mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Merge branch 'galaxyproject:dev' into dev
This commit is contained in:
Boris Depoortere
@@ -7,7 +7,7 @@ aiosignal==1.4.0
|
||||
alabaster==1.0.0
|
||||
annotated-types==0.8.0
|
||||
ase==3.29.0
|
||||
ast-serialize==0.6.0
|
||||
ast-serialize==0.8.0
|
||||
async-timeout==5.0.1 ; python_full_version < '3.11'
|
||||
attrs==26.1.0
|
||||
axe-selenium-python==2.1.6 ; python_full_version < '3.12'
|
||||
@@ -16,23 +16,23 @@ babel==2.18.0
|
||||
backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
|
||||
backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
black==26.5.1
|
||||
boto3==1.43.46
|
||||
botocore==1.43.46
|
||||
boto3==1.43.56
|
||||
botocore==1.43.56
|
||||
build==1.5.0
|
||||
cachecontrol==0.14.4
|
||||
cachetools==7.1.6
|
||||
cachetools==7.1.7
|
||||
cattrs==26.1.0
|
||||
certifi==2026.7.22
|
||||
cffi==2.1.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
|
||||
cffi==2.1.1 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
|
||||
charset-normalizer==3.4.9
|
||||
click==8.4.2
|
||||
cloudbridge==4.3.0
|
||||
cloudbridge==4.3.1
|
||||
codespell==2.4.3
|
||||
colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
|
||||
colorlog==6.12.0
|
||||
contourpy==1.3.2 ; python_full_version < '3.11'
|
||||
contourpy==1.3.3 ; python_full_version >= '3.11'
|
||||
coverage==7.15.2
|
||||
coverage==7.15.4
|
||||
cryptography==50.0.0
|
||||
cwltest==2.6.20251216093331
|
||||
cycler==0.12.1
|
||||
@@ -52,17 +52,17 @@ frozenlist==1.8.0
|
||||
fsspec==2026.7.0
|
||||
galaxy-release-util==0.4.2
|
||||
gcsfs==2026.7.0
|
||||
google-api-core==2.33.0
|
||||
google-auth==2.56.2
|
||||
google-api-core==2.34.0
|
||||
google-auth==2.56.3
|
||||
google-auth-oauthlib==1.4.0
|
||||
google-cloud-core==2.6.0
|
||||
google-cloud-storage==3.13.0
|
||||
google-cloud-storage-control==1.12.0
|
||||
google-cloud-core==2.6.1
|
||||
google-cloud-storage==3.13.1
|
||||
google-cloud-storage-control==1.13.0
|
||||
google-crc32c==1.8.0
|
||||
google-resumable-media==2.10.0
|
||||
googleapis-common-protos==1.75.0
|
||||
google-resumable-media==2.10.1
|
||||
googleapis-common-protos==1.75.1
|
||||
greenlet==3.5.4
|
||||
grpc-google-iam-v1==0.14.4
|
||||
grpc-google-iam-v1==0.14.5
|
||||
grpcio==1.83.0
|
||||
grpcio-status==1.83.0
|
||||
h11==0.16.0
|
||||
@@ -89,7 +89,7 @@ jsonschema-specifications==2025.9.1
|
||||
junit-xml==1.9
|
||||
keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
kiwisolver==1.5.0
|
||||
librt==0.13.0 ; platform_python_implementation != 'PyPy'
|
||||
librt==0.15.0 ; platform_python_implementation != 'PyPy'
|
||||
lxml==6.1.1
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
markdown-it-py==4.2.0 ; python_full_version >= '3.11'
|
||||
@@ -116,19 +116,19 @@ oauthlib==3.3.1
|
||||
onedatafilerestclient==21.2.5.2
|
||||
outcome==1.3.0.post0
|
||||
owlrl==7.6.2
|
||||
packaging==26.2
|
||||
packaging==26.3
|
||||
pathspec==1.1.1
|
||||
pfzy==0.3.4
|
||||
pillow==12.3.0
|
||||
pkce==1.0.3
|
||||
platformdirs==4.11.0
|
||||
platformdirs==4.11.1
|
||||
playwright==1.62.0
|
||||
pluggy==1.6.0
|
||||
port-for==1.0.0
|
||||
prettytable==3.18.0
|
||||
prompt-toolkit==3.0.53
|
||||
propcache==0.5.2
|
||||
proto-plus==1.28.2
|
||||
proto-plus==1.28.3
|
||||
protobuf==7.35.1
|
||||
psutil==7.2.2 ; sys_platform != 'cygwin'
|
||||
psycopg==3.3.4
|
||||
@@ -214,7 +214,7 @@ tenacity==9.1.4
|
||||
testfixtures==8.3.0 ; python_full_version < '3.11'
|
||||
testfixtures==12.3.0 ; python_full_version >= '3.11'
|
||||
text-unidecode==1.3
|
||||
tinydb==4.8.2
|
||||
tinydb==4.9.0
|
||||
toml==0.10.2
|
||||
tomli==2.4.1 ; python_full_version <= '3.11'
|
||||
total-perspective-vortex==3.2.1
|
||||
|
||||
