shape-doctor.py: the `pins` row keeps its gate where `update-shape.py check` says REFUSAL AHEAD beside a merged-away row, so it no longer says that the `apply` `check` prints drops the row when that `apply` is refused, and the `shape currency` counts name every state `check` counts (#676) by brettheap · Pull Request #751 · opensoft/openRepoShape

brettheap · 2026-10-16T23:14:46Z

Lane: openreposhape-3 (openRepoShape-3)
Claim: #676 (comment)

Closes #676.

Stacked on #742 (#683); lands after it. This branch starts at #742's head 3027937d, so until #742 lands this PR's diff shows #742's commits too. Two reasons:

refusals_ahead asks shape-doctor.py and update-shape.py: run from a partial clone of the standard, the shape currency row asks without fetching whether the clone holds what the comparison reads, and is CANNOT ANSWER with a fetch for a person to run where it does not, and a read that fails is refused, never a copy called both (#683) #742's partial_clone_row before it calls prepare.
Both PRs edit check_shape_currency.

Re-measured on main `66b230ed` (with #742, which does not touch either row)

The issue's two lines still hold. The root is tests/test_update_shape_merged_away.py's adopted root, with shape/Makefile merged away and AGENTS-shape.md kept as a committed symlink to the same bytes.

update-shape.py check says merged-away and copy-is-link, and REFUSAL AHEAD: \apply` will refuse while these are unresolved — AGENTS-shape.md`.
pins row: NEXT update-shape.py check. Its reason ends "…reports it `merged-away`, and the `apply` it prints drops its pin row in the re-pin commit: the step the `shape currency` row names too". No refusal_ahead in the detail.
shape currency row: 9 unchanged / 0 upstream-changed / 0 locally-modified / 0 both / 0 upstream-added / 1 merged-away … : shape/Makefile, AGENTS-shape.md. That is 10 counted over 11 rows, with the link's path under no count.
I used AGENTS-shape.md rather than the issue's .gitignore because git does not follow an in-tree .gitignore or .gitattributes kept as a symlink. A copy nothing reads at run time keeps every gate's answer the same.

What changed and why

shape-doctor.py

with_merged_away_rows (shape-doctor.py:2662; new docstring paragraph at :2693; call at :2714). After the linked_record check, it asks refusals_ahead.
- None (the doctor cannot ask): the row is returned untouched, its NEXT the gate.
- Non-empty: the row keeps the gate's NEXT and why. The reason says what check reports: "…so `update-shape.py check` reports it `merged-away`, but it also says REFUSAL AHEAD over AGENTS-shape.md (copy-is-link), and the `apply` it prints refuses while that is unresolved, so it drops no pin row yet". The detail gains merged_away and refusal_ahead ({path: why}).
- Empty: the row and its words are byte for byte as before: NEXT check, and the sentence about the apply dropping the row.
refusals_ahead (:2745, new) asks check's own two REFUSAL AHEAD questions over the rows prepare classifies:
- each row that is a conflict (Row.is_conflict: both, upstream-removed, unmapped, copy-missing, copy-is-link, never merged-away), by its state;
- each file apply would rewrite that has another name (hard_linked_rewrites, update-shape.py apply overwrites a pinned copy, contracts/shape-pin.yaml and the manifest in place (Rollback.write opens the path r+b), so one kept as a HARD link is rewritten through its other name, a file outside the root (or a cp -al snapshot of the whole root) that no check showed and no pin covers, while the README, the one path guarded with st_nlink > 1, is refused #422), as hard-link.
- Beyond the issue's text: the hard-link half is my addition. check prints REFUSAL AHEAD for it too, and apply refuses it (update-rewrite-hardlink), so the old sentence was false there as well.
- It returns None where it cannot ask: the pin does not read; the checkout of the standard is a partial clone short of what the comparison reads, where prepare would fetch (shape-doctor.py and update-shape.py: run from a partial clone of the standard, the shape currency row asks without fetching whether the clone holds what the comparison reads, and is CANNOT ANSWER with a fetch for a person to run where it does not, and a read that fails is refused, never a copy called both (#683) #742's partial_clone_row); or prepare refuses. The shape currency row says which, and the pins row keeps its gate. So the doctor still fetches nothing.
- Cost: a second prepare per doctor run, only where every pins finding is a merged-away row.
check_shape_currency's counts (:4631-4634). The five states print always, as before. Every other state in update-shape.py's ORDER with a non-zero count follows them, in ORDER's order: merged-away, already-at-target, upstream-removed, unmapped, copy-missing, copy-is-link.
- merged-away still comes straight after the five, so a root with none of the new states reads byte for byte as before. detail.counts already held them all.

