prerelease.sh

#!/bin/bash

########## LICENCE ##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
# Software Foundation; either version 3 of the License, or (at your option) any
# later version.
#
# This program 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 Affero General Public License for more
# details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
########## LICENCE ##########

set -eu # exit on first error or undefined value in subtitution

# get current directory
INIT_DIR=`pwd`

rm -rf blib

# get location of this file
MY_PATH="`dirname \"$0\"`"              # relative
MY_PATH="`( cd \"$MY_PATH\" && pwd )`"  # absolutized and normalized
if [ -z "$MY_PATH" ] ; then
  # error; for some reason, the path is not accessible
  # to the script (e.g. permissions re-evaled after suid)
  echo Failed to determine location of script >2
  exit 1  # fail
fi
# change into the location of the script
cd $MY_PATH/perl

echo '### Running perl tests ###'

export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-select='^lib/*\.pm$',-ignore,'^t/'
rm -rf docs
mkdir -p docs/reports_text
prove -w -I lib t


echo '### Generating test/pod coverage reports ###'
# removed 'condition' from coverage as '||' 'or' doesn't work properly
cover -coverage branch,subroutine,pod -report_c0 50 -report_c1 85 -report_c2 100 -report html_basic reports -silent
cover -coverage branch,subroutine,pod -report text reports -silent > docs/reports_text/coverage.txt
rm -rf reports/structure perl.reports/digests reports/cover.13 reports/runs
cp reports/coverage.html reports/index.html
mv reports docs/reports_html
unset HARNESS_PERL_SWITCHES

echo '### Generating POD ###'
mkdir -p docs/pod_html
perl -MPod::Simple::HTMLBatch -e 'Pod::Simple::HTMLBatch::go' lib:bin docs/pod_html > /dev/null

echo '### Archiving docs folder ###'
tar cz -C $MY_PATH/perl -f docs.tar.gz docs

# generate manifest, and cleanup
echo '### Generating MANIFEST ###'
# delete incase any files are moved, the make target just adds stuff
rm -f MANIFEST
# cleanup things which could break the manifest
rm -rf install_tmp
perl Makefile.PL > /dev/null
make manifest &> /dev/null
rm -f Makefile MANIFEST.bak pm_to_blib

# change back to original dir
cd $INIT_DIR