Adds modified files from macbook before deleting repository.

CLAUDE.md

@@ -109,6 +109,10 @@ scripts/specimens/
   38_2026_08_17_tensile_s.py                # Batch S tensile, PA12 White/GF blend, Type IV (S1-S7) — xlsx_only, curve-only
   39_2026_08_18_tensile_t.py                # Batch T tensile, PA12 White/GF blend, Type IV (T1-T14) — xlsx_only, curve-only
   40_2026_08_19_tensile_u.py                # Batch U tensile, PA12 White/GF blend, Type IV (U1-U14) — xlsx_only, curve-only, outline-energy caveat
+  41_2026_08_23_flex_q.py                   # Batch Q flex, Nylon 11 (Q1-Q10) — xlsx_only, raw curve-only (no geometry → strain/stress/metrics null)
+  42_2026_08_23_flex_r.py                   # Batch R flex, Nylon 11 (R1-R10) — xlsx_only, raw curve-only
+  43_2026_08_23_flex_t.py                   # Batch T flex, PA12 White/GF blend (T1-T10) — xlsx_only, raw curve-only
+  44_2026_08_23_flex_u.py                   # Batch U flex, PA12 White/GF blend (U1-U10) — xlsx_only, raw curve-only
 
 data/
   D638/                                 # one JSONL per specimen (HF glob: data/D638/*.jsonl)
@@ -153,10 +157,10 @@ Same TestWorks framework, different schema. Notable renames you have to handle:
 ## Current state
 
