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Merge pull request galaxyproject#18226 from galaxybot/dev_auto_update…
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…_dependencies

Update Python dependencies
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@mvdbeek
mvdbeek committed Jun 10, 2024
2 parents b5e8d50 + 70b5811 commit c42c349
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Showing 12 changed files with 59 additions and 59 deletions.
2 changes: 1 addition & 1 deletion lib/galaxy/datatypes/registry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -864,7 +864,7 @@ def find_conversion_destination_for_dataset_by_extensions(
ext = dataset_or_ext
dataset = None

accepted_datatypes: List["Data"] = []
accepted_datatypes: List[Data] = []
for accepted_format in accepted_formats:
if isinstance(accepted_format, str):
accepted_datatype = self.get_datatype_by_extension(accepted_format)
Expand Down
40 changes: 20 additions & 20 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,28 +1,28 @@
aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13"
ase==3.23.0 ; 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==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
backports-tarfile==1.2.0 ; 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"
boto3==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13"
codespell==2.3.0 ; 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==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.8 ; 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"
Expand All @@ -34,10 +34,10 @@ docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
galaxy-release-util==0.1.9 ; python_version >= "3.8" and python_version < "3.13"
galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13"
graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -86,7 +86,7 @@ pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
pkginfo==1.11.1 ; python_version >= "3.8" and python_version < "3.13"
platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -125,22 +125,22 @@ rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13"
requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
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"
requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
responses==0.25.2 ; 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==0.18.1 ; 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==34.3.0 ; python_version >= "3.9" and python_version < "3.13"
rucio-clients==34.4.2 ; python_version >= "3.9" and python_version < "3.13"
s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240503091721 ; 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"
scipy==1.13.1 ; 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==4.21.0 ; 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"
setuptools==70.0.0 ; 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"
snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -157,7 +157,7 @@ sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_versio
statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
stevedore==5.2.0 ; python_version >= "3.9" and python_version < "3.13"
tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
testfixtures==8.2.0 ; python_version >= "3.8" and python_version < "3.13"
testfixtures==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -167,14 +167,14 @@ trio==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
twine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
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"
watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
werkzeug==3.0.3 ; 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"
zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.13"
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-lint-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ flake8-bugbear==24.4.26
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.4.4
ruff==0.4.8
36 changes: 18 additions & 18 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13"
annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13"
appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -37,7 +37,7 @@ botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -50,8 +50,8 @@ cloudauthz==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
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==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
conda-package-streaming==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.8 ; 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==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -70,7 +70,7 @@ fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
fsspec==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
fsspec==2024.6.0 ; python_version >= "3.8" and python_version < "3.13"
future==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -113,7 +113,7 @@ msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
networkx==2.5 ; python_version >= "3.8" and python_version < "3.13"
nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
nodeenv==1.9.1 ; python_version >= "3.8" and python_version < "3.13"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -127,16 +127,16 @@ pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.46 ; python_version >= "3.8" and python_version < "3.13"
prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13"
pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.7.3 ; python_version >= "3.8" and python_version < "3.13"
pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -164,17 +164,17 @@ 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"
requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
requests==2.32.3 ; 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==0.18.1 ; 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==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
s3fs==2024.6.0 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
shellescape==3.8.1 ; 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"
Expand All @@ -193,16 +193,16 @@ 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"
tornado==6.4 ; python_version >= "3.8" and python_version < "3.13"
tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13"
tqdm==4.66.4 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13"
urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.29.0 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.30.1 ; python_version >= "3.8" and python_version < "3.13"
uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -212,6 +212,6 @@ whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.13"
zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
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