Release 1.5.0 - #21

One-time mechanical pass to satisfy the newly added pre-commit hooks. No
functional changes:
- Ruff format + import sorting (isort) across src/, tests/, examples/.
- Ruff autofixes: remove unused imports, collapse multi-imports; drop dead
  local assignments (conftest esm1 `device`, example script vars).
- Mark the intentional `pepe.api.embed` re-export in __init__.py with noqa.
- Generic fixers: trailing-whitespace + final-newline normalization on
  markdown/json/txt/yaml/workflow files.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Raise the floor to Python 3.10 so packaging metadata, CI, and the type/lint
tooling all agree (mypy and Ruff already targeted 3.10):
- pyproject.toml / setup.py: requires-python >=3.10, drop 3.8/3.9 classifiers.
- .github/workflows/test.yml: unit matrix now [3.10, 3.11].
- .github/conda/meta.yaml: python >=3.10 (host + run).
- pyproject [tool.ruff]: target-version = "py310".
- CHANGELOG: note the removal under [Unreleased].

Bumping the Ruff target to py310 lets the formatter use parenthesized `with`
statements (3.10+ syntax); reformats four files accordingly. No behavior change.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Add pre-commit hooks + drop Python 3.8/3.9

Ship a CPU Docker image alongside PyPI/Conda releases so users can run PEPE without a local Python setup.

Co-authored-by: Cursor <cursoragent@cursor.com>

… release to after Docker publish

Add GHCR Docker publishing to test and main release workflows

Enables metl-*-1d model dispatch, METLEmbedder/METLDataset, typed errors for
missing package and 3D models, CI integration test behind METL_TEST, and docs
in CHANGELOG (1D-only; no logits/attention).

Co-authored-by: Cursor <cursoragent@cursor.com>

Quick start install from GitHub [metl] extra, CLI example, supported models,
and limitations aligned with CHANGELOG.

Co-authored-by: Cursor <cursoragent@cursor.com>

Document pepe-cli[metl] and direct metl-pretrained install, plus CLI/library usage for metl-g-20m-1d.

Co-authored-by: Cursor <cursoragent@cursor.com>

Address review findings on the METL 1D embedder:

- _register_repr_hooks: layer 0 now captures the encoder input embeddings
  (via a forward_pre_hook) instead of aliasing to layers[-1]; the final-layer
  norm hook is guarded so norm-less METL models fall back to the last block
  instead of crashing on None.register_forward_hook. Collapses the duplicated
  make_hook closure into one definition.
- _load_layers: default (layers is None) now returns all transformer layers,
  matching the HuggingFace embedders, instead of only the final layer.

The batch-dimension review item was verified against metl-pretrained source
(batch_first=True throughout) and needs no change.

Adds test_metl_hooks.py (deterministic, no metl download) covering the hook
mapping and layer defaults, and extends the gated integration test with
batch-consistency and multi-layer checks.

Add METL 1D embeddings (Option A)

…-publish-test

…dency

PyPI/TestPyPI reject packages with direct URL dependencies (PEP 440).
Remove `metl-pretrained @ git+https://...` from [project.optional-dependencies]
in pyproject.toml and from extras_require in setup.py. Users should install
metl-pretrained directly from GitHub. Update README, CHANGELOG, and error
messages accordingly.

…sh-test

Fix TestPyPI publish failure: remove git URL from metl optional dependency

Cut the Unreleased section into [1.5.0], covering METL 1D embeddings and
GHCR Docker publishing. Restores the Docker/GHCR changelog entry dropped
during an earlier merge into test.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>