feat: add runtime TypeSpec support by MilesCranmerBot · Pull Request #1280 · astroautomata/PySR

MilesCranmerBot · 2026-08-07T23:09:33Z

Summary

add TypeSpec(name, fields, sample, ...) for symbolic regression over custom Julia value types
compile each TypeSpec into one deterministic private Julia module per process, with exact-source reuse, replacement warnings, and conflicting checkpoint-restore protection
make fitting transactional so failed searches and rejected warm starts leave the previously fitted Julia state intact
preserve and replay operators, objectives, complexity mappings, early-stop conditions, templates, and worker definitions across serialization and multiprocessing
support discrete constants through mutate and continuous constant optimization through scalar_constants and with_scalar_constants
support typed OperatorEnum evaluation, full objectives, ExpressionSpec, explicit-keyword TemplateExpressionSpec, and custom expression specs that declare TypeSpec support
remove the legacy positional TemplateExpressionSpec constructor and its obsolete compatibility machinery
pin SymbolicRegression.jl v2.0.0-beta.5 for custom-value mutation support

Example

type_spec = TypeSpec(
    name="Vec2",
    fields={"data": "Vector{Float64}"},
    sample="rng -> Vec2(randn(rng, 2))",
    scalar_constants="value -> value.data",
    with_scalar_constants="(value, constants) -> Vec2(constants)",
)

model = PySRRegressor(
    type_spec=type_spec,
    operators={
        1: ["rotate90(x::Vec2) = Vec2([-x.data[2], x.data[1]])"],
        2: ["add_vectors(x::Vec2, y::Vec2) = Vec2(x.data + y.data)"],
    },
    elementwise_loss=(
        "vector_loss(x::Vec2, y::Vec2)::Float64 = "
        "sum(abs2, x.data - y.data)"
    ),
)

The documentation includes custom full objectives plus vector-valued, string-valued, heterogeneous tensor, variable-length constant, template, multiprocessing, and checkpoint examples.

Verification

44 passed, 36 subtests passed in pysr/test/test_type_specs.py
157 passed, 38 subtests passed in pysr/test/test_main.py
changed-file pre-commit hooks passed
git diff --check passed

codecov · 2026-08-08T00:29:21Z

Codecov Report

✅ All modified and coverable lines are covered by tests.

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MilesCranmer · 2026-08-08T00:44:48Z

@MilesCranmerBot please address the above

MilesCranmer · 2026-08-08T00:46:53Z

@MilesCranmerBot also we need 100% diff coverage

MilesCranmerBot · 2026-08-08T02:42:13Z

Addressed in 9601b5a:

renamed the TypeSpec setup method to instantiate
replaced the @eval wrappers with direct jl.seval definitions
removed the serial-only restriction and added a multithreaded TypeSpec regression test
added coverage for TypeSpec conversions and callback variants

Checks: normal numeric regression test passes; TypeSpec direct-instantiation coverage is 100%.

MilesCranmer · 2026-08-09T16:00:36Z

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Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

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Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

…nd pickling

…pespec example

`names(...; all=true)` reports gensym symbols such as `#1#2` for the anonymous functions in a TypeSpec module. Copying those into the configuration module reserved the same names that Julia 1.11 assigns to that module's own closures, so loading any configuration failed with an invalid constant redefinition. Also correct the runtime boundary annotations for numeric early stopping and the search output tuple. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

A configuration source that raised left the module holding the constants for the sources that had already run, so retrying the same definition redefined them and failed on Julia 1.10 and 1.11. Replace the module on every install and stop binding the per-source values, which nothing read. Also state what a preamble shares with configuration sources. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

SymbolicRegression wraps the equation in quotes without escaping its contents, so an equation holding a string constant is not valid CSV: pandas either raises or shifts a later field into the complexity column, which then fails arithmetic. The file has three columns in a fixed order, so read the equation as the rest of the line. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

for more information, see https://pre-commit.ci

The fixtures wrote a leading index column, so the file had four fields where the Julia writer emits three, and the equation was read as the last two. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

