diff --git a/poetry.lock b/poetry.lock index 5d4ebed..53165df 100644 --- a/poetry.lock +++ b/poetry.lock @@ -75,6 +75,81 @@ python-versions = ">=2.7" 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 = "4.10.0" +description = "Screen-scraping library" +category = "main" +optional = false +python-versions = ">3.0.0" + +[package.dependencies] +soupsieve = ">1.2" + +[package.extras] +html5lib = ["html5lib"] +lxml = ["lxml"] + +[[package]] +name = "bioregistry" +version = "0.3.27" +description = "Integrated registry of biological databases and nomenclatures" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +beautifulsoup4 = "*" +click = "*" +defusedxml = "*" +more-click = "*" +more-itertools = "*" +pydantic = "*" +pystow = ">=0.1.13" +pyyaml = "*" +rdflib = "*" +rdflib-jsonld = "*" +requests = "*" +requests-ftp = "*" +tabulate = "*" +tqdm = "*" + +[package.extras] +charts = ["matplotlib", "matplotlib-venn", "seaborn"] +docs = ["sphinx", "sphinx-rtd-theme", "sphinx-click", "sphinx-autodoc-typehints", "sphinx-automodapi"] +health = ["click-default-group", "pandas"] +web = ["flask", "flasgger", "bootstrap-flask"] + +[[package]] +name = "bioversions" +version = "0.3.5" +description = "What's the current version for each biological database?" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +beautifulsoup4 = "*" +bioregistry = ">=0.2.6" +cachier = "<=1.5.0" +click = "*" +click-default-group = "*" +dataclasses-json = "*" +lxml = "*" +more-click = "*" +pystow = ">=0.1.0" +pyyaml = "*" +requests = "*" +requests-ftp = "*" +tabulate = "*" +tqdm = "*" + +[package.extras] +charts = ["matplotlib", "seaborn"] +slack = ["slack-sdk"] +twitter = ["tweepy"] +web = ["flask", "bootstrap-flask"] + [[package]] name = "black" version = "21.9b0" @@ -115,6 +190,22 @@ packaging = "*" six = ">=1.9.0" webencodings = "*" +[[package]] +name = "cachier" +version = "1.5.0" +description = "Persistent, stale-free, local and cross-machine caching for Python functions." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +pathtools = "*" +portalocker = "*" +watchdog = "*" + +[package.extras] +test = ["pytest", "coverage", "pytest-cov", "pymongo", "pandas", "collective.checkdocs", "pygments"] + [[package]] name = "certifi" version = "2021.10.8" @@ -155,7 +246,7 @@ unicode_backport = ["unicodedata2"] [[package]] name = "click" -version = "8.0.1" +version = "8.0.3" description = "Composable command line interface toolkit" category = "main" optional = false @@ -164,6 +255,17 @@ python-versions = ">=3.6" [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} +[[package]] +name = "click-default-group" +version = "1.2.2" +description = "Extends click.Group to invoke a command without explicit subcommand name" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +click = "*" + [[package]] name = "colorama" version = "0.4.4" @@ -180,6 +282,22 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "dataclasses-json" +version = "0.5.6" +description = "Easily serialize dataclasses to and from JSON" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +marshmallow = ">=3.3.0,<4.0.0" +marshmallow-enum = ">=1.5.1,<2.0.0" +typing-inspect = ">=0.4.0" + +[package.extras] +dev = ["pytest (>=6.2.3)", "ipython", "mypy (>=0.710)", "hypothesis", "portray", "flake8", "simplejson", "types-dataclasses"] + [[package]] name = "debugpy" version = "1.5.0" @@ -399,6 +517,17 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "isodate" +version = "0.6.0" +description = "An ISO 8601 date/time/duration parser and formatter" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +six = "*" + [[package]] name = "jedi" version = "0.18.0" @@ -430,7 +559,7 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "jsonschema" -version = "4.0.1" +version = "4.1.0" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -488,6 +617,20 @@ python-versions = "*" [package.dependencies] pygments = ">=2.4.1,<3" +[[package]] +name = "lxml" +version = "4.6.3" +description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" + +[package.extras] +cssselect = ["cssselect (>=0.7)"] +html5 = ["html5lib"] +htmlsoup = ["beautifulsoup4"] +source = ["Cython (>=0.29.7)"] + [[package]] name = "markupsafe" version = "2.0.1" @@ -496,6 +639,31 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "marshmallow" +version = "3.13.0" +description = "A lightweight library for converting complex datatypes to and from native Python datatypes." +category = "main" +optional = false +python-versions = ">=3.5" + +[package.extras] +dev = ["pytest", "pytz", "simplejson", "mypy (==0.910)", "flake8 (==3.9.2)", "flake8-bugbear (==21.4.3)", "pre-commit (>=2.4,<3.0)", "tox"] +docs = ["sphinx (==4.1.1)", "sphinx-issues (==1.2.0)", "alabaster (==0.7.12)", "sphinx-version-warning (==1.1.2)", "autodocsumm (==0.2.6)"] +lint = ["mypy (==0.910)", "flake8 (==3.9.2)", "flake8-bugbear (==21.4.3)", "pre-commit (>=2.4,<3.0)"] +tests = ["pytest", "pytz", "simplejson"] + +[[package]] +name = "marshmallow-enum" +version = "1.5.1" +description = "Enum field for Marshmallow" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +marshmallow = ">=2.0.0" + [[package]] name = "matplotlib-inline" version = "0.1.3" @@ -515,6 +683,25 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "more-click" +version = "0.0.6" +description = "More click." +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +click = "*" + +[[package]] +name = "more-itertools" +version = "8.10.0" +description = "More routines for operating on iterables, beyond itertools" +category = "main" +optional = false +python-versions = ">=3.5" + [[package]] name = "mypy-extensions" version = "0.4.3" @@ -754,6 +941,14 @@ category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +[[package]] +name = "pathtools" +version = "0.1.2" +description = "File system general utilities" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "pexpect" version = "4.8.0" @@ -797,6 +992,22 @@ python-versions = ">=3.6" dev = ["pre-commit", "tox"] testing = ["pytest", "pytest-benchmark"] +[[package]] +name = "portalocker" +version = "2.3.2" +description = "Wraps the portalocker recipe for easy usage" +category = "main" +optional = false +python-versions = ">=3.5" + +[package.dependencies] +pywin32 = {version = ">=226", markers = "platform_system == \"Windows\""} + +[package.extras] +docs = ["sphinx (>=1.7.1)"] +redis = ["redis"] +tests = ["pytest (>=5.4.1)", "pytest-cov (>=2.8.1)", "sphinx (>=3.0.3)", "pytest-flake8 (>=1.0.5)", "pytest-mypy (>=0.8.0)", "redis"] + [[package]] name = "pre-commit" version = "2.15.0" @@ -867,6 +1078,21 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +[[package]] +name = "pydantic" +version = "1.8.2" +description = "Data validation and settings management using python 3.6 type hinting" +category = "main" +optional = false +python-versions = ">=3.6.1" + +[package.dependencies] +typing-extensions = ">=3.7.4.3" + +[package.extras] +dotenv = ["python-dotenv (>=0.10.4)"] +email = ["email-validator (>=1.0.3)"] + [[package]] name = "pygments" version = "2.10.0" @@ -891,6 +1117,26 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "pystow" +version = "0.1.13" +description = "Easily pick a place to store data for your python package." +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +click = "*" +requests = "*" +tqdm = "*" + +[package.extras] +aws = ["boto3"] +docs = ["sphinx", "sphinx-rtd-theme", "sphinx-click", "sphinx-autodoc-typehints", "sphinx-automodapi"] +pandas = ["pandas"] +rdf = ["rdflib"] +xml = ["lxml"] + [[package]] name = "pytest" version = "6.2.5" @@ -933,7 +1179,7 @@ python-versions = "*" [[package]] name = "pywin32" -version = "301" +version = "302" description = "Python for Window Extensions" category = "main" optional = false @@ -967,9 +1213,37 @@ python-versions = ">=3.6" cffi = {version = "*", markers = "implementation_name == \"pypy\""} py = {version = "*", markers = "implementation_name == \"pypy\""} +[[package]] 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(>=1.5.6,!=1.5.7)", "win-inet-pton"] use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] +[[package]] +name = "requests-ftp" +version = "0.3.1" +description = "FTP Transport Adapter for Requests." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +requests = "*" + [[package]] name = "send2trash" version = "1.8.0" @@ -1014,6 +1299,14 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" +[[package]] +name = "soupsieve" +version = "2.2.1" +description = "A modern CSS selector implementation for Beautiful Soup." +category = "main" +optional = false +python-versions = ">=3.6" + [[package]] name = "sqlalchemy" version = "1.4.25" @@ -1186,6 +1479,18 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "typing-inspect" +version = "0.7.1" +description = "Runtime inspection utilities for typing module." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +mypy-extensions = ">=0.3.0" +typing-extensions = ">=3.7.4" + [[package]] name = "urllib3" version = "1.26.7" @@ -1218,6 +1523,17 @@ six = ">=1.9.0,<2" docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=19.9.0rc1)"] testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "packaging (>=20.0)"] +[[package]] +name = "watchdog" +version = "2.1.6" +description = "Filesystem events monitoring" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.extras] +watchmedo = ["PyYAML (>=3.10)"] + [[package]] name = "wcwidth" version = "0.2.5" @@ -1237,7 +1553,7 @@ python-versions = "*" [metadata] lock-version = "1.1" python-versions = "^3.9" -content-hash = "8583e8a280ca9b65e6cfc7f74f04b11885807135afc455a2e1b7b1cd265bac06" +content-hash = 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