3. Plotting and Debugging

Plotting

For Errors & debugging it is necessary to visualize the graph-operation. You may plot any plottable and annotate on top the execution plan and solution of the last computation, calling methods with arguments like this:

pipeline.plot(True)                   # open a matplotlib window
pipeline.plot("pipeline.svg")            # other supported formats: png, jpg, pdf, ...
pipeline.plot()                       # without arguments return a pydot.DOT object
pipeline.plot(solution=solution)      # annotate graph with solution values
solution.plot()                    # plot solution only

… or for the last …:

solution.plot(...)
execution plan
Graphtik Legend

The legend for all graphtik diagrams, generated by legend().

The same Plottable.plot() method applies also for:

each one capable to producing diagrams with increasing complexity.

For instance, when a pipeline has just been composed, plotting it will come out bare bone, with just the 2 types of nodes (data & operations), their dependencies, and (optionally, if plot theme include_steps is true) the sequence of the execution-steps of the plan.

barebone graph

But as soon as you run it, the net plot calls will print more of the internals. Internally it delegates to ExecutionPlan.plot() of the plan. attribute, which caches the last run to facilitate debugging. If you want the bare-bone diagram, plot the network:

pipeline.net.plot(...)

If you want all details, plot the solution:

solution.net.plot(...)

Note

For plots, Graphviz program must be in your PATH, and pydot & matplotlib python packages installed. You may install both when installing graphtik with its plot extras:

pip install graphtik[plot]

Tip

A description of the similar API to pydot.Dot instance returned by plot() methods is here: https://pydotplus.readthedocs.io/reference.html#pydotplus.graphviz.Dot

Jupyter notebooks

The pydot.Dot instances returned by Plottable.plot() are rendered directly in Jupyter/IPython notebooks as SVG images.

You may increase the height of the SVG cell output with something like this:

pipeline.plot(jupyter_render={"svg_element_styles": "height: 600px; width: 100%"})

See default_jupyter_render for those defaults and recommendations.

Plot customizations

Rendering of plots is performed by the active plotter (class plot.Plotter). All Graphviz styling attributes are controlled by the active plot theme, which is the plot.Theme instance installed in its Plotter.default_theme attribute.

The following style expansion\s apply in the attribute-values of Theme instances:

  • Resolve any Ref instances, first against the current nx_attrs and then against the attributes of the current theme.

  • Render jinja2 templates (see _expand_styles()) with template-arguments all the attributes of the plot_args instance in use (hence much more flexible than Ref).

  • Call any callables with current plot_args and replace them by their result (even more flexible than templates).

  • Any Nones results above are discarded.

  • Workaround pydot/pydot#228 pydot-cstor not supporting styles-as-lists.

You may customize the theme and/or plotter behavior with various strategies, ordered by breadth of the effects (most broadly effecting method at the top):

  1. (zeroth, because it is discouraged!)

    Modify in-place Theme class attributes, and monkeypatch Plotter methods.

    This is the most invasive method, affecting all past and future plotter instances, and future only(!) themes used during a Python session.

Attention

It is recommended to use other means for Plot customizations instead of modifying directly theme’s class-attributes.

All Theme class-attributes are deep-copied when constructing new instances, to avoid modifications by mistake, while attempting to update instance-attributes instead (hint: allmost all its attributes are containers i.e. dicts). Therefore any class-attributes modification will be ignored, until a new Theme instance from the patched class is used .

  1. Modify the default_theme attribute of the default active plotter, like that:

    get_active_plotter().default_theme.kw_op["fillcolor"] = "purple"
    

    This will affect all Plottable.plot() calls for a Python session.

  2. Create a new Plotter with customized Plotter.default_theme, or clone and customize the theme of an existing plotter by the use of its Plotter.with_styles() method, and make that the new active plotter.

    • This will affect all calls in context.

    • If customizing theme constants is not enough, you may subclass and install a new Plotter class in context.

  3. Pass theme or plotter arguments when calling Plottable.plot():

    pipeline.plot(plotter=Plotter(kw_legend=None))
    pipeline.plot(theme=Theme(include_steps=True)
    

    You may clone and customize an existing plotter, to preserve any pre-existing customizations:

    active_plotter = get_active_plotter()
    pipeline.plot(theme={"include_steps": True})
    

    … OR:

    pipeline.plot(plotter=active_plotter.with_styles(kw_legend=None))
    

    You may create a new class to override Plotter’s methods that way.

