Commit d49bc365 authored by galaxybot's avatar galaxybot Committed by github-actions[bot]
Browse files

Update Python dependencies 

by running `make update-dependencies`.
parent 3b68c38a

lib/galaxy/dependencies/dev-requirements.txt

+15 −16
Original line number Diff line number Diff line
@@ -29,7 +29,7 @@ colorlog==6.9.0 
contourpy==1.3.0 ; python_full_version < '3.10'

contourpy==1.3.2 ; python_full_version == '3.10.*'

contourpy==1.3.3 ; python_full_version >= '3.11'

coverage==7.10.4

coverage==7.10.6

cryptography==45.0.6

cwltest==2.6.20250818005349

cycler==0.12.1
@@ -38,12 +38,12 @@ darkgraylib==1.2.1 
decorator==5.2.1

defusedxml==0.7.1

docutils==0.21.2

dogpile-cache==1.2.2

dogpile-cache==1.4.0

enum-tools==0.12.0 ; python_full_version >= '3.10'

exceptiongroup==1.3.0 ; python_full_version < '3.11'

filelock==3.19.1

fluent-logger==0.11.1

fonttools==4.59.1

fonttools==4.59.2

frozenlist==1.7.0

galaxy-release-util==0.3.1

graylint==1.1.1
@@ -68,6 +68,8 @@ jaraco-functools==4.3.0 ; platform_machine != 'ppc64le' and platform_machine != 
jeepney==0.9.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'

jinja2==3.1.6

jmespath==1.0.1

jsonpatch==1.33

jsonpointer==3.0.0

jsonschema==4.25.1

jsonschema-specifications==2025.4.1

junit-xml==1.9
@@ -79,7 +81,7 @@ markdown-it-py==3.0.0 
markdown-it-reporter==0.0.2

markupsafe==3.0.2

matplotlib==3.9.4 ; python_full_version < '3.10'

matplotlib==3.10.5 ; python_full_version >= '3.10'

matplotlib==3.10.6 ; python_full_version >= '3.10'

mdit-py-plugins==0.4.2 ; python_full_version < '3.10'

mdit-py-plugins==0.5.0 ; python_full_version >= '3.10'

mdurl==0.1.2
@@ -102,16 +104,15 @@ owlrl==7.1.4 ; python_full_version >= '3.10' 
packaging==24.2 ; python_full_version < '3.10'

packaging==25.0 ; python_full_version >= '3.10'

pathspec==0.12.1

pbr==7.0.1

pfzy==0.3.4

pillow==11.3.0

pkce==1.0.3

platformdirs==4.3.8

playwright==1.54.0

platformdirs==4.4.0

playwright==1.55.0

pluggy==1.6.0

port-for==0.7.4

prettytable==3.16.0

prompt-toolkit==3.0.51

prompt-toolkit==3.0.52

propcache==0.3.2

psutil==7.0.0 ; sys_platform != 'cygwin'

psycopg==3.2.9
@@ -139,7 +140,7 @@ pytest-playwright==0.7.0 
pytest-postgresql==7.0.2

pytest-shard==0.1.2

python-dateutil==2.9.0.post0

python-irodsclient==3.1.1

python-irodsclient==3.2.0

python-slugify==8.0.4

pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'

pyyaml==6.0.2
@@ -157,20 +158,18 @@ 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==0.7.3 ; python_full_version >= '3.10'

roman-numerals-py==3.1.0 ; python_full_version >= '3.11'

rpds-py==0.27.0

rpds-py==0.27.1

ruamel-yaml==0.18.15

ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'

rucio-clients==37.7.1

rucio-clients==38.0.0

s3transfer==0.13.1

schema-salad==8.9.20250723145140

scipy==1.13.1 ; python_full_version < '3.10'

scipy==1.15.3 ; python_full_version == '3.10.*'

scipy==1.16.1 ; python_full_version >= '3.11'

secretstorage==3.3.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'

selenium==4.32.0 ; python_full_version < '3.10'

selenium==4.35.0 ; python_full_version >= '3.10'

selenium==4.32.0

seletools==1.5.0

setuptools==80.9.0

six==1.17.0

sniffio==1.3.1

snowballstemmer==3.0.1
@@ -187,7 +186,7 @@ sphinxcontrib-jsmath==1.0.1 
sphinxcontrib-qthelp==2.0.0

