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from __future__ import print_function
import argparse
import pickle
import numpy as np
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
from sklearn.datasets import make_moons, make_circles
from sklearn.neural_network import MLPClassifier
from sklearn.neighbors impor... | pdedumast/ShapeVariationAnalyzer | ShapeVariationAnalyzer/Resources/Classifier/ML_algorithms.py | Python | apache-2.0 | 2,294 | [
"Gaussian",
"VTK"
] | 7553f321913a6abac0c2a7e8ce95b5e330fc903246b974379decffe6fa2e7aa8 |
from __future__ import division
import zstackLib
import numpy as np
import matplotlib.pyplot as plt
plt.rcParams.update({'font.size':11})
filename = '/home/brian/local/drumCreep/20x_gfp_stack_t2.tif'
z1 = zstackLib.zstack(filename)
z1.focusScan(threshValue=127,blurWindow=5,particleAnalysis=0)
fig=plt.figure(figsize... | gtg556h/pyZstack | call.py | Python | mit | 584 | [
"Brian"
] | 4be279767d2ec32c0ab62de4139f309442cbfe353c1ee3071527a8d366d15694 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/manipulating/writing exciting input files.
"""
import xml.etree.ElementTree as ET
import numpy as np
import scipy.constants as const
from monty.io import zopen
from monty.json import MSONable
from py... | vorwerkc/pymatgen | pymatgen/io/exciting/inputs.py | Python | mit | 15,394 | [
"CRYSTAL",
"exciting",
"pymatgen"
] | 2d7cbfe97c0dd008a337174aaec0171157d6617197813ba2e05fedf4e810f6ef |
from operator import itemgetter, attrgetter
import math
from math import copysign
from random import *
import timeit
from timeit import Timer as t
from matplotlib.pyplot import *
from numpy import *
def sigmoid (x):
return math.tanh(x)
class NN:
# ni,nh,no = n of input (i), hidden (h) and output (o) nodes
# ai,... | ActiveState/code | recipes/Python/578242_Artificial_Neuroglial_Network_ANGN_/recipe-578242.py | Python | mit | 29,104 | [
"NEURON"
] | cbef43c0a56634700ca5e6b3aaa3fe2f90bf9c7586b130ea09b5a3d9f031aa36 |
"""Collection of aospy.Var objects for use in my research."""
from aospy.constants import r_e
from aospy.var import Var
from . import calcs, units
# Define pressure, pressure thickness, and their dependencies first.
p = Var(
name='p',
units=units.Pa,
domain='atmos',
description='Pressure of model hal... | spencerahill/aospy-obj-lib | aospy_user/variables.py | Python | apache-2.0 | 99,756 | [
"NetCDF"
] | fe89d9efb63f15daba6d9a73c3885dc67fbd6e6b1cf38059abb471d6987e4f99 |
#!/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/example_microcircuit_lognormalweights.py | Python | gpl-3.0 | 23,391 | [
"NEURON"
] | fa0475b45a513a53e5c70b40b7235d5fa84455b4c9ac9310775e0c923690372d |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | dongjoon-hyun/tensorflow | tensorflow/contrib/model_pruning/examples/cifar10/cifar10_pruning.py | Python | apache-2.0 | 13,962 | [
"Gaussian"
] | 87e93e1eb768816d7534457ed48841b8d018b52ac4b581cb742a3bf1fbbf3fa9 |
# tr.po
val = {"" : "Project-Id-Version: sheltermanager\nReport-Msgid-Bugs-To: FULL NAME <EMAIL@ADDRESS>\nPOT-Creation-Date: 2013-01-24 10:55+0000\nPO-Revision-Date: 2011-05-21 11:48+0000\nLast-Translator: Sedat Mercan <Unknown>\nLanguage-Team: Turkish <tr@li.org>\nMIME-Version: 1.0\nContent-Type: text/plain; charset=... | aubzen/sheltermanager | src/locale/locale_tr.py | Python | gpl-3.0 | 89,690 | [
"Amber",
"VisIt"
] | 088b1ccd0151ba5afe1c50a0376edf34da6536bbb2983bd9e78b7c3d1f5db7a6 |
# python3
# pylint: disable=g-bad-file-header
# Copyright 2021 DeepMind Technologies Limited. 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... | deepmind/enn | enn/data_noise/bootstrapping.py | Python | apache-2.0 | 8,781 | [
"Gaussian"
] | 8ed007b7af3a17d578ec0567282f04e03aab7e5058bd88f9e1b2cd7a146eb0a6 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-affyexpress/package.py | Python | lgpl-2.1 | 1,854 | [
"Bioconductor"
] | a7f421dcf144c9bfd79032b23d0b5e762597071a385d7af875b88a2464ddbc2c |
""" Module for dealing with VOMS (Virtual Organization Membership Service)
"""
__RCSID__ = "$Id$"
import os
import stat
import tempfile
import shutil
from DIRAC import S_OK, S_ERROR, gConfig, rootPath
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.ProxyFile import multiProxyArgument, deleteMultiPro... | fstagni/DIRAC | Core/Security/VOMS.py | Python | gpl-3.0 | 11,333 | [
"DIRAC"
] | b1ffe781f66cb3a5dcfddc546425eb52c94bc53adc38217e1d4ab5cd3d10441b |
import PIL
from PIL import ImageEnhance, Image, ImageFilter, ImageChops
import PIL.ImageOps
import numpy as np
randint = np.random.randint
__author__ = "Ronny Restrepo"
__copyright__ = "Copyright 2017, Ronny Restrepo"
__credits__ = ["Ronny Restrepo"]
__license__ = "Apache License"
__version__ = "2.0"
# =============... | ronrest/convenience_py | ml/tf/workflow_image_classifier/image_processing.py | Python | apache-2.0 | 30,075 | [
"Gaussian"
] | b7129e4c0cbd3e6f50dc88b15351004773b2e83699e1bf20837a0acfcbf97f46 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# ORCA Importer documentation build configuration file, created by
# sphinx-quickstart on Sat Apr 30 10:03:06 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in thi... | bskinn/excel-orcaimport | doc/source/conf.py | Python | mit | 12,028 | [
"Brian",
"ORCA"
] | d97402b3116dbe6d5974d8b944d6d9d8fd683b21c64ea98d724a909bf78ba10a |
#!/usr/bin/env python
"""
Install.py tool to build the GPU library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, os, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import get_cpus
parser = ... | Pakketeretet2/lammps | lib/gpu/Install.py | Python | gpl-2.0 | 5,125 | [
"LAMMPS"
