Fpl basecase

.github/workflows/R.yml

@@ -46,8 +46,7 @@ jobs:
         os: [ ubuntu-22.04, windows-latest, macos-15-intel, macos-14 ]
         r: [ release ]
         include:
-          # Use 4.0 to check with rtools40's older compiler
-          - { os: windows-latest, r: '4.0' }
+          - { os: windows-latest, r: '4.1' }
           # Use latest ubuntu to make it easier to install dependencies
           - { os: ubuntu-24.04, r: 'devel', http-user-agent: 'release' }
     env:

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ ci:
 
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9014
+    rev: v0.4.3.9017
     hooks:
       - id: parsable-R
       - id: no-browser-statement
@@ -43,19 +43,19 @@ repos:
         exclude: '(\.Rd|python/doc/source/reference/.*|test-doctest-.*)'
 
   - repo: https://github.com/tox-dev/tox-ini-fmt
-    rev: "1.6.0"
+    rev: "1.7.0"
     hooks:
       - id: tox-ini-fmt
 
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.6.0"
+    rev: "v2.11.0"
     hooks:
       - id: pyproject-fmt
         additional_dependencies: ["tox>=4.12.1"]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.13.0
+    rev: v0.14.3
     hooks:
       # Run the formatter.
       - id: ruff-format
@@ -67,6 +67,6 @@ repos:
         require_serial: true
 
   - repo: https://github.com/sphinx-contrib/sphinx-lint
-    rev: v1.0.0
+    rev: v1.0.1
     hooks:
       - id: sphinx-lint

DEVEL-README.md

@@ -24,6 +24,32 @@ How to release
 1. `git ci -a -m "Start development of v{NEW_VERSION}"`
 
 
+Building the code
+=================
+
+C code
+-----
+
+See [*Compilation*](https://github.com/multi-objective/moocore/tree/main/c#compilation) to compile the C code under `c/`.
+
+R and Python packages
+---------------------
+
+Under `r/` or `python/`, the commands `make build` and `make install` will build and install the R and Python packages.
+
+
+Testing
+========
+
+The C code and the Python and R packages have their own testsuites. See [C testsuite](https://github.com/multi-objective/moocore/tree/main/c#testsuite) to setup and run the C testsuite.
+
+The Python and R testsuites are run automatically via Github Actions for every push and pull request. You can run then manually by running `make test` under `r/` or `python/`.
+
+You can run all testsuites at once by executing at the top-level:
+
+    make test
+
+
 How to extend the Python API
 ============================
 

Makefile

@@ -1,4 +1,4 @@
-PACKAGEVERSION=0.1.9
+PACKAGEVERSION=0.2.0
 
 .PHONY: default clean check test pre-commit
 

README.md

@@ -53,6 +53,9 @@ The following projects currently use `moocore`:
  - [`pymoo`](https://pymoo.org/)
  - [`Liger`](https://www.ide.uk/project-liger)
  - [`DESDEO`](https://github.com/industrial-optimization-group/DESDEO/)
+ - [`IOHInspector`](https://github.com/IOHprofiler/IOHinspector?tab=readme-ov-file)
+ - [QuantumAnnealingMOO](https://github.com/andrew-d-king/QuantumAnnealingMOO) (D-Wave Quantum Inc)
+
 
 
 [c-build-badge]: https://github.com/multi-objective/moocore/actions/workflows/C.yml/badge.svg?event=push
@@ -79,5 +82,5 @@ The following projects currently use `moocore`:
 [r-universe-build-link]: https://github.com/r-universe/multi-objective/actions/workflows/build.yml
 [r-universe-version]: https://multi-objective.r-universe.dev/moocore
 [r-universe-version-badge]: https://multi-objective.r-universe.dev/badges/moocore
-[testsuite-badge]: https://github.com/multi-objective/testsuite/actions/workflows/moocore.yml/badge.svg?event=push
+[testsuite-badge]: https://github.com/multi-objective/testsuite/actions/workflows/moocore.yml/badge.svg
 [testsuite-link]: https://github.com/multi-objective/testsuite/actions/workflows/moocore.yml

c/Makefile

@@ -1,7 +1,7 @@
 #-----------------------------------------------------------------------
 #  Makefile for moocore
 #-----------------------------------------------------------------------
-VERSION = 0.17.0
+VERSION = 0.17.0$(REVISION)
 
