saturn-notebook 1.2.2

Plain-text Python notebooks with checkpointing

Saturn

Screenshots

Features

• Plain-text format. Notebooks are regular Python files. Different types of cells are comments with special formatting. Markdown rendering and syntax highlighting in the terminal thanks to rich.

• Checkpoints. Special checkpoint cells allow to save the state of the session or individual variables.

• Terminal graphics support. When using kitty terminal (or in principle anything that supports its graphics protocol) matplotlib figures are rendered inline in the terminal.

• MPI awareness. When running under MPI, only rank 0 will write out the modified notebook. The REPL will take input on rank 0 and broadcast to other ranks. It's also possible to suppress output from all ranks other than 0.

• Ability to convert from Jupyter to Saturn notebooks. This also allows to view Jupyter notebooks in the terminal.

Installation

pip install saturn-notebook

Commands and options

• saturn show notebook.py

  Display the notebook in the terminal. No computation is performed. Optional --html OUTPUT.html flag will produce HTML output. Use -k, --katex flag to embed KaTeX header into the HTML.

  saturn show notebook.py --html notebook.html -k

• saturn run [notebook.py [output.py]]

  Execute a Python notebook, either modifying it in place, or saving the result into a new notebook output.py. If no input notebook.py is provided, drop into REPL (-i is implied). When leaving, the REPL will ask whether to save the resulting notebook.

  • -c, --clean: run from scratch, ignoring the checkpoints.
  • -a, --auto-capture: automatically capture matplotlib figures, without show().
  • -i, --interactive: drop into REPL (using ptpython) after all the cells are processed; the results of the REPL interaction will be added to the notebook.
  • --no-mpi: disable MPI awareness.
  • -n, --dry-run: don't save the result.
  • --only-root-output: under MPI, suppress output from all ranks other than 0.
  • -e, --external notebook.zip: use external zip archive notebook.zip to store binary content (instead of embedding it inline).

  Any arguments passed after -- will be passed as sys.argv to the notebook.

  saturn run notebook.py -- arguments --to notebook

• saturn clean notebook.py [output.py]

  Remove all binary data from the notebook. Useful for getting rid of large checkpoints.

• saturn image notebook.py [i out.png]

  Save i-th image from notebook.py into out.png. If the last two arguments are omitted, show all the images in the notebook together with their indices.

• saturn version

  Show version of saturn and its dependencies.

• saturn convert notebook.ipynb [notebook.py]

  Convert a Jupyter notebook into a Saturn notebook. If the output name notebook.py is missing, only show the Jupyter notebook. Optional --html OUTPUT.html flag will produce HTML output.

• saturn extract notebook.py notebook.zip

  Extract inline binary content into external archive.

• saturn embed notebook.py notebook.zip

  Embed binary content from external archive into the notebook.

Cell types

• Markdown cells, prefix #m>

  #m> # Sample notebook
  #m>
  #m> Description using markdown **formatting**.
  

• Output cells #o>

  There is not usually a reason to modify these by hand, they are filled by Saturn with the output of code cells. If they contain PNG information, it's base64-encoded and wrapped in {{{ and }}} to allow automatic folding.

  #o> <matplotlib.image.AxesImage object at 0x114217550>
  #o> png{{{
  #o> pngiVBORw0KGgoAAAANSUhEUgAAA8AAAAHgCAYAAABq5QSEAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAP
  ...
  #o> pngGAAAgBQEMAAAACkIYAAAAFL4v5JTyvRQ4v1eAAAAAElFTkSuQmCC
  #o> png}}}
  

  In Vim with foldmethod=marker:

  #o> <matplotlib.image.AxesImage object at 0x114217550>
  +--135 lines: o> png--------------------------------------------------
  

• Checkpoint cells #chk>

  These indicate locations, where the code should checkpoint. Checkpointing serializes the session, which is stored base64-encoded in the same cell. The cell also stores the hash of the previous code blocks, and the checkpoint is valid if the prior code blocks haven't changed. By default saturn will resume from the last valid checkpoint. Same folding markers ({{{ and }}}) are used.

  #chk>{{{
  #chk>gANDIJZCQePiVH9SX7wVtBfgrDpcgWu5HUFFiFEeyNF9sVjFcQB9cQEoWAwAAABfX2J1aWx0aW5zX19x
  ...
  #chk>wAyP55wdmz+qIkdBjBrYP3EjdHEkYnWGcSUu
  #chk>}}}
  

  In Vim with foldmethod=marker:

  +-- 36 lines: chk>----------------------------------------------------
  

• Variable cells #var> x,y,z

  These cells save only the value of the specified variables (which is useful if the full checkpoint is too big). If all the previous code cells haven't changed, the cell's saved content is loaded into the specified variables and the previous code cell is not evaluated.

• Break cells #---#

  These are used to break code cells that don't have any other type of a cell between them.

• REPL cells #-REPL-#

  These instruct Saturn to drop into an interactive REPL loop, just like the -i option. All the cells from the REPL will be inserted after this cell in the notebook. Afterwards, execution proceeds as normal.

• Code cells

  All contiguous lines, not marked as one of the above, are grouped together into code cells.

• Non-skippable code cells #no-skip#

  Adding this line anywhere within the code cell will indicate that it shouldn't be skipped, even if we are restarting from a checkpoint. This is useful, for example, if a cell is modifying sys.path, which won't be captured in a checkpoint.

• Non-hashable code cells #no-hash#

  Adding this line anywhere within the code cell will indicate that it shouldn't be hashed, meaning that changing this cell (or removing it entirely) won't invalidate the checkpoints below. This should be used only with cells that don't change any variables, e.g., purely output or plotting cells.

• Saturn cells #saturn> external=out.zip

  These provide metadata. For now, the only option is to provide the name of the external zip archive to store the binary content.

Vim support

All the binary (non-human-readable) cell content is wrapped in {{{, }}} markers. Adding the following comment to the notebook, ensures that Vim starts with all the binary content folded away.

# vim: foldmethod=marker foldlevel=0

It's also helpful to have Vim recognize the #m> prefix to correctly re-format markdown cells with the gq command. This can be done, for example, by adding the following to ~/.vim/after/ftplugin/python.vim:

setlocal comments=b:#,fb:-,b:#m>

REPL

REPL supports the following keyboard shortcuts:

• Ctrl-d: exits the REPL.
• Ctrl-k: inserts a checkpoint cell. Equivalent to typing in #chk> manually.
• Ctrl-w: exits the REPL and doesn't drop into REPL, even if there are more REPL cells or -i is provided on the command line.
• Ctrl-q: exits the REPL and terminates execution of the entire notebook.
• F10: aborts execution of the entire notebook and doesn't save it out, even if we are not in --dry-run mode.

Screenshots

Running samples/simple.py:

• First run performs full computation and saves the checkpoint, as well as the figure output.

• Second run resumes from the checkpoint, since no code before it has changed.

• Vim folds the binary content.