laurentperrinet

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Remove output from existing Jupyter Notebooks.
Modified from remove_output by Minrk, damianavila, gabraganca.

References: 
    [0]: https://github.com/jupyter/nbformat
    [1]: http://nbformat.readthedocs.org/en/latest/index.html
    [2]: http://blog.jupyter.org/2015/04/15/the-big-split/

laurentperrinet

#FORMAT python
# -*- coding: UTF-8 -*-
"""

A parser to display bibtex code with a nice formatting within MoinMoin wiki pages.

The parsing is done in pure pytho, so that you will not need external programs. This 
parser script should work for MoinMoin 1.9.3.
   
   Copyright: 2012 by Laurent Perrinet -- see https://github.com/meduz/MoinMoin_BibTexParser

laurentperrinet

laurentperrinet

# ! python
# coding: utf-8

import os
import argparse
import glob

import nbformat
from nbconvert.preprocessors import ExecutePreprocessor
from nbconvert.preprocessors.execute import CellExecutionError

laurentperrinet

#!/usr/bin/env python3
"""
How can I list all existing workspaces in JupyterLab?

as answered @
https://stackoverflow.com/questions/52656747/how-can-i-list-all-existing-workspaces-in-jupyterlab/53011827#53011827
"""
import argparse

# construct the argument parse and parse the arguments

laurentperrinet

from flask import Flask, make_response, render_template
app = Flask(__name__)

@app.route("/")
def index():
    render_template("index.html")

@app.route("/simple.png")
def simple():
    import datetime

laurentperrinet

#!/usr/bin/env python3
"""
rename a bunch of files given a glob pattern and change A into B

    rename_files.py -g "**/*.pdf" -a "\\" -b "_" --dry-run
    rename_files.py -g "**/*" -a "\\" -b "_"

 """
import argparse

laurentperrinet

"""
Import your iOS paper © 53 artwork to a folder of png files

Paper is an iOS application to create doodles, created by 53 and now owned by
weTransfer :

    https://paper.bywetransfer.com/

This gist lives at:

laurentperrinet

Dear Editor,

Thank you for inviting me to review this manuscript.

Unfortunately, I cannot review for Nature journals as long as the new and enormous open-access APC fee is in place. The $11,528 now being charged is significantly above the average APC of the biggest for-profit publishers, estimated as around $2,660 (https://undark.org/2021/01/14/big-science-publisher-is-going-open-access/).

‘$11,528’ is not just a large number. It is one semester of a graduate student’s stipend, a neuroimaging study, funds for 4-6 graduate students to attend a scientific meeting. These charges take away money, often from government grants, that would otherwise be spent in important ways - for trainees and for science more broadly.

The ‘Editorial Assessment Charge’ piloted in some Nature journals is also a worrying development. Charging more than $2,000 upon submission is not only excessive, but adds barriers where none should exist.

laurentperrinet

import numpy as np

# https://en.wikipedia.org/wiki/Von_Mises_distribution
def tuning_function(theta, theta0, kappa, fmax, bsl, theta_bound):
    # Von Mises, with kappa the concentration, theta0 the location
    # fmax the firing rate at pref ori, bsl the min firing rate (not the baseline, which was substracted) 
    tf = bsl + np.exp(kappa*(np.cos(2*np.pi/theta_bound*(theta-theta0))-1)) * (fmax-bsl)
    return tf

# we will use the tutorial from https://lmfit.github.io/lmfit-py/model.html :