mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Update Python dependencies
by running `make update-dependencies`.
This commit is contained in:
galaxybot
committed by
github-actions[bot]
github-actions[bot]
parent
c559d7f1bc
commit
223b71cac4
@@ -46,7 +46,8 @@ darker==3.0.0
|
||||
darkgraylib==2.4.1
|
||||
decorator==5.2.1
|
||||
defusedxml==0.7.1
|
||||
docutils==0.21.2
|
||||
docutils==0.21.2 ; python_full_version < '3.11'
|
||||
docutils==0.22.4 ; python_full_version >= '3.11'
|
||||
dogpile-cache==1.4.1 ; python_full_version < '3.10'
|
||||
dogpile-cache==1.5.0 ; python_full_version >= '3.10'
|
||||
enum-tools==0.12.0 ; python_full_version >= '3.10'
|
||||
@@ -77,7 +78,7 @@ isodate==0.7.2 ; python_full_version < '3.11'
|
||||
isort==6.1.0 ; python_full_version < '3.10'
|
||||
isort==7.0.0 ; python_full_version >= '3.10'
|
||||
jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
jaraco-context==6.0.2 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
jaraco-context==6.1.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
jaraco-functools==4.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
jeepney==0.9.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
|
||||
jinja2==3.1.6
|
||||
@@ -91,9 +92,10 @@ junit-xml==1.9
|
||||
keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
kiwisolver==1.4.7 ; python_full_version < '3.10'
|
||||
kiwisolver==1.4.9 ; python_full_version >= '3.10'
|
||||
librt==0.7.7 ; platform_python_implementation != 'PyPy'
|
||||
librt==0.7.8 ; platform_python_implementation != 'PyPy'
|
||||
lxml==6.0.2
|
||||
markdown-it-py==3.0.0
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
markdown-it-py==4.0.0 ; python_full_version >= '3.11'
|
||||
markdown-it-reporter==0.0.2
|
||||
markupsafe==3.0.3
|
||||
matplotlib==3.9.4 ; python_full_version < '3.10'
|
||||
@@ -110,11 +112,12 @@ multidict==6.7.0
|
||||
mypy==1.19.1
|
||||
mypy-extensions==1.1.0
|
||||
myst-parser==3.0.1 ; python_full_version < '3.10'
|
||||
myst-parser==4.0.1 ; python_full_version >= '3.10'
|
||||
myst-parser==4.0.1 ; python_full_version == '3.10.*'
|
||||
myst-parser==5.0.0 ; python_full_version >= '3.11'
|
||||
nh3==0.3.2
|
||||
numpy==2.0.2 ; python_full_version < '3.10'
|
||||
numpy==2.2.6 ; python_full_version == '3.10.*'
|
||||
numpy==2.4.0 ; python_full_version >= '3.11'
|
||||
numpy==2.4.1 ; python_full_version >= '3.11'
|
||||
onedatafilerestclient==21.2.5.2
|
||||
outcome==1.3.0.post0
|
||||
owlrl==6.0.2 ; python_full_version < '3.10'
|
||||
@@ -186,7 +189,6 @@ roc-validator==0.4.2 ; python_full_version < '3.9.20'
|
||||
roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
|
||||
roc-validator==0.8.0 ; python_full_version >= '3.10'
|
||||
roman-numerals==4.1.0 ; python_full_version >= '3.11'
|
||||
roman-numerals-py==4.1.0 ; python_full_version >= '3.11'
|
||||
rpds-py==0.27.1 ; python_full_version < '3.10'
|
||||
rpds-py==0.30.0 ; python_full_version >= '3.10'
|
||||
ruamel-yaml==0.18.17
|
||||
@@ -197,7 +199,7 @@ s3transfer==0.16.0 ; python_full_version >= '3.10'
|
||||
schema-salad==8.9.20251102115403
|
||||
