ci: quiet Codacy code scanning noise

.github/workflows/codacy.yml

@@ -46,7 +46,9 @@ jobs:
       fail-fast: false
       matrix:
         tool:
-          - markdownlint
+          # Upload only repository-owned rules to GitHub Code Scanning.
+          # Advisory quality engines stay in local/Codacy checks so they do
+          # not create empty Security/Quality tool configurations.
           - opengrep
     steps:
       # Checkout the repository to the GitHub Actions runner
@@ -56,8 +58,11 @@ jobs:
       - name: Set Codacy paths
         run: |
           set -euo pipefail
-          echo "CODACY_WORKDIR=$RUNNER_TEMP/codacy-src" >> "$GITHUB_ENV"
-          echo "CODACY_SARIF=$RUNNER_TEMP/results-${{ matrix.tool }}.sarif" >> "$GITHUB_ENV"
+          {
+            echo "CODACY_WORKDIR=$RUNNER_TEMP/codacy-src"
+            echo "CODACY_SARIF=$RUNNER_TEMP/results-${{ matrix.tool }}.sarif"
+            echo "CODACY_HAS_UPLOADABLE_SARIF=false"
+          } >> "$GITHUB_ENV"
 
       - name: Prepare workspace copy without .git
         run: |
@@ -114,8 +119,10 @@ jobs:
               raise SystemExit(f"Codacy produced invalid SARIF JSON: {exc}") from exc
 
           runs = sarif.get("runs")
-          if not isinstance(runs, list) or not runs:
-              sys.exit("Codacy SARIF did not contain any runs to upload")
+          if not isinstance(runs, list):
+              sys.exit("Codacy SARIF did not contain a runs array")
+          if not runs:
+              print("Codacy SARIF did not contain any runs to upload")
 
           out_dir.mkdir(parents=True, exist_ok=True)
           for stale in out_dir.glob("*.sarif"):
@@ -126,7 +133,14 @@ jobs:
               return normalized.strip("-") or "unknown"
 
           seen_categories: dict[str, int] = {}
+          uploadable_count = 0
           for index, run in enumerate(runs, start=1):
+              rules = run.get("tool", {}).get("driver", {}).get("rules")
+              results = run.get("results")
+              if not rules and not results:
+                  print(f"Skipping empty SARIF run {index} with no rules or results")
+                  continue
+
               run_copy = copy.deepcopy(run)
               tool = run_copy.get("tool", {}).get("driver", {}).get("name")
               base_category = f"codacy-{slug(str(tool or f'run-{index}'))}"
@@ -148,13 +162,20 @@ jobs:
               out_file = out_dir / f"{index:02d}-{category}.sarif"
               out_file.write_text(json.dumps(split_sarif, indent=2), encoding="utf-8")
               print(f"Wrote {out_file} with category {category}")
+              uploadable_count += 1
 
           with Path(os.environ["GITHUB_ENV"]).open("a", encoding="utf-8") as env_file:
               env_file.write(f"CODACY_SPLIT_SARIF_DIR={out_dir}\n")
+              env_file.write(f"CODACY_HAS_UPLOADABLE_SARIF={'true' if uploadable_count else 'false'}\n")
+
+          if uploadable_count == 0:
+              print("No non-empty Codacy SARIF runs to upload")
           PY
 
       - name: Upload split SARIF files
+        if: env.CODACY_HAS_UPLOADABLE_SARIF == 'true'
         uses: github/codeql-action/upload-sarif@b25d0ebf40e5b63ee81e1bd6e5d2a12b7c2aeb61 # v4
         with:
           sarif_file: ${{ env.CODACY_SPLIT_SARIF_DIR }}
+          category: codacy-${{ matrix.tool }}
           wait-for-processing: true

