From 50d8d75ddad7bb8a410043237aa70a15d628ed99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Konstantin=20Sch=C3=BCtze?= Date: Sat, 4 Sep 2021 11:43:47 +0900 Subject: [PATCH] Update jaxlib and release v0.2.2 --- .gitlab-ci.yml | 1 + CHANGELOG.md | 5 +- .../extract/bindEmbed21DL/__init__.py | 6 +- .../bindEmbed21DL/binding_residues_cnn.py | 23 +- poetry.lock | 2561 +++++++++-------- pyproject.toml | 6 +- tests/test_bindEmbed21DL.py | 29 +- tests/test_bio_embeddings_simple.py | 2 +- tests/test_conservation.py | 25 +- tests/test_deepblast.py | 4 +- tests/test_embedder_embedding.py | 4 +- tests/test_embedder_other.py | 4 +- tests/test_fasta_processing.py | 30 +- tests/test_hypothesis_bio.py | 9 +- tests/test_mutagenesis.py | 3 +- tests/test_seqvec_fallbacks.py | 12 +- 16 files changed, 1493 insertions(+), 1231 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 09645646..5b52a249 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -28,6 +28,7 @@ stages: <<: *install-deps variables: SKIP_EXPENSIVE_TESTS: 1 + SKIP_AVX2_TESTS: 1 stage: tests coverage: '/TOTAL.*\s(\d+\.\d+\%)/' script: poetry run pytest -v diff --git a/CHANGELOG.md b/CHANGELOG.md index e3b3b523..d7f3bd51 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,11 @@ # Changelog -## Unreleased +## 0.2.2 * Added the `esm1v` embedder from [Meier et al. 2021](https://www.biorxiv.org/content/10.1101/2021.07.09.450648v1), which is part of facebook's [esm](https://github.com/facebookresearch/esm). Note that this is an ensemble model, so you need to pass `ensemble_id` with a value from 1 to 5 to select which weights to use. + * Added the `bindEmbed21DL` extract protocol which is an ensemble of 5 convolutional neural network that predicts of 3 different types of binding residues (metal, nucleic acids, small molecules). + * Fix model download + * Update jaxlib to fix pip installation ## v0.2.1 diff --git a/bio_embeddings/extract/bindEmbed21DL/__init__.py b/bio_embeddings/extract/bindEmbed21DL/__init__.py index ea16f9b4..cdf47c3d 100644 --- a/bio_embeddings/extract/bindEmbed21DL/__init__.py +++ b/bio_embeddings/extract/bindEmbed21DL/__init__.py @@ -1 +1,5 @@ -from bio_embeddings.extract.bindEmbed21DL.bindEmbed21DL_annotation_extractor import BindEmbed21DLAnnotationExtractor +from bio_embeddings.extract.bindEmbed21DL.bindEmbed21DL_annotation_extractor import ( + BindEmbed21DLAnnotationExtractor, +) + +__all__ = ["BindEmbed21DLAnnotationExtractor"] diff --git a/bio_embeddings/extract/bindEmbed21DL/binding_residues_cnn.py b/bio_embeddings/extract/bindEmbed21DL/binding_residues_cnn.py index 1c687450..0c8a421a 100644 --- a/bio_embeddings/extract/bindEmbed21DL/binding_residues_cnn.py +++ b/bio_embeddings/extract/bindEmbed21DL/binding_residues_cnn.py @@ -2,9 +2,9 @@ class BindingResiduesCNN(nn.Module): - """ Convolutional neural network for prediction of 3 different types of binding residues (metal, nucleic acids, + """Convolutional neural network for prediction of 3 different types of binding residues (metal, nucleic acids, small molecules. Final output is determined by taking the average output probability from 5 different models from - 5 cross-validation runs """ + 5 cross-validation runs""" n_features = 1024 bottleneck_dim = 128 @@ -14,13 +14,22 @@ class BindingResiduesCNN(nn.Module): def __init__(self): super(BindingResiduesCNN, self).__init__() self.conv1 = nn.Sequential( - nn.Conv1d(in_channels=self.n_features, out_channels=self.bottleneck_dim, kernel_size=5, stride=1, - padding=2), + nn.Conv1d( + in_channels=self.n_features, + out_channels=self.bottleneck_dim, + kernel_size=5, + stride=1, + padding=2, + ), nn.ELU(), nn.Dropout(self.dropout_rate), - - nn.Conv1d(in_channels=self.bottleneck_dim, out_channels=self.n_classes, kernel_size=5, stride=1, - padding=2), + nn.Conv1d( + in_channels=self.bottleneck_dim, + out_channels=self.n_classes, + kernel_size=5, + stride=1, + padding=2, + ), ) def forward(self, x): diff --git a/poetry.lock b/poetry.lock index 4db8a186..dab156db 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,6 +1,6 @@ [[package]] name = "absl-py" -version = "0.12.0" +version = "0.13.0" description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." category = "main" optional = true @@ -38,18 +38,21 @@ python-versions = "*" [[package]] name = "alembic" -version = "1.6.2" +version = "1.7.1" description = "A database migration tool for SQLAlchemy." category = "main" optional = true -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" +python-versions = ">=3.6" [package.dependencies] +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} +importlib-resources = {version = "*", markers = "python_version < \"3.9\""} Mako = "*" -python-dateutil = "*" -python-editor = ">=0.3" SQLAlchemy = ">=1.3.0" +[package.extras] +tz = ["python-dateutil"] + [[package]] name = "amqp" version = "5.0.6" @@ -74,7 +77,7 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] [[package]] name = "anyio" -version = "3.0.1" +version = "3.3.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" category = "dev" optional = false @@ -87,7 +90,7 @@ typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [package.extras] doc = ["sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"] -test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=6.0)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] +test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=6.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"] trio = ["trio (>=0.16)"] [[package]] @@ -107,30 +110,35 @@ optional = false python-versions = "*" [[package]] -name = "argon2-cffi" -version = "20.1.0" -description = "The secure Argon2 password hashing algorithm." +name = "argcomplete" +version = "1.12.3" +description = "Bash tab completion for argparse" category = "dev" optional = false python-versions = "*" [package.dependencies] -cffi = ">=1.0.0" -six = "*" +importlib-metadata = {version = ">=0.23,<5", markers = "python_version == \"3.7\""} [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest", "sphinx", "wheel", "pre-commit"] -docs = ["sphinx"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] +test = ["coverage", "flake8", "pexpect", "wheel"] [[package]] -name = "async-generator" -version = "1.10" -description = "Async generators and context managers for Python 3.5+" +name = "argon2-cffi" +version = "21.1.0" +description = "The secure Argon2 password hashing algorithm." category = "dev" optional = false python-versions = ">=3.5" +[package.dependencies] +cffi = ">=1.0.0" + +[package.extras] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest", "sphinx", "furo", "wheel", "pre-commit"] +docs = ["sphinx", "furo"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] + [[package]] name = "async-timeout" version = "3.0.1" @@ -161,6 +169,14 @@ docs = ["furo", "sphinx", "zope.interface"] tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"] tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"] +[[package]] +name = "autopage" +version = "0.4.0" +description = "A library to provide automatic paging for console output" +category = "main" +optional = true +python-versions = ">=3.6" + [[package]] name = "babel" version = "2.9.1" @@ -180,6 +196,21 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "backports.entry-points-selectable" +version = "1.1.0" +description = "Compatibility shim providing selectable entry points for older implementations" +category = "dev" +optional = false +python-versions = ">=2.7" + +[package.dependencies] +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} + +[package.extras] +docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +testing = ["pytest (>=4.6)", "pytest-flake8", "pytest-cov", "pytest-black (>=0.3.7)", "pytest-mypy", "pytest-checkdocs (>=2.4)", "pytest-enabler (>=1.0.1)"] + [[package]] name = "beautifulsoup4" version = "4.9.3" @@ -333,35 +364,36 @@ numpy = "*" [[package]] name = "black" -version = "21.7b0" +version = "21.8b0" description = "The uncompromising code formatter." category = "dev" optional = false python-versions = ">=3.6.2" [package.dependencies] -appdirs = "*" click = ">=7.1.2" mypy-extensions = ">=0.4.3" -pathspec = ">=0.8.1,<1" +pathspec = ">=0.9.0,<1" +platformdirs = ">=2" regex = ">=2020.1.8" tomli = ">=0.2.6,<2.0.0" typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""} -typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""} +typing-extensions = ">=3.10.0.0" [package.extras] colorama = ["colorama (>=0.4.3)"] d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"] +jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] python2 = ["typed-ast (>=1.4.2)"] uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "bleach" -version = "3.3.0" +version = "4.1.0" description = "An easy safelist-based HTML-sanitizing tool." