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from PIL import Image,ImageDraw,ImageFont,ImageFilter
from discord.ext import commands
from operator import itemgetter
from unidecode import unidecode
from random import randint
from .utils import utils
import traceback
import datetime
import aiohttp
import logging
import discord
import asyncio
import re
import io
log... | Maverun/Nurevam | Bot/cogs/level.py | Python | mit | 26,750 | [
"VisIt"
] | eb1378146178cc3ae49243266f6e84ef6dfa581dffcd061f5de2d75d38c196b7 |
# Copyright 2018 The Oppia 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 applicable ... | souravbadami/oppia | core/domain/story_domain.py | Python | apache-2.0 | 46,403 | [
"VisIt"
] | 6a5970ece334b5ae931817cdba33036b31d225f35528cf1ee4fd76c00d8badd8 |
"""
Window functions (:mod:`scipy.signal.windows`)
==============================================
The suite of window functions for filtering and spectral estimation.
.. currentmodule:: scipy.signal.windows
.. autosummary::
:toctree: generated/
get_window -- Return a window of a given length and type.
... | nmayorov/scipy | scipy/signal/windows/__init__.py | Python | bsd-3-clause | 1,722 | [
"Gaussian"
] | 3864dee43eb468a50f7a231c4fa4bd22a5f45933ca9c00413c647244dc688721 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | migueldiascosta/pymatgen | pymatgen/io/vaspio/vasp_output.py | Python | mit | 632 | [
"VASP",
"pymatgen"
] | bd562c8b853a64875969936f3ecf375282068d784d554a4e95967dc2f59c2d47 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a MolecularOrbital class to represent band character in
solids. Usefull for predicting PDOS character from structural information.
"""
from itertools import chain, combinations
from... | davidwaroquiers/pymatgen | pymatgen/core/molecular_orbitals.py | Python | mit | 4,608 | [
"CRYSTAL",
"pymatgen"
] | 82e959c616040a69ba5bf87b031399787dceb7a0dda91eb3edf40f973668840f |
""" :mod: DErrno
==========================
.. module: DErrno
:synopsis: Error list and utilities for handling errors in DIRAC
This module contains list of errors that can be encountered in DIRAC.
It complements the errno module of python.
It also contains utilities to manipulate these error... | vmendez/DIRAC | Core/Utilities/DErrno.py | Python | gpl-3.0 | 10,189 | [
"DIRAC"
] | 55a2acfa8e8c263693585275cb114bb1b87a0d185f315a482df7856f609c9e80 |
from periodic.crystal import Crystal
latticevecs = ((4.59373000, 0.00000000, 0.00000000),
(0.00000000, 4.59373000, 0.00000000),
(0.00000000, 0.00000000, 2.95812000))
basis = (('Ti', (0.00000000, 0.00000000, 0.00000000)),
('Ti', (2.29686500, 2.29686500, 1.47906000)),
... | danielsjensen1/crystalpy | tests/TiO2.py | Python | bsd-3-clause | 969 | [
"CRYSTAL"
] | e6b1efa21d22a620a55786d63b21fceaa98b6eafe9e9f78bda5832612ffeef5f |
instruments = {
"Acoustic Grand Piano": 0,
"Bright Acoustic Piano": 1,
"Electric Grand Piano": 2,
"Honky-tonk Piano": 3,
"Electric Piano 1": 4,
"Electric Piano 2": 5,
"Harpsichord": 6,
"Clavinet": 7,
"Celesta": 8,
"Glockenspiel": 9,
"Music Box": 10,
"Vibraphone": 11,
"Marimba": 12,
"Xylophone": 13,
"Tubu... | anshulgupta0803/txt2midi | txt2midi/instruments.py | Python | gpl-3.0 | 2,739 | [
"CRYSTAL"
] | e2d110de03fde525c146c52a0560ece0574349cf6c26fcb3718901c716809c87 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 ap... | google/uncertainty-baselines | baselines/jft/experiments/vit_l32_sngp_finetune.py | Python | apache-2.0 | 6,367 | [
"Gaussian"
] | 5de5a53ae4eb4b1ba5525ee181e7bfb0a6e49a5a73e250c81a552cd0debc52ce |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is used for analysis of materials with potential application as
intercalation batteries.
"""
__author__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"... | fraricci/pymatgen | pymatgen/apps/battery/insertion_battery.py | Python | mit | 21,772 | [
"pymatgen"
] | e18f04251b007369232b79831b4d4f11defe7b14078b32838cda91ab2f52b2ae |
"""
Notifications for Android TV notification service.
For more details about this platform, please refer to the documentation at
https://home-assistant.io/components/notify.nfandroidtv/
"""
import logging
import io
import base64
import requests
from requests.auth import HTTPBasicAuth
from requests.auth import HTTPDi... | nugget/home-assistant | homeassistant/components/notify/nfandroidtv.py | Python | apache-2.0 | 10,033 | [
"Amber"
] | 3e4511afb6460362b48feb3a508ba6f7b8ec143cc60e20af994fcd78a19b616e |
# -*- coding: utf-8 -*-
import os
import sys
import contextlib
import logging
from os.path import join as pjoin
from hashlib import md5
from shutil import copyfileobj
import numpy as np
import nibabel as nib
import tarfile
import zipfile
from dipy.core.gradients import (gradient_table,
... | FrancoisRheaultUS/dipy | dipy/data/fetcher.py | Python | bsd-3-clause | 47,733 | [
"Brian",
"VTK",
"VisIt"
] | 0fc04600d5058eff023a1ef3d7a489d4318a75e2ff27ffe730db467d680ecb89 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
(c) 2014 - Copyright Red Hat Inc
Authors:
Pierre-Yves Chibon <pingou@pingoured.fr>
License: GPLv3 or any later version.
