git: ee993313d167 - main - biology/viennarna: update 2.7.0 → 2.7.2

Go to: [ bottom of page ] [ top of archives ] [ this month ]
From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 28 Jun 2026 06:49:12 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=ee993313d1671cbbb565f4122d39c534b0828a80

commit ee993313d1671cbbb565f4122d39c534b0828a80
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-06-28 04:21:46 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-06-28 06:49:08 +0000

    biology/viennarna: update 2.7.0 → 2.7.2
---
 biology/viennarna/Makefile                         | 12 +++-
 biology/viennarna/distinfo                         |  6 +-
 .../viennarna/files/patch-interfaces_Makefile.am   | 10 ++++
 .../files/patch-m4_ac__rna__build__requirements.m4 |  9 +--
 biology/viennarna/files/patch-m4_ac__rna__swig.m4  | 65 ++++++++++++++++++++++
 biology/viennarna/pkg-plist                        | 10 ++++
 6 files changed, 103 insertions(+), 9 deletions(-)

diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile
index f48bf3a3a2f2..fdc2daa5c55c 100644
--- a/biology/viennarna/Makefile
+++ b/biology/viennarna/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	viennarna
-DISTVERSION=	2.7.0
-PORTREVISION=	3
+DISTVERSION=	2.7.2
 CATEGORIES=	biology
 MASTER_SITES=	https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_7_x/
 DISTNAME=	ViennaRNA-${DISTVERSION}
@@ -63,4 +62,13 @@ post-install:
 	@${RM} ${STAGEDIR}/RNA/RNAconsensus.py
 	@${RMDIR} ${STAGEDIR}/RNA
 
+# tests as of 2.7.2:
+# TOTAL: 83
+# PASS:  83
+# SKIP:  0
+# XFAIL: 0
+# FAIL:  0
+# XPASS: 0
+# ERROR: 0
+
 .include <bsd.port.mk>
diff --git a/biology/viennarna/distinfo b/biology/viennarna/distinfo
index df74d24eeb75..f76e21f9b282 100644
--- a/biology/viennarna/distinfo
+++ b/biology/viennarna/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1730430067
-SHA256 (ViennaRNA-2.7.0.tar.gz) = 9a99fd68ed380894defb4d5e6a8a2871629270028cdf7f16f0a05da6e8c71473
-SIZE (ViennaRNA-2.7.0.tar.gz) = 53185587
+TIMESTAMP = 1782619651
+SHA256 (ViennaRNA-2.7.2.tar.gz) = 1ab5f4a4f76fc85a2243546088e45f5d85f2d7a56cc656e969b005cce9bfab5f
+SIZE (ViennaRNA-2.7.2.tar.gz) = 67253851
diff --git a/biology/viennarna/files/patch-interfaces_Makefile.am b/biology/viennarna/files/patch-interfaces_Makefile.am
new file mode 100644
index 000000000000..29f273242680
--- /dev/null
+++ b/biology/viennarna/files/patch-interfaces_Makefile.am
@@ -0,0 +1,10 @@
+--- interfaces/Makefile.am.orig	2026-04-14 04:48:56 UTC
++++ interfaces/Makefile.am
+@@ -1,6 +1,6 @@ AM_CPPFLAGS = -I$(top_srcdir)/src
+ AM_CPPFLAGS = -I$(top_srcdir)/src
+ 
+-SUBDIRS = @PERL_INTERFACE@ @PYTHON_INTERFACE@ @PYTHON2_INTERFACE@
++SUBDIRS = @PERL_INTERFACE@ @PYTHON_INTERFACE@
+ 
+ SOURCES = \
+     RNA.i \
diff --git a/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4 b/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4
index 67d75c4a94c0..fc2b77cb3e08 100644
--- a/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4
+++ b/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4
@@ -2,13 +2,13 @@
 # - Replace bundled dlib detection with pkg-config
 # - Use system dlib from science/dlib-cpp port
 # - Remove hardcoded paths to bundled dlib-19.24
---- m4/ac_rna_build_requirements.m4.orig	2024-06-01 20:46:46 UTC
+--- m4/ac_rna_build_requirements.m4.orig	2025-12-21 15:30:13 UTC
 +++ m4/ac_rna_build_requirements.m4
-@@ -253,28 +253,18 @@ AC_DEFUN([RNA_CHECK_DLIB], [
+@@ -358,29 +358,18 @@ AC_DEFUN([RNA_CHECK_DLIB], [
  
  AC_DEFUN([RNA_CHECK_DLIB], [
    AX_CXX_COMPILE_STDCXX(17, noext, mandatory)
--  DLIB_VERSION=19.24
+-  DLIB_VERSION=20.0
 -  DLIB_DIR="dlib-${DLIB_VERSION}"
 -  DLIB_PATH="${srcdir}/src/${DLIB_DIR}"
 -  DLIB_SRC_FILE="${DLIB_PATH}/dlib/all/source.cpp"
@@ -36,8 +36,9 @@
 -  AC_SUBST(DLIB_CPPFLAGS, "-I\$(top_srcdir)/src/${DLIB_DIR} -DDLIB_NO_GUI_SUPPORT")
 -  AC_SUBST(DLIB_DIR)
 -  AC_SUBST(DLIB_VERSION)
+-
 +  AC_SUBST(DLIB_CPPFLAGS, "${DLIB_CFLAGS} -DDLIB_NO_GUI_SUPPORT")
 +  AC_SUBST(DLIB_LIBS, "${DLIB_LIBS}")
- 
  ])
  
