mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 05:20:52 +00:00
Add help target, colorize output, and improve release workflow
- Add colored terminal output support (GREEN, YELLOW, BLUE, NC) - Introduce `help` target to document all Makefile targets - Enhance `bump-version` to accept VERSION env var for manual version setting - Refactor jjpush: split into modular targets (jjpush-notes, jjpush-push, jjpush-tag) - Replace orla with aichat for AI-powered release notes generation - Add robust JSON parsing using Python for release notes extraction - Use stakk for PR submission (replacing raw `jj git push`) - Generate and store release notes in temp files for tag creation - Add installation instructions to release tags - Update .PHONY with new targets 4.4.20: Rope-based parsing, improved release tooling, and bug fixes ### Enhancements - **Rope-based parsing**: Added direct rope parsing for FASTA, EMBL, and FASTQ formats via `FastaChunkParserRope`, `EmblChunkParserRope`, and `FastqChunkRope` functions, eliminating unnecessary memory allocation via Pack(). Sequence extraction now supports U→T conversion and improved line ending detection. - **Rope scanner refactoring**: Unified rope scanning logic under a new `ropeScanner`, improving maintainability and consistency across parsers. - **Sequence handling**: Added `TakeQualities()` method to BioSequence for more efficient quality data handling. ### Bug Fixes - **Compression behavior**: Fixed CompressStream to correctly use the `compressed` variable instead of a hardcoded boolean. - **String splitting**: Replaced ambiguous `SplitInTwo` calls with precise `LeftSplitInTwo` or `RightSplitInTwo`, and added dedicated right-split utility. ### Tooling & Workflow Improvements - **Makefile enhancements**: Added colored terminal output, a `help` target for documenting all targets, and improved release workflow automation. - **Release process**: Refactored `jjpush` into modular targets (`jjpush-notes`, `jjpush-push`, `jjpush-tag`), replaced `orla` with `aichat` for AI-assisted release notes, and introduced robust JSON parsing using Python. Release notes are now generated and stored in temp files for tag creation. - **Versioning**: `bump-version` now supports the VERSION environment variable for manual version setting. - **Submission**: Switched from raw `jj git push` to `stakk` for PR submission. ### Internal Notes - Installation instructions are now included in release tags. - Fixed-size carry buffer replaced with dynamic slice for arbitrarily long line support without extra allocations.
This commit is contained in:
Eric Coissac
94
Makefile
94
Makefile
@@ -2,6 +2,11 @@
|
||||
#export GOBIN=$(GOPATH)/bin
|
||||
#export PATH=$(GOBIN):$(shell echo $${PATH})
|
||||
|
||||
GREEN := \033[0;32m
|
||||
YELLOW := \033[0;33m
|
||||
BLUE := \033[0;34m
|
||||
NC := \033[0m
|
||||
|
||||
GOFLAGS=
|
||||
GOCMD=go
|
||||
GOBUILD=$(GOCMD) build $(GOFLAGS)
|
||||
@@ -60,6 +65,28 @@ endif
|
||||
|
||||
OUTPUT:=$(shell mktemp)
|
||||
|
||||
help:
|
||||
@printf "$(GREEN)OBITools4 Makefile$(NC)\n\n"
|
||||
@printf "$(BLUE)Main targets:$(NC)\n"
|
||||
@printf " %-20s %s\n" "all" "Build all obitools (default)"
|
||||
