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DeepLabCut 3.0.2

DeepLabCut 3.0.2 is a patch release bringing several PyTorch workflows fixes, improved config handling and export reliability, broadened compatibility for newer NumPy / Matplotlib versions, and adding a machine-readable docs/API index for agent-assisted interactions with the library.

Highlights

  • Forward-compatibility work for NumPy 2, pandas 3 CoW, and Matplotlib 3.9, including releasing core NumPy / Matplotlib upper bounds (#3420, [#3498], [#3502], [#3508], [#3499], [#3445], [#3394]).
  • More reliable COCO training: model_cfg.metadata is authoritative, with fail-fast validation against annotation JSON (#3435).
  • Safer legacy project configs: empty / null top-level YAML fields are treated as unset; ignore_empty is removed (#3439).
  • Normalized export_model pickles for downstream / real-time consumers (#3473).
  • Detector null thresholds resolve to field defaults instead of crashing (#3470, [#3475]).
  • PyTorch analyze_videos / auto-track honor the overwrite argument instead of hard-coding overwrite=False (#3514).
  • Public LLM-friendly knowledge index (llms.txt, docs.jsonl, api.jsonl) plus hardening follow-up and AGENTS.md (#3453, [#3494], [#3483]).

Important changes

NumPy / Matplotlib dependency bounds (#3420, [#3498], [#3502], [#3508], [#3499])

Core installs no longer pin numpy<2 or a Matplotlib upper bound. Also added numba>=0.60 and an explicit OpenCV dependency. TensorFlow extras still keep a NumPy <2 ceiling where the corresponding TensorFlow build requires it.

  • [#3420] — Prepare for NumPy 2 forward compatibility (including dense SVD for tracklet ranking instead of randomized interpolative SVD)
  • [#3498] — Fix broken NumPy 2.0 compatibility in crossvalutils and predict_multianimal
  • [#3502] — NumPy 2 + numba: take the real part of eig eigenvectors in EllipseFitter
  • [#3508] — Follow-up NumPy 2 fixes (PyTorch snapshot metric loading / Assembly.affinity typing; raise numba floor; declare OpenCV)
  • [#3499] — Remove core NumPy and Matplotlib upper bounds (NumPy <2 remains only where TensorFlow extras still require it; exclude broken Matplotlib 3.7 / 3.7.1)
  • [#3445] — Guard pandas 3 Copy-on-Write read-only .to_numpy() / .values mutations
  • [#3394] — Matplotlib v3.9 compatibility
  • [#3509] — Tighten strict canary CI handling (strict_cells for same-repo pushes/PRs; fork PRs stay non-blocking)

COCOLoader (#3435)

bodyparts / individuals capacity now come from model_cfg.metadata, matching DLCLoader. Construction validates train.json and test.json and raises ValueError if an image exceeds configured capacity or bodyparts do not match. Projects that previously relied on capacity inferred only from the busiest training image should set max_individuals (and bodyparts) explicitly.

ProjectConfig empty / null fields (#3439)

Empty top-level YAML fields are treated as unset and emit an actionable warning. DLCBaseConfig.from_yaml(..., ignore_empty=...) no longer accepts ignore_empty (breaking for that optional parameter). Lower-level read_config(..., ignore_empty=...) deprecates the argument.

Exported models (#3473)

export_model now calls PoseConfig.to_dict(normalize=True), so pickles store primitives (Path → str, enums → str, etc.). Prefer re-exporting models for consumers that load the pickled config.

overwrite in PyTorch video analysis (#3514)

analyze_videos and the auto-track path now forward the caller’s overwrite flag instead of always behaving as overwrite=False. Existing prediction files are skipped only when overwrite is false.

Features and enhancements

  • [#3436] — Add detector_eval_interval to train_from_coco
  • [#3475] — Add DefaultIfNone config validator (null → field default)
  • [#3481] — Harden wandb logger error handling (validate before wandb.init)

Agentic interaction

Coding agents and LLM tools can now discover DeepLabCut knowledge without scraping HTML.

CI builds and deploys a structured index with the docs site:

  • llms.txt — llmstxt.org-style entry point at the docs root (published here after deploy)
  • knowledge/manifest.json — which API versions are indexed and which is current
  • knowledge/main/docs.jsonl — one JSON object per user-docs page and heading
  • knowledge/<version>/api.jsonl — one JSON object per documented API symbol

Also added: AGENTS.md (github.com), shared guidance for humans and coding agents.

  • [#3453] — Knowledge indexing generator + CI deploy (tools/knowledge_indexing)
  • [#3494] — Follow-up hardening for the LLM knowledge index (dependency bounds, stable vs main API links in llms.txt, safer skip/empty-dir publish behavior, anchor/regression fixes)
  • [#3483] — Add AGENTS.md for AI-assisted development

Bug fixes

  • [#3419] — Skip TensorFlow-backed tests cleanly when the tf extra is absent
  • [#3435] — Fix COCOLoader: treat model_cfg.metadata / max_individuals as authoritative instead of inferring solely from train.json
  • [#3439] — Update None-type validation for legacy ProjectConfig templates; remove ignore_empty
  • [#3441] — GUI config editor crash + shared deferred reload on DefaultTab
  • [#3447] — Evaluation visualization fixes, clean-up, and coverage improvements
  • [#3449] — Fix frame extraction failure with pathlib video selections
  • [#3452] — Fix incorrect SuperAnimal HumanBody rename mapping in ModelZoo / Hugging Face download
  • [#3467] — Fix faulty str / Path conversions
  • [#3468] — Fix latent bugs and misleading errors in GUI create_videos
  • [#3469] — Fix WandbLoggerConfig so extra wandb kwargs validate (scoop into wandb_kwargs)
  • [#3470] — Fix Faster R-CNN detector inference crashing on box_score_thresh: null
  • [#3473] — Fix export_model dumping unnormalized objects in pickle
  • [#3480] — Fix GUI tests: use config_path after rename
  • [#3484] — Fix tools imports under a plain pytest invocation
  • [#3486] — Docs: fix dead Model Zoo link in examples/README.md
  • [#3514] — Fix hard-coded overwrite=False in PyTorch analyze_videos / auto-track path

Please let us know if you face any issues with this release, especially related to the latest forward compatibility efforts, we appreciate any issues or reports!

New Contributors

Full Changelog: https://github.com/DeepLabCut/DeepLabCut/compare/v3.0.1...3.0.2

Source: README.md, updated 2026-09-17