multi-objective · pre-commit-ci · Nov 2, 2025 · Oct 31, 2025 · Nov 1, 2025 · Nov 2, 2025
diff --git a/.github/workflows/R.yml b/.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:

diff --git a/.pre-commit-config.yaml b/.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: "v2.11.1"
     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: v0.14.6
     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: v1.0.2
     hooks:
       - id: sphinx-lint
diff --git a/DEVEL-README.md b/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
 ============================
 

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-PACKAGEVERSION=0.1.9
+PACKAGEVERSION=0.2.0
 
 .PHONY: default clean check test pre-commit
 

diff --git a/README.md b/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)
+ - [`seqme`](https://github.com/szczurek-lab/seqme)
 
 
 [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
diff --git a/c/Makefile b/c/Makefile
@@ -1,7 +1,7 @@
 #-----------------------------------------------------------------------
 #  Makefile for moocore
 #-----------------------------------------------------------------------
-VERSION = 0.17.0
+VERSION = 0.18$(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                                                            \
@@ -116,7 +117,8 @@ DIST_ROOT_FILES = Makefile README.md LICENSE
 OBJS  = $(SRCS:.c=.o)
 OBJS := $(OBJS:.cpp=.o)
 
-EXE_LDFLAGS=-lm
+LDLIBS=-lm
+EXE_LDFLAGS=$(LDLIBS)
 
 include gitversion.mk
 
@@ -135,12 +137,12 @@ SHLIB_LDFLAGS = -shared
 # Platform-specific linker flags
 ifeq ($(uname_S),Linux)
   SHLIB_CFLAGS += -fPIC
-  SHLIB_LDFLAGS += -lm -Wl,--no-undefined
+  SHLIB_LDFLAGS += $(LDLIBS) -Wl,--no-undefined
   SHLIB_EXT=so
 endif
 ifeq ($(uname_S),Darwin)
   SHLIB_CFLAGS += -fPIC
-  SHLIB_LDFLAGS += -lm
+  SHLIB_LDFLAGS += $(LDLIBS)
   SHLIB_EXT=dylib
 endif
 ifeq ($(uname_S),Windows)
@@ -156,10 +158,10 @@ EXE_CFLAGS += $(SANITIZERS) $(OPT_CFLAGS) $(MARCH_FLAGS) $(WARN_CFLAGS) \
 
 
 # List of test target base names
-TEST_NAMES := eaf nondominated hv hvapprox igd epsilon dominatedsets
+TEST_NAMES := eaf nondominated hv hvapprox igd epsilon dominatedsets ndsort
 TEST_TARGETS := $(addprefix test-,$(TEST_NAMES))
 TIME_TARGETS := $(addprefix time-,$(TEST_NAMES))
-ALL_NAMES := $(TEST_NAMES) ndsort
+ALL_NAMES := $(TEST_NAMES)
 
 EXE_FILES := $(addsuffix $(EXE), $(addprefix $(BINDIR)/,$(ALL_NAMES)))
 
@@ -195,7 +197,7 @@ $(BINDIR)/nondominated$(EXE): nondominated.o timer.o
 $(EXE_FILES): cmdline.o io.o
 	$(call MKDIR, $(BINDIR)/)
 	$(call ECHO,--> Building $@ version $(VERSION) <---)
-	$(QUIET_LINK)$(CC) -o $@ $^ $(EXE_CFLAGS) $(CFLAGS) $(EXE_LDFLAGS)
+	$(QUIET_LINK)$(CC) -o $@ $^ $(EXE_CFLAGS) $(CFLAGS) $(EXE_LDFLAGS) $(LDFLAGS)
 
 dominatedsets.o: cmdline.h io.h nondominated.h
 eaf_main.o: cmdline.h io.h eaf.h
@@ -224,6 +226,7 @@ $(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)

diff --git a/c/NEWS.md b/c/NEWS.md
@@ -1,5 +1,9 @@
 # moocore C library
 
+## 0.18
+
+ * `pareto_rank()` is now O(k * n log n) in 3D, which is faster than the naive O(n^3).
+
 ## 0.17.0
 
  * `hv_contributions()` gains a parameter `ignore_dominated`.  The 3D case uses the HVC3D algorithm implemented in `hvc3d()`.

diff --git a/c/README.md b/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)
@@ -68,6 +68,38 @@ Most functions are implemented in headers such as `nondominated.h`. For other fu
 Functions exported by the library are marked with `MOOCORE_API`.
 