scipy==1.13.1 ; python_full_version < '3.10'
|
||||
scipy==1.15.3 ; python_full_version == '3.10.*'
|
||||
scipy==1.16.3 ; python_full_version >= '3.11'
|
||||
scipy==1.17.0 ; python_full_version >= '3.11'
|
||||
secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
|
||||
secretstorage==3.5.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
|
||||
selenium==4.32.0 ; python_full_version < '3.10'
|
||||
@@ -209,8 +211,9 @@ snowballstemmer==3.0.1
|
||||
sortedcontainers==2.4.0
|
||||
sphinx==7.4.7 ; python_full_version < '3.10'
|
||||
sphinx==8.1.3 ; python_full_version == '3.10.*'
|
||||
sphinx==8.2.3 ; python_full_version >= '3.11'
|
||||
sphinx-rtd-theme==3.0.2
|
||||
sphinx==9.0.4 ; python_full_version == '3.11.*'
|
||||
sphinx==9.1.0 ; python_full_version >= '3.12'
|
||||
sphinx-rtd-theme==3.1.0
|
||||
sphinxcontrib-applehelp==2.0.0
|
||||
sphinxcontrib-devhelp==2.0.0
|
||||
sphinxcontrib-htmlhelp==2.1.0
|
||||
@@ -227,7 +230,7 @@ testfixtures==10.0.0 ; python_full_version >= '3.11'
|
||||
text-unidecode==1.3
|
||||
tinydb==4.8.2
|
||||
toml==0.10.2
|
||||
tomli==2.3.0 ; python_full_version <= '3.11'
|
||||
tomli==2.4.0 ; python_full_version <= '3.11'
|
||||
total-perspective-vortex==3.1.3
|
||||
trio==0.31.0 ; python_full_version < '3.10'
|
||||
trio==0.32.0 ; python_full_version >= '3.10'
|
||||
|
||||
@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
|
||||
mccabe==0.7.0
|
||||
pycodestyle==2.14.0
|
||||
pyflakes==3.4.0
|
||||
ruff==0.14.11
|
||||
ruff==0.14.13
|
||||
|
||||
@@ -11,11 +11,11 @@ aiohttp==3.13.3
|
||||
aioitertools==0.13.0
|
||||
aiosignal==1.4.0
|
||||
alembic==1.16.5 ; python_full_version < '3.10'
|
||||
alembic==1.18.0 ; python_full_version >= '3.10'
|
||||
alembic==1.18.1 ; python_full_version >= '3.10'
|
||||
amqp==5.3.1
|
||||
annotated-doc==0.0.4
|
||||
annotated-types==0.7.0
|
||||
anthropic==0.75.0
|
||||
anthropic==0.76.0
|
||||
anyio==4.12.1
|
||||
apispec==6.8.4 ; python_full_version < '3.10'
|
||||
apispec==6.9.0 ; python_full_version >= '3.10'
|
||||
@@ -72,7 +72,7 @@ cwl-upgrader==1.2.14 ; python_full_version >= '3.10'
|
||||
cwl-utils==0.40
|
||||
cwltool==3.1.20251031082601 ; python_full_version < '3.10'
|
||||
cwltool==3.1.20260108082145 ; python_full_version >= '3.10'
|
||||
cyclopts==4.4.4 ; python_full_version >= '3.10'
|
||||
cyclopts==4.5.0 ; python_full_version >= '3.10'
|
||||
defusedxml==0.7.1
|
||||
deprecated==1.3.1
|
||||
deprecation==2.1.0
|
||||
@@ -83,7 +83,8 @@ dnspython==2.7.0 ; python_full_version < '3.10'
|
||||
dnspython==2.8.0 ; python_full_version >= '3.10'
|
||||
docopt==0.6.2
|
||||
docstring-parser==0.17.0
|
||||
docutils==0.21.2
|
||||
docutils==0.21.2 ; python_full_version < '3.11'
|
||||
docutils==0.22.4 ; python_full_version >= '3.11'
|
||||
dparse==0.6.4
|
||||
edam-ontology==1.25.3
|
||||
email-validator==2.3.0
|
||||
@@ -94,7 +95,7 @@ executing==2.2.1 ; python_full_version >= '3.10'
|
||||
fakeredis==2.33.0 ; python_full_version >= '3.10'
|
||||
fastapi==0.128.0
|
||||
fastavro==1.12.1 ; sys_platform != 'emscripten'
|
||||
fastmcp==2.14.2 ; python_full_version >= '3.10'
