Forecasting code cleanup by JeffreyCovington · Pull Request #285 · NAU-CCL/Epymorph

JeffreyCovington · 2026-03-25T20:39:02Z

Miscellaneous cleanup which includes:

Renaming likelihoods to be more explicit.
Adding more validation checks.
Adding better type annotations.
Adding and updating documentation.
Fixing typos.

Includes ForecastSimulator, ParticleFilterSimulator, and EnsembleKalmanFilterSimulator as top-level interfaces.

…naries of unknown parameters to have consistent usage of keys when iterating over them.

…hood with an `EnsembleKalmanFilterSimulator`.

… likelihood in terms of standard deviation for consistency. Added and updated documentation and annotations.

…naries of unknown parameters to have consistent usage of keys when iterating over them.

…hood with an `EnsembleKalmanFilterSimulator`.

… likelihood in terms of standard deviation for consistency. Added and updated documentation and annotations.

…/Epymorph into Forecasting-Code-Cleanup

JavadocMD

Looking much better, thanks! Just a few minor things, see inline.

…valued hyperparameters.

…e "realizations" as the first dimension.

Averydx · 2026-04-10T00:40:20Z

Is it possible to split up some of the code in pipeline.py? I'm having difficulties with the dreaded circular imports. For example some of the dataclasses I'm using for type hinting like UnknownParam and PipelineOutput.

JavadocMD · 2026-04-10T17:19:33Z

Is it possible to split up some of the code in pipeline.py?

There are a number of tricks to accomplish this. For instance, notice the epymorph.tools.data module defines its own Output as a Protocol rather than importing the real Output from epymorph.simulator.basic.output. Breaking out of circular imports was the main reason for doing that.

You can also move certain foundational entities to a third module, if they don't require many imports themselves.

There are certain guidelines that can help organize imports; I thought about enforcing them with tools at one point. Anyway, I'm happy to chat about specifics if it's helpful.

Averydx · 2026-04-10T17:24:17Z

Thank you! That’s very helpful.

* Plotting functionality. * Error correction. * Typing * modified: epymorph/forecasting/filter_plot.py * Finally?

* Refactor filter to reduce code repetition. * Added support for non-Gaussian likelihoods in the EnKF. * Added support for observing multiple strata. * Allow unknown params to use wildcards. * Refactor filter to reduce code repetition. * Added support for non-Gaussian likelihoods in the EnKF. * Added support for observing multiple strata. * Allow unknown params to use wildcards. * Cleaned up redundant shape calculations.

JavadocMD

See inline.

* Refactor filter code. * Moved pipeline_messaging * Typing updates. * Updated documentation. * Formatting.

JavadocMD

In addition to the inline comment, I noticed epymorph.forecasting.dynamic_params is importing dataclass from attr instead of dataclasses -- use dataclasses.

There are some documentation warnings, but we don't necessarily have to resolve those here. (uv run mkdocs build to see the list.)

…ulators.

Averydx · 2026-06-10T16:46:48Z

I made some improvements to the typing and handling of parameters to address Tyler's comments.

JavadocMD

Epymorph/epymorph/forecasting/dynamic_params.py

Line 9 in fae74b3

from attr import dataclass

should be: from dataclasses import dataclass

After this (and Jeff's comment), good to merge.

…ots.

JavadocMD

See inline.

JeffreyCovington added 10 commits February 18, 2026 10:33

Implementation of the filtering and forecasting pipeline subsystem.

7451554

Includes ForecastSimulator, ParticleFilterSimulator, and EnsembleKalmanFilterSimulator as top-level interfaces.

Updated type annotations. Added ABC to abstract classes.

bce9d91

Added override decorator as appropriate. Updated operations on dictio…

5bde966

…naries of unknown parameters to have consistent usage of keys when iterating over them.

Added validation upon construction for only using a Gaussian likeli…

38d4996

…hood with an `EnsembleKalmanFilterSimulator`.

Renamed likelihoods to be more explicit. Reparameterized the Gaussian…

2c63513

… likelihood in terms of standard deviation for consistency. Added and updated documentation and annotations.

