feat(gds-examples): add StockFlow DSL version of SIR epidemic model by rororowyourboat · Pull Request #33 · BlockScience/gds-core

rororowyourboat · 2026-02-27T08:13:39Z

Summary

Reimplements SIR epidemic model using gds-stockflow declarative API (StockFlowModel, Stock, Flow, Auxiliary, Converter)
Runs SF-001..SF-005 domain checks + GDS generic/semantic verification
Adds gds-stockflow as dependency to gds-examples

Test plan

48 tests passing (model, DSL verification, spec, canonical, system, GDS verification, query)
Lint clean (ruff check + ruff format)

Closes #27

🤖 Generated with Claude Code

Reimplements the SIR epidemic model using gds-stockflow's declarative API (StockFlowModel, Stock, Flow, Auxiliary, Converter) instead of manual GDS construction. Includes SF-001..SF-005 domain checks, GDS verification, canonical analysis, and 48 tests covering model, compilation, verification, and SpecQuery layers. Closes #27 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Copilot

Pull request overview

Adds a new StockFlow DSL-based SIR epidemic example to gds-examples, showcasing how to declare a stock-flow model via gds-stockflow, compile it into GDS artifacts (spec/system/canonical), and run both StockFlow and GDS verification.

Changes:

Introduces a DSL-declared SIR model (StockFlowModel) with compilation helpers to GDSSpec, SystemIR, and canonical projection.
Adds comprehensive tests covering DSL structure, SF checks, compiled spec/system properties, generic/spec verification, and query API.
Updates gds-examples packaging/docs to include the new example and adds gds-stockflow as a dependency.

Reviewed changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
packages/gds-examples/stockflow/sir_epidemic_dsl/model.py	Declares the SIR model using StockFlow DSL and provides compile/projection helpers.
packages/gds-examples/stockflow/sir_epidemic_dsl/test_sir_epidemic_dsl.py	Adds end-to-end tests for the DSL model, compilation outputs, and verification/query layers.
packages/gds-examples/stockflow/sir_epidemic_dsl/generate_views.py	Adds a script to render all 6 visualization views for the DSL model.
packages/gds-examples/stockflow/sir_epidemic_dsl/init.py	Introduces the new example package.
packages/gds-examples/pyproject.toml	Adds `gds-stockflow` dependency and includes the new example in config lists.
packages/gds-examples/README.md	Documents the new DSL example in the learning path and feature matrix.

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Copilot · 2026-02-27T08:21:58Z

packages/gds-examples/README.md

+
+**Domain:** Stock-flow — built with [gds-stockflow](https://github.com/BlockScience/gds-core/tree/main/packages/gds-stockflow) DSL
+
+**Files:** [model.py](stockflow/sir_epidemic_dsl/model.py) · [tests](stockflow/sir_epidemic_dsl/test_sir_epidemic_dsl.py) · [views](stockflow/sir_epidemic_dsl/VIEWS.md)


This README links to stockflow/sir_epidemic_dsl/VIEWS.md, but this PR doesn’t add that file (only generate_views.py). Either commit the generated VIEWS.md (like the other examples do) or adjust the link/text to point at generate_views.py and explain how to generate the views.

Suggested change

**Files:** [model.py](stockflow/sir_epidemic_dsl/model.py) · [tests](stockflow/sir_epidemic_dsl/test_sir_epidemic_dsl.py) · [views](stockflow/sir_epidemic_dsl/VIEWS.md)

**Files:** [model.py](stockflow/sir_epidemic_dsl/model.py) · [tests](stockflow/sir_epidemic_dsl/test_sir_epidemic_dsl.py) · [view generator](stockflow/sir_epidemic_dsl/generate_views.py) — run `python stockflow/sir_epidemic_dsl/generate_views.py` to regenerate `VIEWS.md`

Copilot · 2026-02-27T08:21:59Z

packages/gds-examples/README.md

+### SIR Epidemic (DSL)
+
+**Same model, declarative style.** Reimplements the SIR epidemic using the `gds-stockflow` DSL. Instead of manually constructing TypeDefs, Entities, Spaces, Blocks, and wiring, you declare Stocks, Flows, Auxiliaries, and Converters — the compiler handles all GDS mapping automatically.
+
+```
+Stocks: Susceptible, Infected, Recovered
+Flows: Infection (S→I), Recovery (I→R)
+Auxiliaries: Infection Rate, Recovery Rate
+Converters: Contact Rate, Recovery Time
+```
+```python
+# The entire model in ~20 lines of declarations
+model = StockFlowModel(name="SIR Epidemic", stocks=[...], flows=[...], auxiliaries=[...], converters=[...])
+spec = compile_model(model)       # → GDSSpec with 9 blocks, 3 entities
+system = compile_to_system(model)  # → SystemIR with temporal loops
+```
+


visualize_examples.py is described as generating diagrams for “all example models”, but it currently doesn’t include the new sir_epidemic_dsl module in its examples = [...] list. Either add sir_epidemic_dsl.model there or clarify in docs that the script only includes a subset of examples.