    Hint

    This project dogfoods (3) in its own docs/source/conf.py sphinx file. In particular, it configures the base-url of operation node links (by default, nodes do not link to any url):

    ## Plot graphtik SVGs with links to docs.
    #
    def _make_py_item_url(fn):
       if not inspect.isbuiltin(fn):
          fn_name = base.func_name(fn, None, mod=1, fqdn=1, human=0)
          if fn_name:
                return f"../reference.html#{fn_name}"
    
    
    plotter = plot.get_active_plotter()
    plot.set_active_plotter(
       plot.get_active_plotter().with_styles(
          kw_op_label={
                **plotter.default_theme.kw_op_label,
                "op_url": lambda plot_args: _make_py_item_url(plot_args.nx_item),
                "fn_url": lambda plot_args: _make_py_item_url(plot_args.nx_item.fn),
          }
       )
    )
    

Sphinx-generated sites

This library contains a new Sphinx extension (adapted from the sphinx.ext.doctest) that can render plottables in sites from python code in “doctests”.

To enabled it, append module graphtik.sphinxext as a string in you docs/conf.py : extensions list, and then intersperse the graphtik or graphtik-output directives with regular doctest-code to embed graph-plots into the site; you may refer to those plotted graphs with the graphtik role referring to their :name: option(see Examples below).

Hint

Note that Sphinx is not doctesting the actual python modules, unless the plotting code has ended up, somehow, in the site (e.g. through some autodoc directive). Contrary to pytest and doctest standard module, the module’s globals are not imported (until sphinx#6590 is resolved), so you may need to import it in your doctests, like this:


Unfortunately, you cannot use relative import, and have to write your module’s full name.

Directives

.. graphtik::

Renders a figure with a graphtik plots from doctest code.

It supports:

  • all configurations from sphinx.ext.doctest sphinx-extension, plus those described below, in Configurations.

  • all options from ‘doctest’ directive,

    • hide

    • options

    • pyversion

    • skipif

  • these options from image directive, except target (plot elements may already link to URLs):

    • height

    • width

    • scale

    • class

    • alt

  • these options from figure directive:

    • name

    • align

    • figwidth

    • figclass

  • and the following new options:

    • graphvar

    • graph-format

    • caption

Specifically the “interesting” options are these:

:graphvar: (string, optional) varname (`str`)

the variable name containing what to render, which it can be:

If missing, it renders the last variable in the doctest code assigned with the above types.

Attention

If no :graphvar: is given and the doctest code fails, it will still render any plottable created from code that has run previously, without any warnings!

:graph-format: png | svg | svgz | pdf | `None` (choice, default: `None`)
if None, format decided according to active builder, roughly:
  • “html”-like: svg

  • “latex”: pdf

Note that SVGs support zooming, tooltips & URL links, while PNGs support image maps for linkable areas.

:zoomable: <empty>, (true, 1, yes, on) | (false, 0, no, off) (`bool`)

Enable/disable interactive pan+zoom of SVGs; if missing/empty, graphtik_zoomable assumed.

:zoomable-opts: <empty>, (true, 1, yes, on) | (false, 0, no, off) (`str`)

A JS-object with the options for the interactive zoom+pan pf SVGs. If missing, graphtik_zoomable_options assumed. Specify {} explicitly to force library’s default options.

:name: link target id (`str`)

Make this pipeline a hyperlink target identified by this name. If :name: given and no :caption: given, one is created out of this, to act as a permalink.

:caption: figure's caption (`str`)

Text to put underneath the pipeline.

:alt: (`str`)

If not given, derived from string representation of the pipeline.

.. graphtik-output::

Like graphtik, but works like doctest’s testoutput directive.

:graphtik:

An interpreted text role to refer to graphs plotted by graphtik or graphtik-output directives by their :name: option.

Configurations

graphtik_default_graph_format
  • type: Union[str, None]

  • default: None

The file extension of the generated plot images (without the leading dot .`), used when no :graph-format: option is given in a graphtik or graphtik-output directive.

If None, the format is chosen from graphtik_graph_formats_by_builder configuration.

graphtik_graph_formats_by_builder
  • type: Map[str, str]

  • default: check the sources

a dictionary defining which plot image formats to choose, depending on the active builder.

  • Keys are regexes matching the name of the active builder;

  • values are strings from the supported formats for pydot library, e.g. png (see supported_plot_formats()).

If a builder does not match to any key, and no format given in the directive, no graphtik plot is rendered; so by default, it only generates plots for html & latex.

