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Merge pull request #17486 from galaxybot/dev_auto_update_dependencies
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Update Python dependencies
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@mvdbeek
mvdbeek authored Feb 22, 2024
2 parents 7b57bf4 + bb6dd68 commit f68ab16
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Showing 6 changed files with 26 additions and 25 deletions.
24 changes: 12 additions & 12 deletions lib/galaxy/dependencies/dev-requirements.txt
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Expand Up @@ -2,7 +2,7 @@ aiohttp==3.9.3 ; 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"
amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.2.0 ; 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"
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"
Expand All @@ -25,8 +25,8 @@ 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]==7.4.1 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
coverage[toml]==7.4.2 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.4 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.4.20240129145612 ; python_version >= "3.8" and python_version < "3.13"
cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
darker==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -36,13 +36,13 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.48.1 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.49.0 ; 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==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
galaxy-release-util==0.1.7 ; 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"
httpcore==1.0.2 ; python_version >= "3.8" and python_version < "3.13"
httpx==0.26.0 ; python_version >= "3.8" and python_version < "3.13"
httpcore==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -61,8 +61,8 @@ 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"
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==3.7.4 ; python_version >= "3.8" and python_version < "3.9"
matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "3.13"
matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
matplotlib==3.8.3 ; python_version >= "3.9" and python_version < "3.13"
mdit-py-plugins==0.4.0 ; 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"
Expand All @@ -85,7 +85,7 @@ platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.41.2 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.43 ; 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"
Expand Down Expand Up @@ -130,7 +130,7 @@ schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version <
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.12.0 ; 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==4.17.2 ; python_version >= "3.8" and python_version < "3.13"
selenium==4.18.1 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.1.0 ; python_version >= "3.8" and python_version < "3.13"
six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -147,7 +147,7 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13
sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
testfixtures==7.2.2 ; python_version >= "3.8" and python_version < "3.13"
testfixtures==8.0.0 ; 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==24.2.6
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.2.1
ruff==0.2.2
16 changes: 8 additions & 8 deletions lib/galaxy/dependencies/pinned-requirements.txt
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@@ -1,4 +1,4 @@
a2wsgi==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
a2wsgi==1.10.2 ; python_version >= "3.8" and python_version < "3.13"
adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.11.2 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -10,7 +10,7 @@ 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==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.4.0 ; 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 Down Expand Up @@ -49,15 +49,15 @@ 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==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.4 ; 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==0.32 ; python_version >= "3.8" and python_version < "3.13"
cwltool==3.1.20240112164112 ; python_version >= "3.8" and python_version < "3.13"
decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13"
dnspython==2.5.0 ; python_version >= "3.8" and python_version < "3.13"
dnspython==2.6.1 ; python_version >= "3.8" and python_version < "3.13"
docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13"
docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -70,7 +70,7 @@ filelock==3.13.1 ; 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"
future @ git+https://github.com/nsoranzo/python-future.git@9ef05b386ce45dd40d2dab5915aec3ed78d81ed9 ; 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"
graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -89,7 +89,7 @@ idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.9"
isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
isal==1.5.3 ; python_version >= "3.8" and python_version < "3.13"
isal==1.6.0 ; 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"
jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -116,7 +116,7 @@ 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==3.9.13 ; python_version >= "3.8" and python_version < "3.13"
orjson==3.9.14 ; python_version >= "3.8" and python_version < "3.13"
oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
packaging==23.2 ; python_version >= "3.8" and python_version < "3.13"
paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -169,7 +169,7 @@ requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
rich==13.7.0 ; python_version >= "3.8" and python_version < "3.13"
rocrate==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.17.1 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
rsa==4.9 ; 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"
Expand Down
5 changes: 3 additions & 2 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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@@ -1,18 +1,19 @@
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==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.4 ; 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==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.13"
types-bleach==6.1.0.20240222 ; python_version >= "3.8" and python_version < "3.13"
types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.20.0.20240201 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20240222 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.4.0.20240205 ; python_version >= "3.8" and python_version < "3.13"
types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
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2 changes: 1 addition & 1 deletion packages/util/setup.cfg
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Expand Up @@ -52,7 +52,7 @@ jstree =
dictobj
template =
Cheetah3!=3.2.6.post2
future @ git+https://github.com/nsoranzo/python-future.git@python312-imp-module_past
future>=1.0.0

[options.packages.find]
exclude =
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -59,7 +59,7 @@ dparse = "*"
edam-ontology = "*"
fastapi = ">=0.108"
fs = "*"
future = { git = "https://github.com/nsoranzo/python-future.git", branch = "python312-imp-module_past" }
future = ">=1.0.0" # Python 3.12 support
galaxy_sequence_utils = "*"
graphene-sqlalchemy = "3.0.0rc1" # need a beta release to be compat. with starlette plugin
gravity = ">=1.0.4"
Expand Down

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