From 49a68202b606f3eaa6c5ed6a630747ba2add2cf9 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 18 Sep 2024 11:50:51 -0400 Subject: [PATCH 1/2] chore: update base image, lockfile deps; bump version to 0.3.0 --- Dockerfile | 2 +- dev.Dockerfile | 2 +- poetry.lock | 1027 ++++++++++++++++++++++++------------------------ pyproject.toml | 6 +- 4 files changed, 522 insertions(+), 515 deletions(-) diff --git a/Dockerfile b/Dockerfile index c53a6d6..372747b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.08.14 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.09.01 WORKDIR /reference diff --git a/dev.Dockerfile b/dev.Dockerfile index 582d9c4..8271502 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.08.14 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.09.01 LABEL org.opencontainers.image.description="Local development image for the Bento reference service." 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-content-hash = "6316d623035b37039f35d3ee9dac7682e1ae0edd02aad37035f92e7c00c6450d" +content-hash = "1dcf6e2bf993ce767e51994b519dab72843d3836fbd2fbd4f4c07c7d76cf867c" diff --git a/pyproject.toml b/pyproject.toml index 54775c5..f7f9b9e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "bento_reference_service" -version = "0.2.3" +version = "0.3.0" description = "Reference data (genomes & annotations) service for the Bento platform." authors = [ "David Lougheed ", @@ -25,9 +25,9 @@ classifiers = [ [tool.poetry.dependencies] python = "^3.10.0" -fastapi = {extras = ["all"], version = "^0.112.1"} +fastapi = {extras = ["all"], version = "^0.115.0"} pydantic = "^2.6.1" -bento-lib = {extras = ["fastapi"], version = "^12.1.0"} +bento-lib = {extras = ["fastapi"], version = "^12.2.2"} aiofiles = "^24.1.0" pysam = "~0.22.1" jsonschema = "^4.23.0" From fed9431be78ec32e50a06bfd4dcdd1f7476590d0 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 20 Sep 2024 14:45:24 -0400 Subject: [PATCH 2/2] chore(deps): remove unused Tox dev dep + update lockfile --- poetry.lock | 129 +++---------------------------------------------- pyproject.toml | 1 - 2 files changed, 7 insertions(+), 123 deletions(-) diff --git a/poetry.lock b/poetry.lock index 47001aa..597c136 100644 --- a/poetry.lock +++ b/poetry.lock @@ -175,13 +175,13 @@ files = [ [[package]] name = "anyio" -version = "4.4.0" +version = "4.5.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, - {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"}, + {file = "anyio-4.5.0-py3-none-any.whl", hash = "sha256:fdeb095b7cc5a5563175eedd926ec4ae55413bb4be5770c424af0ba46ccb4a78"}, + {file = "anyio-4.5.0.tar.gz", hash = "sha256:c5a275fe5ca0afd788001f58fca1e69e29ce706d746e317d660e21f70c530ef9"}, ] [package.dependencies] @@ -191,9 +191,9 @@ sniffio = ">=1.1" typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] -trio = ["trio (>=0.23)"] +doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.21.0b1)"] +trio = ["trio (>=0.26.1)"] [[package]] name = "async-timeout" @@ -357,17 +357,6 @@ d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"] jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] uvloop = ["uvloop (>=0.15.2)"] -[[package]] -name = "cachetools" -version = "5.5.0" -description = "Extensible memoizing collections and decorators" -optional = false -python-versions = ">=3.7" -files = [ - {file = "cachetools-5.5.0-py3-none-any.whl", hash = "sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292"}, - {file = "cachetools-5.5.0.tar.gz", hash = "sha256:2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a"}, -] - [[package]] name = "certifi" version = "2024.8.30" @@ -379,17 +368,6 @@ files = [ {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, ] -[[package]] -name = "chardet" -version = "5.2.0" -description = "Universal encoding detector for Python 3" -optional = false -python-versions = ">=3.7" -files = [ - {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, - {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, -] - [[package]] name = "charset-normalizer" version = "3.3.2" @@ -632,17 +610,6 @@ files = [ {file = "debugpy-1.8.5.zip", hash = "sha256:b2112cfeb34b4507399d298fe7023a16656fc553ed5246536060ca7bd0e668d0"}, ] -[[package]] -name = "distlib" -version = "0.3.8" -description = "Distribution utilities" -optional = false -python-versions = "*" -files = [ - {file = "distlib-0.3.8-py2.py3-none-any.whl", hash = "sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784"}, - {file = "distlib-0.3.8.tar.gz", hash = "sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64"}, -] - [[package]] name = "dnspython" version = "2.6.1" @@ -758,22 +725,6 @@ uvicorn = {version = ">=0.15.0", extras = ["standard"]} [package.extras] standard = ["uvicorn[standard] (>=0.15.0)"] -[[package]] -name = "filelock" -version = "3.16.1" -description = "A platform independent file lock." -optional = false -python-versions = ">=3.8" -files = [ - {file = "filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0"}, - {file = "filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"}, -] - -[package.extras] -docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4.1)"] -testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"] -typing = ["typing-extensions (>=4.12.2)"] - [[package]] name = "frozenlist" version = "1.4.1" @@ -1652,25 +1603,6 @@ files = [ [package.extras] windows-terminal = ["colorama (>=0.4.6)"] -[[package]] -name = "pyproject-api" -version = "1.7.2" -description = "API to interact with the python pyproject.toml based projects" -optional = false -python-versions = ">=3.8" -files = [ - {file = "pyproject_api-1.7.2-py3-none-any.whl", hash = "sha256:17c025105f8d27e22ffe542fe7dff3391b3736191a28294773a1f3b9ed25282b"}, - {file = "pyproject_api-1.7.2.tar.gz", hash = "sha256:dc5b0e0f6e291a4f22b46e182c9c6d4915c62b1f089b8de1b73f2d06ae453593"}, -] - -[package.dependencies] -packaging = ">=24.1" -tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""} - -[package.extras] -docs = ["furo (>=2024.8.6)", "sphinx-autodoc-typehints (>=2.4.1)"] -testing = ["covdefaults (>=2.3)", "pytest (>=8.3.3)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "setuptools (>=75.1)"] - [[package]] name = "pysam" version = "0.22.1" @@ -2089,33 +2021,6 @@ files = [ {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"}, ] -[[package]] -name = "tox" -version = "4.19.0" -description = "tox is a generic virtualenv management and test command line tool" -optional = false -python-versions = ">=3.8" -files = [ - {file = "tox-4.19.0-py3-none-any.whl", hash = "sha256:6e20a520db7710f6980b8ec96bde189d6b8cf41b327ec703b03e1a2a447b1aaf"}, - {file = "tox-4.19.0.tar.gz", hash = "sha256:66177d887f9d7ef8eaa9b58b187f7b865fa4c58650086c01336e82c9831e1867"}, -] - -[package.dependencies] -cachetools = ">=5.5" -chardet = ">=5.2" -colorama = ">=0.4.6" -filelock = ">=3.15.4" -packaging = ">=24.1" -platformdirs = ">=4.2.2" -pluggy = ">=1.5" -pyproject-api = ">=1.7.1" -tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""} -virtualenv = ">=20.26.3" - -[package.extras] -docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-argparse-cli (>=1.17)", "sphinx-autodoc-typehints (>=2.4)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=24.8)"] -testing = ["build[virtualenv] (>=1.2.2)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.2)", "devpi-process (>=1)", "diff-cover (>=9.1.1)", "distlib (>=0.3.8)", "flaky (>=3.8.1)", "hatch-vcs (>=0.4)", "hatchling (>=1.25)", "psutil (>=6)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-xdist (>=3.6.1)", "re-assert (>=1.1)", "setuptools (>=74.1.2)", "time-machine (>=2.15)", "wheel (>=0.44)"] - [[package]] name = "typer" version = "0.12.5" @@ -2318,26 +2223,6 @@ files = [ docs = ["Sphinx (>=4.1.2,<4.2.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)"] test = ["Cython (>=0.29.36,<0.30.0)", "aiohttp (==3.9.0b0)", "aiohttp (>=3.8.1)", "flake8 (>=5.0,<6.0)", "mypy (>=0.800)", "psutil", "pyOpenSSL (>=23.0.0,<23.1.0)", "pycodestyle (>=2.9.0,<2.10.0)"] -[[package]] -name = "virtualenv" -version = "20.26.5" -description = "Virtual Python Environment builder" -optional = false -python-versions = ">=3.7" -files = [ - {file = "virtualenv-20.26.5-py3-none-any.whl", hash = "sha256:4f3ac17b81fba3ce3bd6f4ead2749a72da5929c01774948e243db9ba41df4ff6"}, - {file = "virtualenv-20.26.5.tar.gz", hash = "sha256:ce489cac131aa58f4b25e321d6d186171f78e6cb13fafbf32a840cee67733ff4"}, -] - -[package.dependencies] -distlib = ">=0.3.7,<1" -filelock = ">=3.12.2,<4" -platformdirs = ">=3.9.1,<5" - -[package.extras] -docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] - [[package]] name = "watchfiles" version = "0.24.0" @@ -2653,4 +2538,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = "^3.10.0" -content-hash = "1dcf6e2bf993ce767e51994b519dab72843d3836fbd2fbd4f4c07c7d76cf867c" +content-hash = "7e8967577ca463393d60dcfe65c2c2b06ce9d43fcdd25e95cbd196ba9e1838c1" diff --git a/pyproject.toml b/pyproject.toml index f7f9b9e..f5dc395 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,7 +43,6 @@ httpx = "^0.27.0" pytest = "^8.2.1" pytest-asyncio = "^0.23.5" pytest-cov = "^5.0.0" -tox = "^4.12.1" fasta-checksum-utils = "^0.4.3" [tool.black]