debian/changelog

-raxml (8.2.12+dfsg-3) UNRELEASED; urgency=medium
+raxml (8.2.12+dfsg-4) unstable; urgency=medium
 
-  * Team upload.
+  [ Michael R. Crusoe ]
   * Update SIMDe to for the FMA instruction as well.
 
- -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 20 Dec 2019 09:31:07 -0800
+  [ Helmut Grohne ]
+  * Improve cross building: Let dh_auto_build pass cross tools to make.
+    Closes: #947194
+
+  [ Andreas Tille ]
+  * Add manually created manpage (do not use help2man at build time)
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Set upstream metadata fields: Bug-Database.
+  * Remove obsolete fields Contact, Name from debian/upstream/metadata
+    (already present in machine-readable debian/copyright).
+
+ -- Andreas Tille <tille@debian.org>  Mon, 23 Dec 2019 17:49:16 +0100
 
 raxml (8.2.12+dfsg-2) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -3,9 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
-               help2man
-Standards-Version: 4.1.4
+Build-Depends: debhelper-compat (= 12)
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/raxml
 Vcs-Git: https://salsa.debian.org/med-team/raxml.git
 Homepage: http://www.exelixis-lab.org/

debian/createmanpages

+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=raxmlHPC
+help2man --no-info --no-discard-stderr --help-option="-h" --version-option="-v" \
+         --name="Randomized Axelerated Maximum Likelihood" \
+         --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT

debian/manpages

+debian/*.1

debian/rules

@@ -31,7 +31,7 @@ override_dh_auto_clean:
 override_dh_auto_build:
 	mkdir -p $(BINDIR)
 	set -e ; for mfile in $(MFILES); do \
-	    $(MAKE) -f $${mfile} $(MFLAGS); \
+	    dh_auto_build --buildsystem=makefile -- -f $${mfile} $(MFLAGS); \
 	    curexe=`ls $(exe)* | head -n 1` ; \
 	    if [ -e $(BINDIR)/$${curexe} ] ; then \
 		echo "**** ERROR: $${curexe} was created before!!" && false ; \
@@ -50,9 +50,7 @@ else
 endif
 
 override_dh_installman:
-	help2man --no-info --help-option="-h" --version-option="-v" \
-	         --name="Randomized Axelerated Maximum Likelihood" \
-	         $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/$(exe) > $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/$(exe).1
+	dh_installman
 	for cexe in `ls $(BINDIR)/$(exe)*` ; do \
 	    curexe=`basename $${cexe}` ; \
 	    if [ $${curexe} != $(exe) ] ; then \

debian/upstream/metadata

-Contact: Alexandros Stamatakis <Alexandros.Stamatakis@epfl.ch>
 Bug-Submit: https://groups.google.com/forum/?hl=de#!forum/raxml
-Name: RAxML
 Reference:
- - author: Alexandros Stamatakis
-   title: >
+- author: Alexandros Stamatakis
+  title: >
     RAxML version 8: a tool for phylogenetic analysis and post-analysis
     of large phylogenies
-   journal: Bioinformatics
-   volume: Epub ahead of print
-   year: 2014
-   PMID: 24451623
-   DOI: 10.1093/bioinformatics/btu033
-   URL: "http://bioinformatics.oxfordjournals.org/content/early/\
-    2014/02/07/bioinformatics.btu033"
-   ePrint: "http://bioinformatics.oxfordjournals.org/content/early/\
-    2014/02/07/bioinformatics.btu033.full.pdf+html"
- - author: Alexandros Stamatakis
-   title: >
-     RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
-     thousands of taxa and mixed models
-   journal: Bioinformatics
-   volume: 22
-   number: 21
-   pages: 2688-2690
-   year: 2006
-   PMID: 16928733
-   DOI: 10.1093/bioinformatics/btl446
-   URL: http://bioinformatics.oxfordjournals.org/content/22/21/2688.full
-   ePrint: >
+  journal: Bioinformatics
+  volume: Epub ahead of print
+  year: 2014
+  PMID: 24451623
+  DOI: 10.1093/bioinformatics/btu033
+  URL: http://bioinformatics.oxfordjournals.org/content/early/2014/02/07/bioinformatics.btu033
+  ePrint: http://bioinformatics.oxfordjournals.org/content/early/2014/02/07/bioinformatics.btu033.full.pdf+html
+- author: Alexandros Stamatakis
+  title: >
+    RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
+    thousands of taxa and mixed models
+  journal: Bioinformatics
+  volume: 22
+  number: 21
+  pages: 2688-2690
+  year: 2006
+  PMID: 16928733
+  DOI: 10.1093/bioinformatics/btl446
+  URL: http://bioinformatics.oxfordjournals.org/content/22/21/2688.full
+  ePrint: >
     http://bioinformatics.oxfordjournals.org/content/22/21/2688.full.pdf+html
 Registry:
- - Name: OMICtools
-   Entry: NA
- - Name: bio.tools
-   Entry: raxml
- - Name: SciCrunch
-   Entry: SCR_006086
- - Name: conda:bioconda
-   Entry: raxml
+- Name: OMICtools
+  Entry: NA
+- Name: bio.tools
+  Entry: raxml
+- Name: SciCrunch
+  Entry: SCR_006086
+- Name: conda:bioconda
+  Entry: raxml
+Bug-Database: https://github.com/stamatak/standard-RAxML/issues