sphinxcontrib-serializinghtml==2.0.0

statsd==4.0.1

stevedore==5.4.1

stevedore==5.5.0

tabulate==0.9.0

testfixtures==8.3.0 ; python_full_version < '3.11'

testfixtures==9.1.0 ; python_full_version >= '3.11'
@@ -200,7 +199,7 @@ trio-websocket==0.12.2 
tuspy==1.1.0

twill==3.3

twine==6.1.0

typing-extensions==4.14.1

typing-extensions==4.15.0

tzdata==2025.2 ; sys_platform == 'win32'

url-normalize==2.2.1

urllib3==1.26.20 ; python_full_version < '3.10'

lib/galaxy/dependencies/pinned-lint-requirements.txt

+1 −1
Original line number Diff line number Diff line
@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12 
mccabe==0.7.0

pycodestyle==2.14.0

pyflakes==3.4.0

ruff==0.12.10
 
ruff==0.12.11

lib/galaxy/dependencies/pinned-requirements.txt

+10 −10
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ aiohappyeyeballs==2.6.1 
aiohttp==3.12.15

aioitertools==0.12.0

aiosignal==1.4.0

alembic==1.16.4

alembic==1.16.5

amqp==5.3.1

annotated-types==0.7.0

anyio==4.10.0
@@ -62,7 +62,7 @@ docopt==0.6.2 
docutils==0.21.2

dparse==0.6.4

edam-ontology==1.25.2

email-validator==2.2.0

email-validator==2.3.0

et-xmlfile==2.0.0

exceptiongroup==1.3.0 ; python_full_version < '3.11'

fastapi-slim==0.116.1
@@ -121,7 +121,7 @@ numpy==2.2.6 ; python_full_version == '3.10.*' 
numpy==2.3.2 ; python_full_version >= '3.11'

oauthlib==3.3.1

openpyxl==3.1.5

orjson==3.11.2

orjson==3.11.3

oyaml==1.0

packaging==24.2 ; python_full_version < '3.10'

packaging==25.0 ; python_full_version >= '3.10'
@@ -131,7 +131,7 @@ paste==3.10.1 
pastedeploy==3.1.0

pebble==5.1.3

pillow==11.3.0

prompt-toolkit==3.0.51

prompt-toolkit==3.0.52

propcache==0.3.2

prov==1.5.1

psutil==7.0.0
@@ -164,7 +164,7 @@ pyzmq==27.0.2 
rdflib==7.1.4

referencing==0.36.2

refgenconf==0.12.2

regex==2025.7.34

regex==2025.8.29

repoze-lru==0.7

requests==2.32.5

requests-oauthlib==2.0.0
@@ -174,7 +174,7 @@ rich==13.9.4 
rich-argparse==1.7.1

rocrate==0.14.0

routes==2.5.1

rpds-py==0.27.0

rpds-py==0.27.1

ruamel-yaml==0.18.15

ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'

s3fs==2025.7.0
@@ -189,22 +189,22 @@ sortedcontainers==2.4.0 
spython==0.3.14

sqlalchemy==2.0.43

sqlparse==0.5.3

starlette==0.47.2

starlette==0.47.3

starlette-context==0.4.0

supervisor==4.2.5

supervisor==4.3.0

svgwrite==1.4.3

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==2025.6.11 ; python_full_version >= '3.11'

tifffile==2025.8.28 ; python_full_version >= '3.11'

tinydb==4.8.2

tomli==2.2.1 ; python_full_version < '3.11'

tornado==6.5.2

tqdm==4.67.1

tuspy==1.1.0

tuswsgi==0.5.5

typing-extensions==4.14.1

typing-extensions==4.15.0

typing-inspection==0.4.1

tzdata==2025.2

tzlocal==5.3.1

lib/galaxy/dependencies/pinned-test-requirements.txt

+15 −16
Original line number Diff line number Diff line
@@ -22,17 +22,17 @@ colorlog==6.9.0 
contourpy==1.3.0 ; python_full_version < '3.10'

contourpy==1.3.2 ; python_full_version == '3.10.*'

contourpy==1.3.3 ; python_full_version >= '3.11'

coverage==7.10.4

coverage==7.10.6

cwltest==2.6.20250818005349

cycler==0.12.1

decorator==5.2.1

defusedxml==0.7.1

dogpile-cache==1.2.2

dogpile-cache==1.4.0

enum-tools==0.12.0 ; python_full_version >= '3.10'

