[med-svn] [Git][med-team/pdb2pqr][master] 6 commits: Documentation build depends on python3-sphinx.
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Thu Mar 3 07:40:17 GMT 2022
Andrius Merkys pushed to branch master at Debian Med / pdb2pqr
Commits:
cd5f61c3 by Andrius Merkys at 2022-03-01T08:40:16-05:00
Documentation build depends on python3-sphinx.
- - - - -
9abd4c97 by Andrius Merkys at 2022-03-02T09:12:54-05:00
python3-pdbx is needed to build docs.
- - - - -
7fb36a2c by Andrius Merkys at 2022-03-02T09:14:55-05:00
Documentation build depends on python3-sphinx-rtd-theme.
- - - - -
d88070cc by Andrius Merkys at 2022-03-03T02:11:23-05:00
Removing no longer relevant comment from debian/tests/pdb2pka-test.
- - - - -
874da493 by Andrius Merkys at 2022-03-03T02:25:54-05:00
Updating debian/README.test.
- - - - -
2be98be2 by Andrius Merkys at 2022-03-03T02:39:57-05:00
Updating debian/changelog.
- - - - -
4 changed files:
- debian/README.test
- debian/changelog
- debian/control
- debian/tests/pdb2pka-test
Changes:
=====================================
debian/README.test
=====================================
@@ -1,17 +1,12 @@
-Notes on how this package can be tested.
-────────────────────────────────────────
+Notes on how this package can be tested
+───────────────────────────────────────
This package can be tested by executing
- sh installation-test
+ sh installation-test pdb2pka-test
in order to confirm its integrity.
-If you have both pdb2pqr and pdb2pqr-doc packages installed, you can test their
-installation by executing
-
- sh ligands-test
-
During data processing, pdb2pqr can write multiple warning messages to stderr.
This output means that PDB file contains erranous data, which could be repaired
by pdb2pqr. In `installation-test` and other test scripts these messages should
@@ -29,49 +24,15 @@ Possible PDB IDs can be found in RCSB PDB database [1] and other sources.
To see other options, call `pdb2pqr` without parameters or with `-h` key..
-Notes on PDB2PKA-test
-───────────────────────
-
-For now this test is turned off:
-
- sh pdb2pka-test
-
-It requires `apbs` package with python support to see any sensible results.
-For now current version of `apbs` package doesn't seem to install apbs with
-corresponding headers.
-
-When --ph-calc-method=pdb2pka is used during `pdb2pqr` run, package requires
-python `networkx` library to be installed. Test `pdb2pka-test` passes only if
-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
-
-- tail of program's output look like this:
-
- Missing libraries for interfacing with APBS
- You need to build APBS with Python support using the CMake variable
- -DENABLE_PYTHON=ON.
-
-- even if `apbs` is compiled and installed with -DENABLE_PYTHON flag.
-This output message indicates that command
-
- python -c "from apbslib import *"
-
-- raised python's ImportError.
-
-How to use APBS with PDB2PQR anyway
-───────────────────────────────────
+How to use APBS with PDB2PQR
+────────────────────────────
-1. Call pdb2pqr with --apbs-input flag (since pdb2pka doesn't work,
---ph-calc-method=propka must be used, other arguments can vary) [2]:
+1. Call pdb2pqr with --apbs-input flag:
- pdb2pqr.py --ff PARSE --apbs-input --ph-calc-method=propka 1FAS 1FAS.pqr
+ pdb2pqr --ff PARSE --apbs-input 1FAS 1FAS.pqr
-- this example call produces file `1FAS.in`, which contains valid input data
-for `apbs`. Then call [3]:
+This example call produces file `1FAS.in`, which contains valid input data
+for `apbs`. Then call [2]:
apbs 1FAS.in
@@ -82,7 +43,5 @@ References:
[1]: RCSB PDB database (one of the possible sources of .pdb files)
http://www.rcsb.org/pdb/home/home.do
-[2]: PDB2PQR options
- http://www.poissonboltzmann.org/docs/pdb2pqr-usage/
-[3]: Examples of apbs usage:
+[2]: Examples of apbs usage:
http://www.poissonboltzmann.org/docs/apbs-invocation/
=====================================
debian/changelog
=====================================
@@ -1,7 +1,13 @@
pdb2pqr (3.5.2+dfsg-1) UNRELEASED; urgency=medium
+ * Team upload.
* New upstream version 3.5.2+dfsg (Closes: #1005971)
- * Updating Files-Excluded in debian/copyright.
+ * New binary package for Python3 module.
+ * Propka is no longer provided (separate source package now).
+ * Update Files-Excluded in debian/copyright.
+ * Ignore tests requiring network access.
+ * Update patches, debian/copyright and debian/README.test.
+ * Drop debian/README.Debian: not needed any more.
-- Andrius Merkys <merkys at debian.org> Fri, 18 Feb 2022 05:52:25 -0500
=====================================
debian/control
=====================================
@@ -11,10 +11,12 @@ Build-Depends: debhelper-compat (= 12),
help2man,
python3-dev,
python3-numpy,
+ python3-pdbx,
python3-pandas <!nocheck>,
python3-propka <!nocheck>,
python3-pytest <!nocheck>,
python3-setuptools,
+ python3-sphinx-rtd-theme,
python3-testfixtures <!nocheck>
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/pdb2pqr
=====================================
debian/tests/pdb2pka-test
=====================================
@@ -24,6 +24,3 @@ done
echo "Run pdb2pqr..."
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.
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/-/compare/d5ad46aee12351b00d8a814c334035990c27f9a9...2be98be2085d68aceecbf7a0efa0361c402f1a7c
--
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/-/compare/d5ad46aee12351b00d8a814c334035990c27f9a9...2be98be2085d68aceecbf7a0efa0361c402f1a7c
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