|
||||
fastmcp==2.14.3 ; python_full_version >= '3.10'
|
||||
filelock==3.19.1 ; python_full_version < '3.10'
|
||||
filelock==3.20.3 ; python_full_version >= '3.10'
|
||||
fissix==24.4.24
|
||||
@@ -103,14 +104,14 @@ fs==2.4.16
|
||||
fsspec==2025.10.0 ; python_full_version < '3.10'
|
||||
fsspec==2026.1.0 ; python_full_version >= '3.10'
|
||||
future==1.0.0
|
||||
genai-prices==0.0.50
|
||||
genai-prices==0.0.51
|
||||
google-api-core==2.29.0
|
||||
google-auth==2.47.0
|
||||
google-cloud-batch==0.20.0
|
||||
google-genai==1.47.0 ; python_full_version < '3.10'
|
||||
google-genai==1.57.0 ; python_full_version >= '3.10'
|
||||
google-genai==1.59.0 ; python_full_version >= '3.10'
|
||||
googleapis-common-protos==1.72.0
|
||||
gravity @ git+https://github.com/nsoranzo/gravity.git@a60c911e61c784d37d3eb334c1c68288d2c06ef3
|
||||
gravity @ git+https://github.com/nsoranzo/gravity.git@7c5f457424658ee904694f5566e61b562bce7ed6
|
||||
greenlet==3.2.4 ; (python_full_version < '3.10' and platform_machine == 'AMD64') or (python_full_version < '3.10' and platform_machine == 'WIN32') or (python_full_version < '3.10' and platform_machine == 'aarch64') or (python_full_version < '3.10' and platform_machine == 'amd64') or (python_full_version < '3.10' and platform_machine == 'ppc64le') or (python_full_version < '3.10' and platform_machine == 'win32') or (python_full_version < '3.10' and platform_machine == 'x86_64')
|
||||
greenlet==3.3.0 ; (python_full_version >= '3.10' and platform_machine == 'AMD64') or (python_full_version >= '3.10' and platform_machine == 'WIN32') or (python_full_version >= '3.10' and platform_machine == 'aarch64') or (python_full_version >= '3.10' and platform_machine == 'amd64') or (python_full_version >= '3.10' and platform_machine == 'ppc64le') or (python_full_version >= '3.10' and platform_machine == 'win32') or (python_full_version >= '3.10' and platform_machine == 'x86_64')
|
||||
griffe==1.14.0 ; python_full_version < '3.10'
|
||||
@@ -140,7 +141,7 @@ isa-rwval==0.10.11
|
||||
isal==1.8.0
|
||||
isodate==0.7.2 ; python_full_version < '3.11'
|
||||
jaraco-classes==3.4.0 ; python_full_version >= '3.10'
|
||||
jaraco-context==6.0.2 ; python_full_version >= '3.10'
|
||||
jaraco-context==6.1.0 ; python_full_version >= '3.10'
|
||||
jaraco-functools==4.4.0 ; python_full_version >= '3.10'
|
||||
jeepney==0.9.0 ; python_full_version >= '3.10' and sys_platform == 'linux'
|
||||
jinja2==3.1.6
|
||||
@@ -157,14 +158,15 @@ lagom==2.7.7
|
||||
legacy-cgi==2.6.4 ; python_full_version >= '3.13'
|
||||
limits==4.2 ; python_full_version < '3.10'
|
||||
limits==5.6.0 ; python_full_version >= '3.10'
|
||||
logfire==4.17.0 ; python_full_version >= '3.10'
|
||||
logfire-api==4.17.0
|
||||
logfire==4.19.0 ; python_full_version >= '3.10'
|
||||
logfire-api==4.19.0
|
||||
lupa==2.6 ; python_full_version >= '3.10'
|
||||
lxml==6.0.2
|
||||
mako==1.3.10
|
||||
markdown==3.9 ; python_full_version < '3.10'
|
||||
markdown==3.10 ; python_full_version >= '3.10'
|
||||
markdown-it-py==3.0.0
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
