ontogen 1.2.0__tar.gz

ontogen-1.2.0/.gitignore

@@ -0,0 +1,16 @@
+__pycache__/
+*.pyc
+.venv/
+.pytest_cache/
+build/
+*.egg-info/
+.onto/
+# generated attestations, keys, live config (never commit)
+genomes/attest.json
+genomes/attest.md
+**/attest.json
+**/attest.md
+.pypirc
+*.pypirc
+config.toml
+dist/

ontogen-1.2.0/.python-version

@@ -0,0 +1 @@
+3.13

ontogen-1.2.0/CLAUDE.md

@@ -0,0 +1,46 @@
+# v1 — project operating system (read FIRST in every session)
+
+You are the ribosome of this project: cheap, forgetful, replaceable. Meaning lives in
+the documents, not in the session. This file is your O(k) context.
+
+## What this is
+A living compiler of ontologies (docs/design/SPEC.md §0). Numbering: **v0 = ../archgen**
+(a donor of scars, NOT a donor of code, except what's listed in docs/log/PLAN.md), **v1 = here**.
+
+## Constitution of the method
+docs/design/MODEL.md — the universal model of development (layers, cycle, roles, coverage,
+the UNIVERSAL roadmap). On conflict with it, SPEC refines the mechanisms.
+
+## If you are the OPERATOR of an organism (feature/operation, not core development)
+Read docs/OPERATOR.md + `onto explain <root> <entity>` — that's enough;
+the rest here is for engine developers.
+
+## Reading order (for a new session 1–3 is enough)
+1. this file; 2. docs/log/PLAN.md — where we are (phase statuses); 3. docs/log/JOURNAL.md — the last
+2–3 entries. Deeper as needed: docs/design/SPEC.md (architecture), docs/design/NOT.md (prohibitions),
+docs/log/DECISIONS.md (why it's so), docs/design/SCARS.md (v0), docs/log/PREDICTIONS.md (what to check).
+
+## Hierarchy of truth (on conflict, the upper one wins)
+1. the user's word in the current session → 2. docs/log/DECISIONS.md (accepted decisions)
+→ 3. SPEC/NOT → 4. PLAN → 5. JOURNAL/chats/artifacts (derived).
+A contradiction between documents = a bug: fix the document, record it in JOURNAL.
+
+## Session protocol (mandatory)
+- START: read points 1–3; do NOT begin code if the phase is unclear.
+- WORK: a new decision → a line in docs/log/DECISIONS.md (D-number, status, why);
+  a cancelled one — supersede, don't delete. Inexpressible/dropped → docs/design/UNEXPRESSIBLE.md
+  (create on the first occurrence). An idea outside the current phase → JOURNAL "parking,"
+  do NOT implement (NOT §26).
+- FINISH: an entry in docs/log/JOURNAL.md (what was done/decided/opened, 5–10 lines) +
+  `git add v1 && git commit` — a wave without a commit does not exist (S7 v0).
+- PHASE EXAM: walk through docs/log/PREDICTIONS.md — fulfilled/not, mark it.
+
+## Hard prohibitions (full list — docs/design/NOT.md, 36 items)
+The core knows no languages (I1); no regex-DSL; extra=allow is forbidden;
+F1 — an interpreter WITHOUT code generation; commit only v1/ (don't touch archgen);
+"from the theorem" only for Derived; no batches in the ribosome.
+
+## Artifacts outside the repo
+"Anatomy of v1" diagram: claude.ai/code/artifact/2515e15d-cb36-410d-ab78-e97f94d5ed54
+(source — docs/anatomy.html, edit it and republish to the same URL).
+Claude memory: ~/.claude/projects/-home-the maintainer-dnaContract/memory/.

ontogen-1.2.0/LICENSE

@@ -0,0 +1,190 @@
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+
+   APPENDIX: How to apply the Apache License to your work.
+
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ontogen-1.2.0/PKG-INFO

