Decompose codegen/api.py into a vera/runtime/ package (#421)

[aallan]

Summary

Decomposes the 4,358-line vera/codegen/api.py public-API module, extracting the wasmtime execution runtime into a new vera/runtime/ package. api.py: 4,358 → 1,165 lines (−73%), one layer per commit, each kept green against the #734 characterization harness.

Closes #421.

What moved to vera/runtime/

Infrastructure

• ADT memory-layout utilities (ConstructorLayout, alignment helpers) → vera/codegen/memory.py
• Trap classification + source backtraces (WasmTrapError, _classify_trap, _resolve_trap_frames) → runtime/traps.py
• WASM heap marshalling — memory read/write, GC shadow-rooting, the ADT / Option / Array / Map-Set-bucket codecs — → runtime/heap.py
• The Map/Set value-type dispatch table → runtime/collections.py

The twelve optional effect families → one register_<family>(linker, …) module each:
random, math, md, json, regex, html, map, set, decimal, http, inference, state.

execute() now calls these in sequence instead of inlining ~3,000 lines of branches. Shared state a family needs is passed explicitly (e.g. register_decimal(linker, ops, decimal_store, host_store_refs)).

What stayed inline — and why

The always-on IO family stays in execute() by design. Unlike the twelve pluggable adapters (registered conditionally, owning their own state, feeding nothing back into the result), IO is execute()'s observation channel: its host callbacks write into state that becomes the return value — output_buf/stderr_buf → ExecuteResult.stdout/stderr, last_violation → the trap diagnostic via _classify_trap, tee_stdout → the live-streaming decision — and it shares the _VeraExit Ctrl-C exception with execute()'s exit handling. Extracting the twelve adapters reduced coupling; extracting IO would only relocate a naturally-cohesive unit across a file boundary behind a 7-field context object. The decision and its reasoning are documented in vera/README.md → "Host-binding families (vera/runtime/)", a heading comment on api.py's IO section, and the runtime/__init__ docstring.

Public surface — unchanged

from vera.codegen.api import compile, execute, CompileResult, ExecuteResult, WasmTrapError and from vera.codegen import ConstructorLayout all still resolve. The compiled .wasm import interface is byte-for-byte identical. Internal refactor; no behaviour change.

Verification

• The Characterization harness for execute() ahead of the runtime decomposition #734 characterization harness (22 tests pinning every ExecuteResult field × the three completion modes) stayed green through all 12 layers — it is the gate this decomposition was built behind.
• Each family extraction verified behaviorally: the family's codegen tests and an end-to-end conformance run (vera run); Decimal additionally under VERA_EAGER_GC=1 to stress the GC decref path the lift touched.
• mypy vera/ + ruff clean; full pytest suite + 92 conformance programs + 35 examples green on every layer's pre-commit.
• Source-location tests that pin host-function internals (host_print / host_stderr / host_contract_fail crash with raw Python UnicodeDecodeError on invalid UTF-8 bytes #589/HTTP / Inference network-response decode uses strict UTF-8 (Python error noise leaks into Result Err) #591 UTF-8 hygiene, the heap-string decoder) repointed to the new module homes.

Bonus

Lifting the ~3,000-line runtime out of the public-API module unblocks the deferred whole-vera/ mutation sweep (#387) — api.py's oversized execute() was inflating a 774 MB mutant file mutmut couldn't index.

🤖 Generated with Claude Code

Summary by CodeRabbit

• New Features
  • Expanded runtime-backed effects: HTML, JSON, regex, random, math, state, map, set, HTTP, markdown, inference, decimal, plus improved trap reporting.
• Bug Fixes
  • Reduce leftover temporary .vera files when checks/tests are interrupted.
  • Improved UTF-8 decode handling so errors are reported more cleanly.
• Documentation
  • Updated changelog, testing/coverage totals, known issues, and runtime documentation to reflect the latest capabilities.

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📥 Commits

Reviewing files that changed from the base of the PR and between 902b751 and f539a72.

📒 Files selected for processing (5)

• CHANGELOG.md
• KNOWN_ISSUES.md
• ROADMAP.md
• TESTING.md
• tests/test_codegen.py

📝 Walkthrough

Walkthrough

Decomposes vera/codegen/api.py by extracting memory helpers into vera/codegen/memory.py and host/runtime code into vera/runtime/ modules. Tests, docs, and temp-file handling are updated to reference the new module layout and runtime paths.

