8e03246ab6c71dcffc416732cd3750180981afa6d3fa0f2c27a85e2db2e01c |
# Copyright 2008-2015 by Peter Cock. 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.
"""Bio.SeqIO support for the "tab" (simple tab separated) file format.
You are expected to ... | zjuchenyuan/BioWeb | Lib/Bio/SeqIO/TabIO.py | Python | mit | 4,174 | [
"Biopython"
] | 3b39bba564e80ca76d6e62a33dc57d255c946059bbd4a5ce74d3405546532ac5 |
"""Makes figure with saliency maps."""
import os
import argparse
import numpy
import matplotlib
matplotlib.use('agg')
from matplotlib import pyplot
from PIL import Image
from gewittergefahr.gg_utils import general_utils
from gewittergefahr.gg_utils import radar_utils
from gewittergefahr.gg_utils import file_system_uti... | thunderhoser/GewitterGefahr | gewittergefahr/interpretation_paper_2019/make_saliency_figure.py | Python | mit | 18,459 | [
"Gaussian"
] | bb2d09edaa4c80eb0d1c412a7a62e4ade3920c7eba65daffa82584f9bedaffdf |
# Author: Robin Betz
#
# Copyright (C) 2015 Robin Betz
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option) any
# later version.
#
# This... | Eigenstate/dabble | dabble/molutils.py | Python | gpl-2.0 | 19,999 | [
"VMD"
] | 3de72483eabfe483680d068c096b430cab012b5b683b4053f0be79abba9aaf76 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | scripts/Muon/GUI/FrequencyDomainAnalysis/FFT/fft_view.py | Python | gpl-3.0 | 11,098 | [
"Gaussian"
] | 3ef9f0f85365a014d71c122f7bc7e1d96f2483610152e17483f3fb19827f1227 |
# 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... | pkreissl/espresso | samples/chamber_game.py | Python | gpl-3.0 | 17,459 | [
"ESPResSo"
] | 2a6aeb20260af818843157dd4de7c9046b113815127eea9384504bc066c5cb67 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function
import sys, os
import hashlib
import base64
from datetime import datetime, timedelta
import requests
from requests.exceptions import ConnectionError
from github import Github, UnknownObjectException, GithubException
import click
from jinja2... | jayfk/statuspage | statuspage/statuspage.py | Python | mit | 14,201 | [
"VisIt"
] | 760a469a6f9155c2548be041b1d83dd751c67b612aec00b9f7a71cd6d138e28c |
from .. import Provider as LoremProvider
class Provider(LoremProvider):
"""en_US word list is drawn from Education First's "1000 Most Common Words in English":
http://www.ef.edu/english-resources/english-vocabulary/top-1000-words/
Some words have been removed to make this list appropriate for public testi... | danhuss/faker | faker/providers/lorem/en_US/__init__.py | Python | mit | 17,382 | [
"VisIt"
] | c60a3247d11bd15a6408fb3287f66fcd029e68c67d9be25cdceafc05a7daab93 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#
# Copyright (C) 2012 Canonical Ltd.
# Copyright © 2013-2018 Antergos
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License... | Antergos/Cnchi | src/misc/i18n.py | Python | gpl-3.0 | 3,222 | [
"FEFF"
] | b138bab13f1d15324bb5d999045eabeb537f633f93ab76df683bdd4d0c522989 |
"""
CAD :cite:`cad-Russo2017_e19428` is a method aimed to capture structures of
higher-order correlation in massively parallel spike trains. In particular, it
is able to extract patterns of spikes with arbitrary configuration of time lags
(time interval between spikes in a pattern), and at multiple time scales,
e.g. fr... | INM-6/elephant | elephant/cell_assembly_detection.py | Python | bsd-3-clause | 48,301 | [
"NEURON"
] | 2d399a0af5d0139edb252b431019fa921ef305bebeac61d71378cb87ea3f0366 |
#Author: Carlos Eduardo Leão Elmadjian
import numpy as np
#Class to model a single neuron
#------------------------------
class Neuron():
def __init__(self, idx, eta, inputs):
self.idx = idx
self.eta = eta
self.weight = [0.0 for i in range(inputs+1)]
self.input = [1.0 for i in r... | elmadjian/pcs5735 | aula2/exercise01.py | Python | mpl-2.0 | 3,304 | [
"NEURON"
] | 64d8aa6f25405ca22d1a924f674ef754016e4927076d76990362ba75965b2b90 |
#
# __COPYRIGHT__
#
# 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, merge, publish,
# distribute, sublicen... | andrewyoung1991/scons | src/engine/SCons/Taskmaster.py | Python | mit | 40,474 | [
"VisIt"
] | 205bcd327588e865fc62046ce8cf8c6dab05f2c5f47438f9803eb2549aaede46 |
#!/usr/bin/env python
# *-* coding: UTF-8 *-*
# Copyright 2012-2020 Ronald Römer
#
# 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 ... | zippy84/vtkbool | testing/test_py_module.py | Python | apache-2.0 | 893 | [
"VTK"
] | 89b22a9e21d8696e731bdbf114e51405d41bc3152a86b81fac77b099dd9a1959 |
"""
The Job Path executor determines the chain of Optimizing Agents that must
work on the job prior to the scheduling decision.
