Rolling development → main

.claude/CLAUDE.md

@@ -111,7 +111,7 @@ Edge2Elem: ndarray[n_edges, 2]        # Edge adjacent elements (-1 if boundary)
 - ✅ Skeletonization algorithm behavior
 - ✅ Public method signatures
 - ✅ Mixed-element (tri + quad) support
-- ✅ Test pass rate (currently 57 tests)
+- ✅ Test pass rate (the full pytest suite)
 
 ### Must Improve
 - 🚀 O(n²) edge building → O(n log n) or O(n)

.domi-pin

@@ -4,6 +4,6 @@
 
 upstream: domattioli/DomI
 branch: main
-sha: cfa7f02a4661ed0db8cce9eee7cf3c93b4f0e863
-manifest_sha256: 124153ce0aa71c06ee4836c51488d067032327312c36be5451ad6b0e02af7341
-pinned_at: 2026-07-10T15:13:24Z
+sha: c430fc2d3711e70934d32578a90eb6fc409fdb71
+manifest_sha256: 48c018894b19176816e9d0fb66a62cf5862f401ed575ba83167a66f8b8324094
+pinned_at: 2026-07-15T14:12:54Z

.gitattributes

@@ -1,12 +1,26 @@
 # Exclude Claude/agent + dev-process files from source archives
 # (git archive, PyPI sdist, GitHub release tarball, Zenodo snapshot).
 # Strictly library-running code ships downstream; these stay in the repo.
-.claude/             export-ignore
-CLAUDE.md            export-ignore
-AGENTS.md            export-ignore
-.specify/            export-ignore
-.planning/           export-ignore
-specs/               export-ignore
-docs/sessions/       export-ignore
+
+# >>> release-ignore:begin (generated by DomI release-integrity — do not edit inside; edit .release-ignore.toml + regenerate)
+.claude/ export-ignore
+.claude-plugin/ export-ignore
+.introspect/ export-ignore
+.githooks/ export-ignore
+.specify/ export-ignore
+.planning/ export-ignore
+.domi-pin export-ignore
+.zenodoignore export-ignore
+.release-ignore.toml export-ignore
+CLAUDE.md export-ignore
+AGENTS.md export-ignore
+claude_routine_instructions.md export-ignore
+instructions_on_start.sh export-ignore
+scripts/hooks/ export-ignore
+docs/sessions/ export-ignore
 docs/introspections/ export-ignore
-.domi-pin            export-ignore
+specs/ export-ignore
+*introspect*.yml export-ignore
+.github/ export-ignore
+docs/LEXICON_PROPOSAL.md export-ignore
+# <<< release-ignore:end

.github/workflows/LOCAL.md

@@ -9,3 +9,4 @@ workflows fail the workflow-conformance gate.
 | `python-package.yml` | full cross-OS test matrix incl. macOS lanes (main-push gated) — macOS gating is repo-local by design (spec-010 v2.2 rule 8) |
 | `publish-pypi.yml` | PyPI release, tag-triggered — repo-specific release pipeline |
 | `build-cpp-wheels.yml` | build-only manylinux wheel validation for the chilmesh_cpp binary backend (workflow_dispatch, artifacts only, no publish) — repo-specific packaging (#229) |
+| `publish-cpp-wheels.yml` | release/dispatch-gated PyPI publish of chilmesh_cpp wheels + sdist (no push trigger; `environment: pypi` protected; Trusted Publishing/OIDC) — repo-specific packaging (#256 Phase 2) |

