mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 05:20:52 +00:00
e3c41fc11b
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
154 lines
4.2 KiB
Makefile
154 lines
4.2 KiB
Makefile
#export GOPATH=$(shell pwd)/GO
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#export GOBIN=$(GOPATH)/bin
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#export PATH=$(GOBIN):$(shell echo $${PATH})
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GOFLAGS=
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GOCMD=go
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GOBUILD=$(GOCMD) build $(GOFLAGS)
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GOGENERATE=$(GOCMD) generate
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GOCLEAN=$(GOCMD) clean
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GOTEST=$(GOCMD) test
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GOGET=$(GOCMD) get
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BUILD_DIR=build
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OBITOOLS_PREFIX:=
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PACKAGES_SRC:= $(wildcard pkg/*/*.go pkg/*/*/*.go)
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PACKAGE_DIRS:=$(sort $(patsubst %/,%,$(dir $(PACKAGES_SRC))))
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PACKAGES:=$(notdir $(PACKAGE_DIRS))
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GITHOOK_SRC_DIR=git-hooks
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GITHOOKS_SRC:=$(wildcard $(GITHOOK_SRC_DIR)/*)
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GITHOOK_DIR=.git/hooks
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GITHOOKS:=$(patsubst $(GITHOOK_SRC_DIR)/%,$(GITHOOK_DIR)/%,$(GITHOOKS_SRC))
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OBITOOLS_SRC:= $(wildcard cmd/obitools/*/*.go)
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OBITOOLS_DIRS:=$(sort $(patsubst %/,%,$(dir $(OBITOOLS_SRC))))
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OBITOOLS:=$(notdir $(OBITOOLS_DIRS))
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define MAKE_PKG_RULE
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pkg-$(notdir $(1)): $(1) pkg/obioptions/version.go
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@echo -n - Building package $(notdir $(1))...
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@$(GOBUILD) ./$(1) \
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2> pkg-$(notdir $(1)).log \
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|| cat pkg-$(notdir $(1)).log
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@rm -f pkg-$(notdir $(1)).log
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@echo Done.
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endef
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define MAKE_OBITOOLS_RULE
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$(OBITOOLS_PREFIX)$(notdir $(1)): $(BUILD_DIR) $(1) pkg/obioptions/version.go
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@echo -n - Building obitool $(notdir $(1))...
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@$(GOBUILD) -o $(BUILD_DIR)/$(OBITOOLS_PREFIX)$(notdir $(1)) ./$(1) \
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2> $(OBITOOLS_PREFIX)$(notdir $(1)).log \
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|| cat $(OBITOOLS_PREFIX)$(notdir $(1)).log
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@rm -f $(OBITOOLS_PREFIX)$(notdir $(1)).log
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@echo Done.
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endef
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GIT=$(shell which git 2>&1 >/dev/null && which git)
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GITDIR=$(shell ls -d .git 2>/dev/null && echo .git || echo)
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ifneq ($(strip $(GIT)),)
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ifneq ($(strip $(GITDIR)),)
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COMMIT_ID:=$(shell $(GIT) log -1 HEAD --format=%h)
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LAST_TAG:=$(shell $(GIT) describe --tags $$($(GIT) rev-list --tags --max-count=1) | \
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tr '_' ' ')
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endif
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endif
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OUTPUT:=$(shell mktemp)
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all: install-githook obitools
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obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS))
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install-githook: $(GITHOOKS)
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$(GITHOOK_DIR)/%: $(GITHOOK_SRC_DIR)/%
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@echo installing $$(basename $@)...
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@mkdir -p $(GITHOOK_DIR)
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@cp $< $@
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@chmod +x $@
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update-deps:
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go get -u ./...
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test: .FORCE
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$(GOTEST) ./...
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obitests:
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@for t in $$(find obitests -name test.sh -print) ; do \
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bash $${t} || exit 1;\
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done
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githubtests: obitools obitests
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$(BUILD_DIR):
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mkdir -p $@
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$(foreach P,$(PACKAGE_DIRS),$(eval $(call MAKE_PKG_RULE,$(P))))
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$(foreach P,$(OBITOOLS_DIRS),$(eval $(call MAKE_OBITOOLS_RULE,$(P))))
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pkg/obioptions/version.go: version.txt .FORCE
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@version=$$(cat version.txt); \
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cat $@ \
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| sed -E 's/^var _Version = "[^"]*"/var _Version = "Release '$$version'"/' \
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> $(OUTPUT)
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@diff $@ $(OUTPUT) 2>&1 > /dev/null \
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|| (echo "Update version.go to $$(cat version.txt)" && mv $(OUTPUT) $@)
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@rm -f $(OUTPUT)
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bump-version:
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@echo "Incrementing version..."
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@current=$$(cat version.txt); \
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echo " Current version: $$current"; \
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major=$$(echo $$current | cut -d. -f1); \
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minor=$$(echo $$current | cut -d. -f2); \
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patch=$$(echo $$current | cut -d. -f3); \
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new_patch=$$((patch + 1)); \
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new_version="$$major.$$minor.$$new_patch"; \
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echo " New version: $$new_version"; \
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echo "$$new_version" > version.txt
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@echo "✓ Version updated in version.txt"
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@$(MAKE) pkg/obioptions/version.go
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jjnew:
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@echo "$(YELLOW)→ Creating a new commit...$(NC)"
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@echo "$(BLUE)→ Documenting current commit...$(NC)"
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@jj auto-describe
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@echo "$(BLUE)→ Done.$(NC)"
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@jj new
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@echo "$(GREEN)✓ New commit created$(NC)"
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jjpush:
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@echo "$(YELLOW)→ Pushing commit to repository...$(NC)"
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@echo "$(BLUE)→ Documenting current commit...$(NC)"
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@jj auto-describe
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@echo "$(BLUE)→ Creating new commit for version bump...$(NC)"
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@jj new
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@$(MAKE) bump-version
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@echo "$(BLUE)→ Documenting version bump commit...$(NC)"
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@jj auto-describe
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@version=$$(cat version.txt); \
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echo "$(BLUE)→ Pushing commits and creating tag v$$version...$(NC)"; \
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jj git push --change @; \
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git tag -a "v$$version" -m "Release $$version" 2>/dev/null || echo "Tag v$$version already exists"; \
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git push origin "v$$version" 2>/dev/null || echo "Tag already pushed"
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@echo "$(GREEN)✓ Commits and tag pushed to repository$(NC)"
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jjfetch:
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@echo "$(YELLOW)→ Pulling latest commits...$(NC)"
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@jj git fetch
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@jj new master@origin
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@echo "$(GREEN)✓ Latest commits pulled$(NC)"
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.PHONY: all obitools update-deps obitests githubtests jjnew jjpush jjfetch bump-version .FORCE
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.FORCE:
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