pyproject.toml

[tool.poetry]
name = "bio_embeddings"
version = "0.2.3"
description = "A pipeline for protein embedding generation and visualization"
authors = ["Christian Dallago <christian.dallago@tum.de>", "Michael Heinzinger <mheinzinger@rostlab.org>", "Tobias Olenyi <olenyi@rostlab.org>", "Konstantin Schuetze <schuetze@in.tum.de>"]
maintainers = ["Rostlab <admin@rostlab.org>"]
license = "MIT"
readme = "README.md"
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.7",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "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 = ">=3.8,<3.10"

# Packages which we had to patch
bio-embeddings-cpcprot = { version = "0.0.1", optional = true }
bio-embeddings-tape-proteins = { version = "0.5", optional = true }
bio-embeddings-plus = { version = "0.1.1", optional = true }
bio-embeddings-bepler = { version = "0.0.1", optional = true }
bio-embeddings-allennlp = { version = "0.9.2", optional = true }
bio-embeddings-deepblast = { version = "0.1.0", optional = true }

numpy = "^1.19.2"
gensim = "^4.2.0"
biopython = "^1.79"
"ruamel.yaml" = "^0.17.10"
pandas = "^1.4.2"
h5py = "^3.7.0"
transformers = { version = "^4.19.2", optional = true }
plotly = "^5.8.0"
umap-learn = "^0.5.3"
matplotlib = "^3.5.2"
scikit-learn = "^1.1.1"
scipy = "^1.8.1"
torch = ">=1.8.0,<=1.10.0"
tqdm = "^4.64.0"
lock = "^2018.3.25"
# https://github.com/ElArkk/jax-unirep/issues/107
jax-unirep = { version = "^2.1.0", optional = true }
# https://github.com/google/jax/blob/23b82b99d2e178fc648d5ac9ebc8bf5e4049075e/CHANGELOG.md#jaxlib-0162-march-9-2021
# "jaxlib wheels are now built to require AVX instructions on x86-64 machines by default"
# However, our CI machine is too old for AVX
# We then go even lower due to https://github.com/google/jax/issues/5374
jaxlib = { version = "^0.3.10", optional = true }
appdirs = "^1.4.4"
importlib_metadata = "^4.11.4"
pymongo = { "version" = "^4.1.1", optional = true }
sentry-sdk = { extras = ["flask"],"version" = "^1.5.12", optional = true }
python-slugify = "^6.1.2"
fsspec = { version = "0.8.5", optional = true }
humanize = "^4.1.0"
fair-esm = { version = "0.4.0", optional = true }
flask = { version = "^2.1.2", optional = true }
atomicwrites = "^1.4.0"
pyyaml = "6.0"
# Hiwi addons
sentencepiece="0.1.96"
celery="^5.2.7"
flask-cors="^3.0.10"
gunicorn="^20.1.0"
vespa-effect= {version = "^1.0.0", python="^3.8"}
werkzeug="2.0.3"


[tool.poetry.extras]
# Extras by paper/model name
seqvec = ["bio-embeddings-allennlp", "boto3", "botocore"]
prottrans = ["transformers"]
unirep = ["jax-unirep", "jaxlib"]
esm = ["fair-esm"]
cpcprot = ["bio-embeddings-cpcprot", "bio-embeddings-tape-proteins"]
plus = ["bio-embeddings-plus"]
bepler = ["bio-embeddings-bepler"]
deepblast = ["bio-embeddings-deepblast", "fsspec"]

# General
transformers = ["transformers"]
all = ["bio-embeddings-allennlp", "transformers", "jax-unirep", "fair-esm", "bio-embeddings-cpcprot", "bio-embeddings-tape-proteins", "bio-embeddings-plus", "bio-embeddings-bepler", "bio-embeddings-deepblast"]
# User don't need those, but we need it to run the tests
webserver = ["pymongo", "sentry-sdk", "flask"]

[tool.poetry.dev-dependencies]
black = "21.8b0"
check-manifest = "^0.48"
flask-restx = "^0.5.1"
furo = "^2021.08.31"
hypothesis = "^6.3.4"
hypothesis-bio = { git = "https://github.com/IQTLabs/hypothesis-bio", rev = "393f080772ae7aa7ca0358ce1a6753c0b69546e2" }
invoke = "^1.4.1"
jupyter = "^1.0.0"
mongomock = "^3.22.0"
myst-nb = "^0.13.0"
myst-parser = "^0.15.2"
packaging = "^20.8"
pytest = "^6.0.1"
pytest-celery = "^0.0.0-alpha.1"
pytest-flask = "^1.1.0"
sphinx = "^4"
sphinx-copybutton = "^0.4.0"
toml = "^0.10.1"
tox = "^3.16.1"
wheel = "^0.34.2"
nbconvert = "^6.1.0"


[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 = ['py37']

[build-system]
requires = ["poetry~=1.1.0"]
build-backend = "poetry.masonry.api"