multi-objective · pre-commit-ci · Dec 1, 2025 · Dec 1, 2025 · Dec 1, 2025 · Dec 1, 2025
diff --git a/.github/workflows/R.yml b/.github/workflows/R.yml
@@ -162,9 +162,11 @@ jobs:
         env:
           NOT_CRAN: false
         run: |
-          coverage <- covr::package_coverage(type="all", quiet=FALSE, clean = FALSE,
+          coverage <- withr::with_makevars(c(MOOCORE_DEBUG="1", LTO_OPT=""),
+                        covr::package_coverage(type="all", quiet=FALSE, clean = FALSE,
                            commentDonttest = FALSE, commentDontrun = FALSE, flags="R",
                            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"))
+          )
           print(coverage)
           covr::to_cobertura(coverage)
           list.files("../", pattern="*.xml", recursive=TRUE)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -49,14 +49,14 @@ repos:
       - id: tox-ini-fmt
 
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.11.0"
+    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: v0.14.3
+    rev: v0.14.7
     hooks:
       # Run the formatter.
       - id: ruff-format
@@ -68,6 +68,6 @@ repos:
         require_serial: true
 
   - repo: https://github.com/sphinx-contrib/sphinx-lint
-    rev: v1.0.1
+    rev: v1.0.2
     hooks:
       - id: sphinx-lint
diff --git a/c/Makefile b/c/Makefile
@@ -226,7 +226,7 @@ $(CXXSHLIB): $(LIBHV_OBJS)
 	$(CXX) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $^ $(SHLIB_LDFLAGS)
 
 clean:
-	@-$(RM) *.s *.i
+	@-$(RM) *.s *.i *.gcda mt19937/*.gcda
 	@-$(RM) config.status config.log
 	@-$(RM) Hypervolume_MEX.mex
 	@-$(RM) $(SHLIB) $(CXXSHLIB)

diff --git a/c/cmdline.h b/c/cmdline.h
@@ -270,7 +270,7 @@ static inline void default_cmdline_handler(int opt)
           usage();
           exit(EXIT_SUCCESS);
       default:
-          unreachable();
+          unreachable(); // COVR_EXCL_LINE # nocov
     }
 }
 

diff --git a/c/gcc_attribs.h b/c/gcc_attribs.h
@@ -121,14 +121,14 @@
 
 
 #if (defined(__GNUC__) && __GNUC__ >= 3) || defined(__clang__)
-# define likely(x)	__builtin_expect(!!(x), 1)
-# define unlikely(x)	__builtin_expect(!!(x), 0)
+# define likely(x)	  __builtin_expect(!!(x), 1)
+# define unlikely(x)  __builtin_expect(!!(x), 0)
 #elif (defined(__cplusplus) && __cplusplus >= 202002L) || (defined(_MSVC_LANG) && _MSVC_LANG >= 202002L)
-# define likely(x)	(x) [[likely]]
-# define unlikely(x)	(x) [[unlikely]]
+# define likely(x)	  (x) [[likely]]
+# define unlikely(x)  (x) [[unlikely]]
 #else
-# define likely(x)	(x)
-# define unlikely(x)	(x)
+# define likely(x)	  (x)
+# define unlikely(x)  (x)
 #endif
 
 #ifdef _MSC_VER

diff --git a/c/hv4d_priv.h b/c/hv4d_priv.h
@@ -156,7 +156,7 @@ restart_base_setup_z_and_closest(dlnode_t * restrict list, dlnode_t * restrict n
         }
         p = p->next[0];
     }
-    unreachable();
+    unreachable();  // COVR_EXCL_LINE # nocov
 }
 
 // FIXME: This is very similar to the loop in hvc3d_list() but it doesn't use p->last_slice_z
@@ -211,7 +211,7 @@ one_contribution_3d(dlnode_t * restrict newp)
         lastz = px[2];
         p = p->next[0];
     }
-    unreachable();
+    unreachable();  // COVR_EXCL_LINE # nocov
 }
 
