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Record where the campaign actually is
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1,183 ruff findings left, in five courses. Nine are at zero. The numbers in
here were four hours stale.

Two things worth reading before the next pass: the notebook branch of
scripts/course_run.sh will overwrite tracked notebook outputs the moment it is
used (the same bug already found in TRAK and SPD), and eleven .py files are
now over the 250-line cap -- several because THIS work added the docstrings
and annotations that pushed them over.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0172dj34FDpao6wsix8ZuCzE
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Krzysztof Rudnicki 2026-08-28 21:01:46 +02:00
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TODO-refactor-remaining.md
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REMOVE ME AFTER FINISH REMOVE ME AFTER FINISH
What is done, what is not, and the real numbers. Companion to What is done, what is not, and the real numbers, re-measured 2026-08-28 after
`TODO-file-length-250.md`, which parks one specific blocking decision. the lint campaign started. Companion to `TODO-file-length-250.md`, which parks
one specific blocking decision.
## Done ## Done
| Area | State | | Area | State |
|---|---| |---|---|
| Vendored manifest | `gates/vendored.txt`, mirrored into `~/utils` (`kuhyx/utils@a4a3e0a`) | | Vendored manifest | `gates/vendored.txt`, 8 entries, mirrored into `~/utils` |
| Build artifacts | 189 untracked, `.gitignore` closed, 0 tracked-but-ignored files | | Build artifacts | 189 untracked, `.gitignore` closed, 0 tracked-but-ignored files |
| no-binaries gate | Path-scoped `.binary-allowlist`; verified blocking AND passing | | no-binaries gate | Path-scoped `.binary-allowlist`; verified blocking AND passing |
| Markdown | 4 namespaces, all under 250 lines, `CLAUDE.md` written | | Markdown | 4 namespaces, all under 250 lines, `CLAUDE.md` written |
| pre-commit | 12 hooks, green on all files | | pre-commit | 12 hooks, green on all files |
| pre-push | `pre-commit install --hook-type pre-push` via `install.sh` | | pre-push | `pre-commit install --hook-type pre-push` via `install.sh` |
| GitHub CI | `pre-commit` + `md-naming`, both green. Actions had been DISABLED at repo level | | GitHub CI | `pre-commit` + `md-naming`, both green |
| run.sh | Root harness + 44 course runners over one shared library | | run.sh | Root harness + per-course runners over one shared library |
| Runnability | 38 runnable / 5 no-code / 1 blocked, recorded in `DOCS-runnability.md` | | `pyproject.toml` | `select = ["ALL"]`, mypy strict, coverage config. **No hook wired up yet** |
| LaTeX 250-line cap | 19 reports split, every rebuilt PDF verified identical. 1 left |
| ZPOB | Fixed: builds with `--no-bibtex`, exits 0 |
## Not done, with honest sizes ## The lint campaign
### 1. Python linting — 9,281 ruff findings `select = ["ALL"]`, and by kuhy's decision on 2026-08-28 there are **no
per-file-ignores at all** -- not even the `S101` block for tests that ruff's
own docs and the rest of this fleet carry. A test asserts by raising.
Measured with the fleet config (`select = ["ALL"]`, the five standard ignores): | | ruff findings |
|---|---|
| Baseline, before any of this | 9,281 |
| After the format + safe-fix pass and excluding `TRAK/sightpy` | 3,686 |
| **Now** | **1,183** |
| Rule | Count | Nature | Courses at zero: `WDWR`, `SPD`, `MOM`, `ECRYPT`, `ECRYPT_PROJECT`, `ECOTE`,
`NLP`, `EARIN`, `PORR`. What is left, by course:
| Course | ruff | Can it be verified by running? |
|---|---|---| |---|---|---|
| `Q000` bad-quotes | 2050 | auto-fixable | | `TRAK` | 531 | **Yes** -- `run` ray-traces cornell_box in 37s. `sightpy/` is vendored and excluded; this is kuhy's own code |
| `ANN001`/`ANN201` missing annotations | 1671 | **manual** | | `twm_4` | 228 | No: `jupyter` on PATH is a dead pipx shim. `pip install jupyter` in a venv would fix that |
| `E501` line-too-long | 628 | mostly manual | | `ERSMS-project` | 156 | No: docker-compose course |
| `T201` print | 316 | needs a decision per script | | `PSD` | 152 | No: `run.sh` predates the harness and installs packages with sudo |
| `D1xx` missing docstrings | ~600 | **manual** | | `PBAD` | 115 | No: same dead jupyter shim |
| `W291`/`W293` whitespace | 431 | auto-fixable |
| everything else | ~3600 | mixed |
Roughly 3,000 are auto-fixable and ~6,000 are hand work. The auto-fixable pass **Before running the notebook courses, fix `scripts/course_run.sh` first.**
should be its own commit so the manual diff stays reviewable. Its notebook branch is `jupyter nbconvert --execute --inplace`, and all four
notebooks are tracked WITH their outputs -- that would overwrite a committed
deliverable. This exact bug has already been found twice (TRAK's
`outputs/output.png`, SPD's `results_*.png`); execute to a temp path instead.
**Blocked on:** nothing. Start with `ruff check --fix` on the safe rules, then ## mypy has NOT been run against any of this
add `pyproject.toml` and the ruff/mypy hooks in the same commit as the last fix
(a gate must not land before its subject is clean).
