Command-Line#
Note, you can follow this tutorial by cloning executablebooks/jupyter-cache, and running these commands inside it.: tox
$ jcache --help
Usage: jcache [OPTIONS] COMMAND [ARGS]...
The command line interface of jupyter-cache.
Options:
-v, --version Show the version and exit.
-p, --print-path Print the current cache path and exit.
-a, --autocomplete Print the autocompletion command and exit.
-h, --help Show this message and exit.
Commands:
cache Work with cached execution(s) in a project.
notebook Work with notebook(s) in a project.
project Work with a project.
The first time the cache is required, it will be lazily created:
$ jcache notebook list
Cache path: ../.jupyter_cache
The cache does not yet exist, do you want to create it? [y/N]: y
No notebooks in project
You can specify the path to the cache, with the --cache-path option,
or set the JUPYTERCACHE environment variable.
You can also clear it at any time:
$ jcache project clear
Cache path: ../.jupyter_cache
Are you sure you want to permanently clear the cache!? [y/N]: y
Cache cleared!
$ jcache notebook list
Cache path: ../.jupyter_cache
The cache does not yet exist, do you want to create it? [y/N]: y
No notebooks in project
Tip
Execute this in the terminal for auto-completion:
eval "$(_JCACHE_COMPLETE=source jcache)"
Adding notebooks to the project#
$ jcache notebook --help
Usage: notebook [OPTIONS] COMMAND [ARGS]...
Work with notebook(s) in a project.
Options:
-p, --cache-path TEXT Path to project cache. [default: (.jupyter_cache)]
--help Show this message and exit.
Commands:
add Add notebook(s) to the project.
add-with-assets Add notebook(s) to the project, with possible asset files.
clear Remove all notebooks from the project.
execute Execute specific notebooks in the project.
info Show details of a notebook (by ID).
invalidate Remove any matching cache of the notebook(s) (by ID/URI).
list List notebooks in the project.
merge Create notebook merged with cached outputs (by ID/URI).
remove Remove notebook(s) from the project (by ID/URI).
A project consist of a set of notebooks to be executed.
When adding notebooks to the project, they are recorded by their URI (e.g. file path), i.e. no physical copying takes place until execution time.
$ jcache notebook add tests/notebooks/basic.ipynb tests/notebooks/basic_failing.ipynb tests/notebooks/basic_unrun.ipynb tests/notebooks/complex_outputs.ipynb tests/notebooks/external_output.ipynb
Adding: ../tests/notebooks/basic.ipynb
Adding: ../tests/notebooks/basic_failing.ipynb
Adding: ../tests/notebooks/basic_unrun.ipynb
Adding: ../tests/notebooks/complex_outputs.ipynb
Adding: ../tests/notebooks/external_output.ipynb
Success!
You can list the notebooks in the project, at present none have an existing execution record in the cache:
$ jcache notebook list
ID URI Reader Added Status
---- ------------------------------------- -------- ---------------- --------
1 tests/notebooks/basic.ipynb nbformat 2023-11-08 18:34 -
2 tests/notebooks/basic_failing.ipynb nbformat 2023-11-08 18:34 -
3 tests/notebooks/basic_unrun.ipynb nbformat 2023-11-08 18:34 -
4 tests/notebooks/complex_outputs.ipynb nbformat 2023-11-08 18:34 -
5 tests/notebooks/external_output.ipynb nbformat 2023-11-08 18:34 -
You can remove a notebook from the project by its URI or ID:
$ jcache notebook remove 4
Removing: 4
Success!
$ jcache notebook list
ID URI Reader Added Status
---- ------------------------------------- -------- ---------------- --------
1 tests/notebooks/basic.ipynb nbformat 2023-11-08 18:34 -
2 tests/notebooks/basic_failing.ipynb nbformat 2023-11-08 18:34 -
3 tests/notebooks/basic_unrun.ipynb nbformat 2023-11-08 18:34 -
5 tests/notebooks/external_output.ipynb nbformat 2023-11-08 18:34 -
or clear all notebooks from the project:
$ jcache notebook clear
Are you sure you want to permanently clear the project!? [y/N]: y
Project cleared!
Add a custom reader to read notebook files#
By default, notebook files are read using the nbformat reader.
However, you can also specify a custom reader, defined by an entry point in the jcache.readers group.
