git: e8ad9c30d614 - main - science/silo: update 4.12.0 → 4.12.1

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 04 Oct 2026 09:21:13 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=e8ad9c30d614f49d54d175d6db74685398508edf

commit e8ad9c30d614f49d54d175d6db74685398508edf
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-10-03 21:39:59 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-10-04 09:20:47 +0000

    science/silo: update 4.12.0 → 4.12.1
    
    ChangeLog: https://github.com/llnl/Silo/releases/tag/4.12.1
---
 misc/lbann/Makefile                            |  2 +-
 science/ascent/Makefile                        |  2 +-
 science/axom/Makefile                          |  2 +-
 science/conduit/Makefile                       |  1 +
 science/parthenon/Makefile                     |  2 +-
 science/polytope/Makefile                      |  1 +
 science/silo/Makefile                          | 17 ++++++++++++++---
 science/silo/distinfo                          |  6 +++---
 science/silo/files/patch-CMakeLists.txt        | 13 -------------
 science/silo/files/patch-src_silo_silo__json.c |  6 ++++--
 science/silo/files/patch-tests_checksums       | 18 ++++++++++++++++++
 science/silo/pkg-plist                         |  4 ++--
 science/spheral/Makefile                       |  2 +-
 13 files changed, 48 insertions(+), 28 deletions(-)

diff --git a/misc/lbann/Makefile b/misc/lbann/Makefile
index ca909235e184..0c3b55bb3213 100644
--- a/misc/lbann/Makefile
+++ b/misc/lbann/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	lbann
 DISTVERSIONPREFIX=	v
 DISTVERSION=	0.104
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	misc # machine-learning
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/ascent/Makefile b/science/ascent/Makefile
index 7396717a0ec2..857f7e76f009 100644
--- a/science/ascent/Makefile
+++ b/science/ascent/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	ascent
 DISTVERSIONPREFIX=	v
 DISTVERSION=	0.9.5
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	science
 PKGNAMESUFFIX=	-visualizer
 
diff --git a/science/axom/Makefile b/science/axom/Makefile
index 564cbccde286..eb99ef12c1a3 100644
--- a/science/axom/Makefile
+++ b/science/axom/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	axom
 DISTVERSIONPREFIX=	v
 DISTVERSION=	0.13.0
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/conduit/Makefile b/science/conduit/Makefile
index ab74207b710f..1d4b357cf4fc 100644
--- a/science/conduit/Makefile
+++ b/science/conduit/Makefile
@@ -1,6 +1,7 @@
 PORTNAME=	conduit
 DISTVERSIONPREFIX=	v
 DISTVERSION=	0.9.9
+PORTREVISION=	1
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/parthenon/Makefile b/science/parthenon/Makefile
index c7d15759c1d2..319cb880088c 100644
--- a/science/parthenon/Makefile
+++ b/science/parthenon/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	parthenon
 DISTVERSIONPREFIX=	v
 DISTVERSION=	24.08
-PORTREVISION=	7
+PORTREVISION=	8
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/polytope/Makefile b/science/polytope/Makefile
index 9b5663b188f9..4bc46aa698c4 100644
--- a/science/polytope/Makefile
+++ b/science/polytope/Makefile
@@ -1,6 +1,7 @@
 PORTNAME=	polytope
 DISTVERSIONPREFIX=	v
 DISTVERSION=	0.7.5
+PORTREVISION=	1
 
 CATEGORIES=	science
 
diff --git a/science/silo/Makefile b/science/silo/Makefile
index dac1c6649952..34e91e287342 100644
--- a/science/silo/Makefile
+++ b/science/silo/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	silo
-DISTVERSION=	4.12.0
+DISTVERSION=	4.12.1
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -18,11 +18,16 @@ GH_ACCOUNT=	LLNL
 GH_PROJECT=	Silo
 
 CMAKE_ON=			SILO_ENABLE_INSTALL_LITE_HEADERS
-CMAKE_TESTING_ON=		SILO_ENABLE_TESTS # 3 tests fail, see https://github.com/LLNL/Silo/issues/289
-CMAKE_TESTING_TARGET=		check
+CMAKE_TESTING_ON=		BUILD_TESTING
+# upstream tests share filenames in a common test directory, so they are
+# not safe to run with ctest's default parallelism
+CMAKE_TESTING_JOBS=		1
 
 FFLAGS+=			-fallow-argument-mismatch # needed only for tests
 
+# tests invoke "python3" via $PATH; provide it since only python3.12 is installed
+TEST_ENV=		${MAKE_ENV} PATH=${WRKDIR}/bin:${PATH}
+
 CONFLICTS_INSTALL=		deforaos-browser # bin/browser
 
 OPTIONS_DEFINE=			BROWSER FORTRAN HDF5 PYTHON SILOCK
@@ -47,4 +52,10 @@ PYTHON_USES=			python
 SILOCK_DESC=			Enable building of silock
 SILOCK_CMAKE_BOOL=		SILO_ENABLE_SILOCK
 