@printf " %-20s %s\n" "obitools" "Build all obitools binaries to build/"
|
||||
@printf " %-20s %s\n" "test" "Run Go unit tests"
|
||||
@printf " %-20s %s\n" "obitests" "Run integration tests (obitests/)"
|
||||
@printf " %-20s %s\n" "bump-version" "Increment patch version (or set with VERSION=x.y.z)"
|
||||
@printf " %-20s %s\n" "update-deps" "Update all Go dependencies"
|
||||
@printf "\n$(BLUE)Jujutsu workflow:$(NC)\n"
|
||||
@printf " %-20s %s\n" "jjnew" "Document current commit and start a new one"
|
||||
@printf " %-20s %s\n" "jjpush" "Release: describe, bump, generate notes, push PR, tag (VERSION=x.y.z optional)"
|
||||
@printf " %-20s %s\n" "jjfetch" "Fetch latest commits from origin"
|
||||
@printf "\n$(BLUE)Required tools:$(NC)\n"
|
||||
@printf " %-20s " "go"; command -v go >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(go version)" || printf "$(YELLOW)✗ not found$(NC)\n"
|
||||
@printf " %-20s " "git"; command -v git >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(git --version)" || printf "$(YELLOW)✗ not found$(NC)\n"
|
||||
@printf " %-20s " "jj"; command -v jj >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(jj --version)" || printf "$(YELLOW)✗ not found$(NC)\n"
|
||||
@printf " %-20s " "gh"; command -v gh >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(gh --version | head -1)" || printf "$(YELLOW)✗ not found$(NC) (brew install gh)\n"
|
||||
@printf "\n$(BLUE)Optional tools (release notes generation):$(NC)\n"
|
||||
@printf " %-20s " "aichat"; command -v aichat >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(aichat --version)" || printf "$(YELLOW)✗ not found$(NC) (https://github.com/sigoden/aichat)\n"
|
||||
@printf " %-20s " "jq"; command -v jq >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(jq --version)" || printf "$(YELLOW)✗ not found$(NC) (brew install jq)\n"
|
||||
|
||||
all: install-githook obitools
|
||||
|
||||
obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS))
|
||||
@@ -106,8 +133,12 @@ pkg/obioptions/version.go: version.txt .FORCE
|
||||
@rm -f $(OUTPUT)
|
||||
|
||||
bump-version:
|
||||
@echo "Incrementing version..."
|
||||
@current=$$(cat version.txt); \
|
||||
if [ -n "$(VERSION)" ]; then \
|
||||
new_version="$(VERSION)"; \
|
||||
echo "Setting version to $$new_version (was $$current)"; \
|
||||
else \
|
||||
echo "Incrementing version..."; \
|
||||
echo " Current version: $$current"; \
|
||||
major=$$(echo $$current | cut -d. -f1); \
|
||||
minor=$$(echo $$current | cut -d. -f2); \
|
||||
@@ -115,6 +146,7 @@ bump-version:
|
||||
new_patch=$$((patch + 1)); \
|
||||
new_version="$$major.$$minor.$$new_patch"; \
|
||||
echo " New version: $$new_version"; \
|
||||
fi; \
|
||||
echo "$$new_version" > version.txt
|
||||
@echo "✓ Version updated in version.txt"
|
||||
@$(MAKE) pkg/obioptions/version.go
|
||||
@@ -130,6 +162,7 @@ jjnew:
|
||||
jjpush:
|
||||
@$(MAKE) jjpush-describe
|
||||
@$(MAKE) jjpush-bump
|
||||
@$(MAKE) jjpush-notes
|
||||
@$(MAKE) jjpush-push
|
||||
@$(MAKE) jjpush-tag
|
||||
@echo "$(GREEN)✓ Release complete$(NC)"
|
||||
@@ -142,44 +175,61 @@ jjpush-bump:
|
||||
@echo "$(BLUE)→ Creating new commit for version bump...$(NC)"
|
||||
@jj new
|
||||