Warning

Latex is probably not working :-(

graphtik_zoomable_svg
  • type: bool

  • default: True

Whether to render SVGs with the zoom-and-pan javascript library, unless the :zoomable: directive-option is given (and not empty).

Attention

Zoom-and-pan does not work in Sphinx sites for Chrome locally - serve the HTML files through some HTTP server, e.g. launch this command to view the site of this project:

python -m http.server 8080 --directory build/sphinx/html/
graphtik_zoomable_options
  • type: str

  • default: {controlIconsEnabled: true, zoomScaleSensitivity: 0.4, fit: true}

A JS-object with the options for the interactive zoom+pan pf SVGs, when the :zoomable-opts: directive option is missing. If empty, {} assumed (library’s default options).

graphtik_plot_keywords
  • type: dict

  • default: {}

Arguments or build_pydot() to apply when rendering plottables.

graphtik_save_dot_files
- type: `bool`, `None`
- default: ``None``

For debugging purposes, if enabled, store another <img>.txt file next to each image file with the DOT text that produced it.

When none (default), controlled by config.is_debug() from configurations (which by default obeys to GRAPHTIK_DEBUG environment variable), otherwise, any boolean takes precedence here.

graphtik_warning_is_error
  • type: bool

  • default: false

If false, suppress doctest errors, and avoid failures when building site with -W option, since these are unrelated to the building of the site.

doctest_test_doctest_blocks (foreign config)

Don’t disable doctesting of literal-blocks, ie, don’t reset the doctest_test_doctest_blocks configuration value, or else, such code would be invisible to graphtik directive.

trim_doctest_flags (foreign config)

This configuration is forced to False (default was True).

Attention

This means that in the rendered site, options-in-comments like # doctest: +SKIP and <BLACKLINE> artifacts will be visible.

Examples

The following directive renders a diagram of its doctest code, beneath it:

.. graphtik::
   :graphvar: addmul
   :name: addmul-operation

   >>> from graphtik import compose, operation
   >>> addmul = compose(
   ...       "addmul",
   ...       operation(name="add", needs="abc".split(), provides="ab")(lambda a, b, c: (a + b) * c)
   ... )

addmul-operation

which you may reference with this syntax:

you may :graphtik:`reference <addmul-operation>` with ...

Hint

In this case, the :graphvar: parameter is not really needed, since the code contains just one variable assignment receiving a subclass of Plottable or pydot.Dot instance.

Additionally, the doctest code producing the plottables does not have to be contained in the graphtik directive as a whole.

So the above could have been simply written like this:

>>> from graphtik import compose, operation
>>> addmul = compose(
...       "addmul",
...       operation(name="add", needs="abc".split(), provides="ab")(lambda a, b, c: (a + b) * c)
... )

.. graphtik::
   :name: addmul-operation

Errors & debugging

Graphs may become arbitrary deep. Launching a debugger-session to inspect deeply nested stacks is notoriously hard

Logging

Increase the logging verbosity; logging statements have been placed melticulously to describe the execution flows (but not compilation :-(), with each log statement accompanied by the solution id of that flow, like the (3C40) & (8697) below, important for when running pipelines in parallel:

--------------------- Captured log call ---------------------
DEBUG    === Compiling pipeline(t)...
DEBUG    ... cache-updated key: ((), None, None)
DEBUG    === (3C40) Executing pipeline(t), in parallel, on inputs[], according to ExecutionPlan(needs=[], provides=['b'], x2 steps: op1, op2)...
DEBUG    +++ (3C40) Parallel batch['op1'] on solution[].
DEBUG    +++ (3C40) Executing OpTask(FunctionalOperation|(name='op1', needs=[], provides=[sfx: 'b'], fn{}='<lambda>'), sol_keys=[])...
INFO     graphtik.op.py:534 Results[sfx: 'b'] contained +1 unknown provides[sfx: 'b']
FunctionalOperation|(name='op1', needs=[], provides=[sfx: 'b'], fn{}='<lambda>')
DEBUG    ... (3C40) op(op1) completed in 1.406ms.

...

