biology/biolibc: Update to 0.2.5

Make header files C++ compatible (extern C)
bl_chrom_name_cmp(): Support names with embedded digits, e.g. chr2p
bl_gff_extract_attribute(): Improve performance
gff -> gff3 to distinguish from past and future GFF specs
Silence some compiler warnings

Changes: https://github.com/auerlab/biolibc/releases

3 files changed, 67 insertions, 68 deletions

diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile
index faa55208aa26..e107ad437a58 100644
--- a/biology/biolibc/Makefile
+++ b/biology/biolibc/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	biolibc
-DISTVERSION=	0.2.4-3
-DISTVERSIONSUFFIX=	-g3dc616d
+DISTVERSION=	0.2.5
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo
index 983b7255c1b5..11c338872a43 100644
--- a/biology/biolibc/distinfo
+++ b/biology/biolibc/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1686231530
-SHA256 (auerlab-biolibc-0.2.4-3-g3dc616d_GH0.tar.gz) = a1fd8a7afce75de928ae06711e479f1c653ffd75344b52ee3dfa6ded8cbb6df6
-SIZE (auerlab-biolibc-0.2.4-3-g3dc616d_GH0.tar.gz) = 141067
+TIMESTAMP = 1691785366
+SHA256 (auerlab-biolibc-0.2.5_GH0.tar.gz) = 5273dbf4e5135ac8f11e503c3ef516ec1c73906b1ec196a0a28606d88d3d394a
+SIZE (auerlab-biolibc-0.2.5_GH0.tar.gz) = 141426
diff --git a/biology/biolibc/pkg-plist b/biology/biolibc/pkg-plist
index dfbe6a49d997..a5a415d739ef 100644
--- a/biology/biolibc/pkg-plist
+++ b/biology/biolibc/pkg-plist
@@ -20,14 +20,14 @@ include/biolibc/fastx-accessors.h
 include/biolibc/fastx-mutators.h
 include/biolibc/fastx-rvs.h
 include/biolibc/fastx.h
-include/biolibc/gff-accessors.h
-include/biolibc/gff-index-accessors.h
-include/biolibc/gff-index-mutators.h
-include/biolibc/gff-index-rvs.h
-include/biolibc/gff-index.h
-include/biolibc/gff-mutators.h
-include/biolibc/gff-rvs.h
-include/biolibc/gff.h
+include/biolibc/gff3-accessors.h
+include/biolibc/gff3-index-accessors.h
+include/biolibc/gff3-index-mutators.h
+include/biolibc/gff3-index-rvs.h
+include/biolibc/gff3-index.h
+include/biolibc/gff3-mutators.h
+include/biolibc/gff3-rvs.h
+include/biolibc/gff3.h
 include/biolibc/overlap-accessors.h
 include/biolibc/overlap-mutators.h
 include/biolibc/overlap-rvs.h
@@ -321,61 +321,61 @@ man/man3/bl_fastx_set_fasta.3.gz
 man/man3/bl_fastx_set_fastq.3.gz
 man/man3/bl_fastx_set_format.3.gz
 man/man3/bl_fastx_write.3.gz
-man/man3/bl_gff_copy.3.gz
-man/man3/bl_gff_copy_header.3.gz
-man/man3/bl_gff_dup.3.gz
-man/man3/bl_gff_extract_attribute.3.gz
-man/man3/bl_gff_free.3.gz
-man/man3/bl_gff_index_add.3.gz
-man/man3/bl_gff_index_seek_reverse.3.gz
-man/man3/bl_gff_index_set_array_size.3.gz
-man/man3/bl_gff_index_set_count.3.gz
-man/man3/bl_gff_index_set_end.3.gz
-man/man3/bl_gff_index_set_end_ae.3.gz
-man/man3/bl_gff_index_set_end_cpy.3.gz
-man/man3/bl_gff_index_set_file_pos.3.gz
-man/man3/bl_gff_index_set_file_pos_ae.3.gz
-man/man3/bl_gff_index_set_file_pos_cpy.3.gz
-man/man3/bl_gff_index_set_seqid.3.gz
-man/man3/bl_gff_index_set_seqid_ae.3.gz
-man/man3/bl_gff_index_set_seqid_cpy.3.gz
-man/man3/bl_gff_index_set_start.3.gz
-man/man3/bl_gff_index_set_start_ae.3.gz
-man/man3/bl_gff_index_set_start_cpy.3.gz
-man/man3/bl_gff_init.3.gz
-man/man3/bl_gff_read.3.gz
-man/man3/bl_gff_sam_cmp.3.gz
-man/man3/bl_gff_sam_overlap.3.gz
-man/man3/bl_gff_set_attributes.3.gz
