| [project] | |
| name = "morph" | |
| version = "0.1.0" | |
| description = "Flow-matching molecular generation and scaffold decoration with a molecular DiT" | |
| readme = "README.md" | |
| keywords = ["molecular-generation", "flow-matching", "scaffold-decoration"] | |
| requires-python = ">=3.11" | |
| dependencies = [ | |
| "click>=8.3.1", | |
| "hydra-core>=1.3.2", | |
| "huggingface-hub>=1.0,<2", | |
| "lightning>=2.5.5", | |
| "omegaconf>=2.3.0", | |
| "numpy>=2.0", | |
| "pandas>=2.3.3", | |
| "rdkit>=2025.9.1", | |
| "scipy>=1.15.0", | |
| # Pre-release allowed: the NVIDIA 25.10 container ships a CUDA-enabled | |
| # 2.9.0a0 build. Preserve that container build instead of replacing it with | |
| # a mismatched PyPI Torch/torchvision pair. | |
| "torch>=2.9.0a0, <2.9.1", | |
| "torch-geometric>=2.7.0", | |
| "torchmetrics>=1.8.0", | |
| "wandb>=0.22.2", | |
| "posebusters>=0.6.0", | |
| "matplotlib>=3.10.8", | |
| "lmdb>=2.2.0", | |
| "py3dmol>=2.5.4", | |
| "ipykernel>=7.2.0", | |
| "ase>=3.28.0", | |
| ] | |
| [dependency-groups] | |
| dev = ["pytest>=9.1.1", "ruff>=0.16.5"] | |
| [project.optional-dependencies] | |
| flash-attn = ["flash-attn>=2.8.3, <2.8.4"] | |
| [project.scripts] | |
| morph = "morph.cli:cli" | |
| [tool.uv.extra-build-dependencies] | |
| flash-attn = [{ requirement = "torch", match-runtime = true }] | |
| [build-system] | |
| requires = ["hatchling"] | |
| build-backend = "hatchling.build" | |
| [tool.hatch.build.targets.wheel] | |
| packages = ["src/morph"] | |
| [tool.hatch.build.targets.wheel.force-include] | |
| "configs" = "morph/configs" | |
| [tool.ruff] | |
| # Allow lines to be as long as 88. | |
| line-length = 88 | |
| # Keep attributed third-party implementations close to their upstream sources. | |
| extend-exclude = ["src/morph/_vendor"] | |
| [tool.ruff.format] | |
| docstring-code-format = true | |
| # Correctness, readability, and public API documentation. | |
| [tool.ruff.lint] | |
| # consider selecting "ISC", for implicit string concat | |
| # consider selecting "T201", for print in production code | |
| select = [ | |
| "B", # flake8-bugbear | |
| "C4", # flake8-comprehensions | |
| "D", # pydocstyle | |
| "E", # pycodestyle error | |
| "E501", # line too long | |
| "EXE", # flake8-executable | |
| "F", # pyflakes | |
| "FLY", # flynt | |
| "I", # isort | |
| "ICN", # flake8-import-conventions | |
| "PD", # pandas-vet | |
| "PERF", # perflint | |
| "PIE", # flake8-pie | |
| "PL", # pylint | |
| "PT", # flake8-pytest-style | |
| "PYI", # flakes8-pyi | |
| "Q", # flake8-quotes | |
| "RSE", # flake8-raise | |
| "RUF", # Ruff-specific rules | |
| "SIM", # flake8-simplify | |
| "SLOT", # flakes8-slot | |
| "TCH", # flake8-type-checking | |
| "TID", # flake8-tidy-imports | |
| "UP", # pyupgrade | |
| "W", # pycodestyle warning | |
| "W505", # line too long | |
| "YTT", # flake8-2020 | |
| ] | |
| # also consider ignoring "C901", for high mccabe function complexity | |
| # also consider ignoring "ERA001", for found commented out code | |
| ignore = [ | |
| "EXE002", # shebang is not a python interpreter | |
| "RUF012", # missing classvar type | |
| "RUF013", # Optional prohibited by PEP484 | |
| "B006", # Do not use mutable data structures for argument defaults | |
| "ANN003", # missing type annotations for kwargs | |
| "B019", # Use of functools.lru_cache on methods can lead to memory leaks | |
| "C408", # unnecessary-collection-call | |
| "COM812", # trailing comma missing | |
| "D205", # 1 blank line required between summary line and description | |
| "D415", # first line of docstring must end with punctuation | |
| "DTZ005", # use of datetime.now() without timezone | |
| "E731", # do not assign a lambda expression, use a def | |
| "EM", # flake8-errmsg | |
| "FBT001", # Boolean positional argument in function | |
| "FBT002", # Boolean keyword argument in function | |
| "NPY002", # TODO replace legacy np.random.seed | |
| "PLR", # pylint refactor | |
| "PLW2901", # Outer for loop variable overwritten by inner assignment target | |
| "PT006", # pytest-parametrize-names-wrong-type | |
| "PT011", # pytest-raises-too-broad | |
| "PT013", # pytest-incorrect-pytest-import | |
| "PT019", # pytest-fixture-param-without-value | |
| "PTH", # prefer Path to os.path | |
| "S301", # pickle can be unsafe | |
| "S310", # url open functions can be unsafe | |
| "TRY003", # long exception messages not defined in the exception class itself | |
| "UP015", # unnecessary "r" in open call | |
| "D107", # docstring for __init__ | |
| "D212", # remove whitespace after opening quotes | |
| "D202", # no blank lines after docstring | |
| "D301", | |
| "D100", | |
| "D103", | |
| ] | |
| pydocstyle.convention = "google" | |
| [env] | |
| PROJECT_ROOT = "." | |