 
+Testsuite
+=========
+
+The **moocore** executables are validated using a [comprehensive testsuite](https://github.com/multi-objective/testsuite). Running the testsuite requires [Python](https://www.python.org/downloads/) `>= 3.10` and additional Python packages (see [`testsuite/requirements.txt`](https://github.com/multi-objective/testsuite/blob/main/requirements.txt)).  To run the testsuite yourself, follow these steps:
+
+```bash
+# Download moocore
+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
+    ...
+
+
+
 Command-line executables
 ========================
 
@@ -304,25 +336,6 @@ Options:
                      or maximised (+). By default all are minimised;
 ```
 
-Testsuite
-=========
-
-The **moocore** executables are validated using a [comprehensive testsuite](https://github.com/multi-objective/testsuite). Running the testsuite requires [Python](https://www.python.org/downloads/) `>= 3.10` and additional Python packages (see [`testsuite/requirements.txt`](https://github.com/multi-objective/testsuite/blob/main/requirements.txt)).  To run the testsuite yourself, follow these steps:
-
-```bash
-# Download moocore
-git clone https://github.com/multi-objective/moocore moocore
-# Download the testsuite
-git clone https://github.com/multi-objective/testsuite moocore/testsuite
-# Testing
-make -C moocore/c/ test
-# Timing
-make -C moocore/c/ time
-```
-
-
-
-
 License
 ========
 
@@ -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
diff --git a/c/avl_tiny.h b/c/avl_tiny.h
@@ -119,6 +119,11 @@ avl_init_tree(avl_tree_t *rc, avl_compare_t cmp) {
 /* Reinitializes the tree structure for reuse. Nothing is free()d.
  * Compare and freeitem functions are left alone.
  * O(1) */
+static inline void
+avl_clear_tree(avl_tree_t *avltree) {
+	avltree->top = avltree->head = avltree->tail = NULL;
+}
+
 static void
 avl_clear_node(avl_node_t *newnode) {
 	newnode->left = newnode->right = NULL;

diff --git a/c/common.h b/c/common.h
@@ -5,9 +5,13 @@
 #ifdef R_PACKAGE
 #define R_NO_REMAP
 #include <R.h>
-#define assert(EXP)                                                       \
-    do { if (unlikely(!(EXP))) { Rf_error("error: assertion failed: '%s' at %s:%d", \
-                                #EXP, __FILE__, __LINE__);}} while(0)
+#ifdef NDEBUG
+# define assert(EXP) ((void)0)
+#else
+# define assert(EXP) do { if (unlikely(!(EXP)))                                \
+            Rf_error("error: assertion failed: '%s' at %s:%d",                 \
+                     #EXP, __FILE__, __LINE__);} while(0)
+#endif
 #include "gcc_attribs.h"
 #define fatal_error(...) Rf_error(__VA_ARGS__)
 #define moocore_perror(...) Rf_error(__VA_ARGS__)

diff --git a/c/config.h b/c/config.h
@@ -14,4 +14,10 @@
 # define _CRT_SECURE_NO_WARNINGS 1
 #endif
 
+#if DEBUG == 0 && !defined(NDEBUG)
+# define NDEBUG // Disable assert()
+#elif DEBUG > 0 && defined(NDEBUG)
+# undef NDEBUG // Enable assert()
+#endif
+
 #endif // _MOOCORE_CONFIG_H_
diff --git a/c/eaf.c b/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);
         }

diff --git a/c/epsilon.c b/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);
         }/*