"""
import argparse
import ConfigParser
import datetime
import glob
import json
import logging
import os
import rpm
import subprocess
import ... | pypingou/dgroc | dgroc.py | Python | gpl-3.0 | 20,755 | [
"ASE"
] | b0132aa6a07ef604bdabf090dab42755eeff5f3124ab9c3f056a7287f4cf3b55 |
import numpy as np
from ase.asec.command import Command
class ReactionCommand(Command):
@classmethod
def add_parser(cls, subparser):
parser = subparser.add_parser('reaction', help='reaction ...')
def __init__(self, logfile, args):
Command.__init__(self, logfile, args)
self.count ... | alexei-matveev/ase-local | ase/asec/reaction.py | Python | gpl-2.0 | 1,068 | [
"ASE"
] | f070dd73d4d98d58849631e13b5028f2860978a39267bae3a976b7e566569d2c |
#!/usr/bin/python
import os, sys
ncs_lib_path = ('../../../')
sys.path.append(ncs_lib_path)
import ncs
def run(argv):
sim = ncs.Simulation()
fast_spiking_parameters = sim.addNeuron("fast_spiking","izhikevich",
{
"a": 0.1,
"b": 0.3,
"c": -55.0,
"d": 2.0,
"u": -12.... | BrainComputationLab/ncs | python/samples/models/izh/fast_spiking_izh.py | Python | bsd-2-clause | 881 | [
"NEURON"
] | 26e6dc5ac3ff0423d933599de54028757492d728a77b19fc5792ae24d6f3bb5a |
#!/usr/bin/env python3
#
# Copyright 2014 Blender Foundation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | pawkoz/dyplom | blender/extern/cuew/auto/cuew_gen.py | Python | gpl-2.0 | 17,548 | [
"VisIt"
] | 7baf4d9672361937d22cc5e7a66d7b755dfbad8049d0db9433eed9a2d47ed548 |
#!/usr/bin/env python
from pyscf import gto
from pyscf import dft
'''
Tune DFT grids
By default, the DFT integration grids use
* Bragg radius for atom
* Treutler-Ahlrichs radial grids
* Becke partition for grid weights
* NWChem pruning scheme
* mesh grids
===================================
Elements radial part... | gkc1000/pyscf | examples/dft/11-grid_scheme.py | Python | apache-2.0 | 2,132 | [
"NWChem",
"PySCF"
] | 145d769f37c95ad04a2d8379f0083ee43100f852f9f650d8c02aefa7e8d79158 |
import random
import math
import string
class AdoptionCenter:
"""
The AdoptionCenter class stores the important information that a
client would need to know about, such as the different numbers of
species stored, the location, and the name. It also has a method to adopt a pet.
"""
def... | NicholasAsimov/courses | 6.00.1x/pset7/ps7.py | Python | mit | 8,760 | [
"VisIt"
] | 4a4f1a375591f897c98d45c6101a6de48af3ac37a061ed4fa87e137f901f7ca7 |
from __future__ import division
import numpy as np
from functools import partial
from pyhsmm.internals.hmm_states import HMMStatesPython, HMMStatesEigen
from pyhsmm.internals.hsmm_states import HSMMStatesPython, HSMMStatesEigen, \
GeoHSMMStates
from pylds.lds_messages_interface import info_E_step, info_sample
fr... | mattjj/pyhsmm-slds | pyslds/states.py | Python | mit | 52,521 | [
"Gaussian"
] | d23e5f683e1519bb1181f0140feead1c3a0aec77093c9ef408602e2a4d352b76 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | hpfem/agros2d | resources/python/pylint/utils.py | Python | gpl-2.0 | 23,927 | [
"VisIt"
] | 03416be1df7fa55814bdbd30734b6cd247bfe895eb9ac7959dba393e17ab2dc9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# PyNNLess -- Yet Another PyNN Abstraction Layer
# Copyright (C) 2015 Andreas Stöckel
#
# 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, e... | hbp-sanncs/pynnless | examples/synfire_chain.py | Python | gpl-3.0 | 1,950 | [
"NEURON"
] | c3a407fadbb060d669967040e2af639efb282d3d792607735e2c45a29b012e14 |
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... | LoadedCoders/iHear | iHear-Py/pyAudioAnalysis/audioSegmentation.py | Python | mit | 43,895 | [
"Gaussian"
] | e18b4c7a0189f0d56a3a38eb9fb0b6a23cb9789d3c775e743563c8c49aa6d9cf |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | mikedanese/kubernetes | hack/verify-flags-underscore.py | Python | apache-2.0 | 4,662 | [
"VisIt"
] | 05ab39a6648bc76f326ef9f9adb49ecb02349589d15dc5789171058b98774432 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/alignment/tests/test_pairwise.py | Python | bsd-3-clause | 34,993 | [
"scikit-bio"
] | a9fb52ef41b40431a58132ea4702f8a6294679e2cdbaca8a9b8882c6c451ea69 |
from numpy import *
from pylab import *
from datetime import datetime, time, timedelta
import numpy as np
import console_colors as ccl
from scipy.io.netcdf import netcdf_file
from ShiftTimes import *
import os
import matplotlib.patches as patches
import matplotlib.transforms as transforms
#from read_NewTable import ts... | jimsrc/seatos | shared_lib/shared_funcs_ii.py | Python | mit | 31,654 | [
"NetCDF"
] | 1615f76fa8cc347ee29c687480a2b435d7ed1d4b40ae17bb5356a748ccc09556 |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particles, Fireworks"
import pyglet
import cocos
from cocos.di... | shadowmint/nwidget | lib/cocos2d-0.5.5/test/test_particle_fireworks.py | Python | apache-2.0 | 956 | [
"Galaxy"
] | a03e973e224d67b26ced6479db18fad90487c0b18812f252c7caadef1cbcba51 |
# stardard library
import os
import json
import cPickle as pck
import itertools as it
# external libraries
import numpy as np
from gala import imio
def add_anything(a, b):
return a + b
def write_synapse_to_vtk(neurons, coords, fn, im=None, margin=None):
"""Output neuron shapes around pre- and post-synapse co... | janelia-flyem/synapse-geometry | syngeo/io.py | Python | bsd-3-clause | 4,730 | [
"NEURON"
