[med-svn] [Git][med-team/quicktree][master] 4 commits: routine-update: debhelper-compat 13

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / quicktree


Commits:
3dd0bc8e by Andreas Tille at 2020-06-12T20:47:56+02:00
routine-update: debhelper-compat 13

- - - - -
385a6fdd by Andreas Tille at 2020-06-12T20:48:04+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Fixes: lintian: upstream-metadata-file-is-missing
See-also: https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html


Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html


Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
2e6bf72a by Andreas Tille at 2020-06-12T20:48:48+02:00
routine-update: Ready to upload to unstable

- - - - -
fe426a65 by Andreas Tille at 2020-06-16T14:17:27+02:00
To enable removing quicktree source code copy from libsonlib package a static library is created here

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/libquicktree-dev.install
- + debian/patches/create_lib.patch
- debian/patches/series
- + debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+quicktree (2.5-3) UNRELEASED; urgency=medium
+
+  * To enable removing quicktree source code copy from libsonlib package
+    a static library is created here
+
+ -- Andreas Tille <tille at debian.org>  Tue, 16 Jun 2020 09:35:08 +0200
+
+quicktree (2.5-2) unstable; urgency=medium
+
+  * Team upload.
+  * debhelper-compat 13 (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org>  Fri, 12 Jun 2020 20:48:04 +0200
+
 quicktree (2.5-1) unstable; urgency=medium
 
   * Initial release (Closes: #961375)


=====================================
debian/control
=====================================
@@ -3,8 +3,9 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper-compat (= 12),
-               help2man
+Build-Depends: debhelper-compat (= 13),
+               help2man,
+               dh-exec
 Standards-Version: 4.5.0
 Homepage: https://github.com/khowe/quicktree/
 Vcs-Browser: https://salsa.debian.org/med-team/quicktree
@@ -29,3 +30,26 @@ Description: Neighbor-Joining algorithm for phylogenies
  .
  The tress are written to stdout, in the Newick/New-Hampshire format
  use by PHYLIP and many other programs
+
+Package: libquicktree-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: Neighbor-Joining algorithm for phylogenies (development)
+ QuickTree is an efficient implementation of the Neighbor-Joining
+ algorithm (PMID: 3447015), capable of reconstructing phylogenies from
+ huge alignments in time less than the age of the universe.
+ .
+ QuickTree accepts both distance matrix and multiple-sequence-aligment
+ inputs. The former should be in PHYLIP format. The latter should be
+ in Stockholm format, which is the native alignment format for the Pfam
+ database. Alignments in various formats can be converted to Stockholm
+ format with the sreformat program, which is part of the HMMer package
+ (hmmer.org).
+ .
+ The tress are written to stdout, in the Newick/New-Hampshire format
+ use by PHYLIP and many other programs
+ .
+ This package contains some header files from quicktree that are used
+ by other packages.


=====================================
debian/libquicktree-dev.install
=====================================
@@ -0,0 +1,4 @@
+#!/usr/bin/dh-exec
+
+include/*.h	usr/include/quicktree
+lib*.a		usr/lib/${DEB_HOST_MULTIARCH}


=====================================
debian/patches/create_lib.patch
=====================================
@@ -0,0 +1,32 @@
+--- a/Makefile
++++ b/Makefile
+@@ -10,6 +10,13 @@ COMMON = $(OBJ)/align.o \
+ 	$(OBJ)/options.o \
+ 	$(OBJ)/util.o \
+ 	$(OBJ)/sequence.o
++LIBOBJ =  $(OBJ)/buildtree.o \
++	$(OBJ)/cluster.o \
++	$(OBJ)/distancemat.o \
++	$(OBJ)/options.o \
++	$(OBJ)/util.o \
++	$(OBJ)/sequence.o \
++        $(OBJ)/tree.o \
+ 
+ QUICKTREEOBJ = $(COMMON) $(OBJ)/quicktree.o $(OBJ)/buildtree.o $(OBJ)/tree.o
+ 
+@@ -21,11 +28,14 @@ CFLAGS += -c -I$(INC)
+ 
+ LDFLAGS += -g 
+ 
+-all: quicktree
++all: quicktree libquicktree.a
+ 
+ quicktree : $(QUICKTREEOBJ)
+ 	$(CC) $(LDFLAGS) -o $@ $(QUICKTREEOBJ) -lm
+ 
++libquicktree.a: $(LIBOBJ)
++	ar rc $@ $(LIBOBJ)
++
+ $(OBJ)/quicktree.o : $(SRC)/quicktree.c $(INC)/version.h
+ 	$(CC) $(CFLAGS) -o $(OBJ)/quicktree.o $(SRC)/quicktree.c
+ 


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 fixMake.patch
+create_lib.patch


=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,5 @@
+---
+Bug-Database: https://github.com/khowe/quicktree/issues
+Bug-Submit: https://github.com/khowe/quicktree/issues/new
+Repository: https://github.com/khowe/quicktree.git
+Repository-Browse: https://github.com/khowe/quicktree



View it on GitLab: https://salsa.debian.org/med-team/quicktree/-/compare/0a925f990469319ea72d460c52c96e191e31b10f...fe426a6598742190616d848b8a06773b570106f1

-- 
View it on GitLab: https://salsa.debian.org/med-team/quicktree/-/compare/0a925f990469319ea72d460c52c96e191e31b10f...fe426a6598742190616d848b8a06773b570106f1
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