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pyproject.toml
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[tool.poetry]
name = "bio_embeddings"
version = "0.1.4"
description = "A pipeline for protein embedding generation and visualization"
authors = ["Christian Dallago <[email protected]>", "Michael Heinzinger <[email protected]>", "Tobias Olenyi <[email protected]>", "Konstantin Schuetze <[email protected]>"]
maintainers = ["Rostlab <[email protected]>"]
license = "MIT"
readme = "README.md"
classifiers = [
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Visualization"
]
include = ["README.md", "LICENSE.md", "requirements.txt", "pyproject.toml", "bio_embeddings/utilities/defaults.yml"]
exclude = ["tests/", "examples/", "webserver/", "notebooks/"]
[tool.poetry.scripts]
bio_embeddings = 'bio_embeddings.utilities.cli:main'
[tool.poetry.urls]
issues = "https://github.com/sacdallago/bio_embeddings/issues"
homepage = "https://visualize.protein.properties"
repository = "https://github.com/sacdallago/bio_embeddings"
[tool.poetry.dependencies]
python = "~ 3.6.6 || ^3.7 || ^3.8"
allennlp = { version = "^0.9.0", optional = true }
numpy = "^1.18.3"
gensim = "^3.8.2"
biopython = "^1.76"
"ruamel.yaml" = "^0.16.10"
pandas = "^1.0.3"
h5py = "^2.10.0"
transformers = { version = "^3.1.0", optional = true }
plotly = "^4.6.0"
umap-learn = "^0.4.2"
matplotlib = "^3.2.1"
scikit-learn = "^0.22.2.post1"
scipy = "^1.4.1"
torch = "~1.5.0"
tqdm = "^4.45.0"
lock = "^2018.3.25"
jax-unirep = { version = "^1.0.1", optional = true }
appdirs = "^1.4.4"
# Help the version resolver with allennlp
boto3 = { version = "1.14.18", optional = true }
botocore = { version = "1.17.18", optional = true }
# https://github.com/boto/botocore/issues/2187#issuecomment-712819351
urllib3 = "1.25.10"
importlib_metadata = "^1.7.0"
esm = { git = "https://github.com/facebookresearch/esm.git", tag = "v0.1.0", optional = true }
cpcprot = { git = "https://github.com/amyxlu/CPCProt.git", rev = "df1ad1118544ed349b5e711207660a7c205b3128", optional = true }
tape-proteins = { git = "https://github.com/konstin/tape.git", branch = "patch-1", optional = true }
plus = { git = "https://github.com/konstin/PLUS", optional = true }
[tool.poetry.extras]
seqvec = ["allennlp", "boto3", "botocore"]
transformers = ["transformers"]
unirep = ["jax-unirep"]
esm = ["esm"]
cpcprot = ["cpcprot", "tape-proteins"]
plus = ["plus"]
all = ["allennlp", "transformers", "jax-unirep", "esm", "cpcprot", "tape-proteins", "plus"]
[tool.poetry.dev-dependencies]
pytest = "^6.0.1"
invoke = "^1.4.1"
check-manifest = "^0.41"
wheel = "^0.34.2"
jupyter = "^1.0.0"
tox = "^3.16.1"
black = "^20.8b1"
toml = "^0.10.1"
furo = "^2020.10.15-beta.13"
Sphinx = "^3.2.1"
myst-parser = "^0.12.10"
[tool.pytest.ini_options]
addopts = "--tb=short"
filterwarnings = [
"ignore:::Bio.Alphabet",
"ignore:::thinc.check:4",
"ignore:::thinc.neural.train:7",
"ignore:::plac_ext:6",
"ignore:::scipy.sparse.sparsetools:21",
]
[tool.black]
target-version = ['py36']
include = '/(bio_embeddings|tests)/'
[build-system]
requires = ["poetry~=1.1.0"]
build-backend = "poetry.masonry.api"