CHANGELOG.md

@@ -5,6 +5,116 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Merged Pull Requests
+
+- Enable repo Semgrep rules for issue #338 [#354](https://github.com/acgetchell/delaunay/pull/354)
+- Type repair diagnostics and harden invariants [#332](https://github.com/acgetchell/delaunay/pull/332) [#352](https://github.com/acgetchell/delaunay/pull/352)
+- Harden Python benchmark parsing [#351](https://github.com/acgetchell/delaunay/pull/351)
+- Expand profiling benchmarks around public API workflows [#349](https://github.com/acgetchell/delaunay/pull/349)
+- Bump taiki-e/install-action from 2.75.18 to 2.75.22 [#348](https://github.com/acgetchell/delaunay/pull/348)
+
+### Changed
+
+- Type repair diagnostics and harden invariants [#332](https://github.com/acgetchell/delaunay/pull/332) [#352](https://github.com/acgetchell/delaunay/pull/352)
+  [`a244053`](https://github.com/acgetchell/delaunay/commit/a2440531ae7ee1407e7436379a82fe092f02e7dd)
+
+- Replace stringified flip-repair skip samples with typed diagnostic context.
+  - Make vertex removal transactional across post-removal repair and orientation canonicalization.
+  - Deprecate DelaunayTriangulation::as_triangulation_mut ahead of removal in v0.8.0.
+  - Use scale-aware degeneracy checks for low-dimensional simplex and facet measures.
+  - Add regression and property coverage for rollback behavior, typed diagnostics, and scaled valid measures.
+  - Tolerate throughput formatting precision in benchmark baseline round-trip tests.
+
+### Fixed
+
+- Harden Python benchmark parsing [#351](https://github.com/acgetchell/delaunay/pull/351)
+  [`fea5898`](https://github.com/acgetchell/delaunay/commit/fea58987a2fb84e47603be9f0d1960aaa7e0f5f0)
+
+  - Reject non-finite and unordered Criterion timing estimates before using them in summaries, baselines, or backend comparisons.
+  - Preserve full Criterion benchmark IDs and normalize timing units when comparing storage backend results.
+  - Reuse the shared baseline parser while preserving malformed-section skip behavior and supporting scientific notation.
+  - Fall back from unusable lscpu output to /proc CPU core detection on Linux.
+  - Add regression and round-trip tests for parser behavior, benchmark IDs, unit normalization, and Linux CPU fallback.
+  - Document Python parser/file-format round-trip test expectations.
+
+  **Fixed: Harden Criterion estimate parsing and validation**
+
+  Consolidates estimate validation into a single public helper,
+  `is_valid_criterion_estimate`, now used by `PerformanceSummaryGenerator`
+  and `StorageBackendComparator`. Adds explicit type checks to
+  `PerformanceSummaryGenerator` to reject structurally malformed JSON
+  data, improving parsing robustness.
+
+### Maintenance
+
+- Bump taiki-e/install-action from 2.75.18 to 2.75.22 [#348](https://github.com/acgetchell/delaunay/pull/348)
+  [`31ec720`](https://github.com/acgetchell/delaunay/commit/31ec720a8638103b9acd7ea58c35b2baa5f571b9)
+
+Bumps [taiki-e/install-action](https://github.com/taiki-e/install-action) from 2.75.18 to 2.75.22.
+
+- [Release notes](https://github.com/taiki-e/install-action/releases)
+- [Changelog](https://github.com/taiki-e/install-action/blob/main/CHANGELOG.md)
+- [Commits](https://github.com/taiki-e/install-action/compare/055f5df8c3f65ea01cd41e9dc855becd88953486...cf525cb33f51aca27cd6fa02034117ab963ff9f1)
+
+  ---
+  updated-dependencies:
+
+- dependency-name: taiki-e/install-action
+    dependency-version: 2.75.22
+    dependency-type: direct:production
+    update-type: version-update:semver-patch
+  ...
+