] | cbd18025828ebd8547d67c852e0b52974bd85d061a5ad4228e197a407fdfd661 |
# Zeobuilder is an extensible GUI-toolkit for molecular model construction.
# Copyright (C) 2007 - 2009 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of Zeobuilder.
#
# Zeobuilde... | woutersmet/Zeosummer | share/plugins/molecular/geometry.py | Python | gpl-3.0 | 10,146 | [
"MOPAC"
] | 5b5aaa4b8aa1f07554a097bba4a5426114bb860bfc01a16c45f2c8b020e55576 |
import datetime
from django.conf import settings
from django.contrib.auth.models import Group
from django.core import mail
from django.urls import reverse
from django.test import TestCase
from django.test.utils import override_settings
from django.utils.translation import gettext_lazy as _
from zds.forum.factories im... | ChantyTaguan/zds-site | zds/tutorialv2/tests/tests_views/tests_published.py | Python | gpl-3.0 | 87,293 | [
"VisIt"
] | 1a90a7ac789fb3e7a5e748c58adf94a90af11ad8804c64af2fc55124305b90f4 |
from direct.showbase.PythonUtil import randFloat, normalDistrib, Enum
from direct.showbase.PythonUtil import clampScalar
from toontown.toonbase import TTLocalizer, ToontownGlobals
import random, copy
TraitDivisor = 10000
def getTraitNames():
if not hasattr(PetTraits, 'TraitNames'):
traitNames = []
... | ToonTownInfiniteRepo/ToontownInfinite | toontown/pets/PetTraits.py | Python | mit | 9,405 | [
"Gaussian"
] | 3093cdffe92013ed52711cd7171b2c1e831027f4cf240a37f398af2e6220997a |
#!/usr/bin/env python
"""A class for handling HiC read data."""
import os
import sys
import numpy
import h5py
try:
import pysam
except:
pass
class HiCData(object):
"""This class handles interaction count data for HiC experiments.
This class stores mapped paired-end reads, indexing them by fend-en... | bxlab/HiFive_Paper | Scripts/hifive-1.1.3/hifive/hic_data.py | Python | bsd-3-clause | 37,614 | [
"pysam"
] | 6248f651d65b540a488a25ce2a96f9f64f689b3d86f28b3a49025958f6099bd5 |
"""
KeepNote
Functions for iterating and inserting into textbuffers
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@mit.edu>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | reshadh/Keepnote-LaTeX | keepnote/gui/richtext/textbuffer_tools.py | Python | gpl-2.0 | 18,602 | [
"VisIt"
] | 10709e431dcceb7388fbad3743d2294484930f10f8c81ce044628ac2b9e6486f |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/alignment/tests/test_ssw.py | Python | bsd-3-clause | 32,597 | [
"scikit-bio"
] | f56c1785272183b4273ff6441d1e34a735325d5d06b187d409ad7fffdfd2148a |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
import torch.nn as nn
from torch.distributions import MultivariateNormal, constraints
import pyro.distributions as dist
from pyro.contrib.timeseries.base import TimeSeriesModel
from pyro.nn import PyroParam, pyro_meth... | uber/pyro | pyro/contrib/timeseries/lgssm.py | Python | apache-2.0 | 6,439 | [
"Gaussian"
] | 906c9bd24b6ffd567c8a3aa773cdde1efaf93fa9213a9d78a6f312a7e200ab30 |
""" Builds membrane protein systems """
__version__ = '2.7.12'
__author__ = 'Robin Betz'
import sys
import inspect
#=========================================================================
# Currently supported output formats and description
supported_formats = {
"amber": ".prmtop and .inpcrd Amber PARM7 and R... | Eigenstate/dabble | dabble/__init__.py | Python | gpl-2.0 | 1,456 | [
"Amber",
"CHARMM",
"Desmond",
"Gromacs",
"LAMMPS"
] | 0b4c6df2c9505415c85a194caef45d540bd4e62b8982725d2a4f3080bfa2e696 |
from datetime import datetime
from django.db import transaction
from django.core.management.base import BaseCommand
from schools.models import (
BoundaryType,
Partner
)
from stories.models import (
Question,
QuestionType,
Questiongroup,
QuestiongroupQuestions,
Survey,
Source,
User... | klpdotorg/dubdubdub | apps/stories/management/commands/populatekonnectquestions.py | Python | mit | 3,626 | [
"VisIt"
] | c1f77294bdc6961a9e1cf83b7479f20a56e2089654ac77ec4a4f565ad2aa41ca |
from __future__ import absolute_import
import theano
import sys
from theano.sandbox.rng_mrg import MRG_RandomStreams
import theano.tensor as T
import logging
from emolga.utils.theano_utils import shared_zeros, shared_scalar, floatX
from emolga.utils.generic_utils import get_from_module
from six.moves import zip
from ... | MingyuanXie/CopyNet | emolga/basic/optimizers.py | Python | mit | 9,696 | [
"Gaussian"
] | e069478e4e5cf03dd8d144573e25f92b6aa676b959df4790ef7011847c748ef0 |
# -*- 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 django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | roger-link/tacky | config/urls.py | Python | mit | 1,429 | [
"VisIt"
] | 54600a6f313aadd22ae21da05f053c14b3e4717209e463e2d00007602e79dabb |
"""
Miscellaneous utility functions.