Changes

Runtime extraction and rewiring

Layer / File(s)	Summary
Memory helpers and import rewiring vera/codegen/memory.py, vera/codegen/__init__.py, vera/codegen/closures.py, vera/codegen/core.py, vera/codegen/registration.py	Adds ConstructorLayout plus WASM layout helpers in a new module, then updates codegen imports to source those symbols from vera.codegen.memory.
Runtime traps, heap, and collection primitives vera/runtime/__init__.py, vera/runtime/traps.py, vera/runtime/heap.py, vera/runtime/collections.py	Adds runtime package documentation, trap-frame classification, heap marshalling and wrapper helpers, and the shared value-type dispatch table.
HTTP and inference host bindings vera/runtime/http.py, vera/runtime/inference.py	Adds HTTP scheme validation and request bindings, plus inference provider selection, request execution, and UTF-8 decoding/error handling.
JSON, HTML, Markdown, and regex bindings vera/runtime/json.py, vera/runtime/html.py, vera/runtime/md.py, vera/runtime/regex.py	Adds parse/render/query/extract bindings for structured text effects and regex matching/replacement bindings.
Map and set host bindings vera/runtime/map.py, vera/runtime/set.py	Adds wrapper-based map and set host bindings, including insert/get/remove/query, size, and array conversion operations.
Math, random, state, and decimal bindings vera/runtime/math.py, vera/runtime/random.py, vera/runtime/state.py, vera/runtime/decimal.py	Adds scalar effect bindings for maths, randomness, per-type state stacks, and decimal arithmetic/conversion/rounding.
Tests, temp files, and project docs .gitignore, scripts/check_html_examples.py, tests/test_html.py, tests/test_codegen.py, tests/test_runtime_traps.py, CHANGELOG.md, KNOWN_ISSUES.md, TESTING.md, vera/README.md, ROADMAP.md	Updates temporary .vera file handling, rewires tests to the new runtime modules, adds runtime import-hygiene coverage, and refreshes project documentation and status tables.

Estimated code review effort

🎯 5 (Critical) | ⏱️ ~120 minutes

Possibly related issues

• Decompose vera/codegen/api.py (2,228 lines): extract memory layout and execution runtime #421 — This PR directly carries out the vera/codegen/api.py decomposition into vera/codegen/memory.py and the new vera/runtime/ host layer.
• Standalone WASM runtime package #163 — This PR continues the runtime host-binding extraction from vera/codegen/api.py into dedicated runtime modules.

Possibly related PRs

• aallan/vera#357: The HTTP effect bindings in this PR are extracted into vera/runtime/http.py, matching the HTTP effect surface introduced there.
• aallan/vera#533: This PR moves WasmTrapError and trap classification into vera/runtime/traps.py, which overlaps with the trap-categorisation surface in that PR.
• aallan/vera#546: TrapFrame, _resolve_trap_frames, and trap-frame reporting are part of the same backtrace machinery used in that PR.

Suggested labels

compiler, tests, ci, docs

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Out of Scope Changes check	⚠️ Warning	The PR also includes behaviour hardening and hygiene changes, such as HTTP scheme validation and math/shadow-guard fixes, beyond the decomposition scope.	Keep this PR focused on the api.py split; move the behavioural fixes and other follow-up hardening into separate PRs.
Docstring Coverage	⚠️ Warning	Docstring coverage is 54.71% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly states the main change: decomposing codegen/api.py into runtime package pieces for #421.
Linked Issues check	✅ Passed	The PR extracts the memory helpers and runtime host layer, keeps the public compile/execute surface stable, and adds supporting tests/docs.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feat/421-runtime-decomposition

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[codecov]

Codecov Report

❌ Patch coverage is 96.15680% with 50 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.88%. Comparing base (5452728) to head (f539a72).

Files with missing lines	Patch %	Lines
vera/runtime/heap.py	96.63%	14 Missing ⚠️
vera/runtime/map.py	92.56%	11 Missing ⚠️
vera/runtime/html.py	96.29%	5 Missing ⚠️
vera/runtime/regex.py	92.98%	4 Missing ⚠️
vera/codegen/memory.py	89.65%	3 Missing ⚠️
vera/runtime/http.py	91.66%	3 Missing ⚠️
vera/runtime/decimal.py	97.84%	2 Missing ⚠️
vera/runtime/inference.py	96.82%	2 Missing ⚠️
vera/runtime/math.py	91.66%	2 Missing ⚠️
vera/runtime/md.py	95.23%	2 Missing ⚠️
... and 1 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #789      +/-   ##
==========================================
+ Coverage   91.85%   91.88%   +0.02%     
==========================================
  Files          71       87      +16     
  Lines       26398    26493      +95     
  Branches      321      321              
==========================================
+ Hits        24249    24343      +94     
- Misses       2141     2142       +1     
  Partials        8        8              

Flag	Coverage Δ
javascript	65.33% <ø> (ø)
python	94.96% <96.15%> (+0.01%)	⬆️

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[coderabbitai]

Actionable comments posted: 4

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

scripts/check_html_examples.py (1)

103-113: 🩺 Stability & Availability | 🟠 Major | ⚡ Quick win

Fix Windows-incompatible tempfile handoff in subprocess checks.

