[med-svn] [Git][med-team/pdb2pqr][master] 24 commits: Building and installing sphinx documentation.
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Tue Mar 1 13:36:47 GMT 2022
Andrius Merkys pushed to branch master at Debian Med / pdb2pqr
Commits:
ea8656d1 by Andrius Merkys at 2022-02-23T09:25:44-05:00
Building and installing sphinx documentation.
- - - - -
74cce4dc by Andrius Merkys at 2022-02-23T09:26:32-05:00
Dropping debian/wrapper.sh.
- - - - -
cca910bb by Andrius Merkys at 2022-02-23T09:28:40-05:00
Dropping obsolete dependency on pkg-config.
- - - - -
8ed3af40 by Andrius Merkys at 2022-02-23T09:31:40-05:00
No need to harden arch:all package.
- - - - -
19102336 by Andrius Merkys at 2022-02-23T09:32:15-05:00
No need for dos2unix anymore.
- - - - -
da5e61ff by Andrius Merkys at 2022-02-25T11:59:53-05:00
Adding license statement for pdb2pqr/dat/*.xml.
- - - - -
74f64b0c by Andrius Merkys at 2022-02-25T12:05:24-05:00
Updating debian/copyright.
- - - - -
00db8bdd by Andrius Merkys at 2022-02-25T12:06:01-05:00
Changing Source field in debian/copyright.
- - - - -
be5a15d1 by Andrius Merkys at 2022-02-25T12:13:13-05:00
Fixing debian/pdb2pqr-doc.doc-base.
- - - - -
c13adffc by Andrius Merkys at 2022-02-25T12:13:38-05:00
Dropping debian/pdb2pqr.docs (not much information).
- - - - -
c1453ad9 by Andrius Merkys at 2022-02-25T12:18:13-05:00
Installing only the exsisting tests in debian/docs.
- - - - -
f63b357a by Andrius Merkys at 2022-02-28T05:53:45-05:00
Removing propka autopkgtest as propka is no longer shipped by pdb2pqr.
- - - - -
dbffa2cf by Andrius Merkys at 2022-02-28T05:56:43-05:00
propka is no longer here.
- - - - -
4205c5ce by Andrius Merkys at 2022-02-28T06:54:07-05:00
Web service seems to be gone.
- - - - -
6ad59abd by Andrius Merkys at 2022-02-28T07:50:10-05:00
Removing fix-hashbangs.patch.
- - - - -
7ea4cc8e by Andrius Merkys at 2022-02-28T07:51:52-05:00
Removing patches dealing with hardening.
- - - - -
6c0cd0bc by Andrius Merkys at 2022-02-28T08:34:05-05:00
Dropping commented out reproducible-build.patch.
- - - - -
8e262e6d by Andrius Merkys at 2022-02-28T08:34:50-05:00
Dropping commented out do_not_try_to_build_removed_js_target.patch.
- - - - -
eeddf578 by Andrius Merkys at 2022-02-28T08:43:23-05:00
Adjusting autopkgtest and debian/README.test to CLI changes.
- - - - -
9f2ce8c0 by Andrius Merkys at 2022-02-28T08:50:06-05:00
pdb2pqr CLI options --ph-calc-method and --verbose are gone.
- - - - -
22752487 by Andrius Merkys at 2022-02-28T08:51:39-05:00
Dropping debian/README.Debian: not sure if relatable any more.
- - - - -
1972562c by Andrius Merkys at 2022-02-28T09:06:04-05:00
Running autopkgtest with pytest-3.
- - - - -
5b1dfd61 by Andrius Merkys at 2022-02-28T09:10:08-05:00
python3-networkx is not needed.
- - - - -
d5ad46ae by Andrius Merkys at 2022-02-28T09:16:51-05:00
Build depends on python3-setuptools.
- - - - -
20 changed files:
- − debian/README.Debian
- debian/README.test
- debian/control
- debian/copyright
- debian/docs
- − debian/patches/do_not_try_to_build_removed_js_target.patch
- − debian/patches/fix-hashbangs.patch
- − debian/patches/fix_hardening_no_relro
- − debian/patches/fix_no_debug_symbols_warning
- − debian/patches/reproducible-build.patch
- debian/patches/series
- − debian/patches/use_pkg-config.patch
- debian/pdb2pqr-doc.doc-base
- − debian/pdb2pqr.docs
- debian/rules
- debian/tests/control
- debian/tests/installation-test
- debian/tests/pdb2pka-test
- − debian/tests/propka-test
- − debian/wrapper.sh
Changes:
=====================================
debian/README.Debian deleted
=====================================
@@ -1,26 +0,0 @@
-PDB2PKA
-=======
-
-For now PDB2PQR doesn't produce any results with PDB2PKA, since it requires
-specific versions of `apbs` package. It works only if `apbs` installed and command
-`python -c "from apbslib import *"` doesn't produce error.