"""
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "BSD 3-clause"
import gzip
import numpy as np
import os
import pandas as pd
import sys
import tempfile
import tarfile
import zipfile
try:
from urllib.request import urlretrieve... | ktaneishi/deepchem | deepchem/utils/__init__.py | Python | mit | 3,655 | [
"RDKit"
] | 5a184e170561be12759b01bf6e99d743198ee572ad8b28f07d652a12760f75d6 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | jctanner/ansible | lib/ansible/playbook/conditional.py | Python | gpl-3.0 | 10,451 | [
"VisIt"
] | cf2d386a22c5defa9786d48f8d4848af5c85b1afe70a24d38e8e39e0387bab96 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read a maf and print the text as a fasta file.
usage: %prog < maf > fasta
"""
from __future__ import division
import textwrap
import sys
from bx.align import maf
def __main__():
maf_reader = maf.Reader( sys.stdin )
# Confusing since maf_to_concat_fasta takes n... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_to_fasta.py | Python | bsd-3-clause | 892 | [
"Galaxy"
] | 0c939f569b76c784082bf0b252ce6113c42fcbab21cfa19a9e50b29e34f4b06a |
from django.contrib import admin
from .models import *
from .settings import *
class PlantAdmin(admin.ModelAdmin):
list_display = ('common_name', 'family', 'genus', 'species', 'is_native', 'annual_perennial', 'annualness_index', 'shade_open', 'forb_to_tree_index', 'water_low_medium_high', 'water_needs_index', 'com... | dparizek/newecosystems | newecosystems/apps/core/admin.py | Python | mit | 950 | [
"Firefly"
] | 575586f9900fb0b7de397b7c5dc63b86a86e25af25952960f38c67fda877925f |
#! /usr/bin/python
#Author: Sam Nooij
#Email: sam.nooij [at] rivm [dot] nl
#Date: 28-11-2016
from __future__ import print_function
import urllib
import numpy as np
import glob
import os
import pandas as pd
from Bio import SeqIO
from Bio import Entrez
VIRUS_OF_INTEREST = "mumps virus"
EMAIL_ADDRESS = "[enter your em... | samnooij/sequence_analysis_scripts | genbank/download_all_sequences_of_virus_species.py | Python | gpl-3.0 | 7,994 | [
"Biopython"
] | e941cb2213a8ed5cf87a0ddeec8f36b33f008491d3e37b83a16277778b38896c |
# Copyright 2016 Google 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 or agreed to in writin... | google/svcca | dft_ccas.py | Python | apache-2.0 | 6,768 | [
"NEURON"
] | 3f1cfa079931d1fed737f22f19f0ab9edeb3861d132e248e47bc60ec453929b0 |
from jobTree.scriptTree.target import Target
import re
class AbstractMetaAnalysis(Target):
"""Base class to for meta-analysis targets. Inherit this class to create a meta-analysis.
"""
def __init__(self, outputDir, experiments):
Target.__init__(self)
self.experiments = experiments
s... | mitenjain/nanopore | nanopore/metaAnalyses/abstractMetaAnalysis.py | Python | mit | 1,355 | [
"BWA"
] | 223f8a535fea408e35eec5f48b3706b0f576c3fa8a81a1360751f7c54ceb749f |
import pytest
import numpy as np
from cplpy import run_test, prepare_config
import os
# -----Forces TESTS-----
# EXPLANATION:
MD_FNAME = "lammps_forces.in"
MD_ARGS = "-in " + MD_FNAME
MD_EXEC = "lmp_cpl"
CFD_FNAME = "dummyCFD_forces.py"
CFD_ARGS = CFD_FNAME
CFD_EXEC = "python"
TEST_TEMPLATE_DIR = os.path.join(os.env... | Crompulence/cpl-library | examples/sockets/LAMMPS/LAMMPS-dev/cpl-socket/test/forceC-P/test_forces.py | Python | gpl-3.0 | 3,574 | [
"LAMMPS"
] | 1a3b9dbab27085b768ed45d4495967c223283e88f5df8ee63a36124eb5978961 |
import src.nnload as nnload
from netCDF4 import Dataset
import numpy as np
import pickle
def build_training_dataset(expt, t_step, t_beg, t_end, N_lon_samp=5):
"""Builds training, testing, and cross-validation datasets from an
idealized GCM run folder. Assumes tendencies are stored for
instantaneous ... | jgdwyer/ML-convection | src/nnio.py | Python | apache-2.0 | 21,069 | [
"NetCDF"
] | 660e1cda6a3d5e07f96bfacbc0e9105ddef9bfb4d7812bfa9ceff57f1301a6a3 |
__name__ = "LEDCtrl"
__author__ = "E. A. Tacao <e.a.tacao |at| estadao.com.br>"
__date__ = "29 Dez 2005, 17:00 GMT-03:00"
__version__ = "0.07"
__doc__ = """
LEDCtrl - a LED display control
This is a control that simulates a 7-segment LED display. It accepts decimal
and hexadecimal digits as well as any numb... | jantman/TuxTruck-wxPython | LEDCtrl/LEDCtrl.py | Python | gpl-3.0 | 22,323 | [
"VisIt"
] | a200ff496fa033f52ee4a0fb831fb98559193a4059571f527b8d513c3c03037f |
# Legacy of Insolence version 0.1
# by DrLecter
import sys
from net.sf.l2j.gameserver.model.quest import State
from net.sf.l2j.gameserver.model.quest import QuestState
from net.sf.l2j.gameserver.model.quest.jython import QuestJython as JQuest
print "importing quests:",
# 1- Variables: Maybe you would like to change s... | Barrog/C4-Datapack | data/jscript/quests/372_LegacyOfInsolence/__init__.py | Python | gpl-2.0 | 5,744 | [
"Desmond"
] | 8878c65f7de40affb7c5b6f45b03ebd7705d7000a13d4a2ee69fdc870c72cd9f |
#!/usr/bin/env python3
"""
NAMDBin reads and writes the binary format used by NAMDBin
for restart files. I've written it to support coordinates
and velocities, because that's what LOOS supports, but the
same format is also used to store forces.