.github/workflows/build-cpp-wheels.yml

@@ -1,7 +1,9 @@
 name: build-cpp-wheels
 
-# Build-only validation of the chilmesh_cpp binary (manylinux) wheels.
+# Build + functional-smoke validation of the chilmesh_cpp binary (manylinux) wheels.
 # Manual dispatch; uploads wheels as artifacts ONLY — does NOT publish to PyPI.
+# The cibuildwheel test step RUNS full_init on a tiny mesh (not just a hasattr
+# probe) so a broken/empty binary fails the build (#256 Phase 1a).
 # Linux manylinux runs on the free ubuntu runner (not gated by the macOS/Windows
 # runner-billing question in #225), so the binary path can be validated in the
 # real manylinux container before any publish job is wired up. Refs #229, #163, #234.
@@ -31,7 +33,24 @@ jobs:
           CIBW_BUILD: "cp310-* cp311-* cp312-*"
           CIBW_ARCHS_LINUX: "x86_64"
           CIBW_SKIP: "*-musllinux*"
-          CIBW_TEST_COMMAND: "python -c \"import chilmesh_cpp; assert hasattr(chilmesh_cpp, 'full_init'), 'cpp extension missing full_init'\""
+          CIBW_TEST_REQUIRES: "numpy"
+          # Real functional smoke (#256 Phase 1a): actually RUN full_init on a
+          # 2-triangle unit square and assert the built adjacency + skeleton, not
+          # just that the symbol exists. Topology invariants: 4 verts, 2 elems,
+          # 5 unique edges (4 boundary + 1 shared diagonal), adjacency built,
+          # >=1 peel layer, edge2vert shape (5, 2).
+          CIBW_TEST_COMMAND: >-
+            python -c "import numpy as np, chilmesh_cpp;
+            pts = np.array([[0.,0.],[1.,0.],[1.,1.],[0.,1.]], dtype=np.float64);
+            conn = np.array([[0,1,2],[0,2,3]], dtype=np.int32);
+            m = chilmesh_cpp.full_init(pts, conn);
+            assert m.n_verts == 4, m.n_verts;
+            assert m.n_elems == 2, m.n_elems;
+            assert m.n_edges == 5, m.n_edges;
+            assert m.adjacency_built, 'adjacency not built';
+            assert m.n_layers >= 1, m.n_layers;
+            assert np.asarray(m.edge2vert).shape == (5, 2), np.asarray(m.edge2vert).shape;
+            print('chilmesh_cpp full_init smoke OK:', m.n_verts, 'v', m.n_elems, 'e', m.n_edges, 'edges', m.n_layers, 'layers')"
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:

.github/workflows/publish-cpp-wheels.yml

@@ -0,0 +1,104 @@
+name: publish-cpp-wheels
+
+# Release/tag-gated PyPI publish of the chilmesh_cpp binary wheels + sdist (#256 Phase 2).
+#
+# Triggers ONLY on a published GitHub release or a deliberate manual dispatch —
+# there is NO push trigger, so nothing publishes from `development`. The build
+# leg reuses the manylinux cibuildwheel path validated in build-cpp-wheels.yml
+# (Phase 1a). macOS/Windows legs are intentionally absent here: they are Phase 1b,
+# gated on the runner-billing decision in #225 — add them to the build matrix
+# below once #225 resolves.
+#
+# Auth: PyPI Trusted Publishing (OIDC, id-token: write) is preferred (no
+# long-lived token). A token fallback mirroring publish-pypi.yml is shown as a
+# commented alternative on the publish step. Refs #256, #229, #225, #163, #234.
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build-manylinux:
+    name: cibuildwheel chilmesh_cpp (manylinux x86_64)
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+          cache: pip
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.21.3
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse src/chilmesh_cpp
+        env:
+          CIBW_BUILD: "cp310-* cp311-* cp312-*"
+          CIBW_ARCHS_LINUX: "x86_64"
+          CIBW_SKIP: "*-musllinux*"
+          CIBW_TEST_REQUIRES: "numpy"
+          # Same functional smoke as build-cpp-wheels.yml: run full_init on a
+          # 2-triangle unit square and assert adjacency + skeleton so a broken
+          # binary cannot be published.
+          CIBW_TEST_COMMAND: >-
+            python -c "import numpy as np, chilmesh_cpp;
+            pts = np.array([[0.,0.],[1.,0.],[1.,1.],[0.,1.]], dtype=np.float64);
+            conn = np.array([[0,1,2],[0,2,3]], dtype=np.int32);
+            m = chilmesh_cpp.full_init(pts, conn);
+            assert m.n_verts == 4, m.n_verts;
+            assert m.n_elems == 2, m.n_elems;
+            assert m.n_edges == 5, m.n_edges;
+            assert m.adjacency_built, 'adjacency not built';
+            assert m.n_layers >= 1, m.n_layers;
+            assert np.asarray(m.edge2vert).shape == (5, 2), np.asarray(m.edge2vert).shape;
+            print('chilmesh_cpp full_init smoke OK:', m.n_verts, 'v', m.n_elems, 'e', m.n_edges, 'edges', m.n_layers, 'layers')"
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: chilmesh-cpp-manylinux-wheels
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  sdist:
+    name: build chilmesh_cpp sdist
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v5
+      - name: Build sdist
+        run: pipx run build --sdist --outdir dist src/chilmesh_cpp
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: chilmesh-cpp-sdist
+          path: dist/*.tar.gz
+          if-no-files-found: error
+
+  publish:
+    name: publish chilmesh_cpp to PyPI
+    needs: [build-manylinux, sdist]
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    # Protect with required reviewers in repo settings (Settings → Environments → pypi).
+    environment: pypi
+    permissions:
+      id-token: write   # PyPI Trusted Publishing (OIDC) — no long-lived secret
+    steps:
+      - name: Download all wheel + sdist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        # Token fallback — if PyPI Trusted Publishing is NOT configured for
+        # chilmesh-cpp, drop the `id-token: write` permission above and uncomment:
+        #   with:
+        #     password: ${{ secrets.PYPI_API_TOKEN }}
+        with:
+          packages-dir: dist
+          skip-existing: true

