Enhance benchmarking capabilities and improve performance metrics

.JuliaFormatter.toml

@@ -1,19 +1,19 @@
 style = "default"
 indent = 4
-margin = 92
+margin = 96
 always_for_in = true
 whitespace_typedefs = true
 whitespace_ops_in_indices = true
 remove_extra_newlines = true
 short_to_long_function_def = false
-long_to_short_function_def = false
+long_to_short_function_def = true
 always_use_return = false
-whitespace_in_kwargs = true
+whitespace_in_kwargs = false
 annotate_untyped_fields_with_any = false
 format_docstrings = false
 align_assignment = false
 align_struct_field = false
 align_conditional = false
 align_pair_arrow = false
 trailing_comma = true
-join_lines_based_on_source = true
+join_lines_based_on_source = false

.github/README.md

@@ -0,0 +1,12 @@
+# GitHub Configuration
+
+This directory holds GitHub-specific repository automation and metadata.
+
+## Contents
+
+- `workflows/`: GitHub Actions CI, docs, release, and maintenance workflows.
+
+## Notes
+
+- Workflow behavior is documented in [`../docs/src/ci-testing.md`](../docs/src/ci-testing.md).
+- Generated macOS metadata files such as `.DS_Store` are not meaningful project content.

.github/workflows/README.md

@@ -0,0 +1,18 @@
+# GitHub Actions Workflows
+
+This folder contains the repository's GitHub Actions workflows.
+
+## Files
+
+- `ci.yml`: fast Linux CI for unit tests, notebooks, and coverage upload.
+- `ci-full.yml`: broader matrix CI for pull requests to `develop` and `master`.
+- `docs.yml`: Documenter build and deployment workflow.
+- `TagBot.yml`: release-tag automation.
+
+### Disabled
+
+- `format.yml.disabled`: disabled formatter workflow kept for reference.
+- `CompatHelper.yml.disabled`: dependency update automation. 
+- `nightly.yml.disabled`: scheduled regression sweep on non-Linux platforms.
+
+See [`../../docs/src/ci-testing.md`](../../docs/src/ci-testing.md) for the user-facing workflow overview.

.github/workflows/ci.yml

@@ -38,17 +38,22 @@ jobs:
       - name: Install dependencies
         run: julia --project=. -e 'using Pkg; Pkg.instantiate()'
 
-      - name: Run unit tests
-        run: julia --project=. -e 'using Pkg; Pkg.test()'
+      - name: Run unit tests with coverage
+        run: julia --project=. -e 'using Pkg; Pkg.test(coverage=true)'
 
       - name: Process coverage
-        if: matrix.julia-version == '1.11'
         uses: julia-actions/julia-processcoverage@v1
         with:
           directories: src
 
+      - name: Upload LCOV artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-julia-${{ matrix.julia-version }}-linux
+          path: lcov.info
+          if-no-files-found: warn
+
       - name: Upload coverage to Codecov
-        if: matrix.julia-version == '1.11'
         uses: codecov/codecov-action@v4
         with:
           files: lcov.info

.gitignore

@@ -41,3 +41,4 @@ benchmark/results/
 
 # Developer-specific files
 sc_*
+lcov.info

Makefile

@@ -1,6 +1,7 @@
-.PHONY: test doc format format-check lint clean bench bench-compare bench-compare-py bench-compare-py-label bench-all-label bench-compare-labels check-qmcpy-python
+.PHONY: test coverage doc format format-check lint clean bench bench-compare bench-compare-py bench-compare-py-label bench-all-label bench-compare-labels check-qmcpy-python
 
 FORMATTER_PROJECT=devtools/formatter
+DOC_DEPOT ?= $(if $(TMPDIR),$(TMPDIR),/tmp/)qmcju-doc-depot
 QMCPY_PYTHON_AUTO := $(shell \
 	for py in python python3 "$(HOME)/miniconda3/bin/python" "$(HOME)/miniconda3/envs/qmcpy/bin/python" "$(HOME)/miniconda3/envs/qmcpy-leadership/bin/python"; do \
 		if { [ -x "$$py" ] || command -v "$$py" >/dev/null 2>&1; } && "$$py" -c "import qmcpy" >/dev/null 2>&1; then \
@@ -45,27 +46,35 @@ update:
 test: 
 	julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.test()'
 
