[med-svn] [Git][med-team/pdb2pqr][master] 4 commits: Adding an autopkgtest for propka.

Andrius Merkys (@merkys) gitlab at salsa.debian.org
Thu Feb 10 14:54:40 GMT 2022 


Andrius Merkys pushed to branch master at Debian Med / pdb2pqr


Commits:
e3b11bd9 by Andrius Merkys at 2022-02-10T09:06:33-05:00
Adding an autopkgtest for propka.

- - - - -
b03dc598 by Andrius Merkys at 2022-02-10T09:19:32-05:00
Fixing Python problem causing crashes in propka.

- - - - -
3dd206d1 by Andrius Merkys at 2022-02-10T09:28:18-05:00
Source moved to GitHub.

- - - - -
f24d47ad by Andrius Merkys at 2022-02-10T09:29:11-05:00
Update changelog for 2.1.1+dfsg-8 release

- - - - -


6 changed files:

- debian/changelog
- debian/control
- debian/patches/python3_sundry.patch
- debian/tests/control
- + debian/tests/propka-test
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+pdb2pqr (2.1.1+dfsg-8) unstable; urgency=medium
+
+  * Team upload.
+  * Add an autopkgtest for propka.
+  * Fix Python problem causing crashes in propka.
+  * Source moved to GitHub.
+
+ -- Andrius Merkys <merkys at debian.org>  Thu, 10 Feb 2022 09:28:48 -0500
+
 pdb2pqr (2.1.1+dfsg-7) unstable; urgency=medium
 
   [ Chris Lamb ]


=====================================
debian/control
=====================================
@@ -19,7 +19,7 @@ Build-Depends: debhelper-compat (= 12),
 Standards-Version: 4.5.0
 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
+Homepage: https://www.poissonboltzmann.org
 Rules-Requires-Root: no
 
 Package: pdb2pqr


=====================================
debian/patches/python3_sundry.patch
=====================================
@@ -4298,17 +4298,6 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
  
          self.name             = "Nov30"
          self.Nmin             =  280
---- a/propka30/compare.py
-+++ b/propka30/compare.py
-@@ -39,7 +39,7 @@
- 
- import math
- #import data
--from Source.lib import pka_print
-+from .Source.lib import pka_print
- 
- if False:
-     def compareWithExperiment(protein, file=None, list=None, set=None, label="ALL", **argv):
 --- a/propka30/experiment.py
 +++ b/propka30/experiment.py
 @@ -1,4 +1,4 @@
@@ -4317,15 +4306,6 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
  #
  # * This library is free software; you can redistribute it and/or
  # * modify it under the terms of the GNU Lesser General Public
-@@ -40,7 +40,7 @@
- 
-  
- import string, sys, copy, math
--from Source.lib import pka_print
-+from .Source.lib import pka_print
- 
- 
- def getCatchAllCompareWithExperiment(argv):
 --- a/propka30/propka.py
 +++ b/propka30/propka.py
 @@ -1,4 +1,4 @@
@@ -4334,17 +4314,15 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
  #
  # * This library is free software; you can redistribute it and/or
  # * modify it under the terms of the GNU Lesser General Public
-@@ -41,8 +41,8 @@
+@@ -41,7 +41,7 @@
  
  import string, re, sys, os, math
  
 -import Source.lib as lib
--from Source.protein import Protein
-+from .Source import lib
-+from .Source.protein import Protein
++from Source import lib
+ from Source.protein import Protein
   
  
- 
 --- a/propka30/propka_det.py
 +++ b/propka30/propka_det.py
 @@ -1,4 +1,4 @@
@@ -4353,21 +4331,17 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
  #
  # * This library is free software; you can redistribute it and/or
  # * modify it under the terms of the GNU Lesser General Public
-@@ -39,10 +39,10 @@
+@@ -39,8 +39,8 @@
  #-------------------------------------------------------------------------------------------------------
  
  import string, re, sys, os, math
 -import Source.version as propka
 -import Source.lib as lib
--from Source.protein import Protein
--from Source.mutate import makeCompositeAtomsDictionary
-+from .Source import version as propka
-+from .Source import lib
-+from .Source.protein import Protein
-+from .Source.mutate import makeCompositeAtomsDictionary
++from Source import version as propka
++from Source import lib
+ from Source.protein import Protein
+ from Source.mutate import makeCompositeAtomsDictionary
   
