diff --git a/poetry.lock b/poetry.lock index 5a4c0acc..c30f3004 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2333,6 +2333,45 @@ files = [ {file = "llvmlite-0.42.0.tar.gz", hash = "sha256:f92b09243c0cc3f457da8b983f67bd8e1295d0f5b3746c7a1861d7a99403854a"}, ] +[[package]] +name = "lmdb" +version = "1.4.1" +description = "Universal Python binding for the LMDB 'Lightning' Database" +optional = false +python-versions = "*" +files = [ + {file = "lmdb-1.4.1-cp27-cp27m-macosx_10_14_x86_64.whl", hash = "sha256:dcdbe27f75da9b8f58815c6ac9a1f8fa2d7a8d42abc22abb664e089002d5ffa4"}, + {file = "lmdb-1.4.1-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:032ce6f490caedbec642fc0a79114475e8520d1bf1e1465c6a12b8e5fe39022f"}, + {file = "lmdb-1.4.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:13c5c8504d419039d6617cee24941e420d648a5b15c4b21e6491821400e5750f"}, + {file = "lmdb-1.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6f8018a947608c4be0dc885c90f477a600be1b71285059a9c68280d36b3fb29b"}, + {file = "lmdb-1.4.1-cp310-cp310-win_amd64.whl", hash = "sha256:360ac42a8772f571fdd01156e0466d6be52eea1140556a138281b7c887916ae2"}, + {file = "lmdb-1.4.1-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:f683f3d9a1771f21a7788a9be98fae9f3ce13cb8d549d6074d0402f284572458"}, + {file = "lmdb-1.4.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:73332a830c72d76d57744cd2b29eca2c258bc406273ca4ee07dc9e48ae84d712"}, + {file = "lmdb-1.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0c178c5134e942256a830b0bca7bb052d3d7c645b4b8759d720ab49ec36b3aae"}, + {file = "lmdb-1.4.1-cp311-cp311-win_amd64.whl", hash = "sha256:12047c239ab6ccbbc9db99277aabcfe1c15b1cfc9ea33b92ab30ddd6f0823a10"}, + {file = "lmdb-1.4.1-cp35-cp35m-macosx_10_14_x86_64.whl", hash = "sha256:91930a2a7eb9acc4d687f9067d6f9ec83c9673bbee55823badbbee2f9a3e9970"}, + {file = "lmdb-1.4.1-cp36-cp36m-macosx_10_14_x86_64.whl", hash = "sha256:1b106eb7a23b6a224bc7dfe2bd5a34c84973dda039965ae99106e10d22833dd9"}, + {file = "lmdb-1.4.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9d7779ccfacd5f4c62f28485dd2427b54d19dd7016000e6237816a3750287a82"}, + {file = "lmdb-1.4.1-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0c1f1eff7ae8d8d534309f05e274fd646dd1d4abf5157c59db59a54a55463371"}, + {file = "lmdb-1.4.1-cp36-cp36m-win_amd64.whl", hash = "sha256:b6354df94d241e8c0158f716902224109a5f3f7ed9a24447a25f968427f61d77"}, + {file = "lmdb-1.4.1-cp37-cp37m-macosx_10_15_x86_64.whl", hash = "sha256:64cf7470edfc45ff0369956e40a0784b5225097569299b91f893bd50fa336f52"}, + {file = "lmdb-1.4.1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a3c15d344731507fcfddb911a86d325e867c5574751af28591e82ecf21aad1e5"}, + {file = "lmdb-1.4.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:342550b86bb6275bfb89dbde9e48385da51d57124433bd464cd7681d0702f566"}, + {file = "lmdb-1.4.1-cp37-cp37m-win_amd64.whl", hash = "sha256:3a99a3859427fbc273ae1e932b3e7da946089757e74a05a24a19f5c4a1aba933"}, + {file = "lmdb-1.4.1-cp38-cp38-macosx_10_15_x86_64.whl", hash = "sha256:f71da9bd33fd17c9cdbe2bd4ce87f4b36b8f044927df4220bec4b03f209c78a2"}, + {file = "lmdb-1.4.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4e9ff50ad20d890bc63524230237a61b6eb3be96ad6a6ac475e8ba1a1f2c751f"}, + {file = "lmdb-1.