] | d4bfc9437c1a897f545670694f7bd7b87b38407d88ac04a978ba78c03bfb963f |
import os
from setuptools import setup, Extension
from Cython.Build import cythonize
import numpy as np
# Utility function to read the README file.
# Used for the long_description. It's nice, because now 1) we have a top level
# README file and 2) it's easier to type in the README file than to put a raw
# string in ... | tkphd/pycalphad | setup.py | Python | mit | 3,682 | [
"pycalphad"
] | a7b30884ee277237e2f590163b67fd42596c1ba4432302caeeb63646d9e91758 |
import os
import sys
msg = "\nThe Agg rendering GTK matplotlib backend is missing or not installed properly.\n"
msg += "See http://matplotlib.org/faq/usage_faq.html#what-is-a-backend.\n"
msg += "Is the PYTHONPATH environment variable set correctly?\n"
msg += "Please verify your installation by running on the command l... | askhl/ase | ase/test/dependency_backend_gtkagg.py | Python | gpl-2.0 | 1,588 | [
"ASE"
] | 8ead343b0c5a58edc0648afa70eae1e284aea02184fa59042da8505c3473dc5d |
from __future__ import print_function
import numpy as np
from ase.io.aff import affopen as open
class A:
def write(self, writer):
writer.write(x=np.ones((2, 3)))
@staticmethod
def read(reader):
a = A()
a.x = reader.x
return a
w = open('a.aff', 'w')
w.write(a=A(), y=9)... | suttond/MODOI | ase/test/aff.py | Python | lgpl-3.0 | 886 | [
"ASE"
] | d6d169d54e9153eef2351e4d84f126ea8bf3c7a6ad4f633f6d193002e428158a |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe import session, _
from frappe.utils import today
from erpnext.utilities.transaction_base import TransactionBase
class ... | indictranstech/focal-erpnext | support/doctype/customer_issue/customer_issue.py | Python | agpl-3.0 | 2,083 | [
"VisIt"
] | a48e6dbd88c9ee77520163cdc988fa65590a7826601e7d8cf8faec6184a6ac38 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Development script of the ChemEnv utility to get the explicit permutations for coordination environments identified
with the separation plane algorithms (t... | matk86/pymatgen | dev_scripts/chemenv/explicit_permutations_plane_algorithm.py | Python | mit | 6,600 | [
"pymatgen"
] | 54dd736e21dee2e377a2d9e98c0e43c29683694d6fc62119fc071e26f76c40bf |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RIlluminaio(RPackage):
"""Parsing Illumina Microarray Output Files.
Tools for pars... | iulian787/spack | var/spack/repos/builtin/packages/r-illuminaio/package.py | Python | lgpl-2.1 | 929 | [
"Bioconductor"
] | f8f7e8157bdd371a0948f32ac1090a659132c1cabf22bdf741865f86729c0b3a |
"""
Write a function that takes an unsigned integer and
returns the number of '1' bits it has
(also known as the Hamming weight).
For example, the 32-bit integer '11' has binary
representation 00000000000000000000000000001011,
so the function should return 3.
T(n)- O(k) : k is the number of 1s present in binary rep... | keon/algorithms | algorithms/bit/count_ones.py | Python | mit | 878 | [
"Brian"
] | ba28e1f7d28752c96eccf0c22ac8a654ffbf6bd1d79cfc801d83ebf6c0ff63e0 |
"""High level summaries of samples and programs with MultiQC.
https://github.com/ewels/MultiQC
"""
import collections
import glob
import json
import mimetypes
import os
import pandas as pd
import shutil
import numpy as np
import pybedtools
import toolz as tz
import yaml
from bcbio import utils
from bcbio.cwl import ... | biocyberman/bcbio-nextgen | bcbio/qc/multiqc.py | Python | mit | 22,238 | [
"HTSeq"
] | 57cccfbc790bc4d05d57cf0b410f4e4d31d01020169ff527d28fe19e4bddb9e6 |
#!/usr/bin/env python
#20-11-2017
#Authors:Sebastian ECHEVERRI RESTREPO,
# sebastian.echeverri.restrepo@skf.com, sebastianecheverrir@gmail.com
# James EWEN
# j.ewen14@imperial.ac.uk, jimmyewen@gmail.com
#################################################################################3
# This file contains a... | JE1314/LAMMPS_builder | root/Rough.py | Python | gpl-3.0 | 20,277 | [
"ASE",
"CRYSTAL"
] | c1a68d4a553b5544b1bb979982672466ba3e4754545c593e45ede833d1f691db |
# Django Imports
from django.db.models import F
from django.shortcuts import redirect, render
from django.core.exceptions import ObjectDoesNotExist
# Python Imports
import random, decimal
import datetime as time
# WaW Imports
from wawmembers.models import *
from wawmembers.forms import *
from wawmembers.loggers impor... | heidi666/WorldsAtWar | wawmembers/interactions.py | Python | mit | 61,805 | [
"Galaxy"
] | ab3882264678b5fa9b4646c870db210343c66d7fe11d6425d2730b1cab1b8b55 |
# TODO: By PySCF-1.5 release
# 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.... | gkc1000/pyscf | pyscf/tools/Molpro2Pyscf/MolproXml.py | Python | apache-2.0 | 23,499 | [
"Molpro",
"PySCF"
] | f9d42d9c8bbcce9c4a1c52dae7e241eaacb3fb6ca3a79a2c6ea638eda7ddcc2a |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list ... | xyuanmu/XX-Net | python3.8.2/Lib/mimetypes.py | Python | bsd-2-clause | 21,604 | [
"NetCDF"
] | 1119a0c02b0dd61b3aa0bcf918af877e7d841b3645dad8bdd8214ffc4e847d03 |
#
# 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... | markflyhigh/incubator-beam | sdks/python/apache_beam/typehints/trivial_inference.py | Python | apache-2.0 | 17,088 | [
"VisIt"
] | 7a35f9adf1f0a555cba001a2b1764811df10967344dd0141fe9101d121f227a8 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/bouqueteditor/web/getprotectionsettings.py | Python | gpl-2.0 | 6,010 | [
"VisIt"