 /* Compute the hypervolume indicator in d=4 by iteratively computing the one

diff --git a/c/hvapprox.c b/c/hvapprox.c
@@ -434,7 +434,7 @@ int_of_power_of_sin_from_0_to_b(dimension_t m, double b)
           return 0.13994993409141898*b - cos_b*sin_b*(
               0.03125*POW(sin_b, 30) + 31/960.*POW(sin_b, 28) + 899/26880.*POW(sin_b, 26) + 8091/232960.*POW(sin_b, 24) + 13485/372736.*POW(sin_b, 22) + 310155/8200192.*POW(sin_b, 20) + 186093/4685824.*POW(sin_b, 18) + 392863/9371648.*POW(sin_b, 16) + 6678671/149946368.*POW(sin_b, 14) + 100180065/2099249152.*POW(sin_b, 12) + 33393355/645922816.*POW(sin_b, 10) + 6678671/117440512.*POW(sin_b, 8) + 60108039/939524096.*POW(sin_b, 6) + 0.07463996484875679*POW(sin_b, 4) + 0.093299956060945988*POW(sin_b, 2) + 0.13994993409141898);
       default:
-          unreachable();
+          unreachable();  // COVR_EXCL_LINE # nocov
     }
 #undef POW
 }

diff --git a/c/main-hvapprox.c b/c/main-hvapprox.c
@@ -173,7 +173,7 @@ hvapprox_file (const char *filename, double *reference,
               volume = hv_approx_hua_wang(&data[nobj * cumsize], nobj, cumsizes[n] - cumsize, reference, maximise, nsamples);
               break;
           default:
-              unreachable();
+              unreachable();  // COVR_EXCL_LINE # nocov
         }
 
         if (volume == 0.0) {

diff --git a/c/nondominated.h b/c/nondominated.h
@@ -474,7 +474,7 @@ find_dominated_point_(const double * restrict points, dimension_t dim, size_t si
           return find_dominated_point_agree_(
               points, dim, size, keep_weakly, AGREE_MAXIMISE, /*minmax=*/NULL);
       default:
-          unreachable();
+          unreachable();  // # nocov
     }
 }
 
@@ -525,7 +525,7 @@ find_nondominated_set_(const double * restrict points, dimension_t dim, size_t s
           return find_nondominated_set_agree_(
               points, dim, size, nondom, keep_weakly, AGREE_MAXIMISE, /*minmax=*/NULL);
       default:
-          unreachable();
+          unreachable();  // # nocov
     }
 }
 

diff --git a/c/pow_int.h b/c/pow_int.h
@@ -42,7 +42,7 @@ fast_pow_uint_max32(double base, uint_fast8_t exp)
       case 30: { b15 = fast_pow_uint_max32(base, 15); return b15 * b15; }
       case 31: { b15 = fast_pow_uint_max32(base, 15); return b15 * b15 * base; }
       case 32: { b16 = fast_pow_uint_max32(base, 16); return b16 * b16; }
-      default: unreachable();
+      default: unreachable(); // COVR_EXCL_LINE # nocov
     }
 }
 
@@ -103,7 +103,7 @@ fast_powl_uint_max32(long double base, uint_fast8_t exp)
       case 30: { b15 = fast_powl_uint_max32(base, 15); return b15 * b15; }
       case 31: { b15 = fast_powl_uint_max32(base, 15); return b15 * b15 * base; }
       case 32: { b16 = fast_powl_uint_max32(base, 16); return b16 * b16; }
-      default: unreachable();
+      default: unreachable(); // COVR_EXCL_LINE # nocov
     }
 }
 

diff --git a/python/pyproject.toml b/python/pyproject.toml
@@ -192,6 +192,11 @@ faulthandler_timeout = 10
 doctest_optionflags = "NUMBER"
 addopts = [ "--import-mode=importlib", "--durations=5", "--durations-min=1.0" ]
 
+[tool.coverage.report]
+exclude_also = [
+  '# nocov',
+]
+
 [tool.mypy]
 python_version = "3.11"
 # Strictness (recommended for library code)

diff --git a/python/tox.ini b/python/tox.ini
@@ -35,7 +35,7 @@ commands =
     coverage run --source={envsitepackagesdir}/moocore,tests -m pytest --doctest-modules --import-mode=importlib {envsitepackagesdir}/moocore tests
     coverage report -m
     coverage xml
-    gcovr --print-summary --delete -r {toxinidir} {toxinidir} --xml=c_coverage.xml --exclude '.*/moocore\._libmoocore.c' --fail-under-line 1
+    gcovr --exclude-unreachable-branches --print-summary --delete -r {toxinidir} {toxinidir} --xml=c_coverage.xml --exclude '.*/moocore\._libmoocore.c' --fail-under-line 1
 