-
- -- Tatiana Malygina Mon, 4 Jul 2016 18:49:01 +0300
-
-PROPKA
-======
-
-PDB2PQR can use PROPKA to protonate the structure it converts. PROPKA is
-packaged along with the PDB2PQR in this package.
-
- -- Manuel Prinz Thu, 21 Jun 2012 15:57:01 +0200
-
-
-Web Service
-===========
-
-The Debian package of PDB2PQR currently does not provide the parts that are
-necessary to run PDB2PQR as a web service. If you think that the PDB2PQR
-web service should be available as a package, please file a wishlist bug..
-
- -- Manuel Prinz Sat, 29 Jan 2011 22:53:19 +0100
=====================================
debian/README.test
=====================================
@@ -22,7 +22,7 @@ To test manually, run `pdb2pqr` like this (program output will be saved to
`output.txt` in current directory):
```
-pdb2pqr --ff=amber <valid PDB ID> output.txt
+pdb2pqr --ff AMBER <valid PDB ID> output.txt
```
Possible PDB IDs can be found in RCSB PDB database [1] and other sources..
@@ -47,7 +47,7 @@ this library is installed, otherwise it fails with corresponding error message.
It doesn't fail because of `apbs` installation, but it also doesn't produce any
sensible results. When `pdb2pqr` is run like this:
- pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff=parse --verbose 1a1p 1a1p.pqr
+ pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff PARSE --verbose 1a1p 1a1p.pqr
- tail of program's output look like this:
@@ -68,7 +68,7 @@ How to use APBS with PDB2PQR anyway
1. Call pdb2pqr with --apbs-input flag (since pdb2pka doesn't work,
--ph-calc-method=propka must be used, other arguments can vary) [2]:
- pdb2pqr.py --ff=parse --apbs-input --ph-calc-method=propka 1FAS 1FAS.pqr
+ pdb2pqr.py --ff PARSE --apbs-input --ph-calc-method=propka 1FAS 1FAS.pqr
- this example call produces file `1FAS.in`, which contains valid input data
for `apbs`. Then call [3]:
=====================================
debian/control
=====================================
@@ -14,9 +14,8 @@ Build-Depends: debhelper-compat (= 12),
python3-pandas <!nocheck>,
python3-propka <!nocheck>,
python3-pytest <!nocheck>,
- python3-testfixtures <!nocheck>,
- dos2unix,
- pkg-config
+ python3-setuptools,
+ python3-testfixtures <!nocheck>
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/pdb2pqr
Vcs-Git: https://salsa.debian.org/med-team/pdb2pqr.git
@@ -26,7 +25,6 @@ Rules-Requires-Root: no
Package: pdb2pqr
Architecture: all
Depends: python3-numpy,
- python3-networkx,
python3-pdb2pqr,
${misc:Depends},
${python3:Depends}
@@ -47,7 +45,8 @@ Package: pdb2pqr-doc
Architecture: all
Multi-Arch: foreign
Section: doc
-Depends: ${misc:Depends}
+Depends: ${misc:Depends},
+ ${sphinxdoc:Depends}
Recommends: pdb2pqr
Description: example files accompanying pdb2pqr
Files containing protein structures tend to become large very quickly and
=====================================
debian/copyright
=====================================
@@ -1,89 +1,69 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: pdb2pqr
-Source: http://sourceforge.net/projects/pdb2pqr/
+Source: https://github.com/Electrostatics/pdb2pqr
Files-Excluded:
pdb2pka
site_scons
Files: *
-Copyright: © 2002-2010 Nathan A. Baker
- © 2009 Tommy Carstensen
- © 2004 becker
- © 2006 Mike Bradley
- © 1999-2004 Cambridge Crystallographic Data Centre
- © 2009 Tommy Carstensen
- © 2002-2010 Paul Czodrowski
- © 2005-2010 Todd Dolinsky
- © 2000 EMBL
- © 1992-2008 Free Software Foundation, Inc.
