A first trial of a test for obicount

Makefile

@@ -63,6 +63,11 @@ update-deps:
 
 test:
 	$(GOTEST) ./...
+
+obitests:
+	for t in $$(find obitests -name test.sh -print) ; do \
+		$(SHELL) $${t} ; \
+	done
 	
 man: 
 	make -C doc man
@@ -97,5 +102,5 @@ ifneq ($(strip $(COMMIT_ID)),)
 	@rm -f $(OUTPUT)
 endif
 
-.PHONY: all packages obitools man obibook doc update-deps .FORCE
+.PHONY: all packages obitools man obibook doc update-deps obitests .FORCE
 .FORCE:

obitests/obitools/obicount/test.sh

@@ -0,0 +1,120 @@
+#!/bin/bash -e
+
+#
+# Here give the name of the test serie
+#
+TEST_NAME=obicount
+
+######
+#
+# Some variable and function definitions: please don't change them
+#
+######
+
+TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
+OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
+export PATH="${OBITOOLS_DIR}:${PATH}"
+
+
+TMPDIR="$(mktemp -d)"
+ntest=0
+success=0
+failed=0
+
+cleanup() {
+    echo "========================================" 1>&2
+    echo "## Results of the $TEST_NAME tests:" 1>&2
+
+    echo 1>&2
+    echo "- $ntest tests run" 1>&2
+    echo "- $success successfully completed" 1>&2
+    echo "- $failed failed tests" 1>&2
+    echo 1>&2
+    echo "Cleaning up the temporary directory..." 1>&2
+    echo 1>&2
+    echo "========================================" 1>&2
+
+    rm -rf "$TMPDIR"  # Suppress the temporary directory
+}
+
+log() {
+    echo "[$TEST_NAME @ $(date)] $*" 1>&2
+}
+
+trap cleanup EXIT ERR SIGINT SIGTERM
+
+echo "Testing $TEST_NAME..." 1>&2
+
+
+#################################################
+####
+#### Below are the tests
+####
+#### Before each test :
+####  - increment the variable ntest
+####
+#### Run the command as the condition of a if / then /else
+####
+#### then clause is executed on success of the command
+####  - Write a success message using the log function
+####  - increment the variable success
+####
+#### else clause is executed on failure of the command
+####  - Write a failure message using the log function
+####  - increment the variable failed
+####
+#################################################
+
+((ntest++))
+if obicount "${TEST_DIR}/wolf_F.fasta.gz" \
+    > "${TMPDIR}/wolf_F.fasta_count.csv" ; then
+    log "OBICount: fasta reading OK" 
+    ((success++))
+else
+    log "OBICount: fasta reading failed" 
+    ((failed++))
+fi
+
+((ntest++))
+if obicount "${TEST_DIR}/wolf_F.fastq.gz" \
+    > "${TMPDIR}/wolf_F.fastq_count.csv"
+then
+    log "OBICount: fastq reading OK"
+    ((success++))
+else
+    log "OBICount: fastq reading failed" 
+    ((failed++))
+fi
+
+((ntest++))
+if obicount "${TEST_DIR}/wolf_F.csv.gz" \
+    > "${TMPDIR}/wolf_F.csv_count.csv"
+then
+    log "OBICount: csv reading OK" 
+    ((success++))
+else
+    log "OBICount: csv reading failed"
+    ((failed++))
+fi
+
+((ntest++))
+if diff "${TMPDIR}/wolf_F.fasta_count.csv" \
+    "${TMPDIR}/wolf_F.fastq_count.csv"  > /dev/null
+then
+    log "OBICount: counting on fasta and fastq are identical OK"
+    ((success++))
+else
+    log "OBICount: counting on fasta and fastq are different failed"
+    ((failed++))
+fi
+
+((ntest++))
+if diff "${TMPDIR}/wolf_F.fasta_count.csv" \
+    "${TMPDIR}/wolf_F.csv_count.csv" > /dev/null
+then
+    log "OBICount: counting on fasta and csv are identical OK"
+    ((success++))
+else
+    log "OBICount: counting on fasta and csv are different failed"
+    ((failed++))
+fi

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "6a8061c"
+var _Commit = "4774438"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.