Drop the legacy experiment_design.csv migration (PP-03)

AGENTS.md

@@ -90,7 +90,7 @@ src/morphobricks_preprocessing/
   design.py         the rows of experiment_design.csv (an output only since v0.5.1): DesignTable/
                     DesignRow (read-only), the run's reconcile_design and design_issues against
                     the folders, write_experiment_design, parse_design_bytes (the strict parser
-                    of the draft's legacy migration); no reader for other bricks (SWEEP-PP)
+                    of a written file; nothing reads the file to prefill a draft); no reader for other bricks (SWEEP-PP)
   design_derive.py  derive_design/write_derived_design: experiment_design.csv from a published
                     description (Spec experiment-v1 11), written by design.write_experiment_design
   design_values.py  the design file's header check (no column twice or unnamed, #83), booleans,
@@ -129,7 +129,7 @@ src/morphobricks_preprocessing/
   draft_ids.py         proposed IDs: the folder label or raw header name only when the reader would
                     accept it as written, else none (never repaired); draft.py the draft
                     (IdSlot proposed/confirmed, open questions, unit_rows with condition_id,
-                    repeat_group, technical_repeat_id) and migrate_legacy_design
+                    repeat_group, technical_repeat_id)
   image_type.py     image type (P4): FLUORESCENCE/RGB, review_image_type (suggestion from
                     TiffMetadata.rgb_samples and the confirmed roles, whether RGB is possible via the
                     brick's check_rgb), image_type_issues (rgb_not_possible)
@@ -663,8 +663,9 @@ functions the tests use.
   `load_design`, the strict `read_confirmed_design`/`ConfirmedDesign`/`DesignCheckError` and
   `RunInputs.design()` are removed; bricks take `repeat_group` from the description
   (`Fov.repeat_group`). `parse_design_bytes` (strict, `DesignFormatError` naming line and
-  column, also for a header naming a column twice or not at all, #83) remains for the draft's
-  experiment-v1 §7 migration of a legacy file.
+  column, also for a header naming a column twice or not at all, #83) remains to check a
+  written file; the draft's legacy migration was removed (Spec ADR 0002 AR10 (9)), and no code
+  path reads an `experiment_design.csv` to propose or prefill a draft.
 - **The run's check:** `reconcile_design` keeps the derived rows of known folders, reopens only
   groups that gain a folder (`design_not_confirmed`), drops removed folders.
 - **v0.5.1: an output only.** Every run is described (`A_DESCRIPTION_REQUIRED` without a

CHANGELOG.md

@@ -8,6 +8,34 @@ v0.5.1: no run before v0.5.1 is read.)
 
 ## Unreleased (v0.5.1)
 
+### The legacy `experiment_design.csv` migration is removed (inventory PP-03)
+
+Spec ADR 0002 AR10 (9) and experiment-v1 §7 (MorphoBricks-Spec PR 25): no backward
+compatibility before the first pipeline release. The Spec is re-vendored at `cc9820f`
+(`tools/vendor.py`; `--check`: identical).
+`draft_format.SPEC_COMMIT` follows the pin, so an answers draft file (`morphobricks.draft.json`)
+saved under `1bed024` is refused as before (`spec_commit_mismatch`) and not carried over.
+
+- **Breaking: an old `experiment_design.csv` is no longer migrated.** Preprocessing never reads
+  an `experiment_design.csv` from an output folder to propose or prefill a draft or a
+  description (Spec §7); `describe` and the notebook build the draft from the folders alone.
+  Describe the experiment in the notebook. The derived `experiment_design.csv` stays an output.
+- Removed: `draft.migrate_legacy_design`, `LegacyMigrationRefused`, `MigrationNote`,
+  `Draft.origin`, `Draft.legacy_missing`, `Draft.notes`, `Draft.unresolved_controls` and the
+  open questions `legacy_folder_missing` and `control_unresolved` (nothing else produced them),
+  with their texts in `describe` and the notebook. `describe` no longer says "cannot be drafted
+  from experiment_design.csv".
+- Kept: `design.parse_design_bytes` and `design_issues` (the run's reconcile check and the tests
+  of the written file still use them).
+- Tests: the Spec scenario P30 follows the amended Spec (`v13` derived twice with a frozen clock
+  moved by a day; both files equal the `v13` golden; the clock is never read). The migration
+  tests are deleted; `tests/test_orphan_design_csv.py` and `test_cli_describe` check that an
+  orphan `experiment_design.csv` in the output folder is ignored by draft creation, `describe`
+  and the notebook (open and reopen).
+- The valid Spec fixtures give byte-identical `plane_histograms.csv`, `experiment_design.csv`
+  and manifest (apart from times) before and after; the refusal codes of the 135 invalid
+  fixtures are unchanged.
+
 ### Fixed: the notebook output is no longer flooded with debug messages
 