@@ -0,0 +1,100 @@
+Metadata-Version: 2.5
+Name: ontogen
+Version: 1.2.0
+Summary: onto: a living ontology compiler — programs are genomes; code is a proven, printed phenotype
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: code-generation,compiler,formal-verification,genome,ontology,smt
+Requires-Python: <3.14,>=3.13
+Requires-Dist: mcp>=2.0.0
+Requires-Dist: pydantic>=2.7
+Requires-Dist: pyyaml>=6
+Requires-Dist: z3-solver>=4.13
+Description-Content-Type: text/markdown
+
+# onto — a living compiler of ontologies
+
+A program is stored not as code, but as a **genome**: entities, rules with
+executable bodies, contracts, invariants. Code is the phenotype: printed into
+dialects (Go, Python), proven by the court (SMT), living under a warden, and
+regrown from scratch. A change in behavior without confirmation is a question with an
+executable counterexample, not a silent merge.
+
+```bash
+uv tool install ontogen                # -> global `onto`
+onto validate genomes/hotel.yaml       # typecheck the genome
+onto court    genomes/hotel.yaml       # SMT court: contracts proven, mutants distinguished
+onto serve    genomes/hotel.yaml --port 8090 --data ./data [--store sqlite]
+onto warden   genomes/hotel.yaml ...   # daemon: watch -> gates -> molt -> monitors
+onto materialize genomes/hotel.yaml --dialect go-stdlib   # print the phenotype
+onto mcp      genomes/hotel.yaml       # a mouth for the LLM (propose = the only write)
+```
+
+## Models: bring your own (any OpenAI-compatible provider)
+
+Configure providers and per-task model ladders in `.onto/config.toml` —
+OpenRouter, OpenAI, Groq, Together, DeepSeek, a local Ollama/vLLM, anything
+OpenAI-compatible. Name a known provider and give only a key (base_url is a
+preset); reference models as `provider:model` or bare. Keys come from
+`${ENV}` or `@keyfile`, never hardcoded. `onto models` shows the registry.
+
+```toml
+[default]
+provider = "openrouter"
+[provider.openrouter]
+api_key = "${OPENROUTER_API_KEY}"
+[provider.local]
+base_url = "http://localhost:11434/v1"   # Ollama
+api_key = "ollama"
+[ladders]
+skills = ["qwen/qwen3-coder", "qwen/qwen3-coder-plus"]
+nl     = ["anthropic/claude-sonnet-4.5", "local:qwen2.5-coder"]
+```
+
+## Quickstart (zero machine)
+
+```bash
+curl -LsSf https://astral.sh/uv/install.sh | sh   # 1. uv (brings its own Python)
+uv tool install ontogen                           # 2. the engine, isolated
+onto init                                         # 3. couple this project + harness
+#    -> .onto/ + genome/ + MCP registration + edit-guard hook + skill
+onto court genome/genome.yaml                     # prove (ALL PROVED)
+onto serve genome/genome.yaml --data .onto/data   # live organism from second zero
+```
+
+The harness (Claude Code) sees the MCP server immediately; it changes
+behavior only through `propose` (checkers + SMT court + semantic diff), and
+a hook blocks any direct edit of the genome or the printed phenotype.
+Dialect toolchains (e.g. Go/JVM) are pulled lazily, only at `materialize`.
+
+## Status: 1.2.0 — the U1-U8 constitution is closed, IR v1.0 is frozen (D72)
+
+## End-to-end scenario (IDEAL, works)
+A natural-language product description -> `nlfront` builds a genome+acceptance -> the COURT proves
+-> the organism lives (warden timers, /admin, /list, /q?params, webhooks)
+-> any language is grown by the model (`growdialect`). Exams: exams/fnl.py,
+exams/fideal.py, exams/fgrow.py.
+
+## Where to look
+| you need | read |
+|---|---|
+| HOW any software is developed under this model | **`docs/design/MODEL.md`** — the method's constitution |
+| to run an organism (features, operation) | `docs/OPERATOR.md` + `onto explain <root> <entity>` |
+| engine development | `CLAUDE.md` -> `docs/log/PLAN.md` -> `docs/log/JOURNAL.md` |
+| architecture and decisions | `docs/design/SPEC.md`, `docs/log/DECISIONS.md` (D1–D87) |
+| what we don't do and why | `docs/design/NOT.md`, `docs/design/SCARS.md` (v0 scars), `docs/design/UNEXPRESSIBLE.md` |
+| visual diagram | `docs/anatomy.html` |
+
+## What the exams have proven (exams/, all green)
+the organism lives via an interpreter without code generation; one judge is green on
+interpreter+Go+Python; contracts are proven (COURT), 21/21 mutants
+distinguished, an equivalent mutant recognized; gene composition (payments in three
+domains byte-for-byte); metabolism by measured heat with failure-with-arithmetic;
+warden: molt in 0.3s, migration of 30k live events by functor, REVOKE of rights;
+live CEGIS with an SLM (~$0.001/skill); a membrane for others' organisms (drift ->
+trust revocation); 25k ev/s ingest, p99 1.8ms, kill -9 -> start from snapshot
+0.01s; jsonl|sqlite store with a byte-identical fold. Running the whole battery:
+`tools/check.sh`.
+
+Status: the engine is built and delivered exam by exam (see `docs/log/PLAN.md`); open —
+calendar operation and the external operator (F7).