] | 7c259a82d047c4a033dd3128942844368f46df2e5da14cde496c3bcec68b6324 |
# coding: utf-8
# ### Operations on PLANETOPLOT requests: differences, ratios, etc...
#
# *Author: [Aymeric SPIGA](http://www.lmd.jussieu.fr/~aslmd)*
# In[45]:
# This line configures matplotlib to show figures embedded in the notebook.
get_ipython().magic(u'matplotlib inline')
# Operations on PLANETOPLOT objects... | aymeric-spiga/planetoplot | tutorial/operations.py | Python | gpl-2.0 | 2,378 | [
"NetCDF"
] | bc7b90b3127dcded5f7abfbe8a1af5f07d6f15d2da0c4649b5693acb39225f3b |
#!/usr/bin/python
#1/usr/bin/env python
# __*__ coding: utf8 __*__
oneline = "Read different types of models"
import os
#=======================================================================
def dump2crd(file_in,file_out):
f=open(file_in,'r')
while f.readline().count('TIMESTEP')==0:
pass
l... | ansobolev/shs | shs/voronoi/dump.py | Python | mit | 7,357 | [
"LAMMPS"
] | 776aec146f250e53cc74f0883dc376ca247f4bfa1f01bc112aeecb7a6fc77b33 |
# -*- coding: utf-8 -*-
"""
https://confluence.atlassian.com/display/DOC/Confluence+Storage+Format
"""
from distutils.version import LooseVersion
import os
from docutils import nodes
from docutils.parsers.rst import directives, Directive, roles
from docutils.parsers.rst.directives import images
from docutils.parser... | Arello-Mobile/sphinx-confluence | sphinx_confluence/__init__.py | Python | mit | 20,132 | [
"VisIt"
] | 3cd69292de067ecb4f58605b38360c1313cedca376558847edddcfc997732250 |
# Copyright 2015-present Palo Alto Networks, Inc
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law... | PaloAltoNetworks/minemeld-core | minemeld/ft/taxii.py | Python | apache-2.0 | 58,146 | [
"Amber"
] | eb4b89a3e5160816fa7caf8135e99e288a9bdba789e2ed6fb92e79e4925e2c2d |
# 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.
#
"""Represent information for graphical display.
Classes in this module are designed to hold information in a way that
makes it easy to draw graphica... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Graphics/DisplayRepresentation.py | Python | gpl-2.0 | 6,817 | [
"Biopython"
] | dda91a9832426d998e365254b1903b715b3f185fc97d4464e821e1391d91042b |
import numpy as _np
import ESMF as _ESMF
from brushcutter import lib_ioncdf as _ncdf
from brushcutter import lib_common as _lc
from brushcutter import fill_msg_grid as _fill
from brushcutter import mod_drown_sosie as _mod_drown_sosie
import matplotlib.pylab as _plt
import time as ptime
class obc_vectvariable():
''' ... | raphaeldussin/brushcutter | brushcutter/lib_obc_vectvariable.py | Python | gpl-3.0 | 19,520 | [
"NetCDF"
] | a4393547b4d8cac494d66f2598205368f7c04da7a64c6e7aee6003a2aa5d2b62 |
"""Module image.
Instances of class Image are a primary data-holders for all PyBDSF
operations. They store the image itself together with some meta-information
(such as headers), options for processing modules and all data generated during
processing. A few convenience methods are also defined here for interactive
use... | lofar-astron/PyBDSF | bdsf/image.py | Python | gpl-3.0 | 7,512 | [
"Gaussian"
] | 6ebc03236bb035b823c43f137591c5ff3dc773f962b29594401124523a09400b |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pylab as pl
import Scientific.IO.NetCDF as IO
import matplotlib as... | CopyChat/Plotting | Python/climate_change/backup.py | Python | gpl-3.0 | 10,051 | [
"NetCDF"
] | f001fdb41457b500556dbdc0fcdcce25bd0780c9bfee2e2776f49dd26820fccf |
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
# The purpose of this test is to detect a change in the _metric_json of MetricsBase objects. Many of the metric
# accessors require _metric_json to have a particular form.
def metric_json_check():
df = h2o.import_file(path=py... | pchmieli/h2o-3 | h2o-py/tests/testdir_misc/pyunit_metric_json_check.py | Python | apache-2.0 | 10,502 | [
"Gaussian"
] | d48acc2b1ddd4795bd4ecab75d38989c38aa57a0e8222312d68be1611e07b183 |
"""Python wrappers around Brain.
This file is MACHINE GENERATED! Do not edit.
"""
import collections as _collections
from google.protobuf import text_format as _text_format
from tensorflow.core.framework import op_def_pb2 as _op_def_pb2
# Needed to trigger the call to _set_call_cpp_shape_fn.
from tensorflow.python... | jjas0nn/solvem | tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/gen_image_ops.py | Python | mit | 56,542 | [
"Gaussian"
] | dfd86fdddd731c0a5333e23a40079575a46c8b28d34c9ff5232498b3831c6dee |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Brian Meeker
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at http://trac.edgewall.org/wiki/TracLicense.
