Introduction

The Python IDE Spyder has a plugin called Spyder notebook. Spyder notebook is a plugin that allows you to edit Jupyter Notebook within Spyder. Not limited to editing Notebooks, by connecting to the Spyder console, you can execute methods described in Jupyter Notebooks, check / rewrite variables, and check variables with the Variable Explorer. I would like to use Jupytext to save Jupyter Notebooks in py file format, but at the moment (2020/7 / In 19), when Jupytext is enabled on Spyder Notebook, an error occurs and saving / updating cannot be performed properly. [It is taken up in Issue] of Spyder notebook [https://github.com/spyder-ide/spyder-notebook/issues/272), and I think that it will be supported in the future.

In this article, I will post as a memorandum how to avoid the above error in the current environment. I think that it will be supported by the main body eventually, so I think that this article will be useless.

Purpose of this article

With Jupytext enabled, connect the Jupyter Notebook kernel to the Spyder console and enable Variable Explorer.

Confirmed environment

OS: Windows 10 Pro 64bit 2004
Python: 3.7.3
Spyder: 4.1.3, 4.1.4
Spyder notebook: 0.1.4.dev1
Jupyter: 1.0.0
Jupytext: 1.5.1

procedure

1. Open the Notebook you want to edit in Spyder Notebook

1) Open the Notebook pane.

Normally, when Spyder notebook is installed, the Notebook tab is automatically added next to the editor tab of Spyder. If the tab is not displayed, you may be able to display it with "Toolbar> View> Pane> Notebook". If it does not exist in the toolbar menu, the installation may not have been successful.

2a) When opening an existing Notebook for editing

Follow the steps below to open the Notebook.

Right-click on a blank area of Notebook → select Open ... Alternatively, select Open ... from the hamburger menu at the top right of the pane.
Select and open the ipynb file in the file selection dialog

2b) When editing with a new Notebook

Save ʻUntitled0.ipynb`, which is open in the initial state, to any location by following the procedure below.

Right-click on the blank area of ʻUntitled0.ipynb` → select Save as ... Alternatively, select Save as ... from the hamburger menu at the top right of the pane.
Specify the save destination of the file in the file selection dialog and save it.

2. Jupytext settings

(Settings when using Jupytext for the first time, unnecessary if already set)

1) Enable file saving in percent format

Check "File> Jupytext> Pair Notebook with percent Script" in Spyder Notebook to enable file saving in percentage format.

When you save, a .py file with the same file name as .ipynb is created in the same folder.

--Example - test_spyder_notebook.ipynb - test_spyder_notebook.py

3. Check the URL of Spyder Notebook

1) Check the running Jupyter Notebook server

ʻStart Anaconda prompt` and enter the following command to check the currently running Jupyter Notebook server.

`Anaconda-prompt`


jupyter notebook list

When the command is executed, the output will be as follows.

`Output example`


Currently running servers:
http://localhost:8888/?token=52a00d3ac13d903245ea6a85611667c45f19ea7d902d6e3d :: C:\Users\<user name>
http://localhost:8889/?token=d1e551f8c2627bccfd18f9e56a08035c800cd4ccb7f4097b :: C:\test

2) Open Notebook in your browser

The URL where the initial directory displayed at the end of each URL line and the directory where the Notebook is saved is the same (the second line in the example) is the URL of the Notebook server currently open in Spyder notebook. Copy all the URLs up to the token and open it in your browser.

3) Check Notebook

Check if the target Notebook (eg test_spyder_notebook.ipynb) exists in the list of Jupyter Notebooks on your browser. If the target Notebook cannot be confirmed, the URL may be incorrect. In that case, select another URL from the URL list confirmed on the console and check it again on the browser.

4) Close the Notebook on the Spyder Notebook

After confirming the target Notebook, ** close the Notebook on Spyder Notebook **. (The default screen of Spyder Notebook is just displayed.)

4. Open the percent format py file in Jupyter Notebook

1) Open the .py file in a Jupyter Notebook on your browser

--Supplement --When you open the .py file, the status will be Running and the file name will be green. --The .ipynb file should be grayed out because you closed it on spyder earlier.

5. Connect the Jupyter Notebook kernel to the Spyder console

1) Connect to an existing kernel

From the Spyder console hamburger menu, select Connect to Existing Kernel.

When the dialog opens, click the "View" button of the connection information file.

A file selection dialog opens. Sort the files in order of modification date and select the JSON file with the latest update date.

--Supplement --This JSON file is the kernel connection information of the test_spyder_notebook.py file that you just opened in Jupyter Notebook. --The default connection information file (json file) is saved in C: \ Users \ <user name> \ AppData \ Roaming \ jupyter \ runtime.

`Contents of json file (example)`


{
  "shell_port": 49552,
  "iopub_port": 49553,
  "stdin_port": 49554,
  "control_port": 49555,
  "hb_port": 49556,
  "ip": "127.0.0.1",
  "key": "591c2e22-fc725f42989c69108b68f974",
  "transport": "tcp",
  "signature_scheme": "hmac-sha256",
  "kernel_name": ""
}

Do not change anything else and press OK to close the dialog.

2) State after connection

You can see that the console has been added. (Here, the console name is "Console 2 / A") If you edited the Notebook before connecting to the console, the Variable Explorer will display the variables.

6. Execution example

1) Input to Jupyter Notebook

You can use it as usual.

2) Check the variable explorer

Because the contents of Jupyter Notebook are not reflected in real time In the initial state, no variables are displayed in the variable explorer.

In this state, if you press the Enter key while leaving a blank line on the Spyder console, the changes will be reflected.

Once the changes are reflected, you will be able to see the variables in the Variable Explorer, just as you would normally use in Spyder.

Example: df_iris

3) Editing py files on Spyder

Since Jupytext is used, the execution contents on Jupyter Notebook are saved in the py file at any time. Since the py file is a script file, it can be opened and edited with Spyder's editor.

important point

If there is a change on the Jupyter Notebook, the Spyder editor will automatically reload the py file, but if you change the py file on the Spyder editor, the Jupyter Notebook will not automatically reload it. If you want to reflect the changes made on the Spyder editor in the Jupyter Notebook, you need to reload the Jupyter Notebook page with the F5 key. (It seems that it can be handled by setting, but I do not know.)

Connect the Jupyter Notebook kernel to Spyder with Jupytext enabled