Posit optimize

.Rbuildignore

@@ -7,6 +7,7 @@
 ^src\-
 ^src\.
 CONTRIBUTING
+AGENTS.md
 README.md
 ^\.github
 ^\.lintr
@@ -34,3 +35,5 @@ revdep
 ^\.vs.*$
 ^\.vscode.*$
 ^CRAN-SUBMISSION$
+^\.positai$
+^\.claude$

.github/workflows/R-CMD-check.yml

@@ -227,3 +227,130 @@ jobs:
         with:
           deps: ${{ matrix.config.deps }}
           extra-packages: ms609/TreeDistData
+
+  benchmark:
+    runs-on: ubuntu-latest
+    needs: check-release
+    if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
+    name: benchmark
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RSPM: "https://packagemanager.posit.co/cran/__linux__/noble/latest"
+      _R_CHECK_BUILD_VIGNETTES_: false
+      _R_CHECK_CRAN_INCOMING_: false
+      _R_CHECK_FORCE_SUGGESTS_: false
+      R_REMOTES_STANDALONE: true
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      R_REALLY_FORCE_SYMBOLS: true
+      PKG_CXXFLAGS: "-O3"
+
+    steps:
+      - name: Checkout PR branch
+        uses: actions/checkout@v5
+        with:
+          path: pr
+
+      - name: Checkout target branch
+        uses: actions/checkout@v5
+        with:
+          ref: ${{ github.event.pull_request.base.ref || 'main' }}
+          path: main
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          extra-repositories: https://ms609.github.io/packages/
+
+      - name: Install R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"hard"'
+          extra-packages: |
+            github::ms609/TreeTools
+          needs: benchmark
+
+      - name: Benchmark PR
+        uses: ms609/actions/benchmark-step@main
+        with:
+          path: pr
+          output: pr
+
+      - name: Benchmark target
+        uses: ms609/actions/benchmark-step@main
+        with:
+          path: main
+          output: main
+
+      - name: Benchmark PR again
+        uses: ms609/actions/benchmark-step@main
+        with:
+          path: pr
+          output: pr2
+
+      - run: dir pr-benchmark-results
+        working-directory: pr
+      - run: dir main-benchmark-results
+        working-directory: pr
+
+      - name: Compare benchmarks
+        id: compare_results
+        working-directory: pr
+        run: |
+          Rscript benchmark/_compare_results.R
+        shell: bash
+
+      - name: Upload PR benchmark results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: pr-benchmark-results
+          path: pr/pr-benchmark-results/*.bench.Rds
+
+      - name: Upload main benchmark results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: main-benchmark-results
+          path: pr/main-benchmark-results/*.bench.Rds
+
+      - name: Comment on PR
+        if: always() && github.event_name == 'pull_request' && steps.compare_results.outputs.report != ''
+        uses: actions/github-script@v7
+        env:
+          BENCHMARK_MESSAGE: ${{ steps.compare_results.outputs.report }}
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const benchmarkIdentifier = '<!-- benchmark-comment -->';
+            const outdatedPrefix = '> **⚠️ This benchmark result is outdated. See the latest comment below.**\n\n';
+
+            const comments = await github.rest.issues.listComments({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number
+            });
+
+            const previousBenchmarkComments = comments.data.filter(comment =>
+              comment.user.type === 'Bot' &&
+              comment.body.includes(benchmarkIdentifier) &&
+              !comment.body.startsWith('> **⚠️ This benchmark result is outdated.')
+            );
+
+            for (const comment of previousBenchmarkComments) {
+              await github.rest.issues.updateComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                comment_id: comment.id,
+                body: outdatedPrefix + comment.body
+              });
+            }
+
+            const newCommentBody = benchmarkIdentifier + '\n' + process.env.BENCHMARK_MESSAGE;
+
+            await github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+              body: newCommentBody
+            });

.positai/settings.json

@@ -0,0 +1,32 @@
+{
+  "permission": {
+    "read": {
+      "*.r": "allow",
+      "*.h": "allow",
+      "*.log": "allow",
+      "*.cpp": "allow",
+      "*.R": "allow",
+      "*": "allow"
+    },
+    "edit": {
+      "*.cpp": "allow",
+      "*.h": "allow",
+      "DESCRIPTION": "allow",
+      "src/Makevars": "allow",
+      "src/Makevars.win": "allow",
+      "*.R": "allow",
+      "*.md": "allow"
+    },
+    "bash": {
+      "cd C:/Users/pjjg18/GitHub/TreeDist": "allow",
+      "cat *": "allow",
+      "echo *": "allow",
+      "find *": "allow",
+      "grep *": "allow",
+      "head *": "allow",
+      "ls *": "allow",
+      "rm -f src/*.o src/*.dll": "allow",
+      "tail *": "allow"
+    }
+  }
+}