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7. Packaging and CI - #7
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A few docstrings and test comments named the clinical outcome this was first built for, a private evaluation pipeline, or a cohort statistic. None of it is needed to read the code: cause 1 is the event of interest, cause 2 the competing event, and the horizon term's labels mirror the landmark evaluation. Renames test_labels_and_weights_match_v3_evaluation to ..._match_landmark_evaluation. No behaviour changes.
…module Nothing imports from the DeepSurvivalMachines submodule since the switch to auton-survival, and its SSH URL made a recursive clone fail without GitHub keys. Remove it. pyproject.toml makes `pip install -e .` work and lists what importing ddh needs: torch, numpy and tqdm for the model, plus the packages auton-survival imports when it loads. auton-survival itself is not a declared dependency: its only PyPI release pins torch<2.0, so the README installs it from source with --no-deps. That combination was checked in a clean virtual environment (torch 2.14, Python 3.11) from a standalone clone: the import resolves to the installed package and the tests pass. .gitignore now refuses common tabular and model-artifact formats, so patient-level data cannot be committed by accident.
GitHub Actions installs CPU torch, auton-survival from its 0.1.0 release commit with --no-deps, and the package with its test extra, then runs pytest on Python 3.11 and 3.12. It installs exactly what the README tells a user to install, so a broken install recipe fails CI too.
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Makes the repository installable and tested by someone who has never seen it.
pyproject.tomldeclares what importingddhneeds. auton-survival is installed from its 0.1.0 release commit with--no-deps, because its PyPI metadata pins torch<2.0. This was verified in a clean environment from a standalone clone..gitignorerefuses tabular and model-artifact formats.