 [testenv:docs]
 description = Build documentation
@@ -55,6 +55,7 @@ passenv = MOOCORE_DEBUG
 setenv =
     .pkg-cov: CFLAGS={env:CFLAGS:--coverage -UNDEBUG -DDEBUG=1}
     .pkg-cov: LDFLAGS=--coverage
+    .pkg-cov: MOOCORE_DEBUG=1
     .pkg-release: MOOCORE_DEBUG=0
     .pkg-debug: MOOCORE_DEBUG=1
 

diff --git a/r/Makefile b/r/Makefile
@@ -89,7 +89,7 @@ check: build
 ifdef TEST
 	_R_CHECK_FORCE_SUGGESTS_=false NOT_CRAN=true $(Reval) 'devtools::test(filter="$(TEST)")'
 else
-	cd $(BINDIR) && (_R_CHECK_FORCE_SUGGESTS_=false NOT_CRAN=true DEBUG=1 R CMD check --run-donttest --run-dontrun --timings $(PACKAGE)_$(PACKAGEVERSION).tar.gz; cat $(PACKAGE).Rcheck/$(PACKAGE)-Ex.timings)
+	cd $(BINDIR) && (_R_CHECK_FORCE_SUGGESTS_=false NOT_CRAN=true MOOCORE_DEBUG=1 R CMD check --run-donttest --run-dontrun --timings $(PACKAGE)_$(PACKAGEVERSION).tar.gz; cat $(PACKAGE).Rcheck/$(PACKAGE)-Ex.timings)
 endif
 
 show:
@@ -112,7 +112,7 @@ winbuild winbuild_:
 	$(Reval) "devtools::check_win_devel()"
 
 covr:
-	$(Reval) "Sys.setenv(NOT_CRAN='true');covr::report(covr::package_coverage(type='all', quiet=FALSE), browse=TRUE)"
+	$(Reval) "Sys.setenv(NOT_CRAN='true');covr::report(withr::with_makevars(c(MOOCORE_DEBUG='1', LTO_OPT=''), covr::package_coverage(type='all', commentDonttest=FALSE, commentDontrun=FALSE, quiet=FALSE)), browse=TRUE)"
 
 benchmarks: quick-install
 	$(RM) ./vignettes/articles/bench/*.rds

diff --git a/r/src/Makevars b/r/src/Makevars
@@ -4,8 +4,8 @@
 # In particular, add the following to ~/.R/Makevars:
 # LTO_OPT=-flto
 LTO=$(LTO_OPT)
-DEBUG=0
-PKG_CPPFLAGS=-DR_PACKAGE -DDEBUG=$(DEBUG) -I./libmoocore/
+MOOCORE_DEBUG?=0
+PKG_CPPFLAGS=-DR_PACKAGE -DDEBUG=$(MOOCORE_DEBUG) -I./libmoocore/
 
 MOOCORE_SRC_FILES = hv3dplus.c hv4d.c hv_contrib.c hv.c hvapprox.c hvc3d.c pareto.c whv.c whv_hype.c avl.c eaf3d.c eaf.c io.c rng.c mt19937/mt19937.c
 SOURCES = $(MOOCORE_SRC_FILES:%=libmoocore/%) init.c Rmoocore.c
@@ -19,7 +19,7 @@ all: exes $(SHLIB)
 $(SHLIB): $(OBJECTS)
 
 exes: $(SHLIB)
-	$(MAKE) -C libmoocore all march=none CC="$(CC)" CFLAGS="$(CFLAGS)" WARN_CFLAGS="" OPT_CFLAGS="" DEBUG=$(DEBUG) EXE=$(EXEEXT) BINDIR=$(PWD)
+	$(MAKE) -C libmoocore all march=none CC="$(CC)" CFLAGS="$(CFLAGS)" WARN_CFLAGS="" OPT_CFLAGS="" DEBUG=$(MOOCORE_DEBUG) EXE=$(EXEEXT) BINDIR=$(PWD)
 	@-$(RM) libmoocore/*.o
 
 clean: