CVS commit: pkgsrc/biology/biolibc

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Oct 28 20:31:40 UTC 2023

Modified Files:
        pkgsrc/biology/biolibc: DESCR Makefile PLIST buildlink3.mk distinfo

Log Message:
biology/biolibc: Update to 0.2.6

Updates for libxtend 0.2.0 API
Add full list of functions to biolibc(3) man page
Other documentation improvements

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


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/biolibc/DESCR
cvs rdiff -u -r1.13 -r1.14 pkgsrc/biology/biolibc/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/biology/biolibc/PLIST \
    pkgsrc/biology/biolibc/buildlink3.mk
cvs rdiff -u -r1.14 -r1.15 pkgsrc/biology/biolibc/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/biolibc/DESCR
diff -u pkgsrc/biology/biolibc/DESCR:1.1 pkgsrc/biology/biolibc/DESCR:1.2
--- pkgsrc/biology/biolibc/DESCR:1.1    Wed Mar 24 15:20:08 2021
+++ pkgsrc/biology/biolibc/DESCR        Sat Oct 28 20:31:40 2023
@@ -1,5 +1,6 @@
-Biolibc is a library of fast, memory-efficient, low-level functions for
-processing biological data.  Like libc, it consists of numerous disparate,
-general-purpose functions which could be used by a wide variety of
-applications.  These include functions for streaming common file formats such
-as SAM and VCF, string functions specific to bioinformatics, etc.
+Biolibc is a library of fast, memory-efficient, low-level functions
+for processing biological data.  Like libc, it consists of numerous
+disparate, general-purpose functions which could be used by a wide
+variety of applications.  These include functions for streaming
+common file formats such as SAM and VCF, string functions specific
+to bioinformatics, etc.

Index: pkgsrc/biology/biolibc/Makefile
diff -u pkgsrc/biology/biolibc/Makefile:1.13 pkgsrc/biology/biolibc/Makefile:1.14
--- pkgsrc/biology/biolibc/Makefile:1.13        Sat Aug 12 14:49:18 2023
+++ pkgsrc/biology/biolibc/Makefile     Sat Oct 28 20:31:40 2023
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.13 2023/08/12 14:49:18 bacon Exp $
+# $NetBSD: Makefile,v 1.14 2023/10/28 20:31:40 bacon Exp $
 
-DISTNAME=      biolibc-0.2.5
+DISTNAME=      biolibc-0.2.6
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
 

Index: pkgsrc/biology/biolibc/PLIST
diff -u pkgsrc/biology/biolibc/PLIST:1.12 pkgsrc/biology/biolibc/PLIST:1.13
--- pkgsrc/biology/biolibc/PLIST:1.12   Sat Aug 12 14:49:18 2023
+++ pkgsrc/biology/biolibc/PLIST        Sat Oct 28 20:31:40 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.12 2023/08/12 14:49:18 bacon Exp $
+@comment $NetBSD: PLIST,v 1.13 2023/10/28 20:31:40 bacon Exp $
 include/biolibc/align-accessors.h
 include/biolibc/align-mutators.h
 include/biolibc/align-rvs.h
@@ -241,6 +241,7 @@ man/man3/bl_align_map_seq_sub.3
 man/man3/bl_align_set_max_mismatch_percent.3
 man/man3/bl_align_set_min_match.3
 man/man3/bl_bed_check_order.3
+man/man3/bl_bed_gff3_cmp.3
 man/man3/bl_bed_gff_cmp.3
 man/man3/bl_bed_read.3
 man/man3/bl_bed_set_block_count.3
@@ -431,6 +432,8 @@ man/man3/bl_sam_copy_header.3
 man/man3/bl_sam_fclose.3
 man/man3/bl_sam_fopen.3
 man/man3/bl_sam_free.3
+man/man3/bl_sam_gff3_cmp.3
+man/man3/bl_sam_gff3_overlap.3
 man/man3/bl_sam_gff_cmp.3
 man/man3/bl_sam_gff_overlap.3
 man/man3/bl_sam_init.3
Index: pkgsrc/biology/biolibc/buildlink3.mk
diff -u pkgsrc/biology/biolibc/buildlink3.mk:1.12 pkgsrc/biology/biolibc/buildlink3.mk:1.13
--- pkgsrc/biology/biolibc/buildlink3.mk:1.12   Sat Aug 12 14:49:18 2023
+++ pkgsrc/biology/biolibc/buildlink3.mk        Sat Oct 28 20:31:40 2023
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.12 2023/08/12 14:49:18 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.13 2023/10/28 20:31:40 bacon Exp $
 
 BUILDLINK_TREE+=       biolibc
 
 .if !defined(BIOLIBC_BUILDLINK3_MK)
 BIOLIBC_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.2.5
+BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.2.6
 BUILDLINK_PKGSRCDIR.biolibc?=  ../../biology/biolibc
 
 .include "../../devel/libxtend/buildlink3.mk"

Index: pkgsrc/biology/biolibc/distinfo
diff -u pkgsrc/biology/biolibc/distinfo:1.14 pkgsrc/biology/biolibc/distinfo:1.15
--- pkgsrc/biology/biolibc/distinfo:1.14        Sat Aug 12 14:49:18 2023
+++ pkgsrc/biology/biolibc/distinfo     Sat Oct 28 20:31:40 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.14 2023/08/12 14:49:18 bacon Exp $
+$NetBSD: distinfo,v 1.15 2023/10/28 20:31:40 bacon Exp $
 
-BLAKE2s (biolibc-0.2.5.tar.gz) = ea2f46e8c6b26da34c2d10603ae1974e680e5df3a1ce8110235dc1afe1d24ec5
-SHA512 (biolibc-0.2.5.tar.gz) = 647d8b19d007775f140b4b2d23bc8048ee6896e34b2d046109c71b1be13955a79991bb7dfbda8887db852265825d18b58e16195173624efb9bd19e6d1f5d13ba
-Size (biolibc-0.2.5.tar.gz) = 141426 bytes
+BLAKE2s (biolibc-0.2.6.tar.gz) = 9895be8848084d1f145b5987a4e3af99f61b1ba55db89873f915e610a7a335a7
+SHA512 (biolibc-0.2.6.tar.gz) = 00dc3b2efa71113c6450191f11217e3b2d99bb31efb703bcd5f5f24e1d6507b9bc98d92329b1ea836397709070f45715e2adb991326ec303b97a8b484ba07712
+Size (biolibc-0.2.6.tar.gz) = 147823 bytes