Alan Grossfield
University of Rochester Medical Center
2017
"""
import st... | GrossfieldLab/loos | Packages/PyLOOS/NAMDBin.py | Python | gpl-3.0 | 3,406 | [
"NAMD"
] | 891a1211b436df01db91b243996bd36cc6d13ba30d4b1bdf0b78c7d8119653bc |
from collections import OrderedDict
from edc_visit_schedule.classes import (
VisitScheduleConfiguration, site_visit_schedules, MembershipFormTuple, ScheduleTuple)
from ..models import SpecimenConsent
class SpecimenConsentVisitSchedule(VisitScheduleConfiguration):
name = 'specimen visit schedule'
app_l... | TshepangRas/tshilo-dikotla | td_maternal/visit_schedule/specimen_consent.py | Python | gpl-2.0 | 685 | [
"VisIt"
] | 2f06707d8a499598c77c7394da1bfa427315461a395c0ab4a8da2156b45254e3 |
import mdtraj as md
import os
import numpy as np
import simtk.unit as u
from simtk.openmm import app
import simtk.openmm as mm
import pdbfixer
name = "1vii"
pdb_filename = os.path.join("./pdbs/%s.pdb" % name)
equil_pdb_filename = os.path.join("./equil/%s.pdb" % name)
equil_dcd_filename = os.path.join("./equil/%s.dcd" ... | kyleabeauchamp/RepexRuns | code/build.py | Python | gpl-2.0 | 1,666 | [
"MDTraj",
"OpenMM"
] | 6d549f1a9e5992e33fbd52c933a41c78bf8351e6cdb70444c29747313fecbcf7 |
# -*- 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 django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | kdagley/midas_pr | config/urls.py | Python | bsd-3-clause | 1,395 | [
"VisIt"
] | 715d94f42e92b9aa693eae2c15499aeb734eda504abf66059fa94595d3e657db |
"""
Module StringFormat
The StringFormat module allows for character-by-character formatting of
strings. It imitates the SPING string drawing and string metrics
interface. The string formatting is done with specialized XML syntax
within the string. Therefore, the interface for the StringFormat module
consists of wrappe... | rdkit/rdkit-orig | rdkit/sping/stringformat.py | Python | bsd-3-clause | 17,143 | [
"RDKit"
] | d443e4ae0ac2bdaa7aba1c587ec0e6592f8bc8272cb6f979d503caf5a93db2f6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module define a WulffShape class to generate the Wulff shape from
a lattice, a list of indices and their corresponding surface energies,
and the total area and volume of the wulff shape,the weighted su... | richardtran415/pymatgen | pymatgen/analysis/wulff.py | Python | mit | 27,788 | [
"pymatgen"
] | fe324a3f3047e7407f6c8f8cd5295cdf4085ea9207e24863fde11d5a89db56aa |
"""
Computational Neurodynamics
Exercise 5
Run an example with two coupled neural oscillators.
(C) Murray Shanahan et al, 2016
"""
import sys
sys.path.append('../Exercise_2')
import numpy as np
import numpy.random as rn
import matplotlib.pyplot as plt
from SynchronisationIndex import SynchronisationIndex
from Power... | pmediano/ComputationalNeurodynamics | Fall2016/Exercise_5/Solutions/Sync2Run.py | Python | gpl-3.0 | 6,828 | [
"NEURON"
] | ef8a302c2b3442f0d1e3d4beaa65078ee0700c8c6c4c9e868bcee1337d0c2361 |
#!/usr/bin/env python
# coding: utf-8
# # 20 - Example Simulation - I Beams
#
# This Journal shows how to model a site including I beams. While the I Beams can be added to the module unit, doing it for the whole row reduces the amount of geometries in the scene and makes raytracing faster.
#
# This particular geomet... | NREL/bifacial_radiance | docs/tutorials/20 - Example Simulation - I Beams.py | Python | bsd-3-clause | 6,424 | [
"Brian"
] | c390760bc683d11e3120fafd39969abef5f76813e01ce60712c77170a1760d41 |
# -*- coding: UTF-8 -*-
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov... | paulojamorim/invesalius3 | invesalius/gui/dialogs.py | Python | gpl-2.0 | 190,014 | [
"Gaussian",
"VTK"
] | 62e2f89497e226a863ee6044ccf4ad30f85c2a20fe57ea7f8d931b107cf5fc72 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | pcu4dros/pandora-core | workspace/lib/python3.5/site-packages/setuptools/command/easy_install.py | Python | mit | 87,125 | [
"VisIt"
] | 60022c521ce6c3fb21befa033fc11eb034b6c5b147eed0f832e604f17df1e987 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import logging
from math import ceil
import sys
import numpy as np
import tensorflow as tf
VGG_MEAN = [103.939, 116.779, 123.68]
class FCN32VGG:
def __init__(self, vgg16_npy_path=None):
... | irashadow/TensorFlow_FCN | fcn32_vgg.py | Python | mit | 15,636 | [
"Gaussian"
] | 1076d8ec13ef4bba756136a38b2cd2e55690ce4fd874126f96b9681042e23763 |
# Copyright (C) 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 versio... | espressomd/espresso | testsuite/scripts/samples/test_diffusion_coefficient.py | Python | gpl-3.0 | 1,177 | [
"ESPResSo"
] | db4bab64da3fe2646816f288a94f23be9126e27f6727658dbf4edc19780136d6 |
import sys, logging, copy, shutil, weakref, cPickle, tempfile, os
from galaxy.util import string_as_bool, relpath, stringify_dictionary_keys, listify
from galaxy.util.odict import odict
from galaxy.web import form_builder
import galaxy.model
from sqlalchemy.orm import object_session
import pkg_resources
pkg_resources... | volpino/Yeps-EURAC | lib/galaxy/datatypes/metadata.py | Python | mit | 30,560 | [
"Galaxy"
] | 6cbd0a8b81f397fdffb91e586d10cd62c22fd3e72e0b789cd6056366c430d2e4 |
import csv
import sys
import numpy
import math
from numpy import genfromtxt
from numpy.linalg import inv
import random
from random import randint
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import axes3d, Axes3D
#import time
#start_time = time.time()
PrintEnabled = 0
X = genfromtxt(sys.argv[1], delimit... | Labonneguigue/Machine-Learning | Project 3/hw3_clustering.py | Python | mit | 13,773 | [
"Gaussian"
] | c276bde22e0dab3bb795d5f0fbc3a49856ecda75a36f7e89d60e16260e6e1682 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | gift/tasks/style_transfer_ops.py | Python | apache-2.0 | 7,380 | [
"Gaussian"
] | d11656455ebcfedecff33a0fae89367e7c9f5bcd5af3c90b7d5652cb5d88b556 |
"""Deal with an Organism in a Genetic Algorithm population.