- 
- 
 --- a/propka30/propka_gui.py
 +++ b/propka30/propka_gui.py
 @@ -1,4 +1,4 @@
@@ -4376,21 +4350,17 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
  #
  # * This library is free software; you can redistribute it and/or
  # * modify it under the terms of the GNU Lesser General Public
-@@ -39,10 +39,10 @@
+@@ -39,8 +39,8 @@
  #-------------------------------------------------------------------------------------------------------
  
  import string, re, sys, os, math
 -import Source.version as propka
 -import Source.lib as lib
--from Source.protein import Protein
--from Source.mutate import makeCompositeAtomsDictionary
-+from .Source import version as propka
-+from .Source import lib
-+from .Source.protein import Protein
-+from .Source.mutate import makeCompositeAtomsDictionary
++from Source import version as propka
++from Source import lib
+ from Source.protein import Protein
+ from Source.mutate import makeCompositeAtomsDictionary
  pka_print = lib.pka_print
- 
- 
 --- a/propka30/propka_mut.py
 +++ b/propka30/propka_mut.py
 @@ -1,4 +1,4 @@
@@ -4405,14 +4375,12 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
  
 -import Source.lib as lib
 -import Source.mutate as mutate
--from Source.protein import Protein
--from Source.pdb import readPDB
++from Source import lib
++from Source import mutate
+ from Source.protein import Protein
+ from Source.pdb import readPDB
 -import Source.version as propka
-+from .Source import lib
-+from .Source import mutate
-+from .Source.protein import Protein
-+from .Source.pdb import readPDB
-+from .Source import version as propka
++from Source import version as propka
  pka_print = lib.pka_print
  
  
@@ -4424,17 +4392,15 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
  #
  # * This library is free software; you can redistribute it and/or
  # * modify it under the terms of the GNU Lesser General Public
-@@ -40,8 +40,8 @@
+@@ -40,7 +40,7 @@
  
  import string, re, sys, os, math
  
 -import Source.lib as lib
--from Source.protein import Protein
-+from .Source import lib
-+from .Source.protein import Protein
++from Source import lib
+ from Source.protein import Protein
   
  
- 
 --- a/querystatus.py
 +++ b/querystatus.py
 @@ -9,7 +9,7 @@


=====================================
debian/tests/control
=====================================
@@ -5,3 +5,6 @@ Restrictions: allow-stderr
 Tests: pdb2pka-test
 Depends: @, python3-networkx
 Restrictions: allow-stderr
+
+Tests: propka-test
+Depends: @


=====================================
debian/tests/propka-test
=====================================
@@ -0,0 +1,6 @@
+#!/bin/sh
+
+TMP_DIR=$(mktemp --directory)
+cp examples/1a1p/1a1p.pdb ${TMP_DIR}
+cd ${TMP_DIR}
+propka 1a1p.pdb


=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
-version=3
-opts="repacksuffix=+dfsg,dversionmangle=s/[~+]dfsg[0-9]*//,uversionmangle=s/src-//,repack,compression=xz" \
-  http://sf.net/pdb2pqr/pdb2pqr-[src-]*(\d[\d.]+)\.tar\.gz
+version=4
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*@ARCHIVE_EXT@)%@PACKAGE at -$1%,repacksuffix=+dfsg,dversionmangle=s/[~+]dfsg[0-9]*//,repack,compression=xz" \
+ https://github.com/Electrostatics/pdb2pqr/tags \
+ (?:.*?/)?v?@ANY_VERSION@@ARCHIVE_EXT@



View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/-/compare/0495d695b3927e88ecef947a7f752adb07327e62...f24d47ad70988603f85bb178535a9f9fb07cea93

-- 
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/-/compare/0495d695b3927e88ecef947a7f752adb07327e62...f24d47ad70988603f85bb178535a9f9fb07cea93
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