ontogen-1.2.0/README.md

@@ -0,0 +1,86 @@
+# onto — a living compiler of ontologies
+
+A program is stored not as code, but as a **genome**: entities, rules with
+executable bodies, contracts, invariants. Code is the phenotype: printed into
+dialects (Go, Python), proven by the court (SMT), living under a warden, and
+regrown from scratch. A change in behavior without confirmation is a question with an
+executable counterexample, not a silent merge.
+
+```bash
+uv tool install ontogen                # -> global `onto`
+onto validate genomes/hotel.yaml       # typecheck the genome
+onto court    genomes/hotel.yaml       # SMT court: contracts proven, mutants distinguished
+onto serve    genomes/hotel.yaml --port 8090 --data ./data [--store sqlite]
+onto warden   genomes/hotel.yaml ...   # daemon: watch -> gates -> molt -> monitors
+onto materialize genomes/hotel.yaml --dialect go-stdlib   # print the phenotype
+onto mcp      genomes/hotel.yaml       # a mouth for the LLM (propose = the only write)
+```
+
+## Models: bring your own (any OpenAI-compatible provider)
+
+Configure providers and per-task model ladders in `.onto/config.toml` —
+OpenRouter, OpenAI, Groq, Together, DeepSeek, a local Ollama/vLLM, anything
+OpenAI-compatible. Name a known provider and give only a key (base_url is a
+preset); reference models as `provider:model` or bare. Keys come from
+`${ENV}` or `@keyfile`, never hardcoded. `onto models` shows the registry.
+
+```toml
+[default]
+provider = "openrouter"
+[provider.openrouter]
+api_key = "${OPENROUTER_API_KEY}"
+[provider.local]
+base_url = "http://localhost:11434/v1"   # Ollama
+api_key = "ollama"
+[ladders]
+skills = ["qwen/qwen3-coder", "qwen/qwen3-coder-plus"]
+nl     = ["anthropic/claude-sonnet-4.5", "local:qwen2.5-coder"]
+```
+
+## Quickstart (zero machine)
+
+```bash
+curl -LsSf https://astral.sh/uv/install.sh | sh   # 1. uv (brings its own Python)
+uv tool install ontogen                           # 2. the engine, isolated
+onto init                                         # 3. couple this project + harness
+#    -> .onto/ + genome/ + MCP registration + edit-guard hook + skill
+onto court genome/genome.yaml                     # prove (ALL PROVED)
+onto serve genome/genome.yaml --data .onto/data   # live organism from second zero
+```
+
+The harness (Claude Code) sees the MCP server immediately; it changes
+behavior only through `propose` (checkers + SMT court + semantic diff), and
+a hook blocks any direct edit of the genome or the printed phenotype.
+Dialect toolchains (e.g. Go/JVM) are pulled lazily, only at `materialize`.
+
+## Status: 1.2.0 — the U1-U8 constitution is closed, IR v1.0 is frozen (D72)
+
+## End-to-end scenario (IDEAL, works)
+A natural-language product description -> `nlfront` builds a genome+acceptance -> the COURT proves
+-> the organism lives (warden timers, /admin, /list, /q?params, webhooks)
+-> any language is grown by the model (`growdialect`). Exams: exams/fnl.py,
+exams/fideal.py, exams/fgrow.py.
+
+## Where to look
+| you need | read |
+|---|---|
+| HOW any software is developed under this model | **`docs/design/MODEL.md`** — the method's constitution |
+| to run an organism (features, operation) | `docs/OPERATOR.md` + `onto explain <root> <entity>` |
+| engine development | `CLAUDE.md` -> `docs/log/PLAN.md` -> `docs/log/JOURNAL.md` |
+| architecture and decisions | `docs/design/SPEC.md`, `docs/log/DECISIONS.md` (D1–D87) |
+| what we don't do and why | `docs/design/NOT.md`, `docs/design/SCARS.md` (v0 scars), `docs/design/UNEXPRESSIBLE.md` |
+| visual diagram | `docs/anatomy.html` |
+
+## What the exams have proven (exams/, all green)
+the organism lives via an interpreter without code generation; one judge is green on
+interpreter+Go+Python; contracts are proven (COURT), 21/21 mutants
+distinguished, an equivalent mutant recognized; gene composition (payments in three
+domains byte-for-byte); metabolism by measured heat with failure-with-arithmetic;
+warden: molt in 0.3s, migration of 30k live events by functor, REVOKE of rights;
+live CEGIS with an SLM (~$0.001/skill); a membrane for others' organisms (drift ->
+trust revocation); 25k ev/s ingest, p99 1.8ms, kill -9 -> start from snapshot
+0.01s; jsonl|sqlite store with a byte-identical fold. Running the whole battery:
+`tools/check.sh`.
+
+Status: the engine is built and delivered exam by exam (see `docs/log/PLAN.md`); open —
+calendar operation and the external operator (F7).