 S=
 ## Quiet / verbose output:
@@ -96,6 +96,7 @@ HDRS =  avl.h                                                                \
         hvapprox.h                                                           \
         hv_priv.h                                                            \
         hv3d_priv.h                                                          \
+        hv4d_priv.h                                                          \
         igd.h                                                                \
         io.h                                                                 \
         io_priv.h                                                            \
@@ -224,6 +225,7 @@ $(CXXSHLIB): $(LIBHV_OBJS)
 	$(CXX) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $^ $(SHLIB_LDFLAGS)
 
 clean:
+	@-$(RM) *.s *.i
 	@-$(RM) config.status config.log
 	@-$(RM) Hypervolume_MEX.mex
 	@-$(RM) $(SHLIB) $(CXXSHLIB)

c/README.md

@@ -45,17 +45,17 @@ This uses the option `"-march=native"`. If your GCC version does not support `"n
 
     make all MARCH=x86-64-v2
 
-See the [GCC manual](https://gcc.gnu.org/onlinedocs/gcc/Submodel-Options.html** for the names of the architectures supported by your version of GCC.
+See the [GCC manual](https://gcc.gnu.org/onlinedocs/gcc/Submodel-Options.html) for the names of the architectures supported by your version of GCC.
 
-You can compile the code with various runtime checks enabled using the option `DEBUG=1`.  This will slow down the code significantly.
+You can compile the code with various runtime checks enabled using the option `DEBUG=1`.  This will slow down the code significantly.  If this is too slow for your purposes, you can disable the [sanitizers](https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Options.html#index-fsanitize_003daddress) using `make all DEBUG=1 SANITIZERS=""`.
 
 The build system will try to pick good compiler flags for you, but if you need to, you can override them by passing the option `OPT_CFLAGS`. For example, to disable compiler optimization and enabled debug symbols, you could run:
 
     make all OPT_CFLAGS="-O0 -g"
 
 
 If you do not want to see the command line of each compiler
-invocation, pass `S=1` to `make`.
+invocation, you pass `S=1` to `make`.
 
