From 0d2c75627a964d35ec5c951c611507c7766f73cf Mon Sep 17 00:00:00 2001 From: Blake Sweeney Date: Fri, 21 Jun 2024 10:54:21 +0100 Subject: [PATCH] Add black and isort as dev deps These should always be used to format the code. --- poetry.lock | 170 ++++++++++++++++++++++++++++--------------------- pyproject.toml | 4 +- 2 files changed, 102 insertions(+), 72 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6b851332..082c2047 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "argcomplete" version = "3.0.8" description = "Bash tab completion for argparse" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -19,7 +18,6 @@ test = ["coverage", "mypy", "pexpect", "ruff", "wheel"] name = "argh" version = "0.28.1" description = "An unobtrusive argparse wrapper with natural syntax" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -37,7 +35,6 @@ test = ["iocapture (>=0.1.2)", "pytest (>=7.2)", "pytest-cov (>=4.0)", "tox (>=4 name = "attrs" version = "21.4.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -55,7 +52,6 @@ tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy" name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" -category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -74,7 +70,6 @@ lxml = ["lxml"] name = "biopython" version = "1.81" description = "Freely available tools for computational molecular biology." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -107,11 +102,54 @@ files = [ [package.dependencies] numpy = "*" +[[package]] +name = "black" +version = "24.4.2" +description = "The uncompromising code formatter." +optional = false +python-versions = ">=3.8" +files = [ + {file = "black-24.4.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dd1b5a14e417189db4c7b64a6540f31730713d173f0b63e55fabd52d61d8fdce"}, + {file = "black-24.4.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e537d281831ad0e71007dcdcbe50a71470b978c453fa41ce77186bbe0ed6021"}, + {file = "black-24.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eaea3008c281f1038edb473c1aa8ed8143a5535ff18f978a318f10302b254063"}, + {file = "black-24.4.2-cp310-cp310-win_amd64.whl", hash = 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(>=3.7.4,!=3.9.0)"] +jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] +uvloop = ["uvloop (>=0.15.2)"] + [[package]] name = "certifi" version = "2022.12.7" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -123,7 +161,6 @@ files = [ name = "charset-normalizer" version = "3.1.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -208,7 +245,6 @@ files = [ name = "click" version = "8.1.3" description = "Composable command line interface toolkit" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -223,7 +259,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "click-aliases" version = "1.0.1" description = "Enable aliases for Click" -category = "main" optional = false python-versions = "*" files = [ @@ -241,7 +276,6 @@ dev = ["coveralls", "flake8", "flake8-import-order", "pytest", "pytest-cov", "to name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -253,7 +287,6 @@ files = [ name = "cython" version = "0.29.34" description = "The Cython compiler for writing C extensions for the Python language." -category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -303,7 +336,6 @@ files = [ name = "decorator" version = "5.1.1" description = "Decorators for Humans" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -315,7 +347,6 @@ files = [ name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -327,7 +358,6 @@ files = [ name = "furl" version = "2.1.3" description = "URL manipulation made simple." -category = "main" optional = false python-versions = "*" files = [ @@ -343,7 +373,6 @@ six = ">=1.8.0" name = "gffutils" version = "0.11.1" description = "Work with GFF and GTF files in a flexible database framework" -category = "main" optional = false python-versions = "*" files = [ @@ -361,7 +390,6 @@ six = ">=1.12.0" name = "humanfriendly" version 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for Python 2 and 3" -category = "main" optional = false python-versions = "*" files = [ @@ -498,11 +522,24 @@ files = [ [package.dependencies] sortedcontainers = ">=2.0,<3.0" +[[package]] +name = "isort" +version = "5.13.2" +description = "A Python utility / library to sort Python imports." +optional = false +python-versions = ">=3.8.0" +files = [ + {file = "isort-5.13.2-py3-none-any.whl", hash = "sha256:8ca5e72a8d85860d5a3fa69b8745237f2939afe12dbf656afbcb47fe72d947a6"}, + {file = "isort-5.13.2.tar.gz", hash = "sha256:48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109"}, +] + +[package.extras] +colors = ["colorama (>=0.4.6)"] + [[package]] name = "joblib" version = "1.2.0" description = "Lightweight pipelining with Python functions" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -514,7 +551,6 @@ files = [ name = "jsonschema" version = "4.17.3" description = "An implementation of JSON Schema validation for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -534,7 +570,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "lxml" version = "4.9.2" 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.