+ ##
diff --git a/biology/viennarna/files/patch-m4_ac__rna__swig.m4 b/biology/viennarna/files/patch-m4_ac__rna__swig.m4
new file mode 100644
index 000000000000..ee200a37b6ce
--- /dev/null
+++ b/biology/viennarna/files/patch-m4_ac__rna__swig.m4
@@ -0,0 +1,65 @@
+--- m4/ac_rna_swig.m4.orig	2026-04-14 04:46:13 UTC
++++ m4/ac_rna_swig.m4
+@@ -18,7 +18,6 @@ AC_DEFUN([RNA_ENABLE_SWIG_INTERFACES],[
+ 
+   AM_CONDITIONAL(HAS_SWIG, test "x$has_swig" != "xno")
+   RNA_ENABLE_SWIG_PERL
+-  RNA_ENABLE_SWIG_PYTHON2
+   RNA_ENABLE_SWIG_PYTHON
+ 
+ ])
+@@ -130,54 +129,5 @@ AC_DEFUN([RNA_ENABLE_SWIG_PYTHON],[
+     AC_CONFIG_FILES([interfaces/Python/Makefile interfaces/Python/version.i])
+     AC_CONFIG_FILES([interfaces/Python/RNA/__init__.py])
+     AC_CONFIG_FILES([setup.py setup.cfg pyproject.toml])
+-  ])
+-])
+-
+-AC_DEFUN([RNA_ENABLE_SWIG_PYTHON2],[
+-
+-  AX_REQUIRE_DEFINED([AX_PYTHON2_DEVEL])
+-
+-  RNA_ADD_PACKAGE([python2],
+-                  [Python2 interface],
+-                  [no],[],[],
+-                  [${srcdir}/interfaces/Python2/Makefile.am])
+-
+-
+-  ## check for python2 requirements
+-  AS_IF([test "x$with_python2" != "xno"],[
+-    AS_IF([test "x$wants_swig" = "xno"],[
+-      with_python2="no"
+-    ],[
+-      ## if swig is not available, check whether we already have swig generated sources
+-      if test "x$has_swig" != "xyes"
+-      then
+-        AC_RNA_TEST_FILE([${srcdir}/interfaces/Python2/RNA_wrap.cpp],[],[
+-          with_python2="no"
+-        ])
+-        AC_RNA_TEST_FILE([${srcdir}/interfaces/Python2/RNA.py],[],[
+-          with_python2="no"
+-        ])
+-      fi
+-    ])
+-  ])
+-
+-  AS_IF([test "x$with_python2" != "xno"],[
+-
+-    ## check for python2 config
+-    AX_PYTHON2_DEVEL
+-
+-    if test "x$python2_enabled_but_failed" != "x"
+-    then
+-      with_python2="no"
+-    else
+-      AC_SUBST(PYTHON2DIR,$python2dir)
+-      AC_SUBST(PKGPYTHON2DIR,$pkgpython2dir)
+-      AC_SUBST(PYEXEC2DIR,$py2execdir)
+-      AC_SUBST(PKGPYEXEC2DIR,$pkgpy2execdir)
+-
+-      AC_DEFINE([WITH_PYTHON2_INTERFACE], [1], [Create the Python 2.x interface to RNAlib])
+-      AC_SUBST([PYTHON2_INTERFACE], [Python2])
+-      AC_CONFIG_FILES([interfaces/Python2/Makefile interfaces/Python2/version.i])
+-    fi
+   ])
+ ])
diff --git a/biology/viennarna/pkg-plist b/biology/viennarna/pkg-plist
index ee361b469586..99620f5550e6 100644
--- a/biology/viennarna/pkg-plist
+++ b/biology/viennarna/pkg-plist
@@ -74,6 +74,7 @@ include/ViennaRNA/constraints_hard.h
 include/ViennaRNA/constraints_ligand.h
 include/ViennaRNA/constraints_soft.h
 include/ViennaRNA/convert_epars.h
+include/ViennaRNA/data/transform.h
 include/ViennaRNA/data_structures.h
 include/ViennaRNA/datastructures/array.h
 include/ViennaRNA/datastructures/basic.h
@@ -134,6 +135,7 @@ include/ViennaRNA/loops/external.h
 include/ViennaRNA/loops/hairpin.h
 include/ViennaRNA/loops/internal.h
 include/ViennaRNA/loops/multibranch.h
+include/ViennaRNA/math/functions.h
 include/ViennaRNA/mconf.h
 include/ViennaRNA/mfe.h
 include/ViennaRNA/mfe/exterior.h
@@ -189,6 +191,10 @@ include/ViennaRNA/probabilities/basepairs.h
 include/ViennaRNA/probabilities/structures.h
 include/ViennaRNA/probing/SHAPE.h
 include/ViennaRNA/probing/basic.h
+include/ViennaRNA/probing/strategy_deigan.h
+include/ViennaRNA/probing/strategy_eddy.h
+include/ViennaRNA/probing/strategy_nlogp.h
+include/ViennaRNA/probing/strategy_zarringhalam.h
 include/ViennaRNA/profiledist.h
 include/ViennaRNA/read_epars.h
 include/ViennaRNA/ribo.h
@@ -266,6 +272,10 @@ share/ViennaRNA/bin/rotate_ss.pl
 share/ViennaRNA/bin/switch.pl
 share/ViennaRNA/dna_mathews1999.par
 share/ViennaRNA/dna_mathews2004.par
+share/ViennaRNA/prior_probing_1M7_paired.data
+share/ViennaRNA/prior_probing_1M7_unpaired.data
+share/ViennaRNA/prior_probing_DMS_paired.data
+share/ViennaRNA/prior_probing_DMS_unpaired.data
 share/ViennaRNA/rna_andronescu2007.par
 share/ViennaRNA/rna_langdon2018.par
 share/ViennaRNA/rna_misc_special_hairpins.par