Line 103 and Line 124 keep the temporary .vera file open with delete=True while passing its path to subprocess.run(...). That is not portable on Windows and can fail to reopen the file. Use delete=False, close before subprocess invocation, and unlink in finally; also pass encoding="utf-8" explicitly.

Suggested patch

 def try_check(content: str, root: Path) -> str | None:
     """Try to type-check content. Returns error message or None."""
-    with tempfile.NamedTemporaryFile(
-        mode="w", suffix=".vera", delete=True
-    ) as f:
-        f.write(content)
-        f.flush()
+    f = tempfile.NamedTemporaryFile(
+        mode="w", suffix=".vera", delete=False, encoding="utf-8"
+    )
+    try:
+        f.write(content)
+        f.close()
         result = subprocess.run(
             [sys.executable, "-m", "vera.cli", "check", f.name],
             capture_output=True,
             text=True,
             cwd=str(root),
             timeout=30,
         )
         if "OK:" in result.stdout:
             return None
         # Return first line of stderr or stdout for diagnostics
         err = result.stderr.strip() or result.stdout.strip()
         return err.split("\n")[0][:200]
+    finally:
+        Path(f.name).unlink(missing_ok=True)
@@
 def try_verify(content: str, root: Path) -> str | None:
     """Try to verify contracts. Returns error message or None."""
-    with tempfile.NamedTemporaryFile(
-        mode="w", suffix=".vera", delete=True
-    ) as f:
-        f.write(content)
-        f.flush()
+    f = tempfile.NamedTemporaryFile(
+        mode="w", suffix=".vera", delete=False, encoding="utf-8"
+    )
+    try:
+        f.write(content)
+        f.close()
         result = subprocess.run(
             [sys.executable, "-m", "vera.cli", "verify", f.name],
             capture_output=True,
             text=True,
             cwd=str(root),
             timeout=60,
         )
         if "OK:" in result.stdout:
             return None
         err = result.stderr.strip() or result.stdout.strip()
         return err.split("\n")[0][:200]
+    finally:
+        Path(f.name).unlink(missing_ok=True)

As per coding guidelines, “In Python code, explicitly pass encoding="utf-8" to open(), read_text(), and write_text() calls,” and as per path instructions (TESTING.md), tempfile paths passed to subprocesses must use delete=False with manual unlink for Windows portability.

Also applies to: 124-134

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/check_html_examples.py` around lines 103 - 113, The tempfile handoff
in the subprocess checks is Windows-incompatible because the `.vera` file stays
open with `delete=True` while `subprocess.run(...)` tries to reopen it. Update
the tempfile usage in the check helper around the `subprocess.run` call to
create it with `delete=False`, close it before invoking `vera.cli check`, and
remove it in a `finally` block; also make sure the file write uses
`encoding="utf-8"` explicitly.

Sources: Coding guidelines, Path instructions

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@vera/runtime/decimal.py`:
- Around line 89-92: The Decimal wrapper returned from _wrap_handle is being
held across _alloc_option_some_i32, which can allocate and leave the WASM heap
pointer unrooted under GC pressure. Update the decimal_from_string and
decimal_div paths to use the existing _ShadowGuard pattern so the wrapped
Decimal is rooted on the shadow stack before calling _alloc_option_some_i32,
then unroot it after the Option.Some allocation completes.

In `@vera/runtime/heap.py`:
- Around line 174-204: The heap shadow-stack push path in push() only guards sp
against limit, so it can still write a partial 4-byte slot when fewer than 4
bytes remain. Update the overflow check in Heap.push to reject any case where sp
+ 4 would exceed the shadow-stack limit before calling memory.data_ptr and
writing the packed pointer, preserving the existing RuntimeError diagnostic
shape for overflow.

In `@vera/runtime/http.py`:
- Around line 26-29: Validate the parsed URL scheme in the Http handling path
before calling urllib.request.urlopen so only http and https are allowed; reject
any other scheme (such as file) for both the GET and POST branches. Update the
logic around _read_wasm_string and the urlopen call site to parse/check the
scheme first, then proceed only when the scheme is permitted, keeping the
existing _HTTP_TIMEOUT behavior unchanged.