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.6" [package.dependencies] packaging = "*" @@ -389,24 +421,27 @@ numpy = ">=1.15.0" [[package]] name = "boto3" -version = "1.17.72" +version = "1.18.36" description = "The AWS SDK for Python" category = "main" optional = true -python-versions = ">= 2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">= 3.6" [package.dependencies] -botocore = ">=1.20.72,<1.21.0" +botocore = ">=1.21.36,<1.22.0" jmespath = ">=0.7.1,<1.0.0" -s3transfer = ">=0.4.0,<0.5.0" +s3transfer = ">=0.5.0,<0.6.0" + +[package.extras] +crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.20.72" +version = "1.21.36" description = "Low-level, data-driven core of boto 3." category = "main" optional = true -python-versions = ">= 2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">= 3.6" [package.dependencies] jmespath = ">=0.7.1,<1.0.0" @@ -414,7 +449,7 @@ python-dateutil = ">=2.1,<3.0.0" urllib3 = ">=1.25.4,<1.27" [package.extras] -crt = ["awscrt (==0.11.15)"] +crt = ["awscrt (==0.11.24)"] [[package]] name = "cached-property" @@ -445,29 +480,29 @@ importlib-metadata = {version = ">=0.20", markers = "python_version < \"3.8\""} [[package]] name = "celery" -version = "5.0.5" +version = "5.1.2" description = "Distributed Task Queue." category = "dev" optional = false python-versions = ">=3.6," [package.dependencies] -billiard = ">=3.6.3.0,<4.0" +billiard = ">=3.6.4.0,<4.0" click = ">=7.0,<8.0" click-didyoumean = ">=0.0.3" click-plugins = ">=1.1.1" click-repl = ">=0.1.6" -kombu = ">=5.0.0,<6.0" +kombu = ">=5.1.0,<6.0" pytz = ">0.0-dev" vine = ">=5.0.0,<6.0" [package.extras] arangodb = ["pyArango (>=1.3.2)"] auth = ["cryptography"] -azureblockblob = ["azure-storage (==0.36.0)", "azure-common (==1.1.5)", "azure-storage-common (==1.1.0)"] +azureblockblob = ["azure-storage-blob (==12.6.0)"] brotli = ["brotli (>=1.0.0)", "brotlipy (>=0.7.0)"] cassandra = ["cassandra-driver (<3.21.0)"] -consul = ["python-consul"] +consul = ["python-consul2"] cosmosdbsql = ["pydocumentdb (==2.3.2)"] couchbase = ["couchbase (>=3.0.0)"] couchdb = ["pycouchdb"] @@ -477,7 +512,6 @@ elasticsearch = ["elasticsearch"] eventlet = ["eventlet (>=0.26.1)"] gevent = ["gevent (>=1.0.0)"] librabbitmq = ["librabbitmq (>=1.5.0)"] -lzma = ["backports.lzma"] memcache = ["pylibmc"] mongodb = ["pymongo[srv] (>=3.3.0)"] msgpack = ["msgpack"] @@ -497,7 +531,7 @@ zstd = ["zstandard"] [[package]] name = "certifi" -version = "2020.12.5" +version = "2021.5.30" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false @@ -505,7 +539,7 @@ python-versions = "*" [[package]] name = "cffi" -version = "1.14.5" +version = "1.14.6" description = "Foreign Function Interface for Python calling C code." category = "main" optional = false @@ -519,9 +553,20 @@ name = "chardet" version = "4.0.0" description = "Universal encoding detector for Python 2 and 3" category = "main" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +[[package]] +name = "charset-normalizer" +version = "2.0.4" +description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" +optional = false +python-versions = ">=3.5.0" + +[package.extras] +unicode_backport = ["unicodedata2"] + [[package]] name = "check-manifest" version = "0.41" @@ -572,7 +617,7 @@ dev = ["pytest (>=3.6)", "pytest-cov", "wheel", "coveralls"] [[package]] name = "click-repl" -version = "0.1.6" +version = "0.2.0" description = "REPL plugin for Click" category = "dev" optional = false @@ -585,13 +630,14 @@ six = "*" [[package]] name = "cliff" -version = "3.7.0" +version = "3.9.0" description = "Command Line Interface Formulation Framework" category = "main" optional = true python-versions = ">=3.6" [package.dependencies] +autopage = ">=0.4.0" cmd2 = ">=1.0.0" pbr = ">=2.0.0,<2.1.0 || >2.1.0" PrettyTable = ">=0.7.2" @@ -612,11 +658,11 @@ numpy = "*" [[package]] name = "cmd2" -version = "1.5.0" +version = "2.1.2" description = "cmd2 - quickly build feature-rich and user-friendly interactive command line applications in Python" category = "main" optional = true -python-versions = ">=3.5" +python-versions = ">=3.6" [package.dependencies] attrs = ">=16.3.0" @@ -625,11 +671,13 @@ importlib-metadata = {version = ">=1.6.0", markers = "python_version < \"3.8\""} pyperclip = ">=1.6" pyreadline = {version = "*", markers = "sys_platform == \"win32\" and python_version < \"3.8\""} pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_version >= \"3.8\""} +typing-extensions = {version = "*", markers = "python_version < \"3.8\""} wcwidth = ">=0.1.7" [package.extras] -dev = ["pytest (>=4.6)", "codecov", "pytest-cov", "pytest-mock", "flake8", "sphinx", "sphinx-rtd-theme", "sphinx-autobuild", "doc8", "invoke", "twine (>=1.11)", "mock", "nox (==2019.11.9)", "nox"] -test = ["codecov", "coverage", "pytest (>=4.6)", "pytest-cov", "pytest-mock", "mock", "gnureadline"] +dev = ["codecov", "doc8", "flake8", "invoke", "mypy (==0.902)", "nox", "pytest (>=4.6)", "pytest-cov", "pytest-mock", "sphinx", "sphinx-rtd-theme", "sphinx-autobuild", "twine (>=1.11)"] +test = ["codecov", "coverage", "pytest (>=4.6)", "pytest-cov", "pytest-mock", "gnureadline"] +validate = ["flake8", "mypy (==0.902)"] [[package]] name = "colorama" @@ -641,15 +689,18 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "colorlog" -version = "5.0.1" +version = "6.4.1" description = "Add colours to the output of Python's logging module." category = "main" optional = true -python-versions = "*" +python-versions = ">=3.6" [package.dependencies] colorama = {version = "*", markers = "sys_platform == \"win32\""} +[package.extras] +development = ["black", "flake8", "mypy", "pytest", "types-colorama"] + [[package]] name = "conllu" version = "4.4" @@ -685,9 +736,17 @@ category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +[[package]] +name = "debugpy" +version = "1.4.1" +description = "An implementation of the Debug Adapter Protocol for Python" +category = "dev" +optional = false +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" + [[package]] name = "decorator" -version = "5.0.7" +version = "5.0.9" description = "Decorators for Humans" category = "dev" optional = false @@ -703,7 +762,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "distlib" -version = "0.3.1" +version = "0.3.2" description = "Distribution utilities" category = "dev" optional = false @@ -789,7 +848,7 @@ Six = "*" [[package]] name = "flask-restx" -version = "0.5.0" +version = "0.5.1" description = "Fully featured framework for fast, easy and documented API development with Flask" category = "dev" optional = false @@ -846,7 +905,7 @@ ssh = ["paramiko"] [[package]] name = "ftfy" -version = "6.0.1" +version = "6.0.3" description = "Fixes some problems with Unicode text after the fact" category = "main" optional = true @@ -860,7 +919,7 @@ docs = ["furo", "sphinx"] [[package]] name = "furo" -version = "2021.4.11b34" +version = "2021.6.18b36" description = "A clean customisable Sphinx documentation theme." category = "dev" optional = false @@ -868,7 +927,7 @@ python-versions = ">=3.6" [package.dependencies] beautifulsoup4 = "*" -sphinx = ">=3.0,<4.0" +sphinx = ">=3.0,<5.0" [package.extras] doc = ["myst-parser", "sphinx-copybutton", "sphinx-inline-tabs", "docutils (!=0.17)"] @@ -899,21 +958,21 @@ smart-open = ">=1.8.1" [package.extras] distributed = ["Pyro4 (>=4.27)"] -docs = ["pytest", "pytest-rerunfailures", "mock", "cython", "nmslib", "pyemd", "testfixtures", "Morfessor (==2.0.2a4)", "python-Levenshtein (>=0.10.2)", "visdom (>=0.1.8,!=0.1.8.7)", "scikit-learn", "Pyro4 (>=4.27)", "sphinx (<=2.4.4)", "sphinx-gallery", "sphinxcontrib.programoutput", "sphinxcontrib-napoleon", "matplotlib", "plotly", "memory-profiler", "annoy", "pyro4", "nltk", "statsmodels", "pandas"] -test = ["pytest", "pytest-rerunfailures", "mock", "cython", "nmslib", "pyemd", "testfixtures", "Morfessor (==2.0.2a4)", "python-Levenshtein (>=0.10.2)", "visdom (>=0.1.8,!=0.1.8.7)", "scikit-learn"] -test-win = ["pytest", "pytest-rerunfailures", "mock", "cython", "nmslib", "pyemd", "testfixtures", "Morfessor (==2.0.2a4)", "python-Levenshtein (>=0.10.2)", "visdom (>=0.1.8,!