-
Notifications
You must be signed in to change notification settings - Fork 66
/
pyproject.toml
140 lines (127 loc) · 4.71 KB
/
pyproject.toml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
[tool.poetry]
name = "bio_embeddings"
version = "0.2.3"
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 :: 3.7",
"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"