Initially this takes jobs in the received state and starts the jobs on the
optimizer chain.
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import List
from DIRAC.Worklo... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Executor/JobPath.py | Python | gpl-3.0 | 4,662 | [
"DIRAC"
] | 44f17cab34f8436bda86d434eff37364a58a1c394d82bd4d55be9850da722024 |
"""
Determine which packages need updates after pinning change
"""
import enum
from itertools import chain
import logging
import re
import string
from .utils import RepoData
# FIXME: trim_build_only_deps is not exported via conda_build.api!
# Re-implement it here or ask upstream to export that functionality.
f... | bioconda/bioconda-utils | bioconda_utils/update_pinnings.py | Python | mit | 13,007 | [
"BLAST",
"Bioconda"
] | 385038da29598c62c18cb92f8fa4f5418157ed504b48fa4125ed1fd4911f92f3 |
################################################################################
# The Neural Network (NN) based Speech Synthesis System
# https://svn.ecdf.ed.ac.uk/repo/inf/dnn_tts/
#
# Centre for Speech Technology Research
# University of Edinburgh, UK
# ... | bajibabu/merlin | src/layers/mdn_layers.py | Python | apache-2.0 | 15,599 | [
"Gaussian"
] | fdeaa08f14ac4ff99a9ebae7ba9f89297fc982e60b4fd364791d525f34b05aab |
# 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 ... | Hybrid-Cloud/badam | patches_tool/aws_patch/aws_deps/libcloud/compute/providers.py | Python | apache-2.0 | 8,232 | [
"VisIt"
] | efe1764a556b904ad5fdb1abaee3576828973092f838b918b6ef0cc92a491e84 |
"""
Elastic basis pursuit
"""
import numpy as np
import numpy.linalg as nla
import leastsqbound as lsq
import sklearn.linear_model as lm
import scipy.optimize as opt
def err_func(params, x, y, func):
"""
Error function for fitting a function
Parameters
----------
para... | vistalab/elastic_basis_pursuit | ebp/elastic_basis_pursuit.py | Python | mit | 8,059 | [
"Gaussian"
] | b2718bd1c43d5f77ab46391b38f36cca5874a96aef4512b0e36f7d5ae8942182 |
# Test
import bvp
dbi = bvp.DBInterface()
db_update_script = """
import bvp
import bpy
import numpy as np
# Parameters
n_samples = 5
# Set scene to particular action
scn = bpy.data.scenes["{act_name}"]
bvp.utils.blender.set_scene(scn.name)
# Make sure armature object for action is selected
grp = bpy.data.groups["{... | marklescroart/bvp | Scripts/update_val_script.py | Python | bsd-2-clause | 2,207 | [
"VisIt"
] | 7b44519ff67cdb320e53037a503e309a8447a8f534f7b47d086716c3b2c5cc9f |
"""
objectstore package, abstraction for storing blobs of data for use in Galaxy,
all providers ensure that data can be accessed on the filesystem for running
tools
"""
import os
import random
import shutil
import logging
import threading
from xml.etree import ElementTree
from galaxy.util import umask_fix_perms, forc... | jmchilton/pulsar | galaxy/objectstore/__init__.py | Python | apache-2.0 | 29,544 | [
"Galaxy"
] | f3b95dd654d87aa1d9838c867f06727c716978634e8ac159bb038ac5bffc5916 |
from django.urls import reverse
from django.test import TestCase
from .views import error
class SimpleTest(TestCase):
def test_home(self):
response = self.client.get('/')
self.assertEqual(response.status_code, 200)
def test_error_route(self):
visit = lambda: self.client.get(reverse('... | gregazevedo/gregazevedo | gregazevedo/home/tests.py | Python | mit | 417 | [
"VisIt"
] | 451b4df3f876a2e83cc6b227b722c68f6a71b4ae3717635d6debfb74977cf855 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/py-ase/package.py | Python | lgpl-2.1 | 1,729 | [
"ASE"
] | 49936d7e320c265799dfd8be13519451463c94e7915a3a0da439b63b8d68c598 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from brew.grains import Grain
from brew.grains import GrainAddition
from brew.hops import Hop
from brew.hops import HopAddition
from brew.recipes import Recipe
from brew.yeasts import Yeast
"""
Build a recipe from known ingredients.