- © 1993 Noah Friedman <friedman at prep.ai.mit.edu>
- © 2010 Wes Goodman
- © David J. Heisterberg
- © 1994-2000 Michael Holst
- © 2007-2010 Yong Huang
- © 2004-2005 Hui Li
- © 2005,2010 Jan H. Jensen
- © 2000-2010 Gerhard Klebe
- © 2000-2004 Daniel Kuhn
- © 2010 Predrag Kukic (kukaq)
- © 2006 Jan Labanowski
- © 1991 Massachusetts Institute of Technology
- © 2007 Julie C. Mitchell
- © 2002-2010 Jens Erik Nielsen
- © The Ohio Supercomputer Center, Columbus
- © 2004 Philipps-University, Marburg
- © J. Ren
- © 2000-2004 Stefan Schmitt
- © 2008 Dave Sept
- © 2002-2003 UCSD/HHMI
- © 2003-2008 University College Dublin
- © 2007-2010 Samir Unni
- © 2004-2007 Washington University St. Louis
- © 2004 Nils Weskamp
-License: BSD3-clause
- All rights reserved.
- .
- Redistribution and use in source and binary forms, with or without modification,
- are permitted provided that the following conditions are met:
+Copyright: 2002-2020, Jens Erik Nielsen, University College Dublin
+ 2002-2020, Nathan A. Baker, Battelle Memorial Institute
+ 2002-2020, Paul Czodrowski & Gerhard Klebe, University of Marburg
+License: BSD-3-Clause
+Comment:
+ Developed at the Pacific Northwest National Laboratory, operated by Battelle
+ Memorial Institute, Pacific Northwest Division for the U.S. Department Energy.
+
+License: BSD-3-Clause
+ 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,
- 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
- 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
- specific prior written permission.
+ * 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
+ 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
+ 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
- OF THE POSSIBILITY OF SUCH DAMAGE.
+ 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: pdb2pqr/dat/AA.xml
+ pdb2pqr/dat/HYDROGENS.xml
+ pdb2pqr/dat/NA.xml
+ pdb2pqr/dat/PATCHES.xml
+ pdb2pqr/dat/TOPOLOGY.xml
+Copyright: 2002-2011, Jens Erik Nielsen, University College Dublin
+License: BSD-3-Clause
Files: debian/*
-Copyright: © 2007-2010 Steffen Moeller <moeller at debian.org>
- © 2010-2012 Manuel Prinz <manuel at debian.org>
- © 2013-2018 Andreas Tille <tille at debian.org>
+Copyright: 2007-2010, Steffen Moeller <moeller at debian.org>
+ 2010-2012, Manuel Prinz <manuel at debian.org>
+ 2013-2018, Andreas Tille <tille at debian.org>
+ 2022, Andrius Merkys <merkys at debian.org>
License: GPL-2+
License: GPL-2+
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Library General Public
- License as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later version.
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
.
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Library General Public License for more details.
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Library General Public License for more details.
.
- On Debian systems, the complete text of the GNU Library General Public License
- can be found in /usr/share/common-licenses/GPL-2.
-
+ On Debian systems, the complete text of the GNU Library General Public License
+ can be found in /usr/share/common-licenses/GPL-2.
=====================================
debian/docs
=====================================
@@ -1,4 +1,2 @@
debian/README.test
-debian/tests/installation-test
-debian/tests/ligands-test
-debian/tests/pdb2pka-test
+debian/tests/*-test
=====================================
debian/patches/do_not_try_to_build_removed_js_target.patch deleted
=====================================
@@ -1,19 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 08 Jan 2016 10:56:05 +0100
-Description: Since some minimised JS files without source were
- contained inside the upstream source which are not used in the
- resulting binary package these were removed from the source.
- This patch prevents the build system from accessing missing files.
