debian/changelog

+conservation-code (20110309.0-8) unstable; urgency=medium
+
+  * Rename test dir in autopktest from ADTTMP to AUTOPKGTEST_TMP
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #942925
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Remove trailing whitespace in debian/changelog
+  * Do not parse d/changelog
+  * Trim trailing whitespace.
+  * Use secure URI in Homepage field.
+  * Remove obsolete fields Contact, Name from debian/upstream/metadata.
+  * Remove unnecessary get-orig-source-target.
+
+ -- Andreas Tille <tille@debian.org>  Sun, 15 Dec 2019 16:24:28 +0100
+
 conservation-code (20110309.0-7) unstable; urgency=medium
 
   * debhelper 11
@@ -25,10 +41,10 @@ conservation-code (20110309.0-5) unstable; urgency=medium
   * upstream fix - to load identity matrix without error when no alignment
     matrix is found
   * add hardening
-  * allow-stderr for testsuite to allow test pass instead of fail when matrix 
+  * allow-stderr for testsuite to allow test pass instead of fail when matrix
     file is not found
   * verbose output in test + check distributions usage
-  * simplified debian/tests/non-default-params-test, but made more verbose 
+  * simplified debian/tests/non-default-params-test, but made more verbose
     debian/README.test
   * cme fix dpkg-copyright
 

debian/compat

-11

debian/control

@@ -4,19 +4,19 @@ Uploaders: Laszlo Kajan <lkajan@rostlab.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python
-Standards-Version: 4.2.1
+               python3
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/conservation-code
 Vcs-Git: https://salsa.debian.org/med-team/conservation-code.git
-Homepage: http://compbio.cs.princeton.edu/conservation/
+Homepage: https://compbio.cs.princeton.edu/conservation/
 
 Package: conservation-code
 Architecture: all
 Depends: ${misc:Depends},
-         ${python:Depends},
-         python-numpy
+         ${python3:Depends},
+         python3-numpy
 Enhances: concavity
 Description: protein sequence conservation scoring tool
  This package provides score_conservation(1), a tool to score protein sequence

debian/patches/series

@@ -7,3 +7,4 @@ stockholm_format
 Python3-prints
 usage
 fix_load_identity_matrix
+2to3.patch

debian/rules

@@ -15,7 +15,7 @@ pkgdatadir:=${datarootdir}/$(DEB_SOURCE)
 
 
 %:
-	dh $@ --with python2
+	dh $@ --with python3
 
 override_dh_auto_build: $(MANS)
 
@@ -37,19 +37,3 @@ override_dh_auto_clean:
 	rm -f $(MANS) ChangeLog
 
 # Policy §4.9 says that the get-orig-source target 'may be invoked in any directory'. So we do not use variables set from dpkg-parsechangelog.
-get-orig-source:
-	set -e; \
-	if ! ( which xz >/dev/null ); then \
-		echo "Could not find 'xz' tool for compression. Please install the package 'xz-utils'." >&2; \
-		exit 1; \
-	fi ; \
-	t=$$(mktemp -d) || exit 1; \
-	trap "rm -rf -- '$$t'" EXIT; \
-	( cd "$$t"; \
-		wget -O conservation-code_20110309.0.orig.tar.gz http://compbio.cs.princeton.edu/conservation/conservation_code.tar.gz; \
-		gunzip *.tar.gz; \
-		tar --owner=root --group=root --mode=a+rX --delete -f *.tar --wildcards '*/._*'; \
-		xz --best *.tar; \
-	); \
-	mv $$t/*.tar.?z ./
-

debian/tests/installation-test

@@ -6,12 +6,12 @@ set -e
 
 pkg=conservation-code
 
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
 
 cp -a /usr/share/doc/${pkg}/examples/* .
 

debian/tests/non-default-params-test

@@ -6,12 +6,12 @@ set -e
 
 pkg=conservation-code
 
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
 
 cp -a /usr/share/doc/${pkg}/examples/* .
 

debian/upstream/metadata

-Name: conservation-code
-Contact: Tony Capra <http://compbio.cs.princeton.edu/conservation/>
 Reference:
- - Author: John A. Capra and Mona Singh
-   Title: Predicting functionally important residues from sequence conservation
-   Journal: Bioinformatics
-   Volume: 23
-   Number: 15
-   Pages: 1875-82
-   Year: 2007
-   URL: http://bioinformatics.oxfordjournals.org/content/23/15/1875.full
-   DOI: 10.1093/bioinformatics/btm270
-   PMID: 17519246
+- Author: John A. Capra and Mona Singh
+  Title: Predicting functionally important residues from sequence conservation
+  Journal: Bioinformatics
+  Volume: 23
+  Number: 15
+  Pages: 1875-82
+  Year: 2007
+  URL: http://bioinformatics.oxfordjournals.org/content/23/15/1875.full
+  DOI: 10.1093/bioinformatics/btm270
+  PMID: 17519246
 Registry:
- - Name: OMICtools
-   Entry: OMICS_06943
- - Name: SciCrunch
-   Entry: NA
- - Name: bio.tools
-   Entry: NA
+- Name: OMICtools
+  Entry: OMICS_06943
+- Name: SciCrunch
+  Entry: NA
+- Name: bio.tools
+  Entry: NA