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feat: add codebase genome pipeline foundation #710

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Rockachopa commented 2026-04-15 04:15:42 +00:00
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Refs #665

This lands the executable foundation for the Codebase Genome lane without pretending the full multi-repo epic is finished.

What changed

  • add pipelines/codebase_genome.py deterministic analyzer that writes GENOME.md
  • add pipelines/codebase-genome.py wrapper matching the expected pipeline entrypoint style
  • add scripts/codebase_genome_nightly.py nightly org rotator with dry-run mode and persisted state
  • generate and commit GENOME.md for timmy-home as the proof artifact
  • document usage, nightly rotation, and cron wiring in docs/CODEBASE_GENOME_PIPELINE.md
  • add regression tests for the generator, nightly runner, and committed genome artifact

Verification

  • python3 -m pytest -q tests/test_codebase_genome_pipeline.py tests/test_big_brain_repo_audit.py
  • python3 -m py_compile pipelines/codebase_genome.py pipelines/codebase-genome.py scripts/codebase_genome_nightly.py
  • python3 scripts/codebase_genome_nightly.py --dry-run > /tmp/codebase_genome_nightly_dry_run.json
  • python3 -m json.tool /tmp/codebase_genome_nightly_dry_run.json >/dev/null
  • python3 scripts/detect_secrets.py pipelines/codebase_genome.py pipelines/codebase-genome.py scripts/codebase_genome_nightly.py docs/CODEBASE_GENOME_PIPELINE.md GENOME.md tests/test_codebase_genome_pipeline.py docs/RUNBOOK_INDEX.md

Scope note

This PR advances epic #665 by landing the generator, nightly rotation scaffold, and one real genome artifact. Automatic test generation across all repos remains a follow-on lane.

Refs #665 This lands the executable foundation for the Codebase Genome lane without pretending the full multi-repo epic is finished. ## What changed - add `pipelines/codebase_genome.py` deterministic analyzer that writes `GENOME.md` - add `pipelines/codebase-genome.py` wrapper matching the expected pipeline entrypoint style - add `scripts/codebase_genome_nightly.py` nightly org rotator with dry-run mode and persisted state - generate and commit `GENOME.md` for `timmy-home` as the proof artifact - document usage, nightly rotation, and cron wiring in `docs/CODEBASE_GENOME_PIPELINE.md` - add regression tests for the generator, nightly runner, and committed genome artifact ## Verification - `python3 -m pytest -q tests/test_codebase_genome_pipeline.py tests/test_big_brain_repo_audit.py` - `python3 -m py_compile pipelines/codebase_genome.py pipelines/codebase-genome.py scripts/codebase_genome_nightly.py` - `python3 scripts/codebase_genome_nightly.py --dry-run > /tmp/codebase_genome_nightly_dry_run.json` - `python3 -m json.tool /tmp/codebase_genome_nightly_dry_run.json >/dev/null` - `python3 scripts/detect_secrets.py pipelines/codebase_genome.py pipelines/codebase-genome.py scripts/codebase_genome_nightly.py docs/CODEBASE_GENOME_PIPELINE.md GENOME.md tests/test_codebase_genome_pipeline.py docs/RUNBOOK_INDEX.md` ## Scope note This PR advances epic #665 by landing the generator, nightly rotation scaffold, and one real genome artifact. Automatic test generation across all repos remains a follow-on lane.
Rockachopa added 1 commit 2026-04-15 04:15:42 +00:00
feat: add codebase genome pipeline (#665)
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Timmy approved these changes 2026-04-15 05:14:33 +00:00
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Review: feat: add codebase genome pipeline foundation

This PR adds the foundational codebase genome pipeline: pipelines/codebase_genome.py for generating genome documents from any repo, scripts/codebase_genome_nightly.py for rotating through org repos on a nightly schedule, a generated GENOME.md for timmy-home itself, and comprehensive tests.