exceptiongroup==1.3.0 ; python_full_version < '3.11'

filelock==3.19.1

fluent-logger==0.11.1

fonttools==4.59.1

fonttools==4.59.2

frozenlist==1.7.0

greenlet==3.2.4

h11==0.16.0
@@ -48,6 +48,8 @@ inquirerpy==0.3.4 
isodate==0.7.2 ; python_full_version < '3.11'

jinja2==3.1.6

jmespath==1.0.1

jsonpatch==1.33

jsonpointer==3.0.0

jsonschema==4.25.1

jsonschema-specifications==2025.4.1

junit-xml==1.9
@@ -57,7 +59,7 @@ lxml==5.4.0 
markdown-it-py==3.0.0

markupsafe==3.0.2

matplotlib==3.9.4 ; python_full_version < '3.10'

matplotlib==3.10.5 ; python_full_version >= '3.10'

matplotlib==3.10.6 ; python_full_version >= '3.10'

mdurl==0.1.2

mirakuru==2.6.1

mistune==3.0.2
@@ -73,16 +75,15 @@ owlrl==6.0.2 ; python_full_version < '3.10' 
owlrl==7.1.4 ; python_full_version >= '3.10'

packaging==24.2 ; python_full_version < '3.10'

packaging==25.0 ; python_full_version >= '3.10'

pbr==7.0.1

pfzy==0.3.4

pillow==11.3.0

pkce==1.0.3

platformdirs==4.3.8

playwright==1.54.0

platformdirs==4.4.0

playwright==1.55.0

pluggy==1.6.0

port-for==0.7.4

prettytable==3.16.0

prompt-toolkit==3.0.51

prompt-toolkit==3.0.52

propcache==0.3.2

psutil==7.0.0 ; sys_platform != 'cygwin'

psycopg==3.2.9
@@ -106,7 +107,7 @@ pytest-playwright==0.7.0 
pytest-postgresql==7.0.2

pytest-shard==0.1.2

python-dateutil==2.9.0.post0

python-irodsclient==3.1.1

python-irodsclient==3.2.0

python-slugify==8.0.4

pyyaml==6.0.2

rdflib==7.1.4
@@ -119,24 +120,22 @@ rich-click==1.8.9 
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==0.7.3 ; python_full_version >= '3.10'

rpds-py==0.27.0

rpds-py==0.27.1

ruamel-yaml==0.18.15

ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'

rucio-clients==37.7.1

rucio-clients==38.0.0

s3transfer==0.13.1

schema-salad==8.9.20250723145140

scipy==1.13.1 ; python_full_version < '3.10'

scipy==1.15.3 ; python_full_version == '3.10.*'

scipy==1.16.1 ; python_full_version >= '3.11'

selenium==4.32.0 ; python_full_version < '3.10'

selenium==4.35.0 ; python_full_version >= '3.10'

selenium==4.32.0

seletools==1.5.0

setuptools==80.9.0

six==1.17.0

sniffio==1.3.1

sortedcontainers==2.4.0

statsd==4.0.1

stevedore==5.4.1

stevedore==5.5.0

tabulate==0.9.0

testfixtures==8.3.0 ; python_full_version < '3.11'

testfixtures==9.1.0 ; python_full_version >= '3.11'
@@ -148,7 +147,7 @@ trio==0.30.0 
trio-websocket==0.12.2

tuspy==1.1.0

twill==3.3

typing-extensions==4.14.1

typing-extensions==4.15.0

tzdata==2025.2 ; sys_platform == 'win32'

url-normalize==2.2.1

urllib3==1.26.20 ; python_full_version < '3.10'

lib/galaxy/dependencies/pinned-typecheck-requirements.txt

+2 −2
Original line number Diff line number Diff line 
# 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==1.40.16

boto3-stubs==1.40.21

botocore-stubs==1.38.46

cffi==1.17.1 ; platform_python_implementation != 'PyPy'

cryptography==45.0.6
@@ -32,6 +32,6 @@ types-s3transfer==0.13.0 
types-setuptools==80.9.0.20250822

types-six==1.17.0.20250515

types-urllib3==1.26.25.14 ; python_full_version < '3.10'

typing-extensions==4.14.1

typing-extensions==4.15.0

typing-inspection==0.4.1

urllib3==2.5.0 ; python_full_version >= '3.10'