-
---- a/SConscript-main.py
-+++ b/SConscript-main.py
-@@ -190,8 +190,7 @@ subFiles = [('pdb2pqr.py', 'pdb2pqr.py.i
- ('visualize.cgi', 'visualize.py', True),
- ('querystatus.cgi', 'querystatus.py', True),
- ('src/aconf.py', 'src/aconf.py.in', False),
-- ('html/server.html', 'html/server.html.in', False),
-- ('3dmol/js/3dmol.js', '3dmol/js/3dmol.js.in', False)]
-+ ('html/server.html', 'html/server.html.in', False)]
-
- compile_targets = []
-
=====================================
debian/patches/fix-hashbangs.patch deleted
=====================================
@@ -1,35 +0,0 @@
-Subject: Fixes "broken" hashbangs
-From: Manuel Prinz <manuel at debian.org>
-Last-Update: 2012-06-21
---- a/pdb2pka/inputgen_pKa.py
-+++ b/pdb2pka/inputgen_pKa.py
-@@ -1,4 +1,4 @@
--#!/bin/env python
-+#!/usr/bin/python
- #
- # $Id$
- #
---- a/propka30/Source/corresponding_atoms.py
-+++ b/propka30/Source/corresponding_atoms.py
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/python3.0
-+#!/usr/bin/python
-
- #
- # * This library is free software; you can redistribute it and/or
---- a/propka30/Source/rotate.py
-+++ b/propka30/Source/rotate.py
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/python3.0
-+#!/usr/bin/python
- #
- # * This library is free software; you can redistribute it and/or
- # * modify it under the terms of the GNU Lesser General Public
---- a/propka30/propka.py
-+++ b/propka30/propka.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python
- #
- # * This library is free software; you can redistribute it and/or
- # * modify it under the terms of the GNU Lesser General Public
=====================================
debian/patches/fix_hardening_no_relro deleted
=====================================
@@ -1,17 +0,0 @@
-Author: Tatiana Malygina <merlettaia at gmail.com>
-Last-Update: 2016-06-14
-Description: this fix prevents hardening-no-relro warning from appearing during
- lintian run
-
---- a/SConscript-main.py
-+++ b/SConscript-main.py
-@@ -100,6 +100,9 @@ if env['EXTRA_CXXFLAGS']:
- if env['EXTRA_LINKFLAGS']:
- env.Append(LINKFLAGS = [env['EXTRA_LINKFLAGS']])
-
-+if 'LDFLAGS' in os.environ:
-+ env.Append(LINKFLAGS = os.environ['LDFLAGS'])
-+
- if os.name == 'nt':
- #Check to see if we are running in a virtualenv
- if hasattr(sys, 'real_prefix'):
=====================================
debian/patches/fix_no_debug_symbols_warning deleted
=====================================
@@ -1,23 +0,0 @@
-Author: Tatiana Malygina <merlettaia at gmail.com>
-Last-Update: 2016-06-15
-Description: this fix prevents debug-file-with-no-debug-symbols warning from
-appearing during lintian run
-
---- a/build_config.py
-+++ b/build_config.py
-@@ -58,7 +58,7 @@
- #Set to True to build compiled extentions with debug headers.
- #Defaults to False
-
--#DEBUG=True
-+DEBUG=True
-
- #CXXFLAGS
- #Set to add extra CXX flags to the build.
-@@ -78,4 +78,4 @@
- # Requires swig on the the user path.
- # Defaults to False
-
--#REBUILD_SWIG=True
-\ No newline at end of file
-+#REBUILD_SWIG=True
=====================================
debian/patches/reproducible-build.patch deleted
=====================================
@@ -1,16 +0,0 @@
-Description: Make the build reproducible
-Author: Chris Lamb <lamby at debian.org>
-Last-Update: 2020-03-29
-Bug-Debian: https://bugs.debian.org/955287
-
---- a/src/aconf.py.in
-+++ b/src/aconf.py.in
-@@ -53,7 +53,7 @@ PDB2PQR_VERSION = "@PDB2PQR_VERSION@"
- MAXATOMS = @MAXATOMS@
-
- """ The absolute path to root HTML directory"""
--SRCPATH = "@srcpath@/"
-+SRCPATH = "/nonexistent"
-
- """ The path to the web site *directory* """
- WEBSITE = "@website@"
=====================================
debian/patches/series
=====================================
@@ -1,10 +1,4 @@
-#fix-hashbangs.patch
#no_privacy_breach_logo.patch
-#do_not_try_to_build_removed_js_target.patch
-#fix_hardening_no_relro
-#fix_no_debug_symbols_warning
#python3_PR516.patch
#python3_scriptbang.patch
-#use_pkg-config.patch
-#reproducible-build.patch
skip-network-tests.patch
=====================================
debian/patches/use_pkg-config.patch deleted
=====================================
@@ -1,16 +0,0 @@
-Description: Use pkg-config to correctly detect libpython3.7m
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
-
---- a/SConscript-main.py
-+++ b/SConscript-main.py
-@@ -81,7 +81,8 @@ env = Environment(variables=vars,
-
-
- python_lib = 'python' + gcv('VERSION')
--env.Append(LIBS=[python_lib])
-+env.ParseConfig('pkg-config --cflags --libs python3')
-+# env.Append(LIBS=[python_lib])
- #To get swig to work on windows.