+- Enable repo Semgrep rules for issue #338 [#354](https://github.com/acgetchell/delaunay/pull/354)
+  [`9d51d30`](https://github.com/acgetchell/delaunay/commit/9d51d3038ae3f3316102ecaf39429bdfb73ff1cc)
+
+  - Enable project-owned Semgrep rules in local checks, CodeRabbit, and Codacy/OpenGrep scanning.
+  - Harden Semgrep execution with strict mode, a higher timeout, and fixture coverage for hot-path hash collection rules.
+  - Replace flagged diagnostics and silent numeric fallbacks with explicit tracing, expectations, and typed Hilbert quantization errors.
+  - Centralize Delaunay triangulation cache invalidation through the existing repair-cache helper.
+
+  **Maintenance: Enable repository Semgrep rules**
+
+  - Rename the Semgrep config to semgrep.yaml and wire it into local checks, CodeRabbit, and Codacy/OpenGrep.
+  - Add strict Semgrep execution plus fixture coverage for hot-path hash collections and targeted panic bypasses.
+  - Make Hilbert errors non-exhaustive and document quantization-scale conversion failures on APIs that can return them.
+  - Replace fragile VertexBuilder expect paths with infallible Vertex point constructors.
+
+  **Maintenance: Expand repository Semgrep rules**
+
+  - Add project-specific Semgrep checks for Rust dynamic errors, lint suppression reasons, Python subprocess mocks, and typed script helpers.
+  - Add focused Semgrep fixtures for hot-path hash collections, Rust project rules, and Python test conventions.
+  - Wire the expanded Semgrep fixture suite into `just check`.
+  - Replace stale Clippy `allow` suppressions with documented `expect` attributes and remove dynamic error trait-object usage from tests.
+
+  **Maintenance: Refresh quality tooling and diagnostics**
+
+  - Pin GitHub workflow tool versions and update action SHAs for cache, artifact upload, install-action, and SARIF upload.
+  - Exclude Semgrep fixtures from Codacy analysis so intentional rule-test violations do not surface as production issues.
+  - Add a cargo-machete backed just unused-deps recipe for checking unused direct dependencies.
+  - Gate convex hull test diagnostics behind test-debug tracing instead of unconditional stdout output.
+  - Add Hilbert ordering and zero-dimensional sort coverage for Codecov patch gaps.
+
+  **Fixed: Harden Hilbert ordering errors and prelude checks [#338](https://github.com/acgetchell/delaunay/pull/338)**
+
+  - Return typed Hilbert errors for non-finite quantization inputs and failed u32 coordinate conversions instead of silently collapsing values.
+  - Preserve item order when Hilbert sort key construction fails, and add regression coverage for the new error paths.
+  - Add the focused ordering prelude and update doctests, examples, benchmarks, and integration tests to use orthogonal prelude imports.
+  - Add a Semgrep rule and fixture coverage for examples and benchmarks that bypass focused preludes.
+  - Verify pinned shfmt binaries in CI with explicit SHA256 values instead of downloading a missing upstream checksum file.
+
+### Performance
+
+- Expand profiling benchmarks around public API workflows [#349](https://github.com/acgetchell/delaunay/pull/349)
+  [`0acbf65`](https://github.com/acgetchell/delaunay/commit/0acbf651b57c287aecc10bd51eea55fdbcbe2442)
+
+- Run profiling comparisons with the checked-out crate toolchain by default
+  - Add local `just profile` support for comparing code refs and compiler versions
+  - Expand `ci_performance_suite` beyond construction to cover hulls, boundary traversal, validation, and bistellar flips
+  - Emit a versioned API benchmark manifest so benchmark logs show which public workflows were measured
+
 ## [0.7.6] - 2026-04-25
 