"""
def main():
# Define Grains
... | chrisgilmerproj/brewday | examples/pale_ale_recipe.py | Python | mit | 1,317 | [
"CRYSTAL"
] | 5ffc2f2aa22b63457fcf6bf4a353c529108b7fddf884d95f77077a48f2a38e4f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from lib.meos import MEoS
from lib import unidades
class N2(MEoS):
"""Multiparamente equation of state for nitrogen"""
name = "nitrogen"
CASNumber = "7727-37-9"
formula = "N2"
synonym = "R-728"
rhoc = unidades.Density(313.3)
Tc = unidades.Temperat... | edusegzy/pychemqt | lib/mEoS/N2.py | Python | gpl-3.0 | 39,327 | [
"Jmol"
] | 33ffa27ae167d1669d7ff79b932bdafdef70f344e813ebe4f8a82ecf384659d7 |
# Copyright 2009 by Osvaldo Zagordi. All rights reserved.
# Revisions copyright 2010 by Peter Cock.
# 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.
"""Command line wrapper for the short read aligner ... | zjuchenyuan/BioWeb | Lib/Bio/Sequencing/Applications/_Novoalign.py | Python | mit | 8,246 | [
"Biopython"
] | a1be22cab51f2419d77abea4f39e55444d54b9a93fa0e7233ad11eb892ead50f |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | catchupMail.py | Python | gpl-3.0 | 5,380 | [
"Galaxy"
] | 64a2ca6a9f6606be227bbb060ee2364869e39ef1ee84c00359bbe5f1e1aa337f |
# Licensed to the StackStorm, Inc ('StackStorm') 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 use th... | Itxaka/st2 | st2common/st2common/hooks.py | Python | apache-2.0 | 11,784 | [
"GULP"
] | 01be3c135be2088b077d877103932cc3fd3973ac07aeacde92de98a08c7c239b |
#! /usr/bin/python
# -*- coding: utf-8 -*-
import logging
logger = logging.getLogger(__name__)
# import funkcí z jiného adresáře
import os
import os.path
import pytest
path_to_script = os.path.dirname(os.path.abspath(__file__))
import unittest
import numpy as np
import sys
try:
import skelet3d
data3d = np... | mjirik/teigen | tests/tube_tree_test.py | Python | apache-2.0 | 9,295 | [
"VTK"
] | 465f62296756b6d822a2cd602e3452a28a84b3a21d0877fbd40f1e8a91e4caf1 |
from rest_framework import serializers
from elixir.models import *
from elixir.validators import *
class LegacyDownloadSerializer(serializers.ModelSerializer):
url = serializers.CharField(allow_blank=False, validators=[IsURLFTPValidator], required=True)
type = serializers.CharField(allow_blank=True, max_length=300, ... | bio-tools/biotoolsregistry | backend/elixir/serialization/resource_serialization/v2/download.py | Python | gpl-3.0 | 1,739 | [
"Galaxy"
] | b7973b0aabadcd1d5387d3df2e8e822b7218ddc10360884a3275cc566806bd87 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module for interfacing with phonopy, see https://atztogo.github.io/phonopy/
"""
from typing import Any, Dict, List
import numpy as np
from monty.dev import requires
from monty.serialization import loadfn
from scipy.interp... | materialsproject/pymatgen | pymatgen/io/phonopy.py | Python | mit | 25,305 | [
"phonopy",
"pymatgen"
] | a8513f349d31cf16c06f4d4c015dc041f0c1f02ef8d2172a433ecf4c8d134b1a |
#
# This file is part of Healpy.
#
# Healpy is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# Healpy is distributed in the hope... | cjcopi/healpy | healpy/sphtfunc.py | Python | gpl-2.0 | 41,728 | [
"Gaussian"
] | 6935eec374ab02d6a6d466128991898f62d3e6ef441581b56adc6587975c9035 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | leeping/mdtraj | tests/test_lh5.py | Python | lgpl-2.1 | 4,054 | [
"MDTraj"
] | acc95c4b6b1a15ae8cf0daa88011720fddb8bedecdd7bb78fc125368668f4a83 |
# -*- coding: utf-8 -*-
# Copyright 2014-2022 Mike Fährmann
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
"""Extractors for https://danbooru.donmai.us/ and other Danbooru instanc... | mikf/gallery-dl | gallery_dl/extractor/danbooru.py | Python | gpl-2.0 | 12,770 | [
"MOE"
] | 7d12f50ed3f45f6d9300eea3ab27ebc60f4491c7a9e409852b9ea3e10994bbb7 |
"""
This file run the pipeline of doing differential expression analysis of
Contaminated CHO samples.
