Axiomize

Reproducible scientific modeling that survives contact with reality. Axiomize turns a vague idea into an explicit, versioned mathematical model, validates it dimensionally and numerically, and exports an artifact someone else can re-run years from now.

This is not the numerical-methods library. That door is scientific-computing-system. Axiomize is the modeling layer: mandatory units, a versioned Model IR, and export to SBML, CellML, and Modelica. The MCP server is axiomize mcp.

mcp-name: io.github.Furox-Art/axiomize

Current package line: 1.14.1 on PyPI and npm.

Documentation: furox-art.github.io/axiomize · Changelog: CHANGELOG.md · Roadmap: ROADMAP.md · Security: SECURITY.md · Contributing: CONTRIBUTING.md · Code of conduct: CODE_OF_CONDUCT.md · Cite: CITATION.cff

Why

I got tired of scientific models that live in Jupyter notebooks and die there.

Someone writes a beautiful simulation, it works on their machine, they graduate or change jobs, and six months later nobody can run it. The dependencies are broken, the data is missing, and the "documentation" is a 47-cell notebook with no explanation.

Axiomize forces models to be explicit, versioned, testable code instead of exploratory spaghetti. Every assumption is written down. Every parameter carries a unit. Every result carries enough provenance that another person, on another machine, can reproduce it.

Who it is for

If you are…	Start here
A scientist whose result has to be defensible in review	Why and the example gallery
An engineer sizing capacity, reliability, or inventory	CLI quickstart and axiomize solve / axiomize fit
Building an agent that should reason with numbers, not vibes	axiomize capabilities, then MCP or REST
Reproducing or auditing someone else's published model	axiomize model --action numerical-verify and portable export

Not a fit: if you want a black-box predictor with no inspectable assumptions, or if you need the engine to make scientific claims for you without a human in the loop.

Install

pip install axiomize

Optional extras: pip install "axiomize[full]" for PyMC/JAX Bayesian sampling.

The playground extra installs gradio and pandas but ships no UI: playground/app.py is not in the wheel or the sdist, so pip install "axiomize[playground]" alone leaves you with dependencies and nothing to run. To use it, get the file from the repository:

git clone https://github.com/Furox-Art/axiomize
pip install "axiomize[playground]"
python axiomize/playground/app.py

Python in five minutes

Declare the model, then let Axiomize check it. Units are mandatory, so dimensional mistakes fail loudly instead of producing a meaningless number. This block is the model in examples/quickstart_sir.py, field for field.

from axiomize.general_engine import simulate_model
from axiomize.model_ir import ModelIR

model = ModelIR.from_dict({
    "schema_version": "1.0",
    "name": "sir-outbreak",
    "domain": "epidemiology",
    "family": "ode",
    "independent_variable": "t",
    "independent_unit": "day",
    "variables": [
        {"name": "S", "unit": "person", "initial": 990.0, "bounds": [0.0, None]},
        {"name": "I", "unit": "person", "initial": 10.0, "bounds": [0.0, None]},
    ],
    "parameters": [
        {"name": "beta", "unit": "1/day", "value": 0.3, "bounds": [0.0, None]},
        {"name": "gamma", "unit": "1/day", "value": 0.1, "bounds": [0.0, None]},
        {"name": "N", "unit": "persons", "value": 1000.0},
    ],
    "equations": [
        {"target": "S", "expression": "-beta*I*S/N", "kind": "derivative"},
        {"target": "I", "expression": "beta*I*S/N - gamma*I", "kind": "derivative"},
    ],
    "constraints": [
        {"name": "cases_nonnegative", "expression": "I", "relation": "ge",
         "threshold": 0.0, "scientific_basis": "case counts cannot be negative"},
    ],
    "assumptions": ["closed population of 1000", "homogeneous mixing"],
})

result = simulate_model(model, t_span=(0.0, 30.0), points=4)
print(f"status: {result['status']}")
print(f"solver: {result['solver']['backend']} / {result['solver']['method']}")
print(f"days:   {result['time']}")
print(f"infected: {[round(v, 3) for v in result['states']['I']]}")
print(f"checks: {result['validation']['status']} ({len(result['validation']['checks'])} of them)")

Real output, and byte-identical to python examples/quickstart_sir.py:

status: PASS
solver: scipy / DOP853
days:   [0.0, 10.0, 20.0, 30.0]
infected: [10.0, 65.393, 239.869, 290.024]
checks: PASS (25 of them)

CLI in five minutes

Every command prints JSON you can pipe.

# What is actually installed, and is it usable? Backends report honestly.
axiomize capabilities

# Clarify a vague idea before any numbers get committed.
axiomize intake "Reduce traffic congestion in a mid-size city"

# Check a model against closed-form theory, not just vibes.
axiomize-validate --model sir --beta 0.3 --gamma 0.1

axiomize-validate output on those inputs:

=== SIR validation ===
horizon                = 180 days  (final-size theory is the t->infinity limit)
R0                     = 3.000  (outbreak)
Peak infected          = 300,465 at day 61.4
Final size (simulated) = 0.9404
Final size (theory)    = 0.9405
Theory match           = True

--- sanity checks ---
population_conserved                PASS
compartments_nonnegative            PASS
R_monotonic_increase                PASS

The two flags that matter once you leave the reference model are --input-json (the Model IR request as a file) and --approve-heavy (authorizes repeated refinement runs):

# Without --approve-heavy the study is refused rather than run silently.
axiomize model --action numerical-verify --input-json request.json
# status: APPROVAL_REQUIRED, study: solver_tolerance_refinement

axiomize model --action numerical-verify --input-json request.json --approve-heavy
# status: PASS, uncertainty_separation.numerical: 6.6100987239990846e-11

Step-by-step versions of all of this, with the request files, are in docs/quickstart.md.

Surface map

The engine is 68 public modules behind four interfaces. This README names the whole CLI and the shape of the two servers; the per-module detail belongs in docs/integrations.md.

Console scripts (8)

Command	Does
axiomize	The main CLI. 14 subcommands, below.
axiomize-validate	Closed-form theory checks for the three reference models: sir, gillespie, queue
axiomize-fit	Calibrate sir or logistic against a time,value CSV; --selftest runs the built-in checks
axiomize-csv-check	Data quality on an observation file: gaps, duplicates, outliers via modified z-score
axiomize-benchmark	Grades a produced report against a case in benchmarks/ideas.json
axiomize-to-latex	Converts a standardized report to LaTeX, optionally --pdf. This is the only LaTeX path in the project; it is not a model export format.
axiomize-index-reports	Rebuilds reports/INDEX.md from the reports in a directory
axiomize-sweep	Parallel parameter sweeps (--job sweep, --job mc)

axiomize subcommands (14)

intake · policy · model · clean-data · compare-runs · solve · fit · validate · tools · capabilities · reproduce · benchmark · serve · mcp

tools and capabilities report backend availability; policy reports what the agent is allowed to spend; reproduce and compare-runs work on stored run directories.

axiomize model --action (16)

Family	Values
Model lifecycle	plan · validate · simulate · fit · compare · repair · export
Analysis	stability · validity · discover · experiment-design · uncertainty · bifurcation
Verification	numerical-verify · stop-check · surrogate

MCP and REST

The MCP server exposes 35 tools named axiomize.<verb>. axiomize.model_* mirrors the model --action values above; the unprefixed names (solve, fit_model, cross_validate, sensitivity_analysis, uncertainty_analysis, falsify, compare_models, intake, workflow_policy, clean_data, compare_runs, experiment_design, inspect_run, reproduce, get_capabilities, list_tools, select_tools) cover the surrounding workflow. Enumerate them rather than trusting a list:

axiomize mcp        # stdio transport; send tools/list over stdin

The REST server serves 30 route handlers (26 POST, plus GET /tools, /capabilities, /workflow-policy and /runs/{id}) under a /v1 prefix, on loopback by default:

axiomize serve --port 8765
curl -s http://127.0.0.1:8765/v1/capabilities

Both surfaces are larger than any README can enumerate honestly, which is why the naming convention matters more than the list. Both counts come from the installed handlers.

Model export formats

axiomize model --action export --input-json request.json dispatches on the "format" field. What actually returns PASS for a given model:

Format	Status	Notes
json	yes	Canonical Model IR, sorted keys
python	yes	Rerunnable script that re-imports the IR
yaml	yes	Needs PyYAML; otherwise TOOL_UNAVAILABLE
ipynb	yes	nbformat 4 notebook
sbml-l3v2	yes	SBML Level 3 Version 2 Core
modelica	yes	Modelica 3.6 text
portable-bundle	yes	axiomize.portable-bundle.v1 with a SHA-256 over canonical IR
graphml	conditional	Needs family: network IR with metadata.network
causal-dot	conditional	Needs family: causal IR with identification metadata
cellml-2.0	conditional	Passes for supported units; ADAPTER_REQUIRED naming the ones it will not reinterpret
sbml, cellml	no	Unversioned aliases deliberately return ADAPTER_REQUIRED

LaTeX is not in this dispatch chain. latex, tex and pdf raise ValueError: format must be json, python, yaml, sbml, or cellml. Use axiomize-to-latex on a written report instead.

