diff --git a/README.md b/README.md index f2e77374e..26edcc8ba 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,16 @@ $ poetry publish ## Release notes + +### 0.5.0 + +* Add `Ag3.snp_allele_frequencies()`. +* Add `Ag3.snp_effects()`. +* Add `Ag3.cnv_hmm()`, `Ag3.cnv_coverage_calls()` and `Ag3.cnv_discordant_read_calls()`. +* Speed up test suite via caching. +* Add configuration for pre-commit hooks. + + ### 0.4.3 * Performance improvements for faster reading a indexing diff --git a/poetry.lock b/poetry.lock index ca43b1ea3..2ab93a3ce 100644 --- a/poetry.lock +++ b/poetry.lock @@ -85,17 +85,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "20.3.0" +version = "21.2.0" description = "Classes Without Boilerplate" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"] -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"] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"] +docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"] [[package]] name = "backcall" @@ -118,26 +118,27 @@ numpy = "*" [[package]] name = "black" -version = "20.8b1" +version = "21.5b1" description = "The uncompromising code formatter." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.6.2" [package.dependencies] appdirs = "*" click = ">=7.1.2" dataclasses = {version = ">=0.6", markers = "python_version < \"3.7\""} mypy-extensions = ">=0.4.3" -pathspec = ">=0.6,<1" +pathspec = ">=0.8.1,<1" regex = ">=2020.1.8" toml = ">=0.10.1" -typed-ast = ">=1.4.0" -typing-extensions = ">=3.7.4" +typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""} +typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""} [package.extras] colorama = ["colorama (>=0.4.3)"] -d = ["aiohttp (>=3.3.2)", "aiohttp-cors"] +d = ["aiohttp (>=3.6.0)", "aiohttp-cors"] +python2 = ["typed-ast (>=1.4.2)"] [[package]] name = "bleach" @@ -154,7 +155,7 @@ webencodings = "*" [[package]] name = "cachetools" -version = "4.2.1" +version = "4.2.2" description = "Extensible memoizing collections and decorators" category = "main" optional = false @@ -327,7 +328,7 @@ ssh = ["paramiko"] [[package]] name = "gcsfs" -version = "0.8.0" +version = "2021.4.0" description = "Convenient Filesystem interface over GCS" category = "main" optional = false @@ -336,11 +337,10 @@ python-versions = ">=3.6" [package.dependencies] aiohttp = "*" decorator = "*" -fsspec = ">=0.8.0" +fsspec = "2021.04.0" google-auth = ">=1.2" google-auth-oauthlib = "*" requests = "*" -ujson = "*" [package.extras] crc = ["crcmod"] @@ -348,7 +348,7 @@ gcsfuse = ["fusepy"] [[package]] name = "google-auth" -version = "1.29.0" +version = "1.30.0" description = "Google Authentication Library" category = "main" optional = false @@ -449,20 +449,9 @@ category = "dev" optional = false python-versions = "*" -[[package]] -name = "intervaltree" -version = "3.1.0" -description = "Editable interval tree data structure for Python 2 and 3" -category = "main" -optional = false -python-versions = "*" - 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