Included with jupyter_cache is the jupytext reader, for formats like MyST Markdown:
$ jcache notebook add --reader nbformat tests/notebooks/basic.ipynb tests/notebooks/basic_failing.ipynb
Adding: ../tests/notebooks/basic.ipynb
Adding: ../tests/notebooks/basic_failing.ipynb
Success!
$ jcache notebook add --reader jupytext tests/notebooks/basic.md
Adding: ../tests/notebooks/basic.md
Success!
$ jcache notebook list
ID URI Reader Added Status
---- ----------------------------------- -------- ---------------- --------
1 tests/notebooks/basic.ipynb nbformat 2023-11-08 18:34 -
2 tests/notebooks/basic_failing.ipynb nbformat 2023-11-08 18:34 -
3 tests/notebooks/basic.md jupytext 2023-11-08 18:34 -
Important
To use the jupytext reader, you must have the jupytext package installed.
Executing the notebooks#
Simply call the execute command, to execute all notebooks in the project that do not have an existing record in the cache.
Executors are defined by entry points in the jcache.executors group.
jupyter-cache includes these executors:
local-serial: execute notebooks with the working directory set to their path, in serial mode (using a single process).local-parallel: execute notebooks with the working directory set to their path, in parallel mode (using multiple processes).temp-serial: execute notebooks with a temporary working directory, in serial mode (using a single process).temp-parallel: execute notebooks with a temporary working directory, in parallel mode (using multiple processes).
$ jcache project execute --executor local-serial
Executing 3 notebook(s) in serial
Executing: ../tests/notebooks/basic.ipynb
Execution Successful: ../tests/notebooks/basic.ipynb
Executing: ../tests/notebooks/basic_failing.ipynb
warning: Execution Excepted: ../tests/notebooks/basic_failing.ipynb
warning: CellExecutionError: An error occurred while executing the following cell:
warning: ------------------
warning: raise Exception('oopsie!')
warning: ------------------
warning:
warning:
warning: ---------------------------------------------------------------------------
warning: Exception Traceback (most recent call last)
warning: Cell In[1], line 1
warning: ----> 1 raise Exception('oopsie!')
warning:
warning: Exception: oopsie!
Executing: ../tests/notebooks/basic.md
Execution Successful: ../tests/notebooks/basic.md
Finished! Successfully executed notebooks have been cached.
succeeded:
- ../tests/notebooks/basic.ipynb
- ../tests/notebooks/basic.md
excepted:
- ../tests/notebooks/basic_failing.ipynb
errored: []
Successfully executed notebooks will now have a record in the cache, uniquely identified by the a hash of their code and metadata content:
$ jcache cache list --hashkeys
ID Origin URI Created Accessed Hashkey
---- ------------------------ ---------------- ---------------- --------------------------------
1 tests/notebooks/basic.md 2023-11-08 18:34 2023-11-08 18:34 94c17138f782c75df59e989fffa64e3a
These records are then compared to the hashes of notebooks in the project, to find which have up-to-date executions.
Note here both notebooks share the same cached notebook (denoted by [1] in the status):
$ jcache notebook list
ID URI Reader Added Status
---- ----------------------------------- -------- ---------------- --------
1 tests/notebooks/basic.ipynb nbformat 2023-11-08 18:34 ✅ [1]
2 tests/notebooks/basic_failing.ipynb nbformat 2023-11-08 18:34 ❌
3 tests/notebooks/basic.md jupytext 2023-11-08 18:34 ✅ [1]
Next time you execute the project, only notebooks which don’t match a cached record will be executed:
$ jcache project execute --executor local-serial -v CRITICAL
Finished! Successfully executed notebooks have been cached.
succeeded: []
excepted:
- ../tests/notebooks/basic_failing.ipynb
errored: []
You can also force all notebooks to be re-executed:
$ jcache project execute --force
Executing 3 notebook(s) in serial
Executing: ../tests/notebooks/basic.ipynb
Execution Successful: ../tests/notebooks/basic.ipynb
Executing: ../tests/notebooks/basic_failing.ipynb
warning: Execution Excepted: ../tests/notebooks/basic_failing.ipynb
warning: CellExecutionError: An error occurred while executing the following cell:
warning: ------------------
warning: raise Exception('oopsie!')
warning: ------------------
warning:
warning:
warning: ---------------------------------------------------------------------------
warning: Exception Traceback (most recent call last)
warning: Cell In[1], line 1
warning: ----> 1 raise Exception('oopsie!')
warning:
warning: Exception: oopsie!
