mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-08-24 05:41:19 +00:00
Eric Coissac
90cf780f23
Corrects expected values for division and comparison operations in the uint128 test suite. Updates obilandmark to use log.Fatalf instead of log.Fatal, ensuring sequence ID, taxid, and taxonomy name are correctly interpolated in fatal error messages.
246 lines
11 KiB
Makefile
246 lines
11 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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.DEFAULT_GOAL := all
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GREEN := \033[0;32m
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YELLOW := \033[0;33m
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BLUE := \033[0;34m
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NC := \033[0m
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GOFLAGS=
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LDFLAGS=
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GOCMD=go
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GOBUILD=$(GOCMD) build $(GOFLAGS) $(if $(LDFLAGS),-ldflags="$(LDFLAGS)")
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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; rm -f $(OBITOOLS_PREFIX)$(notdir $(1)).log; exit 1; }
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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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help:
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@printf "$(GREEN)OBITools4 Makefile$(NC)\n\n"
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@printf "$(BLUE)Main targets:$(NC)\n"
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@printf " %-20s %s\n" "all" "Build all obitools (default)"
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@printf " %-20s %s\n" "obitools" "Build all obitools binaries to build/"
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@printf " %-20s %s\n" "test" "Run Go unit tests"
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@printf " %-20s %s\n" "obitests" "Run integration tests (obitests/)"
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@printf " %-20s %s\n" "bump-version" "Increment patch version (or set with VERSION=x.y.z)"
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@printf " %-20s %s\n" "update-deps" "Update all Go dependencies"
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@printf "\n$(BLUE)Jujutsu workflow:$(NC)\n"
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@printf " %-20s %s\n" "jjnew" "Document current commit and start a new one"
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@printf " %-20s %s\n" "jjpush" "Release: describe, bump, generate notes, push PR, tag (VERSION=x.y.z optional)"
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@printf " %-20s %s\n" "jjfetch" "Fetch latest commits from origin"
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@printf "\n$(BLUE)Required tools:$(NC)\n"
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@printf " %-20s " "go"; command -v go >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(go version)" || printf "$(YELLOW)✗ not found$(NC)\n"
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@printf " %-20s " "git"; command -v git >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(git --version)" || printf "$(YELLOW)✗ not found$(NC)\n"
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@printf " %-20s " "jj"; command -v jj >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(jj --version)" || printf "$(YELLOW)✗ not found$(NC)\n"
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@printf " %-20s " "gh"; command -v gh >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(gh --version | head -1)" || printf "$(YELLOW)✗ not found$(NC) (brew install gh)\n"
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@printf "\n$(BLUE)Optional tools (release notes generation):$(NC)\n"
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@printf " %-20s " "aichat"; command -v aichat >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(aichat --version)" || printf "$(YELLOW)✗ not found$(NC) (https://github.com/sigoden/aichat)\n"
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@printf " %-20s " "jq"; command -v jq >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(jq --version)" || printf "$(YELLOW)✗ not found$(NC) (brew install jq)\n"
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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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@current=$$(cat version.txt); \
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if [ -n "$(VERSION)" ]; then \
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new_version="$(VERSION)"; \
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echo "Setting version to $$new_version (was $$current)"; \
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else \
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echo "Incrementing version..."; \
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echo " Current version: $$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: $$new_version"; \
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fi; \
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echo "$$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 undocumented commits...$(NC)"
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@jj auto-doc
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@echo "$(BLUE)→ Done.$(NC)"
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@jj new
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@echo "$(GREEN)✓ New commit created$(NC)"
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jjpush:
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@$(MAKE) jjpush-describe
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@$(MAKE) jjpush-bump
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@$(MAKE) jjpush-notes
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@$(MAKE) jjpush-push
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@$(MAKE) jjpush-tag
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@echo "$(GREEN)✓ Release complete$(NC)"
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jjpush-describe:
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@echo "$(BLUE)→ Documenting undocumented commits...$(NC)"
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@jj auto-doc
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jjpush-bump:
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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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jjpush-notes:
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@version=$$(cat version.txt); \
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echo "$(BLUE)→ Generating release notes for version $$version...$(NC)"; \
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release_title="Release $$version"; \
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release_body=""; \