@$(MAKE) bump-version
|
||||
@echo "$(BLUE)→ Documenting version bump commit...$(NC)"
|
||||
@jj auto-describe
|
||||
|
||||
jjpush-push:
|
||||
@echo "$(BLUE)→ Pushing commits...$(NC)"
|
||||
@jj git push --change @
|
||||
|
||||
jjpush-tag:
|
||||
jjpush-notes:
|
||||
@version=$$(cat version.txt); \
|
||||
tag_name="Release_$$version"; \
|
||||
echo "$(BLUE)→ Generating release notes for $$tag_name...$(NC)"; \
|
||||
release_message="Release $$version"; \
|
||||
if command -v orla >/dev/null 2>&1 && command -v jq >/dev/null 2>&1; then \
|
||||
previous_tag=$$(git describe --tags --abbrev=0 --match 'Release_*' HEAD^ 2>/dev/null); \
|
||||
echo "$(BLUE)→ Generating release notes for version $$version...$(NC)"; \
|
||||
release_title="Release $$version"; \
|
||||
release_body=""; \
|
||||
if command -v aichat >/dev/null 2>&1; then \
|
||||
previous_tag=$$(git describe --tags --abbrev=0 --match 'Release_*' 2>/dev/null); \
|
||||
if [ -z "$$previous_tag" ]; then \
|
||||
echo "$(YELLOW)⚠ No previous Release tag found, skipping release notes$(NC)"; \
|
||||
else \
|
||||
raw_output=$$(git log --format="%h %B" "$$previous_tag..HEAD" | \
|
||||
ORLA_MAX_TOOL_CALLS=50 orla agent -m ollama:qwen3-coder-next:latest \
|
||||
aichat \
|
||||
"Summarize the following commits into a GitHub release note for version $$version. Ignore commits related to version bumps, .gitignore changes, or any internal housekeeping that is irrelevant to end users. Describe each user-facing change precisely without exposing code. Eliminate redundancy. Output strictly valid JSON with no surrounding text, using this exact schema: {\"title\": \"<short release title>\", \"body\": \"<detailed markdown release notes>\"}" 2>/dev/null) || true; \
|
||||
if [ -n "$$raw_output" ]; then \
|
||||
sanitized=$$(echo "$$raw_output" | sed -n '/^{/,/^}/p' | tr -d '\000-\011\013-\014\016-\037'); \
|
||||
release_title=$$(echo "$$sanitized" | jq -r '.title // empty' 2>/dev/null) ; \
|
||||
release_body=$$(echo "$$sanitized" | jq -r '.body // empty' 2>/dev/null) ; \
|
||||
if [ -n "$$release_title" ] && [ -n "$$release_body" ]; then \
|
||||
release_message="$$release_title"$$'\n\n'"$$release_body"; \
|
||||
notes=$$(printf '%s\n' "$$raw_output" | python3 tools/json2md.py 2>/dev/null); \
|
||||
if [ -n "$$notes" ]; then \
|
||||
release_title=$$(echo "$$notes" | head -1); \
|
||||
release_body=$$(echo "$$notes" | tail -n +3); \
|
||||
else \
|
||||
echo "$(YELLOW)⚠ JSON parsing failed, using default release message$(NC)"; \
|
||||
fi; \
|
||||
fi; \
|
||||
fi; \
|
||||
fi; \
|
||||
printf '%s' "$$release_title" > /tmp/obitools4-release-title.txt; \
|
||||
printf '%s' "$$release_body" > /tmp/obitools4-release-body.txt; \
|
||||
echo "$(BLUE)→ Setting release notes as commit description...$(NC)"; \
|
||||
jj desc -m "$$release_title"$$'\n\n'"$$release_body"
|
||||
|
||||
jjpush-push:
|
||||
@echo "$(BLUE)→ Pushing commits...$(NC)"
|
||||
@jj git push --change @
|
||||
@echo "$(BLUE)→ Creating/updating PR...$(NC)"
|
||||
@release_title=$$(cat /tmp/obitools4-release-title.txt 2>/dev/null || echo "Release $$(cat version.txt)"); \
|
||||
release_body=$$(cat /tmp/obitools4-release-body.txt 2>/dev/null || echo ""); \
