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[amoschoomy]

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Pull request overview

This PR renames the Python package from tcrgnn to graffit, updates tests/docs/scripts accordingly, and introduces/rewrites several core modules (graph generation, training, evaluation, plotting, utilities) to support the new package layout and updated serialization behavior.

Changes:

• Rename imports across tests, docs, and scripts from tcrgnn to graffit.
• Add/port graffit implementation modules (graph/edge generation, training loop/config, evaluation utilities, plotting, posthoc adjustment).
• Update packaging metadata and dependency constraints in pyproject.toml, plus Sphinx API docs structure.

Reviewed changes

Copilot reviewed 58 out of 83 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/utils_tests/test_data_loading.py	Update imports/monkeypatch targets to graffit.utils._data_loading.
tests/utils_tests/test_common_utils.py	Update module import path to graffit.utils._common_utils.
tests/training_tests/test_train_api.py	Update training API/config imports and monkeypatch paths to graffit.
tests/training_tests/test_loop.py	Update training loop imports to graffit.training._loop.
tests/training_tests/test_config.py	Update training config import to graffit.training._config.
tests/test_import.py	Update package import smoke test to graffit.
tests/posthoc_adjustment_tests/test_transform.py	Update posthoc transform import path to graffit.
tests/posthoc_adjustment_tests/test_out.py	Update posthoc API imports and monkeypatch paths to graffit.
tests/posthoc_adjustment_tests/test_clonal_frequency.py	Update clonal frequency import path to graffit.
tests/plotting_tests/test_charts.py	Update plotting import path to graffit.plotting.charts.
tests/model_tests/test_model.py	Update model import path to graffit.models.gatv2.
tests/generate_graph_tests/test_io.py	Update graph IO imports; switch roundtrip load to load_graphs_from_disk.
tests/generate_graph_tests/test_encoding.py	Update encoding import path to graffit.graph_gen.encodings.
tests/generate_graph_tests/test_build_graph.py	Update build-graph import path to graffit.graph_gen._build_graph.
tests/generate_graph_tests/test_api.py	Update graph generation API import/monkeypatch paths to graffit.
tests/generate_edge_tests/test_io.py	Update edge IO import path to graffit.edge_gen._io.
tests/generate_edge_tests/test_generate_edge.py	Update edge generation module import path to graffit.
tests/generate_edge_tests/test_api.py	Update edge API imports and patch decorators to graffit.
tests/evaluate_tests/test_utils.py	Update evaluate utils import path to graffit.evaluate._utils.
tests/evaluate_tests/test_predict.py	Update evaluate predict module import path to graffit.
tests/evaluate_tests/test_api.py	Update evaluate API import path to graffit.evaluate.api.
src/tcrgnn/graph_gen/_io.py	Remove legacy tcrgnn graph-gen IO module.
src/graffit/utils/_data_loading.py	Add safer load_graphs behavior with legacy fallback; keep train/test loaders.
src/graffit/utils/_common_utils.py	Add tar extraction/archive/temp/cleanup helpers.
src/graffit/utils/init.py	Export common utils + data loading functions from graffit.utils.
src/graffit/training/api.py	Update model import to graffit.models.gatv2.
src/graffit/training/_loop.py	Add training loop implementation with early stopping and checkpointing.
src/graffit/training/_config.py	Add training configuration and path container dataclasses.
src/graffit/training/init.py	Export training public API (train_model, config types).
src/graffit/posthoc_adjustment/api.py	Update internal imports to graffit posthoc modules.
src/graffit/posthoc_adjustment/_transform.py	Add percentile + blending + distribution-aware score adjustment functions.
src/graffit/posthoc_adjustment/_clonal_frequency.py	Add clonal frequency merge helper for model output tables.
src/graffit/posthoc_adjustment/init.py	Export posthoc adjustment API symbols.
src/graffit/posthoc_adjustment/README.md	Add conceptual + mathematical documentation for posthoc calibration.
src/graffit/plotting/charts.py	Add plotting utilities for score distributions, logits summaries, ROC.
src/graffit/plotting/init.py	Export plotting entry points.
src/graffit/models/gatv2.py	Add GATv2 model implementation.
src/graffit/models/init.py	Export GATv2 model.
src/graffit/graph_gen/encodings.py	Add PCA encoding loader + amino-acid mapping.
src/graffit/graph_gen/api.py	Add graph generation APIs for dirs and tar.gz sources.
src/graffit/graph_gen/_io.py	Add stable graph serialization payload format + load/save helpers.
src/graffit/graph_gen/_build_graph.py	Add edgelist-to-PyG graph construction pipeline.
src/graffit/graph_gen/init.py	Export graph generation API entry points.
src/graffit/fold_backend/init.py	Package stub for fold backend namespace.
src/graffit/fold_backend/README.md	Add placeholder README for fold backend.
src/graffit/evaluate/api.py	Update evaluate imports to graffit.* and model import path.
src/graffit/evaluate/_utils.py	Add device selection, loader creation, model loading, and score writing helpers.
src/graffit/evaluate/_predict.py	Update import path to graffit.evaluate._utils.
src/graffit/evaluate/init.py	Export evaluate API entry points.
src/graffit/edge_gen/cli.py	Add placeholder CLI module.
src/graffit/edge_gen/api.py	Update logger name to graffit.edgegen.
src/graffit/edge_gen/_io.py	Update logger name to graffit.edgegen.io.
src/graffit/edge_gen/_generate_edge.py	Add PDB parsing and edge list generation helpers.
src/graffit/edge_gen/init.py	Export edge generation public API.
src/graffit/init.py	Provide top-level package exports for core APIs.
scripts/train.py	Update script imports to graffit.
pyproject.toml	Rename project to graffit, update dependencies, and switch coverage target.
docs/source/tutorial/05_train_model.ipynb	Update tutorial install/import commands to graffit.
docs/source/tutorial/04_posthoc_scoring_adjustment.ipynb	Update tutorial install/import commands to graffit.
docs/source/tutorial/03_evaluating_model.ipynb	Update tutorial install command to graffit.
docs/source/tutorial/02_generating_graph.ipynb	Update tutorial install/import commands to graffit.
docs/source/tutorial/01_generating_edge.ipynb	Update tutorial install/import commands to graffit.
docs/source/index.rst	Update project name and API toctree to graffit.*.
docs/source/conf.py	Update Sphinx project name and apidoc settings for graffit.
docs/source/api/tcrgnn.training.rst	Remove old tcrgnn API doc stub.
docs/source/api/tcrgnn.posthoc_adjustment.rst	Remove old tcrgnn API doc stub.
docs/source/api/tcrgnn.plotting.rst	Remove old tcrgnn API doc stub.
docs/source/api/tcrgnn.models.rst	Remove old tcrgnn API doc stub.
docs/source/api/tcrgnn.graph_gen.rst	Remove old tcrgnn API doc stub.
docs/source/api/tcrgnn.fold_backend.rst	Remove old tcrgnn API doc stub.
docs/source/api/tcrgnn.evaluate.rst	Remove old tcrgnn API doc stub.
docs/source/api/modules.rst	Add graffit root modules toctree.
docs/source/api/graffit.utils.rst	Point API docs at graffit.utils.
docs/source/api/graffit.training.rst	Add Sphinx API docs for graffit.training.
docs/source/api/graffit.rst	Add Sphinx API docs for root graffit package and subpackages.
docs/source/api/graffit.posthoc_adjustment.rst	Add Sphinx API docs for graffit.posthoc_adjustment.
docs/source/api/graffit.plotting.rst	Add Sphinx API docs for graffit.plotting.
docs/source/api/graffit.models.rst	Add Sphinx API docs for graffit.models.
docs/source/api/graffit.graph_gen.rst	Add Sphinx API docs for graffit.graph_gen.
docs/source/api/graffit.fold_backend.rst	Add Sphinx API docs for graffit.fold_backend.
docs/source/api/graffit.evaluate.rst	Add/update Sphinx API docs for graffit.evaluate.
docs/source/api/graffit.edge_gen.rst	Add Sphinx API docs for graffit.edge_gen.
README.md	Update installation instructions to pip install graffit and note torch versioning.

