libpll: imported to biology/libpll

[Dr. Thomas Orgis <thomas.orgis%uni-hamburg.de@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Dr. Thomas Orgis <thomas.orgis%uni-hamburg.de@localhost>
Pushed By:	thor
Date:		Sat Dec 23 14:32:28 2023 +0100
Changeset:	66d1c9e279547f76fe30173f46bee50f84d8baf5

Modified Files:
	Makefile
Removed Files:
	libpll/DESCR
	libpll/Makefile
	libpll/PLIST
	libpll/distinfo
	libpll/patches/patch-configure
	libpll/patches/patch-configure.ac

Log Message:
libpll: imported to biology/libpll

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=66d1c9e279547f76fe30173f46bee50f84d8baf5

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

diffstat:
 Makefile                          |  1 -
 libpll/DESCR                      | 15 ---------------
 libpll/Makefile                   | 20 --------------------
 libpll/PLIST                      | 40 ---------------------------------------
 libpll/distinfo                   |  7 -------
 libpll/patches/patch-configure    | 20 --------------------
 libpll/patches/patch-configure.ac | 20 --------------------
 7 files changed, 123 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index 94d512c358..f44cb2c4d3 100644
--- a/Makefile
+++ b/Makefile
@@ -1976,7 +1976,6 @@ SUBDIR+=	libpare
 SUBDIR+=	libparsifal
 SUBDIR+=	libpatterns
 SUBDIR+=	libplist2
-SUBDIR+=	libpll
 SUBDIR+=	libpsurface
 SUBDIR+=	libpthread-stubs
 SUBDIR+=	libpusb
diff --git a/libpll/DESCR b/libpll/DESCR
deleted file mode 100644
index 3c6e5efd2f..0000000000
--- a/libpll/DESCR
+++ /dev/null
@@ -1,15 +0,0 @@
-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.
diff --git a/libpll/Makefile b/libpll/Makefile
deleted file mode 100644
index 0e80e90fad..0000000000
--- a/libpll/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	libpll-src-0.3.2
-PKGNAME=	${DISTNAME:S/-src//}
-CATEGORIES=	# TODO: add primary category
-MASTER_SITES=	${MASTER_SITE_GITHUB:=xflouris/}
-GITHUB_PROJECT=	libpll
-GITHUB_RELEASE=	0.3.2
-
-MAINTAINER=	thomas.orgis%uni-hamburg.de@localhost
-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"
diff --git a/libpll/PLIST b/libpll/PLIST
deleted file mode 100644
index 733e79e17e..0000000000
--- a/libpll/PLIST
+++ /dev/null
@@ -1,40 +0,0 @@
-@comment $NetBSD$
-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
diff --git a/libpll/distinfo b/libpll/distinfo
deleted file mode 100644
index b9901893a5..0000000000
--- a/libpll/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD$
-
-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
diff --git a/libpll/patches/patch-configure b/libpll/patches/patch-configure
deleted file mode 100644
index 4c9dfec7a4..0000000000
--- a/libpll/patches/patch-configure
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD$
-
-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
- 
diff --git a/libpll/patches/patch-configure.ac b/libpll/patches/patch-configure.ac
deleted file mode 100644
index 9f7bc04a04..0000000000
--- a/libpll/patches/patch-configure.ac
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD$
-
-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
-