debian/changelog

+alter-sequence-alignment (1.3.4-3) unstable; urgency=medium
+
+  * Replace python-markdown by markdown
+    Closes: #942948
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Remove trailing whitespace in debian/rules
+  * Set upstream metadata fields: Bug-Database, Repository, Repository-
+    Browse.
+
+ -- Andreas Tille <tille@debian.org>  Sun, 15 Dec 2019 16:31:47 +0100
+
 alter-sequence-alignment (1.3.4-2) unstable; urgency=medium
 
   * Architecture: all

debian/compat

-11

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: java
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                javahelper,
                maven-debian-helper,
                libproperties-maven-plugin-java,
@@ -12,8 +12,8 @@ Build-Depends: debhelper (>= 11~),
                libmaven-assembly-plugin-java,
                libargs4j-java,
                rename,
-               python-markdown
-Standards-Version: 4.2.1
+               markdown
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/alter-sequence-alignment
 Vcs-Git: https://salsa.debian.org/med-team/alter-sequence-alignment.git
 Homepage: http://sing.ei.uvigo.es/ALTER/

debian/rules

@@ -7,7 +7,7 @@ JAVA_HOME=/usr/lib/jvm/default-java
 
 override_dh_auto_build:
 	dh_auto_build
-	markdown_py -f README.html README.md
+	markdown README.md > README.html
 
 override_jh_installlibs:
 	file-rename 's/ALTER-([\d.]+)-jar-with-dependencies.jar/alter-\1.jar/' alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar

debian/upstream/metadata

 Reference:
- Author: >
-  Daniel Glez-Peña and Daniel Gómez-Blanco and Miguel Reboiro-Jato and
-  Florentino Fdez-Riverola and David Posada
- Title: >
-  ALTER: program-oriented conversion of DNA and protein alignments"
- Journal: Nucl. Acids Res.
- Year: 2010
- Volume: 38
- Number: suppl 2
- Pages: W14-W18
- DOI: 10.1093/nar/gkq321
- PMID: 20439312
- URL: http://nar.oxfordjournals.org/content/38/suppl_2/W14
- ePrint: >
-  http://nar.oxfordjournals.org/content/38/suppl_2/W14.full.pdf+html
+  Author: >
+    Daniel Glez-Peña and Daniel Gómez-Blanco and Miguel Reboiro-Jato and
+    Florentino Fdez-Riverola and David Posada
+  Title: >
+    ALTER: program-oriented conversion of DNA and protein alignments"
+  Journal: Nucl. Acids Res.
+  Year: 2010
+  Volume: 38
+  Number: suppl 2
+  Pages: W14-W18
+  DOI: 10.1093/nar/gkq321
+  PMID: 20439312
+  URL: http://nar.oxfordjournals.org/content/38/suppl_2/W14
+  ePrint: >
+    http://nar.oxfordjournals.org/content/38/suppl_2/W14.full.pdf+html
 Registry:
- - Name: OMICtools
-   Entry: OMICS_19786
- - Name: bio.tools
-   Entry: alter
- - Name: SciCrunch
-   Entry: SCR_015968
+- Name: OMICtools
+  Entry: OMICS_19786
+- Name: bio.tools
+  Entry: alter
+- Name: SciCrunch
+  Entry: SCR_015968
+Bug-Database: https://github.com/sing-group/ALTER/issues
+Repository: https://github.com/sing-group/ALTER.git
+Repository-Browse: https://github.com/sing-group/ALTER