fix: remove non-existent hovernet_infer_compare from doesnt_contain_max_epochs; fix stale pending table

- runner.sh: hovernet_infer_compare.ipynb does not exist in the repo;
  the exemption was a dead entry that could never match. Removed.
- diagnose_1_6_release.md: PEP8 row removed from the 'Still pending'
  table (autofix was already applied and marked done at line 401).
  Also updated runner.sh change summary to reflect the actual skip list
  entries (deep_atlas_tutorial, 05_spleen_segmentation_lightning).

Signed-off-by: R. Garcia-Dias <rafaelagd@gmail.com>

Author: garciadias

diagnose_1_6_release.md

@@ -438,7 +438,7 @@ Changes committed to bring Docker run to parity with Eric's run:
 
 | File | Change |
 |---|---|
-| `runner.sh` | Add `msd_crossval_datalist_generator.ipynb` and `hovernet_infer_compare.ipynb` to `doesnt_contain_max_epochs`; add `image_restoration.ipynb` to `skip_run_papermill` |
+| `runner.sh` | Add `msd_crossval_datalist_generator.ipynb` to `doesnt_contain_max_epochs`; add `image_restoration.ipynb`, `05_spleen_segmentation_lightning.ipynb`, `deep_atlas_tutorial.ipynb` to `skip_run_papermill` |
 | `computer_assisted_intervention/endoscopic_inbody_classification.ipynb` | Reverted `return_state_dict=False` — upstream MONAI ≥1.5 already returns `nn.Module` by default; the extra kwarg caused `TypeError` in CI |
 | `bundle/05_spleen_segmentation_lightning.ipynb` | Change `pytorch-lightning~=2.0.0` → `pytorch-lightning>=2.1` to avoid mlflow eager-import failure (R7) |
 
@@ -449,5 +449,4 @@ Changes committed to bring Docker run to parity with Eric's run:
 | Disk space (R2) | Free `/data` disk or bind-mount scratch volume; `deep_atlas` (~2 GB), `deployment/bentoml`, `experiment_management/bundle_integrate_mlflow`, `microscopy` notebooks |
 | Socket FD limit (R8) | ✓ Confirmed fixed — `--ulimit nofile=65536:65536` resolves ancdata error; isolated run completed in 3m1s (2026-06-11) |
 | pytorch-lightning/mlflow import chain (R7) | ✓ Fixed: `pytorch-lightning>=2.1` in notebook (PR #2065) |
-| PEP8 in 3 notebooks | Run `bash runner.sh --autofix` for `surgtoolloc/preprocess_detect_scene_and_split_fold.ipynb`, `deep_atlas/deep_atlas_tutorial.ipynb`, `modules/interpretability/class_lung_lesion.ipynb` |
 | Restormer in MONAI dev | Cherry-pick Restormer network class commit; remove from skip list once merged |

runner.sh

@@ -85,7 +85,6 @@ doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" realism_diversity_m
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" omniverse_integration.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" hugging_face_pipeline_for_monai.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" msd_crossval_datalist_generator.ipynb)  # inference/datalist-only notebook, no training loop
-doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" hovernet_infer_compare.ipynb)  # inference-only notebook
 
 # Execution of the notebook in these folders / with the filename cannot be automated
 skip_run_papermill=()