- #env.Append(ENV={'PATH' : os.environ['PATH']})
-
=====================================
debian/pdb2pqr-doc.doc-base
=====================================
@@ -5,5 +5,5 @@ Abstract: This guide explains the use of PDB2PQR
Section: Science/Chemistry
Format: HTML
-Index: /usr/share/doc/pdb2pqr/userguide.html
-Files: /usr/share/doc/pdb2pqr/userguide.html
+Index: /usr/share/doc/pdb2pqr/html/index.html
+Files: /usr/share/doc/pdb2pqr/html/index.html
=====================================
debian/pdb2pqr.docs deleted
=====================================
@@ -1 +0,0 @@
-README*
=====================================
debian/rules
=====================================
@@ -2,14 +2,6 @@
include /usr/share/dpkg/pkg-info.mk
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-
-# Compile with -fPIC on all platforms (fix for #636204, #654240)
-export DEB_CFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
-export DEB_CPPFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
-export DEB_CXXFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
-export DEB_FFLAGS_MAINT_APPEND = -fPIC
-
# Prevent network access:
export http_proxy = 127.0.0.1:9
export https_proxy = 127.0.0.1:9
@@ -21,6 +13,10 @@ override_dh_auto_build:
dh_auto_build
PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html
+override_dh_installdocs:
+ dh_installdocs
+ dh_installdocs -p pdb2pqr-doc --doc-main-package pdb2pqr build/html
+
override_dh_installman:
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/dx2cube --no-info --version-string $(DEB_VERSION_UPSTREAM) > dx2cube.1
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/inputgen --no-info --version-string $(DEB_VERSION_UPSTREAM) > inputgen.1
=====================================
debian/tests/control
=====================================
@@ -3,8 +3,8 @@ Depends: pdb2pqr
Restrictions: allow-stderr
Tests: pdb2pka-test
-Depends: @, python3-networkx
+Depends: @,
Restrictions: allow-stderr
-Tests: propka-test
-Depends: @
+Test-Command: pytest-3
+Depends: @, python3-pytest
=====================================
debian/tests/installation-test
=====================================
@@ -5,5 +5,5 @@
set -e
echo "Run pdb2pqr..."
-pdb2pqr --ff=amber examples/1a1p/1a1p.pdb ${AUTOPKGTEST_TMP}/output.txt
-[ -s ${AUTOPKGTEST_TMP}/output.txt ]
+pdb2pqr --ff AMBER examples/1a1p/1a1p.pdb ${AUTOPKGTEST_TMP}/output.txt
+test -s ${AUTOPKGTEST_TMP}/output.txt
=====================================
debian/tests/pdb2pka-test
=====================================
@@ -23,7 +23,7 @@ done
echo "Run pdb2pqr..."
-pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff=parse --verbose 1a1p/1a1p.pdb 1a1p/1a1p.pqr
+pdb2pqr --with-ph 7.0 --ff PARSE 1a1p/1a1p.pdb 1a1p/1a1p.pqr
# error messages fixed, at my VM this still appears:
## Missing libraries for interfacing with APBS
## You need to build APBS with Python support using the CMake variable -DENABLE_PYTHON=ON.
=====================================
debian/tests/propka-test deleted
=====================================
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-TMP_DIR=$(mktemp --directory)
-cp examples/1a1p/1a1p.pdb ${TMP_DIR}
-cd ${TMP_DIR}
-propka 1a1p.pdb
=====================================
debian/wrapper.sh deleted
=====================================
@@ -1,8 +0,0 @@
-#!/bin/sh
-app=@SCRIPT@
-if [ -x $app ]; then
- $app $*
-else
- echo "No executable at '$app'."
- exit 64
-fi
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/-/compare/faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0...d5ad46aee12351b00d8a814c334035990c27f9a9
--
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/-/compare/faaa68ce8d5f63148a87d83e8b4ff5dbda8966a0...d5ad46aee12351b00d8a814c334035990c27f9a9
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