In `@vera/runtime/math.py`:
- Around line 21-43: The blanket ValueError-to-NaN handling in _math_unary_host
is too broad for logarithms. Update the host wrapper so math.log, math.log2, and
math.log10 preserve zero inputs as -Infinity while still translating
negative-domain ValueError cases to NaN. Use the existing _math_unary_host and
its inner host callback to special-case x == 0.0 for the log functions, keeping
parity with browser/IEEE semantics without changing other math.* behavior.

---

Outside diff comments:
In `@scripts/check_html_examples.py`:
- Around line 103-113: The tempfile handoff in the subprocess checks is
Windows-incompatible because the `.vera` file stays open with `delete=True`
while `subprocess.run(...)` tries to reopen it. Update the tempfile usage in the
check helper around the `subprocess.run` call to create it with `delete=False`,
close it before invoking `vera.cli check`, and remove it in a `finally` block;
also make sure the file write uses `encoding="utf-8"` explicitly.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: ASSERTIVE

Plan: Pro

Run ID: 2fa83f7b-4761-48ff-b0a9-16ce67428fe5

📥 Commits

Reviewing files that changed from the base of the PR and between 5452728 and e635061.

📒 Files selected for processing (31)

• .gitignore
• CHANGELOG.md
• KNOWN_ISSUES.md
• TESTING.md
• scripts/check_html_examples.py
• tests/test_codegen.py
• tests/test_html.py
• tests/test_runtime_traps.py
• vera/README.md
• vera/codegen/__init__.py
• vera/codegen/api.py
• vera/codegen/closures.py
• vera/codegen/core.py
• vera/codegen/memory.py
• vera/codegen/registration.py
• vera/runtime/__init__.py
• vera/runtime/collections.py
• vera/runtime/decimal.py
• vera/runtime/heap.py
• vera/runtime/html.py
• vera/runtime/http.py
• vera/runtime/inference.py
• vera/runtime/json.py
• vera/runtime/map.py
• vera/runtime/math.py
• vera/runtime/md.py
• vera/runtime/random.py
• vera/runtime/regex.py
• vera/runtime/set.py
• vera/runtime/state.py
• vera/runtime/traps.py

💤 Files with no reviewable changes (2)

• KNOWN_ISSUES.md
• tests/test_html.py

[aallan]

Review round — outcome

Internal (pr-review-toolkit). code-reviewer approved — a faithful, behavior-preserving extraction (the #734 characterization gate plus 1,277 codegen/runtime tests green; the byte-for-byte move audit came back clean). Two findings became fixes in 3d1379d:

• Import cycle (pr-test-analyzer). _validate_wrap_handle had been parked in the compile-time codegen/memory.py, but it is a runtime heap concern (only heap.py's _wrap_handle calls it). That created heap -> codegen.memory -> codegen/__init__ -> api -> runtime.decimal -> heap, so a cold import vera.runtime.<x> (no prior vera.codegen import) raised ImportError — undercutting the modularity the decomposition adds. Moved it to heap.py (no other runtime -> codegen edge remains) and added TestRuntimePackageImportHygiene421, which cold-imports all 15 runtime submodules in fresh interpreters (RED before the move, green after).
• State docs (comment-analyzer). Corrected the "registered conditionally / owns its own state / feeds nothing back" generalization — State registers unconditionally and threads state_store into ExecuteResult.state. Fixed the line counts (api.py is 1,182 after the IO comment).

CodeRabbit. The scripts/check_html_examples.py tempfile-portability finding is fixed in 03c83da (delete=False + manual close/unlink + encoding="utf-8", matching tests/test_html.py and TESTING.md). The four inline findings are replied to individually: decimal.py:92 is a false positive (_alloc_option_some_i32 already shadow-roots its payload); heap.py:204, http.py:29, and math.py:43 are pre-existing (verbatim in codegen/api.py on main) and out of scope for this behavior-preserving move — recommended as follow-ups:

• Http accepts non-http(s) schemes (# noqa: S310 on main) — security.
• Math.log(0) returns NaN vs JS/IEEE −∞ — parity.
• shadow-stack push could use a stricter sp + 4 > limit — defensive.

@coderabbitai — thanks; the three pre-existing items are noted for a follow-up.

[coderabbitai]

Tip

For best results, initiate chat on the files or code changes.