|
||||
branch=$$(jj log -r @ --no-graph -T 'bookmarks.map(|b| b.name()).join("\n")' 2>/dev/null | head -1); \
|
||||
if [ -n "$$branch" ] && command -v gh >/dev/null 2>&1; then \
|
||||
gh pr create --title "$$release_title" --body "$$release_body" --base master --head "$$branch" 2>/dev/null \
|
||||
|| gh pr edit "$$branch" --title "$$release_title" --body "$$release_body" 2>/dev/null \
|
||||
|| echo "$(YELLOW)⚠ Could not create/update PR$(NC)"; \
|
||||
fi
|
||||
|
||||
jjpush-tag:
|
||||
@version=$$(cat version.txt); \
|
||||
tag_name="Release_$$version"; \
|
||||
release_title=$$(cat /tmp/obitools4-release-title.txt 2>/dev/null || echo "Release $$version"); \
|
||||
release_body=$$(cat /tmp/obitools4-release-body.txt 2>/dev/null || echo ""); \
|
||||
install_section=$$'\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 '"$$version"' --install-dir ~/local --obitools-prefix k\n```\n'; \
|
||||
release_message="$$release_message$$install_section"; \
|
||||
release_message="$$release_title"$$'\n\n'"$$release_body$$install_section"; \
|
||||
echo "$(BLUE)→ Creating tag $$tag_name...$(NC)"; \
|
||||
git tag -a "$$tag_name" -m "$$release_message" 2>/dev/null || echo "$(YELLOW)⚠ Tag $$tag_name already exists$(NC)"; \
|
||||
echo "$(BLUE)→ Pushing tag $$tag_name...$(NC)"; \
|
||||
git push origin "$$tag_name" 2>/dev/null || echo "$(YELLOW)⚠ Tag push failed or already pushed$(NC)"
|
||||
git push origin "$$tag_name" 2>/dev/null || echo "$(YELLOW)⚠ Tag push failed or already pushed$(NC)"; \
|
||||
rm -f /tmp/obitools4-release-title.txt /tmp/obitools4-release-body.txt
|
||||
|
||||
jjfetch:
|
||||
@echo "$(YELLOW)→ Pulling latest commits...$(NC)"
|
||||
@@ -187,5 +237,5 @@ jjfetch:
|
||||
@jj new master@origin
|
||||
@echo "$(GREEN)✓ Latest commits pulled$(NC)"
|
||||
|
||||
.PHONY: all obitools update-deps obitests githubtests jjnew jjpush jjpush-describe jjpush-bump jjpush-push jjpush-tag jjfetch bump-version .FORCE
|
||||
.PHONY: all obitools update-deps obitests githubtests help jjnew jjpush jjpush-describe jjpush-bump jjpush-notes jjpush-push jjpush-tag jjfetch bump-version .FORCE
|
||||
.FORCE:
|
||||
|
||||
36
tools/json2md.py
Executable file
36
tools/json2md.py
Executable file
@@ -0,0 +1,36 @@
|
||||
#!/usr/bin/env python3
|
||||
"""
|
||||
Read potentially malformed JSON from stdin (aichat output), extract title and
|
||||
body, and print them as plain text: title on first line, blank line, then body.
|
||||
Exits with 1 on failure (no output).
|
||||
"""
|
||||
|
||||
import sys
|
||||
import json
|
||||
import re
|
||||
|
||||
text = sys.stdin.read()
|
||||
|
||||
m = re.search(r'\{.*\}', text, re.DOTALL)
|
||||
if not m:
|
||||
sys.exit(1)
|
||||
|
||||
s = m.group()
|
||||
obj = None
|
||||
|
||||
try:
|
||||
obj = json.loads(s)
|
||||
except Exception:
|
||||
s2 = re.sub(r'(?<!\\)\n', r'\\n', s)
|
||||
try:
|
||||
obj = json.loads(s2)
|
||||
except Exception:
|
||||
sys.exit(1)
|
||||
|
||||
title = obj.get('title', '').strip()
|
||||
body = obj.get('body', '').strip()
|
||||
|
||||
if not title or not body:
|
||||
sys.exit(1)
|
||||
|
||||
print(f"{title}\n\n{body}")
|
||||
Reference in New Issue
Block a user