ontogen-1.2.0/cache_skills/0c200ceb12f4186b.py

@@ -0,0 +1,45 @@
+def fast_match_orders(bids, asks):
+    # Filter out orders with qty <= 0
+    bids = [b for b in bids if b.qty > 0]
+    asks = [a for a in asks if a.qty > 0]
+    
+    # Sort bids: highest price first, then earliest ts, then lex id
+    bids.sort(key=lambda x: (-x.price, x.ts, x.id))
+    # Sort asks: lowest price first, then earliest ts, then lex id
+    asks.sort(key=lambda x: (x.price, x.ts, x.id))
+    
+    trades = []
+    i, j = 0, 0  # pointers for bids and asks
+    
+    while i < len(bids) and j < len(asks):
+        bid = bids[i]
+        ask = asks[j]
+        
+        # Check if they can match
+        if bid.price >= ask.price:
+            # Match quantity is the minimum of remaining quantities
+            match_qty = min(bid.qty, ask.qty)
+            if match_qty > 0:
+                # Create trade at ask's price
+                trade = {
+                    "bid": bid.id,
+                    "ask": ask.id,
+                    "price": ask.price,
+                    "qty": match_qty
+                }
+                trades.append(trade)
+                
+                # Update remaining quantities
+                bid.qty -= match_qty
+                ask.qty -= match_qty
+            
+            # Move to next order if current is fully filled
+            if bid.qty == 0:
+                i += 1
+            if ask.qty == 0:
+                j += 1
+        else:
+            # No more matches possible due to price mismatch
+            break
+    
+    return trades

ontogen-1.2.0/cache_skills/664dcf149808d805.py

@@ -0,0 +1,34 @@
+def fast_allocate(demands, stocks):
+    # Aggregate available stock by SKU
+    stock_dict = {}
+    for st in stocks:
+        stock_dict[st.sku] = stock_dict.get(st.sku, 0) + st.available
+    
+    # Sort demands: higher priority first, then by id ascending
+    sorted_demands = sorted(demands, key=lambda d: (-d.priority, d.id))
+    
+    allocations = []
+    # Track how much has been allocated per demand and per sku
+    allocated_to_demand = {d.id: 0 for d in demands}
+    allocated_per_sku = {sku: 0 for sku in stock_dict}
+
+    for demand in sorted_demands:
+        remaining_demand = demand.qty - allocated_to_demand[demand.id]
+        if remaining_demand <= 0:
+            continue
+        
+        available_stock = stock_dict.get(demand.sku, 0) - allocated_per_sku.get(demand.sku, 0)
+        if available_stock <= 0:
+            continue
+
+        alloc_qty = min(remaining_demand, available_stock)
+        if alloc_qty > 0:
+            allocations.append({
+                "id": demand.id,
+                "sku": demand.sku,
+                "qty": alloc_qty
+            })
+            allocated_to_demand[demand.id] += alloc_qty
+            allocated_per_sku[demand.sku] += alloc_qty
+
+    return allocations

ontogen-1.2.0/cache_skills/allocate.fast.py

@@ -0,0 +1,34 @@
+def fast_allocate(demands, stocks):
+    # Aggregate available stock by SKU
+    stock_dict = {}
+    for st in stocks:
+        stock_dict[st.sku] = stock_dict.get(st.sku, 0) + st.available
+    
+    # Sort demands: higher priority first, then by id ascending
+    sorted_demands = sorted(demands, key=lambda d: (-d.priority, d.id))
+    
+    allocations = []
+    # Track how much has been allocated per demand and per sku
+    allocated_to_demand = {d.id: 0 for d in demands}
+    allocated_per_sku = {sku: 0 for sku in stock_dict}
+
+    for demand in sorted_demands:
+        remaining_demand = demand.qty - allocated_to_demand[demand.id]
+        if remaining_demand <= 0:
+            continue
+        
+        available_stock = stock_dict.get(demand.sku, 0) - allocated_per_sku.get(demand.sku, 0)
+        if available_stock <= 0:
+            continue
+
+        alloc_qty = min(remaining_demand, available_stock)
+        if alloc_qty > 0:
+            allocations.append({
+                "id": demand.id,
+                "sku": demand.sku,
+                "qty": alloc_qty
+            })
+            allocated_to_demand[demand.id] += alloc_qty
+            allocated_per_sku[demand.sku] += alloc_qty
+
+    return allocations

