John Kitchin

Connecting to kernel in a Docker image

8

I tried following the clues at https://github.com/emacs-jupyter/jupyter/issues/61, but I did not succeed. First, I ran: ``` #+BEGIN_SRC sh docker pull jupyter/base-notebook docker run --rm --name test -p 56406-56410:56406-56410 \ jupyter/base-notebook...

Create a kernel with specified custom ports

6

I am trying to start a jupyter kernel like this: ``` jupyter-kernel \ --ip=0.0.0.0 \ --KernelManager.control_port=56406 \ --KernelManager.hb_port=56407 \ --KernelManager.iopub_port=56408 \ --KernelManager.shell_port=56409 \ --KernelManager.stdin_port=56410 ``` It starts, and I see...

In this code: ``` #+BEGIN_SRC bibtex :tangle test.bib @article{kitchin-2015-examp, author = {Kitchin, John R.}, title = {Examples of Effective Data Sharing in Scientific Publishing}, journal = {ACS Catalysis}, volume =...

This line `params = gryffin.recommend(observations=observations)[0]` eventually fails with `AttributeError: module 'numpy' has no attribute 'float'` The issue is np.float was deprecated, and removed (https://numpy.org/devdocs/release/1.24.0-notes.html#expired-deprecations). It works fine with numpy 1.23.5....

I am moderately sure that Python 3.10 breaks the install. With This Dockerfile the install works fine: ``` FROM jupyter/scipy-notebook:python-3.9 RUN pip install gryffin ``` But with this one, it...

or syntax for a filter?

11

Is it possible to write a filter that shows entries tagged important or relevant? Or perhaps filter on some truthy function?

it is deprecated and not in Python3

It would be nice to be able to recover constraints, energy, forces, stress, and convergence from the json serialized calculator.

In increasing number of species? In increasing atomic number? In alphabetical order?