Executing: ../tests/notebooks/basic.md
Execution Successful: ../tests/notebooks/basic.md
Finished! Successfully executed notebooks have been cached.
succeeded:
- ../tests/notebooks/basic.ipynb
- ../tests/notebooks/basic.md
excepted:
- ../tests/notebooks/basic_failing.ipynb
errored: []
If you modify a code cell, the notebook will no longer match a cached notebook or, if you wish to re-execute unchanged notebook(s) (for example if the runtime environment has changed), you can remove their records from the cache (keeping the project record):
$ jcache cache clear
Are you sure you want to permanently clear the cache!? [y/N]: n
Aborted!
Note
The number of notebooks in the cache is limited
(current default 1000).
Once this limit is reached, the oldest (last accessed) notebooks begin to be deleted.
change this default with jcache config cache-limit
Analysing executed/excepted notebooks#
You can see the elapsed execution time of a notebook via its ID in the cache:
$ jcache cache info 1
ID: 1
Origin URI: ../tests/notebooks/basic.md
Created: 2023-11-08 18:34
Accessed: 2023-11-08 18:34
Hashkey: 94c17138f782c75df59e989fffa64e3a
Data:
execution_seconds: 1.0625380310002583
Failed execution tracebacks are also available on the project record:
$ jcache notebook info --tb tests/notebooks/basic_failing.ipynb
ID: 2
URI: ../tests/notebooks/basic_failing.ipynb
Reader:
name: nbformat
type: plugin
Added: 2023-11-08 18:34
Status: ❌
Failed Last Execution!
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/jupyter-cache/envs/latest/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
executenb(
File "/home/docs/checkouts/readthedocs.org/user_builds/jupyter-cache/envs/latest/lib/python3.11/site-packages/nbclient/client.py", line 1314, in execute
return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/docs/checkouts/readthedocs.org/user_builds/jupyter-cache/envs/latest/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 173, in wrapped
return loop.run_until_complete(inner)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/docs/.asdf/installs/python/3.11.6/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
return future.result()
^^^^^^^^^^^^^^^
File "/home/docs/checkouts/readthedocs.org/user_builds/jupyter-cache/envs/latest/lib/python3.11/site-packages/nbclient/client.py", line 709, in async_execute
await self.async_execute_cell(
File "/home/docs/checkouts/readthedocs.org/user_builds/jupyter-cache/envs/latest/lib/python3.11/site-packages/nbclient/client.py", line 1062, in async_execute_cell
await self._check_raise_for_error(cell, cell_index, exec_reply)
File "/home/docs/checkouts/readthedocs.org/user_builds/jupyter-cache/envs/latest/lib/python3.11/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
raise Exception('oopsie!')
------------------
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
Cell In[1], line 1
----> 1 raise Exception('oopsie!')
Exception: oopsie!
Tip
Code cells can be tagged with raises-exception to let the executor known that a cell may raise an exception
(see this issue on its behaviour).
Retrieving executed notebooks#
Notebooks added to the project are not modified in any way during or after execution:
You can create a new “final” notebook, with the cached outputs merged into the source notebook with:
$ jcache notebook merge tests/notebooks/basic.md final_notebook.ipynb
Merged with cache PK 1
Success!
Invalidating cached notebooks#
If you want to invalidate a notebook’s cached execution,
for example if you have changed the notebook’s execution environment,
you can do so by calling the invalidate command:
$ jcache notebook invalidate tests/notebooks/basic.ipynb
Invalidating: tests/notebooks/basic.ipynb
Success!
$ jcache notebook list
ID URI Reader Added Status
---- ----------------------------------- -------- ---------------- --------
1 tests/notebooks/basic.ipynb nbformat 2023-11-08 18:34 -
2 tests/notebooks/basic_failing.ipynb nbformat 2023-11-08 18:34 ❌
3 tests/notebooks/basic.md jupytext 2023-11-08 18:34 -
Specifying notebooks with assets#
When executing in a temporary directory, you may want to specify additional “asset” files that also need to be be copied to this directory for the notebook to run.
$ jcache notebook remove tests/notebooks/basic.ipynb
Removing: tests/notebooks/basic.ipynb
Success!