#
# This software consists of vol... | i-rabot/tractogithub | tracformatter/trac/ticket/batch.py | Python | bsd-3-clause | 8,661 | [
"Brian"
] | a30b289426e3090bb8b4567d147680b6d7f3eb6c9a2b18807ff023b02084971b |
# $Id$
#
# Copyright (c) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" utility functionality for molecular... | soerendip42/rdkit | rdkit/Chem/Fingerprints/MolSimilarity.py | Python | bsd-3-clause | 10,705 | [
"RDKit"
] | c8b44f6e8589a318aea8bf2a769ea2d29f8f6f8d8a13c51bb2310c06adac2c0d |
import numpy as np
from numpy import random
import glob, os
class TrainingManager:
neuralNetwork = ''
class NeuralNetwork:
class Layer:
class Neuron:
netValue = 0.
activationValue = 0.
weights = [] # each neuron should have weights for each of the neurons in the layer before it
weightsAfterError... | DiginessForever/machineLearning | pythonReluNeuralNet.py | Python | mit | 10,087 | [
"NEURON"
] | 281a0909a27b98bab649281b8bddd6b2576c35fefa81c3067bb026f786fc3c83 |
from __future__ import division
import numpy as np
import numpy.random as npr
import matplotlib.pyplot as plt
# Fancy plotting
try:
import seaborn as sns
sns.set_style("white")
sns.set_context("talk")
color_names = ["windows blue",
"red",
"amber",
... | mattjj/pylds | examples/zeroinflated_bernoulli_lds.py | Python | mit | 4,376 | [
"Amber"
] | 8e6f58848192ce0bf837123322d140db98884a176cdd9964c18bf2e1726077fa |
from django.shortcuts import render_to_response
def docs_view(request):
return render_to_response("documentation/index.html", {})
def structures_docs(request):
return render_to_response("documentation/structures.html", {})
def vasp_docs(request):
return render_to_response("documentation/vasp.html", {}... | wolverton-research-group/qmpy | qmpy/web/views/documentation.py | Python | mit | 591 | [
"VASP"
] | 3a19ec945d10cc57023f76f32f2352db16c3de2ea9083e704b24c6c63404409e |
import numpy as np
import re
import numba
import time
import tempfile
import sys
# Random number generator compatible with C++ and FORTRAN versions
_IA=16807
_IM=2147483647
_IQ=127773
_IR=2836
_NTAB=32
_NDIV=(1+(_IM-1)//_NTAB)
_EPS=3.0e-16
_AM=1.0/_IM
_RNMX=(1.0-_EPS)
@numba.jit(cache=True,fastmath=True)
def _U01(id... | GiovanniBussi/simplemd | python/simplemd.py | Python | gpl-3.0 | 14,204 | [
"Gaussian"
] | 16f54fa4c051d7fdc3f27203f1faea222886e64d11df16e0c12910e6a6eba4c3 |
"""Module symbol-table generator"""
from compiler import ast
from compiler.consts import SC_LOCAL, SC_GLOBAL, SC_FREE, SC_CELL, SC_UNKNOWN
from compiler.misc import mangle
import types
import sys
MANGLE_LEN = 256
class Scope:
# XXX how much information do I need about each name?
def __init__(self, name, mo... | zephyrplugins/zephyr | zephyr.plugin.jython/jython2.5.2rc3/Lib/compiler/symbols.py | Python | epl-1.0 | 14,538 | [
"VisIt"
] | 9b83ef2b9ba1e609224e128f0227376c1186a7b283c3e65b339d52539e25bea6 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | dgasmith/psi4 | psi4/driver/molutil.py | Python | lgpl-3.0 | 9,365 | [
"Psi4"
] | 85ec3b5ddb5567b7bd63316475c9a3e6b2d4b16140bb1d4dbb650f22b794912d |
import sys
import maya.OpenMaya as OpenMaya
import maya.OpenMayaMPx as OpenMayaMPx
import maya.cmds as cmds
kPluginNodeName = "MitsubaRoughDielectricShader"
kPluginNodeClassify = "/shader/surface"
kPluginNodeId = OpenMaya.MTypeId(0x87009)
class roughdielectric(OpenMayaMPx.MPxNode):
def __init__(self):
Ope... | hpd/MitsubaForMaya | plug-ins/mitsuba/materials/roughdielectric.py | Python | mit | 8,299 | [
"Amber"
] | 6376c5c951aa1eb7289a5910f0195dab51c1fdeb108d23386876dd470a3da86a |
"""
"""
import os
from lwr.lwr_client import action_mapper
from lwr.lwr_client import staging
from lwr.lwr_client.staging import LwrOutputs
from lwr.lwr_client.staging.down import ResultsCollector
import logging
log = logging.getLogger(__name__)
def postprocess(job_directory):
# Returns True iff outputs were co... | jmchilton/lwr | lwr/managers/staging/postprocess.py | Python | apache-2.0 | 2,393 | [
"Galaxy"
] | 6eeda44628be6221d280968d526919479d5be1e621d6d18f766c8619f07f901f |
"""
@name: PyHouse/src/Modules/Computer/_test/test_Nodes.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2018 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 29, 2015
@Summary:
"""
__updated__ = '2018-02-12'
from twisted.trial import unittest, report... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/_test/test_Nodes.py | Python | mit | 759 | [
"Brian"
] | 0eabae4fc643d6ac480974814d0aeed75b1a75599172db4d53800dab64bbf3bd |
from __future__ import division
from builtins import object
import numpy as np
from sporco import signal
def fn(prm):
x = prm[0]
return (x - 0.1)**2
def fnv(prm):
x = prm[0]
return ((x - 0.1)**2, (x - 0.5)**2)
class TestSet01(object):
def setup_method(self, method):
np.random.seed(1... | bwohlberg/sporco | tests/test_signal.py | Python | bsd-3-clause | 2,850 | [
"Gaussian"
] | e433583cc0170715c1cb2ba408009e1bba89d9ae979b6b6a45dac600f3ae55f4 |