### 2. Coverage — 19 tests for ~28k lines `pyproject.toml` sets `strict = true` and `CLAUDE.md` says the repo runs mypy,
but mypy is not installed on this machine (pip is externally managed; use a
venv) and no commit so far has type-checked. **"Zero findings" in the commit
messages means zero RUFF findings.** Measured after installing it:
`gates/coverage.tsv` (per-directory floors, `target` always 100, floors may | Course | mypy --strict errors |
only rise) is designed but not written. Nothing exists for the non-Python |---|---|
languages yet. This is the largest remaining item by a wide margin and is | `WDWR`, `SPD`, `MOM`, `ECRYPT_PROJECT` | 0 |
measured in weeks. | `ECOTE` | 14 |
| `NLP` | 29 |
| `EARIN/lab1` alone | 46 |
| `TRAK` | 1 |
| `PSD/zin1` | 5 |
Two structural notes for whoever runs it next:
- It cannot be pointed at the whole repo. There are many `main.py` files and
mypy stops at `Duplicate module named "main"`. Run it per directory.
- Most errors are `Returning Any` from untyped third-party calls (openai,
pandas) and genuinely-wrong unions this pass introduced by hand, e.g.
`str | bool` returns in `gpt_chunks.reformat`. They are real.
## Still open
### 1. The 250-line cap: 51 files
| Type | Count | Note |
|---|---|---|
| `.txt` | 27 | Blocked -- see `TODO-file-length-250.md` |
| `.py` | 11 | Several GREW during the lint pass, because docstrings and annotations are lines: `NLP/gpt_chunks.py` 911 -> 973, `EARIN/lab2/main.py` 581 -> 647, `PORR/.../linear_algebra_utils.py` 422 -> 553. Split them AFTER the lint work, not during |
| `.cpp` | 9 | |
| `.c` | 4 | |
| `.java` | 2 | |
| `.tex` | 1 | `ELAC/.../03-building-nfa-...tex`, 418 lines of consecutive tikz figures with no subsection to split on |
### 2. Coverage
`gates/coverage.tsv` is designed but not written, and there are 125 tests for
~28k lines. The largest remaining item by a wide margin.
### 3. Dependency freshness ### 3. Dependency freshness
9 `requirements.txt`, 5 `package.json`, 7 `pom.xml`, 1 `.csproj`, none pinned. 9 `requirements.txt`, 5 `package.json`, 7 `pom.xml`, 1 `.csproj`, none pinned.
**The upgrade and the gate must land in the SAME commit** or the repo is **The upgrade and the gate must land in the SAME commit.**
instantly and permanently red -- see the warning in
`~/utils/scripts/install_dependency_freshness_gate.sh`.
### 4. The 250-line cap ### 4. File-rewriting hooks
73 files still over. Breakdown: 27 `.txt` (blocked -- see `trailing-whitespace` and `end-of-file-fixer` are deliberately absent; they
`TODO-file-length-250.md`), 19 `.tex`, 10 `.py`, 9 `.cpp`, 4 `.c`, 2 `.java`. want their own reviewed commit.
The `.tex` splits are `\input{}` per section, and the acceptance test is that
the rebuilt PDF is unchanged. **Do not split the source files before their
tests exist** -- splitting untested code is the highest-risk action here.
### 5. File-rewriting hooks ### 5. Three checks that must be run on every future pass
`trailing-whitespace` and `end-of-file-fixer` are deliberately absent. They `scripts/check_refactor_safety.py` exists because ruff and a smoke run BOTH
will touch hundreds of submitted coursework files, so they want their own missed three regressions this campaign introduced. Run it before and after any
reviewed commit rather than being buried in a config change. automated rewrite:
### 6. Two courses still fail `run` ```bash
cp -r <course> /tmp/before
# ...do the pass...
./scripts/check_refactor_safety.py --signatures /tmp/before <course>
./scripts/check_refactor_safety.py --logging --print-keywords <course>
```
- `Programming/PORR` -- its pytest suite solves systems up to 10000x10000 and And run mypy per directory afterwards: it found 12 latent TypeErrors in EARIN
runs for many minutes at full CPU. Under the 2G/2-core cap it will be that ruff could not see -- call sites still passing positionally to arguments
OOM-killed rather than finish. It needs either a smaller default parameter the pass had made keyword-only.
set for `run`, or to be marked as a deliberately heavy target.
- `Programming/ZPOB` -- latexmk exits 12 from bibtex even though `esej.pdf` is ### 6. Disk
produced. Probably a missing/!stale .bib entry; needs a clean-room rebuild
to see the first real error rather than the cached one. `Programming/PORR/code/` holds 3.8 GB of generated .npz caches (poli3 alone is
2.3 GB). All gitignored, all regenerable, none of it needed unless the full
benchmark is re-run.
## Standing rule ## Standing rule
A gate lands only once the thing it gates is clean, so A gate lands only once the thing it gates is clean, so `pre-commit run
`pre-commit run --all-files` is green at every commit. Every hook still missing --all-files` is green at every commit. Every hook still missing from
from `.pre-commit-config.yaml` is listed there with what blocks it. `.pre-commit-config.yaml` is listed there with what blocks it.