ensure test_trtools.sh can be run with a dev install but explain the …

…caveats

test/cmdline_tests.sh

@@ -25,13 +25,15 @@ if [ $# -eq 0 ]; then
     # use default example location
     EXDATADIR="example-files"
     BEAGLEDIR="trtools/testsupport/sample_vcfs/beagle"
-elif (( $# != 2 )) ; then
-    echo "usage: cmdline_tests.sh {example_dir} {beagle_dir}" 2>&1
-    echo "Expected 2 arguments but recieved $#" 2>&1
+    BEAGLESCRIPT="scripts/trtools_prep_beagle_vcf.sh"
+elif (( $# != 3 )) ; then
+    echo "usage: cmdline_tests.sh {example_dir} {beagle_dir} {beagle_script}" 2>&1
+    echo "Expected 3 arguments but recieved $#" 2>&1
     exit 1
 else
     EXDATADIR=$1
     BEAGLEDIR=$2
+    BEAGLESCRIPT=$3
 fi
 
 TMPDIR=$(mktemp -d -t tmp-XXXXXXXXXX)
@@ -220,10 +222,10 @@ prep_beagle_out="$TMPDIR"/test_prep_beagle_vcf.vcf.gz
 ref_panel="$BEAGLEDIR"/1kg_snpstr_21_first_100k_first_50_annotated.vcf.gz
 imputed_vcf="$BEAGLEDIR"/1kg_snpstr_21_first_100k_second_50_STRs_imputed.vcf.gz
 
-runcmd_fail "trtools_prep_beagle_vcf.sh hipstr nonexistent.vcf.gz $imputed_vcf $prep_beagle_out"
-runcmd_fail "trtools_prep_beagle_vcf.sh hipstr $ref_panel nonexistent.vcf.gz $prep_beagle_out"
+runcmd_fail "$BEAGLESCRIPT hipstr nonexistent.vcf.gz $imputed_vcf $prep_beagle_out"
+runcmd_fail "$BEAGLESCRIPT hipstr $ref_panel nonexistent.vcf.gz $prep_beagle_out"
 
-trtools_prep_beagle_vcf.sh hipstr "$ref_panel" "$imputed_vcf" "$prep_beagle_out"
+$BEAGLESCRIPT hipstr "$ref_panel" "$imputed_vcf" "$prep_beagle_out"
 
 if ! [[ -f "$prep_beagle_out" ]] ; then
     echo "prep_beagle_vcf test didn't produce output file" >&2

trtools/testsupport/test_trtools.sh

@@ -3,6 +3,12 @@
 # Run the tests for an installed copy of trtools
 # If not already present, megabytes of test data will be downloaded before test running
 
+# If TRTools was installed normally, this script can be executed by simply running
+# 'test_trtools.sh' on the command line.
+# Otherwise, if TRTools was installed via poetry, you should run the command
+# 'poetry run trtools/testsupport/test_trtools.sh'. However, please note that this
+# script should not be used to test TRTools against any recent/unpublished changes.
+
 echo "Running test_trtools.sh"
 
 command -v git >/dev/null 2>&1 || { echo >&2 "git is not available, but is required for downloading the test data. Aborting."; exit 1; }
@@ -41,4 +47,4 @@ cd "$loc" || exit 1
 # run unit tests
 python -m pytest . -p trtools.testsupport.dataloader --datadir "$TMP"/trtools/testsupport
 # run command line tests
-$TMP/test/cmdline_tests.sh $TMP/example-files $TMP/trtools/testsupport/sample_vcfs/beagle
+$TMP/test/cmdline_tests.sh $TMP/example-files $TMP/trtools/testsupport/sample_vcfs/beagle $TMP/scripts/trtools_prep_beagle_vcf.sh