diff --git a/science/cif-tools/Makefile b/science/cif-tools/Makefile
index 297be4c78553..7f82466380ea 100644
--- a/science/cif-tools/Makefile
+++ b/science/cif-tools/Makefile
@@ -1,24 +1,23 @@
 PORTNAME=	cif-tools
 DISTVERSIONPREFIX=	v
-DISTVERSION=	1.0.12 # chemistry
-PORTREVISION=	5
-CATEGORIES=	science
+DISTVERSION=	1.0.13
+CATEGORIES=	science # chemistry
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Suite of programs to manipulate and examine mmCIF files
 WWW=		https://github.com/PDB-REDO/cif-tools
 
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	libmcfp>0:devel/libmcfp \
 		mrc:devel/mrc
 LIB_DEPENDS=	libboost_iostreams.so:devel/boost-libs \
 		libcifpp.so:science/libcifpp
 
 USES=		cmake:noninja compiler:c++17-lang # ninja: error: build.ninja:890: multiple rules generate ALL
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	PDB-REDO
 
 .include <bsd.port.mk>
diff --git a/science/cif-tools/distinfo b/science/cif-tools/distinfo
index b7800477bf75..e81d1d7f7fb0 100644
--- a/science/cif-tools/distinfo
+++ b/science/cif-tools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1722210600
-SHA256 (PDB-REDO-cif-tools-v1.0.12_GH0.tar.gz) = 5a29cef3557830de859cb01b8f327eb459b341cc085f5bf77dc56a8aabda5288
-SIZE (PDB-REDO-cif-tools-v1.0.12_GH0.tar.gz) = 1828300
+TIMESTAMP = 1774151757
+SHA256 (PDB-REDO-cif-tools-v1.0.13_GH0.tar.gz) = 0d18a69c18fbaf8f4fc59b85b3a171de613734ea34f524e86ee79f17c50cc4be
+SIZE (PDB-REDO-cif-tools-v1.0.13_GH0.tar.gz) = 1839479
diff --git a/science/cif-tools/files/patch-src_cif-diff.cpp b/science/cif-tools/files/patch-src_cif-diff.cpp
new file mode 100644
index 000000000000..32f536844126
--- /dev/null
+++ b/science/cif-tools/files/patch-src_cif-diff.cpp
@@ -0,0 +1,42 @@
+--- src/cif-diff.cpp.orig	2026-03-22 05:31:17 UTC
++++ src/cif-diff.cpp
+@@ -133,7 +133,7 @@ class templateParser : public cif::sac_parser
+ 	{
+ 	}
+ 
+-	void produce_item(std::string_view category, std::string_view item, std::string_view value) override
++	void produce_item(std::string_view category, std::string_view item, cif::item_value value) override
+ 	{
+ 		std::ostringstream tag;
+ 		tag << '_' << category << '.' << item;
+@@ -195,7 +195,7 @@ void compareCategories(cif::category &a, cif::category
+ 
+ 			tie(tag, compare) = tags[kix];
+ 
+-			d = compare(a[tag].text(), b[tag].text());
++			d = compare(a[tag].sv(), b[tag].sv());
+ 
+ 			if (d != 0)
+ 				break;
+@@ -334,10 +334,10 @@ void compareCategories(cif::category &a, cif::category
+ 
+ 			// make it an option to compare unapplicable to empty or something
+ 
+-			std::string_view ta = ra[tag].text();
++			std::string_view ta = ra[tag].sv();
+ 			if (ta == ".")
+ 				ta = "";
+-			std::string_view tb = rb[tag].text();
++			std::string_view tb = rb[tag].sv();
+ 			if (tb == ".")
+ 				tb = "";
+ 
+@@ -361,7 +361,7 @@ void compareCategories(cif::category &a, cif::category
+ 
+ 	if (not diffs.empty())
+ 	{
+-		std::cout << std::string(mcfp::get_terminal_width(), '-') << '\n'
++		std::cout << std::string(cif::get_terminal_width(), '-') << '\n'
+ 				  << "Differences in values for category " << a.name() << '\n'
+ 				  << '\n';
+ 
diff --git a/science/cif-tools/files/patch-src_cif-grep.cpp b/science/cif-tools/files/patch-src_cif-grep.cpp
new file mode 100644
index 000000000000..aff0c6720114
--- /dev/null
+++ b/science/cif-tools/files/patch-src_cif-grep.cpp
