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Merge pull request #18095 from galaxybot/dev_auto_update_dependencies
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Update Python dependencies
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@mvdbeek
mvdbeek authored May 7, 2024
2 parents 3611778 + e6b7b4c commit 1bb139a
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Showing 5 changed files with 25 additions and 24 deletions.
20 changes: 10 additions & 10 deletions lib/galaxy/dependencies/dev-requirements.txt
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Expand Up @@ -19,8 +19,8 @@ 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"
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]==7.5.0 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.5 ; 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"
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 @@ -31,11 +31,11 @@ deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
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==3.13.4 ; python_version >= "3.8" and python_version < "3.13"
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"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
galaxy-release-util==0.1.7 ; python_version >= "3.8" and python_version < "3.13"
galaxy-release-util==0.1.9 ; 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 @@ -72,7 +72,7 @@ more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
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"
myst-parser==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
nh3==0.2.17 ; 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"
Expand All @@ -93,11 +93,11 @@ psycopg==3.1.18 ; 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"
pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13"
pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.6 ; python_version >= "3.8" and python_version < "3.13"
pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -112,14 +112,14 @@ 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"
python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
python-irodsclient==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
python-irodsclient==2.0.1 ; python_version >= "3.8" and python_version < "3.13"
python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9"
pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
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==0.35.0 ; python_version >= "3.9" 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"
Expand Down Expand Up @@ -152,7 +152,7 @@ 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==8.1.0 ; python_version >= "3.8" and python_version < "3.13"
testfixtures==8.2.0 ; 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"
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2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-lint-requirements.txt
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Expand Up @@ -4,4 +4,4 @@ flake8-bugbear==24.4.26
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.4.2
ruff==0.4.3
22 changes: 11 additions & 11 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Expand Up @@ -25,7 +25,7 @@ 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"
bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13"
bcrypt==4.1.2 ; python_version >= "3.8" and python_version < "3.13"
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"
Expand All @@ -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==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.6 ; 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"
Expand All @@ -66,8 +66,8 @@ dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13"
email-validator==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
fastapi==0.110.2 ; python_version >= "3.8" and python_version < "3.13"
filelock==3.13.4 ; python_version >= "3.8" and python_version < "3.13"
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==2023.12.2 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -117,12 +117,12 @@ nodeenv==1.8.0 ; 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"
orjson==3.10.1 ; python_version >= "3.8" and python_version < "3.13"
orjson==3.10.3 ; python_version >= "3.8" and python_version < "3.13"
oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
paste==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13"
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"
Expand All @@ -140,7 +140,7 @@ pydantic[email]==2.7.1 ; 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"
pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13"
pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
pyjwt==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -155,11 +155,11 @@ python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13"
pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
pyzmq==26.0.2 ; python_version >= "3.8" and python_version < "3.13"
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==0.35.0 ; 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==2024.4.16 ; python_version >= "3.8" and python_version < "3.13"
regex==2024.4.28 ; 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"
Expand Down Expand Up @@ -194,7 +194,7 @@ 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"
tqdm==4.66.2 ; 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"
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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@@ -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==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.6 ; 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"
Expand Down
3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -57,7 +57,7 @@ dnspython = "*"
docutils = "!=0.17, !=0.17.1"
dparse = "*"
edam-ontology = "*"
fastapi = ">=0.108"
fastapi-slim = ">=0.111.0"
fs = "*"
future = ">=1.0.0" # Python 3.12 support
galaxy_sequence_utils = "*"
Expand All @@ -69,6 +69,7 @@ h5grove = ">=1.2.1"
h5py = "*"
importlib-resources = { version = "*", python = "<3.9" } # for importlib.{abc.Traversable,resources.{files, Package}}
isa-rwval = ">=0.10.10"
jinja2 = "*"
kombu = ">=5.3" # for importlib-metadata fix
isal = "*"
lagom = "*"
Expand Down

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