Tested

The tests are in tests/test_update_shape_merged_away.py, which owns #502's merged-away root and its helpers.

The pins row beside a copy kept as a link (:450, through the linked_beside_merged fixture at :420): refusal_ahead == {"AGENTS-shape.md": "copy-is-link"}, NEXT without update-shape.py, no "the `apply` it prints drops", and the REFUSAL AHEAD clause named. The fixture first asserts that check itself says merged-away, copy-is-link and REFUSAL AHEAD over the link.
The counts over the same root (:461): the summary ends / 1 merged-away / 1 copy-is-link, and its counts add up to detail.counts. The old merged-away counts test now shares that helper, assert_the_counts_sum_to_the_rows (:403).
The pins row beside a hard-linked pin (:472): refusal_ahead == {"contracts/shape-pin.yaml": "hard-link"}, and the gate is kept.
Run from a partial clone short of what check reads (:486): nothing is fetched (rev-list --missing=print, as shape-doctor.py and update-shape.py: run from a partial clone of the standard, the shape currency row asks without fetching whether the clone holds what the comparison reads, and is CANNOT ANSWER with a fetch for a person to run where it does not, and a read that fails is refused, never a copy called both (#683) #742's tests ask), and the gate is kept. It imports shape-doctor.py and update-shape.py: run from a partial clone of the standard, the shape currency row asks without fetching whether the clone holds what the comparison reads, and is CANNOT ANSWER with a fetch for a person to run where it does not, and a read that fails is refused, never a copy called both (#683) #742's moved, partial_clone_of and doctored (:48).
Mutants:
- Against shape-doctor.py and update-shape.py: run from a partial clone of the standard, the shape currency row asks without fetching whether the clone holds what the comparison reads, and is CANNOT ANSWER with a fetch for a person to run where it does not, and a read that fails is refused, never a copy called both (#683) #742's head, without this change, the four new tests fail; the old counts test passes.
- With refusals_ahead's partial-clone guard removed, the fourth fails on "the doctor fetched".

Command, run in three groups at once (stub gh first on PATH, GH_TOKEN=bogus, empty GH_CONFIG_DIR):

/usr/bin/python3 -m pytest -q -p no:cacheprovider --basetemp=<scratch>/bt-w676-<group> -o tmp_path_retention_policy=failed <files>

Results, all on b7312258:

tests/test_shape_doctor.py: 428 passed, 3 skipped, 1 xfailed in 356.07s (0:05:56).
tests/test_update_shape_merged_away.py, tests/test_update_shape_hardlink.py, tests/test_doctor_partial_clone.py, tests/test_doctor_gitlink_repairs.py and tests/test_doctor_pin_restore_merges.py, together: 98 passed in 135.01s (0:02:15).
tests/test_doctor_next_is_a_command.py, tests/test_doctor_legs_members_next.py, tests/test_pin_source_env_collisions.py, tests/test_shape_pin_files_not_a_list.py, tests/test_update_shape_next_quoting.py, tests/test_repo_hygiene.py and tests/test_cli_reference.py, together: 496 passed in 254.38s (0:04:14).

Pinned copies

None. shape-doctor.py is not copied into projects.

Docs

No doc states the pins row's merged-away sentence or the shape currency row's list of counted states, so README.md, AGENTS.md, the handbook and docs/cli.md are unchanged.

Lands after

shape-doctor.py and update-shape.py: run from a partial clone of the standard, the shape currency row asks without fetching whether the clone holds what the comparison reads, and is CANNOT ANSWER with a fetch for a person to run where it does not, and a read that fails is refused, never a copy called both (#683) #742 (shape-doctor.py: run from a partial clone of the standard, the shape currency row fetches what the clone lacks, and with its remote out of reach calls each copy the standard changed since the pin both, so a doctor that fetches nothing fetches, and offline says DRIFTED of copies nobody edited #683). This PR is stacked on it.
On Tracking: update-shape.py and bump-leg.py, keeping a project's shape copies and leg pins current #458, the issue asks for its line in comment 6158353941 to be marked → #676 and ticked when this closes. That is not done here.

🤖 Generated with Claude Code

Summary by Sourcery

Make shape diagnosis refuse safely when upstream data is unavailable and accurately reflect update-shape refusal behavior and state counts.

New Features:

Detect partial upstream clones that cannot safely answer shape comparisons and provide a refetch command for users to resolve them.
Preserve pin-gate findings when update-shape reports REFUSAL AHEAD conditions that prevent the proposed apply from removing merged-away rows.