+# Run tests with Julia coverage instrumentation
+coverage:
+	find src test -name '*.cov' -delete
+	rm -f lcov.info
+	julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.test(coverage=true)'
+	julia --project=. devtools/process_coverage.jl
+
 # Run specific test file
 test-%:
 	julia --project=. -e 'include("test/$*.jl")'
 
 # Build documentation
 doc:
-	julia --project=docs -e 'using Pkg; Pkg.instantiate(); Pkg.resolve()'
-	julia --project=docs docs/make.jl
+	rm -rf docs/build
+	JULIA_DEPOT_PATH="$(DOC_DEPOT):$(HOME)/.julia" julia --project=docs -e 'using Pkg; Pkg.instantiate(); Pkg.resolve()'
+	JULIA_DEPOT_PATH="$(DOC_DEPOT):$(HOME)/.julia" julia --project=docs docs/make.jl
 
-# Format code with JuliaFormatter
+# Format code with JuliaFormatter (uses the repo .JuliaFormatter.toml for all paths)
 format:
-	julia --project=$(FORMATTER_PROJECT) -e 'using Pkg; Pkg.instantiate(); using JuliaFormatter; format("src/"); format("test/")'
+	julia --project=$(FORMATTER_PROJECT) -e 'using Pkg; Pkg.instantiate(); using JuliaFormatter; format(["src/", "test/", "benchmark/"])'
 
 # Check formatting (CI-friendly, fails if changes needed)
 format-check:
-	julia --project=$(FORMATTER_PROJECT) -e 'using Pkg; Pkg.instantiate(); using JuliaFormatter; @assert format("src/", overwrite=false); @assert format("test/", overwrite=false)'
+	julia --project=$(FORMATTER_PROJECT) -e 'using Pkg; Pkg.instantiate(); using JuliaFormatter; @assert format(["src/", "test/", "benchmark/"], overwrite=false)'
 
 # Clean build artifacts
 clean:
 	rm -rf docs/build
-	rm -rf *.jl.cov *.jl.*.cov *.jl.mem
+	rm -rf *.jl.cov *.jl.*.cov *.jl.mem lcov.info
 
 # Instantiate project dependencies (includes Plots and all other deps). Download what Manifest.toml says.
 setup:

README.md

@@ -96,10 +96,23 @@ julia -e 'using IJulia; notebook(dir="demos")'
 Run the benchmark suite:
 
 ```bash
-julia --project=. benchmark/benchmarks.jl
+make bench
+# or
+julia benchmark/runbenchmarks.jl
 ```
 
-This benchmarks sampling, transforms, integrand evaluation, and end-to-end integration across all DD types. Results are saved to `benchmark/results/latest.json`.
+This benchmarks sampling, transforms, integrand evaluation, and end-to-end integration across all DD types. Results are saved under `benchmark/results/`. See [`benchmark/README.md`](benchmark/README.md) for the full workflow, comparison scripts, and the Julia-vs-QMCPy accuracy sidecars.
+
+## Repository Layout
+
+Most top-level and source subdirectories now include a local `README.md` describing
+their purpose and the files they contain. Useful starting points:
+
+- [`benchmark/README.md`](benchmark/README.md) — standalone benchmarking and comparison tooling
+- [`demos/README.md`](demos/README.md) — notebook demos and how to run them
+- [`docs/README.md`](docs/README.md) — Documenter build/deploy layout
+- [`src/README.md`](src/README.md) — package source tree and component folders
+- [`test/README.md`](test/README.md) — unit tests, notebook tests, and coverage commands
 
 ## Documentation
 
@@ -119,14 +132,21 @@ using QMC
 # Unit tests
 julia --project=. -e 'using Pkg; Pkg.test()'
 
+# Unit tests with coverage instrumentation
+julia --project=. -e 'using Pkg; Pkg.test(coverage=true)'
+# or
+make coverage
+
 # Demo notebooks
 julia --project=. test/run_notebooks.jl
 
