graphtik

Graphtik

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.. epigraph::

It's a DAG all the way down!

|sample-plot|

Computation graphs for Python & Pandas

Graphtik is a library to compose, solve, execute & plot graphs of python functions (a.k.a pipelines) that consume and populate named data (a.k.a dependencies), whose names may be nested (such as. pandas dataframe columns), based on whether values for those dependencies exist in the inputs or have been calculated earlier.

In mathematical terms, given:

• a partially populated data-tree, and
• a set of functions operating on (consuming/producing) branches of the data tree,

graphtik collects a subset of functions in a graph that when executed consume & produce as many values as possible in the data-tree.

|usage-overview|

• Its primary use case is building flexible algorithms for data science/machine learning projects.

• It should be extendable to implement the following:

  • an IoC dependency resolver <https://en.wikipedia.org/wiki/Dependency_injection>_ (e.g. Java Spring, Google Guice);
  • an executor of interdependent tasks based on files (e.g. GNU Make);
  • a custom ETL engine;
  • a spreadsheet calculation engine.

Graphtik sprang <https://docs.google.com/spreadsheets/d/1HPgtg2l6v3uDS81hLOcFOZxIBLCnHGrcFOh3pFRIDio/edit#gid=0>_ from Graphkit_ (summer 2019, v1.2.2) to experiment <https://github.com/yahoo/graphkit/issues/>_ with Python 3.6+ features, but has diverged significantly with enhancements ever since.

.. _features:

Features

• Deterministic pre-decided execution plan (unless partial-outputs or endured operations defined, see below).
• Can assemble existing functions without modifications into pipeline\s.
• dependency resolution can bypass calculation cycles based on data given and asked.
• Support functions with optional <optionals> input args and/or varargs <varargish>.
• Support functions with partial outputs; keep working even if certain endured operations fail.
• Facilitate trivial conveyor operation\s and alias on provides.
• Support cycles, by annotating repeated updates of dependency values as sideffects, (e.g. to add columns into pandas.DataFrame\s).
• Hierarchical dependencies <subdoc> may access data values deep in solution with json pointer path expressions.
• Hierarchical dependencies annotated as implicit imply which subdoc dependency the function reads or writes in the parent-doc.
• Merge <operation merging> or nest <operation nesting> sub-pipelines.
• Early eviction of intermediate results from solution, to optimize memory footprint.
• Solution tracks all intermediate overwritten <overwrite> values for the same dependency.
• Elaborate Graphviz_ plotting with configurable plot theme\s.
• Integration with Sphinx sites with the new graphtik directive.
• Authored with debugging in mind.
• Parallel execution (but underdeveloped & DEPRECATED).

Anti-features ^^^^^^^^^^^^^

• It's not meant to follow complex conditional logic based on dependency values (though it does support that to a limited degree <partial outputs>).

• It's not an orchestrator for long-running tasks, nor a calendar scheduler - Apache Airflow <https://airflow.apache.org/>, Dagster <https://github.com/dagster-io/dagster> or Luigi <https://luigi.readthedocs.io/>_ may help for that.

• It's not really a parallelizing optimizer, neither a map-reduce framework - look additionally at Dask <https://dask.org/>, IpyParallel <https://ipyparallel.readthedocs.io/en/latest/>, Celery <https://docs.celeryproject.org/en/stable/getting-started/introduction.html>_, Hive, Pig, Hadoop, etc.

• It's not a stream/batch processor, like Spark, Storm, Fink, Kinesis, because it pertains function-call semantics, calling only once each function to process data-items.

Differences with schedula %%%%%%%%%%%%%%%%%%%%%%%%%%%

schedula <https://schedula.readthedocs.io/>_ is a powerful library written roughly for the same purpose, and works differently along these lines (ie features below refer to schedula):

• terminology ( := ):

  • pipeline := dispatcher
  • plan := workflow
  • solution := solution

• Dijkstra planning runs while calling operations:

  • Powerful & flexible (ie all operations are dynamic, domains are possible, etc).
  • Supports weights.
  • Cannot pre-calculate & cache execution plans (slow).