Comments suppressed due to low confidence (1)

src/graffit/utils/_data_loading.py:38

• allow_unsafe_legacy defaults to True, which means a failed "safe" load will automatically fall back to weights_only=False (unsafe pickle loading). For a library function, it’s safer to default this to False and require callers to opt in explicitly when loading trusted legacy files.

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[Copilot]

graffit.utils.device (and set_seed) doesn’t exist in the current package layout, so this script will fail to import. Consider importing get_device from graffit.evaluate._utils (or adding a dedicated graffit/utils/device.py module) and providing a set_seed helper if it’s still needed.

[Copilot]

With the src/ layout, apidoc_module_dir = "../../graffit" is likely incorrect (the package lives under ../../src/graffit). As written, Sphinx apidoc may fail to find modules or generate empty docs; consider pointing apidoc to the src package directory and adjusting sys.path.insert accordingly.

[amoschoomy]

@copilot open a new pull request to apply changes based on this feedback

[Copilot]

from graffit import ... train will fail because graffit.__init__ doesn’t export a train symbol. Either import train from graffit.training._loop here, or re-export it from graffit/training/__init__.py (and then from graffit/__init__.py) if it’s intended to be part of the public API.

Suggested change

	from graffit import GATv2, TrainConfig, TrainPaths, train
	from graffit import GATv2, TrainConfig, TrainPaths
	from graffit.training._loop import train

[amoschoomy]

@copilot open a new pull request to apply changes based on the comments in this thread

[amoschoomy]

@copilot open a new pull request to apply changes based on the comments in this thread