"""
# standard modules
import sys #for Python 3 hack
import random
import array
# Sequence objects from Biopython
from Bio.Seq import MutableSeq
def function_population(new_genome, num_organisms, fitness_calculator):
"""Generate a population given a func... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/GA/Organism.py | Python | gpl-2.0 | 6,137 | [
"Biopython"
] | 4c6e1b01f79f8ae9132674a27b64ac663fe5614866226f876cb395c205dc7f78 |
from ase.lattice.spacegroup import crystal
from gpaw import GPAW, PW
a = 4.0351 # Experimental lattice constant in Angstrom
Ecut = 250 # Energy cut off for PW calculation
k = 5 # Number of kpoints per each direction
# This gives the typical NaCl structure:
LiF = crystal(['Li', 'F'],
[(0, 0, 0), (0.5,... | robwarm/gpaw-symm | doc/exercises/bse/LiF_gs.py | Python | gpl-3.0 | 773 | [
"ASE",
"CRYSTAL",
"GPAW"
] | cca4ef3a4c2df69685f4c7816ed234e79ca81fa7c17b30770d968eba4bf49462 |
#!/usr/bin/env python3
"""The influence of windowing of log. sweep signals when using a
Kaiser Window by fixing beta (=2) and fade_out (=0).
fstart = 1 Hz
fstop = 22050 Hz
Unwindowed Deconvolution
"""
import sys
sys.path.append('..')
import measurement_chain
import plotting
import calculation
import ge... | spatialaudio/sweep | log_sweep_kaiser_window_script1/log_sweep_kaiser_window_script1_1.py | Python | mit | 2,181 | [
"DIRAC"
] | 1a26442f9b60bc1c5b4abd3d0e4f4ac48700d9f2ba2168401cc9125ef0d79e60 |
from __future__ import absolute_import
import logging
from django.utils.translation import ugettext_lazy as _
from sentry import options
from sentry.integrations import (
IntegrationInstallation,
IntegrationFeatures,
IntegrationProvider,
IntegrationMetadata,
FeatureDescription,
)
from sentry.pip... | beeftornado/sentry | src/sentry/integrations/msteams/integration.py | Python | bsd-3-clause | 3,780 | [
"VisIt"
] | 777d0dc8a5f5bf3c5ed74b92ad711e61a918defb81f13df57380b2cba1404e06 |
# -*- encoding:utf-8 -*-
from eve import Eve
from werkzeug.security import generate_password_hash
from eve.auth import TokenAuth
import genToken
from datetime import datetime
import base64
import json
from flask import abort, Response
class TokAuth(TokenAuth):
def check_auth(self, token, allowed_roles, resource, ... | damoyelang1992/restserver | src/test.py | Python | gpl-3.0 | 2,434 | [
"VisIt"
] | f74b32485347a1c1ddf1b32af9d4cb961a6cccb9586e13ada0909d8517c1de88 |
import logging
import tempfile
from epanettools.epanettools import EPANetSimulation
from epanettools.epanettools import Link
from epanettools.epanettools import Links
from epanettools.epanettools import Node
from epanettools.epanettools import Nodes
logger = logging.getLogger()
class _Link:
pass
class _Node:
... | asselapathirana/RRPam-WDS | src/rrpam_wds/hydraulic_services.py | Python | gpl-3.0 | 6,458 | [
"ADF"
] | f1ca1b00a0fe8a8dda866cdb5c570320c4f9691a154f83d4d217ca7dd1c77a35 |
r"""OS routines for Mac, DOS, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, mac, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, ntpath, or macpath
- os.name is 'posix', 'nt', 'os2', 'mac', 'ce' or 'riscos'
- os.curdir is a string r... | kontais/EFI-MIPS | ToolKit/cmds/python/Lib/os.py | Python | bsd-3-clause | 24,528 | [
"VisIt"
] | 4c8d10f3668edb59115908d115dc5f0c1f2442bf6b1a89ef1931864783a7367e |
#!/usr/bin/env python
""" Illustrates the Glyph3D class and some basic texturing of the
glyph. Notice how easy it is to create a simple PolyData object as
the input of the Glyph using Python lists.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2004-2006, Enthought, Inc.
# License: BSD Sty... | dmsurti/mayavi | examples/tvtk/texture_glyph.py | Python | bsd-3-clause | 2,472 | [
"VTK"
] | cba96d317e0b56223ae8dc257c713437b8e84958e1235df88626441662c1fdce |
from __future__ import print_function
import sys
from setuptools import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import platform
try:
import numpy # NOQA
except ImportError:
print('numpy is required during installation')
sys.exit(1)
try:
import scipy # NOQA... | skggm/skggm | setup.py | Python | mit | 2,029 | [
"Gaussian"
] | 38f9ec977571d00fa2c2a0852af8ee6a3ef298ef19b317f095e44651f18bd80a |
"""Treat Cartesian Gaussian basis set information.
High-level module that allows for reading in basis set information and
transforming it in a format suitable for further processing.
"""
# This file is part of ManipulateAggregates.
#
# Copyright (C) 2016 by Torsten Sachse
#
# ManipulateAggregates is free software: yo... | razziel89/ManipulateAggregates | ManipulateAggregates/orbitalcharacter/read_MO_basis.py | Python | gpl-3.0 | 12,560 | [
"Gaussian"
] | f0d24c61b6097633d28362400ac78bd983da665b21832cb2c354058276f5d6ab |
# Author: Cole Howard
#
# Tests for Network Class of linear_neuron project
import unittest
from ..source.network import append_bias, Network, Neuron
from ..source.neuron import Neuron
class NetworkHelperTests(unittest.TestCase):
def test_append_bias(self):
self.assertEqual(append_bias([0, 0, 0]), [0, 0... | uglyboxer/linear_neuron | tests/test_network.py | Python | mit | 1,120 | [
"NEURON"
] | fbd4f98cd12e6577793147b5daf14c9927d753ebfc643e4977d8b310e7128d7e |
"""
Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml).