 
 Embedding (shared library)
@@ -314,12 +314,25 @@ The **moocore** executables are validated using a [comprehensive testsuite](http
 git clone https://github.com/multi-objective/moocore moocore
 # Download the testsuite
 git clone https://github.com/multi-objective/testsuite moocore/testsuite
+# Install required python packages
+python3 -m pip install -r testsuite/requirements.txt
 # Testing
 make -C moocore/c/ test
 # Timing
 make -C moocore/c/ time
 ```
 
+Under `moocore/c/`, `make test` will compile the code with `DEBUG=1 SANTIZERS="" OPT_CFLAGS="-Og -g3"`. This is useful for debugging failures.
+
+`make time` will compile the code with `DEBUG=0 SANITIZERS="" OPT_CLAGS="-O3 -ftlo -march=native"`. This is useful for benchmarking code and making sure compiler optimizations do not break anything.
+
+Neither `make test` nor `make time` recompile the code that has not been modified. So you can compile the code first with your preferred compiler flags and then run the testsuite. For example, if you compile with `make all DEBUG=1`, the code will be compiler with several [sanitizers](https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Options.html#index-fsanitize_003daddress) enabled. You can then call `make test` to run the testsuite with the sanitizers enabled.  This is much slower, but very helpful to track crashes.
+
+Under `c/` there are various targets to run only parts of the testsuite, for example:
+
+    make test-hv
+    make test-nondominated
+    ...
 
 
 
@@ -348,5 +361,5 @@ See the [LICENSE](/LICENSE) and [COPYRIGHTS](/r/inst/COPYRIGHTS) files.
 [r-moocore-cran]: https://cran.r-project.org/package=moocore
 [r-moocore-github]: https://github.com/multi-objective/moocore/tree/main/r#readme
 [r-moocore-homepage]: https://multi-objective.github.io/moocore/r/
-[testsuite-badge]: https://github.com/multi-objective/testsuite/actions/workflows/moocore.yml/badge.svg?event=push
+[testsuite-badge]: https://github.com/multi-objective/testsuite/actions/workflows/moocore.yml/badge.svg
 [testsuite-link]: https://github.com/multi-objective/testsuite/actions/workflows/moocore.yml

c/eaf.c

@@ -563,7 +563,7 @@ eaf_check_polygons(eaf_polygon_t *p, int nobj)
                 polygon_print(pi, nobj);
                 polygon_print(pj, nobj);
 #endif
-                assert(!polygons_intersect(pi, pj, nobj));
+                assert(false);
             }
             pj = next_polygon(pj, nobj, end);
         }

c/epsilon.c

@@ -143,7 +143,7 @@ do_file (const char *filename, double *reference, size_t reference_size,
         //        time_elapsed = Timer_elapsed_virtual ();
         fprintf (outfile, indicator_printf_format "\n", epsilon);
         if ((additive_flag && epsilon < 0) || (!additive_flag && epsilon < 1)) {
-            errprintf ("%s: some points are not  dominated by the reference set",
+            errprintf ("%s: some points are not dominated by the reference set",
                        filename);
             exit (EXIT_FAILURE);
         }/*

c/epsilon.h

@@ -14,11 +14,12 @@
 static inline bool
 all_positive(const double * restrict points, size_t size, dimension_t dim)
 {
-    ASSUME(dim <= 32);
-    for (size_t a = 0; a < size; a++)
-        for (dimension_t d = 0; d < dim; d++)
-            if (points[a * dim + d] <= 0)
-                return false;
+    ASSUME(size > 0);
+    ASSUME(1 <= dim && dim <= 32);
+    const size_t len = size * dim;
+    for (size_t a = 0; a < len; a++)
+        if (points[a] <= 0)
+            return false;
 
     return true;
 }
@@ -43,19 +44,19 @@ all_positive(const double * restrict points, size_t size, dimension_t dim)
    for negative values doesn't make sense.
  */
 
-static inline double
-eps_value_(bool do_ratio, double a, double b)
-{
-    return do_ratio ? a / b : a - b;
-}
 
+_attr_optimize_finite_math
 static inline double
 epsilon_helper_(bool do_mult, const enum objs_agree_t agree,
                 const signed char * restrict minmax, dimension_t dim,
                 const double * restrict points_a, size_t size_a,
                 const double * restrict points_b, size_t size_b)
 {
+// Converting this macro to an inline function hinders vectorization.
+#define eps_value_(X,Y) (do_mult ? ((X) / (Y)) : ((X) - (Y)))
+
     ASSUME(2 <= dim && dim <= 32);
+    ASSUME(size_a > 0 && size_b > 0);
     ASSUME(agree == AGREE_MINIMISE || agree == AGREE_MAXIMISE || agree == AGREE_NONE);
     ASSUME(minmax == NULL || agree != AGREE_NONE);
     double epsilon = do_mult ? 0 : -INFINITY;
@@ -65,29 +66,25 @@ epsilon_helper_(bool do_mult, const enum objs_agree_t agree,
         const double * restrict pb = &points_b[b * dim];
         for (size_t a = 0; a < size_a; a++) {
             const double * restrict pa = &points_a[a * dim];
-            double epsilon_max;
-            if (agree == AGREE_NONE) {
-                epsilon_max = MAX(minmax[0] * eps_value_(do_mult, pb[0], pa[0]),
-                                  minmax[1] * eps_value_(do_mult, pb[1], pa[1]));
-                if (epsilon_max >= epsilon_min)
-                    continue;
-                for (dimension_t d = 2; d < dim; d++) {
-                    double epsilon_temp = minmax[d] * eps_value_(do_mult, pb[d], pa[d]);
-                    epsilon_max = MAX(epsilon_max, epsilon_temp);
-                }
-            } else {
-                epsilon_max = (agree == AGREE_MINIMISE)
-                    ? MAX(eps_value_(do_mult, pa[0], pb[0]), eps_value_(do_mult, pa[1], pb[1]))
-                    : MAX(eps_value_(do_mult, pb[0], pa[0]), eps_value_(do_mult, pb[1], pa[1]));
-                if (epsilon_max >= epsilon_min)
-                    continue;
-                for (dimension_t d = 2; d < dim; d++) {
-                    double epsilon_temp = (agree == AGREE_MINIMISE)
-                        ? eps_value_(do_mult, pa[d], pb[d])
