abmfact 0.1.0__tar.gz

abmfact-0.1.0/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+.venv/
+venv/
+build/
+dist/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+coverage.xml
+htmlcov/
+abmfact-results/
+results/
+.DS_Store
+.env

abmfact-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes are recorded here. The format follows
+[Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and the project uses
+[semantic versioning](https://semver.org/).
+
+## [Unreleased]
+
+## [0.1.0] - 2026-10-18
+
+### Added
+
+- Audit files in YAML: model, parameters, claims and budget.
+- Claims with threshold, range and monotone tests, and a safe metric grammar.
+- Seven checks: determinism, update order, agent order, random streams, grid placement, time step and
+  population scale.
+- Verdicts ROBUST, SHIFTED, FRAGILE, INCONCLUSIVE, BASELINE_FAILS, NOT_TESTABLE and SKIPPED, with
+  reasons, seeds needed and reproducer commands.
+- Diagnosis of the likely cause from the pattern of flagged checks.
+- Python, Mesa, NetLogo and command adapters.
+- Outputs: results.json, a self-contained report.html and an RO-Crate 1.1 record.
+- The planted-fault zoo and an acceptance test requiring a diagonal detection matrix.
+- Command line: run, check, demo, init and replay.

abmfact-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use ABMfact, please cite it as below."
+title: "ABMfact: is it a finding or an artefact?"
+abstract: >-
+  ABMfact audits the conclusions of agent-based models against implementation artefacts. It reruns a
+  model under changes that a correct implementation must not care about, such as activation order,
+  agent labels, random streams, grid placement, time step and population size, and reports which
+  stated conclusions survive, with intervals and reproducible commands.
+type: software
+authors:
+  - family-names: Hemedan
+    given-names: Ahmed
+version: 0.1.0
+license: Apache-2.0
+repository-code: "https://github.com/a7med7emedan/ABMfact"
+keywords:
+  - agent-based modelling
+  - verification
+  - reproducibility
+  - artefacts
+  - simulation
+references:
+  - type: article
+    title: "Errors and artefacts in agent-based modelling"
+    authors:
+      - family-names: Galán
+        given-names: José Manuel
+      - family-names: Izquierdo
+        given-names: Luis R.
+      - family-names: Izquierdo
+        given-names: Segismundo S.
+      - family-names: Santos
+        given-names: José Ignacio
+      - family-names: del Olmo
+        given-names: Ricardo
+      - family-names: López-Paredes
+        given-names: Adolfo
+      - family-names: Edmonds
+        given-names: Bruce
+    journal: "Journal of Artificial Societies and Social Simulation"
+    volume: 12
+    issue: 1
+    year: 2009
+    url: "https://www.jasss.org/12/1/1.html"

abmfact-0.1.0/LICENSE

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abmfact-0.1.0/NOTICE

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+ABMfact
+Copyright 2026 Ahmed Hemedan
+
+This product is licensed under the Apache License, Version 2.0 (see LICENSE).

