mirror of
https://github.com/RosettaCommons/foundry.git
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3ae4ee81e6
* refactor(mypy): un-ignore 5 easy-tier modules Fix each module's single pre-existing type error with a pure annotation or setattr change (no behavior change) and remove it from the [[tool.mypy.overrides]] ignore_errors list: - callbacks/train_logging: loss_trackers: dict[str, MeanMetric] - callbacks/metrics_logging: seen_examples: set[str] - common: setattr(wrapper, "_has_run", True) for the @wraps wrapper - hydra/resolvers: attribute_path: str | None (body already guards) - inference_engines/base: base_overrides: dict[str, Any] 13 modules remain on the ignore list. mypy now type-checks the 5 newly-included modules cleanly. Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * refactor(mypy): un-ignore 7 medium-tier modules Resolve the type errors in and remove from the [[tool.mypy.overrides]] ignore_errors list. Mostly narrowing / annotation fixes; two deliberate type-honesty fixes flagged below. - utils/weights: lowercase `any` -> `Any` in _PatternPolicyMixin (4x); assert-narrow fallback_policy at the call site (matches get_policy idiom) - model/layers/blocks: class-level w/b: torch.Tensor for the registered buffers (avoids nn.Module's Tensor | Module __getattr__ fallback) - utils/components: is-None narrowing + tip_names local in get_name_mask's TIP branch (exists() can't narrow for mypy); drop orphaned exists import - utils/logging: str(field) for the tree key; assign to a new hparams local rather than reassigning the typed cfg param - foundry_cli/download_checkpoints: guard on `hasher is not None`; total_size = 0.0 for the float accumulation - training/schedulers: SchedulerConfig.scheduler is now a required field (was = None, but documented required and assumed non-None everywhere) - utils/xpu/xpu_accelerator: name @property -> @staticmethod to match lightning's Accelerator ABC 6 hard-tier modules remain on the ignore list. Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * refactor(mypy): un-ignore metrics/metric module Fix the 11 type errors in foundry.metrics.metric and remove it from the [tool.mypy.overrides] ignore_errors list (5 hard-tier modules remain). - str(name) coercion of DictConfig.items() keys (str|bytes|int|... union) - exists() -> 'is not None' narrowing; drop orphaned atomworks import - widen compute_from_kwargs -> dict|list and kwargs_to_compute_args -> dict|None to match the actual returns / documented contract (callers already handle them) - three type: ignore[arg-type] on nested_dict.get/getitem for an upstream atomworks annotation bug (param typed dict[tuple,...] but navigated as nested dict[str,Any]); warn_unused_ignores will flag them if upstream is fixed No behavior change. All gates green (ruff, mypy 41 files, pytest 27 passed). Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * refactor(mypy): un-ignore utils/{ddp,rigid,datasets} Clear the three remaining foundry.utils.* modules off the mypy ignore_errors list (47 errors: ddp 12, rigid 16, datasets 19). Type-honesty and annotation fixes only, no behavior change: narrow DictConfig|dict params to DictConfig where attribute access requires it (item access kept where a plain-dict default is real), honest int|None / Tensor|None widenings, variable renames to avoid type-reuse, str() coercion of DictConfig keys, the file's own if/elif/else narrowing pattern, and documented type: ignore / cast for genuine torch and atomworks stub limitations. Two hard-tier modules remain (callbacks/health_logging, trainers/fabric). Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com> * refactor(mypy): un-ignore callbacks/health_logging Clear foundry.callbacks.health_logging off the mypy ignore_errors list by fixing its 23 type errors (annotation / type-honesty only, no behavior change): - import the stdlib 'types' module directly instead of relying on 'from typing import types' (worked at runtime but fragile/untyped) - replace 'callable'-used-as-a-type with Mapping[str, Callable[..., Any]] on the stat/histogram dict params and Callable[..., bool] | None on the filter params; annotate the two MappingProxyType default constants to match - annotate the _hooks / _temp_cache / _cache instance vars - make implicit-Optional defaults explicit (... | None) on the two plot_tensor_* helpers, matching their is-not-None guards - in plot_tensor_hist, replace two type-changing param reassignments with equivalent always-set locals (display_values, step_labels) Only trainers/fabric remains on the ignore list. Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com> * refactor(mypy): un-ignore trainers/fabric (ratchet complete) Clear foundry.trainers.fabric (the last and largest module) off the mypy ignore_errors list and remove the now-empty override block. The ratchet ignore list is now empty: all of src/foundry + src/foundry_cli type-checks with no per-module exemptions. Fixes are annotation / type-honesty only, no behavior change: - annotate self.state as dict[str, Any] (a heterogeneous, dynamically- keyed training-state bag, also merged with arbitrary checkpoint keys); this collapses ~69 union-attr/operator/arg-type errors. Also annotate default_state and declare _current_train_return (set by subclass training_step implementations). - dataloader types: Fabric.setup_dataloaders is stub-typed to return DataLoader | list[DataLoader], so cast its single-loader results to DataLoader and change train_loop/validation_loop params from _FabricDataLoader to DataLoader (drop the now-unused import). - precision: widen the param to str | int | None (the body sets it None when an XPU plugin takes over), cast to the guarded Literal at the XPUMixedPrecision call, and add one documented type: ignore[arg-type] where our public API is wider than Fabric's precision Literal. - narrow the parameter-freezing guard to direct attribute access; type get_latest_checkpoint as Path | None (matching its returns) with a cast at the single caller; drop a stale type: ignore. Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com> * chore(mypy): bring models/rfd3 into scope behind an ignore_errors ratchet Add models/rfd3/src/rfd3 to [tool.mypy].files so the rfd3 model package is type-checked by the standard gate (mypy now covers 99 files: foundry + rfd3). Seed a fresh [[tool.mypy.overrides]] ignore_errors ratchet listing the 32 rfd3 modules with pre-existing type errors (194 total), mirroring the original src/foundry bootstrap; the 26 already-clean rfd3 modules are type-checked immediately. Modules are cleared from the ratchet one slice at a time in follow-up work. Config only, no code changes. rfd3 is an editable install, so imports resolve without an added mypy_path. Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com> --------- Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> Co-authored-by: Hope Woods <hope.woods@omsf.io>
277 lines
7.3 KiB
TOML
277 lines
7.3 KiB
TOML
[project]
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name = "rc-foundry"
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dynamic = ["version"]
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description = "Shared utilities and training infrastructure for biomolecular structure prediction models."