Copilot · 2026-02-27T08:21:59Z

packages/gds-examples/stockflow/sir_epidemic_dsl/test_sir_epidemic_dsl.py

+"""Tests for the SIR Epidemic model (gds-stockflow DSL)."""
+
+from gds.blocks.roles import BoundaryAction, Mechanism, Policy
+from gds.ir.models import FlowDirection
+from gds.query import SpecQuery


For consistency with the other examples (and the documented example layout), consider renaming this test module to test_model.py. Several scripts/docs in this repo assume each example directory has a test_model.py, so keeping the naming uniform helps discovery and maintenance.

Copilot · 2026-02-27T08:21:59Z

packages/gds-examples/stockflow/sir_epidemic_dsl/model.py

+    No numerical values are specified — GDS is structural, not numerical.
+    The compiler infers all types, spaces, entities, blocks, and wirings
+    from these declarations.


The docstring says “No numerical values are specified”, but this model does specify numeric initial stock values (999.0/1.0/0.0). Please reword this to clarify that the DSL example omits rate equations/parameters (or other behavioral coefficients), while still providing initial conditions.

Suggested change

No numerical values are specified — GDS is structural, not numerical.

The compiler infers all types, spaces, entities, blocks, and wirings

from these declarations.

Numerical initial conditions for the stocks are provided, but no

specific rate equations or parameter values are hard-coded here — the

DSL declaration is structural, and the compiler infers all types,

spaces, entities, blocks, and wirings from these declarations.

Copilot · 2026-02-27T08:21:59Z

packages/gds-examples/stockflow/sir_epidemic_dsl/generate_views.py

+    uv run python stockflow/sir_epidemic_dsl/generate_views.py
+    uv run python stockflow/sir_epidemic_dsl/generate_views.py --save   # write VIEWS.md


The usage examples in this module docstring don’t match the repo’s documented invocation pattern from the repository root (e.g. uv run python packages/gds-examples/...). As written, uv run python stockflow/... will fail unless the current working directory is packages/gds-examples. Please update the paths to be unambiguous and consistent with packages/gds-examples/README.md.

Suggested change

uv run python stockflow/sir_epidemic_dsl/generate_views.py

uv run python stockflow/sir_epidemic_dsl/generate_views.py --save # write VIEWS.md

uv run python packages/gds-examples/stockflow/sir_epidemic_dsl/generate_views.py

uv run python packages/gds-examples/stockflow/sir_epidemic_dsl/generate_views.py --save # write VIEWS.md

- Fix model.py docstring: clarify that initial conditions are provided while rate equations/parameters are omitted (not "no numerical values") - Fix generate_views.py usage paths to match repo convention (packages/gds-examples/stockflow/sir_epidemic_dsl/...) - Generate VIEWS.md with all 6 visualization views - Add sir_epidemic_dsl to visualize_examples.py examples list - Add sir_epidemic_dsl to README.md generate-all-views shell snippet Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Copilot AI review requested due to automatic review settings February 27, 2026 08:13

Copilot started reviewing on behalf of rororowyourboat February 27, 2026 08:14 View session

Copilot AI reviewed Feb 27, 2026

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rororowyourboat merged commit 2e617b1 into main Feb 27, 2026
9 checks passed

rororowyourboat mentioned this pull request Feb 27, 2026

feat: merge all outstanding PRs (#36-#41) #42

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3 tasks

rororowyourboat deleted the feat/examples-stockflow-sir-dsl branch February 27, 2026 09:14

This was referenced Feb 27, 2026

docs: build and validate mkdocs site #43

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test: run full test suite post-merge validation #46

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feat(gds-examples): add StockFlow DSL version of SIR epidemic model#33

feat(gds-examples): add StockFlow DSL version of SIR epidemic model#33
rororowyourboat merged 2 commits intomainfrom
feat/examples-stockflow-sir-dsl

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		Domain: Stock-flow — built with [gds-stockflow](https://github.com/BlockScience/gds-core/tree/main/packages/gds-stockflow) DSL

		Files: [model.py](stockflow/sir_epidemic_dsl/model.py) · [tests](stockflow/sir_epidemic_dsl/test_sir_epidemic_dsl.py) · [views](stockflow/sir_epidemic_dsl/VIEWS.md)

-    No numerical values are specified — GDS is structural, not numerical.
-    The compiler infers all types, spaces, entities, blocks, and wirings
-    from these declarations.
+    Numerical initial conditions for the stocks are provided, but no
+    specific rate equations or parameter values are hard-coded here — the
+    DSL declaration is structural, and the compiler infers all types,
+    spaces, entities, blocks, and wirings from these declarations.

		uv run python stockflow/sir_epidemic_dsl/generate_views.py
		uv run python stockflow/sir_epidemic_dsl/generate_views.py --save # write VIEWS.md

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rororowyourboat commented Feb 27, 2026

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