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fhamood wants to merge 729 commits into
fhamood:developmentfrom
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Open

Pain#3
fhamood wants to merge 729 commits into
fhamood:developmentfrom
daisybio:development

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@fhamood

@fhamood fhamood commented Nov 28, 2025

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JudithBernett and others added 30 commits January 20, 2026 13:54
…opment/actions/cache-5.0.2

[DEPENDABOT]: Bump actions/cache from 5.0.1 to 5.0.2
Bumps [actions/cache](https://github.com/actions/cache) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@v5.0.2...v5.0.3)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: 5.0.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Leaderboard was not shown properly in docs
Bumps [crazy-max/ghaction-github-labeler](https://github.com/crazy-max/ghaction-github-labeler) from 5.3.0 to 6.0.0.
- [Release notes](https://github.com/crazy-max/ghaction-github-labeler/releases)
- [Commits](crazy-max/ghaction-github-labeler@v5.3.0...v6.0.0)

---
updated-dependencies:
- dependency-name: crazy-max/ghaction-github-labeler
  dependency-version: 6.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 6 to 7.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v6...v7)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Added a new baseline model AdaBoostDecisionTree
tereshchuk1 and others added 30 commits June 20, 2026 01:35
Add tissue term to mean effects baseline
Allow advanced users to supply create_splits(response_data) scripts validated
by test_mode semantics, wired through the experiment loop, CLI, and make-cv-pkls
while preserving the existing fold-dict training contract.
Add sphinx docstrings, replace Protocol with Callable, fix isort/black
formatting, and document tests so CI pre-commit passes.
Satisfy flake8-darglint DAR101 for pytest fixture parameters.
Expose pipeline split settings via a frozen CustomSplitParams dataclass
passed as the second argument to create_splits(response_data, params).
Document private validation helpers with sphinx param/returns/raises sections.
Move built-in and external split logic into drevalpy.datasets.splits with a shared create_and_record_splits path, JSON manifests that record split_label vs test_mode, and explicit result discovery so reports resolve the semantic test mode correctly.
Add missing docstrings and isort fixes for the split provider refactor, and sync with development.
Make tests.datasets a proper package for mypy, skip row-overlap validation on trusted built-in splits, and keep external split validation unchanged.
Use len(splits) instead of the requested params value so external scripts that return a different fold count are reflected accurately.
feat: add user-defined custom CV split scripts
MultiViewLightGBM was merged into development via #430 after this branch
was created. The earlier 'remove LightGBM' change would delete the file
and unregister the model on merge; restore it verbatim from development
and re-add its registry entries, keeping SparseGO.
load() only recorded the checkpoint path; _load_weights_if_needed was
never called, so a reloaded model predicted with freshly initialised
weights. Call it at the end of _build_network (the single point where the
network is constructed), so the saved state_dict is applied on the first
train()/predict() or build_model() after load(). The checkpoint path is
cleared after loading to avoid reloading stale weights on later rebuilds.
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10 participants