 - `D638` config — 180 rows: 164 SLS across batches A-U (batch counts: A5 B5 C7 D5 E5 F5 G5 H3 I5 J4 J_MB5 K5 L6 M17 N5 O4 P11 Q13 R14 S7 T14 U14) + 3 PLA + 3 PETG + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White.
-- `D790` config — 90 rows: 80 SLS across batches C-P (batch counts: C9 D8 E10 F9 G4 H5 I5 J2 J_MB2 K3 L4 M5 N5 P9) + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White.
-- **Batches K-P have `db_print_date=None`** (print jobs not yet backfilled into Database) — SLS rows through J/J_MB have Database FKs (2026-07-12 backfill: E ← 2026-06-07 (same as D), F ← 2026-06-13, G ← 2026-06-09, H ← 2026-06-24, I ← 2026-06-25, J/J_MB ← 2026-06-27 (`D790 and D638 and other objects`)); K, L, M, N, O, P, Q still need the same treatment once their print jobs land.
+- `D790` config — 130 rows: 120 SLS across batches C-U (no O or S; batch counts: C9 D8 E10 F9 G4 H5 I5 J2 J_MB2 K3 L4 M5 N5 P9 Q10 R10 T10 U10) + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White.
+- **Batches K-U have `db_print_date=None`** (print jobs not yet backfilled into Database) — SLS rows through J/J_MB have Database FKs (2026-07-12 backfill: E ← 2026-06-07 (same as D), F ← 2026-06-13, G ← 2026-06-09, H ← 2026-06-24, I ← 2026-06-25, J/J_MB ← 2026-06-27 (`D790 and D638 and other objects`)); K, L, M, N, O, P, Q, R, S, T, U still need the same treatment once their print jobs land.
 - **`_lib.py` disambiguates same-date jobs by STL content.** Two 2026-06-27 prints share a date in Database; `resolve_database_fk` picks the one whose object list contains the standard's STL needle (`d638` / `d790`). Same fix will apply to any future same-date collision (e.g. 06-29 already has two jobs, though no ASTM specimens map there yet).
-- Total: 270 specimens, produced by 40 per-session scripts (some date folders — 2026_06_10, 2026_06_30, 2026_07_21 — contain more than one Test project/batch/specimen type).
+- Total: 310 specimens, produced by 44 per-session scripts (some date folders — 2026_06_10, 2026_06_30, 2026_07_21, 2026_08_23 — contain more than one Test project/batch/specimen type).
 - Batch I flex is missing TSR4 (excluded: `test_end_reason` is "Test Stopped", not a detected break) — sample_ids I1-I5 map to TSR{1,2,3,5,6}.
 - Batch H's 5 flex rows are `xlsx_only` (no raw TestRuns folder survived — see architectural decisions above); Batches K, L, M, N are `xlsx_only` too (no TestRuns/h5 handed off for those sessions at all, not just one project overwriting another) — every other row has full h5-derived curves.
 - **Batch J / J_MB (2026-07-06 print, tested 07/06 and 07/08) is the first split-batch label.** Both are the same physical print batch; `J` specimens were tested as-printed, `J_MB` specimens were media blasted post-print before testing. This deviates from the single-letter `batch_label` convention (see architectural decisions above) — deliberately, per user instruction, to keep the surface-treatment distinction visible without adding a new schema field. If more media-blast-vs-not comparisons get added, consider promoting this to a real `surface_treatment` field instead of continuing to overload `batch_label`.
@@ -169,10 +173,11 @@ Same TestWorks framework, different schema. Notable renames you have to handle:
   - **Its xlsx export is curve-only** — each sheet is just cols A-B (the already-analyzed strain/stress trace, col A mm/mm, col B kN/mm²) with **no cols D-F scalar block and no Width/Thickness**, unlike Batches K-P whose exports still carried Modulus/PeakStress/geometry. `build_row_from_xlsx`'s analyzed-curve branch handles it unchanged (populates strain/stress, leaves metrics null since `read_xlsx_scalars` finds nothing), but every Batch Q row's `geometry` and `metrics` come out fully null — the honest representation of a curve-only file; consumers re-derive peak/modulus from the curve. `notes` is set on the session so it flags this rather than emitting the generic xlsx-only caveat.
   - **13 specimens on 14 tabs, one "broken".** Tabs are named `"1"`..`"14"` (plain numbers, not `"SheetN"`), so `_resolve_sheet_name` falls back to positional order — fine here since the tabs are in order, so tab position == sheet index. Tab `"7"` holds only the text "broken" (physical specimen 7 broke, no curve); the `test_runs` list skips it and passes tab position as the explicit 4th-element sample number, giving Q1-Q6, Q8-Q14 (never Q7). Same skip-a-number pattern as Batch P.
   - **`load_database_jobs()` now degrades gracefully when the `Agentic-SLS-Database` sibling checkout is absent** (returns `{}` + warns instead of crashing on the missing `jobs.jsonl`). Batch Q — like all K-Q — passes `db_print_date=None`, so no FK lookup is needed; `resolve_database_fk` short-circuits on the None date. A row that *does* declare a `db_print_date` in a repo-less environment now warns "no Database job" instead of crashing. Check out the sibling repo to backfill real FKs.
-- **Batch R (2026-08-08) is the fourth Nylon 11 print** (D638 Type IV tensile only, `37_2026_08_08_tensile_r.py`, from the 188C/34mJ print of 2026-08-07), same curve-only xlsx export and figure treatment as Batch Q — except all 14 tabs (`Sheet1`..`Sheet14`, standard names this time) hold real curves, so sample_ids run R1-R14 with no gaps. D790 specimens from the Q/R prints exist physically but haven't been tested/handed off yet.
+- **Batch R (2026-08-08) is the fourth Nylon 11 print** (D638 Type IV tensile only, `37_2026_08_08_tensile_r.py`, from the 188C/34mJ print of 2026-08-07), same curve-only xlsx export and figure treatment as Batch Q — except all 14 tabs (`Sheet1`..`Sheet14`, standard names this time) hold real curves, so sample_ids run R1-R14 with no gaps. (The Q/R prints' D790 flex specimens were later tested on 2026-08-23 — see the Batch Q/R/T/U flex bullet below.)