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readme = "README.md"
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requires-python = ">=3.12,<3.13"
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authors = [
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{ name = "Institute for Protein Design", email = "contact@ipd.uw.edu" },
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]
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license = { file = "LICENSE.md" }
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classifiers = [
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"Natural Language :: English",
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"Operating System :: POSIX :: Linux",
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"Operating System :: MacOS",
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"Operating System :: Microsoft :: Windows",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: Implementation :: CPython",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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"License :: OSI Approved :: BSD License",
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]
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dependencies = [
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# ... configuration & CLI
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"rootutils>=1.0.7,<1.1",
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"hydra-core>=1.3.0,<1.4",
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"environs>=11.0.0,<12",
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# ... logging
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"wandb>=0.15.10,<1",
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"rich>=13.9.4",
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# ... typing & documentation
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"jaxtyping>=0.2.17,<1",
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"beartype>=0.18.0,<1",
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"typer>=0.20.0,<1",
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# ... ml tools (core)
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"torch>=2.2.0,<3",
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"lightning>=2.5.0",
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"loralib>=0.1.1",
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"einops>=0.8.0,<1",
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"einx>=0.1.0,<1",
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"opt_einsum>=3.4.0,<4",
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"dm-tree>=0.1.6,<1",
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"zstandard",
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"pandas",
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# "biotite",
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"atomworks[ml]>=2.1.1",
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"ipykernel>=6.31.0",
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"assertpy",
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"toolz",
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]
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[project.optional-dependencies]
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rfd3na = [
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"pydantic>=2.8",
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]
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rfd3 = [
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"pydantic>=2.8",
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]
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rf3 = [
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"cuequivariance_ops_cu12>=0.6.1; sys_platform == 'linux'",
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"cuequivariance_ops_torch_cu12>=0.6.1; sys_platform == 'linux'",
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"cuequivariance_torch>=0.6.1; sys_platform == 'linux'",
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]
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all = [
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"rc-foundry[rfd3na]",
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"rc-foundry[rfd3]",
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"rc-foundry[rf3]",
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]
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dev = [
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# Linters & formatters
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"assertpy",
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"ruff==0.8.3",
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"ipdb",
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# Type checking
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"mypy>=1.13,<2",
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# Debugger/interactive
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"debugpy>=1.8.5,<2",
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"ipykernel>=6.29.4,<7",
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# Testing tools
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"pytest>=8.2.0,<9", # testing framework
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"pytest-testmon>=2.1.1,<3", # run only tests related to changed code
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"pytest-xdist>=3.6.1,<4", # run tests in parallel
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"pytest-dotenv>=0.5.2,<1", # load environment variables from .env file
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"pytest-cov>=4.1.0,<5", # generate coverage report
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"pytest-benchmark>=5.0.0,<6", # benchmark tests for speed
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"atomworks[ml,dev,openbabel]>=2.1.1",
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"pre-commit"
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]
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[project.scripts]
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rf3 = "rf3.cli:app"
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rfd3 = "rfd3.cli:app"
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rfd3na = "rfd3na.cli:app"
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mpnn = "mpnn.inference:main"
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foundry = "foundry_cli.download_checkpoints:app"
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# Build settings ----------------------------------------------------------------------
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[build-system]
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requires = [
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"hatchling",
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"hatch-vcs == 0.4",
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]
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build-backend = "hatchling.build"
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[tool.hatch.version]
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source = "vcs"
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fallback-version = "0.0.0"
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local-scheme = "no-local-version"
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[tool.hatch.build.hooks.vcs]
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version-file = "src/foundry/version.py"
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tag-pattern = "^v(?P<version>.*)$"
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[tool.hatch.metadata]
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allow-direct-references = true
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[tool.hatch.build.targets.wheel]
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packages = [
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"src/foundry",
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"src/foundry_cli",
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"models/rf3/src/rf3",
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"models/rfd3/src/rfd3",
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"models/rfd3na/src/rfd3na",
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"models/mpnn/src/mpnn",
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]
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[tool.hatch.build.targets.wheel.force-include]
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"models/rfd3na/configs" = "rfd3na/configs"
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"models/rfd3/configs" = "rfd3/configs"
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"models/rf3/configs" = "rf3/configs"
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# Formatting & linting settings -------------------------------------------------------
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[tool.ruff]
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line-length = 88
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indent-width = 4
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target-version = "py310"
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exclude = [
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".bzr",
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".direnv",
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".eggs",
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".git",
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".git-rewrite",
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".hg",
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".ipynb_checkpoints",
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".mypy_cache",
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".nox",
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".pants.d",
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".pyenv",
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".pytest_cache",
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".pytype",
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".ruff_cache",
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".svn",
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".tox",
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".venv",
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".vscode",
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"__pypackages__",
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"_build",
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"buck-out",
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"build",
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"dist",
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"node_modules",
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"site-packages",
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"env",
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".venv",
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"venv",
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"*.ipynb",
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"dev.py",
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"archive",
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]
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[tool.ruff.format]
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# Like Black, use double quotes for strings.
