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-rw-r--r--math/4ti2/Makefile6
-rw-r--r--math/4ti2/distinfo6
-rw-r--r--math/Makefile1
-rw-r--r--math/R-cran-Rmpfr/Makefile2
-rw-r--r--math/R-cran-Rmpfr/distinfo6
-rw-r--r--math/R-cran-pbkrtest/Makefile2
-rw-r--r--math/R-cran-pbkrtest/distinfo6
-rw-r--r--math/octave-forge-geometry/Makefile4
-rw-r--r--math/py-grandalf/Makefile18
-rw-r--r--math/py-grandalf/distinfo3
-rw-r--r--math/py-grandalf/files/patch-setup.py10
-rw-r--r--math/py-grandalf/pkg-descr7
-rw-r--r--math/py-mathics/Makefile3
-rw-r--r--math/py-narwhals/Makefile4
-rw-r--r--math/py-narwhals/distinfo6
-rw-r--r--math/py-networkx/Makefile3
-rw-r--r--math/py-pandas-datareader/Makefile4
-rw-r--r--math/py-pandas/Makefile4
-rw-r--r--math/scipoptsuite/Makefile3
-rw-r--r--math/scipoptsuite/distinfo6
-rw-r--r--math/scipoptsuite/pkg-plist6
-rw-r--r--math/vtk8/Makefile1
22 files changed, 77 insertions, 34 deletions
diff --git a/math/4ti2/Makefile b/math/4ti2/Makefile
index 1de8b4ef38c4..a80b86a0c114 100644
--- a/math/4ti2/Makefile
+++ b/math/4ti2/Makefile
@@ -1,6 +1,6 @@
PORTNAME= 4ti2
DISTVERSIONPREFIX= Release_
-DISTVERSION= 1_6_10
+DISTVERSION= 1_6_13
CATEGORIES= math
MAINTAINER= yuri@FreeBSD.org
@@ -13,10 +13,12 @@ LICENSE_FILE= ${WRKSRC}/COPYING
LIB_DEPENDS= libglpk.so:math/glpk \
libgmp.so:math/gmp
-USES= autoreconf compiler:c++11-lang gmake libtool
+USES= autoreconf compiler:c++11-lang gmake libtool shebangfix
USE_GITHUB= yes
USE_LDCONFIG= yes
+SHEBANG_FILES= test/check.template.in
+
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --disable-static --enable-shared --with-glpk=${LOCALBASE} --with-gmp=${LOCALBASE}
diff --git a/math/4ti2/distinfo b/math/4ti2/distinfo
index c5266ed4badb..1d0872a1335c 100644
--- a/math/4ti2/distinfo
+++ b/math/4ti2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1682583538
-SHA256 (4ti2-4ti2-Release_1_6_10_GH0.tar.gz) = 2f1bce3203da65b651d68cbd0ace0f89a16d1f436cf5f24e22bc15ec22df936a
-SIZE (4ti2-4ti2-Release_1_6_10_GH0.tar.gz) = 5005427
+TIMESTAMP = 1753038439
+SHA256 (4ti2-4ti2-Release_1_6_13_GH0.tar.gz) = 37b36536f0b9185afa8e0c9badf6a6b5277b7a4a8409726d599cf254946e94fa
+SIZE (4ti2-4ti2-Release_1_6_13_GH0.tar.gz) = 4991075
diff --git a/math/Makefile b/math/Makefile
index 8858e9aa98a9..7dcdaa9510e1 100644
--- a/math/Makefile
+++ b/math/Makefile
@@ -989,6 +989,7 @@
SUBDIR += py-gau2grid
SUBDIR += py-gimmik
SUBDIR += py-gmpy2
+ SUBDIR += py-grandalf
SUBDIR += py-graphillion
SUBDIR += py-gym
SUBDIR += py-gym-notices
diff --git a/math/R-cran-Rmpfr/Makefile b/math/R-cran-Rmpfr/Makefile
index c309b1ac5faa..3d91c007db9d 100644
--- a/math/R-cran-Rmpfr/Makefile
+++ b/math/R-cran-Rmpfr/Makefile
@@ -1,5 +1,5 @@
PORTNAME= Rmpfr
-DISTVERSION= 1.1-0
+DISTVERSION= 1.1-1
CATEGORIES= math
DISTNAME= ${PORTNAME}_${DISTVERSION}
diff --git a/math/R-cran-Rmpfr/distinfo b/math/R-cran-Rmpfr/distinfo
index 9dcf4ed25f35..daea6428910d 100644
--- a/math/R-cran-Rmpfr/distinfo
+++ b/math/R-cran-Rmpfr/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1747455080
-SHA256 (Rmpfr_1.1-0.tar.gz) = ae3e148dc7f003960a81fd4f2b8285c8f8b951be3f34fc2779dfca20b1af141f
-SIZE (Rmpfr_1.1-0.tar.gz) = 618436
+TIMESTAMP = 1753008029
+SHA256 (Rmpfr_1.1-1.tar.gz) = 1f67af9baba9e9939db9757783b90caa6054035a0d27bbd07c8403b250294bd2
+SIZE (Rmpfr_1.1-1.tar.gz) = 655307
diff --git a/math/R-cran-pbkrtest/Makefile b/math/R-cran-pbkrtest/Makefile
index 4c5ee41dd81b..3d1536c57692 100644
--- a/math/R-cran-pbkrtest/Makefile
+++ b/math/R-cran-pbkrtest/Makefile
@@ -1,5 +1,5 @@
PORTNAME= pbkrtest
-DISTVERSION= 0.5.4
+DISTVERSION= 0.5.5
CATEGORIES= math