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if command -v aichat >/dev/null 2>&1; then \
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previous_tag=$$(git describe --tags --abbrev=0 --match 'Release_*' 2>/dev/null); \
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if [ -z "$$previous_tag" ]; then \
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echo "$(YELLOW)⚠ No previous Release tag found, skipping release notes$(NC)"; \
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else \
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raw_output=$$(git log --format="%h %B" "$$previous_tag..HEAD" | \
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aichat \
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"Summarize the following commits into a GitHub release note for version $$version. Ignore commits related to version bumps, .gitignore changes, or any internal housekeeping that is irrelevant to end users. Describe each user-facing change precisely without exposing code. Eliminate redundancy. Output strictly valid JSON with no surrounding text, using this exact schema: {\"title\": \"<short release title>\", \"body\": \"<detailed markdown release notes>\"}" 2>/dev/null) || true; \
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if [ -n "$$raw_output" ]; then \
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notes=$$(printf '%s\n' "$$raw_output" | python3 tools/json2md.py 2>/dev/null); \
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if [ -n "$$notes" ]; then \
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release_title=$$(echo "$$notes" | head -1); \
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release_body=$$(echo "$$notes" | tail -n +3); \
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else \
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echo "$(YELLOW)⚠ JSON parsing failed, using default release message$(NC)"; \
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fi; \
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fi; \
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fi; \
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fi; \
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printf '%s' "$$release_title" > /tmp/obitools4-release-title.txt; \
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printf '%s' "$$release_body" > /tmp/obitools4-release-body.txt; \
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echo "$(BLUE)→ Setting release notes as commit description...$(NC)"; \
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jj desc -m "$$release_title"$$'\n\n'"$$release_body"
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jjpush-push:
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@echo "$(BLUE)→ Pushing commits...$(NC)"
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@jj git push --change @
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@echo "$(BLUE)→ Creating/updating PR...$(NC)"
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@release_title=$$(cat /tmp/obitools4-release-title.txt 2>/dev/null || echo "Release $$(cat version.txt)"); \
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release_body=$$(cat /tmp/obitools4-release-body.txt 2>/dev/null || echo ""); \
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branch=$$(jj log -r @ --no-graph -T 'bookmarks.map(|b| b.name()).join("\n")' 2>/dev/null | head -1); \
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if [ -n "$$branch" ] && command -v gh >/dev/null 2>&1; then \
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gh pr create --title "$$release_title" --body "$$release_body" --base master --head "$$branch" 2>/dev/null \
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|| gh pr edit "$$branch" --title "$$release_title" --body "$$release_body" 2>/dev/null \
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|| echo "$(YELLOW)⚠ Could not create/update PR$(NC)"; \
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fi
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jjpush-tag:
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@version=$$(cat version.txt); \
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tag_name="Release_$$version"; \
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release_title=$$(cat /tmp/obitools4-release-title.txt 2>/dev/null || echo "Release $$version"); \
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release_body=$$(cat /tmp/obitools4-release-body.txt 2>/dev/null || echo ""); \
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install_section=$$'\n## Installation\n\n### Pre-built binaries\n\nDownload the appropriate archive for your system from the\n[release assets](https://github.com/metabarcoding/obitools4/releases/tag/Release_'"$$version"')\nand extract it:\n\n#### Linux (AMD64)\n```bash\ntar -xzf obitools4_'"$$version"'_linux_amd64.tar.gz\n```\n\n#### Linux (ARM64)\n```bash\ntar -xzf obitools4_'"$$version"'_linux_arm64.tar.gz\n```\n\n#### macOS (Intel)\n```bash\ntar -xzf obitools4_'"$$version"'_darwin_amd64.tar.gz\n```\n\n#### macOS (Apple Silicon)\n```bash\ntar -xzf obitools4_'"$$version"'_darwin_arm64.tar.gz\n```\n\nAll OBITools4 binaries are included in each archive.\n\n### From source\n\nYou can also compile and install OBITools4 directly from source using the\ninstallation script:\n\n```bash\ncurl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version '"$$version"'\n```\n\nBy default binaries are installed in `/usr/local/bin`. Use `--install-dir` to\nchange the destination and `--obitools-prefix` to add a prefix to command names:\n\n```bash\ncurl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \\\n bash -s -- --version '"$$version"' --install-dir ~/local --obitools-prefix k\n```\n'; \
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release_message="$$release_title"$$'\n\n'"$$release_body$$install_section"; \
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echo "$(BLUE)→ Creating tag $$tag_name...$(NC)"; \
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commit_hash=$$(jj log -r @ --no-graph -T 'commit_id' 2>/dev/null); \
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git tag -a "$$tag_name" $${commit_hash:+"$$commit_hash"} -m "$$release_message" 2>/dev/null || echo "$(YELLOW)⚠ Tag $$tag_name already exists$(NC)"; \
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echo "$(BLUE)→ Pushing tag $$tag_name...$(NC)"; \
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git push origin "$$tag_name" 2>/dev/null || echo "$(YELLOW)⚠ Tag push failed or already pushed$(NC)"; \
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rm -f /tmp/obitools4-release-title.txt /tmp/obitools4-release-body.txt
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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 help jjnew jjpush jjpush-describe jjpush-bump jjpush-notes jjpush-push jjpush-tag jjfetch bump-version .FORCE
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.FORCE:
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