ontogen-1.2.0/cache_skills/allocate.naive.py

@@ -0,0 +1,34 @@
+def naive_allocate(demands, stocks):
+    # Aggregate available stock by SKU
+    stock_dict = {}
+    for st in stocks:
+        stock_dict[st.sku] = stock_dict.get(st.sku, 0) + st.available
+    
+    # Sort demands: higher priority first, then by id ascending
+    sorted_demands = sorted(demands, key=lambda d: (-d.priority, d.id))
+    
+    allocations = []
+    # Track how much has been allocated per demand and per sku
+    allocated_to_demand = {d.id: 0 for d in demands}
+    allocated_per_sku = {sku: 0 for sku in stock_dict}
+
+    for demand in sorted_demands:
+        remaining_demand = demand.qty - allocated_to_demand[demand.id]
+        if remaining_demand <= 0:
+            continue
+        
+        available_stock = stock_dict.get(demand.sku, 0) - allocated_per_sku.get(demand.sku, 0)
+        if available_stock <= 0:
+            continue
+
+        alloc_qty = min(remaining_demand, available_stock)
+        if alloc_qty > 0:
+            allocations.append({
+                "id": demand.id,
+                "sku": demand.sku,
+                "qty": alloc_qty
+            })
+            allocated_to_demand[demand.id] += alloc_qty
+            allocated_per_sku[demand.sku] += alloc_qty
+
+    return allocations

ontogen-1.2.0/cache_skills/c5f84ddd6a2c7547.py

@@ -0,0 +1,28 @@
+def fast_allocate(demands, stocks):
+    # Create a copy of available stock quantities that we can modify
+    stock_available = {st.sku: st.available for st in stocks}
+    
+    # Sort demands by priority (descending) then by id (ascending)
+    sorted_demands = sorted(demands, key=lambda d: (-d.priority, d.id))
+    
+    allocations = []
+    
+    for demand in sorted_demands:
+        # Check if there's any stock available for this SKU
+        if demand.sku in stock_available and stock_available[demand.sku] > 0:
+            # Allocate the minimum of what's demanded and what's available
+            alloc_qty = min(demand.qty, stock_available[demand.sku])
+            
+            # Only create an allocation if qty > 0
+            if alloc_qty > 0:
+                # Create allocation as a dict
+                allocations.append({
+                    "id": demand.id,
+                    "sku": demand.sku,
+                    "qty": alloc_qty
+                })
+                
+                # Reduce available stock
+                stock_available[demand.sku] -= alloc_qty
+    
+    return allocations

ontogen-1.2.0/cache_skills/e254e5f29b990b38.py

@@ -0,0 +1,34 @@
+def naive_allocate(demands, stocks):
+    # Aggregate available stock by SKU
+    stock_dict = {}
+    for st in stocks:
+        stock_dict[st.sku] = stock_dict.get(st.sku, 0) + st.available
+    
+    # Sort demands: higher priority first, then by id ascending
+    sorted_demands = sorted(demands, key=lambda d: (-d.priority, d.id))
+    
+    allocations = []
+    # Track how much has been allocated per demand and per sku
+    allocated_to_demand = {d.id: 0 for d in demands}
+    allocated_per_sku = {sku: 0 for sku in stock_dict}
+
+    for demand in sorted_demands:
+        remaining_demand = demand.qty - allocated_to_demand[demand.id]
+        if remaining_demand <= 0:
+            continue
+        
+        available_stock = stock_dict.get(demand.sku, 0) - allocated_per_sku.get(demand.sku, 0)
+        if available_stock <= 0:
+            continue
+
+        alloc_qty = min(remaining_demand, available_stock)
+        if alloc_qty > 0:
+            allocations.append({
+                "id": demand.id,
+                "sku": demand.sku,
+                "qty": alloc_qty
+            })
+            allocated_to_demand[demand.id] += alloc_qty
+            allocated_per_sku[demand.sku] += alloc_qty
+
+    return allocations