 ### ⚠️ Breaking Changes
@@ -14,6 +124,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Merged Pull Requests
 
+- Release v0.7.6 [#347](https://github.com/acgetchell/delaunay/pull/347)
 - Preserve fallback rebuild cell data [#305](https://github.com/acgetchell/delaunay/pull/305) [#346](https://github.com/acgetchell/delaunay/pull/346)
 - Switch coverage reporting to cargo-llvm-cov [#345](https://github.com/acgetchell/delaunay/pull/345)
 - Clarify research scope and changelog hygiene [#344](https://github.com/acgetchell/delaunay/pull/344)
@@ -502,6 +613,13 @@ Bumps [actions/setup-node](https://github.com/actions/setup-node) from 6.3.0 to
   - Add GitHub issue templates and clarify private vulnerability reporting guidance.
   - Tighten Python lint/typecheck settings and clean up benchmark/changelog utility diagnostics.
   - Add changelog post-processing coverage for version-heading reset behavior.
+- Release v0.7.6 [#347](https://github.com/acgetchell/delaunay/pull/347)
+  [`6e437fb`](https://github.com/acgetchell/delaunay/commit/6e437fb5869f7ada49d6760114c4d25f15eb9b29)
+
+- Bump version to v0.7.6
+  - Update changelog with latest changes
+  - Update documentation for release
+  - Add performance results for v0.7.6
 
 ## [0.7.5] - 2026-04-10
 
@@ -2866,6 +2984,7 @@ Older releases are archived by minor series:
 - [0.3.x](docs/archive/changelog/0.3.md)
 - [0.2.x](docs/archive/changelog/0.2.md)
 
+[unreleased]: https://github.com/acgetchell/delaunay/compare/v0.7.6..HEAD
 [0.7.6]: https://github.com/acgetchell/delaunay/compare/v0.7.5..v0.7.6
 [0.7.5]: https://github.com/acgetchell/delaunay/compare/v0.7.4..v0.7.5
 [0.7.4]: https://github.com/acgetchell/delaunay/compare/v0.7.3..v0.7.4

README.md

@@ -88,6 +88,26 @@ Add the library to your crate:
 cargo add delaunay
 ```
 
+Choose the smallest prelude that matches the task:
+
+| Task | Import |
+|---|---|
+| Build, configure, insert, or remove vertices | `use delaunay::prelude::triangulation::*` |
+| Read-only traversal, adjacency, convex hulls, and comparison helpers | `use delaunay::prelude::query::*` |
+| Points, kernels, predicates, and geometric measures | `use delaunay::prelude::geometry::*` |
+| Random points or triangulations for examples, tests, and benchmarks | `use delaunay::prelude::generators::*` |
+| Bistellar flips / Edit API | `use delaunay::prelude::triangulation::flips::*` |
+| Delaunay repair diagnostics and policies | `use delaunay::prelude::triangulation::repair::*` |
+| Delaunayize workflow | `use delaunay::prelude::triangulation::delaunayize::*` |
+| Hilbert ordering and quantization utilities | `use delaunay::prelude::ordering::*` |
+| Low-level TDS cells, facets, keys, and validation reports | `use delaunay::prelude::tds::*` |
+| Collection aliases and small buffers | `use delaunay::prelude::collections::*` |
+| Topology validation and Euler characteristic helpers | `use delaunay::prelude::topology::validation::*` |
+| Topological spaces and topology traits | `use delaunay::prelude::topology::spaces::*` |
+
+`use delaunay::prelude::*` remains available for quick experiments, but examples
+and benchmarks in this repository prefer focused preludes so imports document intent.
+
 ```rust
 use delaunay::prelude::triangulation::*;
 

docs/api_design.md

@@ -88,7 +88,6 @@ use `DelaunayTriangulationBuilder`:
 
 ```rust
 use delaunay::prelude::triangulation::*;
-use delaunay::core::triangulation::{TopologyGuarantee, ValidationPolicy};
 
 // Toroidal (periodic) triangulation in 2D
 let vertices = vec![

docs/dev/rust.md

@@ -547,17 +547,33 @@ pub mod core {
 
 ## Prelude Design
 
-Preludes should remain **small and purpose‑specific**.
+Focused preludes should remain **small and purpose-specific**.
 
-A prelude should import only the items needed for a specific task.
+A focused prelude should import only the items needed for a specific task.
+Prefer these focused preludes in doctests, integration tests, examples, and
+benchmarks because they make intent visible at the import site.
 
-Example:
+Examples:
 
 ```text
 delaunay::prelude::triangulation
-```
-
-Avoid giant catch‑all preludes.
+delaunay::prelude::triangulation::flips
+delaunay::prelude::triangulation::repair
+delaunay::prelude::triangulation::delaunayize
+delaunay::prelude::query
+delaunay::prelude::geometry
+delaunay::prelude::generators
+delaunay::prelude::ordering
+delaunay::prelude::collections
+delaunay::prelude::tds
+delaunay::prelude::topology::validation
+delaunay::prelude::topology::spaces
+```
+
+The root `delaunay::prelude::*` is intentionally available as a convenience for
+new users and quick experiments. Avoid using it in committed examples,
+benchmarks, and doctests when a focused prelude communicates the workflow more
+clearly.
 
