[med-svn] [Git][med-team/pdb2pqr][master] 13 commits: Re-activate other part of autopkgtest

Andreas Tille gitlab at salsa.debian.org
Thu Dec 12 18:14:54 GMT 2019



Andreas Tille pushed to branch master at Debian Med / pdb2pqr


Commits:
a5e59615 by Andreas Tille at 2019-12-12T14:42:51Z
Re-activate other part of autopkgtest

- - - - -
a19972b9 by Andreas Tille at 2019-12-12T15:07:27Z
Use 2to3 to port from Python2 to Python3

- - - - -
08c6271a by Andreas Tille at 2019-12-12T15:10:39Z
Python3 in packaging

- - - - -
4afcb08f by Andreas Tille at 2019-12-12T15:11:01Z
May be there are some more test options

- - - - -
ba914801 by Andreas Tille at 2019-12-12T15:11:28Z
routine-update: debhelper-compat 12

- - - - -
182a35fa by Andreas Tille at 2019-12-12T15:11:32Z
routine-update: Standards-Version: 4.4.1

- - - - -
832282bd by Andreas Tille at 2019-12-12T15:11:33Z
R-U: Trailing whitespace in debian/changelog

- - - - -
494315be by Andreas Tille at 2019-12-12T15:11:33Z
R-U: Trailing whitespace in debian/control

- - - - -
559225c6 by Andreas Tille at 2019-12-12T15:11:33Z
R-U: Trailing whitespace in debian/copyright

- - - - -
ab9d9355 by Andreas Tille at 2019-12-12T15:11:42Z
Remove obsolete field Name from debian/upstream/metadata.
- - - - -
a21fc819 by Andreas Tille at 2019-12-12T15:53:29Z
Test script was missing from 2to3 batch

- - - - -
06f020d5 by Andreas Tille at 2019-12-12T15:54:10Z
Use Debian packaged scons

- - - - -
f3f79c56 by Andreas Tille at 2019-12-12T15:55:24Z
Add TODO about build error - may be due to issues in scons?

- - - - -


10 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
- debian/tests/pdb2pka-test
- + debian/tests/todo
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,31 @@
+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 at debian.org>  Thu, 12 Dec 2019 15:41:47 +0100
+
 pdb2pqr (2.1.1+dfsg-5) unstable; urgency=medium
 
   * Team upload.
@@ -49,7 +77,7 @@ pdb2pqr (2.1.1+dfsg-2) unstable; urgency=medium
   * add patch to remove hardening-no-relro warning
   * improved tests: add separate tests for use with pdb2pqr-doc installed and
     without it
-  * found parameter set when error raised (described in `pdb2pka-test` 
+  * found parameter set when error raised (described in `pdb2pka-test`
     in testsuite), updated d/docs
   * fixed `pdb2pqr-test` - now should work ok (haven't checked with apbs yet)
   * add patch to remove debug-file-with-no-debug-symbols warning (turn on debug)


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -5,17 +5,17 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
            Andreas Tille <tille at 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
@@ -44,7 +44,7 @@ Description: Preparation of protein structures for electrostatics calculations
  .
  This package also includes PropKa, a tool to modify the protonation state of
  protein structures in the Protein Data Bank (PDB) format to match a given pKa
- value. It can also be used to refine NMR structures, which often yield 
+ value. It can also be used to refine NMR structures, which often yield
  inaccurate pKa values for some residues.
 
 Package: pdb2pqr-doc


=====================================
debian/copyright
=====================================
@@ -47,28 +47,28 @@ Copyright: © 2002-2010  Nathan A. Baker
 License: BSD3-clause
     All rights reserved.
  .
-    Redistribution and use in source and binary forms, with or without modification, 
+    Redistribution and use in source and binary forms, with or without modification,
     are permitted provided that the following conditions are met:
  .
-        * Redistributions of source code must retain the above copyright notice, 
+        * Redistributions of source code must retain the above copyright notice,
           this list of conditions and the following disclaimer.
-        * Redistributions in binary form must reproduce the above copyright notice, 
-          this list of conditions and the following disclaimer in the documentation 
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
-        * Neither the names of University College Dublin, Washington University in 
-          St. Louis, or University of Marburg nor the names of its contributors may 
-          be used to endorse or promote products derived from this software without 
+        * Neither the names of University College Dublin, Washington University in
+          St. Louis, or University of Marburg nor the names of its contributors may
+          be used to endorse or promote products derived from this software without
           specific prior written permission.
  .
-    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-    IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-    INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
-    BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 
-    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
-    LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE 
-    OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+    IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+    INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+    BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+    LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+    OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
     OF THE POSSIBILITY OF SUCH DAMAGE.
 