SymbolicRegression 2.0.0-beta.8 escapes quotes in the equation column, so the file is valid CSV and the hand-rolled reader added for beta.7 is unnecessary. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

A type module that failed partway stayed defined in Main, so every later load skipped reinstall and failed with a missing binding. Mark the module as installed with its last statement and reinstall whenever that marker is absent. Evaluating an expression through its callable let DynamicExpressions fill the output with NaN, which cannot convert to a generated type. Evaluate with eval_tree_array and report the rejected value instead. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

The parameter test only checked fingerprint stability, so nothing proved that a parameter holding a TypeSpec value actually changes during a search. Fit a model whose only route to zero loss is the mutate hook rewriting the parameter, and document how parameters are created, mutated, and optimized. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

MilesCranmer · 2026-08-17T10:54:51Z

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TypeSpec and TemplateExpressionSpec models hold live Julia objects in `julia_expression` and `lambda_format`, which cannot be revived in a fresh Julia session. Drop both columns for either spec when pickling and rebuild them from the search output whenever equations are accessed, so `get_best`, `from_file`, and the export helpers all work after a restore instead of only `predict`. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

Every error branch reported uncovered by codecov on this PR now runs under the test suite: spec and configuration validation, fit and prediction data validation, array conversion failures, the runtime value-ordering guard, warm-start toggling, and the fitted-model score/predict guards. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

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MilesCranmerBot force-pushed the codex/type-spec branch 5 times, most recently from 0069e72 to 0bfdb21 Compare August 10, 2026 22:21

MilesCranmerBot and others added 17 commits August 10, 2026 18:22

feat: add runtime TypeSpec compiler

3470dcd

feat: integrate TypeSpec with PySRRegressor

6adbeb9

fix: isolate TypeSpec prediction validation

6b0e6c6

test: include TypeSpec tests in main suite

ecd95a5

Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

df59be2

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fix: address TypeSpec review feedback

db320fc

Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

fix: allow full objectives with TypeSpec

3f966f5

Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

refactor: remove TypeSpec expression spec override

327598a

Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

refactor: simplify runtime typespec support

b47b1a7

fix: satisfy TypeSpec runtime and static checks

22bcda3

fix: initialize TypeSpec on multiprocessing workers

d2b5a57

docs: add heterogeneous tensor TypeSpec example

5817852

fix: address typespec review findings on data handling, validation, a…

a3dfc28

…nd pickling

feat: default can_optimize to false for non-numeric typespec value types

d401bed

feat: add sample_weight alias for weights in fit

a98326a

fix: satisfy sklearn sample_weight estimator checks

1269a63

fix: correct count_scalar_constants and sample all ranks in tensor ty…

d2e9743

…pespec example

MilesCranmerBot and others added 4 commits August 14, 2026 11:22

Remove redundant TypeSpec codegen version

785216d

Remove TypeSpec runtime fingerprint salt

575e7f9

Enable TypeSpec template parameters

27e8ae5

MilesCranmerBot force-pushed the codex/type-spec branch from b94051c to 6667c13 Compare August 14, 2026 22:31

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Write test hall of fame files without a pandas index

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The fixtures wrote a leading index column, so the file had four fields where the Julia writer emits three, and the equation was read as the last two. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

Read the hall of fame with pandas again

009cdc1

SymbolicRegression 2.0.0-beta.8 escapes quotes in the equation column, so the file is valid CSV and the hand-rolled reader added for beta.7 is unnecessary. Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

Mark the TypeSpec runtime as internal

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Co-authored-by: Miles Cranmer <miles.cranmer@gmail.com>

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docs: write TemplateExpressionSpec keywords explicitly in the skill

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docs: improve writeup for type spec example

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docs: greatly improve type spec docs

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chore: cleanup

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docs: clean up

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chore(master): release 2.0.0-beta.2 #1293

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