diff --git a/poetry.lock b/poetry.lock index c6b853e7..38dc0026 100644 --- a/poetry.lock +++ b/poetry.lock @@ -158,7 +158,7 @@ python-versions = ">=3.5" name = "atomicwrites" version = "1.4.0" description = "Atomic file writes." -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" @@ -532,6 +532,31 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "etils" +version = "0.9.0" +description = "Collection of common python utils" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +all = ["etils[array-types]", "etils[eapp]", "etils[ecolab]", "etils[edc]", "etils[enp]", "etils[epath]", "etils[epy]", "etils[etqdm]", "etils[etree-dm]", "etils[etree-jax]", "etils[etree-tf]", "etils[etree]"] +array-types = ["etils[enp]"] +dev = ["chex", "pylint (>=2.6.0)", "pytest", "pytest-subtests", "pytest-xdist", "yapf"] +eapp = ["absl-py", "simple_parsing"] +ecolab = ["etils[enp]", "etils[epy]", "jupyter", "mediapy", "numpy"] +edc = ["etils[epy]", "typing_extensions"] +enp = ["etils[epy]", "numpy"] +epath = ["etils[epy]", "importlib_resources", "typing_extensions", "zipp"] +epy = ["typing_extensions"] +etqdm = ["absl-py", "etils[epy]", "tqdm"] +etree = ["etils[array_types]", "etils[enp]", "etils[epy]", "etils[etqdm]"] +etree-dm = ["dm-tree", "etils[etree]"] +etree-jax = ["etils[etree]", "jax[cpu]"] +etree-tf = ["etils[etree]", "tf-nightly"] +lazy-imports = ["etils[ecolab]"] + [[package]] name = "fastjsonschema" version = "2.15.3" @@ -1240,7 +1265,7 @@ python-versions = "*" name = "more-itertools" version = "8.13.0" description = "More routines for operating on iterables, beyond itertools" -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -1571,6 +1596,30 @@ jaxlib = ">=0.1.37" numpy = ">=1.18.0" typing-extensions = ">=3.10.0" +[[package]] +name = "orbax" +version = "0.1.0" +description = "Orbax" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +absl-py = "*" +cached_property = "*" +etils = "*" +flax = "*" +importlib_resources = "*" +jax = "*" +jaxlib = "*" +numpy = "*" +pytest = "*" +pyyaml = "*" +tensorstore = ">=0.1.20" + +[package.extras] +dev = ["pytest-xdist"] + [[package]] name = "packaging" version = "21.3" @@ -1712,7 +1761,7 @@ tenacity = ">=6.2.0" name = "pluggy" version = "0.13.1" description = "plugin and hook calling mechanisms for python" -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" @@ -1931,7 +1980,7 @@ python-versions = ">=3.7" name = "pytest" version = "5.4.3" description = "pytest: simple powerful testing with Python" -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -2615,6 +2664,17 @@ tensorflow-cpu = ["tensorflow-cpu (>=2.9.0,<2.10.0)"] tensorflow-gpu = ["tensorflow-gpu (>=2.9.0,<2.10.0)"] tensorflow-rocm = ["tensorflow-rocm (>=2.9.0,<2.10.0)"] +[[package]] +name = "tensorstore" +version = "0.1.28" +description = "Read and write large, multi-dimensional arrays" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +numpy = ">=1.16.0" + [[package]] name = "termcolor" version = "1.1.0" @@ -3079,7 +3139,7 @@ testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>= [metadata] lock-version = "1.1" python-versions = ">=3.7.13,<3.11" -content-hash = "db5defb9399c241fa31cdcf16bd146a8d8792e120aca451d581e2e9954b19aa2" +content-hash = "b160ee414fd912b6d7095cb1cfd1df52cea8482337d68d533f68bee6899c5bea" [metadata.files] absl-py = [ @@ -3460,6 +3520,10 @@ et-xmlfile = [ {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"}, {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"}, ] +etils = [ + {file = "etils-0.9.0-py3-none-any.whl", hash = "sha256:635d6f7d1c519eb194304228543a4c5c7df0e6b58243302473e34c18cf720588"}, + {file = "etils-0.9.0.tar.gz", hash = "sha256:489103e9e499a566765c60458ee15d185cf0065f2060a4d16a68f8f46962ed0d"}, +] fastjsonschema = [ {file = "fastjsonschema-2.15.3-py3-none-any.whl", hash = "sha256:ddb0b1d8243e6e3abb822bd14e447a89f4ab7439342912d590444831fa00b6a0"}, {file = "fastjsonschema-2.15.3.tar.gz", hash = "sha256:0a572f0836962d844c1fc435e200b2e4f4677e4e6611a2e3bdd01ba697c275ec"}, @@ -4321,6 +4385,10 @@ optax = [ {file = "optax-0.1.2-py3-none-any.whl", hash = "sha256:4e3cb24b70e87acd65700da77c570c468e701d32a2393ae4a5ec35719d90ade6"}, {file = "optax-0.1.2.tar.gz", hash = "sha256:c2963ffa3b3ac47f72c2866625207c9468558ed18e6e471baac69d4de2ac3f58"}, ] +orbax = [ + {file = "orbax-0.1.0-py3-none-any.whl", hash = "sha256:df2b5534cb379e1c72a8829bbb62a2c7ebc0e06567ad98e4b06e6aced5d231b1"}, + {file = "orbax-0.1.0.tar.gz", hash = "sha256:317fae101b504dfea9204d667fd79ad7039395b123356995e13a01332e996595"}, +] packaging = [ {file = "packaging-21.3-py3-none-any.whl", hash = "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"}, {file = "packaging-21.3.tar.gz", hash = "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb"}, @@ -5140,6 +5208,24 @@ tensorflow-io-gcs-filesystem = [ {file = "tensorflow_io_gcs_filesystem-0.26.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:bd285595afe03740553710ccdbd1397d69a8e48d758c731c0de1f1c5a71a9fe5"}, {file = "tensorflow_io_gcs_filesystem-0.26.0-cp39-cp39-win_amd64.whl", hash = "sha256:2940b4ab6848ef5ec34dc3c140b5ae9eba0da13453da839c30ebe3461a6eb51d"}, ] +tensorstore = [ + {file = "tensorstore-0.1.28-cp310-cp310-macosx_10_14_x86_64.whl", hash = "sha256:deb32f1e74ab7b836ecec02a759a558fc57522a8dea0db4f19a01a78e93abab5"}, + {file = "tensorstore-0.1.28-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:bd8615308ad3e29111238dfdd3aca1f3fb79b55c3dac1c04c96c8a319985addf"}, + {file = "tensorstore-0.1.28-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ee16297a9493ed0d6d1000f216e79d29a0b80e7e97646e8520afd44138165839"}, + {file = "tensorstore-0.1.28-cp310-cp310-win_amd64.whl", hash = "sha256:b6f7e0c7455d9e164e6143714519e7c96cc4166b61ed7d268a8ab84a77e0d593"}, + {file = "tensorstore-0.1.28-cp37-cp37m-macosx_10_14_x86_64.whl", hash = "sha256:1c53e1e0e7996b8ba41854135d748c2bc8802b94a79122b56448aeb1f77efd9f"}, + {file = "tensorstore-0.1.28-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6bd122a44db81369808c84b7739ad2d8453f89c548c5d61d62f2b1f3331dbe9f"}, + {file = "tensorstore-0.1.28-cp37-cp37m-win_amd64.whl", hash = "sha256:197159da3ee97c08d8769fa151ff167328108bf07a13886f688b21f64abfb7d6"}, + {file = "tensorstore-0.1.28-cp38-cp38-macosx_10_14_x86_64.whl", hash = "sha256:e480da4f95f7c95302c4b3e2a7fc32b8cfe1aa51742d72f84a335e49462a2465"}, + {file = "tensorstore-0.1.28-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:7948ead0d5a55303ffa97a35659aa56a20c60bd89d9487643f51ac8d2e19b52c"}, + {file = "tensorstore-0.1.28-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:818aeb015b249069a686fb20f0c0b71663410ac6411cee88df18b8e05b567cbc"}, + {file = "tensorstore-0.1.28-cp38-cp38-win_amd64.whl", hash = "sha256:6719eaba4ec2692d890c3c67c389fcae073d40d9e8c27e2dabd27fc9fd745e5c"}, + {file = "tensorstore-0.1.28-cp39-cp39-macosx_10_14_x86_64.whl", hash = "sha256:d7c86f63a6d4d7a84e3201ba9746ca51015612d375d77b9302eb93e9b88bc7aa"}, + {file = "tensorstore-0.1.28-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:dc82cbb77255fd2f7aa191f1e030f13276bf7272ea1027fcc6900537b30bfbcb"}, + {file = "tensorstore-0.1.28-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c4de09e3fae30f8a9ab7648600c78e109ddd1d14af4280e055439fdd52a6dca9"}, + {file = "tensorstore-0.1.28-cp39-cp39-win_amd64.whl", hash = "sha256:f9270586401ee60ff79a4cd54c62ab5b06831d69b561df1fb9ebbeade4d4929c"}, + {file = "tensorstore-0.1.28.tar.gz", hash = "sha256:cd8d8185136632c58edcd7cf4c43d301bf8ad61a197c632cb495d7d33b7be04e"}, +] termcolor = [ {file = "termcolor-1.1.0.tar.gz", hash = "sha256:1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b"}, ] diff --git a/pyproject.toml b/pyproject.toml index ff5369cd..3779c274 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ homepage = "https://github.com/bowang-lab/scGPT" readme = "README.md" [tool.poetry.dependencies] -python = ">=3.7.13,<4" +python = ">=3.7.13,<3.11" pandas = "1.3.5" scvi-tools = "^0.16.0" llvmlite = "^0.38.0" @@ -25,6 +25,7 @@ datasets = "^2.3.0" typing-extensions = "^4.2.0" scib = "^1.0.3" flash-attn = "^1.0.1" +orbax = "<0.1.8" [tool.poetry.dev-dependencies] pytest = "^5.2" diff --git a/scgpt/scbank/databank.py b/scgpt/scbank/databank.py index 6b74b656..a938db24 100644 --- a/scgpt/scbank/databank.py +++ b/scgpt/scbank/databank.py @@ -8,7 +8,6 @@ from scipy.sparse import spmatrix, csr_matrix from anndata import AnnData from datasets import Dataset, load_dataset -from scvi import settings from scgpt.tokenizer import GeneVocab from .data import DataTable, MetaInfo