[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
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/compare/b2177025e88006b17d68bc6636f6b06a037ba24c...f3f79c56ccccd6a55763bea792cf0537e7d0ad92
--
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/compare/b2177025e88006b17d68bc6636f6b06a037ba24c...f3f79c56ccccd6a55763bea792cf0537e7d0ad92
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