Strict type-checking + tests for foundry.utils (instantiators, ddp, logging); remove dead rf3.data.paired_msa#322
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instantiators is already fully annotated, so this adds it to the per-module strict mypy override (a lock-in for future defs) and fills the test gap with tests/test_instantiators.py covering the callback/logger instantiation control flow. Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
…st logging Adds the three remaining small foundry.utils modules to the per-module strict mypy override. squashfs was already fully annotated (pure lock-in); ddp needed one annotation (RankedLogger.log varargs); logging needed five. New tests/test_logging.py covers the two pure helpers (CachedDataFilter.filter and condense_count_columns_of_grouped_df). Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
rf3.data.paired_msa no longer imports against the installed atomworks: MultiInputDatasetWrapper subclasses StructuralDatasetWrapper, which atomworks turned into a deprecated factory function, so subclassing it raises TypeError at import. The module was reachable only through domain_distillation.yaml, which is itself referenced only in commented-out lines of pdb_and_distillation.yaml, and its LoadPairedMSAs class was used nowhere. Remove the module, its orphaned domain_distillation.yaml config, the dangling commented references in pdb_and_distillation.yaml, and the stale pyproject mypy-exemption comment. rf3 now type-checks fully with no in-file suppressions. Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
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Continues bringing the shared
foundry.utilslayer under strict type-checking with unit tests, and removes a dead module inrf3.Type stubs + tests (foundry.utils)
instantiators— added unit tests covering the hydra instantiation control flow (callbacks/loggers,None/empty handling, missing-_target_errors) and tightened it to strict type-checking. Already fully annotated, so this is a strictness lock-in.ddp/squashfs/logging— tightened to strict type-checking and added the missing annotations (RankedLogger.log,CachedDataFilter.filter, warning/print helpers). New tests forlogging's two pure helpers (CachedDataFilter.filter,condense_count_columns_of_grouped_df). The rest of these modules is side-effecting glue (Rich output, subprocess mounts, rank state) and is intentionally left untested.Remove dead code (rf3)
rf3.data.paired_msa. It subclassedStructuralDatasetWrapper, which the installedatomworksnow exposes as a factory function rather than a class, so the module raisedTypeErroron import. It was reachable only through a dataset config that is itself referenced solely from commented-out lines, so it was dead in practice. Removed the module, its orphaneddomain_distillation.yamlconfig, the dangling commented references to it, and the now-stale type-checker exemption comment.With this, all of
rf3type-checks with no in-file suppressions.