Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup

Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup

This commit introduces Jaccard distance and similarity methods for KmerSet and KmerSetGroup.

For KmerSet:
- Added JaccardDistance method to compute the Jaccard distance between two KmerSets
- Added JaccardSimilarity method to compute the Jaccard similarity between two KmerSets

For KmerSetGroup:
- Added JaccardDistanceMatrix method to compute a pairwise Jaccard distance matrix
- Added JaccardSimilarityMatrix method to compute a pairwise Jaccard similarity matrix

Also includes:
- New DistMatrix implementation in pkg/obidist for storing and computing distance/similarity matrices
- Updated version handling with bump-version target in Makefile
- Added tests for all new methods

Makefile

@@ -62,10 +62,10 @@ OUTPUT:=$(shell mktemp)
 
 all: install-githook obitools
 
-obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS)) 
+obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS))
 
 install-githook: $(GITHOOKS)
-	
+
 $(GITHOOK_DIR)/%: $(GITHOOK_SRC_DIR)/%
 	@echo installing $$(basename $@)...
 	@mkdir -p $(GITHOOK_DIR)
@@ -79,10 +79,10 @@ update-deps:
 test: .FORCE
 	$(GOTEST) ./...
 
-obitests: 
+obitests:
 	@for t in $$(find obitests -name test.sh -print) ; do \
 		bash $${t} || exit 1;\
-	done 
+	done
 
 githubtests: obitools obitests
 
@@ -94,19 +94,30 @@ $(foreach P,$(PACKAGE_DIRS),$(eval $(call MAKE_PKG_RULE,$(P))))
 
 $(foreach P,$(OBITOOLS_DIRS),$(eval $(call MAKE_OBITOOLS_RULE,$(P))))
 
-pkg/obioptions/version.go: .FORCE
-ifneq ($(strip $(COMMIT_ID)),)
-	@cat $@ \
-	| sed  -E 's/^var _Commit = "[^"]*"/var _Commit = "'$(COMMIT_ID)'"/' \
-	| sed  -E 's/^var _Version = "[^"]*"/var _Version = "'"$(LAST_TAG)"'"/' \
+pkg/obioptions/version.go: version.txt .FORCE
+	@version=$$(cat version.txt); \
+	cat $@ \
+	| sed  -E 's/^var _Version = "[^"]*"/var _Version = "Release '$$version'"/' \
 	> $(OUTPUT)
 
 	@diff $@ $(OUTPUT) 2>&1 > /dev/null \
-    	|| echo "Update version.go : $@ to $(LAST_TAG) ($(COMMIT_ID))" \
-    	&& mv $(OUTPUT) $@
+    	|| (echo "Update version.go to $$(cat version.txt)" && mv $(OUTPUT) $@)
 
 	@rm -f $(OUTPUT)
-endif
+
+bump-version:
+	@echo "Incrementing version..."
+	@current=$$(cat version.txt); \
+	echo "  Current version: $$current"; \
+	major=$$(echo $$current | cut -d. -f1); \
+	minor=$$(echo $$current | cut -d. -f2); \
+	patch=$$(echo $$current | cut -d. -f3); \
+	new_patch=$$((patch + 1)); \
+	new_version="$$major.$$minor.$$new_patch"; \
+	echo "  New version: $$new_version"; \
+	echo "$$new_version" > version.txt
+	@echo "✓ Version updated in version.txt"
+	@$(MAKE) pkg/obioptions/version.go
 
 jjnew:
 	@echo "$(YELLOW)→ Creating a new commit...$(NC)"
@@ -116,13 +127,21 @@ jjnew:
 	@jj new
 	@echo "$(GREEN)✓ New commit created$(NC)"
 
-jjpush: 
+jjpush:
 	@echo "$(YELLOW)→ Pushing commit to repository...$(NC)"
 	@echo "$(BLUE)→ Documenting current commit...$(NC)"
 	@jj auto-describe
-	@echo "$(BLUE)→ Done.$(NC)"
-	@jj git push --change @
-	@echo "$(GREEN)✓ Commit pushed to repository$(NC)"
+	@echo "$(BLUE)→ Creating new commit for version bump...$(NC)"
+	@jj new
+	@$(MAKE) bump-version
+	@echo "$(BLUE)→ Documenting version bump commit...$(NC)"
+	@jj auto-describe
+	@version=$$(cat version.txt); \
+	echo "$(BLUE)→ Pushing commits and creating tag v$$version...$(NC)"; \
+	jj git push --change @; \
+	git tag -a "v$$version" -m "Release $$version" 2>/dev/null || echo "Tag v$$version already exists"; \
+	git push origin "v$$version" 2>/dev/null || echo "Tag already pushed"
+	@echo "$(GREEN)✓ Commits and tag pushed to repository$(NC)"
 
 jjfetch:
 	@echo "$(YELLOW)→ Pulling latest commits...$(NC)"
@@ -130,5 +149,5 @@ jjfetch:
 	@jj new master@origin
 	@echo "$(GREEN)✓ Latest commits pulled$(NC)"
 
-.PHONY: all obitools update-deps obitests githubtests jjnew jjpush jjfetch .FORCE
-.FORCE:
+.PHONY: all obitools update-deps obitests githubtests jjnew jjpush jjfetch bump-version .FORCE
+.FORCE: