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Date: Mon, 18 Dec 2023 01:39:13 +0000
From: "Dr. Thomas Orgis" <thor@netbsd.org>
Subject: CVS commit: pkgsrc/biology/libpll
To: pkgsrc-changes@NetBSD.org
Approved: commit_and_comment
Reply-To: thor@netbsd.org
Message-Id: <20231218013913.8CBC2FA42@cvs.NetBSD.org>

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Module Name:	pkgsrc
Committed By:	thor
Date:		Mon Dec 18 01:39:13 UTC 2023

Added Files:
	pkgsrc/biology/libpll: DESCR Makefile PLIST distinfo
	pkgsrc/biology/libpll/patches: patch-configure patch-configure.ac

Log Message:
biology/libpll: added package for PLL phylogenetic analysis

The aim of this project is to implement a versatile high-performance
software library for phylogenetic analysis. The library should serve
as a lower-level interface of PLL (Flouri et al. 2015) and should
have the following properties:

    open source code with an appropriate open source license.
    64-bit multi-threaded design that handles very large datasets.
    easy to use and well-documented.
    SIMD implementations of time-consuming parts.
    as fast or faster likelihood computations than RAxML (Stamatakis 2014).
    fast implementation of the site repeats algorithm (Kobert 2017).
    functions for tree visualization.
    bindings for Python.
    generic and clean design.
    Linux, Mac, and Microsoft Windows compatibility.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/libpll/DESCR \
    pkgsrc/biology/libpll/Makefile pkgsrc/biology/libpll/PLIST \
    pkgsrc/biology/libpll/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/libpll/patches/patch-configure \
    pkgsrc/biology/libpll/patches/patch-configure.ac

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


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Added files:

Index: pkgsrc/biology/libpll/DESCR
diff -u /dev/null pkgsrc/biology/libpll/DESCR:1.1
--- /dev/null	Mon Dec 18 01:39:13 2023
+++ pkgsrc/biology/libpll/DESCR	Mon Dec 18 01:39:13 2023
@@ -0,0 +1,15 @@
+The aim of this project is to implement a versatile high-performance
+software library for phylogenetic analysis. The library should serve
+as a lower-level interface of PLL (Flouri et al. 2015) and should
+have the following properties:
+
+    open source code with an appropriate open source license.
+    64-bit multi-threaded design that handles very large datasets.
+    easy to use and well-documented.
+    SIMD implementations of time-consuming parts.
+    as fast or faster likelihood computations than RAxML (Stamatakis 2014).
+    fast implementation of the site repeats algorithm (Kobert 2017).
+    functions for tree visualization.
+    bindings for Python.
+    generic and clean design.
+    Linux, Mac, and Microsoft Windows compatibility.
Index: pkgsrc/biology/libpll/Makefile
diff -u /dev/null pkgsrc/biology/libpll/Makefile:1.1
--- /dev/null	Mon Dec 18 01:39:13 2023
+++ pkgsrc/biology/libpll/Makefile	Mon Dec 18 01:39:13 2023
@@ -0,0 +1,20 @@
+# $NetBSD: Makefile,v 1.1 2023/12/18 01:39:13 thor Exp $
+
+DISTNAME=	libpll-src-0.3.2
+PKGNAME=	${DISTNAME:S/-src//}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=xflouris/}
+GITHUB_PROJECT=	libpll
+GITHUB_RELEASE=	0.3.2
+
+MAINTAINER=	thomas.orgis@uni-hamburg.de
+HOMEPAGE=	https://github.com/xflouris/libpll/
+COMMENT=	High-performance software library for phylogenetic analysis
+LICENSE=	gnu-agpl-v3
+
+GNU_CONFIGURE=	yes
+USE_LIBTOOL=	yes
+
+USE_TOOLS+=	bison flex
+
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/libpll/PLIST
diff -u /dev/null pkgsrc/biology/libpll/PLIST:1.1
--- /dev/null	Mon Dec 18 01:39:13 2023
+++ pkgsrc/biology/libpll/PLIST	Mon Dec 18 01:39:13 2023
@@ -0,0 +1,40 @@
+@comment $NetBSD: PLIST,v 1.1 2023/12/18 01:39:13 thor Exp $
+include/libpll/pll.h
+lib/libpll.la
+man/man3/libpll.3
+share/doc/libpll/examples/heterotachy/Makefile
+share/doc/libpll/examples/heterotachy/README.md
+share/doc/libpll/examples/heterotachy/heterotachy.c
+share/doc/libpll/examples/lg4/Makefile
+share/doc/libpll/examples/lg4/data/example.fas
+share/doc/libpll/examples/lg4/data/example.tree
+share/doc/libpll/examples/lg4/lg4.c
+share/doc/libpll/examples/load-utree/Makefile
+share/doc/libpll/examples/load-utree/README.md
+share/doc/libpll/examples/load-utree/load-utree.c
+share/doc/libpll/examples/newick-fasta-rooted/Makefile
+share/doc/libpll/examples/newick-fasta-rooted/newick-fasta-rooted.c
+share/doc/libpll/examples/newick-fasta-unrooted/Makefile
+share/doc/libpll/examples/newick-fasta-unrooted/newick-fasta-unrooted.c
+share/doc/libpll/examples/newick-phylip-unrooted/Makefile
+share/doc/libpll/examples/newick-phylip-unrooted/newick-phylip-unrooted.c
+share/doc/libpll/examples/newton/Makefile
+share/doc/libpll/examples/newton/README.md
+share/doc/libpll/examples/newton/newton.c
+share/doc/libpll/examples/parsimony/Makefile
+share/doc/libpll/examples/parsimony/npr-pars.c
+share/doc/libpll/examples/partial-traversal/Makefile
+share/doc/libpll/examples/partial-traversal/partial.c
+share/doc/libpll/examples/protein-list/Makefile
+share/doc/libpll/examples/protein-list/protein-list.c
+share/doc/libpll/examples/rooted-tacg/Makefile
+share/doc/libpll/examples/rooted-tacg/rooted-tacg.c
+share/doc/libpll/examples/rooted/Makefile
+share/doc/libpll/examples/rooted/README.md
+share/doc/libpll/examples/rooted/rooted.c
+share/doc/libpll/examples/stepwise/Makefile
+share/doc/libpll/examples/stepwise/stepwise.c
+share/doc/libpll/examples/unrooted/Makefile
+share/doc/libpll/examples/unrooted/README.md
+share/doc/libpll/examples/unrooted/unrooted.c
+share/doc/libpll/libpll_manual.pdf
Index: pkgsrc/biology/libpll/distinfo
diff -u /dev/null pkgsrc/biology/libpll/distinfo:1.1
--- /dev/null	Mon Dec 18 01:39:13 2023
+++ pkgsrc/biology/libpll/distinfo	Mon Dec 18 01:39:13 2023
@@ -0,0 +1,7 @@
+$NetBSD: distinfo,v 1.1 2023/12/18 01:39:13 thor Exp $
+
+BLAKE2s (libpll-src-0.3.2.tar.gz) = 9236f9f3f9d498c205747d4397b0cbd0cc5837e496d2c76a4a6fa78c14d9d90c
+SHA512 (libpll-src-0.3.2.tar.gz) = b264dee8b7796e071b529b6be981ca1cd9b2074fd6af2ecbe79371b5a9187a44dca3b7555502f00ffa135d9d48a236f63180f25d707d8c9d59b27cff40dd86aa
+Size (libpll-src-0.3.2.tar.gz) = 599948 bytes
+SHA1 (patch-configure) = 2238f05ee5d38c4bd2ea4e516cbf9458eb6487bd
+SHA1 (patch-configure.ac) = c14be9e70f5b8db487d22718582a94caa241e48e