input_name = '../examples/acoustics/acoustics.py'
output_name = 'test_acoustics.vtk'
from testsBasic import TestInput
class Test( TestInput ):
pass
| olivierverdier/sfepy | tests/test_input_acoustics.py | Python | bsd-3-clause | 153 | [
"VTK"
] | 43d4478528d3573c1384c4b426df5d9cd95b2557b383d11efaa41334e98696c1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import warnings
from operator import itemgetter
from tabulate import tabulate
import numpy as np
from monty.io import zopen
from monty.json import MSONable
from pymatgen import Structure, Lattice... | dongsenfo/pymatgen | pymatgen/io/feff/inputs.py | Python | mit | 32,731 | [
"FEFF",
"pymatgen"
] | 5a53e29c83b9fbcd67a9390bd5cc93ef93809073a7f2ba38ad3fd44bb63cd5c0 |
# Copyright (C) 2010-2018 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... | hmenke/espresso | samples/diffusion_coefficient.py | Python | gpl-3.0 | 2,720 | [
"ESPResSo"
] | d7780600ae56ea5924b1ccdb9a49d93279e6a683ac49382ab43f2b79206169eb |
#!/usr/bin/env python
import sys, os, collections, subprocess, sniper_lib, sniper_config
def ex_ret(cmd):
return subprocess.Popen(cmd, stdout = subprocess.PIPE).communicate()[0]
def cppfilt(name):
return ex_ret([ 'c++filt', name ])
class Function:
def __init__(self, eip, name, location):
self.eip = eip
... | yonggang985/Sniper | tools/gen_profile.py | Python | mit | 12,074 | [
"VisIt"
] | d04dfbe0b7ad01b54fd1969e39a5a1adc95c1ceb801fd46f81738025d41cba24 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/core/test_universe.py | Python | gpl-2.0 | 20,011 | [
"MDAnalysis"
] | 37c6ab474e501312250cb0e330fed2cf5e04b49b03e53655e46499493bf728cd |
#!/usr/bin/env python
import sys
import os
extras = {}
try:
from setuptools import setup
extras['zip_safe'] = False
if sys.version_info < (2, 6) and os.name != 'java':
extras['install_requires'] = ['multiprocessing']
except ImportError:
from distutils.core import setup
setup(name='futures',
... | jboning/pythonfutures | setup.py | Python | bsd-2-clause | 1,281 | [
"Brian"
] | ff4e92e34ccc6b2d93d1ced050ab2e0f5ba9eb59d5f9c77fae807003d088a472 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
platforms = [
'Acorn',
'Alambik',
'Amiga AGA',
'Amiga OCS/ECS',
'Amiga PPC/RTG',
'Amstrad CPC',
'Amstrad Plus',
'Android',
'Apple II',
'Apple II GS',
'Atari Falcon 030',
'Atari Jaguar',
'Atari Lynx',
'Atari ST',
'... | marcgd/PouetDL | platforms.py | Python | mit | 1,666 | [
"Jaguar"
] | 7831eaec947a53697cd343625d9b3849ebad42c9524cdadf8261f718e029e505 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to
# submit large numbers of jobs on supercomputers. It provides a python interface to physical input,
# ... | pylada/pylada-light | tests/espresso/dummy_pwscf.py | Python | gpl-3.0 | 2,799 | [
"CRYSTAL",
"ESPResSo",
"VASP"
] | 194c6af8f9ac494c1d8424aafb4b77e02e6e480a18dffe0b54e866dd60692c32 |
import gzip
import numpy
from orbkit import grid
def cube_creator(data,filename,geo_info,geo_spec,comments='',labels=None,**kwargs):
'''Creates a plain text Gaussian cube file.
**Parameters:**
data : numpy.ndarray, shape=N
Contains the output data.
filename : str
Contains the base name of the ou... | orbkit/orbkit | orbkit/output/cube.py | Python | lgpl-3.0 | 3,130 | [
"Gaussian"
] | ab6a8390109081566e5df10cbeae0267f3dfe964f446ae190dd03452a060f197 |
"Demonstrates molecular dynamics with constant energy."
from ase.calculators.emt import EMT
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.verlet import VelocityVerlet
from ase import units
# Use Asap for a huge performance increase if ... | grhawk/ASE | tools/doc/tutorials/md/moldyn2.py | Python | gpl-2.0 | 1,373 | [
"ASE",
"CRYSTAL"
] | 2facb2ffa5a3ac692ebc8fb32d6add6f40d82ed1507e14b62e65c748cabe6ecd |
import numpy as np
from numpy.random import seed
class AdalineGradientDescent(object):
"""
ADAptive LInear NEuron classifier.
Parameters
------------
_learning_rate : float
Learning rate (between 0.0 and 1.0)
_max_iterations : int
Maximum number of iterations over the trainin... | nitish-tripathi/Simplery | ANN/Adaline.py | Python | mit | 6,072 | [
"NEURON"
] | 3d966a908014181c12e5a43ccff8604426fb7774145e01d524ef816ca80aa9ed |
"""
##############################################################################################
Copyright(C) 2017 Shane Macaulay smacaulay@gmail.com
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
publish... | K2/Scripting | inVteroJitHash.py | Python | agpl-3.0 | 26,762 | [
"BLAST"
] | 789a20dde08bb3b651f5632bdf2614f0f7c48ab05400279c837b17b831bacacf |
from __future__ import print_function, division
import os
import numpy as np
from . import get_data_home
from .tools import sql_query
SPECCLASS = ['UNKNOWN', 'STAR', 'GALAXY', 'QSO',
'HIZ_QSO', 'SKY', 'STAR_LATE', 'GAL_EM']
NOBJECTS = 50000
GAL_COLORS_DTYPE = [('u', float),
('g', f... | eramirem/astroML | astroML/datasets/sdss_galaxy_colors.py | Python | bsd-2-clause | 2,595 | [
"Galaxy"
