A Python lib for solving & executing graphs of functions, with `pandas` in mind
Project description
It’s a DAG all the way down!
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.
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 (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 from Graphkit (summer 2019, v1.2.2) to experiment with Python 3.6+ features, but has diverged significantly with enhancements ever since.
Features
Deterministic pre-decided execution plan (unless partial-outputs or endured operations defined, see below).
Can assemble existing functions without modifications into pipelines.
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 operations and alias on provides.
Support cycles, by annotating repeated updates of dependency values as sideffects, (e.g. to add columns into pandas.DataFrames).
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 themes.
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, Dagster or Luigi may help for that.
It’s not really a parallelizing optimizer, neither a map-reduce framework - look additionally at Dask, IpyParallel, Celery, 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 is a powerful library written roughly for the same purpose, and works differently along these lines (ie features below refer to schedula):
terminology (<graphtik> := <schedula>):
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 overwrites).
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 pytests,
- 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
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