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quote-style = "double"
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# Like Black, indent with spaces, rather than tabs.
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indent-style = "space"
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# Like Black, respect magic trailing commas.
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skip-magic-trailing-comma = false
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# Like Black, automatically detect the appropriate line ending.
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line-ending = "auto"
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# Enable auto-formatting of code examples in docstrings. Markdown,
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# reStructuredText code/literal blocks and doctests are all supported.
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docstring-code-format = true
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docstring-code-line-length = 88
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[tool.ruff.lint]
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# Allow unused variables when underscore-prefixed.
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dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
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# Sort imports
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extend-select = ["I", "F401"]
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ignore = [
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"F722", # for jaxtyping shape annotation
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"F821", # temporary to avoid jaxtyping warnings, see: https://github.com/astral-sh/ruff/issues/17386
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"E741", # enable us to use variables like "L"
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]
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[tool.pyright]
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typeCheckingMode = "off"
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# Type checking ----------------------------------------------------------------------
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# Lenient baseline so the existing largely-unannotated code does not fail the gate.
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# Per-module strictness is ratcheted up via [tool.mypy.overrides] as annotations land.
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[tool.mypy]
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python_version = "3.12"
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files = ["src/foundry", "src/foundry_cli", "models/rfd3/src/rfd3"]
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ignore_missing_imports = true
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warn_unused_ignores = true
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warn_redundant_casts = true
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disallow_untyped_defs = false
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check_untyped_defs = false
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# rfd3 enablement ratchet. `models/rfd3` was brought into mypy's scope in 0010;
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# these modules had pre-existing type errors at that point and are exempted until
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# annotated. Fix the errors and remove the entry to enable type-checking for that
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# module (same playbook as the now-cleared src/foundry ratchet). Do NOT add modules.
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[[tool.mypy.overrides]]
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module = [
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"rfd3.engine",
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"rfd3.inference.datasets",
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"rfd3.inference.input_parsing",
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"rfd3.inference.legacy_input_parsing",
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"rfd3.inference.parsing",
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"rfd3.inference.symmetry.symmetry_utils",
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"rfd3.metrics.design_metrics",
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"rfd3.model.RFD3",
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"rfd3.model.inference_sampler",
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"rfd3.model.layers.block_utils",
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"rfd3.model.layers.chunked_pairwise",
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"rfd3.run_inference",
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"rfd3.testing.testing_utils",
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"rfd3.trainer.dump_validation_structures",
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"rfd3.trainer.fabric_trainer",
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"rfd3.trainer.rfd3",
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"rfd3.trainer.trainer_utils",
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"rfd3.transforms.conditioning_base",
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"rfd3.transforms.design_transforms",
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"rfd3.transforms.dna_crop",
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"rfd3.transforms.hbonds",
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"rfd3.transforms.hbonds_hbplus",
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"rfd3.transforms.ncaa_transforms",
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"rfd3.transforms.pipelines",
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"rfd3.transforms.ppi_transforms",
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"rfd3.transforms.rasa",
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"rfd3.transforms.training_conditions",
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"rfd3.transforms.util_transforms",
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"rfd3.transforms.virtual_atoms",
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"rfd3.utils.inference",
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"rfd3.utils.io",
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"rfd3.utils.vizualize",
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]
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ignore_errors = true
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# Testing ----------------------------------------------------------------------------
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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addopts = "-ra --strict-markers --strict-config"
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[tool.coverage.run]
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source = ["src/foundry", "src/foundry_cli"]
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branch = true
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[tool.coverage.report]
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show_missing = true
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skip_covered = false
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[dependency-groups]
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dev = [
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"build>=1.3.0",
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"hatchling>=1.28.0",
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]
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