DISTNAME= ${PORTNAME}_${DISTVERSION}
diff --git a/math/R-cran-pbkrtest/distinfo b/math/R-cran-pbkrtest/distinfo
index 72889b767954..30927bfa2864 100644
--- a/math/R-cran-pbkrtest/distinfo
+++ b/math/R-cran-pbkrtest/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1746004088
-SHA256 (pbkrtest_0.5.4.tar.gz) = cd463ff5766c340f576366e45e7a44498e3017083df9c02f332510f8a423d822
-SIZE (pbkrtest_0.5.4.tar.gz) = 75868
+TIMESTAMP = 1753012743
+SHA256 (pbkrtest_0.5.5.tar.gz) = d26c8ef0a6fd73bba184bde8e3434439d62539d93aef0a0b5b480a0f309bc51b
+SIZE (pbkrtest_0.5.5.tar.gz) = 77353
diff --git a/math/octave-forge-geometry/Makefile b/math/octave-forge-geometry/Makefile
index 9933cf303500..abdc8e77b362 100644
--- a/math/octave-forge-geometry/Makefile
+++ b/math/octave-forge-geometry/Makefile
@@ -1,6 +1,6 @@
PORTNAME= octave-forge-geometry
PORTVERSION= 4.1.0
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= math
MASTER_SITES= SF/octave/Octave%20Forge%20Packages/Individual%20Package%20Releases
DISTNAME= ${OCTAVE_PKGNAME}-${DISTVERSIONFULL}
@@ -12,7 +12,7 @@ WWW= https://packages.octave.org/
LICENSE= GPLv3
LICENSE_FILE= ${WRKDIR}/${OCTAVE_SRC}/COPYING
-RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \
+RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \
${OCTAVE_TARBALLS_DIR}/matgeom.tar.gz:math/octave-forge-matgeom
USES= octave python:env
diff --git a/math/py-grandalf/Makefile b/math/py-grandalf/Makefile
new file mode 100644
index 000000000000..d0e8f8ad7eec
--- /dev/null
+++ b/math/py-grandalf/Makefile
@@ -0,0 +1,18 @@
+PORTNAME= grandalf
+DISTVERSION= 0.8
+CATEGORIES= math python
+MASTER_SITES= PYPI
+PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER= yuri@FreeBSD.org
+COMMENT= Graph and drawing algorithms framework
+WWW= https://github.com/bdcht/grandalf
+
+LICENSE= GPLv2
+
+USES= python
+USE_PYTHON= distutils autoplist
+
+RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR}
+
+.include <bsd.port.mk>
diff --git a/math/py-grandalf/distinfo b/math/py-grandalf/distinfo
new file mode 100644
index 000000000000..3027bcc2a6a7
--- /dev/null
+++ b/math/py-grandalf/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1752859612
+SHA256 (grandalf-0.8.tar.gz) = 2813f7aab87f0d20f334a3162ccfbcbf085977134a17a5b516940a93a77ea974
+SIZE (grandalf-0.8.tar.gz) = 38128
diff --git a/math/py-grandalf/files/patch-setup.py b/math/py-grandalf/files/patch-setup.py
new file mode 100644
index 000000000000..795641ece9b4
--- /dev/null
+++ b/math/py-grandalf/files/patch-setup.py
@@ -0,0 +1,10 @@
+--- setup.py.orig 2025-07-18 17:28:03 UTC
++++ setup.py
+@@ -72,7 +72,6 @@ setup(
+ # your project is installed. For an analysis of "install_requires" vs pip's
+ # requirements files see:
+ # https://packaging.python.org/en/latest/requirements.html
+- setup_requires=['pytest-runner',],
+ tests_require=['pytest',],
+
+ install_requires=['pyparsing'],
diff --git a/math/py-grandalf/pkg-descr b/math/py-grandalf/pkg-descr
new file mode 100644
index 000000000000..c6cc12335ca3
--- /dev/null
+++ b/math/py-grandalf/pkg-descr
@@ -0,0 +1,7 @@
+Grandalf is a python package made for experimentations with graphs drawing
+algorithms. It is written in pure python, and currently implements two layouts:
+the Sugiyama hierarchical layout and the force-driven or energy minimization
+approach. While not as fast or featured as graphviz or other libraries like OGDF
+(C++), it provides a way to walk and draw graphs no larger than thousands of
+nodes, while keeping the source code simple enough to make it possible to easily
+tweak and hack any part of it for experimental purpose.