 ImageJ TIFFs have a plain-text description, so reading it as OME-XML failed for every image and

docs/conformance.md

@@ -128,7 +128,7 @@ GS1: a scenario that names fixtures is shown on those fixtures; further fixtures
 | P27 | Deferred to the Stage 2 gate per ADR 0001 GS1 (MorphoBricks-Spec `cdc1841`) | The outcome is a brick's (per-request `binary_mask_policy`). Preprocessing's own parts passed: `A_MASK_NOT_INSTANCES` (`test_a_error_classes`) and the section 2 "Mask fields" row (`i111`, `i112`, below) |
 | P28 | Passed | `test_spec_run_description`: `test_p28_each_new_batch_is_not_yet_checked_until_the_mask_step_has_read_it` (`v08`, with the 0-5 binary batch); `test_spec_run_inputs_semantic`: `test_p28_a_mask_file_not_yet_checked_is_refused_when_read_until_the_step_checked_it` (`v08`), `test_p28_on_v09_each_batch_of_masks_is_unchecked_until_the_mask_step_reads_it` (`v09`: three batches, each `not yet checked` and `A_MASK_UNCHECKED` until the mask step reads it, earlier batches stay `checked`) |
 | P29 | Passed | `test_spec_discovery` on `v07` published with mask folders `NA`, ` cells` and `Cafe\u0301` beside `nuclei` and `cells`: `test_p29_a_run_with_published_v07_refuses_the_mask_type_names` (`run_experiment` refuses with `R_MASK_TYPE_NAME_INVALID` naming ` cells`, `NA` and `R_FOLDER_NOT_NFC` naming `Cafe\u0301`, beside `R_MASK_TYPE_NOT_DECLARED`; nothing renamed), `test_p29_the_mask_step_refuses_the_names_with_a_published_description` (the step is not ready), `test_p29_the_command_line_check_and_masks_refuse_the_mask_type_names` (no `mask_relationships.json`); `test_notebook_name_refusals`: `test_p29_the_described_folder_check_refuses_the_mask_type_names`, `test_p29_pairing_the_masks_again_keeps_the_refusal`, `test_p21_p29_a_refused_name_blocks_check_and_save` (no `morphobricks.toml` is published, so the names never reach `E_ID_TEXT`). Without a description: the four `test_p21_p29_*_as_in_v0_4` above. Also the 5 synthetic-tree `test_p29_*`. Fixed in `0a2e25b` (on `a6a0343` the run gave only `R_MASK_TYPE_NOT_DECLARED`); the new tests fail on `c675f13` except those without a description |
-| P30 | Passed | `test_spec_derived_design`: `test_p30_the_derived_file_of_migrated_legacy_answers_differs_only_in_the_earlier_date` (`v13` tree, 2 cases): the `v13` legacy file migrated, answered with the proposed IDs and derived again is the legacy file byte for byte (and the golden); with `rep1` rows dated 2026-10-01 and 2026-10-15, the repeat takes 2026-10-15, the note lists both dates, and the derived file differs from the legacy file in one line only, the CTRL/rep1 date (the one-date groups `rep2`, `rep3` are byte-identical); under a frozen clock no clock is read. Also `test_draft`: `test_p30_a_group_with_two_dates_takes_the_latest_and_a_note_lists_both`, `test_a_confirmed_group_without_any_date_stays_open_and_takes_no_clock_date`. The answers state each unit's image type ("channels"): since audit batch 33 an unanswered image type is an open question (`unit_image_type_unanswered`), so the test answers it, as the merge `0ea3254` records |
+| P30 | Passed | `test_spec_derived_design`: `test_p30_the_derived_file_of_migrated_legacy_answers_differs_only_in_the_earlier_date` (`v13` tree, 2 cases): the `v13` legacy file migrated, answered with the proposed IDs and derived again is the legacy file byte for byte (and the golden); with `rep1` rows dated 2026-10-01 and 2026-10-15, the repeat takes 2026-10-15, the note lists both dates, and the derived file differs from the legacy file in one line only, the CTRL/rep1 date (the one-date groups `rep2`, `rep3` are byte-identical); under a frozen clock no clock is read. Also `test_draft`: `test_p30_a_group_with_two_dates_takes_the_latest_and_a_note_lists_both`, `test_a_confirmed_group_without_any_date_stays_open_and_takes_no_clock_date`. The answers state each unit's image type ("channels"): since audit batch 33 an unanswered image type is an open question (`unit_image_type_unanswered`), so the test answers it, as the merge `0ea3254` records **Amended after this run** (10 November 2026, re-pin to Spec `cc9820f`, ADR 0002 AR10 (9)): the legacy-CSV case was removed from P30; the test is now `test_p30_v13_derived_twice_with_a_clock_moved_by_a_day_equals_the_golden` and the migration tests named here are deleted. This row records the run on `1bed024`. |
 | P31 | Deferred to the Stage 2 gate per ADR 0001 GS1 (MorphoBricks-Spec `cdc1841`) | The outcome is MorphoCoverage's (prefill, confirmation). Preprocessing's own parts passed: `v27` valid with no warning, and editing `target` or `treatment_key` of `v27` changes no digest and no derived row (section 2 rows below) |
 | P32 | Passed | `test_draft`: `test_p32_forbidden_folders_get_no_proposal_and_nothing_is_adopted`, `test_p32_ordinary_folders_are_proposed_as_their_labels`; `test_spec_derived_design`: golden `v33`, `v34` and `test_the_file_names_folders_never_ids` |
 | P33 | Passed | `test_spec_reconcile`: `test_p33_a_a_renamed_condition_folder_is_not_attached_to_the_old_id`, `test_p33_b_the_statement_keeps_the_id_moves_the_folder_and_reopens_the_repeats`, `test_p33_c_the_old_folder_removal_needs_its_confirmation_and_the_id_stays_used` (`v33`; (a) asserts that the hand-made attachment is `t12` and gives exactly `R_CONFIRMED_ID_CHANGED`); `t10`, `t11`, `t12` against their predecessors in `test_spec_transitions`; `test_condition_folder_reopens` (2) |