libpll: high-performance software library for phylogenetic analysis.

[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:		Mon Feb 13 21:48:48 2023 +0100
Changeset:	04896bc422f0b605ddb3560de74c0cdd108d7e2d

Modified Files:
	Makefile
Added Files:
	libpll/DESCR
	libpll/Makefile
	libpll/PLIST
	libpll/distinfo

Log Message:
libpll: high-performance software library for 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 see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=04896bc422f0b605ddb3560de74c0cdd108d7e2d

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 | 18 ++++++++++++++++++
 libpll/PLIST    | 40 ++++++++++++++++++++++++++++++++++++++++
 libpll/distinfo |  5 +++++
 5 files changed, 79 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index b3350146e2..ca492f97b7 100644
--- a/Makefile
+++ b/Makefile
@@ -2123,6 +2123,7 @@ 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
new file mode 100644
index 0000000000..3c6e5efd2f
--- /dev/null
+++ b/libpll/DESCR
@@ -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.
diff --git a/libpll/Makefile b/libpll/Makefile
new file mode 100644
index 0000000000..02fef5109c
--- /dev/null
+++ b/libpll/Makefile
@@ -0,0 +1,18 @@
+# $NetBSD$
+
+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
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/libpll/PLIST b/libpll/PLIST
new file mode 100644
index 0000000000..733e79e17e
--- /dev/null
+++ b/libpll/PLIST
@@ -0,0 +1,40 @@
+@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
new file mode 100644
index 0000000000..3ff7aa9926
--- /dev/null
+++ b/libpll/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+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