@aallan — clean resolution across the board. A few specific acknowledgements:

• Import cycle — the diagnosis is tight: heap → codegen.memory → codegen/__init__ → api → runtime.decimal → heap is a genuine circular import that would surface only on cold import vera.runtime.* (no prior vera.codegen import), exactly the scenario the decomposition is meant to enable. Moving _validate_wrap_handle to heap.py is the correct fix — it is a runtime heap invariant, not a compile-time layout concern. The TestRuntimePackageImportHygiene421 gate in fresh interpreters is the right regression guard.

• State unconditional registration — noted; the earlier generalisation ("registered conditionally") was incorrect. Threading state_store back through ExecuteResult.state is the correct characterisation.

• decimal.py:92 false positive — withdrawn; _alloc_option_some_i32 does shadow-root its payload before the outer allocation, so there is no GC hazard at that call site.

For the three pre-existing follow-ups, would you like me to open tracking issues now? The three items would be:

1. Security — vera/runtime/http.py: urlopen accepts non-http(s) schemes (mirrors # noqa: S310 suppression on main).
2. Parity — vera/runtime/math.py: math.log(0) returns NaN rather than the IEEE 754 / JS-spec −∞.
3. Defensive — vera/runtime/heap.py: shadow-stack push guard should use sp + 4 > limit rather than the current condition.

Happy to file them against the repo and link back to this PR if that would be useful.

[aallan]

Follow-up round — Http security fix, tracked findings, roadmap

Landed in 902b751:

Http scheme validation (security, fixed now). Http.get/Http.post validate the URL scheme and return Result.Err for file://, ftp://, data:, and any other non-http(s) scheme, instead of handing them to urllib.request.urlopen. New _is_allowed_http_url predicate gates both callbacks; a predicate unit test + an end-to-end file://-reject test; CHANGELOG ### Security entry. (The #591 source-location guards in test_runtime_traps.py got a wider span=2500 window, since the scheme check pushed host_http_post's decode(...) past the old 1500-char default.)

Pre-existing findings filed + tracked. #790 (Math.log(0) / log2(0) / log10(0) return NaN where IEEE-754/JS give −∞) and #791 (shadow-stack push partial-slot guard) — both in KNOWN_ISSUES.md Bugs, labeled bug. decimal.py:92 stays a verified false positive (_alloc_option_some_i32 already shadow-roots its payload).

Roadmap. Tier 1 reprioritised: #387 finish the mutation sweep pulled to the top (whole-vera/ sweep now unblocked by this decomposition), then the two test-file splits #419 / #420 promoted into Tier 1 in order. #421 removed from Tier 1 (closed here).

[coderabbitai]

Actionable comments posted: 3

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@CHANGELOG.md`:
- Line 17: Update the `#421` changelog entry to match the actual placement of
`_validate_wrap_handle`: the note currently says it moved to
`vera/codegen/memory.py`, but the final code/tests reference
`vera.runtime.heap`. Adjust the wording around the `codegen/api.py`
decomposition summary so the symbol location is accurate and consistent with the
rest of the runtime split described in the entry.

In `@TESTING.md`:
- Line 9: The test summary in the overview is mathematically inconsistent, so
update the aggregate count or one of the component counts to make the totals
match. Fix the breakdown in the TESTING.md overview row by verifying the numbers
for passed, stress, and skipped tests, and ensure the “Tests” total aligns with
the sum shown.

In `@tests/test_codegen.py`:
- Around line 12931-12947: The test in
test_http_get_rejects_file_scheme_end_to_end only asserts the Err result and
does not verify that Http.get short-circuits before urlopen is reached. Harden
this test by adding an assertion around the urlopen path in the existing test
body (or its surrounding harness) so the failure of the underlying network call
is explicitly proven, using the test_http_get_rejects_file_scheme_end_to_end and
Http.get symbols to locate the check. Keep the current Err-branch assertion, but
make the test fail if urlopen is invoked so regressions in the scheme guard are
caught reliably.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

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Configuration used: Path: .coderabbit.yaml

Review profile: ASSERTIVE

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📥 Commits

Reviewing files that changed from the base of the PR and between e635061 and 902b751.

📒 Files selected for processing (13)

• CHANGELOG.md
• KNOWN_ISSUES.md
• ROADMAP.md
• TESTING.md
• scripts/check_html_examples.py
• tests/test_codegen.py
• tests/test_runtime_traps.py
• vera/README.md
• vera/codegen/api.py
• vera/codegen/memory.py
• vera/runtime/heap.py
• vera/runtime/http.py
• vera/runtime/state.py