WUT_Computer_Science/TODO-refactor-remaining.md

TODO: remaining work on the gate refactor

REMOVE ME AFTER FINISH

What is done, what is not, and the real numbers, re-measured 2026-08-28 after the lint campaign started. Companion to TODO-file-length-250.md, which parks one specific blocking decision.

Done

Area	State
Vendored manifest	gates/vendored.txt, 8 entries, mirrored into ~/utils
Build artifacts	189 untracked, .gitignore closed, 0 tracked-but-ignored files
no-binaries gate	Path-scoped .binary-allowlist; verified blocking AND passing
Markdown	4 namespaces, all under 250 lines, CLAUDE.md written
pre-commit	15 hooks, green on all files -- ruff, ruff format and no-suppressions landed 2026-08-29
pre-push	pre-commit install --hook-type pre-push via install.sh
GitHub CI	pre-commit + md-naming, both green
run.sh	Root harness + per-course runners over one shared library
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

The lint campaign

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.

	ruff findings
Baseline, before any of this	9,281
After the format + safe-fix pass and excluding TRAK/sightpy	3,686
Now	0

Every course is at zero. 9,281 findings to 0.

What that cost, and what it bought, is in the commit messages; the standing rules for the next pass are below.

mypy: run per directory; the six deliberate errors are gone

pyproject.toml sets strict = true and CLAUDE.md says the repo runs mypy. mypy IS installed now (~/.local/bin/mypy) -- the earlier note here saying it was not is out of date. "Zero findings" in a commit message still means zero RUFF findings unless it says otherwise; only TRAK has been type-checked.

Course	mypy --strict errors
WDWR, SPD, MOM, ECRYPT_PROJECT	0
ECOTE	14
NLP	29
EARIN/lab1 alone	46
TRAK	0 -- cleared 2026-08-29
twm_4	0 -- cleared 2026-08-29
PBAD	not run (no venv; notebooks only)
PSD	0 -- cleared 2026-08-29 (scoped override; see below)
ERSMS-project	0 -- cleared 2026-08-29 (typed DeclarativeBase)

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.
• Point it at the course's own venv or every import is unresolvable: mypy --strict --python-executable Programming/<course>/.venv/bin/python <dir>. Without that, TRAK reported 4 phantom matplotlib import errors on top of the real ones.
• ERSMS-project is at 0 (was 4), fixed 2026-08-29. The old note here claimed a fix "would rewrite both models"; that was wrong. flask-sqlalchemy 3.1.1 does ship py.typed. The actual blocker was that class User(db.Model) is attribute access, which mypy cannot resolve in a base-class position. backend/models.py now declares a named DeclarativeBase with SQLAlchemy 2.0 Mapped[] columns, and the six legacy Model.query call sites became db.session selects, because the Model mixin goes away with the base. Verified by driving the real routes through Flask's test client with Firebase stubbed: 16 scenarios and both CREATE TABLE statements byte-identical to the submitted version. Two traps worth keeping: mapped_column(ForeignKey("user.uid")) silently infers VARCHAR from the referenced column, which changed the submitted user_id INTEGER until an explicit Integer was put back; and backend/Dockerfile copied only app.py, so the split needed it too.
• PSD is at 0 (was 2), by a scoped [[tool.mypy.overrides]] for temperature_anomaly_detector with disallow_subclassing_any = false. pyflink ships no types AND is not installed in that venv, so a hand-written .pyi would assert an API nothing here can check. Recorded in CLAUDE.md as well as here, because this file gets deleted and that one does not.
• Point MYPYPATH at Programming/PSD/zin3/python/code for that tree: the modules import model.* via a runtime sys.path.append, which mypy cannot follow.
• pyproject.toml now carries a [[tool.mypy.overrides]] block with ignore_missing_imports for Imath, OpenEXR, OpenGL and matplotlib. Those (plus keras, tensorflow, sklearn, seaborn, kafka and pyflink) ship neither stubs nor py.typed; without it mypy cannot import them at all and reports nothing else about the file. It is not a suppression of our own code -- do not extend it to anything we wrote.

