From d1f4b05920a499a0dc5517ff1afd6b9f3e9cc3dd Mon Sep 17 00:00:00 2001
From: Robert Edgar <robert@drive5.com>
Date: Sat, 26 Oct 2024 10:04:20 -0700
Subject: [PATCH] All tests passed on commit 32d9850, posting as v2.0

---
 .gitignore                    |  1 +
 test_results/success_list.txt |  1 +
 test_scripts/RUN_TESTS.bash   | 11 +++++++++++
 test_scripts/_run_tests.bash  | 10 +++++-----
 test_scripts/align.bash       |  2 +-
 test_scripts/columns.bash     | 10 +++++-----
 test_scripts/convert.bash     |  8 ++++----
 test_scripts/pdb2mega.bash    |  2 +-
 test_scripts/recompile.bash   |  9 +++++++++
 test_scripts/scop40.bash      |  6 +++---
 test_scripts/search.bash      |  8 ++++----
 11 files changed, 45 insertions(+), 23 deletions(-)
 create mode 100755 test_scripts/recompile.bash

diff --git a/.gitignore b/.gitignore
index da0ea57..4890e35 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,6 +20,7 @@ Makefiled
 tmp/
 tmp
 test_output/
+github_releases/
 
 # User-specific files
 *.rsuser
diff --git a/test_results/success_list.txt b/test_results/success_list.txt
index 9a60a25..9bec612 100644
--- a/test_results/success_list.txt
+++ b/test_results/success_list.txt
@@ -4,3 +4,4 @@ reseekv1.0.i86linux64[95c6b51]	2024-06-30/15:33:08
 reseekv1.0.i86linux64[7e7be2b]	2024-06-30/17:57:37
 reseekv1.1.i86linux64[4214cdc]	2024-08-19/15:36:10
 reseekv2.0.i86linux64[497cb73]	2024-10-24/17:12:16
+reseekv2.0.i86linux64[32d9850]	2024-10-26/09:57:22
diff --git a/test_scripts/RUN_TESTS.bash b/test_scripts/RUN_TESTS.bash
index 98d1185..642d004 100755
--- a/test_scripts/RUN_TESTS.bash
+++ b/test_scripts/RUN_TESTS.bash
@@ -5,6 +5,17 @@ if [ ! -s ./_run_tests.bash ] ; then
 	exit 1
 fi
 
+if [ x$1 == x ] ; then
+	./recompile.bash
+	export reseek=../bin/reseek
+else
+	if [ ! -x $1 ] ; then
+		echo Not executable $x
+		exit 1
+	fi
+	export reseek=$1
+fi
+
 ./_run_tests.bash
 
 if [ $? != 0 ] ; then
diff --git a/test_scripts/_run_tests.bash b/test_scripts/_run_tests.bash
index 9b46c5d..204c29a 100755
--- a/test_scripts/_run_tests.bash
+++ b/test_scripts/_run_tests.bash
@@ -4,10 +4,10 @@ echo
 echo _run_tests.bash
 echo
 
-cd ../src
-rm -rf o/ ../bin/reseek*
-./build_linux_x86.bash
-cd ../test_scripts
+if [ x$reseek == x ] ; then
+	echo "reseek not set"
+	exit 1
+fi
 
 rm -rf ../test_output
 mkdir ../test_output
@@ -16,7 +16,7 @@ mkdir -p ../test_results
 log=../test_output/TEST_LOG.txt
 
 date=`date "+%Y-%m-%d/%H:%M:%S"`
-ver=`../bin/reseek --version | tr -d ' \n\r'`
+ver=`$reseek --version | tr -d ' \n\r'`
 echo $date $ver STARTED >> $log
 git status >> $log
 
diff --git a/test_scripts/align.bash b/test_scripts/align.bash
index 7452e4c..04279cd 100755
--- a/test_scripts/align.bash
+++ b/test_scripts/align.bash
@@ -2,7 +2,7 @@
 
 cd ../test_output
 
-../bin/reseek \
+$reseek \
 	-search dir.bca \
 	-fast \
 	-aln all_vs_all.aln \
diff --git a/test_scripts/columns.bash b/test_scripts/columns.bash
index b65e30d..8d7e031 100755
--- a/test_scripts/columns.bash
+++ b/test_scripts/columns.bash
@@ -2,34 +2,34 @@
 
 cd ../test_output
 
-../bin/reseek \
+$reseek \
 	-search dir.bca \
 	-fast \
 	-output columns_default.tsv \
 	-log columns_default.log
 
-../bin/reseek \
+$reseek \
 	-search dir.bca \
 	-fast \
 	-columns evalue+query+target \
 	-output columns_same_as_default.tsv \
 	-log columns_same_as_default.log
 