 # Build documentation locally
 julia --project=docs docs/make.jl
 ```
 
-See [CI/CD Testing](https://qmcsoftware.github.io/QMC.jl/ci-testing/) for workflow details.
+CI uploads LCOV coverage reports to Codecov and stores the generated `lcov.info`
+as a workflow artifact. See [`test/README.md`](test/README.md) and
+[CI/CD Testing](https://qmcsoftware.github.io/QMC.jl/ci-testing/) for details.
 
 ## Citation
 

benchmark/benchmarks.jl

@@ -53,16 +53,14 @@ const SUITE = BenchmarkGroup()
 #    and Kronecker are pure Julia.
 SUITE["gen_samples"] = BenchmarkGroup()
 for dim in DIMS, n in SAMPLES
-    SUITE["gen_samples"]["IIDStdUniform d=$dim n=$n"] =
-        bench_gen_samples(IIDStdUniform, dim, n)
+    SUITE["gen_samples"]["IIDStdUniform d=$dim n=$n"] = bench_gen_samples(IIDStdUniform, dim, n)
     SUITE["gen_samples"]["Lattice d=$dim n=$n"] =
         bench_gen_samples(Lattice, dim, n; randomize=true)
     SUITE["gen_samples"]["DigitalNetB2 d=$dim n=$n"] =
         bench_gen_samples(DigitalNetB2, dim, n; randomize="LMS_DS")
     SUITE["gen_samples"]["Halton d=$dim n=$n"] =
         bench_gen_samples(Halton, dim, n; randomize=true)
-    SUITE["gen_samples"]["Kronecker d=$dim n=$n"] =
-        bench_gen_samples(Kronecker, dim, n)
+    SUITE["gen_samples"]["Kronecker d=$dim n=$n"] = bench_gen_samples(Kronecker, dim, n)
 end
 
 # 2. Transform (pure Julia: inverse-CDF + covariance factor)
@@ -200,25 +198,35 @@ end
 
 function _int_cubmcclt_asian()
     dd = IIDStdUniform(50; seed=42)
-    tm = GeometricBrownianMotion(dd; volatility=0.2, start_price=100.0,
-                                  interest_rate=0.05, t_final=1.0)
+    tm = GeometricBrownianMotion(
+        dd;
+        volatility=0.2,
+        start_price=100.0,
+        interest_rate=0.05,
+        t_final=1.0,
+    )
     f = FinancialOption(tm; option_type=:asian, strike_price=100.0)
     CubMCCLT(f; abs_tol=0.5)
 end
 
 function _int_cubqmcnetg_european()
     dd = DigitalNetB2(50; seed=42, randomize="LMS_DS")
-    tm = GeometricBrownianMotion(dd; volatility=0.2, start_price=100.0,
-                                  interest_rate=0.05, t_final=1.0)
+    tm = GeometricBrownianMotion(
+        dd;
+        volatility=0.2,
+        start_price=100.0,
+        interest_rate=0.05,
+        t_final=1.0,
+    )
     f = FinancialOption(tm; option_type=:european, strike_price=100.0)
     CubQMCNetG(f; abs_tol=0.5)
 end
 
-const INTEGRATE_CASES = Pair{String,Function}[
-    "CubMCCLT Keister"          => _int_cubmcclt_keister,
-    "CubQMCLatticeG Keister"    => _int_cubqmclatticeg_keister,
-    "CubQMCNetG Keister"        => _int_cubqmcnetg_keister,
-    "CubMCCLT AsianOption"      => _int_cubmcclt_asian,
+const INTEGRATE_CASES = Pair{String, Function}[
+    "CubMCCLT Keister" => _int_cubmcclt_keister,
+    "CubQMCLatticeG Keister" => _int_cubqmclatticeg_keister,
+    "CubQMCNetG Keister" => _int_cubqmcnetg_keister,
+    "CubMCCLT AsianOption" => _int_cubmcclt_asian,
     "CubQMCNetG EuropeanOption" => _int_cubqmcnetg_european,
 ]