Content in the repository

What	Where	Count
Domain packs	packs/	12
Perspective lenses	skills/axiomize/perspectives/	15
Report templates	skills/axiomize/templates/	5
Worked examples	examples/	18 .md + quickstart_sir.py
MCP registry manifest	server.json	1

server.json is what the MCP registry reads to publish axiomize mcp; its mcp-name line is repeated at the top of this README for clients that scrape it.

Adoption path

1. Try it on something you already believe. Recreate a model you trust with axiomize-validate. If the engine disagrees with a result you can defend, stop here and open an issue.
2. Move one real question onto Model IR. Declare units and constraints explicitly. The dimensional checks are where the value shows up first.
3. Gate the expensive steps. Discretized families return APPROVAL_REQUIRED until you pass --approve-heavy. Approval authorizes compute; it never disables a resource ceiling.
4. Export something portable. axiomize model --action export emits canonical IR JSON, and SBML, CellML or Modelica for supported models, so the artifact outlives this library.
5. Wire it into review. Ship the exported IR and the validation record alongside the result, not just a figure.

What it actually does

• Validates dimensional consistency, so you cannot add meters to seconds
• Refuses to simulate a model that fails those checks: execution goes through the same validation as axiomize model --action validate, and a mismatch raises ModelDimensionMismatch carrying the failing checks instead of returning numbers
• Enforces scientific constraints as named, justified checks rather than prose
• Separates numerical error from stochastic variability before claiming convergence
• Compares candidate model families and records why one was chosen
• Exports to JSON, Python, YAML, notebooks, SBML Level 3, CellML 2.0, Modelica, GraphML, Graphviz DOT and a SHA-256 portable bundle; see the format table for which of those are conditional. Values and units round-trip bit-exactly, and that is asserted in the suite rather than assumed
• Converts written reports to LaTeX via axiomize-to-latex, which is a separate path
• Keeps an integrity-checked run ledger, so a stored result can be verified before use

Honest limits

• It does not make a bad model good. It makes a bad model fail loudly.
• Bayesian sampling needs the full extra (PyMC/JAX); FEM needs FEniCS/DOLFINx. Both are reported as unavailable rather than silently substituted.
• Benchmark results grade report structure in blind runs, not modeling correctness. Only the table carrying script, case-set and commit hashes is reproducible; the older waves are kept as history and cannot be rerun.
• Worked examples use illustrative parameter ranges labelled lit. / data / est.. No example cites an external source, so treat the numbers as reading material rather than literature-backed results.
• Generated-code execution and theorem elaboration are not an OS sandbox. See SECURITY.md.

Documentation

• Quickstart and workflow: furox-art.github.io/axiomize
• Worked examples: example gallery, or the 19 files in examples/
• Domain packs (which lenses matter per field): packs/domain-packs.md
• Agent integration (MCP, REST, CLI): docs/integrations.md
• Portable export formats: docs/portable-export.md
• Trust boundaries and reporting: SECURITY.md, docs/security.md
• Agent skill pack: skills/axiomize/SKILL.md, plus the 15 perspective lenses

Supply chain

PyPI 1.12.5 is published with PEP 740 attestations: both the wheel and the sdist serve a Sigstore bundle naming Furox-Art/axiomize via release.yml, environment pypi, and each attested digest matches the file you download. You can confirm that before installing.

npm 1.12.5 is not attested. It was published with a long-lived NPM_TOKEN, which cannot mint an attestation, so that tarball is digest-verifiable only:

npm view axiomize@1.12.5 dist.integrity   # pin this; npm ci enforces it from a lockfile

Three different things are easy to confuse. A PEP 740 attestation says a build workflow signed this exact file digest. npm dist.signatures says only that the registry has not altered its own metadata — every npm version has those, token or OIDC, and they are not build provenance. dist.integrity / digests.sha256 say the bytes you have are the bytes that were published, but not who built them.

Pinning by digest is the honest recommendation today. Registering the npm trusted publisher (owner Furox-Art, repository axiomize, workflow release.yml, environment npm) is what would close the npm gap; PyPI's is already registered. Verification commands, the per-file PyPI endpoint shape, and what each of the three proves are in docs/documentation.md, and CI re-checks the claims above against both registries on every run.

npm

npx axiomize works and forwards to python -m axiomize.cli, so it needs Python and pip install axiomize underneath; it is not a standalone binary. npm 1.12.2 is published and broken (index.js had a syntax error); 1.12.4 is the first working release.

License

MIT. Use it, break it, fix it.