@@ -0,0 +1,16 @@
+--- src/cif-grep.cpp.orig	2026-03-22 05:31:17 UTC
++++ src/cif-grep.cpp
+@@ -70,11 +70,11 @@ class statsParser : public cif::sac_parser
+ 	{
+ 	}
+ 
+-	void produce_item(std::string_view category, std::string_view item, std::string_view value) override
++	void produce_item(std::string_view category, std::string_view item, cif::item_value value) override
+ 	{
+ 		if ((mCat.empty() or cif::iequals(category, mCat)) and
+ 			(mItem.empty() or cif::iequals(item, mItem)) and
+-			std::regex_search(value.begin(), value.end(), mRx) == not mInvertMatch)
++			std::regex_search(value.sv().begin(), value.sv().end(), mRx) == not mInvertMatch)
+ 		{
+ 			++mMatches;
+ 
diff --git a/science/cif-tools/files/patch-src_cif-validate.cpp b/science/cif-tools/files/patch-src_cif-validate.cpp
new file mode 100644
index 000000000000..fd845a559b6c
--- /dev/null
+++ b/science/cif-tools/files/patch-src_cif-validate.cpp
@@ -0,0 +1,26 @@
+--- src/cif-validate.cpp.orig	2026-03-22 05:31:17 UTC
++++ src/cif-validate.cpp
+@@ -52,7 +52,7 @@ class dummy_parser : public cif::sac_parser
+ 	{
+ 	}
+ 
+-	void produce_item(std::string_view category, std::string_view item, std::string_view value) override
++	void produce_item(std::string_view category, std::string_view item, cif::item_value value) override
+ 	{
+ 	}
+ };
+@@ -112,12 +112,12 @@ int pr_main(int argc, char *argv[])
+ 		for (auto &db : f)
+ 		{
+ 			if (config.count("dict"))
+-				db.set_validator(&cif::validator_factory::instance().get(config.get<std::string>("dict")));
++				db.set_validator(cif::validator_factory::instance().get(config.get<std::string>("dict")));
+ 			else
+ 				db.load_dictionary();
+ 			
+ 			if (db.get_validator() == nullptr)
+-				db.set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
++				db.set_validator(cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+ 
+ 			if (not const_cast<const cif::datablock &>(db).is_valid())
+ 				result = 1;
diff --git a/science/cif-tools/files/patch-src_cif2pdb.cpp b/science/cif-tools/files/patch-src_cif2pdb.cpp
new file mode 100644
index 000000000000..e5d17751ffdf
--- /dev/null
+++ b/science/cif-tools/files/patch-src_cif2pdb.cpp
@@ -0,0 +1,14 @@
+--- src/cif2pdb.cpp.orig	2026-03-22 05:31:17 UTC
++++ src/cif2pdb.cpp
+@@ -92,9 +92,9 @@ int pr_main(int argc, char *argv[])
+ 
+ 	// Load dict, if any
+ 	if (config.has("dict"))
+-		f.front().set_validator(&cif::validator_factory::instance().get(config.get<std::string>("dict")));
++		f.front().set_validator(cif::validator_factory::instance().get(config.get<std::string>("dict")));
+ 	else if (f.front().get_validator() == nullptr)
+-		f.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
++		f.front().set_validator(cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+ 
+ 	if (f.empty() or (not config.has("no-validate") and not f.is_valid()))
+ 	{
diff --git a/science/cif-tools/files/patch-src_mmCQL.cpp b/science/cif-tools/files/patch-src_mmCQL.cpp
new file mode 100644
index 000000000000..c18f5e4d38a2
--- /dev/null
+++ b/science/cif-tools/files/patch-src_mmCQL.cpp
@@ -0,0 +1,11 @@
+--- src/mmCQL.cpp.orig	2026-03-22 05:31:17 UTC
++++ src/mmCQL.cpp
+@@ -1182,7 +1182,7 @@ StatementPtr Parser::ParseUpdate()
+ 		}
+ 
+ 		if (iv)
+-			iv->operator()(value);
++			iv->validate_value(value);
+ 
+ 		itemValuePairs.emplace_back(item, value);
+