-man/man3/bl_gff_set_attributes_ae.3.gz
-man/man3/bl_gff_set_attributes_array_size.3.gz
-man/man3/bl_gff_set_attributes_cpy.3.gz
-man/man3/bl_gff_set_attributes_len.3.gz
-man/man3/bl_gff_set_end.3.gz
-man/man3/bl_gff_set_feature_id.3.gz
-man/man3/bl_gff_set_feature_id_ae.3.gz
-man/man3/bl_gff_set_feature_id_cpy.3.gz
-man/man3/bl_gff_set_feature_name.3.gz
-man/man3/bl_gff_set_feature_name_ae.3.gz
-man/man3/bl_gff_set_feature_name_cpy.3.gz
-man/man3/bl_gff_set_feature_parent.3.gz
-man/man3/bl_gff_set_feature_parent_ae.3.gz
-man/man3/bl_gff_set_feature_parent_cpy.3.gz
-man/man3/bl_gff_set_file_pos.3.gz
-man/man3/bl_gff_set_gene_name_cpy.3.gz
-man/man3/bl_gff_set_phase.3.gz
-man/man3/bl_gff_set_score.3.gz
-man/man3/bl_gff_set_seqid_ae.3.gz
-man/man3/bl_gff_set_seqid_cpy.3.gz
-man/man3/bl_gff_set_source_ae.3.gz
-man/man3/bl_gff_set_source_cpy.3.gz
-man/man3/bl_gff_set_start.3.gz
-man/man3/bl_gff_set_strand.3.gz
-man/man3/bl_gff_set_type_ae.3.gz
-man/man3/bl_gff_set_type_cpy.3.gz
-man/man3/bl_gff_skip_header.3.gz
-man/man3/bl_gff_to_bed.3.gz
-man/man3/bl_gff_write.3.gz
+man/man3/bl_gff3_copy.3.gz
+man/man3/bl_gff3_copy_header.3.gz
+man/man3/bl_gff3_dup.3.gz
+man/man3/bl_gff3_extract_attribute.3.gz
+man/man3/bl_gff3_free.3.gz
+man/man3/bl_gff3_index_add.3.gz
+man/man3/bl_gff3_index_seek_reverse.3.gz
+man/man3/bl_gff3_index_set_array_size.3.gz
+man/man3/bl_gff3_index_set_count.3.gz
+man/man3/bl_gff3_index_set_end.3.gz
+man/man3/bl_gff3_index_set_end_ae.3.gz
+man/man3/bl_gff3_index_set_end_cpy.3.gz
+man/man3/bl_gff3_index_set_file_pos.3.gz
+man/man3/bl_gff3_index_set_file_pos_ae.3.gz
+man/man3/bl_gff3_index_set_file_pos_cpy.3.gz
+man/man3/bl_gff3_index_set_seqid.3.gz
+man/man3/bl_gff3_index_set_seqid_ae.3.gz
+man/man3/bl_gff3_index_set_seqid_cpy.3.gz
+man/man3/bl_gff3_index_set_start.3.gz
+man/man3/bl_gff3_index_set_start_ae.3.gz
+man/man3/bl_gff3_index_set_start_cpy.3.gz
+man/man3/bl_gff3_init.3.gz
+man/man3/bl_gff3_read.3.gz
+man/man3/bl_gff3_sam_cmp.3.gz
+man/man3/bl_gff3_sam_overlap.3.gz
+man/man3/bl_gff3_set_attributes.3.gz
+man/man3/bl_gff3_set_attributes_ae.3.gz
+man/man3/bl_gff3_set_attributes_array_size.3.gz
+man/man3/bl_gff3_set_attributes_cpy.3.gz
+man/man3/bl_gff3_set_attributes_len.3.gz
+man/man3/bl_gff3_set_end.3.gz
+man/man3/bl_gff3_set_feature_id.3.gz
+man/man3/bl_gff3_set_feature_id_ae.3.gz
+man/man3/bl_gff3_set_feature_id_cpy.3.gz
+man/man3/bl_gff3_set_feature_name.3.gz
+man/man3/bl_gff3_set_feature_name_ae.3.gz
+man/man3/bl_gff3_set_feature_name_cpy.3.gz
+man/man3/bl_gff3_set_feature_parent.3.gz
+man/man3/bl_gff3_set_feature_parent_ae.3.gz
+man/man3/bl_gff3_set_feature_parent_cpy.3.gz
+man/man3/bl_gff3_set_file_pos.3.gz
+man/man3/bl_gff3_set_gene_name_cpy.3.gz
+man/man3/bl_gff3_set_phase.3.gz
+man/man3/bl_gff3_set_score.3.gz
+man/man3/bl_gff3_set_seqid_ae.3.gz
+man/man3/bl_gff3_set_seqid_cpy.3.gz
+man/man3/bl_gff3_set_source_ae.3.gz
+man/man3/bl_gff3_set_source_cpy.3.gz
+man/man3/bl_gff3_set_start.3.gz
+man/man3/bl_gff3_set_strand.3.gz
+man/man3/bl_gff3_set_type_ae.3.gz
+man/man3/bl_gff3_set_type_cpy.3.gz
+man/man3/bl_gff3_skip_header.3.gz
+man/man3/bl_gff3_to_bed.3.gz
+man/man3/bl_gff3_write.3.gz
 man/man3/bl_next_start_codon.3.gz
 man/man3/bl_next_stop_codon.3.gz
 man/man3/bl_overlap_print.3.gz