-                        : eps_value_(do_mult, pb[d], pa[d]);
-                    epsilon_max = MAX(epsilon_max, epsilon_temp);
-                }
+            double epsilon_max = (agree == AGREE_NONE)
+                ? MAX(minmax[0] * eps_value_(pb[0], pa[0]),
+                      minmax[1] * eps_value_(pb[1], pa[1]))
+                : ((agree == AGREE_MINIMISE)
+                   ? MAX(eps_value_(pa[0], pb[0]), eps_value_(pa[1], pb[1]))
+                   : MAX(eps_value_(pb[0], pa[0]), eps_value_(pb[1], pa[1])));
+
+            if (epsilon_max >= epsilon_min)
+                continue;
+
+            for (dimension_t d = 2; d < dim; d++) {
+                double epsilon_temp = (agree == AGREE_NONE)
+                    ? minmax[d] * eps_value_(pb[d], pa[d])
+                    : ((agree == AGREE_MINIMISE)
+                       ? eps_value_(pa[d], pb[d])
+                       : eps_value_(pb[d], pa[d]));
+                epsilon_max = MAX(epsilon_max, epsilon_temp);
             }
+
             if (epsilon_max <= epsilon) {
                 skip_max = true;
                 break;
@@ -100,6 +97,63 @@ epsilon_helper_(bool do_mult, const enum objs_agree_t agree,
     return epsilon;
 }
 
+_attr_optimize_finite_math
+static inline double
+epsilon_mult_agree_none(const signed char * restrict minmax, dimension_t dim,
+                        const double * restrict points_a, size_t size_a,
+                        const double * restrict points_b, size_t size_b)
+{
+    return epsilon_helper_(/* do_mult=*/true, AGREE_NONE, minmax, dim, points_a, size_a, points_b, size_b);
+}
+
+_attr_optimize_finite_math
+static inline double
+epsilon_mult_agree_min(dimension_t dim,
+                        const double * restrict points_a, size_t size_a,
+                        const double * restrict points_b, size_t size_b)
+{
+    return epsilon_helper_(/* do_mult=*/true, AGREE_MINIMISE, /*minmax=*/NULL, dim, points_a, size_a, points_b, size_b);
+}
+
+_attr_optimize_finite_math
+static inline double
+epsilon_mult_agree_max(dimension_t dim,
+                        const double * restrict points_a, size_t size_a,
+                        const double * restrict points_b, size_t size_b)
+{
+    return epsilon_helper_(/* do_mult=*/true, AGREE_MAXIMISE, /*minmax=*/NULL, dim, points_a, size_a, points_b, size_b);
+}
+
+
+_attr_optimize_finite_math
+static inline double
+epsilon_addi_agree_none(const signed char * restrict minmax, dimension_t dim,
+                        const double * restrict points_a, size_t size_a,
+                        const double * restrict points_b, size_t size_b)
+{
+    return epsilon_helper_(/* do_mult=*/false, AGREE_NONE, minmax, dim, points_a, size_a, points_b, size_b);
+}
+
+_attr_optimize_finite_math
+static inline double
+epsilon_addi_agree_min(dimension_t dim,
+                        const double * restrict points_a, size_t size_a,
+                        const double * restrict points_b, size_t size_b)
+{
+    return epsilon_helper_(/* do_mult=*/false, AGREE_MINIMISE, /*minmax=*/NULL, dim, points_a, size_a, points_b, size_b);
+}
+
+_attr_optimize_finite_math
+static inline double
+epsilon_addi_agree_max(dimension_t dim,
+                        const double * restrict points_a, size_t size_a,
+                        const double * restrict points_b, size_t size_b)
+{
+    return epsilon_helper_(/* do_mult=*/false, AGREE_MAXIMISE, /*minmax=*/NULL, dim, points_a, size_a, points_b, size_b);
+}
+
+
+_attr_optimize_finite_math
 static inline double
 epsilon_mult_minmax(const signed char * restrict minmax, dimension_t dim,
                     const double * restrict points_a, size_t size_a,
@@ -114,14 +168,15 @@ epsilon_mult_minmax(const signed char * restrict minmax, dimension_t dim,
     // This forces the compiler to generate three specialized versions of the function.
     switch (check_all_minimize_maximize(minmax, dim)) {
       case AGREE_MINIMISE:
-          return epsilon_helper_(/* do_mult=*/true, AGREE_MINIMISE, /*minmax=*/NULL, dim, points_a, size_a, points_b, size_b);
+          return epsilon_mult_agree_min(dim, points_a, size_a, points_b, size_b);
       case AGREE_MAXIMISE:
-          return epsilon_helper_(/* do_mult=*/true, AGREE_MAXIMISE, /*minmax=*/NULL, dim, points_a, size_a, points_b, size_b);
+          return epsilon_mult_agree_max(dim, points_a, size_a, points_b, size_b);
       default:
-          return epsilon_helper_(/* do_mult=*/true, AGREE_NONE, minmax, dim, points_a, size_a, points_b, size_b);
+          return epsilon_mult_agree_none(minmax, dim, points_a, size_a, points_b, size_b);
     }
 }
 
+_attr_optimize_finite_math
 static inline double
 epsilon_additive_minmax(const signed char * restrict minmax, dimension_t dim,
                         const double * restrict points_a, size_t size_a,
@@ -130,11 +185,11 @@ epsilon_additive_minmax(const signed char * restrict minmax, dimension_t dim,
     // This forces the compiler to generate three specialized versions of the function.
     switch (check_all_minimize_maximize(minmax, dim)) {
       case AGREE_MINIMISE:
-          return epsilon_helper_(/* do_mult=*/false, AGREE_MINIMISE, /*minmax=*/NULL, dim, points_a, size_a, points_b, size_b);
+          return epsilon_addi_agree_min(dim, points_a, size_a, points_b, size_b);
       case AGREE_MAXIMISE:
-          return epsilon_helper_(/* do_mult=*/false, AGREE_MAXIMISE, /*minmax=*/NULL, dim, points_a, size_a, points_b, size_b);
+          return epsilon_addi_agree_max(dim, points_a, size_a, points_b, size_b);
       default:
-          return epsilon_helper_(/* do_mult=*/false, AGREE_NONE, minmax, dim, points_a, size_a, points_b, size_b);
+          return epsilon_addi_agree_none(minmax, dim, points_a, size_a, points_b, size_b);
     }
 }