=0.1.8.7)", "scikit-learn"] +docs = ["pytest", "pytest-rerunfailures", "mock", "cython", "nmslib", "pyemd", "testfixtures", "Morfessor (==2.0.2a4)", "python-Levenshtein (>=0.10.2)", "visdom (>0.1.8.7)", "scikit-learn", "Pyro4 (>=4.27)", "sphinx (<=2.4.4)", "sphinx-gallery", "sphinxcontrib.programoutput", "sphinxcontrib-napoleon", "matplotlib", "plotly", "memory-profiler", "annoy", "pyro4", "nltk", "statsmodels", "pandas"] +test = ["pytest", "pytest-rerunfailures", "mock", "cython", "nmslib", "pyemd", "testfixtures", "Morfessor (==2.0.2a4)", "python-Levenshtein (>=0.10.2)", "visdom (>0.1.8.7)", "scikit-learn"] +test-win = ["pytest", "pytest-rerunfailures", "mock", "cython", "nmslib", "pyemd", "testfixtures", "Morfessor (==2.0.2a4)", "python-Levenshtein (>=0.10.2)", "visdom (>0.1.8.7)", "scikit-learn"] [[package]] name = "gevent" -version = "21.1.2" +version = "21.8.0" description = "Coroutine-based network library" category = "main" optional = true -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5" [package.dependencies] cffi = {version = ">=1.12.2", markers = "platform_python_implementation == \"CPython\" and sys_platform == \"win32\""} -greenlet = {version = ">=0.4.17,<2.0", markers = "platform_python_implementation == \"CPython\""} +greenlet = {version = ">=1.1.0,<2.0", markers = "platform_python_implementation == \"CPython\""} "zope.event" = "*" "zope.interface" = "*" @@ -921,8 +980,8 @@ greenlet = {version = ">=0.4.17,<2.0", markers = "platform_python_implementation dnspython = ["dnspython (>=1.16.0,<2.0)", "idna"] docs = ["repoze.sphinx.autointerface", "sphinxcontrib-programoutput", "zope.schema"] monitor = ["psutil (>=5.7.0)"] -recommended = ["dnspython (>=1.16.0,<2.0)", "idna", "cffi (>=1.12.2)", "selectors2", "backports.socketpair", "psutil (>=5.7.0)"] -test = ["dnspython (>=1.16.0,<2.0)", "idna", "requests", "objgraph", "cffi (>=1.12.2)", "selectors2", "futures", "mock", "backports.socketpair", "contextvars (==2.4)", "coverage (>=5.0)", "coveralls (>=1.7.0)", "psutil (>=5.7.0)"] +recommended = ["cffi (>=1.12.2)", "dnspython (>=1.16.0,<2.0)", "idna", "selectors2", "backports.socketpair", "psutil (>=5.7.0)"] +test = ["requests", "objgraph", "cffi (>=1.12.2)", "dnspython (>=1.16.0,<2.0)", "idna", "selectors2", "futures", "mock", "backports.socketpair", "contextvars (==2.4)", "coverage (>=5.0)", "coveralls (>=1.7.0)", "psutil (>=5.7.0)"] [[package]] name = "gitdb" @@ -937,19 +996,19 @@ smmap = ">=3.0.1,<5" [[package]] name = "gitpython" -version = "3.1.17" +version = "3.1.20" description = "Python Git Library" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [package.dependencies] gitdb = ">=4.0.1,<5" -typing-extensions = {version = ">=3.7.4.0", markers = "python_version < \"3.8\""} +typing-extensions = {version = ">=3.7.4.3", markers = "python_version < \"3.10\""} [[package]] name = "google-auth" -version = "1.30.0" +version = "1.35.0" description = "Google Authentication Library" category = "main" optional = true @@ -962,13 +1021,13 @@ rsa = {version = ">=3.1.4,<5", markers = "python_version >= \"3.6\""} six = ">=1.9.0" [package.extras] -aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)"] +aiohttp = ["requests (>=2.20.0,<3.0.0dev)", "aiohttp (>=3.6.2,<4.0.0dev)"] pyopenssl = ["pyopenssl (>=20.0.0)"] reauth = ["pyu2f (>=0.1.5)"] [[package]] name = "google-auth-oauthlib" -version = "0.4.4" +version = "0.4.6" description = "Google Authentication Library" category = "main" optional = true @@ -983,10 +1042,10 @@ tool = ["click (>=6.0.0)"] [[package]] name = "greenlet" -version = "1.1.0" +version = "1.1.1" description = "Lightweight in-process concurrent programming" category = "main" -optional = true +optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] @@ -994,7 +1053,7 @@ docs = ["sphinx"] [[package]] name = "grpcio" -version = "1.37.1" +version = "1.39.0" description = "HTTP/2-based RPC framework" category = "main" optional = true @@ -1004,11 +1063,11 @@ python-versions = "*" six = ">=1.5.2" [package.extras] -protobuf = ["grpcio-tools (>=1.37.1)"] +protobuf = ["grpcio-tools (>=1.39.0)"] [[package]] name = "h5py" -version = "3.2.1" +version = "3.4.0" description = "Read and write HDF5 files from Python" category = "main" optional = false @@ -1024,7 +1083,7 @@ numpy = [ [[package]] name = "huggingface-hub" -version = "0.0.8" +version = "0.0.16" description = "Client library to download and publish models on the huggingface.co hub" category = "main" optional = true @@ -1033,18 +1092,21 @@ python-versions = ">=3.6.0" [package.dependencies] filelock = "*" importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} +packaging = ">=20.9" requests = "*" tqdm = "*" +typing-extensions = "*" [package.extras] all = ["pytest", "black (>=20.8b1)", "isort (>=5.5.4)", "flake8 (>=3.8.3)"] dev = ["pytest", "black (>=20.8b1)", "isort (>=5.5.4)", "flake8 (>=3.8.3)"] quality = ["black (>=20.8b1)", "isort (>=5.5.4)", "flake8 (>=3.8.3)"] testing = ["pytest"] +torch = ["torch"] [[package]] name = "humanize" -version = "3.5.0" +version = "3.11.0" description = "Python humanize utilities" category = "main" optional = false @@ -1055,7 +1117,7 @@ tests = ["freezegun", "pytest", "pytest-cov"] [[package]] name = "hypothesis" -version = "6.12.0" +version = "6.17.4" description = "A library for property-based testing" category = "dev" optional = false @@ -1104,11 +1166,11 @@ resolved_reference = "393f080772ae7aa7ca0358ce1a6753c0b69546e2" [[package]] name = "idna" -version = "2.10" +version = "3.2" description = "Internationalized Domain Names in Applications (IDNA)" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.5" [[package]] name = "imagesize" @@ -1120,7 +1182,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.6.1" +version = "4.8.1" description = "Read metadata from Python packages" category = "main" optional = false @@ -1135,6 +1197,21 @@ docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] perf = ["ipython"] testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] +[[package]] +name = "importlib-resources" +version = "5.2.2" +description = "Read resources from Python packages" +category = "main" +optional = true +python-versions = ">=3.6" + +[package.dependencies] +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} + +[package.extras] +docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"] + [[package]] name = "iniconfig" version = "1.1.1" @@ -1145,7 +1222,7 @@ python-versions = "*" [[package]] name = "invoke" -version = "1.5.0" +version = "1.6.0" description = "Pythonic task execution" category = "dev" optional = false @@ -1153,25 +1230,30 @@ python-versions = "*" [[package]] name = "ipykernel" -version = "5.5.5" +version = "6.3.1" description = "IPython Kernel for Jupyter" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.7" [package.dependencies] appnope = {version = "*", markers = "platform_system == \"Darwin\""} -ipython = ">=5.0.0" -jupyter-client = "*" -tornado = ">=4.2" -traitlets = ">=4.1.0" +argcomplete = {version = ">=1.12.3", markers = "python_version < \"3.8.0\""} +debugpy = ">=1.0.0,<2.0" +importlib-metadata = {version = "<5", markers = "python_version < \"3.8.0\""} +ipython = ">=7.23.1,<8.0" +ipython-genutils = "*" +jupyter-client = "<8.0" +matplotlib-inline = ">=0.1.0,<0.2.0" +tornado = ">=4.2,<7.0" +traitlets = ">=4.1.0,<6.0" [package.extras] -test = ["pytest (!=5.3.4)", "pytest-cov", "flaky", "nose", "jedi (<=0.17.2)"] +test = ["pytest (!=5.3.4)", "pytest-cov", "flaky", "nose", "ipyparallel"] [[package]] name = "ipython" -version = "7.23.1" +version = "7.27.0" description = "IPython: Productive Interactive Computing" category = "dev" optional = false @@ -1191,7 +1273,7 @@ pygments = "*" traitlets = ">=4.2" [package.extras] -all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.16)", "pygments", "qtconsole", "requests", "testpath"] +all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.17)", "pygments", "qtconsole", "requests", "testpath"] doc = ["Sphinx (>=1.3)"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] @@ -1199,7 +1281,7 @@ nbformat = ["nbformat"] notebook = ["notebook", "ipywidgets"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] -test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.16)"] +test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"] [[package]] name = "ipython-genutils" @@ -1211,7 +1293,7 @@ python-versions = "*" [[package]] name = "ipywidgets" -version = "7.6.3" +version = "7.6.4" description = "IPython HTML widgets for Jupyter" category = "dev" optional = false @@ -1220,6 +1302,7 @@ python-versions = "*" [package.dependencies] ipykernel = ">=4.5.1" ipython = {version = ">=4.0.0", markers = "python_version >= \"3.3\""} +ipython-genutils = ">=0.2.0,<0.3.0" jupyterlab-widgets = {version = ">=1.0.0", markers = "python_version >= \"3.6\""} nbformat = ">=4.2.0" traitlets = ">=4.3.1" @@ -1268,16 +1351,16 @@ tqdm = "*" [[package]] name = "jaxlib" -version = "0.1.57" +version = "0.1.71" description = "XLA library for JAX" category = "main" optional = true -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] absl-py = "*" -flatbuffers = "*" -numpy = ">=1.12" +flatbuffers = ">=1.12,<3.0" +numpy = ">=1.18" scipy = "*" [[package]] @@ -1385,7 +1468,7 @@ qtconsole = "*" [[package]] name = "jupyter-cache" -version = "0.4.2" +version = "0.4.3" description = "A defined interface for working with a cache of jupyter notebooks." category = "dev" optional = false @@ -1396,23 +1479,24 @@ attrs = "*" nbclient = ">=0.2,<0.6" nbdime = "*" nbformat = "*" -sqlalchemy = ">=1.3.12,<1.4.0" +sqlalchemy = ">=1.3.12,<1.5" [package.extras] cli = ["click", "click-completion", "click-log", "tabulate", "pyyaml"] code_style = ["flake8 (>=3.7.0,<3.8.0)", "black", "pre-commit (==1.17.0)"] rtd = ["myst-nb (>=0.7,<1.0)", "sphinx-copybutton", "pydata-sphinx-theme"] -testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions", "matplotlib", "numpy", "sympy", "pandas", "nbformat (>=5.1)"] +testing = ["ipykernel", "coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions", "matplotlib", "numpy", "sympy", "pandas", "nbformat (>=5.1)"] [[package]] name = "jupyter-client" -version = "6.2.0" +version = "7.0.2" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false python-versions = ">=3.6.1" [package.dependencies] +entrypoints = "*" jupyter-core = ">=4.6.0" nest-asyncio = ">=1.5" python-dateutil = ">=2.1" @@ -1421,8 +1505,8 @@ tornado = ">=4.1" traitlets = "*" [package.extras] -doc = ["sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] -test = ["async-generator", "ipykernel", "ipython", "mock", "pytest-asyncio", "pytest-timeout", "pytest", "mypy", "pre-commit", "jedi (<0.18)"] +doc = ["myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] +test = ["codecov", "coverage", "ipykernel", "ipython", "mock", "mypy", "pre-commit", "pytest", "pytest-asyncio", "pytest-cov", "pytest-timeout", "jedi (<0.18)"] [[package]] name = "jupyter-console" @@ -1456,14 +1540,14 @@ traitlets = "*" [[package]] name = "jupyter-server" -version = "1.7.0" +version = "1.10.2" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." category = "dev" optional = false python-versions = ">=3.6" [package.dependencies] -anyio = {version = ">=3.0.1,<4", markers = "python_version >= \"3.7\""} +anyio = ">=3.1.0,<4" argon2-cffi = "*" ipython-genutils = "*" jinja2 = "*" @@ -1473,6 +1557,7 @@ nbconvert = "*" nbformat = "*" prometheus-client = "*" pyzmq = ">=17" +requests-unixsocket = "*" Send2Trash = "*" terminado = ">=0.8.3" tornado = ">=6.1.0" @@ -1480,11 +1565,11 @@ traitlets = ">=4.2.1" websocket-client = "*" [package.extras] -test = ["coverage", "pytest", "pytest-cov", "pytest-mock", "requests", "pytest-tornasync", "pytest-console-scripts", "ipykernel"] +test = ["coverage", "pytest (>=6.0)", "pytest-cov", "pytest-mock", "requests", "pytest-tornasync", "pytest-console-scripts", "ipykernel"] [[package]] name = "jupyter-server-mathjax" -version = "0.2.2" +version = "0.2.3" description = "MathJax resources as a Jupyter Server Extension." category = "dev" optional = false @@ -1513,7 +1598,7 @@ Sphinx = ">=2" [[package]] name = "jupyterlab-widgets" -version = "1.0.0" +version = "1.0.1" description = "A JupyterLab extension." category = "dev" optional = false @@ -1521,26 +1606,28 @@ python-versions = ">=3.6" [[package]] name = "kiwisolver" -version = "1.3.1" +version = "1.3.2" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "kombu" -version = "5.0.2" +version = "5.1.0" description = "Messaging library for Python." category = "dev" optional = false python-versions = ">=3.6" [package.dependencies] -amqp = ">=5.0.0,<6.0.0" +amqp = ">=5.0.6,<6.0.0" +cached-property = {version = "*", markers = "python_version < \"3.8\""} importlib-metadata = {version = ">=0.18", markers = "python_version < \"3.8\""} +vine = "*" [package.extras] -azureservicebus = ["azure-servicebus (>=0.21.1)"] +azureservicebus = ["azure-servicebus (>=7.0.0)"] azurestoragequeues = ["azure-storage-queue"] consul = ["python-consul (>=0.6.0)"] librabbitmq = ["librabbitmq (>=1.5.2)"] @@ -1551,7 +1638,7 @@ qpid = ["qpid-python (>=0.26)", "qpid-tools (>=0.26)"] redis = ["redis (>=3.3.11)"] slmq = ["softlayer-messaging (>=1.0.3)"] sqlalchemy = ["sqlalchemy"] -sqs = ["boto3 (>=1.4.4)", "pycurl (==7.43.0.2)"] +sqs = ["boto3 (>=1.4.4)", "pycurl (==7.43.0.2)", "urllib3 (<1.26)"] yaml = ["PyYAML (>=3.10)"] zookeeper = ["kazoo (>=1.3.1)"] @@ -1584,7 +1671,7 @@ python-versions = "*" [[package]] name = "mako" -version = "1.1.4" +version = "1.1.5" description = "A super-fast templating language that borrows the best ideas from the existing templating languages." category = "main" optional = true @@ -1632,7 +1719,7 @@ testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions", [[package]] name = "markupsafe" -version = "2.0.0" +version = "2.0.1" description = "Safely add untrusted strings to HTML/XML markup." category = "main" optional = false @@ -1640,7 +1727,7 @@ python-versions = ">=3.6" [[package]] name = "matplotlib" -version = "3.4.2" +version = "3.4.3" description = "Python plotting package" category = "main" optional = false @@ -1690,7 +1777,7 @@ python-versions = "*" [[package]] name = "mongomock" -version = "3.22.1" +version = "3.23.0" description = "Fake pymongo stub for testing simple MongoDB-dependent code" category = "dev" optional = false @@ -1786,14 +1873,13 @@ testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest [[package]] name = "nbclient" -version = "0.5.3" +version = "0.5.4" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." category = "dev" optional = false python-versions = ">=3.6.1" [package.dependencies] -async-generator = "*" jupyter-client = ">=6.1.5" nbformat = ">=5.0" nest-asyncio = "*" @@ -1834,7 +1920,7 @@ test = ["pytest", "pytest-cov", "ipykernel", "jupyter-client (>=5.3.1)", "ipywid [[package]] name = "nbdime" -version = "3.0.0" +version = "3.1.0" description = "Diff and merge of Jupyter Notebooks" category = "dev" optional = false @@ -1849,7 +1935,6 @@ jupyter-server-mathjax = ">=0.2.2" nbformat = "*" pygments = "*" requests = "*" -six = "*" tornado = "*" [package.extras] @@ -1906,7 +1991,7 @@ twitter = ["twython"] [[package]] name = "notebook" -version = "6.3.0" +version = "6.4.3" description = "A web-based notebook environment for interactive computing" category = "dev" optional = false @@ -1929,7 +2014,7 @@ tornado = ">=6.1" traitlets = ">=4.2.1" [package.extras] -docs = ["sphinx", "nbsphinx", "sphinxcontrib-github-alt", "sphinx-rtd-theme"] +docs = ["sphinx", "nbsphinx", "sphinxcontrib-github-alt", "sphinx-rtd-theme", "myst-parser"] json-logging = ["json-logging"] test = ["pytest", "coverage", "requests", "nbval", "selenium", "pytest-cov", "requests-unixsocket"] @@ -1947,11 +2032,11 @@ numpy = ">=1.15" [[package]] name = "numpy" -version = "1.20.3" +version = "1.21.2" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.7,<3.11" [[package]] name = "numpydoc" @@ -1970,16 +2055,16 @@ testing = ["matplotlib", "pytest", "pytest-cov"] [[package]] name = "oauthlib" -version = "3.1.0" +version = "3.1.1" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" category = "main" optional = true -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.extras] -rsa = ["cryptography"] -signals = ["blinker"] -signedtoken = ["cryptography", "pyjwt (>=1.0.0)"] +rsa = ["cryptography (>=3.0.0,<4)"] +signals = ["blinker (>=1.4.0)"] +signedtoken = ["cryptography (>=3.0.0,<4)", "pyjwt (>=2.0.0,<3)"] [[package]] name = "opt-einsum" @@ -1998,7 +2083,7 @@ tests = ["pytest", "pytest-cov", "pytest-pep8"] [[package]] name = "optuna" -version = "2.7.0" +version = "2.9.1" description = "A hyperparameter optimization framework" category = "main" optional = true @@ -2011,20 +2096,21 @@ cmaes = ">=0.8.2" colorlog = "*" numpy = "*" packaging = ">=20.0" +PyYAML = "*" scipy = "!