$ jcache notebook add-with-assets -nb tests/notebooks/basic.ipynb tests/notebooks/artifact_folder/artifact.txt
Success!
$ jcache notebook info tests/notebooks/basic.ipynb
ID: 4
URI: ../tests/notebooks/basic.ipynb
Reader:
name: nbformat
type: plugin
Added: 2023-11-08 18:34
Status: '-'
Assets:
- ../tests/notebooks/artifact_folder/artifact.txt
Adding notebooks directly to the cache#
Pre-executed notebooks can be added to the cache directly, without executing them.
A check will be made that the notebooks look to have been executed correctly, i.e. the cell execution counts go sequentially up from 1.
$ jcache cache add tests/notebooks/complex_outputs.ipynb
Caching: ../tests/notebooks/complex_outputs.ipynb
Validity Error: Expected cell 0 to have execution_count 1 not None
The notebook may not have been executed, continue caching? [y/N]: y
Success!
Or to skip the validation:
$ jcache cache add --no-validate tests/notebooks/external_output.ipynb
Caching: ../tests/notebooks/external_output.ipynb
Success!
$ jcache cache list
ID Origin URI Created Accessed
---- ------------------------------------- ---------------- ----------------
2 tests/notebooks/external_output.ipynb 2023-11-08 18:34 2023-11-08 18:34
1 tests/notebooks/complex_outputs.ipynb 2023-11-08 18:34 2023-11-08 18:34
Tip
To only show the latest versions of cached notebooks.
$ jcache cache list --latest-only
Diffing notebooks#
You can diff any of the cached notebooks with any (external) notebook:
Warning
This requires pip install nbdime
$ jcache cache diff 1 tests/notebooks/basic_unrun.ipynb
nbdiff
--- cached pk=1
+++ other: ../tests/notebooks/basic_unrun.ipynb
## inserted before nb/cells/0:
+ code cell:
+ source:
+ a=1
+ print(a)
## deleted nb/cells/0-6:
- code cell:
- metadata (unknown keys):
- init_cell: True
- slideshow:
- slide_type: skip
- source:
- from ipypublish.scripts.ipynb_latex_setup import *
- code cell:
- execution_count: 3
- metadata (unknown keys):
- ipub:
- text:
- format:
- backgroundcolor: \color{blue!10}
- source:
- print("""
- This is some printed text,
- with a nicely formatted output.
- """)
- outputs:
- output 0:
- output_type: stream
- name: stdout
- text:
-
- This is some printed text,
- with a nicely formatted output.
-
- code cell:
- execution_count: 3
- metadata (unknown keys):
- ipub:
- figure:
- caption: A nice picture.
- label: fig:example
- placement: !bh
- source:
- Image('example.jpg',height=400)
- outputs:
- output 0:
- output_type: execute_result
- execution_count: 3
- data:
- image/jpeg: /9j/4RB6...<snip base64, md5=b3f071e0466de0eb...>
- text/plain: <IPython.core.display.Image object>
- metadata (unknown keys):
- image/jpeg:
- height: 400
- code cell:
- execution_count: 9
- metadata (unknown keys):
- ipub:
- code:
- asfloat: True
- caption: a
- label: code:example_mpl
- widefigure: False
- figure:
- caption:
- label: fig:example_mpl
- widefigure: False
- source:
- plt.scatter(np.random.rand(10), np.random.rand(10),
- label='data label')
- plt.ylabel(r'a y label with latex $\alpha$')
- plt.legend();
- outputs:
- output 0:
- output_type: display_data
- data:
- application/pdf: JVBERi0x...<snip base64, md5=e244f7ca0e270cb0...>
- image/svg+xml:
- <?xml version="1.0" encoding="utf-8" standalone="no"?>
- <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
- "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
- <!-- Created with matplotlib (http://matplotlib.org/) -->
- <svg height="258pt" version="1.1" viewBox="0 0 455 258" width="455pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
- <defs>
- <style type="text/css">
- *{stroke-linecap:butt;stroke-linejoin:round;}
- </style>
- </defs>
- <g id="figure_1">
- <g id="patch_1">
- <path d="M 0 258.561146
- L 455.384887 258.561146
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- </g>
- <g id="axes_1">
- <g id="patch_2">
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- <g id="PathCollection_1">
- <defs>
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Success!