Index: pkgsrc/biology/libpll/patches/patch-configure
diff -u /dev/null pkgsrc/biology/libpll/patches/patch-configure:1.1
--- /dev/null	Mon Dec 18 01:39:13 2023
+++ pkgsrc/biology/libpll/patches/patch-configure	Mon Dec 18 01:39:13 2023
@@ -0,0 +1,20 @@
+$NetBSD: patch-configure,v 1.1 2023/12/18 01:39:13 thor Exp $
+
+Make stupid check for bison and flex a bit less stupid.
+
+--- configure.orig	2023-02-13 21:30:40.779472369 +0000
++++ configure
+@@ -11880,11 +11880,11 @@ test -n "$YACC" || YACC="yacc"
+ 
+ 
+ 
+-if test "x$LEX" != xflex; then
++if test "x$(basename "$LEX")" != xflex; then
+   as_fn_error $? "could not find required installation of FLEX" "$LINENO" 5
+ fi
+ 
+-if test "x$YACC" != x"bison -y"; then
++if test "x$(basename "$YACC")" != x"bison -y"; then
+   as_fn_error $? "could not find required installation of BISON" "$LINENO" 5
+ fi
+ 
Index: pkgsrc/biology/libpll/patches/patch-configure.ac
diff -u /dev/null pkgsrc/biology/libpll/patches/patch-configure.ac:1.1
--- /dev/null	Mon Dec 18 01:39:13 2023
+++ pkgsrc/biology/libpll/patches/patch-configure.ac	Mon Dec 18 01:39:13 2023
@@ -0,0 +1,20 @@
+$NetBSD: patch-configure.ac,v 1.1 2023/12/18 01:39:13 thor Exp $
+
+Make stupid checks for bison and flex a bit less stupid.
+
+--- configure.ac.orig	2023-02-13 21:28:47.785056736 +0000
++++ configure.ac
+@@ -20,11 +20,11 @@ AC_PROG_LEX
+ AC_PROG_YACC
+ AC_PROG_INSTALL
+ 
+-if test "x$LEX" != xflex; then
++if test "x$(basename "$LEX")" != xflex; then
+   AC_MSG_ERROR(could not find required installation of FLEX)
+ fi
+ 
+-if test "x$YACC" != x"bison -y"; then
++if test "x$(basename "$YACC")" != x"bison -y"; then
+   AC_MSG_ERROR(could not find required installation of BISON)
+ fi
+ 


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