git: 8aff1f2722e8 - main - science/cif-tools: update 1.0.12 → 1.0.13
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Date: Sun, 22 Mar 2026 05:38:20 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=8aff1f2722e825e4110baa71c4cd2a7fbab7c6a3
commit 8aff1f2722e825e4110baa71c4cd2a7fbab7c6a3
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-03-22 05:37:55 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-03-22 05:38:13 +0000
science/cif-tools: update 1.0.12 → 1.0.13
---
science/cif-tools/Makefile | 5 ++-
science/cif-tools/distinfo | 6 ++--
science/cif-tools/files/patch-src_cif-diff.cpp | 42 ++++++++++++++++++++++
science/cif-tools/files/patch-src_cif-grep.cpp | 16 +++++++++
science/cif-tools/files/patch-src_cif-validate.cpp | 26 ++++++++++++++
science/cif-tools/files/patch-src_cif2pdb.cpp | 14 ++++++++
science/cif-tools/files/patch-src_mmCQL.cpp | 11 ++++++
7 files changed, 114 insertions(+), 6 deletions(-)
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
@@ -1,8 +1,7 @@
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
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);
+