Strengths:

  • The pipeline architecture is sound: generate_genome_markdown() takes a repo path and produces a structured analysis. The nightly runner rotates through repos using persistent state, ensuring each repo gets analyzed in turn.
  • The nightly script has good operational design: fetch_org_repos() calls the Gitea API, select_next_repo() rotates with modular arithmetic, ensure_checkout() handles both fresh clones and updates, and build_run_plan() produces a deterministic command.
  • The --dry-run flag on the nightly script is valuable for operational validation.
  • Tests cover the pipeline output structure, nightly rotation logic, and the existence of the generated genome.

Concerns:

  1. Security: Token handling in _authenticated_clone_url() — The function reads a token from a file and embeds it directly in the clone URL (https://{token}@{host}/...). This is a common pattern but means the token appears in process argument lists visible via ps. Consider using GIT_ASKPASS or credential helpers instead. The token file path defaults to ~/.config/gitea/token which is reasonable.

  2. ensure_checkout() uses git reset --hard — This silently discards any local changes in the workspace directory. Since this is a nightly automation workspace this is probably intentional, but it means any manual work in the workspace directory will be destroyed without warning.

  3. The generated GENOME.md is relatively shallow compared to the hand-crafted genomes in PRs #714 and #717. The automated pipeline produces section headings and basic structure but may lack the nuanced analysis of the manual versions. This is expected for an automated tool and can be improved iteratively.

  4. No error handling around subprocess.run(..., check=True) in ensure_checkout() and run_plan() — if git clone/fetch fails, the script will crash with a raw CalledProcessError. Consider catching and logging a more actionable error message.

None of these are blocking. The pipeline foundation is solid and the nightly rotation pattern is well-designed for incremental improvement.

APPROVED.

## Review: feat: add codebase genome pipeline foundation This PR adds the foundational codebase genome pipeline: `pipelines/codebase_genome.py` for generating genome documents from any repo, `scripts/codebase_genome_nightly.py` for rotating through org repos on a nightly schedule, a generated `GENOME.md` for timmy-home itself, and comprehensive tests. **Strengths:** - The pipeline architecture is sound: `generate_genome_markdown()` takes a repo path and produces a structured analysis. The nightly runner rotates through repos using persistent state, ensuring each repo gets analyzed in turn. - The nightly script has good operational design: `fetch_org_repos()` calls the Gitea API, `select_next_repo()` rotates with modular arithmetic, `ensure_checkout()` handles both fresh clones and updates, and `build_run_plan()` produces a deterministic command. - The `--dry-run` flag on the nightly script is valuable for operational validation. - Tests cover the pipeline output structure, nightly rotation logic, and the existence of the generated genome. **Concerns:** 1. **Security: Token handling in `_authenticated_clone_url()`** — The function reads a token from a file and embeds it directly in the clone URL (`https://{token}@{host}/...`). This is a common pattern but means the token appears in process argument lists visible via `ps`. Consider using `GIT_ASKPASS` or credential helpers instead. The token file path defaults to `~/.config/gitea/token` which is reasonable. 2. **`ensure_checkout()` uses `git reset --hard`** — This silently discards any local changes in the workspace directory. Since this is a nightly automation workspace this is probably intentional, but it means any manual work in the workspace directory will be destroyed without warning. 3. **The generated `GENOME.md` is relatively shallow** compared to the hand-crafted genomes in PRs #714 and #717. The automated pipeline produces section headings and basic structure but may lack the nuanced analysis of the manual versions. This is expected for an automated tool and can be improved iteratively. 4. **No error handling around `subprocess.run(..., check=True)`** in `ensure_checkout()` and `run_plan()` — if git clone/fetch fails, the script will crash with a raw `CalledProcessError`. Consider catching and logging a more actionable error message. None of these are blocking. The pipeline foundation is solid and the nightly rotation pattern is well-designed for incremental improvement. APPROVED.
Timmy approved these changes 2026-04-15 06:12:48 +00:00
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Auto-approved: clean merge, no conflicts, no CI failures.

Auto-approved: clean merge, no conflicts, no CI failures.
Rockachopa commented 2026-04-16 04:03:01 +00:00
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Merged via git (conflict resolved with -X theirs)

Merged via git (conflict resolved with -X theirs)
Rockachopa closed this pull request 2026-04-16 04:03:02 +00:00
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Reference: Timmy_Foundation/timmy-home#710
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