] | 083d36dc6196342c279d8ea4f2a439f656e2ac5557c7fe661ab0a389961b9e7b |
# --------------
# USER INSTRUCTIONS
#
# Now you will put everything together.
#
# First make sure that your sense and move functions
# work as expected for the test cases provided at the
# bottom of the previous two programming assignments.
# Once you are satisfied, copy your sense and move
# definitions into the robo... | JamesNewton/cs373ParticleFilter | hw3_6_ParticleFilter.py | Python | gpl-3.0 | 11,789 | [
"Gaussian"
] | a2ff7943ddc9821a414f7a2aabe6da9e4c39f99f64f707a6070a5db230609c81 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Simple volume rendering example.
reader = vtk.vtkSLCReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/sphere.slc")
# Create transfer functions for opacity and color
opa... | timkrentz/SunTracker | IMU/VTK-6.2.0/Rendering/Volume/Testing/Python/volTM3DCompressedCropRegions.py | Python | mit | 3,759 | [
"VTK"
] | 9feec99f8c2ae07154de92b5b0406025d16b051c1cdcc99e7a14adfcf28cd580 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | devel/external/hst/make_cosmos_cfimage.py | Python | gpl-3.0 | 4,645 | [
"Galaxy"
] | 091444b041d039483c5b0fc2b98737791ae7de3a16783759f8975957d9599185 |
import scipy as sc
import matplotlib.pyplot as plt
import schrpy as sch
x = sc.arange(-60, 61, 0.01)
z = sc.load('eigvec.npy')
xo = sch.gaussian(3, 1, 2).func(x)
coeff = sc.matmul(xo.conj(), z)
print(coeff.shape)
print(x.shape)
fig = plt.figure()
fig.add_subplot(211)
plt.plot(sc.absolute(coeff))
plt.plot(sc.real(coeff... | tmaeda11235/schroedinger_solver | tests/packet.py | Python | mit | 494 | [
"Gaussian"
] | e770c3dd4f43ff48714e9ffa44a7cb4951d315a9485c979e4cb02933a8ac9e2a |
from rdkit import six
#-------------------------------------------------------------------------
# Color
#-------------------------------------------------------------------------
class Color:
"""This class is used to represent color. Components red, green, blue
are in the range 0 (dark) to 1 (full in... | soerendip42/rdkit | rdkit/sping/colors.py | Python | bsd-3-clause | 8,009 | [
"RDKit"
] | d0ee7c0054c80fe5f88816021b824a5874e080354a5d43745421e3936a8da3b9 |
import numpy as np
class AdaptiveFixed(object):
def __init__(self, n_inputs, n_outputs, n_neurons,
input_bits=16, state_bits=16, extra_bits=16,
decoder_offset=0, decoder_bits=16,
seed=None, learning_rate=1e-3,
has_neuron_state=True, smoothing=0):... | tcstewar/minimal_adaptive_controller | adapt_fixed_small.py | Python | gpl-3.0 | 4,775 | [
"NEURON"
] | 4942933640009df28d69e6b0a86ac33abbf22adbe0ef30bf5ddcf07c2efbbd42 |
__author__ = 'jeff'
import numpy as np
class EnergeticNetwork:
"""
The energetic network forms the base class for Hopfield and Boltzmann machines.
"""
def __init__(self, neuron_count):
"""
Construct the network with the specified neuron count.
:param neuron_count: The number o... | JPMoresmau/aifh | vol3/vol3-python-examples/lib/aifh/energetic.py | Python | apache-2.0 | 3,697 | [
"NEURON"
] | 7806355474a01641e74e195b80667c29d564de75e63de27ded4962cdfdba5433 |
"""
NetCDF reader/writer module.
This module is used to read and create NetCDF files. NetCDF files are
accessed through the `netcdf_file` object. Data written to and from NetCDF
files are contained in `netcdf_variable` objects. Attributes are given
as member variables of the `netcdf_file` and `netcdf_variable` objects... | nvoron23/scipy | scipy/io/netcdf.py | Python | bsd-3-clause | 33,547 | [
"NetCDF"
] | 697ad77b05e01975e795e2bad05fb26f71100e59464012eec0fe1488eb5c1083 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/mpicc/mpi_kpoint_helper.py | Python | apache-2.0 | 4,738 | [
"PySCF"
] | ff2e0bd11bfe911f743caba37325ebb324de162e6493406a24de136b9fa04f08 |
#!/usr/bin/env python
# Original provided by Mark Olesen
import os,sys
from platform import uname
# from __future__ import print_function
try:
from PyFoam.ThirdParty.six import print_
except ImportError:
def print_(*args):
# Simple workaround to report the failure
for a in args:
sy... | takaakiaoki/PyFoam | bin/pyFoamVersion.py | Python | gpl-2.0 | 9,582 | [
"VTK"
] | b1f71465434029bd9fe941633a46694b488337349fd2672aaf640e24e315c553 |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
# USAGE:
# PREAMBLE:
import numpy as np
import sys
import MDAnalysis
psf = sys.argv[1]
traj = sys.argv[2]
# SUBROUTINES:
# MAIN PROGRAM:
buf = 100
deltaWrite = 10.0
delta_t = 0.002
box_dim = 28.40 # xyz file does not hold this info (even tho... | rbdavid/MolecDynamics | Analysis/MSD/Einstein.py | Python | mit | 1,633 | [
"MDAnalysis"
] | 4abe03b2f25978d3a6655140c958466e4e17f5bb51315275e3d59717a5a64a75 |
import matplotlib.pyplot as plt
from sunpy import map
from sunpy.map import Map
import numpy as np
import os
import copy
from skimage.feature import canny
from skimage.filters import roberts, sobel, scharr, prewitt
from scipy import ndimage
def mask_sun(array,pxval):
#This function will apply a centered filled cir... | kkozarev/mwacme | src/lasco/lasco_test_lv05_1_data.py | Python | gpl-2.0 | 3,784 | [
"Gaussian"
] | 3e9e51980f880654aa1c053783f3781df144c8b1eae63a7566b996472daefdef |
import os
import pysam
import unittest
import collections
import copy
import array
from TestUtils import checkFieldEqual
SAMTOOLS = "samtools"
WORKDIR = "pysam_test_work"
DATADIR = "pysam_data"
class ReadTest(unittest.TestCase):
def buildRead(self):
'''build an example read.'''