diff --git a/math/py-mathics/Makefile b/math/py-mathics/Makefile
index 65d3cf8ed8ad..56ec33321e68 100644
--- a/math/py-mathics/Makefile
+++ b/math/py-mathics/Makefile
@@ -1,5 +1,6 @@
PORTNAME= Mathics3
PORTVERSION= 8.0.1
+PORTREVISION= 1
CATEGORIES= math python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -30,7 +31,7 @@ RUN_DEPENDS= ${PYNUMPY} \
${PY_PILLOW} \
bash:shells/bash \
${PYTHON_PKGNAMEPREFIX}py>0:devel/py-py@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pint>0:devel/py-pint@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}sympy>0:math/py-sympy@${PY_FLAVOR} \
diff --git a/math/py-narwhals/Makefile b/math/py-narwhals/Makefile
index 5777052a57e3..5b4d4a35a8d9 100644
--- a/math/py-narwhals/Makefile
+++ b/math/py-narwhals/Makefile
@@ -1,5 +1,5 @@
PORTNAME= narwhals
-PORTVERSION= 1.46.0
+PORTVERSION= 1.47.0
CATEGORIES= math python
MASTER_SITES= PYPI \
https://github.com/narwhals-dev/narwhals/releases/download/v${PORTVERSION}/
@@ -34,7 +34,7 @@ DUCKDB_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}duckdb>=1.0:databases/py-duckdb@${PY_
PANDAS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pandas>=1.1.3,1:math/py-pandas@${PY_FLAVOR}
MODIN_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}modin>=0:math/py-modin@${PY_FLAVOR}
POLARS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}polars>=0.20.4:misc/py-polars@${PY_FLAVOR}
-PYARROW_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pyarrow>=11.0.0:databases/py-pyarrow@${PY_FLAVOR}
+PYARROW_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pyarrow>=13.0.0:databases/py-pyarrow@${PY_FLAVOR}
SQLFRAME_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}sqlframe>=3.22.0:databases/py-sqlframe@${PY_FLAVOR}
.include <bsd.port.mk>
diff --git a/math/py-narwhals/distinfo b/math/py-narwhals/distinfo
index 9aafed610074..5a9d356010df 100644
--- a/math/py-narwhals/distinfo
+++ b/math/py-narwhals/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1752266156
-SHA256 (narwhals-1.46.0.tar.gz) = fd7e53860b233c2b5566d8b4e1b3e8e9c01b5a87649a9f9a322742000f207a60
-SIZE (narwhals-1.46.0.tar.gz) = 512060
+TIMESTAMP = 1752566720
+SHA256 (narwhals-1.47.0.tar.gz) = 38238882f3ab2bbc8e7121bc9be951a8a58f1a810bdb14aa2b18792bafac01f8
+SIZE (narwhals-1.47.0.tar.gz) = 514799
diff --git a/math/py-networkx/Makefile b/math/py-networkx/Makefile
index acfdb7a850a8..687730db26cb 100644
--- a/math/py-networkx/Makefile
+++ b/math/py-networkx/Makefile
@@ -1,5 +1,6 @@
PORTNAME= networkx
DISTVERSION= 3.5
+PORTREVISION= 1
PORTEPOCH= 2
CATEGORIES= math python
MASTER_SITES= PYPI
@@ -47,7 +48,7 @@ GRAPHVIZ_DESC= Additional graph layout and rendering algorithms
GRAPHVIZ_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pygraphviz>=1.2:graphics/py-pygraphviz@${PY_FLAVOR}
LXML_DESC= Binding for the libxml2 and libxslt libraries
-LXML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR}
+LXML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR}
PANDAS_DESC= Data analysis
PANDAS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pandas>=1.3:math/py-pandas@${PY_FLAVOR}
diff --git a/math/py-pandas-datareader/Makefile b/math/py-pandas-datareader/Makefile
index 82f4f3440d19..4e941b803578 100644
--- a/math/py-pandas-datareader/Makefile
+++ b/math/py-pandas-datareader/Makefile
@@ -1,6 +1,6 @@
PORTNAME= pandas-datareader
DISTVERSION= 0.9.0
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= math finance python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -12,7 +12,7 @@ WWW= https://github.com/pydata/pandas-datareader
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE.md
-RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \
+RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pandas>0.19.2:math/py-pandas@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}requests>=2.3.0:www/py-requests@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}requests-file>0:www/py-requests-file@${PY_FLAVOR} \
diff --git a/math/py-pandas/Makefile b/math/py-pandas/Makefile
index c3ffab971454..70c2f9abe9b6 100644
--- a/math/py-pandas/Makefile
+++ b/math/py-pandas/Makefile
@@ -1,6 +1,6 @@
PORTNAME= pandas
PORTVERSION= 2.2.3
-PORTREVISION= 1
+PORTREVISION= 2
PORTEPOCH= 1
CATEGORIES= math devel python
MASTER_SITES= PYPI
@@ -79,7 +79,7 @@ HTML5LIB_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}beautifulsoup>=4.2.1:www/py-beautif
${PYTHON_PKGNAMEPREFIX}html5lib>0:www/py-html5lib@${PY_FLAVOR}
JINJA2_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}Jinja2>0:devel/py-Jinja2@${PY_FLAVOR}
LXML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}beautifulsoup>=4.2.1:www/py-beautifulsoup@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR}
+ ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR}
MPL_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.0.0:math/py-matplotlib@${PY_FLAVOR}
NUMEXPR_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numexpr>=2.6.1:math/py-numexpr@${PY_FLAVOR}
OPENPYXL_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}openpyxl>=2.4.0:textproc/py-openpyxl@${PY_FLAVOR}
diff --git a/math/scipoptsuite/Makefile b/math/scipoptsuite/Makefile
index f10c7a538453..ce001d0eb252 100644
--- a/math/scipoptsuite/Makefile
+++ b/math/scipoptsuite/Makefile
@@ -1,6 +1,5 @@
PORTNAME= scipoptsuite
-DISTVERSION= 9.2.1
-PORTREVISION= 1
+DISTVERSION= 9.2.3
CATEGORIES= math
MASTER_SITES= https://scipopt.org/download/release/
diff --git a/math/scipoptsuite/distinfo b/math/scipoptsuite/distinfo
index 1f8e70d74fa3..23a32f5a0226 100644
--- a/math/scipoptsuite/distinfo
+++ b/math/scipoptsuite/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1742782011
-SHA256 (scipoptsuite-9.2.1.tgz) = 41b71a57af773403e9a6724f78c37d8396ac4b6b270a9bbf3716d67f1af12edf
-SIZE (scipoptsuite-9.2.1.tgz) = 17608938
+TIMESTAMP = 1752906975
+SHA256 (scipoptsuite-9.2.3.tgz) = 9cb8278ce40b59939a200a36bd1ee3b9a7923b3c6df5c31b135a5a42ecabac5a
+SIZE (scipoptsuite-9.2.3.tgz) = 17627327
diff --git a/math/scipoptsuite/pkg-plist b/math/scipoptsuite/pkg-plist
index 102d232f0959..59f2544e4a17 100644
--- a/math/scipoptsuite/pkg-plist
+++ b/math/scipoptsuite/pkg-plist
@@ -1095,15 +1095,15 @@ lib/cmake/zimpl/zimpl-targets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/zimpl/zimpl-targets.cmake
lib/libgcg.so
lib/libgcg.so.3.7
-lib/libgcg.so.3.7.1.0
+lib/libgcg.so.3.7.2.0
lib/libpapilo-core.a
lib/libscip.so
lib/libscip.so.9.2
-lib/libscip.so.9.2.1.0
+lib/libscip.so.9.2.3.0
lib/libsoplex-pic.a
lib/libsoplex.a
lib/libsoplexshared.so
lib/libsoplexshared.so.7.1
-lib/libsoplexshared.so.7.1.3.0
+lib/libsoplexshared.so.7.1.5.0
lib/libzimpl-pic.a
lib/libzimpl.a
diff --git a/math/vtk8/Makefile b/math/vtk8/Makefile
index d0a3a97bdb2d..06d0030f5f76 100644
--- a/math/vtk8/Makefile
+++ b/math/vtk8/Makefile
@@ -12,6 +12,7 @@ WWW= https://www.vtk.org
LICENSE= BSD3CLAUSE
+BROKEN_FreeBSD_13= complation fails: error: no member named 'derived' in 'Transpose<TranspositionsBase<type-parameter-0-0>>'
BROKEN_FreeBSD_15= complation fails: error: no member named 'derived' in 'Transpose<TranspositionsBase<type-parameter-0-0>>'
LIB_DEPENDS= libtiff.so:graphics/tiff \
generated by cgit v1.2.3 (git 2.25.1) at 2025-07-24 03:50:32 +0000