[gentoo-commits] repo/gentoo:master commit in: sci-biology/newick-utils/files/, sci-biology/newick-utils/

[David Seifert]

commit:     f812704e44f3d927dd47f3901c59ee7716adefd0
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Nov  1 18:36:11 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Nov  1 18:36:11 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f812704e

sci-biology/newick-utils: Port to EAPI 7

* Don't build static libraries by default
* Fix GCC 10 / -fno-common
* Disable automagic guile and lua

Closes: https://bugs.gentoo.org/708534
Closes: https://bugs.gentoo.org/712312
Closes: https://bugs.gentoo.org/727986
Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 .../files/newick-utils-1.6-deduplicate-libnw.patch | 153 +++++++++++++++++++++
 .../files/newick-utils-1.6-fno-common.patch        |  41 ++++++
 sci-biology/newick-utils/metadata.xml              |  11 +-
 .../newick-utils/newick-utils-1.6-r1.ebuild        |  44 ++++++
 sci-biology/newick-utils/newick-utils-1.6.ebuild   |  20 ---
 5 files changed, 245 insertions(+), 24 deletions(-)

diff --git a/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch b/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch
new file mode 100644
index 00000000000..ca997830ace
--- /dev/null
+++ b/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch
@@ -0,0 +1,153 @@
+Don't rebuild all of libnw.la pointlessly
+
+--- a/tests/Makefile.am
++++ b/tests/Makefile.am
+@@ -8,6 +8,8 @@
+ showsrc:
+ 	@echo $(srcdir)
+ 
++LDADD = $(top_builddir)/src/libnw.la
++
+ TESTS = test_newick_scanner test_newick_parser test_rnode test_list \
+ 	test_link test_masprintf test_svg_graph_radial \
+ 	test_canvas test_concat test_hash test_lca test_enode \
+@@ -37,100 +39,57 @@
+ 
+ SRC = $(top_builddir)/src
+ 
+-test_newick_scanner_SOURCES = test_newick_scanner.c $(SRC)/newick_scanner.c \
+-	$(SRC)/newick_parser.c $(SRC)/rnode.c $(SRC)/rnode_iterator.c \
+-	$(SRC)/list.c $(SRC)/hash.c $(SRC)/masprintf.c $(SRC)/link.c
+-
+-test_newick_parser_SOURCES = test_newick_parser.c $(SRC)/parser.c \
+-	$(SRC)/newick_scanner.c $(SRC)/newick_parser.c $(SRC)/list.c \
+-	$(SRC)/rnode.c $(SRC)/link.c $(SRC)/hash.c $(SRC)/rnode_iterator.c \
+-	$(SRC)/masprintf.c $(SRC)/to_newick.c $(SRC)/concat.c
+-
+-test_rnode_SOURCES = test_rnode.c $(SRC)/rnode.c $(SRC)/list.c \
+-	$(SRC)/rnode_iterator.c $(SRC)/hash.c $(SRC)/masprintf.c \
+-	tree_stubs.c $(SRC)/nodemap.c $(SRC)/link.c
+-
+-test_list_SOURCES = test_list.c $(SRC)/list.c
+-
+-test_link_SOURCES = test_link.c $(SRC)/link.c $(SRC)/nodemap.c \
+-	$(SRC)/list.c $(SRC)/to_newick.c $(SRC)/rnode.c \
+-	$(SRC)/concat.c $(SRC)/hash.c tree_stubs.c \
+-	$(SRC)/rnode_iterator.c $(SRC)/masprintf.c
++test_newick_scanner_SOURCES = test_newick_scanner.c
++
++test_newick_parser_SOURCES = test_newick_parser.c
++
++test_rnode_SOURCES = test_rnode.c tree_stubs.c
++
++test_list_SOURCES = test_list.c
++
++test_link_SOURCES = test_link.c tree_stubs.c
+ 
+ test_canvas_SOURCES = test_canvas.c $(SRC)/canvas.c
+ 
+-test_concat_SOURCES = test_concat.c $(SRC)/concat.c
++test_concat_SOURCES = test_concat.c
++
++test_hash_SOURCES = test_hash.c
++
++test_lca_SOURCES = test_lca.c tree_stubs.c
++
++test_nodemap_SOURCES = test_nodemap.c tree_stubs.c
+ 
+-test_hash_SOURCES = test_hash.c $(SRC)/hash.c $(SRC)/list.c $(SRC)/masprintf.c
++test_to_newick_SOURCES = test_to_newick.c tree_stubs.c
+ 
+-test_lca_SOURCES = test_lca.c $(SRC)/lca.c $(SRC)/list.c $(SRC)/nodemap.c \
+-	$(SRC)/link.c $(SRC)/rnode.c $(SRC)/hash.c \
+-	$(SRC)/rnode_iterator.c tree_stubs.c $(SRC)/masprintf.c \
+-	$(SRC)/error.c
+-
+-test_nodemap_SOURCES = test_nodemap.c $(SRC)/nodemap.c \
