Eric Coissac
6acafa7f2c
Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
118 lines
3.9 KiB
Makefile
118 lines
3.9 KiB
Makefile
VENV := .venv
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PYTHON := $(VENV)/bin/python
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PIP := $(VENV)/bin/pip
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MKDOCS := $(VENV)/bin/mkdocs
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CARGO_DIR := src
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DOC_DIR := docmd
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DOC_FILE := mkdocs.yml
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DOC_SITE := doc
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DOC_PORT := 8001
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DOC_USER_DIR := UserDocMD
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DOC_USER_FILE := mkdocs-user.yml
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DOC_USER_SITE := doc-user
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DOC_USER_PORT := 8002
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# ── virtualenv ────────────────────────────────────────────────────────────────
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$(VENV)/bin/activate:
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python3 -m venv $(VENV)
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$(MKDOCS): $(VENV)/bin/activate
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$(PIP) install --quiet --upgrade pip
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$(PIP) install --quiet \
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livereload watchdog \
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mkdocs mkdocs-material \
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mkdocs-mermaid2-plugin \
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mkdocs-bibtex
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$(PIP) install --quiet --upgrade InSilicoSeq
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# ── obikmer binary ───────────────────────────────────────────────────────────
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PROFILE_FILE := profile.pb
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PPROF_PORT := 8081
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.PHONY: obikmer
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obikmer:
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cargo build --release --manifest-path $(CARGO_DIR)/Cargo.toml --bin obikmer
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.PHONY: debug
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debug:
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cargo build --manifest-path $(CARGO_DIR)/Cargo.toml --bin obikmer
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.PHONY: profile-build
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profile-build:
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cargo build --release --manifest-path $(CARGO_DIR)/Cargo.toml \
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--bin obikmer --features obikmer/profiling
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.PHONY: profile-view
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profile-view:
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go tool pprof -http=127.0.0.1:$(PPROF_PORT) $(PROFILE_FILE)
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# ── documentation ─────────────────────────────────────────────────────────────
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.PHONY: doc
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doc: $(MKDOCS)
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$(MKDOCS) build -f $(DOC_FILE)
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.PHONY: doc-serve
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doc-serve: $(MKDOCS)
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$(MKDOCS) serve -f $(DOC_FILE) \
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--dev-addr=127.0.0.1:$(DOC_PORT) \
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--livereload
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.PHONY: clean-doc
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clean-doc:
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rm -rf $(DOC_SITE)/
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.PHONY: doc-user
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doc-user: $(MKDOCS)
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$(MKDOCS) build -f $(DOC_USER_FILE)
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.PHONY: doc-user-serve
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doc-user-serve: $(MKDOCS)
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$(MKDOCS) serve -f $(DOC_USER_FILE) \
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--dev-addr=127.0.0.1:$(DOC_USER_PORT) \
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--livereload
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.PHONY: clean-doc-user
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clean-doc-user:
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rm -rf $(DOC_USER_SITE)/
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.PHONY: clean
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clean: clean-doc clean-doc-user
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rm -rf $(VENV)
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# ── release ───────────────────────────────────────────────────────────────────
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CARGO_TOML := $(CARGO_DIR)/obikmer/Cargo.toml
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.PHONY: bump-version
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bump-version:
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@current=$$(grep '^version = ' $(CARGO_TOML) | head -n 1 | sed 's/version = "\(.*\)"/\1/'); \
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if [ -n "$(RELEASE)" ]; then \
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new_version="$(RELEASE)"; \
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else \
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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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fi; \
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echo "Version: $$current -> $$new_version"; \
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sed -i.bak "s/^version = \"$$current\"/version = \"$$new_version\"/" $(CARGO_TOML) && \
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rm $(CARGO_TOML).bak
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.PHONY: release
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release: bump-version
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@jj auto-describe
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@jj git push --change @
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@new_version=$$(grep '^version = ' $(CARGO_TOML) | head -n 1 | sed 's/version = "\(.*\)"/\1/'); \
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git_hash=$$(jj log -r @ --no-graph -T 'commit_id'); \
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commits=$$(jj log -r 'latest(tags())..@' --no-graph -T 'description ++ "\n"' 2>/dev/null || \
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jj log --no-graph -T 'description ++ "\n"' --limit 30); \
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notes=$$(printf 'Write concise markdown release notes for obikmer (a Rust kmer genomics tool). Be technical and direct. Base them strictly on these commit messages:\n\n%s' "$$commits" | aichat 2>/dev/null); \
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tag_msg="$${notes:-Release v$$new_version}"; \
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git tag -a "v$$new_version" -m "$$tag_msg" "$$git_hash" && \
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git push origin "v$$new_version"
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