Found while proving the run guard, not yet fixed

NotProgramming/MOM was recorded as runnable and was not: _first_file '*.tex' used find -print -quit, which handed back report_three/sections/02-model-dwukryterialny.tex, and latexmk faithfully tried to typeset a bare \section. It picks a file containing \documentclass now, and MOM, ELAC, AIS, SPD, ZPOB, SDM, DPZ and ESOEN all exit 0.

Two things surfaced on the way and are still true:

• A multi-report course builds one arbitrary report. PARTLY FIXED 2026-08-29: run.sh run <dir> now enumerates every document and either asks which, or builds all of them when not interactive, so nothing depends on readdir order any more. What is still open is that some of those documents are broken -- see below. MOM has three, ELAC two, AIS several drafts. Sorting looked like the fix until it swapped ELAC to projectA and AIS to report/final/ver1, both of which then failed with latexmk exit 12. That claim did not survive re-testing on 2026-08-29. With the build directories deleted first, ./run.sh run NotProgramming/ELAC --batch and ./run.sh run Programming/AIS --batch both build every document and exit 0. The exit 12 reproduced once in this session against pre-existing build/ state and not once from clean, so the likeliest cause is stale artifacts rather than a broken document -- but the original failing state is gone and that is an inference, not something re-verified. If it comes back, delete build/ before concluding anything about the document.
• unityhub --version never returns on this machine, which is why _works carries a timeout 5. Use _works only for tools that answer --version; _have is still right for the other ten probe call sites.

Found by actually running the programs, not yet fixed

run.sh run executes what it builds as of 2026-08-29, and the first thing that fell out is a course that had never been run by the harness at all:

• EPFU/labs/krudnic3_lab1.c dies with SIGFPE (exit 136) on printf("\n%f", i_one / i_two) -- an integer division by zero. It was invisible before because EPFU's stub pins --entry to penguins/src, so the lab was never compiled, let alone run. gcc also warns twice about %d/%f against the wrong argument types on lines 12 and 14. Left alone for now: it is a submitted deliverable and fixing it is a separate decision from making the runner work.
• ECOAR overwrites a tracked deliverable when it runs. C/puzzle.out writes C/dest.bmp beside its source, so the before/after tree guard fails the run -- correctly. It was invisible before for the same reason as EPFU's lab: the runner built puzzle.out and never executed it. The fix is to make the program write into build/, which means touching a submitted .c, so it is recorded rather than done. git checkout -- restores the file meanwhile; the guard is what makes that recoverable at all.

Still open

1. The 250-line cap: 50 files

Type	Count	Note
.txt	27	Blocked -- see TODO-file-length-250.md
.py	10	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. TRAK is already clear: its three over-cap files were split in the same pass that linted them, each verified by a byte-identical render. twm_4/TWM_KerasIntro.py joined the list at 407 lines and should NOT be split: it is an nbconvert export, and a partial one
.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

9 requirements.txt, 5 package.json, 7 pom.xml, 1 .csproj, none pinned. The upgrade and the gate must land in the SAME commit.

4. File-rewriting hooks

trailing-whitespace and end-of-file-fixer are deliberately absent; they want their own reviewed commit.

5. Three checks that must be run on every future pass

scripts/check_refactor_safety.py exists because ruff and a smoke run BOTH missed three regressions this campaign introduced. Run it before and after any automated rewrite:

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>

And run mypy per directory afterwards: it found 12 latent TypeErrors in EARIN that ruff could not see -- call sites still passing positionally to arguments the pass had made keyword-only.

Prefer a check the program itself settles. TRAK's ray_tracing0 path has no RNG at all, so main.py --algorithm ray_tracing0 --output ../build/x.png renders byte-identically every time: refactoring 109 findings out of rendering.py and splitting it in two was verified by one md5 comparison. The cornell_box path is stochastic and cannot be used that way -- its ray count drifts by ~20 between runs on its own. Where an RNG is unavoidable, do the restructure and the NPY002 swap as SEPARATE steps: the first must be bit-identical under an external seed, only the second may move the pixels.

6. Disk

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

A gate lands only once the thing it gates is clean, so pre-commit run --all-files is green at every commit. Every hook still missing from .pre-commit-config.yaml is listed there with what blocks it.