+-	$(SRC)/rnode.c $(SRC)/list.c $(SRC)/hash.c $(SRC)/link.c \
+-	$(SRC)/rnode_iterator.c $(SRC)/masprintf.c tree_stubs.c
+-
+-test_to_newick_SOURCES = test_to_newick.c $(SRC)/to_newick.c \
+-	$(SRC)/rnode.c $(SRC)/link.c $(SRC)/concat.c \
+-	$(SRC)/list.c $(SRC)/rnode_iterator.c $(SRC)/hash.c \
+-	$(SRC)/masprintf.c $(SRC)/parser.c $(SRC)/newick_scanner.c \
+-	$(SRC)/newick_parser.c tree_stubs.c
+-
+-test_tree_SOURCES = test_tree.c $(SRC)/tree.c $(SRC)/rnode.c $(SRC)/list.c \
+-	$(SRC)/to_newick.c $(SRC)/nodemap.c $(SRC)/link.c $(SRC)/concat.c \
+-	$(SRC)/hash.c tree_stubs.c $(SRC)/rnode_iterator.c \
+-	$(SRC)/masprintf.c
+-
+-test_node_set_SOURCES = test_node_set.c tree_stubs.c $(SRC)/node_set.c \
+-	$(SRC)/hash.c $(SRC)/rnode.c $(SRC)/list.c $(SRC)/link.c \
+-	$(SRC)/rnode_iterator.c $(SRC)/masprintf.c
+-
+-test_enode_SOURCES = test_enode.c $(SRC)/enode.c $(SRC)/rnode.c \
+-	$(SRC)/link.c $(SRC)/list.c $(SRC)/rnode_iterator.c \
+-	$(SRC)/hash.c $(SRC)/masprintf.c
+-
+-test_rnode_iterator_SOURCES = test_rnode_iterator.c $(SRC)/rnode_iterator.c \
+-  	$(SRC)/list.c $(SRC)/link.c $(SRC)/rnode.c $(SRC)/to_newick.c \
+-       	$(SRC)/hash.c $(SRC)/nodemap.c tree_stubs.c $(SRC)/masprintf.c \
+-	$(SRC)/parser.c $(SRC)/newick_scanner.c $(SRC)/newick_parser.c \
+-	$(SRC)/concat.c
++test_tree_SOURCES = test_tree.c tree_stubs.c
++
++test_node_set_SOURCES = test_node_set.c tree_stubs.c $(SRC)/node_set.c
++
++test_enode_SOURCES = test_enode.c $(SRC)/enode.c
++
++test_rnode_iterator_SOURCES = test_rnode_iterator.c tree_stubs.c
+ 
+ test_readline_SOURCES = test_readline.c $(SRC)/readline.c
+ 
+-test_tree_models_SOURCES = test_tree_models.c $(SRC)/tree_models.c \
+-	$(SRC)/rnode.c $(SRC)/list.c $(SRC)/to_newick.c $(SRC)/link.c \
+-	$(SRC)/concat.c $(SRC)/rnode_iterator.c \
+-	$(SRC)/hash.c $(SRC)/masprintf.c
+-
+-test_xml_utils_SOURCES = test_xml_utils.c $(SRC)/xml_utils.c \
+-	$(SRC)/masprintf.c
+-
+-test_masprintf_SOURCES = test_masprintf.c $(SRC)/masprintf.c
+-
+-test_error_SOURCES = test_error.c $(SRC)/error.c
+-
+-test_order_tree_SOURCES = test_order_tree.c $(SRC)/order_tree.c tree_stubs.c \
+-	$(SRC)/link.c $(SRC)/to_newick.c $(SRC)/rnode.c $(SRC)/list.c \
+-	$(SRC)/masprintf.c $(SRC)/concat.c $(SRC)/hash.c $(SRC)/nodemap.c \
+-	$(SRC)/rnode_iterator.c
+-
+-test_graph_common_SOURCES = test_graph_common.c $(SRC)/graph_common.c \
+-	tree_stubs.c $(SRC)/link.c $(SRC)/list.c $(SRC)/tree.c \
+-	$(SRC)/rnode_iterator.c $(SRC)/hash.c $(SRC)/masprintf.c \
+-	$(SRC)/rnode.c $(SRC)/nodemap.c
++test_tree_models_SOURCES = test_tree_models.c $(SRC)/tree_models.c
++
++test_xml_utils_SOURCES = test_xml_utils.c $(SRC)/xml_utils.c
++
++test_masprintf_SOURCES = test_masprintf.c
++
++test_error_SOURCES = test_error.c
++
++test_order_tree_SOURCES = test_order_tree.c tree_stubs.c $(SRC)/order_tree.c
++
++test_graph_common_SOURCES = test_graph_common.c tree_stubs.c $(SRC)/graph_common.c
+ 
+ test_svg_graph_radial_SOURCES = test_svg_graph_radial.c \
+-	$(SRC)/svg_graph_radial.c $(SRC)/tree.c $(SRC)/svg_graph.c \
+-	$(SRC)/rnode.c $(SRC)/hash.c $(SRC)/list.c $(SRC)/masprintf.c \
+-	$(SRC)/rnode_iterator.c $(SRC)/svg_graph_ortho.c $(SRC)/error.c \
++	$(SRC)/svg_graph_radial.c $(SRC)/svg_graph.c \
++	$(SRC)/svg_graph_ortho.c \
+ 	$(SRC)/readline.c $(SRC)/xml_utils.c $(SRC)/graph_common.c \
+-	$(SRC)/node_pos_alloc.c $(SRC)/nodemap.c $(SRC)/lca.c $(SRC)/link.c
++	$(SRC)/node_pos_alloc.c
+ 
+-test_subtree_SOURCES = test_subtree.c $(SRC)/subtree.c $(SRC)/rnode.c \
+-	$(SRC)/list.c $(SRC)/hash.c $(SRC)/link.c $(SRC)/rnode_iterator.c \
+-	$(SRC)/masprintf.c $(SRC)/nodemap.c
++test_subtree_SOURCES = test_subtree.c $(SRC)/subtree.c
+ 
+ clean-local:
+ 	$(RM) *.out