Bug Fixes:

Distinguish unreadable upstream files from files that are absent, preventing failed reads from being misclassified as upstream changes or both-sided changes.
Ensure pin findings do not claim that a refused apply will drop rows.

Enhancements:

Report every non-zero update-shape state in shape currency counts, keeping the output aligned with the states check classifies.
Recognize git promisor remotes and partial-clone configuration consistently with Git's behavior.

Tests:

Add coverage for partial-clone detection, non-fetching behavior, unreadable upstreams, promisor configuration, REFUSAL AHEAD handling, hard-linked pins, and comprehensive state counts.

…standard, the `shape currency` row asks without fetching whether the clone holds what the comparison reads, and is CANNOT ANSWER with a fetch for a person to run where it does not, and a read that fails is refused, never a copy called `both` (#683) Measured again on main de92614 with git 2.43: run from a `--filter=blob:none` clone of the standard, the doctor made five lazy fetches, one under each `git show` of a copy the standard changed since the pin (missing objects at the pin 1255 -> 1250), and with the clone's remote out of reach it said `DRIFTED (5 both)` of copies nobody edited; `update-shape.py check` printed the same five `both` rows. shape-doctor.py: - `partial_clone_row`: where `partial_clone` holds, `objects_lacking` asks `git rev-list --objects --no-walk --missing=print` of the pinned commit and of HEAD, before `prepare` or any `ls-tree` reads them. Where either lacks an object, the row is CANNOT ANSWER (`environment`, exit 3, error `shape-doctor-partial-clone`), and its NEXT is `git -C <shape> fetch --refetch --no-filter <promisor remote>`. - `promisor_remotes`: git 2.43's own reading of a promisor remote. `promisor = false` alone is no longer partial (git fetches nothing there), a `partialclonefilter` is (git fetches there whatever `promisor` says), and `extensions.partialclone` names one. - `check_shape_currency`: a `prepare` refusal of a read that failed (`update-upstream-unreadable`) gets a `why` of its own and no `fetch --all`, which would bring nothing to read it. - `as_the_standard_wrote_it` takes that refusal as "not proved", as it took a None. update-shape.py: - `Upstream.blob` reads with `git cat-file blob`, and where that fails, `files_at` (one `ls-tree -r` per revision) says whether the revision lists a file at the path: None where it does not, a directory included, and `update-upstream-unreadable` where it does, so `check` and `apply` refuse rather than print `both`. tests/test_doctor_partial_clone.py: new; nothing is fetched where `rev-list --missing=print` lists the same objects before and after. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

One conflict, in shape-doctor.py's EXIT CODES list, exit 3: this branch added a partial clone lacking what the comparison reads (#683), and main added a validator that crashed or cannot be given what it needs (#278, #410) and a naming policy that does not load (#678). All are kept, in main's form. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

… check` says REFUSAL AHEAD beside a merged-away row, so it no longer says that the `apply` `check` prints drops the row when that `apply` is refused, and the `shape currency` counts name every state `check` counts (#676) The `pins` row: `with_merged_away_rows` named `check`, and said the `apply` it prints drops each merged-away row, wherever the gate's only findings were merged-away rows and neither the pin nor the manifest is a link. A pinned COPY kept as a link is `copy-is-link` to `check`, which says REFUSAL AHEAD over it, and its `apply` exits 2 writing nothing; so does `both`, `upstream-removed`, `unmapped`, and a file `apply` would rewrite that has a hard link. `refusals_ahead` now asks `check`'s own two questions over the rows `prepare` classifies (`Row.is_conflict`, and `hard_linked_rewrites`). Where either names a file, the row keeps the gate as its NEXT, names what `check` reports, and leaves out the sentence about `apply`. Where the doctor cannot ask -- the pin does not read, the checkout is a partial clone short of what the comparison reads (`partial_clone_row`, #683), or `prepare` refuses -- it keeps the gate too, so it never fetches. The `shape currency` row: the reason printed the five original states and `merged-away` only, so a `copy-is-link`, `copy-missing`, `upstream-removed`, `unmapped` or `already-at-target` row stood under no count. Every non-zero state of `update-shape.py`'s `ORDER` now follows the five, in that order, so a root with none of them reads as before. Stacked on #742 (#683): `refusals_ahead` uses its `partial_clone_row`. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

sourcery-ai · 2026-10-16T23:15:09Z

Reviewer's Guide

The PR corrects merged-away pin guidance by modeling update-shape.py's refusal conditions, expands shape-currency counts to every nonzero check state, and adds defensive partial-clone handling so the doctor never fetches or reports false drift when comparison objects are unavailable.