 - **Batch S (2026-08-17) is the first PA12 White / PA12 GF blend print** (D638 Type IV tensile only, `38_2026_08_17_tensile_s.py`, recorder build 77 of 2026-08-16), curve-only xlsx like Q/R. Only S1-S7 exist: the stacked layout's upper level was never printed — the build was soft-canceled as it began. The laser energy was changed MID-PRINT via agent setup overrides (28 → 38 → 48 mJ/mm within the bottom stack's first ~0.3 mm), so the effective process point (48 mJ/mm, [48, 38] outlines, 168C, 50% overlap, 110% powder) is recorded in the row `notes` and in the printer's "…v2 As-Printed B77" profile — the pre-print profile does NOT describe these specimens. When a print has overrides, the recorder's `agent_actions`/`setup_overrides` history is the authoritative parameter record.
 - **Batch T (2026-08-18) is the second PA12 White/GF blend print** (D638 Type IV, `39_2026_08_18_tensile_t.py`, recorder build 78 of 2026-08-17): full stacked layout completed (T1-T14), uniform 56 mJ/mm fill / [56, 48] outlines / 168C / 130% powder — the outline-array setup override on this build landed BEFORE the first sintered layer (it re-staged the stale legacy array), so unlike Batch S it defines the process point rather than perturbing it.
 - **Batch U (2026-08-19) is the third PA12 White/GF blend print** (D638 Type IV, `40_2026_08_19_tensile_u.py`, recorder build 79 of 2026-08-18, full layout U1-U14): v4 profile — 56 mJ/mm fill, 172C surface, begin-layer 176C +20 s dwell, 130% powder. OUTLINE CAVEAT: the profile's outline scalars say [56, 48] but its legacy laserOutlineEnergyDensities array was stale at [28, 18] and build 79 had no pre-print staging override (unlike build 78/Batch T), so per the stale-array-wins firmware behavior the outlines most likely printed at [28, 18] — recorded in the row notes; don't trust the profile/job name for this batch's outline energies.
+- **Batch Q/R/T/U flex (2026-08-23) is the first curve-only *raw* D790 session** (`41`-`44_2026_08_23_flex_{q,r,t,u}.py`, 10 specimens each → Q1-Q10, R1-R10, T1-T10, U1-U10; the three-point-flex counterparts to those batches' Type IV tensile specimens — Q/R Nylon 11, T/U PA12 White/GF blend — same physical print batches). All four `.xlsx` files live directly under `source/2026_08_23/` (`Q.xlsx`..`U.xlsx`) and share that `session_folder`, so each script sets `xlsx_tag` (`"Q"`../`"U"`) to keep `specimen_id`s distinct (`2026_08_23/Q/Sheet1`, etc.). Each sheet (tabs named `"0"`..`"9"`, so `_resolve_sheet_name` falls back to positional order — fine, they're in order) is just cols A-B of the **raw load-deflection trace** (col A mm deflection, col B N load) with no `Width`/`Thickness` — unlike Batch P flex, whose export carried geometry and let `build_row_from_xlsx` derive the D790 chord stress/strain + modulus. With no geometry, `flexural_stress_strain_pa`/`flexural_modulus_pa` have nothing to work from, so these rows carry only the raw `curves.extension_m`/`curves.load_n`; `curves.strain`/`curves.stress_pa`, `geometry`, and every `metrics` field come out null (honest curve-only, like the tensile Q/R/S/T/U rows but *raw* rather than already-analyzed). Consequence: these batches have **no** D790 stress-strain figures — `03_batch_clusters.py`/`04_batch_details.py` skip them for lack of a plottable curve (no code change needed; D790 clusters stayed at 14, and no `assets/batches/D790_{Q,R,T,U}.png` are emitted) until specimen geometry is supplied. Each session sets an explicit `notes` so the rows flag this rather than emitting the generic derived-from-chord-formulas caveat. Print jobs not yet in Database; `db_print_date=None`.
 - **`NYLON12_WHITE_FL` is a new `material_class`** (FormLabs Nylon 12 White SLS control, tested 2026-07-23, no `batch_label`/`sample_id`, no Database FK) — a second FormLabs reference material alongside `PA12GF_FL`, unfilled/white nylon rather than glass-filled. Per user instruction it's excluded from the cluster/batch-averages figures and rendered on its own (`{standard}_nylon12white_control.png`, see `scripts/plots/_lib.py`'s `NYLON_CONTROLS`). **D638 (tensile) `tensile_nylon12white_fl.xlsx` is a raw load/extension export with no gauge-length scalar in the file** — unlike D790 there's no chord-formula fallback for tensile, so strain/stress can't be derived from geometry alone. User confirmed the test used a 25mm-starting-length extensometer, so `31_2026_07_23_tensile_nylon12white_fl.py` sets `gauge_length_mm: 25` explicitly and `build_row_from_xlsx` derives strain = extension/gauge_length, stress = load/area from that (see the `gauge_length_mm` session key, added for this case — `geometry.gauge_length_mm` on xlsx_only rows is null unless a session declares it). D790 (flex) rows derive normally since flexural strain/stress only need width/thickness. **The D638 curves are cut at their stress peak for plotting only** (`VERTICAL_BREAK_MATERIALS` in `scripts/plots/_lib.py`) — past peak, the raw trace continues as extension keeps increasing after the specimen separates while load reads ~0, and with few points sampled through the break itself this drew as a misleading diagonal line back to zero rather than the near-vertical drop a real break shows. Per user instruction, each figure applies this differently: `01_controls.py`'s raw-curve Nylon 12 White figure uses `vertical_break_at_peak` (cuts at peak, appends a point at zero stress/same strain so it plots as a vertical drop, matching the other SLS batches' visual convention); `02_batch_averages.py`'s mean ± SD figure now trims **every** specimen at its peak inside `group_average` (via `truncate_at_peak`) so no fracture branch — Nylon's included — reaches the averaging grid (this replaced the old per-Nylon special-case). Both `vertical_break_at_peak` and `truncate_at_peak` are applied by the calling code, not baked into `load_standard`, since the figures need different treatments. Either way this only affects what gets plotted — the underlying JSONL `curves.strain`/`curves.stress_pa` arrays are untouched (full raw trace still there for anyone querying the dataset directly). D790 Nylon 12 White isn't affected — its curves don't show this artifact.
 
