Added -version switch

.github/workflows/deploy.yml

@@ -60,6 +60,9 @@ jobs:
     steps:
     - name: help
       run: ./kmer-db
+
+    - name: version
+      run: ./kmer-db -version
 
 ########################################################################################
   upload:

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: GitHub Actions CI
+name: Build and tests
 
 on:
   push:
@@ -54,8 +54,13 @@ jobs:
         path: ./
 
     - name: untar artifacts
-      run: |
-        tar -xf kmer-db.tar
+      run: tar -xf kmer-db.tar
+
+    - name: help
+      run: ./kmer-db
+
+    - name: version
+      run: ./kmer-db -version
 
     - name: build 
       run: |

.github/workflows/self-hosted.yml

@@ -83,8 +83,10 @@ jobs:
 
     steps:
     - name: help (${{matrix.compiler}}, ${{matrix.mode}})
-      run: | 
-       ${EXEC} ${{matrix.mode}} -help
+      run: ${EXEC} ${{matrix.mode}} -help
+
+    - name: run (${{matrix.compiler}})
+      run: ${EXEC} -version  
 
 
  ########################################################################################

README.md

@@ -1,7 +1,7 @@
 # Kmer-db
 [![GitHub downloads](https://img.shields.io/github/downloads/refresh-bio/kmer-db/total.svg?style=flag&label=GitHub%20downloads)](https://github.com/refresh-bio/kmer-db/releases)
 [![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/kmer-db.svg?style=flag&label=Bioconda%20downloads)](https://anaconda.org/bioconda/kmer-db)
-[![GitHub Actions CI](../../workflows/GitHub%20Actions%20CI/badge.svg)](../../actions/workflows/main.yml)
+[![Build and tests](../../workflows/Build%20and%20tests/badge.svg)](../../actions/workflows/main.yml)
 [![License](https://anaconda.org/bioconda/famsa/badges/license.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
 
 ![x86-64](https://img.shields.io/static/v1?label=%E2%80%8B&message=x86-64&color=yellow&logo=PCGamingWiki&logoColor=white)

src/main.cpp

@@ -23,9 +23,6 @@ int main(int argc, char **argv)
 {
 	Log::getInstance(Log::LEVEL_NORMAL).enable();
 
-	LOG_NORMAL << "Kmer-db version " << VERSION << " (" << DATE << ")" << endl
-		<< "S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018" << endl << endl;
-
 	Params params;
 
 	try {

src/params.cpp

@@ -1,5 +1,6 @@
 #include "params.h"
 #include "types.h"
+#include "version.h"
 
 #include <iostream>
 #include <stdexcept>
@@ -61,6 +62,13 @@ bool Params::parse(int argc, char** argv) {
 	std::vector<string> params(argc - 1);
 	std::transform(argv + 1, argv + argc, params.begin(), [](char* c)->string { return c; });
 
+	if (findSwitch(params, SWITCH_VERSION)) {
+		LOG_NORMAL << VERSION;
+		return false;
+	}
+
+	showHeader();
+
 	bool helpWanted = findSwitch(params, SWITCH_HELP);
 	if (params.size() == 0) {
 		// no arguments or -help switch already consumed
@@ -71,7 +79,7 @@ bool Params::parse(int argc, char** argv) {
 	mode = str2mode(params.front());
 	params.erase(params.begin());
 
-	if (helpWanted && params.size() == 0) {
+	if (helpWanted || params.size() == 0 || mode == Mode::unknown) {
 		// help for particular mode
 		showInstructions(mode);
 		return false;
@@ -116,7 +124,7 @@ bool Params::parse(int argc, char** argv) {
 			parse_minhash(params); break;
 		default:
 			showInstructions(mode);
-
+			return false;
 		}
 
 		// set default fration in minhash mode if not specified
@@ -130,6 +138,14 @@ bool Params::parse(int argc, char** argv) {
 	return true;
 }
 
+// *****************************************************************************************
+//
+void Params::showHeader() const {
+
+	LOG_NORMAL << "Kmer-db version " << VERSION << " (" << DATE << ")" << endl
+		<< "S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018" << endl << endl;
+}
+
 // *****************************************************************************************
 //
 void Params::showInstructions(Mode mode) const {

src/params.h

@@ -37,6 +37,7 @@ class Params {
 	const std::string MODE_DISTANCE = "distance";
 
 	const std::string SWITCH_HELP = "-help";
+	const std::string SWITCH_VERSION = "-version";
 	const std::string SWITCH_KMC_SAMPLES = "-from-kmers";
 	const std::string SWITCH_MINHASH_SAMPLES = "-from-minhash";
 	const std::string SWITCH_MULTISAMPLE_FASTA = "-multisample-fasta";
@@ -104,6 +105,8 @@ class Params {
 
 	void showInstructions(Mode mode) const;
 
+	void showHeader() const;
+
 
 	bool findSwitch(std::vector<std::string>& params, const std::string& name) const {
 		auto it = std::find(params.begin(), params.end(), name); // verbose mode

src/version.h

@@ -1,12 +1,15 @@
 #pragma once
 
-#define VERSION "2.2.2"
-#define DATE "04.10.2024"
+#define VERSION "2.2.3"
+#define DATE "21.10.2024"
 
 /* 
 
 Version history
 
+2.2.3 (21.10.2024)
+- Added `-version` switch.
+
 2.2.2 (04.10.2024)
 - Fixed bug with filtering/sampling in all2all variants and new2all always using 18 as a kmer length.