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commit 6252a5c1b8376a3302ba8b7ea1328ca951b6b1f5 Author: latticetower-guest <[email protected]> Date: Tue Jun 14 23:53:25 2016 +0300 fixes in testsuite: 1. removed examples for pdb2pqr (unnecessary) 2. split installation-test to 2 different files - to use with and without pdb2pqr-doc package 3. updated README.test --- debian/README.test | 13 +++++++++---- debian/examples | 1 - debian/tests/control | 4 ++++ debian/tests/installation-test | 26 -------------------------- debian/tests/ligands-test | 33 +++++++++++++++++++++++++++++++++ 5 files changed, 46 insertions(+), 31 deletions(-) diff --git a/debian/README.test b/debian/README.test index 9ab7270..915a3ad 100644 --- a/debian/README.test +++ b/debian/README.test @@ -6,11 +6,16 @@ This package can be tested by executing sh installation-test in order to confirm its integrity. -During data processing, package 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` script these messages should appear. -For this to be processed in autopkgtest testsuite, `allow-stderr` restriction +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 +appear. For this to be processed in autopkgtest testsuite, `allow-stderr` restriction is set. To test manually, run `pdb2pqr` like this (program output will be saved to diff --git a/debian/examples b/debian/examples deleted file mode 100644 index e39721e..0000000 --- a/debian/examples +++ /dev/null @@ -1 +0,0 @@ -examples/* diff --git a/debian/tests/control b/debian/tests/control index 8d154a1..2999c55 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -1,3 +1,7 @@ Tests: installation-test +Depends: pdb2pqr +Restrictions: allow-stderr + +Tests: ligands-test Depends: @ Restrictions: allow-stderr diff --git a/debian/tests/installation-test b/debian/tests/installation-test index 5c89640..d2b4791 100644 --- a/debian/tests/installation-test +++ b/debian/tests/installation-test @@ -13,32 +13,6 @@ fi cd $ADTTMP -cp -a /usr/share/doc/${pkg}/examples/* . -find . -type f -name "*.gz" -exec gunzip \{\} \; -for lnk in `find . -type l -name "*.gz"` ; do - ln -s `basename $(readlink $lnk) .gz` `echo $lnk | sed 's/\.gz$//'` - rm $lnk -done - echo "Run pdb2pqr..." pdb2pqr --ff=amber "1FAS" output.txt [ -s output.txt ] - -# following were adopted from fabfile.py, -# method "linux_bin_cross_platform_test": -pdb2pqr --ff=parse --verbose --ligand=ligands/LIG_1ABF.mol2 1ABF 1ABF.pqr - -## following fails (this call also present in fabfile.py): -# pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff=parse --verbose 1a1p 1a1p.pqr -## Traceback: -## Running PDB2PKA and applying at pH 7.00... -## Traceback (most recent call last): -## File "/usr/bin/pdb2pqr", line 62, in <module> -## mainCommand(sys.argv) -## File "/usr/share/pdb2pqr/main.py", line 740, in mainCommand -## include_old_header = options.include_header) -## File "/usr/share/pdb2pqr/main.py", line 341, in runPDB2PQR -## myRoutines.runPDB2PKA(ph, ff, pdblist, ligand, verbose, ph_calc_options) -## File "/usr/share/pdb2pqr/src/routines.py", line 1503, in runPDB2PKA -## import pka -## ImportError: No module named pka diff --git a/debian/tests/ligands-test b/debian/tests/ligands-test new file mode 100644 index 0000000..6703807 --- /dev/null +++ b/debian/tests/ligands-test @@ -0,0 +1,33 @@ +#!/bin/sh +# autopkgtest check: build and run with default test data +# Author: Tatiana Malygina <[email protected]> + +set -e + +pkg=pdb2pqr +example_pkg=pdb2pqr-doc + +if [ "$ADTTMP" = "" ] ; then + ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM +fi + +cd $ADTTMP + +cp -a /usr/share/doc/${example_pkg}/examples/* . +find . -type f -name "*.gz" -exec gunzip \{\} \; +for lnk in `find . -type l -name "*.gz"` ; do + ln -s `basename $(readlink $lnk) .gz` `echo $lnk | sed 's/\.gz$//'` + rm $lnk +done + +echo "Run pdb2pqr..." + +# following sample call was adopted from fabfile.py, +# method "linux_bin_cross_platform_test": +for pdb in 1ABF 1HPV 1HPX 1QBS 1XL5; do + echo "******** ${pdb} starting" + pdb2pqr --ff=parse --verbose --ligand="ligands/LIG_${pdb}.mol2" ${pdb} "${pdb}.pqr" + [ -s "${pdb}.pqr" ] + echo "******** ${pdb} done" +done -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pdb2pqr.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