 ## Running the extract

README.md

@@ -106,7 +106,7 @@ Regenerate with `uv run scripts/plots/02_batch_averages.py`.
 | Config | Description | Files |
 |---|---|---|
 | `D638` (default) | Tensile specimens (ASTM D638 Type I, plus 12 Type IV specimens in batch M and Type IV Nylon 11 batches O/P/Q). 115 SLS (batches A–Q) + 3 PLA + 3 PETG + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White = 131 rows. Batches A–J/J_MB have Database FKs; K–Q don't yet (print jobs not backfilled). | `data/D638/*.jsonl` (one row per file) |
-| `D790` | Three-point flex specimens (ASTM D790 Procedure A). 80 SLS rows (batches C–P) + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White = 90 rows. Batches C–J/J_MB have Database FKs; K–P don't yet. | `data/D790/*.jsonl` (one row per file) |
+| `D790` | Three-point flex specimens (ASTM D790 Procedure A). 120 SLS rows (batches C–U; no O or S) + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White = 130 rows. Batches C–J/J_MB have Database FKs; K–U don't yet. | `data/D790/*.jsonl` (one row per file) |
 
 One JSONL file per specimen — SLS rows are named after their `sample_id` (e.g. `data/D638/A1.jsonl`, `data/D790/E10.jsonl`); non-SLS controls use `{material}_TSR{n}.jsonl` (e.g. `data/D638/PLA_TSR6.jsonl`, `data/D790/PA12GF_FL_TSR1.jsonl`). Both configs share the same row schema and are produced by the per-session scripts under `scripts/specimens/`.
 
@@ -172,10 +172,14 @@ Test sessions covered:
 | `2026_08_17/` (`tensile.xlsx`, Type IV) | 7 | D638 | S | not yet in Database |
 | `2026_08_18/` (`tensile.xlsx`, Type IV) | 14 | D638 | T | not yet in Database |
 | `2026_08_19/` (`tensile.xlsx`, Type IV) | 14 | D638 | U | not yet in Database |
+| `2026_08_23/` (`Q.xlsx`) | 10 | D790 | Q | not yet in Database |
+| `2026_08_23/` (`R.xlsx`) | 10 | D790 | R | not yet in Database |
+| `2026_08_23/` (`T.xlsx`) | 10 | D790 | T | not yet in Database |
+| `2026_08_23/` (`U.xlsx`) | 10 | D790 | U | not yet in Database |
 
 TSR11 in `Batch E 3pt test/` exists on disk but has empty `Data/` (aborted run, no DAQ scans) and no corresponding xlsx sheet — it is excluded from the JSONL. TSR4 in Batch I flex (`Flex 6-30/`) is excluded for a similar reason: `test_end_reason` is "Test Stopped" rather than a detected break. Batch Q physical specimen 7 broke — its xlsx tab holds only the text "broken" — so it too is excluded, and Batch Q's `sample_id`s skip `Q7`.
 