diff --git a/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch b/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch
new file mode 100644
index 00000000000..15847a52c48
--- /dev/null
+++ b/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch
@@ -0,0 +1,41 @@
+--- a/src/address_parser.c
++++ b/src/address_parser.c
+@@ -83,6 +83,8 @@
+ #include "enode.h"
+ #include "address_parser_status.h"
+ 
++enum address_parser_status_type address_parser_status;
++
+ extern int adslex (void);
+ 
+ /* The root of the expression (when represented as a parse tree) */
+--- a/src/address_parser_status.h
++++ b/src/address_parser_status.h
+@@ -13,4 +13,4 @@
+  * returns either \c NULL or the top-level enode of the address, so we need to
+  * use an extern variable to convey its status. */
+ 
+-enum address_parser_status_type address_parser_status;
++extern enum address_parser_status_type address_parser_status;
+--- a/tests/test_newick_parser.c
++++ b/tests/test_newick_parser.c
+@@ -11,7 +11,7 @@
+ int nwslex (void);
+ struct rnode *root;
+ struct llist *nodes_in_order;
+-enum parser_status_type newick_parser_status;
++extern enum parser_status_type newick_parser_status;
+ void newick_scanner_set_string_input(char *);
+ 
+ /* NOTE: we can use to_newick() to check the parser's output because this
+--- a/tests/test_newick_scanner.c
++++ b/tests/test_newick_scanner.c
+@@ -20,7 +20,7 @@
+ int nwslex (void);
+ struct rnode *root;
+ struct llist *nodes_in_order;
+-enum parser_status_type newick_parser_status;
++extern enum parser_status_type newick_parser_status;
+ void newick_scanner_set_string_input(char *);
+ void newick_scanner_set_file_input(FILE *);
+ 

diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml
index 959160fe46b..d9bc9150987 100644
--- a/sci-biology/newick-utils/metadata.xml
+++ b/sci-biology/newick-utils/metadata.xml
@@ -1,8 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@g.o</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
+	<maintainer type="project">
+		<email>sci-biology@g.o</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<use>
+		<flag name="xml">Uses <pkg>dev-libs/libxml2</pkg> to handle ornaments</flag>
+	</use>
 </pkgmetadata>

diff --git a/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild b/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
new file mode 100644
index 00000000000..3dcb438832a
--- /dev/null
+++ b/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+DESCRIPTION="Tools for processing phylogenetic trees"
+HOMEPAGE="http://cegg.unige.ch/newick_utils"
+SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="xml"
+
+DEPEND="
+	xml? ( dev-libs/libxml2 )"
+RDEPEND="
+	${DEPEND}
+	!dev-games/libnw"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-deduplicate-libnw.patch
+	"${FILESDIR}"/${P}-fno-common.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--disable-static \
+		--without-guile \
+		--without-lua \
+		$(use_with xml libxml)
+}
+
+src_install() {
+	default
+	find "${ED}" -name '*.la' -delete || die
+}

diff --git a/sci-biology/newick-utils/newick-utils-1.6.ebuild b/sci-biology/newick-utils/newick-utils-1.6.ebuild
deleted file mode 100644
index 845bc011620..00000000000
--- a/sci-biology/newick-utils/newick-utils-1.6.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Tools for processing phylogenetic trees"
-HOMEPAGE="http://cegg.unige.ch/newick_utils"
-SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="!dev-games/libnw"
-
-src_test() {
-	emake -C tests check-TESTS
-}