From b1e281c0e7567b76274a7f1fbe8a2b8ffedbe238 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 11 May 2024 03:12:58 +0000 Subject: [PATCH 1/2] Update Python dependencies --- lib/galaxy/dependencies/dev-requirements.txt | 22 +++++++++---------- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 20 ++++++++--------- .../pinned-typecheck-requirements.txt | 4 ++-- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 57a4854417dc..ca0569b22242 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -6,7 +6,7 @@ ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13" -babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13" +babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13" backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12" backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" black==24.4.2 ; python_version >= "3.8" and python_version < "3.13" @@ -20,7 +20,7 @@ codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13" coverage[toml]==7.5.1 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13" cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13" @@ -52,11 +52,11 @@ jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13" jaraco-context==5.3.0 ; python_version >= "3.8" and python_version < "3.13" jaraco-functools==4.0.1 ; python_version >= "3.8" and python_version < "3.13" jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" -jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13" +jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13" jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13" jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13" junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13" -keyring==25.2.0 ; python_version >= "3.8" and python_version < "3.13" +keyring==25.2.1 ; python_version >= "3.8" and python_version < "3.13" kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13" lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" @@ -64,7 +64,7 @@ markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9" matplotlib==3.8.4 ; python_version >= "3.9" and python_version < "3.13" -mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13" +mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13" mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13" mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13" mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" @@ -89,7 +89,7 @@ pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13" port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13" prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13" psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" -psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13" +psycopg==3.1.19 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13" pygithub==2.3.0 ; python_version >= "3.8" and python_version < "3.13" @@ -107,7 +107,7 @@ pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13" pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13" pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13" pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" -pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13" +pytest-playwright==0.5.0 ; python_version >= "3.8" and python_version < "3.13" pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13" pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13" @@ -125,16 +125,16 @@ requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13" responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13" rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13" rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" -rpds-py==0.18.0 ; python_version >= "3.9" and python_version < "3.13" +rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" -rucio-clients==34.2.0 ; python_version >= "3.9" and python_version < "3.13" +rucio-clients==34.3.0 ; python_version >= "3.9" and python_version < "3.13" schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" selenium==4.20.0 ; python_version >= "3.8" and python_version < "3.13" -seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13" +seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13" setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" @@ -168,7 +168,7 @@ urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13" urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13" watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" -werkzeug==3.0.2 ; python_version >= "3.8" and python_version < "3.13" +werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.13" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13" wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.13" yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 22dfc1d78b88..805eda6a8a58 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.4.26 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.2.0 -ruff==0.4.3 +ruff==0.4.4 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 3a35717114b1..7c5e0d968792 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -20,7 +20,7 @@ argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13" attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" -babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13" +babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13" backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9" bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13" @@ -29,7 +29,7 @@ bcrypt==4.1.3 ; python_version >= "3.8" and python_version < "3.13" bdbag==1.7.2 ; python_version >= "3.8" and python_version < "3.13" beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13" billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13" -bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13" +bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13" bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13" boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13" boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13" @@ -51,7 +51,7 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows" coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13" conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13" cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13" cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13" cwltool==3.1.20240404144621 ; python_version >= "3.8" and python_version < "3.13" @@ -92,7 +92,7 @@ importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9" isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13" isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13" -jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13" +jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13" jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13" jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13" @@ -100,12 +100,12 @@ jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.13" kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13" lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13" lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" -mako==1.3.3 ; python_version >= "3.8" and python_version < "3.13" +mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown==3.6 ; python_version >= "3.8" and python_version < "3.13" markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13" -mercurial==6.7.2 ; python_version >= "3.8" and python_version < "3.13" +mercurial==6.7.3 ; python_version >= "3.8" and python_version < "3.13" mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13" msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13" @@ -159,7 +159,7 @@ pyzmq==26.0.3 ; python_version >= "3.8" and python_version < "3.13" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" referencing==0.35.1 ; python_version >= "3.8" and python_version < "3.13" refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13" -regex==2024.4.28 ; python_version >= "3.8" and python_version < "3.13" +regex==2024.5.10 ; python_version >= "3.8" and python_version < "3.13" repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13" requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13" requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" @@ -168,7 +168,7 @@ requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13" rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13" routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13" -rpds-py==0.18.0 ; python_version >= "3.8" and python_version < "3.13" +rpds-py==0.18.1 ; python_version >= "3.8" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" s3fs==2024.3.1 ; python_version >= "3.8" and python_version < "3.13" @@ -181,7 +181,7 @@ sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13" sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13" spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13" -sqlalchemy==2.0.29 ; python_version >= "3.8" and python_version < "3.13" +sqlalchemy==2.0.30 ; python_version >= "3.8" and python_version < "3.13" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13" sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13" starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13" @@ -189,7 +189,7 @@ starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13" starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13" supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13" svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13" -tenacity==8.2.3 ; python_version >= "3.8" and python_version < "3.13" +tenacity==8.3.0 ; python_version >= "3.8" and python_version < "3.13" tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13" tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 2de65943a6be..07c2b7ea2465 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,6 +1,6 @@ annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" -cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13" lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13" @@ -20,6 +20,6 @@ types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13" types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13" types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13" types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13" -types-six==1.16.21.20240425 ; python_version >= "3.8" and python_version < "3.13" +types-six==1.16.21.20240513 ; python_version >= "3.8" and python_version < "3.13" types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13" typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13" From 7905be93461914c97ce00b45146933db47340036 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 15 May 2024 11:36:21 +0100 Subject: [PATCH 2/2] Update ``playwright_browser`` fixture for pytest-playwright 0.5.0 --- lib/tool_shed/test/functional/conftest.py | 23 +++-------------------- 1 file changed, 3 insertions(+), 20 deletions(-) diff --git a/lib/tool_shed/test/functional/conftest.py b/lib/tool_shed/test/functional/conftest.py index 37bcabc6d661..21172f8ff72e 100644 --- a/lib/tool_shed/test/functional/conftest.py +++ b/lib/tool_shed/test/functional/conftest.py @@ -1,16 +1,11 @@ import os from typing import ( - Any, Callable, - Dict, Generator, ) import pytest -from playwright.sync_api import ( - Browser, - BrowserContext, -) +from playwright.sync_api import Browser from ..base.browser import ShedBrowser from ..base.playwrightbrowser import PlaywrightShedBrowser @@ -23,8 +18,8 @@ def twill_browser() -> Generator[ShedBrowser, None, None]: yield TwillShedBrowser() -def playwright_browser(class_context: BrowserContext) -> Generator[ShedBrowser, None, None]: - page = class_context.new_page() +def playwright_browser(browser: Browser) -> Generator[ShedBrowser, None, None]: + page = browser.new_page() yield PlaywrightShedBrowser(page) @@ -35,15 +30,3 @@ def playwright_browser(class_context: BrowserContext) -> Generator[ShedBrowser, shed_browser = pytest.fixture(scope="class")(playwright_browser) else: raise ValueError(f"Unrecognized value for TOOL_SHED_TEST_BROWSER: {test_browser}") - - -@pytest.fixture(scope="class") -def class_context( - browser: Browser, - browser_context_args: Dict, - pytestconfig: Any, - request: pytest.FixtureRequest, -) -> Generator[BrowserContext, None, None]: - from pytest_playwright.pytest_playwright import context - - yield from context.__pytest_wrapped__.obj(browser, browser_context_args, pytestconfig, request)