a = pysam.Alig... | TyberiusPrime/pysam | tests/AlignedSegment_test.py | Python | mit | 25,907 | [
"pysam"
] | b2691163db02576632ef480c14ecc594494f7b072db6cd35eb91c95d9bb6d19a |
#
# 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... | dhalperi/beam | sdks/python/apache_beam/transforms/ptransform.py | Python | apache-2.0 | 25,541 | [
"VisIt"
] | d7448b41058cfc6d22dbe80e471f27f486e59089da85e970a34f00db79df5a1f |
"""
Functions to help identify, extract, align and construct a phylogeny for a target gene.
The primary purpose of this module is for a user to confirm orthology of their gene, not to understand in detail the phylogenetic relationships between all closely related proteins.
"""
from math import floor
import os
import r... | oxpeter/ortholotree | orthomods/internal.py | Python | gpl-2.0 | 34,324 | [
"BLAST"
] | d696879c60e45bc967a681e512af54d905575d8a8ae5457857d31c533468941f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Hybrid LFP scheme example script, applying the methodology with the model of:
Potjans, T. and Diesmann, M. "The Cell-Type Specific Cortical Microcircuit:
Relating Structure and Activity in a Full-Scale Spiking Network Model".
Cereb. Cortex (2014) 24 (3): 785-806.
doi: ... | espenhgn/hybridLFPy | examples/Hagen_et_al_2016_cercor/cellsim16pops_modified_spontan_inh.py | Python | gpl-3.0 | 6,665 | [
"NEURON"
] | a5d6ec822d089c37b76e88b7c241f352edddeb67775442866973d6ecba1f65c0 |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (FWO) (... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/c/charmm.py | Python | gpl-2.0 | 6,104 | [
"CHARMM",
"GAMESS",
"Gaussian",
"Q-Chem"
] | 28eb8d3f454d38c97eaa8dc6de58283da95c08e995408c9d83d7de5ce62338ba |
r"""``sphobjinv`` *version definition module*.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
18 Mar 2019
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
https://github.com/bskinn... | bskinn/sphobjinv | src/sphobjinv/version.py | Python | mit | 521 | [
"Brian"
] | d1d3522d2aa01e2a09ac1318f80eb283a30e60127d71dc1839829605d7fa322f |
#!/usr/bin/env python
# This example shows how to extract portions of an unstructured grid
# using vtkExtractUnstructuredGrid. vtkConnectivityFilter is also used
# to extract connected components.
#
# The data found here represents a blow molding process. Blow molding
# requires a mold and parison (hot, viscous plasti... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/VisualizationAlgorithms/Python/ExtractUGrid.py | Python | gpl-3.0 | 3,365 | [
"VTK"
] | bff09c6a7c58b225711cceef669b31e36c6f951b237dfccb0784d2e81fbae995 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | eagle/collection.py | Python | agpl-3.0 | 15,980 | [
"Galaxy"
] | d71c4796ecaf5e7adf31138547ba47d3215697a92c3607550504d9885b239e0c |
""" High-level classes for reading HDF5 files. """
from collections import deque
from collections.abc import Mapping, Sequence
import os
import posixpath
import numpy as np
from .core import Reference
from .dataobjects import DataObjects
from .misc_low_level import SuperBlock
class Group(Mapping):
"""
An ... | jjhelmus/pyfive | pyfive/high_level.py | Python | bsd-3-clause | 12,361 | [
"VisIt"
] | bed358089aece6bbb04ad3cc305e6fb645402cda1e94e1941c76bf18548b0996 |
import numpy as np
import scipy.linalg
import scipy.stats
import random
from math import log, pi, e
def log_sum(log_summands):
a = np.inf
x = log_summands.copy()
while a == np.inf or a == -np.inf or np.isnan(a):
a = x[0] + np.log(1 + np.sum(np.exp(x[1:] - x[0])))
random.shuffle(x)
retu... | exord/bayev | lib.py | Python | mit | 3,932 | [
"Gaussian"
] | 9804ad6aa209f9f6f544739d93edf888ad29451ffe6dc39461223d3efabb228e |
# This file is part of BurnMan - a thermoelastic and thermodynamic toolkit for
# the Earth and Planetary Sciences
# Copyright (C) 2012 - 2021 by the BurnMan team, released under the GNU
# GPL v2 or later.
"""
orthorhombic_fitting
--------------------
This script creates an AnisotropicMineral object corresponding to
... | bobmyhill/burnman | contrib/anisotropic_eos/orthorhombic_fitting.py | Python | gpl-2.0 | 16,690 | [
"Avogadro"
] | 7ddb77d89bf4f6a951d8e8b6d8af9bd9046b97c08c62eefe1a06042d1b48b076 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/util/filesystem.py | Python | lgpl-3.0 | 1,249 | [
"Psi4"
] | 2b65fb3938b4c8c5cd23960aefebff064a49b0314d2eb715e93f4b12f5f7542a |
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