=1.4.0" sqlalchemy = ">=1.1.0" tqdm = "*" [package.extras] +benchmark = ["asv", "virtualenv"] checking = ["black", "hacking", "isort", "mypy (==0.790)", "blackdoc"] codecov = ["codecov", "pytest-cov"] -doctest = ["cma", "matplotlib (>=3.0.0)", "pandas", "plotly (>=4.0.0)", "scikit-learn (>=0.19.0,<0.23.0)", "scikit-optimize", "mlflow"] -document = ["sphinx", "sphinx-rtd-theme", "sphinx-copybutton", "sphinx-gallery", "sphinx-plotly-directive", "pillow", "matplotlib", "scikit-learn", "plotly (>=4.0.0)", "pandas", "lightgbm", "torch (==1.8.0)", "torchvision (==0.9.0)", "torchaudio (==0.8.0)", "thop"] -example = ["catboost", "chainer", "lightgbm", "mlflow", "mpi4py", "mxnet", "nbval", "scikit-image", "scikit-learn (>=0.19.0,<0.23.0)", "xgboost", "keras", "tensorflow (>=2.0.0)", "tensorflow-datasets", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "thop", "skorch", "stable-baselines3 (>=0.7.0)", "catalyst (>=21.3)", "torchaudio (==0.8.0)", "allennlp (>=2.2.0)", "dask", "dask-ml", "fastai", "optax", "dm-haiku", "hydra-optuna-sweeper", "ray", "botorch (>=0.4.0)", "torch (==1.8.0+cpu)", "torchvision (==0.9.0+cpu)", "torch (==1.8.0)", "torchvision (==0.9.0)"] +doctest = ["cma", "matplotlib (>=3.0.0)", "pandas", "plotly (>=4.0.0)", "scikit-learn (>=0.24.2)", "scikit-optimize", "mlflow"] +document = ["sphinx (<4.0.0)", "sphinx-rtd-theme", "sphinx-copybutton", "sphinx-gallery", "sphinx-plotly-directive", "pillow", "matplotlib", "scikit-learn", "plotly (>=4.0.0)", "pandas", "lightgbm", "torch (==1.8.0)", "torchvision (==0.9.0)", "torchaudio (==0.8.0)", "thop"] experimental = ["redis"] -integration = ["chainer (>=5.0.0)", "cma", "lightgbm", "mlflow", "mpi4py", "mxnet", "pandas", "scikit-learn (>=0.19.0,<0.23.0)", "scikit-optimize", "xgboost", "keras", "tensorflow", "tensorflow-datasets", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "skorch", "catalyst (>=21.3)", "torchaudio (==0.8.0)", "allennlp (>=2.2.0)", "fastai", "botorch (>=0.4.0)", "torch (==1.8.0+cpu)", "torchvision (==0.9.0+cpu)", "torch (==1.8.0)", "torchvision (==0.9.0)"] -optional = ["bokeh (<2.0.0)", "matplotlib (>=3.0.0)", "pandas", "plotly (>=4.0.0)", "redis", "scikit-learn (>=0.19.0,<0.23.0)"] -testing = ["bokeh (<2.0.0)", "chainer (>=5.0.0)", "cma", "fakeredis", "lightgbm", "matplotlib (>=3.0.0)", "mlflow", "mpi4py", "mxnet", "pandas", "plotly (>=4.0.0)", "pytest", "scikit-learn (>=0.19.0,<0.23.0)", "scikit-optimize", "xgboost", "keras", "tensorflow", "tensorflow-datasets", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "skorch", "catalyst (>=21.3)", "torchaudio (==0.8.0)", "allennlp (>=2.2.0)", "fastai", "botorch (>=0.4.0)", "torch (==1.8.0+cpu)", "torchvision (==0.9.0+cpu)", "torch (==1.8.0)", "torchvision (==0.9.0)"] +integration = ["chainer (>=5.0.0)", "cma", "lightgbm", "mlflow", "wandb", "mpi4py", "mxnet", "pandas", "scikit-learn (>=0.24.2)", "scikit-optimize", "xgboost", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "skorch", "catalyst (>=21.3)", "torchaudio (==0.8.0)", "allennlp (>=2.2.0)", "fastai", "keras", "tensorflow (<2.5.0)", "tensorflow-datasets", "botorch (>=0.4.0)", "torch (==1.8.0+cpu)", "torchvision (==0.9.0+cpu)", "torch (==1.8.0)", "torchvision (==0.9.0)"] +optional = ["bokeh (<2.0.0)", "matplotlib (>=3.0.0)", "pandas", "plotly (>=4.0.0)", "redis", "scikit-learn (>=0.24.2)"] +testing = ["bokeh (<2.0.0)", "chainer (>=5.0.0)", "cma", "fakeredis", "lightgbm", "matplotlib (>=3.0.0)", "mlflow", "mpi4py", "mxnet", "pandas", "plotly (>=4.0.0)", "pytest", "scikit-learn (>=0.24.2)", "scikit-optimize", "xgboost", "keras", "tensorflow-datasets", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "skorch", "catalyst (>=21.3)", "torchaudio (==0.8.0)", "allennlp (>=2.2.0)", "fastai", "tensorflow (<2.5.0)", "botorch (>=0.4.0)", "torch (==1.8.0+cpu)", "torchvision (==0.9.0+cpu)", "torch (==1.8.0)", "torchvision (==0.9.0)"] tests = ["fakeredis", "pytest"] [[package]] @@ -2051,19 +2137,19 @@ pyparsing = ">=2.0.2" [[package]] name = "pandas" -version = "1.2.4" +version = "1.3.2" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false python-versions = ">=3.7.1" [package.dependencies] -numpy = ">=1.16.5" +numpy = ">=1.17.3" python-dateutil = ">=2.7.3" pytz = ">=2017.3" [package.extras] -test = ["pytest (>=5.0.1)", "pytest-xdist", "hypothesis (>=3.58)"] +test = ["hypothesis (>=3.58)", "pytest (>=6.0)", "pytest-xdist"] [[package]] name = "pandocfilters" @@ -2098,11 +2184,11 @@ testing = ["docopt", "pytest (<6.0.0)"] [[package]] name = "pathspec" -version = "0.8.1" +version = "0.9.0" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [[package]] name = "pbr" @@ -2114,7 +2200,7 @@ python-versions = ">=2.6" [[package]] name = "pep517" -version = "0.10.0" +version = "0.11.0" description = "Wrappers to build Python packages using PEP 517 hooks" category = "dev" optional = false @@ -2122,7 +2208,7 @@ python-versions = "*" [package.dependencies] importlib_metadata = {version = "*", markers = "python_version < \"3.8\""} -toml = "*" +tomli = {version = "*", markers = "python_version >= \"3.6\""} zipp = {version = "*", markers = "python_version < \"3.8\""} [[package]] @@ -2146,7 +2232,7 @@ python-versions = "*" [[package]] name = "pillow" -version = "8.2.0" +version = "8.3.2" description = "Python Imaging Library (Fork)" category = "main" optional = false @@ -2160,9 +2246,21 @@ category = "main" optional = true python-versions = "*" +[[package]] +name = "platformdirs" +version = "2.3.0" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.extras] +docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] +test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] + [[package]] name = "plotly" -version = "5.1.0" +version = "5.3.1" description = "An open-source, interactive data visualization library for Python" category = "main" optional = false @@ -2174,17 +2272,18 @@ tenacity = ">=6.2.0" [[package]] name = "pluggy" -version = "0.13.1" +version = "1.0.0" description = "plugin and hook calling mechanisms for python" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} [package.extras] dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] [[package]] name = "preshed" @@ -2200,7 +2299,7 @@ murmurhash = ">=0.28.0,<1.1.0" [[package]] name = "prettytable" -version = "2.1.0" +version = "2.2.0" description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format" category = "main" optional = true @@ -2215,7 +2314,7 @@ tests = ["pytest", "pytest-cov"] [[package]] name = "prometheus-client" -version = "0.10.1" +version = "0.11.0" description = "Python client for the Prometheus monitoring system." category = "dev" optional = false @@ -2226,18 +2325,18 @@ twisted = ["twisted"] [[package]] name = "prompt-toolkit" -version = "3.0.18" +version = "3.0.20" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.6.2" [package.dependencies] wcwidth = "*" [[package]] name = "protobuf" -version = "3.17.0" +version = "3.17.3" description = "Protocol Buffers" category = "main" optional = true @@ -2291,7 +2390,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.9.0" +version = "2.10.0" description = "Pygments is a syntax highlighting package written in Python." category = "main" optional = false @@ -2299,7 +2398,7 @@ python-versions = ">=3.5" [[package]] name = "pymongo" -version = "3.11.4" +version = "3.12.0" description = "Python driver for MongoDB " category = "main" optional = true @@ -2307,9 +2406,9 @@ python-versions = "*" [package.extras] aws = ["pymongo-auth-aws (<2.0.0)"] -encryption = ["pymongocrypt (<2.0.0)"] +encryption = ["pymongocrypt (>=1.1.0,<2.0.0)"] gssapi = ["pykerberos"] -ocsp = ["pyopenssl (>=17.2.0)", "requests (<3.0.0)", "service-identity (>=18.1.0)"] +ocsp = ["pyopenssl (>=17.2.0)", "requests (<3.0.0)", "service-identity (>=18.1.0)", "certifi"] snappy = ["python-snappy"] srv = ["dnspython (>=1.16.0,<1.17.0)"] tls = ["ipaddress"] @@ -2317,7 +2416,7 @@ zstd = ["zstandard"] [[package]] name = "pynndescent" -version = "0.5.2" +version = "0.5.4" description = "Nearest Neighbor Descent" category = "main" optional = false @@ -2364,15 +2463,15 @@ python-versions = "*" [[package]] name = "pyrsistent" -version = "0.17.3" +version = "0.18.0" description = "Persistent/Functional/Immutable data structures" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [[package]] name = "pytest" -version = "6.2.4" +version = "6.2.5" description = "pytest: simple powerful testing with Python" category = "main" optional = false @@ -2385,7 +2484,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""} importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} iniconfig = "*" packaging = "*" -pluggy = ">=0.12,<1.0.0a1" +pluggy = ">=0.12,<2.0" py = ">=1.8.2" toml = "*" @@ -2421,7 +2520,7 @@ docs = ["sphinx", "sphinx-rtd-theme"] [[package]] name = "python-dateutil" -version = "2.8.1" +version = "2.8.2" description = "Extensions to the standard Python datetime module" category = "main" optional = false @@ -2430,14 +2529,6 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" [package.dependencies] six = ">=1.5" -[[package]] -name = "python-editor" -version = "1.0.4" -description = "Programmatically open an editor, capture the result." -category = "main" -optional = true -python-versions = "*" - [[package]] name = "python-slugify" version = "5.0.2" @@ -2524,7 +2615,7 @@ python-versions = "*" [[package]] name = "pywin32" -version = "300" +version = "301" description = "Python for Window Extensions" category = "dev" optional = false @@ -2532,11 +2623,11 @@ python-versions = "*" [[package]] name = "pywinpty" -version = "0.5.7" -description = "Python bindings for the winpty library" +version = "1.1.4" +description = "Pseudo terminal support for Windows from Python." category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "pyyaml" @@ -2548,7 +2639,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "pyzmq" -version = "22.0.3" +version = "22.2.1" description = "Python bindings for 0MQ" category = "dev" optional = false @@ -2560,7 +2651,7 @@ py = {version = "*", markers = "implementation_name == \"pypy\""} [[package]] name = "qtconsole" -version = "5.1.0" +version = "5.1.1" description = "Jupyter Qt console" category = "dev" optional = false @@ -2582,15 +2673,15 @@ test = ["flaky", "pytest", "pytest-qt"] [[package]] name = "qtpy" -version = "1.9.0" +version = "1.11.0" description = "Provides an abstraction layer on top of the various Qt bindings (PyQt5, PyQt4 and PySide) and additional custom QWidgets." category = "dev" optional = false -python-versions = "*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" [[package]] name = "regex" -version = "2021.4.4" +version = "2021.8.28" description = "Alternative regular expression module, to replace re." category = "main" optional = false @@ -2598,21 +2689,21 @@ python-versions = "*" [[package]] name = "requests" -version = "2.25.1" +version = "2.26.0" description = "Python HTTP for Humans." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [package.dependencies] certifi = ">=2017.4.17" -chardet = ">=3.0.2,<5" -idna = ">=2.5,<3" +charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""} +idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""} urllib3 = ">=1.21.1,<1.27" [package.extras] -security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"] socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] [[package]] name = "requests-oauthlib" @@ -2629,9 +2720,21 @@ requests = ">=2.0.0" [package.extras] rsa = ["oauthlib[signedtoken] (>=3.0.0)"] +[[package]] +name = "requests-unixsocket" +version = "0.2.0" +description = "Use requests to talk HTTP via a UNIX domain socket" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +requests = ">=1.1" +urllib3 = ">=1.8" + [[package]] name = "responses" -version = "0.13.3" +version = "0.13.4" description = "A utility library for mocking out the `requests` Python library." category = "main" optional = true @@ -2643,7 +2746,7 @@ six = "*" urllib3 = ">=1.25.10" [package.extras] -tests = ["coverage (>=3.7.1,<6.0.0)", "pytest-cov", "pytest-localserver", "flake8", "pytest (>=4.6,<5.0)", "pytest (>=4.6)", "mypy"] +tests = ["coverage (>=3.7.1,<6.0.0)", "pytest-cov", "pytest-localserver", "flake8", "types-mock", "types-requests", "types-six", "pytest (>=4.6,<5.0)", "pytest (>=4.6)", "mypy"] [[package]] name = "rsa" @@ -2658,7 +2761,7 @@ pyasn1 = ">=0.1.3" [[package]] name = "ruamel.yaml" -version = "0.17.10" +version = "0.17.16" description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" category = "main" optional = false @@ -2673,19 +2776,19 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"] [[package]] name = "ruamel.yaml.clib" -version = "0.2.2" +version = "0.2.6" description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.5" [[package]] name = "s3transfer" -version = "0.4.2" +version = "0.5.0" description = "An Amazon S3 Transfer Manager" category = "main" optional = true -python-versions = "*" +python-versions = ">= 3.6" [package.dependencies] botocore = ">=1.12.36,<2.0a.0" @@ -2730,7 +2833,7 @@ tests = ["matplotlib (>=2.1.1)", "scikit-image (>=0.13)", "pandas (>=0.25.0)", " [[package]] name = "scipy" -version = "1.6.3" +version = "1.7.1" description = "SciPy: Scientific Library for Python" category = "main" optional = false @@ -2741,15 +2844,20 @@ numpy = ">=1.16.5,<1.23.0" [[package]] name = "send2trash" -version = "1.5.0" +version = "1.8.0" description = "Send file to trash natively under Mac OS X, Windows and Linux." category = "dev" optional = false python-versions = "*" +[package.extras] +nativelib = ["pyobjc-framework-cocoa", "pywin32"] +objc = ["pyobjc-framework-cocoa"] +win32 = ["pywin32"] + [[package]] name = "sentencepiece" -version = "0.1.95" +version = "0.1.96" description = "SentencePiece python wrapper" category = "main" optional = true @@ -2804,11 +2912,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "smart-open" -version = "5.0.0" +version = "5.2.1" description = "Utils for streaming large files (S3, HDFS, GCS, Azure Blob Storage, gzip, bz2...)" category = "main" optional = false -python-versions = ">=3.6.*" +python-versions = ">=3.6,<4.0" [package.extras] all = ["boto3", "google-cloud-storage", "azure-storage-blob", "azure-common", "azure-core", "requests"] @@ -2816,7 +2924,7 @@ azure = ["azure-storage-blob", "azure-common", "azure-core"] gcs = ["google-cloud-storage"] http = ["requests"] s3 = ["boto3"] -test = ["boto3", "google-cloud-storage", "azure-storage-blob", "azure-common", "azure-core", "requests", "mock", "moto[server] (==1.3.14)", "pathlib2", "responses", "paramiko", "parameterizedtestcase", "pytest", "pytest-rerunfailures"] +test = ["boto3", "google-cloud-storage", "azure-storage-blob", "azure-common", "azure-core", "requests", "moto[server] (==1.3.14)", "pathlib2", "responses", "paramiko", "parameterizedtestcase", "pytest", "pytest-rerunfailures"] webhdfs = ["requests"] [[package]] @@ -2845,7 +2953,7 @@ python-versions = "*" [[package]] name = "sortedcontainers" -version = "2.3.0" +version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" category = "dev" optional = false @@ -2861,7 +2969,7 @@ python-versions = ">=3.6" [[package]] name = "spacy" -version = "2.3.5" +version = "2.3.7" description = "Industrial-strength Natural Language Processing (NLP) in Python" category = "main" optional = true @@ -2984,11 +3092,11 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-htmlhelp" -version = "1.0.3" +version = "2.0.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [package.extras] lint = ["flake8", "mypy", "docutils-stubs"] @@ -3019,7 +3127,7 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-serializinghtml" -version = "1.1.4" +version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." category = "main" optional = false @@ -3031,23 +3139,35 @@ test = ["pytest"] [[package]] name = "sqlalchemy" -version = "1.3.24" +version = "1.4.23" description = "Database Abstraction Library" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" + +[package.dependencies] +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine in \"x86_64 X86_64 aarch64 AARCH64 ppc64le PPC64LE amd64 AMD64 win32 WIN32\""} +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [package.extras] +aiomysql = ["greenlet (!=0.4.17)", "aiomysql"] +aiosqlite = ["greenlet (!=0.4.17)", "aiosqlite"] +asyncio = ["greenlet (!=0.4.17)"] +mariadb_connector = ["mariadb (>=1.0.1)"] mssql = ["pyodbc"] mssql_pymssql = ["pymssql"] mssql_pyodbc = ["pyodbc"] -mysql = ["mysqlclient"] -oracle = ["cx-oracle"] -postgresql = ["psycopg2"] -postgresql_pg8000 = ["pg8000 (<1.16.6)"] +mypy = ["sqlalchemy2-stubs", "mypy (>=0.910)"] +mysql = ["mysqlclient (>=1.4.0,<2)", "mysqlclient (>=1.4.0)"] +mysql_connector = ["mysqlconnector"] +oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"] +postgresql = ["psycopg2 (>=2.7)"] +postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"] +postgresql_pg8000 = ["pg8000 (>=1.16.6)"] postgresql_psycopg2binary = ["psycopg2-binary"] postgresql_psycopg2cffi = ["psycopg2cffi"] pymysql = ["pymysql (<1)", "pymysql"] +sqlcipher = ["sqlcipher3-binary"] [[package]] name = "sqlparse" @@ -3067,7 +3187,7 @@ python-versions = "*" [[package]] name = "stevedore" -version = "3.3.0" +version = "3.4.0" description = "Manage dynamic plugins for Python applications" category = "main" optional = true @@ -3090,11 +3210,11 @@ doc = ["reno", "sphinx", "tornado (>=4.5)"] [[package]] name = "tensorboard" -version = "2.4.1" +version = "2.6.0" description = "TensorBoard lets you watch Tensors Flow" category = "main" optional = true -python-versions = ">= 2.7, != 3.0.*, != 3.1.