Updated type annotations. Added ABC to abstract classes.

177a276

Added override decorator as appropriate. Updated operations on dictio…

5c03a53

…naries of unknown parameters to have consistent usage of keys when iterating over them.

Added validation upon construction for only using a Gaussian likeli…

02e772f

…hood with an `EnsembleKalmanFilterSimulator`.

Renamed likelihoods to be more explicit. Reparameterized the Gaussian…

f490cf9

… likelihood in terms of standard deviation for consistency. Added and updated documentation and annotations.

Merge branch 'Forecasting-Code-Cleanup' of https://github.com/NAU-CCL…

b959342

…/Epymorph into Forecasting-Code-Cleanup

JeffreyCovington requested a review from JavadocMD March 25, 2026 20:39

Updated line formatting.

fb84578

JavadocMD reviewed Mar 30, 2026

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Comment thread epymorph/forecasting/likelihood.py Outdated

Comment thread epymorph/forecasting/likelihood.py

Comment thread epymorph/forecasting/pipeline.py

Averydx reviewed Apr 1, 2026

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Comment thread epymorph/forecasting/likelihood.py

JeffreyCovington added 3 commits April 2, 2026 10:51

Updated documentation.

e4b5f2d

Changed validation of dynamic parameters to work properly with array-…

633cc99

…valued hyperparameters.

Changed the posterior_values of the particle filter and EnKF to hav…

54dc719

…e "realizations" as the first dimension.

JeffreyCovington requested a review from JavadocMD April 2, 2026 18:58

Averydx and others added 2 commits May 20, 2026 09:10

Forecasting code cleanup (#293)

40230fa

* Plotting functionality. * Error correction. * Typing * modified: epymorph/forecasting/filter_plot.py * Finally?

JavadocMD reviewed May 22, 2026

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Messaging and refactor of pipeline simulators. (#295)

51715b2

* Refactor filter code. * Moved pipeline_messaging * Typing updates. * Updated documentation. * Formatting.

JeffreyCovington requested a review from JavadocMD June 1, 2026 20:12

JavadocMD reviewed Jun 2, 2026

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Comment thread epymorph/forecasting/forecast.py Outdated

JeffreyCovington added 2 commits June 3, 2026 16:35

Reorganized internal forecasting utility functions.

6932d56

Updated typing in FilterOutput.

859e97e

JeffreyCovington linked an issue Jun 9, 2026 that may be closed by this pull request

Add a data_mode flag to PipelineOutput #287

Closed

JeffreyCovington and others added 4 commits June 9, 2026 14:37

Added support for movement data by visit or home node in pipeline sim…

2fe5fba

…ulators.

Typing and doc improvements in the munge.

f364ae3

modified: tests/fast/tools/data_test.py

1a51d45

modified: epymorph/forecasting/munge_realizations.py

fae74b3

JeffreyCovington requested a review from JavadocMD June 10, 2026 17:16

JeffreyCovington commented Jun 24, 2026

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Comment thread epymorph/forecasting/pipeline.py

JavadocMD requested changes Jun 25, 2026

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JeffreyCovington commented Jun 25, 2026

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Comment thread epymorph/forecasting/filter_plot.py

JeffreyCovington commented Jun 25, 2026

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Comment thread epymorph/forecasting/filter_plot.py Outdated

JeffreyCovington added 3 commits June 29, 2026 14:03

Updated typing, documentation, and naming conventions for pipeline pl…

6b71f82

…ots.

Fixed incorrect import.

2ba1322

Adjusted typing for plotting on multiple matplotlib axes.

a96133b

JavadocMD reviewed Jun 30, 2026

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Comment thread epymorph/forecasting/filter_plot.py Outdated

Comment thread epymorph/forecasting/filter_plot.py

Updated documentation and typing.

d6d2b76

JeffreyCovington merged commit 1abed28 into 2.0-beta Jun 30, 2026
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JeffreyCovington deleted the Forecasting-Code-Cleanup branch June 30, 2026 19:37

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