.planning/008-DECISION.md

@@ -4,6 +4,15 @@
 **Date:** 2026-05-22  
 **Status:** FINAL (pending benchmark data)
 
+> **UPDATE 2026-07-14 — superseded outcome.** The Rust/quad-edge port described
+> here was built (`src/chilmesh_core`) and has since been measured and **FROZEN**:
+> it is output-equivalent to Python but ~2–5× slower than the C++ backend on full
+> init, with no performance niche over it. The "pending benchmark data" is now
+> filled — see [`docs/RUST_EVALUATION.md`](../docs/RUST_EVALUATION.md) and
+> `src/chilmesh_core/STATUS.md`. C++ is the acceleration path; the forward plan is
+> prebuilt C++ wheels ([`docs/dev/PREBUILT_WHEELS_PLAN.md`](../docs/dev/PREBUILT_WHEELS_PLAN.md)),
+> not further Rust work. This decision record is retained as history.
+
 ---
 
 ## Executive Summary

.planning/codebase/CONCERNS.md

@@ -2,6 +2,14 @@
 
 **Analysis Date:** 2026-05-21
 
+> **UPDATE 2026-07-14.** The "Rust/C++ extension" optimization opportunity below
+> has been resolved: the **C++** half-edge backend is built, bit-identical, and is
+> the acceleration path (~5× faster than the Rust port). The **Rust** extension was
+> also built, measured, and is now **FROZEN** (no perf niche over C++) — see
+> [`docs/RUST_EVALUATION.md`](../../docs/RUST_EVALUATION.md). The remaining lever is
+> distribution (prebuilt C++ wheels), not a new language port:
+> [`docs/dev/PREBUILT_WHEELS_PLAN.md`](../../docs/dev/PREBUILT_WHEELS_PLAN.md).
+
 ## Language & Performance Optimization Opportunities
 
 ### 1. Skeletonization Bottleneck (Medium Priority)

.planning/project_plan.md

@@ -1,5 +1,10 @@
 # CHILmesh Project Plan & Roadmap
 
+> ⚠️ **STALE — historical, not the live roadmap (banner added 2026-07-27).**
+> This document describes the 2026-04-26 `v0.1.1 → v0.2.0` plan. The repo is now **v1.4.1** (stable; C++/Rust half-edge backends, full mutation API `#94`, fort.14/.2dm/fort.13 I/O, lazy `summary()`). The "You are here" / Phase-0 markers below are ~15 months out of date.
+> **Live status & roadmap → [README §Status & Roadmap](../README.md#status--roadmap).**
+> Disposition (retire this file vs. refresh it) is an open operator decision — see [#261](https://github.com/domattioli/CHILmesh/issues/261). Banner added pending that call; the content below is preserved unmodified as a historical record.
+
 **Current Version:** 0.1.1 (Alpha)
 **Planning Date:** 2026-04-26
 **Horizon:** 12 months (through Q1 2027)

.release-ignore.toml

@@ -0,0 +1,10 @@
+# Repo-local extension of DomI's canonical release-ignore baseline
+# (DomI skills/release-integrity/policy/release-ignore.toml). Additive only.
+# Regenerate channel files: python release_ignore.py generate (release-integrity skill).
+
+[extend]
+# docs/BENCHMARK.md and other computational docs ship (operator ruling
+# 2026-07-14); only AI dev-workflow material is excluded.
+exclude = [
+    "docs/LEXICON_PROPOSAL.md",
+]