-../bin/reseek \
+$reseek \
 	-search dir.bca \
 	-fast \
 	-columns std \
 	-output columns_std.tsv \
 	-log columns_std.log
 
-../bin/reseek \
+$reseek \
 	-search dir.bca \
 	-fast \
 	-columns query+target+qlo+qhi+ql+tlo+thi+tl+cigar+qrow+trow \
 	-output columns_local_rows.tsv \
 	-log columns_local_rows.log
 
-../bin/reseek \
+$reseek \
 	-search dir.bca \
 	-fast \
 	-columns query+target+qlo+qhi+ql+tlo+thi+tl+cigar+qrowg+trowg \
diff --git a/test_scripts/convert.bash b/test_scripts/convert.bash
index 18dc54c..d7fe310 100755
--- a/test_scripts/convert.bash
+++ b/test_scripts/convert.bash
@@ -6,7 +6,7 @@ cd ../test_output
 ls ../test_structures/* \
 	> test_structures.files
 
-../bin/reseek \
+$reseek \
 	-convert test_structures.files \
 	-fasta files.fa \
 	-cal files.cal \
@@ -14,7 +14,7 @@ ls ../test_structures/* \
 	-chainsep : \
 	-log convert_files.log
 
-../bin/reseek \
+$reseek \
 	-convert ../test_structures/ \
 	-fasta dir.fa \
 	-cal dir.cal \
@@ -26,7 +26,7 @@ function cvt() {
 	from=$1
 	opt=$2
 	to=$3
-	../bin/reseek \
+	$reseek \
 		-convert $from \
 		-$opt $to \
 		-log $to.log
@@ -39,7 +39,7 @@ cvt dir.bca cal cvt_dir_bca.cal
 rm -f scop40.cal*
 cp ../test_data/scop40.cal.gz .
 gunzip scop40.cal.gz
-../bin/reseek \
+$reseek \
 	-convert scop40.cal \
 	-minchainlength 5 \
 	-bca scop40.bca
diff --git a/test_scripts/pdb2mega.bash b/test_scripts/pdb2mega.bash
index 7a19ca2..32d47c3 100755
--- a/test_scripts/pdb2mega.bash
+++ b/test_scripts/pdb2mega.bash
@@ -2,7 +2,7 @@
 
 cd ../test_output
 
-../bin/reseek \
+$reseek \
 	-pdb2mega ../test_structures/4v40.cif \
 	-output ../test_output/4v40.mega \
 	-log pdb2mega.log
diff --git a/test_scripts/recompile.bash b/test_scripts/recompile.bash
new file mode 100755
index 0000000..0715cda
--- /dev/null
+++ b/test_scripts/recompile.bash
@@ -0,0 +1,9 @@
+#!/bin/bash -e
+
+echo
+echo recompile.bash
+echo
+
+cd ../src
+rm -rf o/ ../bin/reseek*
+./build_linux_x86.bash
diff --git a/test_scripts/scop40.bash b/test_scripts/scop40.bash
index d64c57f..5076d12 100755
--- a/test_scripts/scop40.bash
+++ b/test_scripts/scop40.bash
@@ -2,19 +2,19 @@
 
 cd ../test_output
 
-../bin/reseek \
+$reseek \
 	-search scop40.bca \
 	-output scop40-fast.tsv \
 	-fast \
 	-log scop40-fast.log
 
-../bin/reseek \
+$reseek \
 	-search scop40.bca \
 	-output scop40-sensitive.tsv \
 	-sensitive \
 	-log scop40-sensitive.log
 
-../bin/reseek \
+$reseek \
 	-search scop40.bca \
 	-output scop40-evalue1.tsv \
 	-fast \
diff --git a/test_scripts/search.bash b/test_scripts/search.bash
index d0906b7..b76f4a9 100755
--- a/test_scripts/search.bash
+++ b/test_scripts/search.bash
@@ -2,26 +2,26 @@
 
 cd ../test_output
 
-../bin/reseek \
+$reseek \
 	-search dir.bca \
 	-fast \
 	-output search_dir.bca.tsv \
 	-log search_dir_bca.log
 
-../bin/reseek \
+$reseek \
 	-search dir.cal \
 	-output search_dir.cal.tsv \
 	-fast \
 	-log search_dir_cal.log
 
-../bin/reseek \
+$reseek \
 	-search dir.cal \
 	-db dir.bca \
 	-output search_dir_cal_bca.tsv \
 	-fast \
 	-log search_dir_cal_bca.log
 
-../bin/reseek \
+$reseek \
 	-search dir.bca \
 	-db dir.cal \
 	-output search_dir_bca_cal.tsv \