markdown-it-py==4.0.0 ; python_full_version >= '3.11'
|
||||
markupsafe==3.0.3
|
||||
mcp==1.25.0 ; python_full_version >= '3.10'
|
||||
mdurl==0.1.2
|
||||
@@ -186,7 +188,7 @@ nodejs-wheel==22.20.0
|
||||
nodejs-wheel-binaries==22.20.0
|
||||
numpy==2.0.2 ; python_full_version < '3.10'
|
||||
numpy==2.2.6 ; python_full_version == '3.10.*'
|
||||
numpy==2.4.0 ; python_full_version >= '3.11'
|
||||
numpy==2.4.1 ; python_full_version >= '3.11'
|
||||
oauthlib==3.3.1
|
||||
openai==2.15.0
|
||||
openapi-pydantic==0.5.1 ; python_full_version >= '3.10'
|
||||
@@ -215,12 +217,12 @@ pebble==5.1.3
|
||||
pillow==11.3.0 ; python_full_version < '3.10'
|
||||
pillow==12.1.0 ; python_full_version >= '3.10'
|
||||
platformdirs==4.5.1 ; python_full_version >= '3.10'
|
||||
prometheus-client==0.23.1 ; python_full_version >= '3.10'
|
||||
prometheus-client==0.24.1 ; python_full_version >= '3.10'
|
||||
prompt-toolkit==3.0.52
|
||||
propcache==0.4.1
|
||||
proto-plus==1.27.0
|
||||
protobuf==5.29.5 ; python_full_version < '3.10'
|
||||
protobuf==6.33.3 ; python_full_version >= '3.10'
|
||||
protobuf==6.33.4 ; python_full_version >= '3.10'
|
||||
prov==1.5.1
|
||||
psutil==7.2.1
|
||||
pulsar-galaxy-lib==0.15.13
|
||||
@@ -232,14 +234,14 @@ pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementat
|
||||
pycryptodome==3.23.0
|
||||
pydantic==2.12.5
|
||||
pydantic-ai==0.8.1 ; python_full_version < '3.10'
|
||||
pydantic-ai==1.41.0 ; python_full_version >= '3.10'
|
||||
pydantic-ai==1.44.0 ; python_full_version >= '3.10'
|
||||
pydantic-ai-slim==0.8.1 ; python_full_version < '3.10'
|
||||
pydantic-ai-slim==1.41.0 ; python_full_version >= '3.10'
|
||||
pydantic-ai-slim==1.44.0 ; python_full_version >= '3.10'
|
||||
pydantic-core==2.41.5
|
||||
pydantic-evals==0.8.1 ; python_full_version < '3.10'
|
||||
pydantic-evals==1.41.0 ; python_full_version >= '3.10'
|
||||
pydantic-evals==1.44.0 ; python_full_version >= '3.10'
|
||||
pydantic-graph==0.8.1 ; python_full_version < '3.10'
|
||||
pydantic-graph==1.41.0 ; python_full_version >= '3.10'
|
||||
pydantic-graph==1.44.0 ; python_full_version >= '3.10'
|
||||
pydantic-settings==2.11.0 ; python_full_version < '3.10'
|
||||
pydantic-settings==2.12.0 ; python_full_version >= '3.10'
|
||||
pydantic-tes==0.2.0
|
||||
@@ -275,7 +277,7 @@ rdflib==7.5.0 ; python_full_version >= '3.10'
|
||||
redis==7.1.0 ; python_full_version >= '3.10'
|
||||
referencing==0.36.2
|
||||
refgenconf==0.12.2
|
||||
regex==2025.11.3
|
||||
regex==2026.1.15
|
||||
repoze-lru==0.7
|
||||
requests==2.32.5
|
||||
requests-oauthlib==2.0.0
|
||||
@@ -320,11 +322,11 @@ tenacity==9.1.2
|
||||
text-unidecode==1.3
|
||||
tifffile==2024.8.30 ; python_full_version < '3.10'
|
||||
tifffile==2025.5.10 ; python_full_version == '3.10.*'
|
||||
tifffile==2025.12.20 ; python_full_version >= '3.11'
|
||||
tifffile==2026.1.14 ; python_full_version >= '3.11'
|
||||
tiktoken==0.12.0 ; python_full_version >= '3.10'
|
||||
tinydb==4.8.2
|
||||
tokenizers==0.22.2 ; sys_platform != 'emscripten'
|
||||
tomli==2.3.0 ; python_full_version < '3.11'
