Date: Sun, 22 Mar 2026 05:38:20 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 8aff1f2722e8 - main - science/cif-tools: update 1.0.=?utf-8?Q?12 =E2=86=92 1?=.0.13 Message-ID: <69bf804c.33195.54a7c0f9@gitrepo.freebsd.org>
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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); +home | help
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