 Files: propka30/*


=====================================
debian/patches/2to3.patch
=====================================
The diff for this file was not included because it is too large.

=====================================
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 at 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
=====================================
@@ -0,0 +1,7 @@
+
+
+
+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
=====================================
@@ -1,51 +1,49 @@
-Name: PDB2PQR
-Registration: "http://spreadsheets.google.com/viewform?\
- hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA.."
+Registration: "http://spreadsheets.google.com/viewform?hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA.."
 Reference:
- - Author: >
+- Author: >
     Todd J Dolinsky and Paul Czodrowski and Hui Li and Jens E Nielsen
     and Jan H Jensen and Gerhard Klebe and Nathan A Baker
-   Title: >
+  Title: >
     PDB2PQR: Expanding and upgrading automated preparation of biomolecular
     structures for molecular simulations
-   Journal: Nucleic Acids Research
-   Year: 2007
-   Volume: 35
-   Pages: W522-5
-   DOI: 10.1093/nar/gkm276
-   PMID: 17488841
-   URL: http://nar.oxfordjournals.org/content/35/suppl_2/W522
-   eprint: http://nar.oxfordjournals.org/content/35/suppl_2/W522.full.pdf+html
- - Author: >
+  Journal: Nucleic Acids Research
+  Year: 2007
+  Volume: 35
+  Pages: W522-5
+  DOI: 10.1093/nar/gkm276
+  PMID: 17488841
+  URL: http://nar.oxfordjournals.org/content/35/suppl_2/W522
+  eprint: http://nar.oxfordjournals.org/content/35/suppl_2/W522.full.pdf+html
+- Author: >
     Todd J Dolinsky and Jens E Nielsen and J Andrew McCammon and Nathan A Baker
-   Title: >
+  Title: >
     PDB2PQR: an automated pipeline for the setup, execution, and analysis
     of Poisson-Boltzmann electrostatics calculations
-   Journal: Nucleic Acids Research
-   Year: 2004
-   Volume: 32
-   Pages: W665-W667
-   DOI: 10.1093/nar/gkh381
-   PMID: 15215472
-   URL: http://nar.oxfordjournals.org/content/32/suppl_2/W665.abstract
-   eprint: http://nar.oxfordjournals.org/content/32/suppl_2/W665.full.pdf+html
- - Debian-Package: propka
-   Author: Hui Li and Andrew D Robertson and Jan H Jensen
-   Title: >
+  Journal: Nucleic Acids Research
+  Year: 2004
+  Volume: 32
+  Pages: W665-W667
+  DOI: 10.1093/nar/gkh381
+  PMID: 15215472
+  URL: http://nar.oxfordjournals.org/content/32/suppl_2/W665.abstract
+  eprint: http://nar.oxfordjournals.org/content/32/suppl_2/W665.full.pdf+html
+- Debian-Package: propka
+  Author: Hui Li and Andrew D Robertson and Jan H Jensen
+  Title: >
     Very fast empirical prediction and rationalization of protein pKa values
-   Journal: Proteins
-   Year: 2005
-   Volume: 61
-   Number: 4
-   Pages: 704-21
-   DOI: 10.1002/prot.20660
-   PMID: 16231289
-   URL: http://onlinelibrary.wiley.com/doi/10.1002/prot.20660/abstract
-   eprint: http://onlinelibrary.wiley.com/doi/10.1002/prot.20660/pdf
+  Journal: Proteins
+  Year: 2005
+  Volume: 61
+  Number: 4
+  Pages: 704-21
+  DOI: 10.1002/prot.20660
+  PMID: 16231289
+  URL: http://onlinelibrary.wiley.com/doi/10.1002/prot.20660/abstract
+  eprint: http://onlinelibrary.wiley.com/doi/10.1002/prot.20660/pdf
 Registry:
- - Name: OMICtools
-   Entry: OMICS_14370
- - Name: bio.tools
-   Entry: NA
- - Name: RRID
-   Entry: NA
+- Name: OMICtools
+  Entry: OMICS_14370
+- Name: bio.tools
+  Entry: NA
+- Name: RRID
+  Entry: NA



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