-Batches K through U (2026-07-15 through 2026-08-19) have no raw `TestRuns/`/h5 folders at all — only TestWorks xlsx exports were handed off, so all of these rows are `xlsx_only` (see `scripts/specimens/_lib.py`'s `build_row_from_xlsx`). Batch M's 12 Type IV specimens are a narrow-section ASTM D638 geometry (6mm × 4.15mm vs Type I's 12.8mm × 3.1mm) from the same print as its 5 Type I specimens — same `batch_label`, distinguished by `astm.type`. Batches O, P, Q, and R are entirely Type IV as well, but of a different SLS powder (Nylon 11, first used in this dataset in these batches — see `notes` on their rows) rather than a geometry variant of an existing batch, so they're excluded from the batch-average/cluster figures the same way Type IV rows always are, but get their own per-batch detail figures rather than sharing Batch M's combined Type IV figure (see `scripts/plots/_lib.py`'s `TYPE_IV_DEDICATED_BATCHES`). Batch Q's and R's exports are more minimal still: each sheet holds only the already-analyzed strain/stress curve with no geometry (`Width`/`Thickness`) or scalar-metric columns, so those rows' `geometry` and metrics are null — except `peak_stress_pa`, which the extract derives from the curve itself (max stress; see `derive_d638_peak` in `scripts/specimens/_lib.py`) — while `curves.strain`/`curves.stress_pa` are populated (consumers re-derive modulus from the curve). The FormLabs Nylon 12 White tensile control's xlsx export is a raw load/extension curve with no gauge length in the file — `strain`/`stress_pa` are derived using a user-confirmed 25mm extensometer gauge length declared in the script itself (see Composite stress–strain above); its flex counterpart derives normally via the D790 chord formulas.
+Batches K through U (2026-07-15 through 2026-08-19) have no raw `TestRuns/`/h5 folders at all — only TestWorks xlsx exports were handed off, so all of these rows are `xlsx_only` (see `scripts/specimens/_lib.py`'s `build_row_from_xlsx`). Batch M's 12 Type IV specimens are a narrow-section ASTM D638 geometry (6mm × 4.15mm vs Type I's 12.8mm × 3.1mm) from the same print as its 5 Type I specimens — same `batch_label`, distinguished by `astm.type`. Batches O, P, Q, and R are entirely Type IV as well, but of a different SLS powder (Nylon 11, first used in this dataset in these batches — see `notes` on their rows) rather than a geometry variant of an existing batch, so they're excluded from the batch-average/cluster figures the same way Type IV rows always are, but get their own per-batch detail figures rather than sharing Batch M's combined Type IV figure (see `scripts/plots/_lib.py`'s `TYPE_IV_DEDICATED_BATCHES`). Batch Q's and R's exports are more minimal still: each sheet holds only the already-analyzed strain/stress curve with no geometry (`Width`/`Thickness`) or scalar-metric columns, so those rows' `geometry` and metrics are null — except `peak_stress_pa`, which the extract derives from the curve itself (max stress; see `derive_d638_peak` in `scripts/specimens/_lib.py`) — while `curves.strain`/`curves.stress_pa` are populated (consumers re-derive modulus from the curve). The FormLabs Nylon 12 White tensile control's xlsx export is a raw load/extension curve with no gauge length in the file — `strain`/`stress_pa` are derived using a user-confirmed 25mm extensometer gauge length declared in the script itself (see Composite stress–strain above); its flex counterpart derives normally via the D790 chord formulas. The Batch Q, R, T, and U **flex** specimens (D790, tested 2026-08-23) are curve-only in the opposite way: each sheet holds only the *raw* load-deflection trace (col A mm deflection, col B N load) with no `Width`/`Thickness`, so the D790 chord formulas have no geometry to work from — `curves.strain`/`curves.stress_pa` and all `metrics` (including flexural modulus) are null, and only `curves.extension_m`/`curves.load_n` are populated. Consequently these batches do not appear on the D790 stress–strain figures (there is no derivable stress/strain to plot until specimen geometry is supplied).
 
 Batch H's 5 flex specimens (`2026_06_30/Flex 6-30/`) don't have a raw TestRuns folder — it looks like it was overwritten when the Batch I TestWorks project reused the same default `TST1.Test` name in the same directory. `flex_h_6.30.xlsx` is the only surviving record, so those 5 rows are built from that xlsx export alone: the raw load/extension curve (`curves.load_n`/`curves.extension_m`) comes from its embedded columns, but `curves.strain`/`curves.stress_pa` are empty and several `metrics` fields (`modulus_pa`, `strain_at_peak`, `strain_at_yield`, etc.) are null, since deriving them requires the support span, which this export doesn't surface. See each row's `notes` field.
 

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