• Calculated values are stored inside a graph (mimicking the structure of the functions):

  • graph visualizations absolutely needed to inspect & debug its solutions.
  • graphs imply complex pre/post processing & traversal algos (vs constructing/traversing data-trees).

• Reactive plotted diagrams, web-server runs behind the scenes.

• Operation graphs are stackable:

  • plotted nested-graphs support drill-down.
  • graphtik emulates that with data/operation names (operation nesting), but always a unified graph is solved at once, bc it is impossible to dress nesting-funcs as a python-funcs and pre-solve plan (schedula does not pre-solve plan, Dijkstra runs all the time). See TODO about plotting such nested graphs.

• Schedula does not calculate all possible values (ie no overwrite\s).

• Schedula computes precedence based on weights and lexicographical order of function name.

  • Re-inserting operation does not overrides its current function - must remove it first.
  • graphtik precedence based insertion order during composition.

• Virtual start and end data-nodes needed for Dijkstra to solve the dag.

• No domains (execute-time conditionals deciding whether a function must run).

• Probably recompute is more straightforward in graphtik.

• TODO: more differences with schedula exist.

Quick start

Here’s how to install:

::

pip install graphtik

OR with various "extras" dependencies, such as, for plotting::

pip install graphtik[plot]

. Tip:: Supported extras:

**plot**
    for plotting with `Graphviz`_,
**matplot**
    for plotting in *maplotlib* windows
**sphinx**
    for embedding plots in *sphinx*\-generated sites,
**test**
    for running *pytest*\s,
**dill**
    may help for pickling `parallel` tasks - see `marshalling` term
    and ``set_marshal_tasks()`` configuration.
**all**
    all of the above, plus development libraries, eg *black* formatter.
**dev**
    like *all*

Let's build a graphtik computation graph that produces x3 outputs out of 2 inputs α and β:

• α x β
• α - αxβ
• |α - αxβ| ^ 3

..

from graphtik import compose, operation from operator import mul, sub

@operation(name="abs qubed", ... needs=["α-α×β"], ... provides=["|α-α×β|³"]) ... def abs_qubed(a): ... return abs(a) ** 3

Compose the abs_qubed function along the mul & sub built-ins into a computation graph:

graphop = compose("graphop", ... operation(needs=["α", "β"], provides=["α×β"])(mul), ... operation(needs=["α", "α×β"], provides=["α-α×β"])(sub), ... abs_qubed, ... ) graphop Pipeline('graphop', needs=['α', 'β', 'α×β', 'α-α×β'], provides=['α×β', 'α-α×β', '|α-α×β|³'], x3 ops: mul, sub, abs qubed)

Run the graph and request all of the outputs (notice that unicode characters work also as Python identifiers):

graphop(α=2, β=5) {'α': 2, 'β': 5, 'α×β': 10, 'α-α×β': -8, '|α-α×β|³': 512}

... or request a subset of outputs:

solution = graphop.compute({'α': 2, 'β': 5}, outputs=["α-α×β"]) solution {'α-α×β': -8}

... and plot the results (if in jupyter, no need to create the file):

solution.plot('executed_3ops.svg') # doctest: +SKIP

|sample-sol|

|plot-legend|

.. |sample-plot| image:: docs/source/images/sample.svg :alt: sample graphtik plot :width: 380px :align: middle .. |usage-overview| image:: docs/source/images/GraphkitUsageOverview.svg :alt: Usage overview of graphtik library :width: 640px :align: middle .. |sample-sol| image:: docs/source/images/executed_3ops.svg :alt: sample graphtik plot :width: 380px :align: middle .. |plot-legend| image:: docs/source/images/GraphtikLegend.svg :alt: graphtik legend :align: middle

.. _Graphkit: https://github.com/yahoo/graphkit .. _Graphviz: https://graphviz.org .. _badges_substs:

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