DEBUG    === Compiling pipeline(t)...
DEBUG    ... cache-hit key: ((), None, None)
DEBUG    === (8697) Executing pipeline(t), evicting, on inputs[], according to ExecutionPlan(needs=[], provides=['b'], x3 steps: op1, op2, sfx: 'b')...
DEBUG    +++ (8697) Executing OpTask(FunctionalOperation(name='op1', needs=[], provides=[sfx: 'b'], fn{}='<lambda>'), sol_keys=[])...
INFO     graphtik.op.py:534 Results[sfx: 'b'] contained +1 unknown provides[sfx: 'b']
FunctionalOperation(name='op1', needs=[], provides=[sfx: 'b'], fn{}='<lambda>')
DEBUG    ... (8697) op(op1) completed in 0.149ms.
DEBUG    +++ (8697) Executing OpTask(FunctionalOperation(name='op2', needs=[sfx: 'b'], provides=['b'], fn='<lambda>'), sol_keys=[sfx: 'b'])...
DEBUG    ... (8697) op(op2) completed in 0.08ms.
DEBUG    ... (8697) evicting 'sfx: 'b'' from solution[sfx: 'b', 'b'].
DEBUG    === (8697) Completed pipeline(t) in 0.229ms.

DEBUG flag

Enable the set_debug() in configurations, or externally, by setting the GRAPHTIK_DEBUG environment variable, to enact the following:

  • net objects print details recursively;

  • plotted SVG diagrams include style-provenance as tooltips;

  • Sphinx extension also saves the original DOT file next to each image (see graphtik_save_dot_files).

Tip

From code you may wrap the code you are interested in with config.debug_enabled() “context-manager”, to get augmented print-outs for selected code-paths only.

Jetsam on exceptions

Additionally, when some operation fails, the original exception gets annotated with the following properties, as a debug aid:

>>> from graphtik import compose, operation
>>> from pprint import pprint
>>> def scream(*args):
...     raise ValueError("Wrong!")
>>> try:
...     compose("errgraph",
...             operation(name="screamer", needs=['a'], provides=["foo"])(scream)
...     )(a=None)
... except ValueError as ex:
...     pprint(ex.jetsam)
{'aliases': None,
 'args': {'kwargs': {}, 'positional': [None], 'varargs': []},
 'network': Network(x3 nodes, x1 ops: screamer),
 'operation': FunctionalOperation(name='screamer', needs=['a'], provides=['foo'], fn='scream'),
 'outputs': None,
 'plan': ExecutionPlan(needs=['a'], provides=['foo'], x1 steps: screamer),
 'results_fn': None,
 'results_op': None,
 'solution': {'a': None},
 'task': OpTask(FunctionalOperation(name='screamer', needs=['a'], provides=['foo'], fn='scream'), sol_keys=['a'])}

In interactive REPL console you may use this to get the last raised exception:

import sys

sys.last_value.jetsam

The following annotated attributes might have meaningful value on an exception:

network

the innermost network owning the failed operation/function

plan

the innermost plan that executing when a operation crashed

operation

the innermost operation that failed

args

either the input arguments list fed into the function, or a dict with both args & kwargs keys in it.

outputs

the names of the outputs the function was expected to return

provides

the names eventually the graph needed from the operation; a subset of the above, and not always what has been declared in the operation.

fn_results

the raw results of the operation’s function, if any

op_results

the results, always a dictionary, as matched with operation’s provides

solution

an instance of Solution, contains inputs & outputs till the error happened; note that Solution.executed contain the list of executed operations so far.

Of course you may use many of the above “jetsam” values when plotting.

Debugger

The Plotting capabilities, along with the above annotation of exceptions with the internal state of plan/operation often renders a debugger session unnecessary. But since the state of the annotated values might be incomplete, you may not always avoid one.

You may to enable “post mortem debugging”.

If you set a breakpoint() in one of your functions, move up a few frames to find the ExecutionPlan._handle_task() method, where the “live” ExecutionPlan & Solution instances live, useful when investigating problems with computed values.

Accessing wrapper operation from task-context

Alternatively, when the debugger is stopped inside an underlying function, you may access the wrapper FunctionalOperation and the Solution through the graphtik.execution.task_context context-var. This is populated with the _OpTask instance of the currently executing operation, as shown in the pdb session printout, below:

(Pdb) from graphtik.execution import task_context
(Pdb) op_task = task_context.get()

Get possible completions on the returned operation-task with [TAB]:

(Pdb) p op_task.[TAB][TAB]
op_task.__call__
op_task.__class__
...
op_task.get
op_task.logname
op_task.marshalled
op_task.op
op_task.result
op_task.sol
op_task.solid

Printing the operation-task gives you a quick overview of the operation and the available solution keys (but not the values, not to clutter the debugger console):

(Pdb) p op_task
OpTask(FunctionalOperation(name=..., needs=..., provides=..., fn=...), sol_keys=[...])

Print the wrapper operation:

(Pdb) p op_task.op
...

Print the solution:

(Pdb) p op_task.sol
...