Flow diagram for partial-clone safety checks

flowchart TD
    A[check_shape_currency] --> B[read_pin]
    B --> C{partial_clone}
    C -- no --> D[prepare]
    C -- yes --> E[objects_lacking]
    E --> F{objects missing}
    F -- yes --> G[partial_clone_row]
    G --> H[CANNOT ANSWER; person runs fetch --refetch --no-filter]
    F -- no --> D
    D --> I{upstream readable}
    I -- no --> J[update-upstream-unreadable]
    I -- yes --> K[classify rows and count states]

File-Level Changes

Change	Details	Files
Keep the `pins` finding gated when `update-shape.py check` reports REFUSAL AHEAD, instead of claiming the generated apply will drop the merged-away row.	Added a second preparation-based check for conflicting rows and hard-linked rewrites that cause apply refusals. Preserved the gate and added structured `refusal_ahead` details when refusals are found or the doctor cannot safely ask. Updated reason text and documentation to distinguish refused applies from successful re-pin drops.	`shape-doctor.py` `tests/test_update_shape_merged_away.py`
Make shape currency report all nonzero states counted by update-shape.py, not only the original five states and merged-away.	Emit nonzero states from update-shape.py's ORDER after the always-present states. Added coverage ensuring printed counts sum to all classified rows, including copy-is-link.	`shape-doctor.py` `tests/test_update_shape_merged_away.py`
Prevent partial-clone reads from fetching implicitly or producing misleading drift classifications.	Detect promisor remotes and inspect pinned and standard commits with rev-list --missing=print before comparison. Return a CANNOT ANSWER shape-currency row with a person-run --refetch --no-filter command when required objects are missing. Distinguish missing files from unreadable upstream files using git cat-file and ls-tree, raising update-upstream-unreadable for failed reads. Cover blob and tree filters, promisor configuration variants, no-fetch behavior, and recovery commands.	`shape-doctor.py` `update-shape.py` `tests/test_doctor_partial_clone.py`

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#676	Make the `pins` row’s explanation and NEXT command reflect `update-shape.py check`’s refusal state when merged-away rows coexist with other conflicts, rather than claiming a refused `apply` would drop pin rows.	✅
#676	Make the `shape currency` summary count every non-zero state in `update-shape.py`’s `ORDER`, while continuing to print the five established states even when their counts are zero.	✅

Possibly linked issues

shape-doctor.py: the pins row says check's apply drops merged-away rows where check says REFUSAL AHEAD (a pinned copy kept as a link), and the shape currency counts leave out five of check's states #676: Link: it implements both requested shape-doctor fixes, with additional partial-clone and hard-link safeguards.

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sonarqubecloud · 2026-10-16T23:15:39Z

Quality Gate passed

Issues
2 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

brettheap · 2026-10-16T23:32:59Z

(lane openRepoShape-3, 2026-10-16T23:33:01Z) Lane 3's independent review of #751 at b7312258, stacked on #742 (RV-f, ruling 8): READY. Two test gaps (surviving mutants) go to a v1.1.1 follow-up. It lands after #742, once its Linux tests job is green.

#676's claims hold on main and on #742's head:

check says REFUSAL AHEAD … AGENTS-shape.md, while the pins row says the apply it prints "drops its pin row".
The counts read 11 over 12 rows.

On the head, the row agrees with check in every state RV-f built. Each root has a merged-away shape/Makefile, and the last column is the printed apply, pasted:

root	`check` says	`pins` row	counts	the pasted `apply`
merged-away only	nothing ahead	NEXT `check`, unchanged	`/ 1 merged-away`	exit 0, row dropped
a copy kept as a link	`AGENTS-shape.md`	gate kept, `copy-is-link`	`… / 1 copy-is-link`	exit 2 `update-rewrite-symlink`
the pin hard-linked	the pin	gate kept, `hard-link`	`/ 1 merged-away`	exit 2 `update-rewrite-hardlink`
an unmapped row	`extra/notes.txt`	gate kept, `unmapped`	`… / 1 unmapped`	exit 2 `update-conflict`
`both`	`scripts/validate-pins.py`	gate kept, `both`	`1 both`	exit 2 `update-conflict`
upstream-removed	`AGENTS-shape.md`	gate kept, `upstream-removed`	`… / 1 upstream-removed`	exit 2 `update-conflict`

