debian/changelog

+pdb2pqr (2.1.1+dfsg-6) UNRELEASED; urgency=medium
+
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #937262
+  * Re-activate other part of autopkgtest
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/control
+  * Remove trailing whitespace in debian/copyright
+  * Remove obsolete field Name from debian/upstream/metadata.
+  * Use Debian packaged scons
+  TODO:
+      scons: Building targets ...
+      CopySubAction("pdb2pqr.py", "pdb2pqr.py.in")
+      scons: *** [pdb2pqr.py] TypeError : a bytes-like object is required, not 'str'
+      Traceback (most recent call last):
+        File "/usr/lib/scons/SCons/Action.py", line 1209, in execute
+          result = self.execfunction(target=target, source=rsources, env=env)
+        File "/usr/lib/scons/SCons/Action.py", line 1371, in __call__
+          return self.parent.actfunc(*args, **kw)
+        File "./site_scons/site_init.py", line 123, in CopySubAction
+          contents = contents.replace(k, v)
+      TypeError: a bytes-like object is required, not 'str'
+      scons: building terminated because of errors.
+
+ -- Andreas Tille <tille@debian.org>  Thu, 12 Dec 2019 15:41:47 +0100
+
 pdb2pqr (2.1.1+dfsg-5) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11

debian/control

@@ -5,17 +5,17 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
                gfortran,
                swig,
                xmlto,
                openbabel,
-               python-dev,
-               python-numpy,
-               scons,
+               python3-dev,
+               python3-numpy,
+               scons (>= 3.1.1-4),
                dos2unix
-Standards-Version: 4.1.5
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/pdb2pqr
 Vcs-Git: https://salsa.debian.org/med-team/pdb2pqr.git
 Homepage: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
@@ -24,9 +24,9 @@ Package: pdb2pqr
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${python:Depends},
-         python-numpy,
-         python-networkx
+         ${python3:Depends},
+         python3-numpy,
+         python3-networkx
 Suggests: apbs
 Enhances: autodocktools
 Provides: propka

debian/patches/series

@@ -4,3 +4,4 @@ do_not_try_to_build_removed_js_target.patch
 fix_hardening_no_relro
 fix_no_debug_symbols_warning
 spelling.patch
+2to3.patch

debian/rules

@@ -10,7 +10,7 @@ export DEB_CXXFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/includ
 export DEB_FFLAGS_MAINT_APPEND   = -fPIC
 
 %:
-	dh $@ --with python2
+	dh $@ --with python3
 
 override_dh_auto_clean:
 	( cd pdb2pka && \
@@ -28,7 +28,7 @@ override_dh_auto_configure:
 	  cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \
 	  cp -a pMC_mult.py pMC_mult.py.saved && \
 	  swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i )
-	python scons/scons.py \
+	scons \
 		URL="http://localhost/pdb2pqr/" \
 		PREFIX="/usr/share/pdb2pqr"
 

debian/tests/pdb2pka-test

@@ -2,20 +2,21 @@
 # autopkgtest check: build and run with default test data
 # Author: Tatiana Malygina <merlettaia@gmail.com>
 
-echo "This test is skipped since apbs Python support does not work"
-exit 0
+#  Hmmm, lets see, whether this might work with our 2to3 Python3 port
+# echo "This test is skipped since apbs Python support does not work"
+# exit 0
 
 set -e
 
 pkg=pdb2pqr
 example_pkg=pdb2pqr
 
-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/${example_pkg}/examples/* .
 find . -type f -name "*.gz" -exec gunzip \{\} \;

debian/tests/todo

+
+
+
+python3 scons/scons.py basic-test    # for a basic functionality test
+python3 scons/scons.py advanced-test # for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled
+python3 scons/scons.py complete-test # for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled
+python3 scons/scons.py pdb2pka-test

debian/upstream/metadata

-Name: PDB2PQR
-Registration: "http://spreadsheets.google.com/viewform?\
- hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA.."
+Registration: "http://spreadsheets.google.com/viewform?hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA.."
 Reference:
 - Author: >
     Todd J Dolinsky and Paul Czodrowski and Hui Li and Jens E Nielsen