+pre-test-PYTHON-on: # tests don't work w/out the PYTHON option; BINARY_ALIAS can't be easily used because this is option-conditional
+	@${MKDIR} ${WRKDIR}/bin
+	@${LN} -sf ${PYTHON_CMD} ${WRKDIR}/bin/python3
+
+# tests as of 4.12.1: 100% tests passed, 0 tests failed out of 180
+
 .include <bsd.port.mk>
diff --git a/science/silo/distinfo b/science/silo/distinfo
index 2fe4efe79810..4b97a9fbbdee 100644
--- a/science/silo/distinfo
+++ b/science/silo/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1763923185
-SHA256 (LLNL-Silo-4.12.0_GH0.tar.gz) = 5251816e43b08c19c925480b2daf85cc9b75e494b91df37df0eacc092279cfd0
-SIZE (LLNL-Silo-4.12.0_GH0.tar.gz) = 99198889
+TIMESTAMP = 1790854313
+SHA256 (LLNL-Silo-4.12.1_GH0.tar.gz) = 5ae33320eb545544c3e5d5c11723093d5c02eef88f0f7fd816190353d2986856
+SIZE (LLNL-Silo-4.12.1_GH0.tar.gz) = 12153371
diff --git a/science/silo/files/patch-CMakeLists.txt b/science/silo/files/patch-CMakeLists.txt
deleted file mode 100644
index 1d76b4832b67..000000000000
--- a/science/silo/files/patch-CMakeLists.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-- workaround for https://github.com/LLNL/Silo/issues/501
-
---- CMakeLists.txt.orig	2025-11-23 19:03:43 UTC
-+++ CMakeLists.txt
-@@ -700,7 +700,7 @@ install(FILES ${silo_public_headers} DESTINATION ${CMA
-                     WORLD_READ)
- 
- # Symlink old style silo_f77.inc
--if(SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER)
-+if(FALSE AND SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER)
-     install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink silo.inc silo_f77.inc
-         WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})")
- endif()
diff --git a/science/silo/files/patch-src_silo_silo__json.c b/science/silo/files/patch-src_silo_silo__json.c
index 331a87c8890e..05757b49c39e 100644
--- a/science/silo/files/patch-src_silo_silo__json.c
+++ b/science/silo/files/patch-src_silo_silo__json.c
@@ -1,6 +1,8 @@
---- src/silo/silo_json.c.orig	2025-11-21 05:30:59 UTC
+-- do not use stat64
+
+--- src/silo/silo_json.c.orig	2026-07-28 07:31:59 UTC
 +++ src/silo/silo_json.c
-@@ -446,11 +446,7 @@ json_object_from_binary_file(char const *filename)
+@@ -423,11 +423,7 @@ json_object_from_binary_file(char const *filename)
  #ifndef SIZEOF_OFF64_T
  #error missing definition for SIZEOF_OFF64_T in silo_private.h
  #else
diff --git a/science/silo/files/patch-tests_checksums b/science/silo/files/patch-tests_checksums
new file mode 100644
index 000000000000..f8ac64cf2467
--- /dev/null
+++ b/science/silo/files/patch-tests_checksums
@@ -0,0 +1,18 @@
+-- Force decimal interpretation of $minoffset before passing it to head -c.
+-- Needed because FreeBSD's head(1) parses its byte count with strtol(3)
+-- using base 0, so a value with a leading zero (as produced by `od -A d`,
+-- which zero-pads the decimal offset) is misread as octal and rejected
+-- with "illegal byte count" whenever it contains an 8 or 9 digit. This
+-- caused the checksums test to fail on FreeBSD.
+
+--- tests/checksums.orig	2026-07-28 07:31:59 UTC
++++ tests/checksums
+@@ -133,7 +133,7 @@ rm -f multi_ucd3d_corrupt.h5
+ # and the last part of the file (minus the part we've zeroed)
+ #
+ rm -f multi_ucd3d_corrupt.h5
+-head -c $minoffset h5_check_files/multi_ucd3d.h5 > multi_ucd3d_corrupt.h5
++head -c $(awk -v n="$minoffset" 'BEGIN{printf "%d", n}') h5_check_files/multi_ucd3d.h5 > multi_ucd3d_corrupt.h5
+ dd if=/dev/zero bs=16 count=1 >> multi_ucd3d_corrupt.h5 2>/dev/null
+ leftover=$(expr $size - $minoffset - 16)
+ tail -c $leftover h5_check_files/multi_ucd3d.h5 >> multi_ucd3d_corrupt.h5
diff --git a/science/silo/pkg-plist b/science/silo/pkg-plist
index fc056e66313d..e663ae044141 100644
--- a/science/silo/pkg-plist
+++ b/science/silo/pkg-plist
@@ -10,12 +10,12 @@ include/silo.h
 %%FORTRAN%%include/silo.inc
 %%FORTRAN%%include/silo_FC.h
 include/silo_exports.h
-include/silo_f9x.inc
+%%FORTRAN%%include/silo_f9x.inc
 %%PYTHON%%lib/Silo.so
 lib/cmake/Silo/SiloConfig.cmake
 lib/cmake/Silo/SiloConfigVersion.cmake
 lib/cmake/Silo/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake
 lib/cmake/Silo/SiloTargets.cmake
 lib/libsilo%%SUFX_HDF5%%.so
-lib/libsilo%%SUFX_HDF5%%.so.4.12.0
+lib/libsilo%%SUFX_HDF5%%.so.4.12.1
 lib/libsilo%%SUFX_HDF5%%.so.412
diff --git a/science/spheral/Makefile b/science/spheral/Makefile
index c861b1aa99fd..4219d7e88e44 100644
--- a/science/spheral/Makefile
+++ b/science/spheral/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	spheral
 DISTVERSIONPREFIX=	v
 DISTVERSION=	2026.06.0
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	science # physics
 
 MAINTAINER=	yuri@FreeBSD.org