abmfact-0.1.0/PKG-INFO

@@ -0,0 +1,244 @@
+Metadata-Version: 2.5
+Name: abmfact
+Version: 0.1.0
+Summary: Is it a finding or an artefact? Audits the conclusions of agent-based models against implementation artefacts.
+Project-URL: Homepage, https://github.com/a7med7emedan/ABMfact
+Project-URL: Source, https://github.com/a7med7emedan/ABMfact
+Project-URL: Documentation, https://github.com/a7med7emedan/ABMfact/tree/main/docs
+Project-URL: Issues, https://github.com/a7med7emedan/ABMfact/issues
+Project-URL: Changelog, https://github.com/a7med7emedan/ABMfact/blob/main/CHANGELOG.md
+Author: Ahmed Hemedan
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Keywords: abm,agent-based-model,agent-based-modelling,artefacts,computational-science,mesa,metamorphic-testing,netlogo,reproducibility,research-software,robustness,simulation,validation,verification
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Software Development :: Testing
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: numpy>=1.26
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: scipy>=1.11
+Provides-Extra: mesa
+Requires-Dist: mesa>=3.1; extra == 'mesa'
+Requires-Dist: networkx>=3.0; extra == 'mesa'
+Provides-Extra: netlogo
+Requires-Dist: pynetlogo>=0.5; extra == 'netlogo'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/a7med7emedan/ABMfact/main/assets/logo-dark.svg">
+    <img src="https://raw.githubusercontent.com/a7med7emedan/ABMfact/main/assets/logo.svg" alt="ABMfact" width="420">
+  </picture>
+</p>
+
+<p align="center">
+  <a href="https://github.com/a7med7emedan/ABMfact/actions/workflows/tests.yml"><img src="https://github.com/a7med7emedan/ABMfact/actions/workflows/tests.yml/badge.svg" alt="tests"></a>
+  <img src="https://img.shields.io/badge/python-3.11%20%7C%203.12%20%7C%203.13-blue" alt="Python 3.11 to 3.13">
+  <a href="https://github.com/a7med7emedan/ABMfact/blob/main/LICENSE"><img src="https://img.shields.io/badge/licence-Apache--2.0-green" alt="Apache-2.0"></a>
+</p>
+
+**ABMfact tells you whether the conclusions of an agent-based model are findings or implementation
+artefacts.**
+
+You state your model's conclusions as checkable claims. ABMfact reruns the model under changes that a
+correct implementation must not care about: activation order, agent labels, random streams, where the
+world sits on the grid, the time step and the population size. It then reports, claim by claim, which
+conclusions survive. Every verdict comes with an interval, a reason and a one-line command that
+reproduces it.
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/a7med7emedan/ABMfact/main/assets/how-it-works-dark.svg">
+    <img src="https://raw.githubusercontent.com/a7med7emedan/ABMfact/main/assets/how-it-works.svg" alt="The audit pipeline: a model and its claims run under a baseline and six perturbed conditions, over many seeds; intervals and equivalence tests give a verdict per claim and check (ROBUST, SHIFTED or FRAGILE), written to report.html, results.json and an RO-Crate record." width="100%">
+  </picture>
+</p>
+
+## Why
+
+Galán et al. (2009) separated two ways a model can mislead. An *error* is code that does not do what
+the modeller meant. An *artefact* is a result produced by an implementation choice that is not part of
+the theory, such as the order agents act in. Both are hard to see by reading code, and both survive
+peer review. ABMfact turns that distinction into automatic, repeatable tests, so the question "is this
+an artefact?" gets an answer with a seed attached.
+
+## Quick start
+
+```bash
+pip install abmfact            # add [mesa] or [netlogo] for those frameworks
+abmfact demo --jobs 4          # audit the planted-fault zoo (about a minute on four cores)
+abmfact init                   # write a commented audit.yaml for your model
+abmfact run audit.yaml --out results/
+```
+
+`results/report.html` opens in any browser. `abmfact check audit.yaml` exits with status 1 when any claim
+is fragile, so it fits in continuous integration.
+
+## What you write
+
+One YAML file: the model, its parameters, the claims and a budget.
+
+```yaml
+model:
+  adapter: python
+  target: mypackage.model:run          # run(params, seed, knobs) -> dict of outputs
+  supports:                            # the implementation choices your model can vary
+    update_order: {values: [random, id, synchronous], default: random}
+    agent_order: true
+    grid: true
+    dt_scale: true
+    pop_scale: true
+
+params: {beta: 0.4, gamma: 0.1}
+
+claims:
+  - id: C1
+    statement: "most of the population is infected"
+    metric: attack_rate
+    test: greater_than
+    value: 0.6
+  - id: C2
+    statement: "the attack rate rises with transmission"
+    metric: attack_rate
+    test: monotone_increasing
+    over: beta
+    where: {beta: [0.25, 0.4]}
+  - id: C3
+    statement: "the epidemic peaks within 25 time units"
+    metric: peak_time
+    test: less_than
+    value: 25
+    skip_checks:
+      population_scale: "peak time legitimately grows with system size"
+
+budget: {seeds: 100, jobs: 4}
+```
+
+Claims test conclusions, not raw numbers, because a number can move while the conclusion holds. Write
+them from the paper or the abstract before running anything.
+
+## What you get
+
+For example, auditing the zoo model with a stale-buffer bug (`abmfact.zoo:fault_stale_state`, claims as
+in [examples/zoo/audit.yaml](https://github.com/a7med7emedan/ABMfact/blob/main/examples/zoo/audit.yaml)) gives:
+
+| Claim | determinism | update order | agent order | rng streams | grid | time step | population |
+|---|---|---|---|---|---|---|---|
+| C1 most are infected | ROBUST | **SHIFTED** | ROBUST | ROBUST | ROBUST | ROBUST | ROBUST |
+| C2 rises with beta | ROBUST | **SHIFTED** | ROBUST | ROBUST | ROBUST | ROBUST | ROBUST |
+| C3 peak below 50% | ROBUST | **SHIFTED** | ROBUST | ROBUST | ROBUST | ROBUST | ROBUST |
+| C4 peaks by t = 25 | ROBUST | **FRAGILE** | ROBUST | ROBUST | ROBUST | ROBUST | SKIPPED |
+
+with the likely cause: *stale or partial state reads: agents see a state that depends on the scheduling
+path*.
+
+Each run writes three files:
+
+- `report.html`: the verdict table, one interval plot per claim and condition, likely causes, and