|
||||
tomli==2.4.0 ; python_full_version < '3.11'
|
||||
tornado==6.5.4
|
||||
tqdm==4.67.1
|
||||
tuspy==1.1.0
|
||||
|
||||
@@ -69,9 +69,10 @@ jsonschema-specifications==2025.9.1
|
||||
junit-xml==1.9
|
||||
kiwisolver==1.4.7 ; python_full_version < '3.10'
|
||||
kiwisolver==1.4.9 ; python_full_version >= '3.10'
|
||||
librt==0.7.7 ; platform_python_implementation != 'PyPy'
|
||||
librt==0.7.8 ; platform_python_implementation != 'PyPy'
|
||||
lxml==6.0.2
|
||||
markdown-it-py==3.0.0
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
markdown-it-py==4.0.0 ; python_full_version >= '3.11'
|
||||
markupsafe==3.0.3
|
||||
matplotlib==3.9.4 ; python_full_version < '3.10'
|
||||
matplotlib==3.10.8 ; python_full_version >= '3.10'
|
||||
@@ -85,7 +86,7 @@ mypy==1.19.1
|
||||
mypy-extensions==1.1.0
|
||||
numpy==2.0.2 ; python_full_version < '3.10'
|
||||
numpy==2.2.6 ; python_full_version == '3.10.*'
|
||||
numpy==2.4.0 ; python_full_version >= '3.11'
|
||||
numpy==2.4.1 ; python_full_version >= '3.11'
|
||||
onedatafilerestclient==21.2.5.2
|
||||
outcome==1.3.0.post0
|
||||
owlrl==6.0.2 ; python_full_version < '3.10'
|
||||
@@ -157,7 +158,7 @@ s3transfer==0.16.0 ; python_full_version >= '3.10'
|
||||
schema-salad==8.9.20251102115403
|
||||
scipy==1.13.1 ; python_full_version < '3.10'
|
||||
scipy==1.15.3 ; python_full_version == '3.10.*'
|
||||
scipy==1.16.3 ; python_full_version >= '3.11'
|
||||
scipy==1.17.0 ; python_full_version >= '3.11'
|
||||
selenium==4.32.0 ; python_full_version < '3.10'
|
||||
selenium==4.39.0 ; python_full_version >= '3.10'
|
||||
seletools==1.5.0
|
||||
@@ -173,7 +174,7 @@ testfixtures==10.0.0 ; python_full_version >= '3.11'
|
||||
text-unidecode==1.3
|
||||
tinydb==4.8.2
|
||||
toml==0.10.2
|
||||
tomli==2.3.0 ; python_full_version <= '3.11'
|
||||
tomli==2.4.0 ; python_full_version <= '3.11'
|
||||
total-perspective-vortex==3.1.3
|
||||
trio==0.31.0 ; python_full_version < '3.10'
|
||||
trio==0.32.0 ; python_full_version >= '3.10'
|
||||
|
||||
@@ -1,11 +1,11 @@
|
||||
# This file was autogenerated by uv via the following command:
|
||||
# uv export --frozen --no-annotate --no-hashes --only-group=typecheck
|
||||
annotated-types==0.7.0
|
||||
boto3-stubs==1.42.25
|
||||
botocore-stubs==1.42.25
|
||||
boto3-stubs==1.42.30
|
||||
botocore-stubs==1.42.30
|
||||
cffi==2.0.0 ; platform_python_implementation != 'PyPy'
|
||||
cryptography==46.0.3
|
||||
librt==0.7.7 ; platform_python_implementation != 'PyPy'
|
||||
librt==0.7.8 ; platform_python_implementation != 'PyPy'
|
||||
lxml-stubs==0.5.1
|
||||
mypy==1.19.1
|
||||
mypy-boto3-s3==1.42.21
|
||||
@@ -14,8 +14,8 @@ pathspec==1.0.3
|
||||
pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
|
||||
pydantic==2.12.5
|
||||
pydantic-core==2.41.5
|
||||
tomli==2.3.0 ; python_full_version < '3.11'
|
||||
types-awscrt==0.30.0
|
||||
tomli==2.4.0 ; python_full_version < '3.11'
|
||||
types-awscrt==0.31.1
|
||||
types-bleach==6.3.0.20251115
|
||||
types-boto==2.49.18.20241019
|
||||
types-contextvars==2.4.7.3
|
||||
|
||||
Reference in New Issue
Block a user