*" files = [ @@ -627,7 +662,6 @@ source = ["Cython (>=0.29.7)"] name = "more-itertools" version = "9.1.0" description = "More routines for operating on iterables, beyond itertools" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -635,11 +669,21 @@ files = [ {file = "more_itertools-9.1.0-py3-none-any.whl", hash = "sha256:d2bc7f02446e86a68911e58ded76d6561eea00cddfb2a91e7019bbb586c799f3"}, ] +[[package]] +name = "mypy-extensions" +version = "1.0.0" +description = "Type system extensions for programs checked with the mypy type checker." +optional = false +python-versions = 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description = "Parse OBO formatted ontologies into networkx" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -740,7 +781,6 @@ dev = ["pre-commit", "pytest"] name = "openpyxl" version = "3.1.2" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -755,7 +795,6 @@ et-xmlfile = "*" name = "orderedmultidict" version = "1.0.1" description = "Ordered Multivalue Dictionary" -category = "main" optional = false python-versions = "*" files = [ @@ -770,7 +809,6 @@ six = ">=1.8.0" name = "packaging" version = "23.1" description = "Core utilities for Python packages" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -782,7 +820,6 @@ files = [ name = "pandas" version = "1.5.3" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -816,21 +853,44 @@ 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dir`." +optional = false +python-versions = ">=3.8" +files = [ + {file = "platformdirs-4.2.2-py3-none-any.whl", hash = "sha256:2d7a1657e36a80ea911db832a8a6ece5ee53d8de21edd5cc5879af6530b1bfee"}, + {file = "platformdirs-4.2.2.tar.gz", hash = "sha256:38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3"}, +] + +[package.extras] +docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"] +type = ["mypy (>=1.8)"] + [[package]] name = "pluggy" version = "1.0.0" description = "plugin and hook calling mechanisms for python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -846,7 +906,6 @@ testing = ["pytest", "pytest-benchmark"] name = "psycopg2-binary" version = "2.9.7" description = "psycopg2 - Python-PostgreSQL Database Adapter" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -916,7 +975,6 @@ files = [ name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -928,7 +986,6 @@ files = [ name = "pybedtools" version = "0.9.0" description = "Wrapper around BEDTools for bioinformatics work" -category = "main" optional = false python-versions = "*" files = [] @@ -948,7 +1005,6 @@ resolved_reference = "6021d28b88879057247f4e8fe93c776c98e36f41" name = "pyfaidx" version = "0.7.2.1" description = "pyfaidx: efficient pythonic random access to fasta subsequences" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -964,7 +1020,6 @@ six = "*" name = "pymysql" version = "1.0.3" description = "Pure Python MySQL Driver" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -980,7 +1035,6 @@ rsa = ["cryptography"] name = "pypika" version = "0.48.9" description = "A SQL query builder API for Python" -category = "main" optional = false python-versions = "*" files = [ @@ -991,7 +1045,6 @@ files = [ name = "pyreadline3" version = "3.4.1" description = "A python implementation of GNU readline." -category = "main" optional = false python-versions = "*" files = [ @@ -1003,7 +1056,6 @@ files = [ name = "pyrsistent" version = "0.19.3" description = "Persistent/Functional/Immutable data structures" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1040,7 +1092,6 @@ files = [ name = "pysam" version = "0.21.0" description = "pysam - a python module for reading, manipulating and writing genomic data sets." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1074,7 +1125,6 @@ cython = "*" name = "pytest" version = "7.3.1" description = "pytest: simple powerful testing with Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1095,7 +1145,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -1110,7 +1159,6 @@ six = ">=1.5" name = "pytz" version = "2023.3" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -1122,7 +1170,6 @@ files = [ name = "pyyaml" version = "6.0" description = "YAML parser and emitter for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1172,7 +1219,6 @@ files = [ name = "regex" version = "2023.3.23" description = "Alternative regular expression module, to replace re." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1242,7 +1288,6 @@ files = [ name = "requests" version = "2.28.2" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7, <4" files = [ @@ -1264,7 +1309,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "retry" version = "0.9.2" description = "Easy to use retry decorator." -category = "main" optional = false python-versions = "*" files = [ @@ -1280,7 +1324,6 @@ py = ">=1.4.26,<2.0.0" name = "scikit-learn" version = "1.2.2" description = "A set of python modules for machine learning and data mining" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1323,7 +1366,6 @@ tests = ["black (>=22.3.0)", "flake8 (>=3.8.2)", "matplotlib (>=3.1.3)", "mypy ( name = "scipy" version = "1.9.3" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1362,7 +1404,6 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki name = "semver" version = "2.13.0" description = "Python helper for Semantic Versioning (http://semver.org/)" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1374,7 +1415,6 @@ files = [ name = "setuptools" version = "67.7.2" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1391,7 +1431,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs ( name = "simplejson" version = "3.19.1" description = "Simple, fast, extensible JSON encoder/decoder for Python" -category = "main" optional = false python-versions = ">=2.5, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1486,7 +1525,6 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1498,7 +1536,6 @@ files = [ name = "slack-sdk" version = "3.21.2" description = "The Slack API Platform SDK for Python" -category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -1514,7 +1551,6 @@ testing = ["Flask (>=1,<2)", "Flask-Sockets (>=0.2,<1)", "Jinja2 (==3.0.3)", "We name = "sortedcontainers" version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" -category = "main" optional = false python-versions = "*" files = [ @@ -1526,7 +1562,6 @@ files = [ name = "soupsieve" version = "2.4.1" description = "A modern CSS selector implementation for Beautiful Soup." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1538,7 +1573,6 @@ files = [ name = "sqlitedict" version = "2.1.0" description = "Persistent dict in Python, backed up by sqlite3 and pickle, multithread-safe." -category = "main" optional = false python-versions = "*" files = [ @@ -1549,7 +1583,6 @@ files = [ name = "tatsu" version = "5.8.2" description = "TatSu takes a grammar in a variation of EBNF as input, and outputs a memoizing PEG/Packrat parser in Python." -category = "main" optional = false python-versions = ">=3.10" files = [ @@ -1564,7 +1597,6 @@ future-regex = ["regex"] name = "textblob" version = "0.15.3" description = "Simple, Pythonic text processing. Sentiment analysis, part-of-speech tagging, noun phrase parsing, and more." -category = "main" optional = false python-versions = "*" files = [ @@ -1579,7 +1611,6 @@ nltk = ">=3.1" name = "threadpoolctl" version = "3.1.0" description = "threadpoolctl" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1591,7 +1622,6 @@ files = [ name = "throttler" version = "1.2.2" description = "Zero-dependency Python package for easy throttling with asyncio support" -category = "main" optional = false python-versions = "*" files = [ @@ -1606,7 +1636,6 @@ dev = ["aiohttp (>=3.8)", "codecov (>=2.1)", "flake8 (>=4.0)", "pytest (>=7.0)", name = "tqdm" version = "4.65.0" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1627,7 +1656,6 @@ telegram = ["requests"] name = "urllib3" version = "1.26.15" 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.*, !=3.5.*" files = [ @@ -1643,4 +1671,4 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "af65604dd521498a5a57f8547f7e2d1ca725e3c8c80866d369464b8095ce9653" +content-hash = "0251169cd7315e36570579018b1f17af4ed4b0e1da4ab2b262e670e8113e6546" diff --git a/pyproject.toml b/pyproject.toml index 182a0fee..6fabb57d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,9 @@ openpyxl = "^3.0.10" pybedtools = {git = "https://github.com/afg1/pybedtools.git"} psycopg2-binary = "^2.9.7" -[tool.poetry.dev-dependencies] +[tool.poetry.group.dev.dependencies] +black = "^24.4.2" +isort = "^5.13.2" pytest = "^7.2.0" [build-system]