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:81abf9475a62b7ced1ac0352967106b7ed1ac5d1c1a0d23ed24abe55a28f9884"}, + {file = "lmdb-1.4.1-cp38-cp38-win_amd64.whl", hash = "sha256:c9fa31743b447a3fbbbdaefc858de1c761568d855155dec54d5ad490f88856b6"}, + {file = "lmdb-1.4.1-cp39-cp39-macosx_11_0_x86_64.whl", hash = "sha256:26ef8fa7bd34a64f78f5e16fa9bcce0fe2ad682dd26ef078f95a8847dacb1171"}, + {file = "lmdb-1.4.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9f5dc8a335f7925fd667d62a5e43bed3aa35959b32b233fe0112a6ef02e07877"}, + {file = "lmdb-1.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7ba5d78b0ff130b38a56b7161ceb7e27ba4364d827d2bbb251c24b06c28c64cd"}, + {file = "lmdb-1.4.1-cp39-cp39-win_amd64.whl", hash = "sha256:3b84f6a349ed1bd3fa4e6c3c6b711d0389cc8d9206733cb92feffaf102998e0c"}, + {file = "lmdb-1.4.1-pp27-pypy_73-macosx_10_7_x86_64.whl", hash = "sha256:a428e6b0e298290b91b7d0ce409f595c2c9027d7f2076c39ba006290b90d14cc"}, + {file = "lmdb-1.4.1-pp27-pypy_73-win_amd64.whl", hash = "sha256:885d3f3bf51b9167d368e37b1f1277eabf595dceefd69a489bd81c1ffd3d8ffd"}, + {file = "lmdb-1.4.1-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:4bd8e49d5209c652b2caa18a3a4c30524025d7868d34b7bb249c42f7997da240"}, + {file = "lmdb-1.4.1.tar.gz", hash = "sha256:1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d"}, +] + [[package]] name = "locket" version = "1.0.0" @@ -3098,6 +3137,33 @@ doc = ["nb2plots (>=0.7)", "nbconvert (<7.9)", "numpydoc (>=1.6)", "pillow (>=9. extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.11)", "sympy (>=1.10)"] test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"] +[[package]] +name = "ninja" +version = "1.11.1.1" +description = "Ninja is a small build system with a focus on speed" +optional = false +python-versions = "*" +files = [ + {file = "ninja-1.11.1.1-py2.py3-none-macosx_10_9_universal2.macosx_10_9_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl", hash = "sha256:376889c76d87b95b5719fdd61dd7db193aa7fd4432e5d52d2e44e4c497bdbbee"}, + {file = "ninja-1.11.1.1-py2.py3-none-manylinux1_i686.manylinux_2_5_i686.whl", hash = "sha256:ecf80cf5afd09f14dcceff28cb3f11dc90fb97c999c89307aea435889cb66877"}, + {file = "ninja-1.11.1.1-py2.py3-none-manylinux1_x86_64.manylinux_2_5_x86_64.whl", hash = "sha256:84502ec98f02a037a169c4b0d5d86075eaf6afc55e1879003d6cab51ced2ea4b"}, + {file = "ninja-1.11.1.1-py2.py3-none-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:73b93c14046447c7c5cc892433d4fae65d6364bec6685411cb97a8bcf815f93a"}, + {file = "ninja-1.11.1.1-py2.py3-none-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl", hash = "sha256:18302d96a5467ea98b68e1cae1ae4b4fb2b2a56a82b955193c637557c7273dbd"}, + {file = "ninja-1.11.1.1-py2.py3-none-manylinux2014_s390x.manylinux_2_17_s390x.whl", hash = "sha256:aad34a70ef15b12519946c5633344bc775a7656d789d9ed5fdb0d456383716ef"}, + {file = "ninja-1.11.1.1-py2.py3-none-musllinux_1_1_aarch64.whl", hash = "sha256:d491fc8d89cdcb416107c349ad1e3a735d4c4af5e1cb8f5f727baca6350fdaea"}, + {file = "ninja-1.11.1.1-py2.py3-none-musllinux_1_1_i686.whl", hash = "sha256:7563ce1d9fe6ed5af0b8dd9ab4a214bf4ff1f2f6fd6dc29f480981f0f8b8b249"}, + {file = "ninja-1.11.1.1-py2.py3-none-musllinux_1_1_ppc64le.whl", hash = "sha256:9df724344202b83018abb45cb1efc22efd337a1496514e7e6b3b59655be85205"}, + {file = "ninja-1.11.1.1-py2.py3-none-musllinux_1_1_s390x.whl", hash = "sha256:3e0f9be5bb20d74d58c66cc1c414c3e6aeb45c35b0d0e41e8d739c2c0d57784f"}, + {file = "ninja-1.11.1.1-py2.py3-none-musllinux_1_1_x86_64.whl", hash = "sha256:76482ba746a2618eecf89d5253c0d1e4f1da1270d41e9f54dfbd91831b0f6885"}, + {file = "ninja-1.11.1.1-py2.py3-none-win32.whl", hash = "sha256:fa2ba9d74acfdfbfbcf06fad1b8282de8a7a8c481d9dee45c859a8c93fcc1082"}, + {file = "ninja-1.11.1.1-py2.py3-none-win_amd64.whl", hash = "sha256:95da904130bfa02ea74ff9c0116b4ad266174fafb1c707aa50212bc7859aebf1"}, + {file = "ninja-1.11.1.1-py2.py3-none-win_arm64.whl", hash = "sha256:185e0641bde601e53841525c4196278e9aaf4463758da6dd1e752c0a0f54136a"}, + {file = "ninja-1.11.1.1.tar.gz", hash = "sha256:9d793b08dd857e38d0b6ffe9e6b7145d7c485a42dcfea04905ca0cdb6017cc3c"}, +] + +[package.extras] +test = ["codecov (>=2.0.5)", "coverage (>=4.2)", "flake8 (>=3.0.4)", "pytest (>=4.5.0)", "pytest-cov (>=2.7.1)", "pytest-runner (>=5.1)", "pytest-virtualenv (>=1.7.0)", "virtualenv (>=15.0.3)"] + [[package]] name = "nodeenv" version = "1.8.0" @@ -5395,6 +5461,22 @@ typing-extensions = "*" dynamo = ["jinja2"] opt-einsum = ["opt-einsum (>=3.3)"] +[[package]] +name = "torch-cluster" +version = "1.6.3" +description = "PyTorch Extension Library of Optimized Graph Cluster Algorithms" +optional = false +python-versions = ">=3.8" +files = [ + {file = "torch_cluster-1.6.3.tar.gz", hash = "sha256:78d5a930a5bbd0d8788df8c6d66addd68d6dd292fe3edb401e3dacba26308152"}, +] + +[package.dependencies] +scipy = "*" + +[package.extras] +test = ["pytest", "pytest-cov"] + [[package]] name = "torch-geometric" version = "2.4.0" @@ -5424,6 +5506,44 @@ graphgym = ["hydra-core", "protobuf (<4.21)", "pytorch-lightning", "yacs"] modelhub = ["huggingface_hub"] test = ["onnx", "onnxruntime", "pytest", "pytest-cov"] +[[package]] +name = "torch-scatter" +version = "2.1.2" +description = "PyTorch Extension Library of Optimized Scatter Operations" +optional = false +python-versions = ">=3.8" +files = [ + {file = "torch_scatter-2.1.2.tar.gz", hash = "sha256:69b3aa435f2424ac6a1bfb6ff702da6eb73b33ca0db38fb26989c74159258e47"}, +] + +[package.extras] +test = ["pytest", "pytest-cov"] + +[[package]] +name = "torchdrug" +version = "0.2.1" +description = "A powerful and flexible machine learning platform for drug discovery" +optional = false +python-versions = ">=3.7,<3.11" +files = [ + {file = "torchdrug-0.2.1-py3-none-any.whl", hash = "sha256:f416dbbfb3fc697770e9ee7fa7769611fad060a4749ee49499d87583cfb58ee2"}, +] + +[package.dependencies] +decorator = "*" +fair-esm = "*" +jinja2 = "*" +lmdb = "*" +matplotlib = "*" +networkx = "*" +ninja = "*" +numpy = ">=1.11" +rdkit-pypi = ">=2020.9" +torch = ">=1.8.0" +torch-cluster = ">=1.5.9" +torch-scatter = ">=2.0.8" +tqdm = "*" + [[package]] name = "torchmetrics" version = "1.3.0.post0" @@ -6069,4 +6189,4 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] [metadata] lock-version = "2.0" python-versions = ">= 3.9, < 3.11" -content-hash = "a980d6cf58c0bcd4587931333f68abff976cbed73c96cfd53a5766f1df8782ed" +content-hash = "857700b8c6b32da83cb402c612ed849b511cf6ef392e87f3e88cd3ddff295f6f" diff --git a/pyproject.toml b/pyproject.toml index 9fff6e68..56a58f50 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,6 +61,7 @@ umap-learn = "^0.5.4" matplotlib = "^3.7.2" datashader = "^0.16.0" holoviews = "^1.18.0" +torchdrug = "^0.2.1" [tool.poetry.group.dev.dependencies]