Added --version option

refresh-bio · Oct 22, 2024 · 7b109d4 · 7b109d4
1 parent d80c26a
commit 7b109d4
Show file tree

Hide file tree

Showing 7 changed files with 96 additions and 60 deletions.
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -67,6 +67,8 @@ jobs:
     steps:
     - name: help
       run: ./clusty
+    - name: version
+      run: ./clusty --version
 
 ########################################################################################
   upload:

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -64,10 +64,15 @@ jobs:
       with:
         name: executable-artifact-${{ matrix.machine }}
         path: ./
-
+        
     - name: untar artifacts
-      run: |
-        tar -xf clusty.tar
+      run: tar -xf clusty.tar
+
+    - name: help
+      run: ./clusty-${{matrix.compiler}}
+
+    - name: version
+      run: ./clusty-${{matrix.compiler}} --version
 
     - name: ${{matrix.algo}}, ${{matrix.threshold}} (with representatives, reordered columns)
       run: |

diff --git a/.github/workflows/self-hosted.yml b/.github/workflows/self-hosted.yml
@@ -74,6 +74,10 @@ jobs:
     runs-on: [self-hosted, clusty, '${{ matrix.machine }}']    
 
     steps:
+    - name: help
+      run:  ./clusty-${{matrix.compiler}}
+    - name: version
+      run:  ./clusty-${{matrix.compiler}} --version
     - name: ${{matrix.algo}} (no representatives, numeric ids, singletons in object file)
       run: |
         ./clusty-${{matrix.compiler}} --objects-file ./test/toy.ids.tsv --algo ${{matrix.algo}} --id-cols idx1 idx2 --distance-col tani --similarity --numeric-ids --min tani 0.95 ./test/toy.ani.tsv toy.${{matrix.algo}}.tsv

diff --git a/src/console.cpp b/src/console.cpp
@@ -29,23 +29,32 @@ using namespace std;
 bool Console::init(int argc, char** argv, Params& params) {
 	Log::getInstance(Log::LEVEL_NORMAL).enable();
 
-	LOG_NORMAL << "Clusty" << endl
-		<< "  version " << VERSION
-#ifdef GIT_COMMIT
-		<< "-" << TOSTRING(GIT_COMMIT)
-#endif
-		<< " (" << DATE << ")" << endl << endl;
+	Params::Status status = params.parse(argc, argv);
 
-	if (!params.parse(argc, argv)) {
-		params.printUsage();
+	if (status == Params::Status::ShowVersion) {
+		LOG_NORMAL << VERSION;
 		return false;
 	}
+	else {
 
-	if (params.verbose) {
-		Log::getInstance(Log::LEVEL_VERBOSE).enable();
-	}
+		LOG_NORMAL << "Clusty" << endl
+			<< "  version " << VERSION
+#ifdef GIT_COMMIT
+			<< "-" << TOSTRING(GIT_COMMIT)
+#endif
+			<< " (" << DATE << ")" << endl << endl;
 
-	return true;
+		if (status == Params::Status::Incorrect) {
+			params.printUsage();
+			return false;
+		}
+
+		if (params.verbose) {
+			Log::getInstance(Log::LEVEL_VERBOSE).enable();
+		}
+
+		return true;
+	}
 }
 
 // *******************************************************************************************

diff --git a/src/params.cpp b/src/params.cpp
@@ -10,6 +10,7 @@
 #include "distances.h"
 #include "log.h"
 #include "leiden.h"
+#include "version.h"
 
 #include <vector>
 #include <fstream>
@@ -41,7 +42,8 @@ void Params::printUsage() const {
 		<< "  " + PARAM_MAX + " <column-name> <real-threshold> - accept pairwise connections with values lower or equal given threshold in a specified column" << endl
 		<< "  " + FLAG_NUMERIC_IDS + " - use when sequences in the distances file are represented by numbers (can be mapped to string ids by the object file)" << endl
 		<< "  " + FLAG_OUT_REPRESENTATIVES + " - output a representative object for each cluster instead of a cluster numerical identifier (default: " << std::boolalpha << outputRepresentatives << ")" << endl
-		<< "  " + FLAG_OUT_CSV + " - output a CSV table instead of a default TSV (default: " << std::boolalpha << outputCSV << ")"
+		<< "  " + FLAG_OUT_CSV + " - output a CSV table instead of a default TSV (default: " << std::boolalpha << outputCSV << ")" << endl
+		<< "  " + FLAG_VERSION + " - show Clusty version"
 
 #ifndef NO_LEIDEN
 		<< endl << endl
@@ -53,65 +55,68 @@ void Params::printUsage() const {
 }
 
 
-bool Params::parse(int argc, char** argv) {
+Params::Status Params::parse(int argc, char** argv) {
 
 	vector<string> args;
 	for (int i = 1; i < argc; ++i) {
 		args.emplace_back(argv[i]);
 	}
 
-	if (args.size() < 2) {
-		return false;
+	if (findSwitch(args, FLAG_VERSION)) {
+		return Status::ShowVersion;
 	}
 
-	std::string tmp;
-	findOption(args, PARAM_ALGO, tmp);
-	if (tmp.length()) {
-		algo = str2algo(tmp);
-	}
+	if (args.size() >= 2) {
 
-	findOption(args, PARAM_FILE_OBJECTS, objectsFile);
+		std::string tmp;
+		findOption(args, PARAM_ALGO, tmp);
+		if (tmp.length()) {
+			algo = str2algo(tmp);
+		}
 