Other checks

Nothing fetches: blob:none and tree:0 clones show 0 fetches.
The second prepare leaves the output identical. It costs about 0.1 s and 38 more git processes.
Mutants: four of six are killed. Two survive:
- a prepare refusal returning {} instead of None;
- counting only copy-is-link as a refusal ahead.
Follow-up tests (v1.1.1):
- the prepare-refuses branch (shape-doctor.py:2775), where the row keeps its gate and has no merged_away key;
- one parametrized test over both, upstream-removed and unmapped beside a merged-away row (:2777).
Tests (stub gh): 98 passed and 282 passed. The writer ran test_shape_doctor.py: 428 passed, 3 skipped, 1 xfailed.
Merges: clean with shape-doctor.py: the placement row asks a leg's top-level single-repository.yaml the staying-single record's question only where kind: makes it the record, so one declaring release-config is asked the general question as plan asks it, and an answered entry names that rule (#691) #734, shape-doctor.py: a conflicted shape pin's NEXT reads both sides' pins, so a copy conflicted beside it that only the side not taken has a files: row for is named in its why and left_for_a_person for a person to merge, and never taken (#687) #736, shape-doctor.py: an own-copy validator row whose crash is a root's lost scripts/repo_shape.py names git -C <root> checkout HEAD -- scripts/repo_shape.py as its NEXT (none where HEAD no longer holds it) and the validator in its WHY (#697) #737 and openRepoShape --doctor: a signal sent to the command's shell alone waits for the doctor, so its clone of the standard is never removed while shape-doctor.py runs from it, and a doctor ended by a signal leaves nothing (#680) #740.

Lane: openreposhape-3 (openRepoShape-3)

sourcery-ai · 2026-10-17T00:41:28Z

Sorry @brettheap, you've used your own review budget of 250,000 diff characters for the last 7 days.

You can request another review in 1 day and 1 hour by commenting @sourcery-ai review. Upgrade to get a review now.

main gained 25 pull requests since de92614: #634, #699, #671, #719, #701, #717, #700, #702, #722, #720, #725, #721, #728, #705, #727, #718, #744, #743, #749, #740, #737, #734, #742, #751 and #736. No conflict: AGENTS.md, adopt-project.py and docs/cli.md merged as text, and README.md and docs/handbook.html are unchanged by the merge. README.md is 1473 lines, its cap; AGENTS.md 494, its cap; every handbook marker is current; `render-cli-reference.py --check` is ok. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…es every reason THIS checkout cannot answer, and the notes are current to main bf1f099 with the 25 pull requests since de92614 (#563, #683) - W683 and RV-f's N4 on #742: README's exit-3 list (Keeping a project's shape current, :1208-1220) and its handbook twin (`doctor`) named only a pin whose commit this checkout does not carry. They now say, as shape-doctor.py's EXIT CODES does: a pin's commit it lacks, a partial clone missing what is compared (#683), a read that fails (`update-upstream-unreadable`), a crashed validator of its own (#278, #410), or its own naming policy not loading (#678). +1 line, with tests/readme-cap.d/683.txt; README.md is 1474, its cap (1422 + 2 + 5 + 12 + 22 + 10 + 1). The two `Keeping a project's shape current` markers move: `doctor` text and marker, `current` marker only. - The notes, "What changed since v1.0.1", one entry per pull request from `git log --first-parent de92614..bf1f099`, each from its squash commit and the issues GitHub says it closes: - adopt-project.py: #699, #719, #749, #727, #717, #728 (with #621's hint), #743 + #720 + #718, #722, #721; - update-shape.py, bump-leg.py and a project's own scripts: #702 (with the pinned validators), #634; - scaffold, setup, family and the shared readers: #725, #671, #744; - shape-doctor.py: #742, #701, #737, #751, #736, #734, #700 + #705, #740; - install, CI and the docs: the exit-3 sentence above. - Counts (99 pull requests since bfed143; 109 of 135 milestone issues closed at 10:28Z), the "current to main" sha and the open list (26) are at main bf1f099, still placeholders for tag time. Left for round B: lane 5's eight lines (#630 issuecomment-6227129879), whose pull requests #726, #747, #682, #724, #746, #745 and #738 are open drafts. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Brett Heap and others added 3 commits October 16, 2026 17:51

brettheap marked this pull request as ready for review October 17, 2026 00:41

brettheap merged commit e313701 into main Oct 17, 2026
5 checks passed

brettheap deleted the l3-676-pins-merged-away branch October 17, 2026 00:41

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shape-doctor.py: the `pins` row keeps its gate where `update-shape.py check` says REFUSAL AHEAD beside a merged-away row, so it no longer says that the `apply` `check` prints drops the row when that `apply` is refused, and the `shape currency` counts name every state `check` counts (#676) - #751

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Re-measured on main 66b230ed (with #742, which does not touch either row)

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