All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed.
"""
import json
import os
import shutil
import tempfile
import threading... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/galaxy_install/tool_migration_manager.py | Python | gpl-3.0 | 48,799 | [
"Galaxy"
] | ffc4cff4b73e9bf7a8b35c2d2fe78df268476a4ecb74cb15a0a3f3e688d6af31 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
import urllib
from BeautifulSoup import BeautifulSoup
wiki = "http://sourceforge.net/apps/mediawiki/cclib"
... | gaursagar/cclib | old/downloadwiki.py | Python | bsd-3-clause | 941 | [
"cclib"
] | 16b36543102f25bff1c059a000d763c129888c68f03245d5677437b4ebfedddb |
"""Google Cloud Platform (GCP) compatible extensions of `dicomweb_client`.
Modules under this package may require additional dependencies. Instructions for
installation are available in the Installation Guide here:
https://dicomweb-client.readthedocs.io/en/latest/installation.html#installation-guide
For further detai... | MGHComputationalPathology/dicomweb-client | src/dicomweb_client/ext/gcp/__init__.py | Python | mit | 444 | [
"VisIt"
] | e2f8d46e642e7d7f6d9c2262b5a5b77ce4f638fa3acc26096cde4ea7dde2657d |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#-----------------------------------------------
# Set these parameters for adjoint flagging....
# location... | clawpack/adjoint | paper2_examples/acoustics_2d_ex4/setrun.py | Python | bsd-2-clause | 14,133 | [
"NetCDF"
] | 486b74e3b625053f5725064ab5991259919ffe451b29e6eb7a4b2c1255a3b800 |
#
# @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
#... | susilehtola/psi4 | psi4/driver/qcdb/libmintsbasisset.py | Python | lgpl-3.0 | 65,736 | [
"CFOUR",
"Gaussian",
"Psi4"
] | e05c82e009ca53588c09c323ac0a3f0154253743f82b3bd6297254bf9a1b0d08 |
# -*- coding: utf-8 -*-
"""This module contains helper functions for reading BEL scripts."""
import logging
import os
import re
import time
from typing import Any, Iterable, List, Mapping, Optional, Tuple
from bel_resources import ResourceError, split_file_to_annotations_and_definitions
from pyparsing import ParseEx... | pybel/pybel | src/pybel/io/line_utils.py | Python | mit | 11,090 | [
"Pybel"
] | a01ef99e801e2f610a825d31f823258c535a6ba5b17830267ed522e7b3e96e49 |
# Copyright 2013-2021 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 Gmt(Package):
"""GMT (Generic Mapping Tools) is an open source collection of about 80
... | LLNL/spack | var/spack/repos/builtin/packages/gmt/package.py | Python | lgpl-2.1 | 6,375 | [
"NetCDF"
] | 47233b8979c2eb2f1f65ed7b3be3514d4f15e7b2c17bbe504f45ef87e9d328d9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
from holmes import __version__
tests_require = [
'mock',
'nose',
'coverage',
'yanc',
'preggy',
'tox',
'ipdb',
'coveralls',
'factory_boy',
'sqltap',
'sphinx',
'honcho',
]
setup(
... | marcelometal/holmes-api | setup.py | Python | mit | 2,246 | [
"Octopus"
] | 525e9792dc94ee1fa6de4bbdfaa811ebbb25df87ecd01aaaab9aa1e7dbc2bf40 |
import ase
tol = 1e-9
a = ase.Atoms('CC', [[9.5,5,5],[0.5,5,5]], cell=[10,10,10], pbc=True)
assert abs(a.get_distance(0,1)-9.0) < tol
assert abs(a.get_distance(0,1,mic=True)-1.0) < tol
a.set_distance(0,1, 1.5, mic=True)
assert abs(a.get_distance(0,1)-8.5) < tol
assert abs(a.get_distance(0,1,mic=True)-1.5) < tol
a... | askhl/ase | ase/test/mic.py | Python | gpl-2.0 | 438 | [
"ASE"
] | 24a62015857e34870ce444ed95fb86ebb8cdb951de6f2a3ae876ee46827b38a5 |
#!/usr/bin/env python
from __future__ import unicode_literals, division, print_function
import numpy as np
from abipy.abio.inputs import *
from pymatgen.io.abinit.works import BecWork, PhononWork
from pymatgen.io.abinit.tasks import ScfTask
from pymatgen.io.abinit.flows import PhononFlow
_TOLVARS = set([
'toldfe',
... | mailhexu/pyDFTutils | pyDFTutils/abipy/flow.py | Python | lgpl-3.0 | 6,787 | [
"ABINIT",
"pymatgen"
] | 99f7698fc0f970f6866e6d068a86da24105b50f0c0e6c1844a389f3780453c68 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/ascent/package.py | Python | lgpl-2.1 | 13,518 | [
"VTK"
] | 58109d9b6b2b8e59a821321bc501d37de62ffafa73de28f1a1e3fac212918869 |
# coding: utf-8
from __future__ import unicode_literals
from .mtv import MTVServicesInfoExtractor
from ..compat import compat_urllib_parse_urlencode
from ..utils import update_url_query
class NickIE(MTVServicesInfoExtractor):
IE_NAME = 'nick.com'
_VALID_URL = r'https?://(?:www\.)?nick(?:jr)?\.com/(?:videos/c... | misterhat/youtube-dl | youtube_dl/extractor/nick.py | Python | unlicense | 4,236 | [
"VisIt"
] | 83e086ff7594f8975be4e985fabebd06162f952c42e7ff2af26dccdae30d8897 |
# Orca
#
# Copyright (C) 2010 Joanmarie Diggs
# Copyright (C) 2011-2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; eith... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/toolkits/WebKitGtk/speech_generator.py | Python | gpl-3.0 | 7,897 | [
"ORCA"
] | 2ce0e3d7c0a38913b6146a830b045305c87815eae06d8e5aa45c06b68fa0e8ef |