-	findOption(args, PARAM_ID_COLUMNS, idColumns.first, idColumns.second);
-	numericIds = findSwitch(args, FLAG_NUMERIC_IDS);
+		findOption(args, PARAM_FILE_OBJECTS, objectsFile);
 
-	findOption(args, PARAM_DISTANCE_COLUMN, distanceColumn);
+		findOption(args, PARAM_ID_COLUMNS, idColumns.first, idColumns.second);
+		numericIds = findSwitch(args, FLAG_NUMERIC_IDS);
 
-	bool use_similarity = findSwitch(args, FLAG_SIMILARITY);
-	bool use_percent_similarity = findSwitch(args, FLAG_PERCENT_SIMILARITY);
+		findOption(args, PARAM_DISTANCE_COLUMN, distanceColumn);
 
-	if (use_percent_similarity) {
-		distanceSpecification = DistanceSpecification::PercentSimilarity;
-	}
-	else if (use_similarity) {
-		distanceSpecification = DistanceSpecification::Similarity;
-	}
+		bool use_similarity = findSwitch(args, FLAG_SIMILARITY);
+		bool use_percent_similarity = findSwitch(args, FLAG_PERCENT_SIMILARITY);
 
-	string column;
-	double value;
-	while (findOption(args, PARAM_MIN, column, value)) {
-		columns2filters[column].min = std::max(value, columns2filters[column].min);
-	}
-	while (findOption(args, PARAM_MAX, column, value)) {
-		columns2filters[column].max = std::min(value, columns2filters[column].max);
-	}
+		if (use_percent_similarity) {
+			distanceSpecification = DistanceSpecification::PercentSimilarity;
+		}
+		else if (use_similarity) {
+			distanceSpecification = DistanceSpecification::Similarity;
+		}
+
+		string column;
+		double value;
+		while (findOption(args, PARAM_MIN, column, value)) {
+			columns2filters[column].min = std::max(value, columns2filters[column].min);
+		}
+		while (findOption(args, PARAM_MAX, column, value)) {
+			columns2filters[column].max = std::min(value, columns2filters[column].max);
+		}
 
-	outputRepresentatives = findSwitch(args, FLAG_OUT_REPRESENTATIVES);
-	outputCSV = findSwitch(args, FLAG_OUT_CSV);
+		outputRepresentatives = findSwitch(args, FLAG_OUT_REPRESENTATIVES);
+		outputCSV = findSwitch(args, FLAG_OUT_CSV);
 
-	// leiden parameters
-	findOption(args, PARAM_LEIDEN_RESOLUTION, leidenParams.resolution);
-	findOption(args, PARAM_LEIDEN_BETA, leidenParams.beta);
-	findOption(args, PARAM_LEIDEN_ITERATIONS, leidenParams.numIterations);
+		// leiden parameters
+		findOption(args, PARAM_LEIDEN_RESOLUTION, leidenParams.resolution);
+		findOption(args, PARAM_LEIDEN_BETA, leidenParams.beta);
+		findOption(args, PARAM_LEIDEN_ITERATIONS, leidenParams.numIterations);
 
-	verbose = findSwitch(args, FLAG_VERBOSE);
+		verbose = findSwitch(args, FLAG_VERBOSE);
 
-	if (args.size() == 2) {
-		distancesFile = args[0];
-		output = args[1];
-		return true;
+		if (args.size() == 2) {
+			distancesFile = args[0];
+			output = args[1];
+			return Status::Correct;
+		}
 	}
 
-	return false;
+	return Status::Incorrect;
 }
 
diff --git a/src/params.h b/src/params.h
@@ -29,6 +29,7 @@ enum class DistanceSpecification {
 	PercentSimilarity
 };
 
+
 class Params {
 	const std::string PARAM_ALGO{ "--algo" };
 
@@ -51,8 +52,15 @@ class Params {
 	const std::string PARAM_LEIDEN_ITERATIONS{ "--leiden-iterations" };
 
 	const std::string FLAG_VERBOSE{ "-v" };
+	const std::string FLAG_VERSION{ "--version" };
 
 public:
+	enum Status {
+		Correct,
+		Incorrect,
+		ShowVersion
+	};
+
 	static Algo str2algo(const std::string& str)
 	{
 		if (str == "single") { return Algo::SingleLinkage; }
@@ -101,7 +109,7 @@ class Params {
 	bool verbose{ false };
 
 	void printUsage() const;
-	bool parse(int argc, char** argv);
+	Status parse(int argc, char** argv);
 
 	bool findSwitch(std::vector<std::string>& params, const std::string& name) {
 		auto it = find(params.begin(), params.end(), name); // verbose mode

diff --git a/src/version.h b/src/version.h
@@ -8,13 +8,16 @@
 //
 // *******************************************************************************************
 
-#define VERSION		"1.1.2"
-#define DATE		"2024-10-13"
+#define VERSION		"1.1.3"
+#define DATE		"2024-10-21"
 
 
 /********* Version history *********
 
-1.1.2
+1.1.3 (2024-10-21)
+* Added `--version` switch.
+
+1.1.2 (2024-10-13)
 * Precompiled binaries for macOS include Leiden algorithm.
 * Fixed small bug with `--leiden-iterations` param being displayed in help as `--leiden-resolution`.