Run and debug Jupyter notebook code cells
Code fragments in a Jupyter notebook file are structured as executable cells. Each cell is marked with the
#%% comment and can be executed independently by clicking the icon in the gutter. To execute all cells at once, click on the Jupyter toolbar.
Run code cells
For the target cell press Ctrl+Enter. Alternatively, you can click the icon and select Run Cell. PyCharm launches the Jupyter server, executes the code cell, and renders the output in the Preview pane.
When executing one cell at a time, mind code dependencies. For example, the second cell in the code fragment uses the variables defined in the first cell. So, if you modify the
Nvalue, the changes will be reflected in the scatter chart only after the first cell gets executed. You can use smart shortcuts to execute the current cell and select the below one: Shift+Enter.
To execute all code cells in your notebook, click on the Jupyter notebook toolbar or press Ctrl+Shift+Alt+Enter. To run all code cells above the current cell and handle possible code dependencies, click on the Jupyter toolbar and select the Run All Above command from the quick list.
When you execute a cell, the Variables tab of the Jupyter server tool window opens automatically.
By default, variables are loaded asynchronously. To change the loading policy, click in the Variables tab, select Variables Loading Policy, and select one of the available modes. See Managing Variables Loading Policy for more details.
You can click the link to the right of the variable to preview its values in the tabular form:
Note that Variables tab will appear each time you execute a cell, so if, by some reasons, you need to close it permanently, deselect the corresponding option in the project settings ( ).
In addition to previewing values of the variables in the Variables tab, you can watch the values of the variable usages in the editor. Note that variable assignments are not shown.
This option is enabled by default. To disable it, deselect the Show Inline Values in the Editor checkbox in the project settings ( ).
When you work with a substantial number of code cells, you can effectively navigate between the Editor and Preview panes by using auto scrolling.
Jump to the target output fragment or target code cell
Enable auto scrolling from the source by clicking the icon, then select a code cell in the Editor pane. You will be positioned on the target output fragment in the Preview pane.
Enable auto scrolling to the source code by clicking the icon on the Jupyter toolbar, then select an arbitrary output fragment in the Preview pane. You'll be positioned on the source code cell in the Editor pane.
PyCharm provides the full-functional Jupyter Notebook Debugger.
Debug code in Jupyter notebook
Set the breakpoints in the selected cell and press Shift+Alt+Enter for Windows or ⌥⇧↩ for macOS. Alternatively, you can click the icon, and select Debug Cell.
The Jupyter Notebook Debugger tool window opens.
Use the stepping toolbar buttons to choose on which line you want to stop next and switch to the Debugger tab to preview the variable values:
Debugging is performed within a single code cell. However, if your code cell calls a function from any cell that has been already debugged, you can step into it. The related breakpoints will also work. Note that the cell with the function must be debugged not just executed.
Similarly, you can step into a function called from a Python file that is located in the same project.
Proceed with the debugging steps to complete the execution of the cell.
Clear the notebook output
To erase the execution output in the Preview area, click on the Jupyter notebook toolbar and select the command from the quick list. Evaluate the results in the Preview area.
With PyCharm you can always quickly preview reference documentation for a particular variable, type, or argument.
Preview reference documentation
To view reference information for any element of a particular code cell, place the caret within the target code cell and type
? <type/variable/argument>. (in this example, you will preview documentation for
plt.scatter). Note that a code element should be accessible within the code cell.
Execute the cell. The Introspection tab opens in the Jupyter tool window.
Preview reference documentation in the Introspection tab.
Note that the Introspection tab shows documentation for the latest requested code element. Even though you proceed with executing other code cells, restart the server, or delete the line with your request, this information will be shown.