*" +python-versions = ">=3.6" [package.dependencies] absl-py = ">=0.4" @@ -3105,10 +3225,18 @@ markdown = ">=2.6.8" numpy = ">=1.12.0" protobuf = ">=3.6.0" requests = ">=2.21.0,<3" -six = ">=1.10.0" +tensorboard-data-server = ">=0.6.0,<0.7.0" tensorboard-plugin-wit = ">=1.6.0" werkzeug = ">=0.11.15" +[[package]] +name = "tensorboard-data-server" +version = "0.6.1" +description = "Fast data loading for TensorBoard" +category = "main" +optional = true +python-versions = ">=3.6" + [[package]] name = "tensorboard-plugin-wit" version = "1.8.0" @@ -3119,7 +3247,7 @@ python-versions = "*" [[package]] name = "tensorboardx" -version = "2.2" +version = "2.4" description = "TensorBoardX lets you watch Tensors Flow without Tensorflow" category = "main" optional = true @@ -3131,7 +3259,7 @@ protobuf = ">=3.8.0" [[package]] name = "terminado" -version = "0.9.5" +version = "0.11.1" description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library." category = "dev" optional = false @@ -3139,7 +3267,7 @@ python-versions = ">=3.6" [package.dependencies] ptyprocess = {version = "*", markers = "os_name != \"nt\""} -pywinpty = {version = ">=0.5,<1", markers = "os_name == \"nt\""} +pywinpty = {version = ">=1.1.0", markers = "os_name == \"nt\""} tornado = ">=4" [package.extras] @@ -3147,14 +3275,14 @@ test = ["pytest"] [[package]] name = "testpath" -version = "0.4.4" +version = "0.5.0" description = "Test utilities for code working with files and commands" category = "dev" optional = false -python-versions = "*" +python-versions = ">= 3.5" [package.extras] -test = ["pathlib2"] +test = ["pytest", "pathlib2"] [[package]] name = "text-unidecode" @@ -3198,15 +3326,15 @@ cuda92 = ["cupy-cuda92 (>=5.0.0b4)"] [[package]] name = "threadpoolctl" -version = "2.1.0" +version = "2.2.0" description = "threadpoolctl" category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [[package]] name = "tokenizers" -version = "0.10.2" +version = "0.10.3" description = "Fast and Customizable Tokenizers" category = "main" optional = true @@ -3225,7 +3353,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "tomli" -version = "1.2.0" +version = "1.2.1" description = "A lil' TOML parser" category = "dev" optional = false @@ -3263,7 +3391,7 @@ python-versions = ">= 3.5" [[package]] name = "tox" -version = "3.23.1" +version = "3.24.3" description = "tox is a generic virtualenv management and test command line tool" category = "dev" optional = false @@ -3286,12 +3414,15 @@ testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "psutil (>=5.6.1)", "pytes [[package]] name = "tqdm" -version = "4.60.0" +version = "4.62.2" description = "Fast, Extensible Progress Meter" category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + [package.extras] dev = ["py-make (>=0.1.0)", "twine", "wheel"] notebook = ["ipywidgets (>=6)"] @@ -3299,21 +3430,18 @@ telegram = ["requests"] [[package]] name = "traitlets" -version = "5.0.5" +version = "5.1.0" description = "Traitlets Python configuration system" category = "dev" optional = false python-versions = ">=3.7" -[package.dependencies] -ipython-genutils = "*" - [package.extras] test = ["pytest"] [[package]] name = "transformers" -version = "4.6.0" +version = "4.10.0" description = "State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch" category = "main" optional = true @@ -3321,10 +3449,11 @@ python-versions = ">=3.6.0" [package.dependencies] filelock = "*" -huggingface-hub = "0.0.8" +huggingface-hub = ">=0.0.12" importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} numpy = ">=1.17" packaging = "*" +pyyaml = ">=5.1" regex = "!=2019.12.17" requests = "*" sacremoses = "*" @@ -3332,30 +3461,39 @@ tokenizers = 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vision = ["pillow"] [[package]] @@ -3368,7 +3506,7 @@ python-versions = "*" [[package]] name = "typing-extensions" -version = "3.10.0.0" +version = "3.10.0.2" description = "Backported and Experimental Type Hints for Python 3.5+" category = "main" optional = false @@ -3376,7 +3514,7 @@ python-versions = "*" [[package]] name = "typing-utils" -version = "0.0.3" +version = "0.1.0" description = "utils to inspect Python type annotations" category = "main" optional = true @@ -3414,16 +3552,16 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "urllib3" -version = "1.26.4" +version = "1.26.6" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" [package.extras] +brotli = ["brotlipy (>=0.6.0)"] secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"] socks = ["PySocks 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b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "bio_embeddings" -version = "0.2.1" +version = "0.2.2" description = "A pipeline for protein embedding generation and visualization" authors = ["Christian Dallago ", "Michael Heinzinger ", "Tobias Olenyi ", "Konstantin Schuetze "] maintainers = ["Rostlab "] @@ -60,7 +60,7 @@ jax-unirep = { version = "^1.0.0", optional = true } # "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 = "0.1.57", optional = true } +jaxlib = { version = "^0.1.71", optional = true } appdirs = "^1.4.4" importlib_metadata = "^4.6.1" pymongo = { "version" = "^3.11.2", optional = true } @@ -92,7 +92,7 @@ check-manifest = "^0.41" wheel = "^0.34.2" jupyter = "^1.0.0" tox = "^3.16.1" -black = "21.7b0" +black = "21.8b0" toml = "^0.10.1" furo = "^2021.2.28b28" Sphinx = "^3.2.1" # Sphinx 4 is blocked on https://github.com/executablebooks/MyST-NB/issues/338 diff --git a/tests/test_bindEmbed21DL.py b/tests/test_bindEmbed21DL.py index 07cfd6ba..95fab327 100644 --- a/tests/test_bindEmbed21DL.py +++ b/tests/test_bindEmbed21DL.py @@ -4,15 +4,11 @@ import pytest import torch -from bio_embeddings.embed import ( - EmbedderInterface, - ProtTransT5XLU50Embedder, -) - +from bio_embeddings.embed import EmbedderInterface, ProtTransT5XLU50Embedder from bio_embeddings.extract.bindEmbed21DL import BindEmbed21DLAnnotationExtractor # >P58568 -FASTA = 'MADKADQSSYLIKFISTAPVAATIWLTITAGILIEFNRFFPDLLFHPLP' +FASTA = "MADKADQSSYLIKFISTAPVAATIWLTITAGILIEFNRFFPDLLFHPLP" # groundtruth values for small molecule binding Y = list("------------------S-SSSSSS-SSSSSS-SSSSS--SSS-S-S-") @@ -23,18 +19,16 @@ "get_embedder,get_extractor,expected_accuracy", [ ( - lambda: ProtTransT5XLU50Embedder(half_precision_model=True), - lambda: BindEmbed21DLAnnotationExtractor(), - 0.714, - ), + lambda: ProtTransT5XLU50Embedder(half_precision_model=True), + lambda: BindEmbed21DLAnnotationExtractor(), + 0.714, + ) ], ) def test_binding_residue_annotation_extractor( - get_embedder: Callable[[], EmbedderInterface], - get_extractor: Callable[ - [], Union[BindEmbed21DLAnnotationExtractor] - ], - expected_accuracy: float, + get_embedder: Callable[[], EmbedderInterface], + get_extractor: Callable[[], Union[BindEmbed21DLAnnotationExtractor]], + expected_accuracy: float, ): """Check that BasicAnnotationExtractor passes (without checking correctness)""" extractor = get_extractor() @@ -43,7 +37,10 @@ def test_binding_residue_annotation_extractor( embedding = embedder.embed(FASTA) prediction = extractor.get_binding_residues(embedding) - results = [actual.value == predicted for actual, predicted in zip(prediction.small_molecules, Y)] + results = [ + actual.value == predicted + for actual, predicted in zip(prediction.small_molecules, Y) + ] actual_accuracy = round(sum(results) / len(results), 3) assert actual_accuracy == pytest.approx(expected_accuracy) diff --git a/tests/test_bio_embeddings_simple.py b/tests/test_bio_embeddings_simple.py index e48ab178..e2c3d930 100644 --- a/tests/test_bio_embeddings_simple.py +++ b/tests/test_bio_embeddings_simple.py @@ -70,5 +70,5 @@ def test_files(tmp_path): def simple_behavior_test(test_files): - """ Run the pipeline using a simple setup once """ + """Run the pipeline using a simple setup once""" parse_config_file_and_execute_run(test_files, overwrite=True) diff --git a/tests/test_conservation.py b/tests/test_conservation.py index c4b3cc97..4b9fe91e 100644 --- a/tests/test_conservation.py +++ b/tests/test_conservation.py @@ -1,14 +1,10 @@ - import os from typing import Callable, Union import pytest import torch -from bio_embeddings.embed import ( - EmbedderInterface, - ProtTransT5XLU50Embedder, -) +from bio_embeddings.embed import EmbedderInterface, ProtTransT5XLU50Embedder from bio_embeddings.extract.prott5cons import ProtT5consAnnotationExtractor @@ -17,7 +13,9 @@ MVKVGGEAGPSVTLPCHYSGAVTSMCWNRGSCSLFTCQNGIVWTNGTHVTYRKDTRYKLLGDLSRRDVSLTIENTAVSDSGVYCCRVEHRGWFNDMKITVSLEIVPP """.strip() # groundtruth scores from ConSurf-DB -Y = list("65183814944769491851316369976516613393436647651173341728948172511877999915534296919899766491899371431937196") +Y = list( + "65183814944769491851316369976516613393436647651173341728948172511877999915534296919899766491899371431937196" +) @pytest.mark.skipif(os.environ.get("SKIP_SLOW_TESTS"), reason="Uses T5") @@ -29,14 +27,12 @@ lambda: ProtTransT5XLU50Embedder(half_precision_model=True), lambda: ProtT5consAnnotationExtractor("prott5cons"), 0.262, - ), + ) ], ) def test_conservation_annotation_extractor( get_embedder: Callable[[], EmbedderInterface], - get_extractor: Callable[ - [], Union[ProtT5consAnnotationExtractor] - ], + get_extractor: Callable[[], Union[ProtT5consAnnotationExtractor]], expected_accuracy: float, ): """Check that BasicAnnotationExtractor passes (without checking correctness)""" @@ -45,7 +41,10 @@ def test_conservation_annotation_extractor( embedding = embedder.embed(FASTA) prediction = extractor.get_conservation(embedding) - results = [actual.value == predicted for actual, predicted in zip(prediction.conservation, Y)] - - actual_accuracy = sum(results)/len(results) + results = [ + actual.value == predicted + for actual, predicted in zip(prediction.conservation, Y) + ] + + actual_accuracy = sum(results) / len(results) assert actual_accuracy == pytest.approx(expected_accuracy) diff --git a/tests/test_deepblast.py b/tests/test_deepblast.py index d657fa71..bd2bcfa3 100644 --- a/tests/test_deepblast.py +++ b/tests/test_deepblast.py @@ -15,4 +15,6 @@ def test_pairwise_alignments_to_msa(): "HQDIRQRTAKS-LA-DHYNIDRE-QARRVLE-TT-E-QL--Y-----T--Q-WL-A-QNTKLV-Q--P--QLEALLKWAAXLHEVG-LSINH-SGXHRH-S-AYILQN-TNLPG-F-N-Q----E-Q-QTLL--ATLV-RXHRKAIKLDELPRL-NL-F-KK--K-YYLPLIQLL-----R-L-S-T-LL-NNQRQSTTTP--E-S-L-R-LITD-DS-HWTL-RFPHGYLTQNSLVQLDFER--EQAYWDDV-VGW-KLV-IEE-EEP-D-EAAKVAPEE", "AKEINLTGEEVVALAAK-Y----M-N-E-TDAAFVKK--A-LD-Y-ATAA-HF-Y-QVR-K--SGEPYIVHPIQVAG---------I-LADL-HLDAVTV-ACGFLH----D-V-VE-D-TDITLDNI-E--F---D-F----G----KDV-RDI--V-DGVTK-LGKVEYKSHEEQLAE-N-H--RKMLM-AMS--KDI-RV---I-L-VKLADRLHNMRTLKHLRKD---KQE-RISRETMEI-YAPLAH-R-L-G-I-SR-IKWE-L-E-DLAFRYLN", ] - assert expected_query, expected_targets == pairwise_alignments_to_msa(queries, targets) + assert expected_query, expected_targets == pairwise_alignments_to_msa( + queries, targets + ) diff --git a/tests/test_embedder_embedding.py b/tests/test_embedder_embedding.py index d6f033ef..bbda69d8 100644 --- a/tests/test_embedder_embedding.py +++ b/tests/test_embedder_embedding.py @@ -60,6 +60,7 @@ Word2VecEmbedder, ] + # Those embedder aren't ran by default on CI neglected_embedders: List[Any] = [ ESMEmbedder, @@ -84,7 +85,7 @@ def embedder_test_impl( embedder_class: Type[EmbedderInterface], device: Optional[str] = None ): - """ Compute embeddings and check them against a stored reference file """ + """Compute embeddings and check them against a stored reference file""" if embedder_class == SeqVecEmbedder: embedder = embedder_class(warmup_rounds=0, device=device) elif embedder_class == ESM1vEmbedder: @@ -129,6 +130,7 @@ def test_embedder_cpu(embedder_class: Type[EmbedderInterface]): @pytest.mark.skipif(os.environ.get("SKIP_SLOW_TESTS"), reason="This test is very slow") +@pytest.mark.skipif(os.environ.get("SKIP_AVX2_TESTS"), reason="This test needs AVX2") @pytest.mark.parametrize("embedder_class", [UniRepEmbedder]) def test_embedder_other(embedder_class: Type[EmbedderInterface]): """UniRep does not allow configuring the device""" diff --git a/tests/test_embedder_other.py b/tests/test_embedder_other.py index 3b256d5d..1ed65a47 100644 --- a/tests/test_embedder_other.py +++ b/tests/test_embedder_other.py @@ -31,7 +31,7 @@ ], ) def test_model_download(embedder_class): - """ We want to check that models are downloaded if the model_directory isn't given """ + """We want to check that models are downloaded if the model_directory isn't given""" module_name = embedder_class.__module__ model_class = typing.get_type_hints(embedder_class)["_model"].__name__ model_name = f"{module_name}.{model_class}" @@ -56,7 +56,7 @@ def test_model_download(embedder_class): ], ) def test_model_no_download(embedder_class): - """ We want to check that models aren't downloaded if the model_directory is given """ + """We want to check that models aren't downloaded if the model_directory is given""" with mock.patch( "bio_embeddings.embed.embedder_interfaces.get_model_directories_from_zip", return_value="/dev/null", diff --git a/tests/test_fasta_processing.py b/tests/test_fasta_processing.py index e526b5e2..e186fe2c 100644 --- a/tests/test_fasta_processing.py +++ b/tests/test_fasta_processing.py @@ -25,7 +25,7 @@ def reduce_per_protein(embedding: ndarray) -> ndarray: def test_simple_remapping(pytestconfig, tmp_path: Path): - """ https://github.com/sacdallago/bio_embeddings/issues/50 """ + """https://github.com/sacdallago/bio_embeddings/issues/50""" global_parameters = { "sequences_file": str( pytestconfig.rootpath.joinpath("test-data/seqwence-protein.fasta") @@ -34,20 +34,13 @@ def test_simple_remapping(pytestconfig, tmp_path: Path): "simple_remapping": True, } global_parameters = _process_fasta_file(**global_parameters) - embed_and_write_batched( - FakeEmbedder(), - FileSystemFileManager(), - global_parameters, - ) + embed_and_write_batched(FakeEmbedder(), FileSystemFileManager(), global_parameters) def test_illegal_amino_acids(caplog, pytestconfig, tmp_path: Path): - """ https://github.com/sacdallago/bio_embeddings/issues/54 """ + """https://github.com/sacdallago/bio_embeddings/issues/54""" input_file = pytestconfig.rootpath.joinpath("test-data/illegal_amino_acids.fasta") - _process_fasta_file( - sequences_file=str(input_file), - prefix=str(tmp_path), - ) + _process_fasta_file(sequences_file=str(input_file), prefix=str(tmp_path)) assert caplog.messages == [ f"The entry 'lowercase' in {input_file} contains lower " "case amino acids. Lower case letters are uninterpretable by most language " @@ -65,10 +58,7 @@ def test_unparsable_fasta(caplog, pytestconfig, tmp_path: Path): ValueError, match=f"Could not parse '{input_file}'. Are you sure this is a valid fasta file?", ): - _process_fasta_file( - sequences_file=str(input_file), - prefix=str(tmp_path), - ) + _process_fasta_file(sequences_file=str(input_file), prefix=str(tmp_path)) assert caplog.messages == [] @@ -96,16 +86,10 @@ def test_broken_fasta(pytestconfig, tmp_path: Path): """ input_file = pytestconfig.rootpath.joinpath("test-data/embeddings.npz") with pytest.raises(ValueError, match="Are you sure this is a valid fasta file?"): - _process_fasta_file( - sequences_file=input_file, - prefix=str(tmp_path), - ) + _process_fasta_file(sequences_file=input_file, prefix=str(tmp_path)) def test_missing_fasta(tmp_path: Path): input_file = tmp_path.joinpath("non_existant.fasta") with pytest.raises(FileNotFoundError, match="No such file or directory"): - _process_fasta_file( - sequences_file=input_file, - prefix=str(tmp_path), - ) + _process_fasta_file(sequences_file=input_file, prefix=str(tmp_path)) diff --git a/tests/test_hypothesis_bio.py b/tests/test_hypothesis_bio.py index b6ce1d9d..66d7da98 100644 --- a/tests/test_hypothesis_bio.py +++ b/tests/test_hypothesis_bio.py @@ -20,13 +20,10 @@ def cached_embedder(request) -> EmbedderInterface: @pytest.mark.skipif( - not os.environ.get("RUN_VERY_SLOW_TESTS"), reason="Hypothesis is the slowest of them all" -) -@pytest.mark.parametrize( - "cached_embedder", - name_to_embedder.values(), - indirect=True, + not os.environ.get("RUN_VERY_SLOW_TESTS"), + reason="Hypothesis is the slowest of them all", ) +@pytest.mark.parametrize("cached_embedder", name_to_embedder.values(), indirect=True) @settings(deadline=timedelta(seconds=10)) @given(sequence=protein(uppercase_only=True)) def test_foo(sequence, cached_embedder: EmbedderInterface): diff --git a/tests/test_mutagenesis.py b/tests/test_mutagenesis.py index f6c65c98..7cdb3fab 100644 --- a/tests/test_mutagenesis.py +++ b/tests/test_mutagenesis.py @@ -8,8 +8,7 @@ @pytest.mark.skipif( - not os.environ.get("RUN_VERY_SLOW_TESTS"), - reason="This is experimental", + not os.environ.get("RUN_VERY_SLOW_TESTS"), reason="This is experimental" ) def test_protbert_bfd_mutagenesis(pytestconfig, tmp_path: Path): result_kwargs = run_mutagenesis( diff --git a/tests/test_seqvec_fallbacks.py b/tests/test_seqvec_fallbacks.py index cd5d8f76..1d894eef 100644 --- a/tests/test_seqvec_fallbacks.py +++ b/tests/test_seqvec_fallbacks.py @@ -53,17 +53,9 @@ def test_fallbacks(caplog): cuda_device, elmo_log ), ), mock.patch( - "bio_embeddings.utilities.helpers.torch.cuda.is_available", - lambda: True, + "bio_embeddings.utilities.helpers.torch.cuda.is_available", lambda: True ): - sequences = [ - "M" * 20, - "M" * 8, - "M" * 8, - "M" * 7, - "M" * 7, - "M" * 7, - ] + sequences = ["M" * 20, "M" * 8, "M" * 8, "M" * 7, "M" * 7, "M" * 7] embeddings_generator = SeqVecEmbedder( weights_file="/invalid/path", options_file="/invalid/path", warmup_rounds=0 ).embed_many(sequences, given_limit)