import string, sys
from datetime import datetime, timedelta
from galaxy import util, datatypes
from galaxy.web.base.controller import *
from galaxy.util.odict import odict
from galaxy.model.orm import *
from galaxy.web.framework.helpers import time_ago, iff, grids
import logging
log = logging.getLogger( __name__ )
# S... | volpino/Yeps-EURAC | lib/galaxy/web/controllers/admin.py | Python | mit | 61,790 | [
"Galaxy"
] | 08614576731e6b1ae76042e6b8f123d46e773efb8b76b447acc3c5239a2bdbf8 |
import numpy as np
from gpaw.lfc import LocalizedFunctionsCollection as LFC
from gpaw.grid_descriptor import GridDescriptor
from gpaw.spline import Spline
a = 4.0
gd = GridDescriptor(N_c=[16, 20, 20], cell_cv=[a, a + 1, a + 2],
pbc_c=(0, 1, 1))
spos_ac = np.array([[0.25, 0.15, 0.35], [0.5, 0.5, 0.5]... | robwarm/gpaw-symm | gpaw/test/derivatives.py | Python | gpl-3.0 | 1,578 | [
"GPAW"
] | da0482b6db64fd98fd9ec719ec849b159ede4b16f06bd672be79c256be26878d |
# $HeadURL $
''' DIRAC.ResourceStatusSystem.DB package
'''
__RCSID__ = '$Id: $'
################################################################################
#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF | Sbalbp/DIRAC | ResourceStatusSystem/DB/__init__.py | Python | gpl-3.0 | 244 | [
"DIRAC"
] | 0508a0baf11f008878ee73ae764600e626a98e5e0cf94a4065c8c26e947f527c |
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
import sys
timestep = float(sys.argv[1]) * u.femtoseconds
cas = "126492-54-4"
target_length = 200 * u.nanoseconds
n_steps = int(target_length / timestep)
output_frequency = int(250 * u.femtoseconds / timestep)
barostat_frequency = i... | choderalab/LiquidBenchmark | src/test_stepsize/production_amber.py | Python | gpl-2.0 | 1,723 | [
"OpenMM"
] | 035bef6cfb426209a23c8768bdf1727a8cc77ee7525a3c5dd95fc273cf6670a4 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 F... | andrebellafronte/stoq | stoqlib/gui/editors/taxclasseditor.py | Python | gpl-2.0 | 3,401 | [
"VisIt"
] | bb55561824dd70d1d83d04df4c4db3c971b97e5dffb262c5c744ac2beae74071 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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... | caio2k/RIDE | src/robotide/lib/robot/output/console/dotted.py | Python | apache-2.0 | 3,003 | [
"VisIt"
] | a4a3828d6e5f98db446a19f85cf471aaa015bafb3f72073f5de4f0f3131aa5f1 |
# -*- coding: UTF-8 -*-
try:
import biggles # Requires biggles: http://biggles.sourceforge.net/
has_biggles = True
except ImportError:
#print("Biggles is not installed. If you wish to automatically plot some nice statistics please install it: http://biggles.sourceforge.net/")
has_biggles = False
try:
... | davidmfinol/py3NEAT | neat/visualize.py | Python | gpl-3.0 | 5,503 | [
"NEURON"
] | 1a6e4cbbf2ff5d1dd48b58b9f384ff7fb2a0e3174e4549bbef06d06dbce0885a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Cluster sequence IDs into groups of IDs whose sequences blast together.
Input file is the result file (outfmt 0) of fasta file blasted against itself.
Usage:
%program <input_file> <output_file>"""
import sys
from collections import defaultdict
from copy import de... | wkh124/wkh124 | blast_cluster_sequences.py | Python | gpl-3.0 | 1,426 | [
"BLAST"
] | ac0523e37746e0704f106475c63ae4d63d60d6859ffb0d7e4c1e42023fbc5734 |
import gc, os, sys, string, re, pdb, scipy.stats, cPickle
import Mapping2, getNewer1000GSNPAnnotations, Bowtie, binom, GetCNVAnnotations, dictmerge, utils, InBindingSite
TABLE=string.maketrans('ACGTacgt', 'TGCAtgca')
USAGE="%s mindepth snpfile readfiletmplt maptmplt bindingsites cnvfile outfile logfile ksfile"
def r... | gersteinlab/AlleleDB | alleledb_pipeline/CombineSnpCounts.py | Python | cc0-1.0 | 5,465 | [
"Bowtie"
] | 56c1339514dc7d5e16e734a7d425039890b9eb0c984cd096ce6afa6e8e4d19ac |
"""
Define some
"""
from __future__ import print_function
from builtins import range
from builtins import object
from copy import deepcopy as copy
import numpy as n
import numpy as np
import dashi as d
import pylab as p
import matplotlib.ticker
from hepbasestack.colors import get_color_palette
#from .colors import... | achim1/HErmes | HErmes/visual/plotting.py | Python | gpl-2.0 | 42,350 | [
"Gaussian"
] | 28f6ba85dd96e3badb3c23445f990894b4a112f067ce58acdafbd8449dc5cfee |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/auxiliary/__init__.py | Python | gpl-2.0 | 19,868 | [
"Gromacs",
"MDAnalysis"
] | adbd1e6d2ce6bb49f73a41cfc90aff6b38bfd0aa88c300326523c68f610bed0f |
import sys
import json
import uuid
import re
from girder.api.rest import Resource
### Convenience function to check if all keys are in a dictionary
def allIn(keyTuple, dictionary) :
return all(k in dictionary for k in keyTuple)
class RemoteConnection(Resource):
"""
API endpoint for remote connections.... | scottwittenburg/web-hpc-manager | python/girder/plugins/remoteconnections/server/__init__.py | Python | bsd-3-clause | 13,464 | [
"ParaView"