 ---
 

docs/numerical_robustness_guide.md

@@ -80,7 +80,7 @@ The convenience constructors (`DelaunayTriangulation::new()`, `::empty()`, etc.)
 `AdaptiveKernel`. To opt into a different kernel, use the explicit-kernel constructors:
 
 ```rust
-use delaunay::geometry::kernel::RobustKernel;
+use delaunay::prelude::geometry::RobustKernel;
 use delaunay::prelude::triangulation::*;
 
 let kernel = RobustKernel::<f64>::new();

docs/workflows.md

@@ -137,7 +137,7 @@ If repair fails to converge within the flip budget, you get
 detections, etc.).
 
 ```rust
-use delaunay::core::algorithms::flips::DelaunayRepairError;
+use delaunay::prelude::triangulation::repair::DelaunayRepairError;
 use delaunay::prelude::triangulation::*;
 
 let vertices = vec![

examples/memory_analysis.rs

@@ -3,6 +3,7 @@
 //! This example demonstrates basic memory usage analysis for Delaunay triangulations
 //! using the existing allocation counter infrastructure from the tests.
 
+use delaunay::prelude::generators::generate_random_triangulation;
 use delaunay::prelude::query::*;
 use std::any::Any;
 use std::backtrace::Backtrace;

examples/zero_allocation_iterator_demo.rs

@@ -5,7 +5,7 @@
 //! zero-allocation `vertex_uuid_iter()` method compared to the traditional
 //! `vertex_uuids()` method that allocates a Vec.
 
-use delaunay::prelude::query::*;
+use delaunay::prelude::generators::generate_random_triangulation;
 use std::hint::black_box;
 use std::time::Instant;
 

semgrep.yaml

@@ -367,6 +367,27 @@ rules:
       - pattern-regex: '^\s*use\s+delaunay::(core|geometry|triangulation|topology)::'
       - pattern-not-regex: '^\s*use\s+delaunay::prelude::'
 
+  - id: delaunay.rust.prefer-prelude-imports-in-triangulation-doctests
+    languages:
+      - rust
+    severity: WARNING
+    message: >-
+      Use focused delaunay::prelude imports in public triangulation doctests
+      instead of deep crate module paths.
+    metadata:
+      category: maintainability
+      tracking_issue: "https://github.com/acgetchell/delaunay/issues/355"
+      rationale: >-
+        Public doctests should model the small, orthogonal prelude import
+        surfaces that users can copy into their own code.
+    paths:
+      include:
+        - "/src/**/*.rs"
+        - "/tests/semgrep/src/project_rules/**/*.rs"
+    patterns:
+      - pattern-regex: '^\s*//[/!]\s*(?:#\s*)?use\s+delaunay::(core|geometry|triangulation|topology)::'
+      - pattern-not-regex: '^\s*//[/!]\s+use\s+delaunay::prelude::'
+
   - id: delaunay.python.no-broad-exception
     languages:
       - python

src/core/adjacency.rs

@@ -23,8 +23,8 @@ use thiserror::Error;
 /// # Examples
 ///
 /// ```rust
-/// use delaunay::core::adjacency::AdjacencyIndexBuildError;
-/// use delaunay::core::tds::{CellKey, VertexKey};
+/// use delaunay::prelude::query::AdjacencyIndexBuildError;
+/// use delaunay::prelude::tds::{CellKey, VertexKey};
 /// use slotmap::KeyData;
 ///
 /// let cell_key = CellKey::from(KeyData::from_ffi(1));