+  reproducer commands. Self-contained, light and dark.
+- `results.json`: every interval, comparison and verdict, for scripts and CI. Identical across reruns
+  apart from the timestamp.
+- `ro-crate-metadata.json`: an RO-Crate 1.1 record of the audit file, results and report, with SHA-256
+  hashes, so the audit itself can be archived and cited.
+
+## The checks
+
+| Check | Question | Typical cause when it fails |
+|---|---|---|
+| `determinism` | Does the same seed always give the same result? | an unseeded generator, set or dict iteration order, wall-clock time |
+| `update_order` | Does the conclusion survive a different activation order? | stale or partial state reads, buffers reused between steps |
+| `agent_order` | Does it survive relabelling the agents? | `agents[:k]`, ties broken by id |
+| `rng_streams` | Does it survive fresh, independent random streams? | a hard-coded seed, streams shared between processes |
+| `grid` | Does it survive moving or rotating the world on the torus? | a boundary that does not wrap, absolute array positions |
+| `time_step` | Does it survive halving the time step? | probabilities not converted with the current step |
+| `population_scale` | Does it survive doubling the population at fixed density? | a size or count fixed at the calibration value |
+
+A check needs the model to honour its knob. When a model does not, the check is reported as
+`NOT_TESTABLE`, never skipped silently. The `rng_streams` check always runs: when a model does not manage
+its own streams, ABMfact remaps the seed.
+
+## Verdicts
+
+| Verdict | Meaning |
+|---|---|
+| `ROBUST` | the claim holds under every variant, and every result is statistically equivalent to baseline |
+| `SHIFTED` | the claim still holds, but a result moved beyond its tolerance, or its spread doubled or halved |
+| `FRAGILE` | the claim fails under a variant, or the same seed gave a different result |
+| `INCONCLUSIVE` | the intervals are too wide to decide; the report says how many seeds would settle it |
+| `BASELINE_FAILS` | the claim does not hold even before anything is changed |
+| `NOT_TESTABLE`, `SKIPPED` | the model does not expose the knob, or the claim declares the check out of scope, with a reason |
+
+Decisions use one-sided tests at `alpha` (0.05 by default, so 90% intervals) and a three-outcome
+equivalence test against a tolerance, 10% of the baseline mean unless the claim sets one. See
+[docs/statistics.md](https://github.com/a7med7emedan/ABMfact/blob/main/docs/statistics.md).
+
+## Validation: the planted-fault zoo
+
+A checker is only as good as its evidence that it catches what it claims to catch, and nothing else.
+`abmfact.zoo` holds one clean SIR model on a torus and seven copies of it, each with one realistic bug.
+`abmfact demo` audits all eight with every check. The figure below is drawn from a real run with 100 seeds
+per condition by [scripts/make_figures.py](https://github.com/a7med7emedan/ABMfact/blob/main/scripts/make_figures.py).
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/a7med7emedan/ABMfact/main/assets/matrix-dark.svg">
+    <img src="https://raw.githubusercontent.com/a7med7emedan/ABMfact/main/assets/matrix.svg" alt="Planted-fault detection matrix: each of the seven faulty models is caught only by its own check, and the clean model by none." width="100%">
+  </picture>
+</p>
+
+The test suite requires this exact matrix:
+
+```
+                determinism  update order  agent order  rng streams  grid    time step  population scale
+clean           .            .             .            .            .       .          .
+nondeterminism  CAUGHT       .             .            .            .       .          .
+stale_state     .            CAUGHT        .            .            .       .          .
+id_dependence   .            .             CAUGHT       .            .       .          .
+ignored_seed    .            .             .            CAUGHT       .       .          .
+boundary        .            .             .            .            CAUGHT  .          .
+dt_unscaled     .            .             .            .            .       CAUGHT     .
+density         .            .             .            .            .       .          CAUGHT
+```
+
+Each fault is caught by its own check and by no other, and the clean model is robust everywhere. The
+bugs are described in [docs/zoo.md](https://github.com/a7med7emedan/ABMfact/blob/main/docs/zoo.md) and marked `# FAULT` in the source.
+
+## Adapters
+
+| Adapter | For | Notes |
+|---|---|---|
+| `python` | any `run(params, seed, knobs)` callable | the fastest path |
+| `mesa` | Mesa 3 model classes | knobs map to constructor keywords; `pip install "abmfact[mesa]"` |
+| `netlogo` | `.nlogo` models through pynetlogo | knobs map to globals; needs a local NetLogo |
+| `command` | anything else: R, Julia, Java, C++ | reads JSON on stdin, prints JSON on stdout |
+
+Working examples for each live in [examples/](https://github.com/a7med7emedan/ABMfact/tree/main/examples). See [docs/adapters.md](https://github.com/a7med7emedan/ABMfact/blob/main/docs/adapters.md).
+
+## Limits
+
+ABMfact checks implementation choices that should not matter. It does not check whether the model is a
+good description of the world, and it cannot find a bug that changes no stated claim. Its power depends
+on the seeds you give it: an `INCONCLUSIVE` verdict is an honest answer, not a pass. Many comparisons are
+made in one audit, so treat a single marginal `SHIFTED` as a lead to investigate, not a conclusion.
+
+## Citing
+
+If ABMfact helps your work, please cite it using [CITATION.cff](https://github.com/a7med7emedan/ABMfact/blob/main/CITATION.cff) (GitHub shows a "Cite this
+repository" button). The idea it implements comes from:
+
+> Galán, J. M., Izquierdo, L. R., Izquierdo, S. S., Santos, J. I., del Olmo, R., López-Paredes, A., &
+> Edmonds, B. (2009). Errors and artefacts in agent-based modelling. *Journal of Artificial Societies and
+> Social Simulation*, 12(1), 1. https://www.jasss.org/12/1/1.html
+
+## Licence
+
+Apache-2.0. See [LICENSE](https://github.com/a7med7emedan/ABMfact/blob/main/LICENSE).