] | 8c9449156763af1d840f2d024f4cc0bece22c76fb95191df91412c6a1efa54e6 |
# Copyright (C) 2017-2018 Michael Freitag, Shahin Amiriparian, Sergey Pugachevskiy, Nicholas Cummins, Björn Schuller
#
# This file is part of auDeep.
#
# auDeep 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,... | auDeep/auDeep | audeep/cli/modify.py | Python | gpl-3.0 | 3,618 | [
"NetCDF"
] | 606f5b9fa76c0b9b3c7626ba029742fbd48637f40a162a6cf3c968225ea08c40 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Usage messages for bashplotlib system commands
"""
hist = {
"usage": """hist is a command for making histograms. it accepts a series of values in one of the following formats:
1) txt file w/ 1 column of numbers
2) standard in piped from another com... | asbjorn/bashplotlib | bashplotlib/utils/commandhelp.py | Python | mit | 951 | [
"VisIt"
] | 06af63d04330e01e9fa6518b6df60de5019db0f4f46755f0059b40631c5fee0b |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | karllessard/tensorflow | tensorflow/python/autograph/core/unsupported_features_checker.py | Python | apache-2.0 | 2,180 | [
"VisIt"
] | 15b42438ac4a00b260507dc6eb0d26da2e1a0fb32c8ebf6d603ab977d0b20a9f |
from django.test import TestCase
from .models import Molecule
import json
from rdkit.Chem import AllChem
class AddMoleculeTestCase(TestCase):
def setUp(self):
self.propane = """Molecule from ChemDoodle Web Components
http://www.ichemlabs.com
3 2 0 0 0 0 999 V2000
-0.9330 -0.2500 ... | gorgitko/bioinformatics-chemoinformatics | chemoinformatics/molecule_web_database/moldb/tests.py | Python | mit | 3,175 | [
"RDKit"
] | c2ee0beb5f4da50cb1701ba4ddc894ec2163637519972ea24448b9a0b2dc69a0 |
import types
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import Time
from DIRAC.WorkloadManagementSystem.Client.JobState.JobManifest import JobManifest
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.WorkloadManagementSystem.Service.JobPolicy import RIGHT_GET_INFO, RIGHT_RESCHEDULE
f... | sposs/DIRAC | WorkloadManagementSystem/Client/JobState/JobState.py | Python | gpl-3.0 | 19,231 | [
"DIRAC"
] | b9e91b4227a936b8d7924943baa3cf5c4586cb1db4eca2549deb7210bfaf8ec2 |
# This file is part of BenchExec, a framework for reliable benchmarking:
# https://github.com/sosy-lab/benchexec
#
# SPDX-FileCopyrightText: 2007-2020 Dirk Beyer <https://www.sosy-lab.org>
#
# SPDX-License-Identifier: Apache-2.0
import os
import benchexec.util as util
import benchexec.tools.template
import benchexec.... | dbeyer/benchexec | benchexec/tools/blast.py | Python | apache-2.0 | 2,012 | [
"BLAST"
] | a34a2ca57b5c27675f660b1af68dfcf1a8912dcb572bb649dd9c4eb3aa41b185 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Mazecreator/tensorflow | tensorflow/contrib/gan/python/eval/python/classifier_metrics_impl.py | Python | apache-2.0 | 17,492 | [
"Gaussian"
] | d725b5db622108fd5aa4cb62fd327b40386718368fd122f064639f89064ebfb7 |
# encoding: utf-8
# Copyright 2008-2011 California Institute of Technology. ALL RIGHTS
# RESERVED. U.S. Government Sponsorship acknowledged.
from setuptools import setup, find_packages
import os.path
# Package data
# ------------
_name = 'edrn.summarizer'
_version = '0.0.8'
_description = 'EDR... | EDRN/DMCCBackend | src/edrn.summarizer/setup.py | Python | apache-2.0 | 2,742 | [
"Biopython"
] | ff2dc04ed09e1c9f54a696801975c34c26ffb0d937234d63f6baca017b39fd5c |
#!/usr/bin/env python
# Copyright (c) 2012 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.
'''Exception types for GRIT.
'''
class Base(Exception):
'''A base exception that uses the class's docstring in addition to any
... | heke123/chromium-crosswalk | tools/grit/grit/exception.py | Python | bsd-3-clause | 2,972 | [
"xTB"
] | 34d257d38d18865083426a689aaf0cb5475212aa1b65864ee591a4aa988efbeb |
# Maked by Mr. Have fun! Version 0.2
# rewritten by Rolarga, Version 0.3
# Shadow Weapon Coupons contributed by BiTi for the Official L2J Datapack Project
# Visit http://forum.l2jdp.com for more details
import sys
from com.l2scoria.gameserver.model.quest import State
from com.l2scoria.gameserver.model.quest import Que... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/quests/233_TestOfWarspirit/__init__.py | Python | gpl-3.0 | 14,029 | [
"VisIt"
] | 7911474f6338d90f808a0ba79069bdb568a3c38af028febd4ab41f73a132d042 |
"""
Demonstraton of static versus dynamic histograms. Also demonstrates
taking difference between two histograms and plotting it.
@author Paul F. Kunz <Paul_Kunz@slacs.stanford.edu>
"""
import random
from time import sleep
from load_hippo import app, canvas
from hippo import Display, NTuple, NTupleController
# ... | plasmodic/hippodraw | examples/static_vs_dynamic.py | Python | gpl-2.0 | 2,891 | [
"Gaussian"
] | 75611a91c2d282c36a246326b6b63a5c19276ab2bede14a014b4b5fd5942ab51 |
import asyncio
from json.decoder import JSONDecodeError
import json
from concurrent.futures import Executor, ThreadPoolExecutor, ProcessPoolExecutor
from contextlib import contextmanager
from datetime import datetime
from enum import Enum
import io
from multiprocessing import Manager, freeze_support
import os
from path... | psf/black | src/black/__init__.py | Python | mit | 46,769 | [
"VisIt"
] | e8df80e974f57c6c1bf2057376ad54779a49fbee6437a8d1374ea3861d23ce78 |
from __future__ import division, print_function, absolute_import
from sklearn.utils.extmath import logsumexp
from sklearn.utils import check_random_state
from sklearn.base import BaseEstimator
import numpy as np
import random, collections
import scipy.sparse
# Author: Gustav Larsson
# Mark Stoehr <stoehr.mark... | amitgroup/amitgroup | amitgroup/stats/bernoullimm.py | Python | bsd-3-clause | 22,322 | [
"Gaussian"
] | 227b357a0e16d57e79433af212ffdc275a51f579a91578f603a1ce4c6aa18f7b |
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