DO NOT MERGE — review-only mirror of #36 - #47
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Reorganise builtin models under konfai/models/{python,yaml} and ship a declarative YAML model
catalog resolved via 'classpath: default|<Name>.yml' and packaged in the wheel: UNet, NestedUNet,
ResNet (weight-exact vs the KonfAI classes), SegResNet/VNet/DynUNet/ResNet18/VGG16/PlainConvUNet
(weight-exact vs MONAI/torchvision/nnU-Net, real pretrained weights load through the new
konfai.utils.pretrained execution-order bridge), a parametric PlainConvUNet for any nnU-Net topology,
an SMP encoder-backed wrapper, the MIND descriptor, and the ClipNormalize block. The model-builder
registry grows curated primitives (norms, activations, transformer blocks); the classpath resolver is
re-rooted to konfai.models.python (short form unchanged). Also folds the mixed-accumulation
double-backward fix and the point-of-use SimpleITK guard that touch network.py/blocks.py.
BREAKING CHANGE: fully-qualified references 'konfai.models.<task>.<Module>:<Class>' become
'konfai.models.python.<task>.<Module>:<Class>' (no compatibility alias).
FocalLoss batch>1 broadcast, BEST-checkpoint optimisation direction, OneHot.inverse batched argmax, Literal defaults, SLURM rendezvous host, ConvNeXt LayerScaler, DDP shard tail, load_state_dict shrink, and a --resubmit warning instead of a silently dropped flag. SimpleITK is guarded at point-of-use so the package imports without the itk extra. Comments unified in English and SPDX headers completed (incl. the app CLI wrappers); the Slicer-facing core API surface is locked by contract tests.
A runnable synthetic-data registration example (train/predict/evaluate on the builtin VoxelMorph), and the Segmentation and Synthesis examples now ship their model in both a declarative YAML and an equivalent Python form (verified weight-identical), with READMEs explaining when each form applies.
Surface task/finetunable/optional-input defaults on app repositories (relayed over the remote server), so an agent can route to a published app, fine-tune it, or run it from its declared inputs; the get_parameters values/constraints contract is locked by tests.
A FastMCP server exposing the full KonfAI loop to LLM agents: dataset discovery/inspection, config authoring with static review and side-effect-free semantic validation in a spawn subprocess, tracked train/predict/evaluate jobs with process-group cancel and traceback-faithful logs, run comparison and leaderboards, published-app integration (describe/infer/fine-tune), and a first-class model catalog (list/inspect a default|<Name>.yml or session model; guidance that prefers the proven catalog and explains what the KonfAI contract buys). Independent package with its own pyproject and CI.
Unit and integration tests for the MCP tools (dataset, config authoring/validation, jobs, apps, catalog discovery) plus a segmentation end-to-end pipeline and a tool-index anti-drift check.
A problem-led MCP usage page, the konfai-experiments agent skill (canonical loop + generated tool reference), and the AGENTS.md guidance for working on the MCP server.
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✨ Finishing Touches🧪 Generate unit tests (beta)
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Do not merge. Close this once the review is read.
#36 was merged on 14 July, before CodeRabbit was installed, so it refuses it: "Review failed — The pull request is closed." A merged pull request has no diff left to comment on.
This carries the same diff on two throwaway branches so the review can happen:
review/before-36—mainas it stood before #36 (1fbce78~7)review/after-36— the last of its seven commits (1fbce78)Merging this would only fast-forward a throwaway branch. The code is already in
main; anything found here goes out as its own fix.@coderabbitai full review