"""
import os
import sys
import subprocess
sys.path.append('/home/shangzhong/Codes/Pipeline')
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer
from Modules.f00_Message import Message
from Modules.... | shl198/Pipeline | DiffExpression/01_DE_pipeline.py | Python | mit | 3,771 | [
"Bowtie",
"HTSeq"
] | 0496ceff5cee7b9646d150ad29aaa64f78448368a5e0eb6412af649e2ceb0494 |
#!/usr/bin/env python3
from future.utils import iteritems
from past.builtins import cmp
from functools import cmp_to_key
import http.server
import base64
import io
import json
import threading
import time
import hashlib
import os
import sys
from future.moves.urllib.parse import parse_qs
from decimal import Decimal
fro... | undeath/joinmarket-clientserver | scripts/obwatch/ob-watcher.py | Python | gpl-3.0 | 35,777 | [
"VisIt"
] | 7b8aedc5ddf0cb12fc936f5ec157537f5b8997395de7a7dfa7b086a339aa6170 |
'''Read and write DNA sequences.'''
import csv
import os
from Bio import SeqIO
from Bio.Alphabet.IUPAC import ambiguous_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, ExactPosition
from Bio.SeqFeature import CompoundLocation
import coral
import co... | klavinslab/coral | coral/seqio/_dna.py | Python | mit | 11,219 | [
"Biopython"
] | 3e23553f84da76aa18783b1540079bed4b5d39c644afe88bf6237d3b8740f50a |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Classes for representing multi-dimensional data with metadata.
"""
from collections import OrderedDict
from collections.... | SciTools/iris | lib/iris/cube.py | Python | lgpl-3.0 | 164,190 | [
"NetCDF"
] | 6004f07f3e2de9d4d2441ed8b117c82ec93f6ae3d2986d31c66cad4a43e54c82 |
"""
Container page in Studio
"""
from bok_choy.page_object import PageObject
from bok_choy.promise import Promise, EmptyPromise
from . import BASE_URL
from utils import click_css, confirm_prompt
class ContainerPage(PageObject):
"""
Container page in Studio
"""
NAME_SELECTOR = '.page-header-title'
... | peterm-itr/edx-platform | common/test/acceptance/pages/studio/container.py | Python | agpl-3.0 | 14,433 | [
"VisIt"
] | 907da3fc9d7429ac7109cc48e9b3f716b81a01e07bb37e5412e1da45ad3a3a19 |
#!/usr/bin/env python
# file test_exclude_seqs_by_blast.py
__author__ = "Jesse Zaneveld"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Zaneveld", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Jesse Zaneveld"
__email__ = "zaneveld@gmail.com"
"""
Test code for... | adamrp/qiime | tests/test_exclude_seqs_by_blast.py | Python | gpl-2.0 | 14,442 | [
"BLAST"
] | 36b380a060704e622961bb25f1e934913432cc867cf07d7a130095e7552ca7bc |
# GoPiGo Connectome
# Written by Timothy Busbice, Gabriel Garrett, Geoffrey Churchill (c) 2014, in Python 2.7
# The GoPiGo Connectome uses a postSynaptic dictionary based on the C Elegans Connectome Model
# This application can be ran on the Raspberry Pi GoPiGo robot with a Sonar that represents Nose Touch when activat... | mattbaker/GoPiGo | disembodiedConnectome.py | Python | gpl-2.0 | 197,938 | [
"NEURON"
] | 184d6fe0cff9f0b8cfa59a63b0a6491f13c3d311eb595789ab5c8329fb0c7b46 |
"""
=============================================
Density Estimation for a mixture of Gaussians
=============================================
Plot the density estimation of a mixture of two Gaussians. Data is
generated from two Gaussians with different centers and covariance
matrices.
"""
import numpy as np
import ma... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/mixture/plot_gmm_pdf.py | Python | bsd-3-clause | 1,528 | [
"Gaussian"
] | dd40ad1dc9ae7ac35da5e9717115ee8e27ef78bd8fabae7237294881d77db295 |
import unittest as ut
from .. import tabular as ta
from ....common import RTOL, ATOL, pandas, requires as _requires
from ....examples import get_path
from ...shapes import Polygon
from ....io import geotable as pdio
from ... import ops as GIS
import numpy as np
PANDAS_EXTINCT = pandas is None
@ut.skipIf(PANDAS_EXTINC... | sjsrey/pysal_core | pysal_core/cg/ops/tests/test_tabular.py | Python | bsd-3-clause | 2,231 | [
"COLUMBUS"
] | f9036421726682ad938f00bde364461a12d61c53eabeae86bae07ec92a0cdfbd |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.