@@ -4,4 +4,4 @@ flake8-bugbear==25.11.29
|
||||
mccabe==0.7.0
|
||||
pycodestyle==2.14.0
|
||||
pyflakes==3.4.0
|
||||
ruff==0.16.1
|
||||
ruff==0.16.2
|
||||
|
||||
@@ -2,24 +2,24 @@
|
||||
# uv export --frozen --no-annotate --no-hashes --no-dev
|
||||
a2wsgi==1.10.10
|
||||
adal==1.2.7
|
||||
aiobotocore==3.8.0
|
||||
aiobotocore==3.9.0
|
||||
aiofile==3.9.0 ; python_full_version < '3.11'
|
||||
aiofile==3.11.1 ; python_full_version >= '3.11'
|
||||
aiofile==3.12.3 ; python_full_version >= '3.11'
|
||||
aiofiles==25.1.0
|
||||
aiohappyeyeballs==2.7.1
|
||||
aiohttp==3.14.3
|
||||
aioitertools==0.13.0
|
||||
aiosignal==1.4.0
|
||||
alembic==1.18.5
|
||||
alembic==1.19.0
|
||||
amqp==5.3.1
|
||||
annotated-doc==0.0.5
|
||||
annotated-types==0.8.0
|
||||
anthropic==0.120.2
|
||||
anthropic==0.121.0
|
||||
anyio==4.14.2
|
||||
apispec==6.10.0
|
||||
appdirs==1.4.4
|
||||
arcp==0.2.1
|
||||
argcomplete==3.7.0
|
||||
argcomplete==3.7.2
|
||||
async-timeout==5.0.1 ; python_full_version < '3.11'
|
||||
attrs==26.1.0
|
||||
authlib==1.7.2
|
||||
@@ -37,14 +37,15 @@ bioblend==1.9.0
|
||||
bleach==6.4.0
|
||||
boltons==26.1.0
|
||||
boto==2.49.0
|
||||
botocore==1.43.46
|
||||
botocore==1.43.56
|
||||
bx-python==0.14.0
|
||||
cachecontrol==0.14.4
|
||||
cachetools==7.1.6
|
||||
caio==0.9.25
|
||||
cachetools==7.1.7
|
||||
caio==0.9.25 ; python_full_version < '3.11'
|
||||
caio==0.12.2 ; python_full_version >= '3.11'
|
||||
celery==5.6.3
|
||||
certifi==2026.7.22
|
||||
cffi==2.1.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
|
||||
cffi==2.1.1 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
|
||||
charset-normalizer==3.4.9
|
||||
circus==0.19.0
|
||||
click==8.4.2
|
||||
@@ -60,7 +61,7 @@ ct3==3.4.0.post5
|
||||
cwl-upgrader==1.2.15
|
||||
cwl-utils==0.42
|
||||
cwltool==3.2.20260720092025
|
||||
cyclopts==4.22.3
|
||||
cyclopts==4.22.5
|
||||
defusedxml==0.7.1
|
||||
deprecated==1.3.1
|
||||
dictobj==0.4
|
||||
@@ -77,20 +78,20 @@ et-xmlfile==2.0.0
|
||||
exceptiongroup==1.3.1
|
||||
executing==2.2.1
|
||||
fastapi==0.141.1
|
||||
fastmcp==3.4.5
|
||||
fastmcp-slim==3.4.5
|
||||
fastmcp==3.4.6
|
||||
fastmcp-slim==3.4.6
|
||||
filelock==3.32.2
|
||||
fissix==24.4.24
|
||||
frozenlist==1.8.0
|
||||
fs==2.4.16
|
||||
fsspec==2026.7.0
|
||||
future==1.0.0
|
||||
genai-prices==0.1.0
|
||||
google-api-core==2.33.0
|
||||
google-auth==2.56.2
|
||||
google-cloud-batch==0.22.1
|
||||
google-genai==2.16.0
|
||||
googleapis-common-protos==1.75.0
|
||||
genai-prices==0.1.1
|
||||
google-api-core==2.34.0
|
||||
google-auth==2.56.3
|
||||
google-cloud-batch==0.22.2
|
||||
google-genai==2.17.0
|
||||
googleapis-common-protos==1.75.1
|
||||
gravity==1.2.3
|
||||
greenlet==3.5.4 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
|
||||
griffelib==2.1.0
|
||||
@@ -132,10 +133,10 @@ kombu==5.6.2
|
||||
lagom==2.7.7
|
||||
legacy-cgi==2.6.4 ; python_full_version >= '3.13'
|
||||
limits==5.8.0
|
||||
logfire==4.39.0
|
||||
logfire-api==4.39.0
|
||||
logfire==4.40.0
|
||||
logfire-api==4.40.0
|
||||
lxml==6.1.1
|
||||
mako==1.3.12
|
||||
mako==1.4.1
|
||||
markdown==3.10.3
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
markdown-it-py==4.2.0 ; python_full_version >= '3.11'
|
||||
@@ -158,7 +159,7 @@ numpy==2.2.6 ; python_full_version < '3.11'
|
||||
numpy==2.4.6 ; python_full_version == '3.11.*'
|
||||
numpy==2.5.1 ; python_full_version >= '3.12'
|
||||
oauthlib==3.3.1
|
||||
openai==2.52.0
|
||||
openai==2.53.0
|
||||
openapi-pydantic==0.5.1
|
||||
openpyxl==3.1.5
|
||||
opentelemetry-api==1.44.0
|
||||
@@ -171,17 +172,17 @@ opentelemetry-sdk==1.44.0
|
||||
opentelemetry-semantic-conventions==0.65b0
|
||||
opentelemetry-util-http==0.65b0
|
||||
orjson==3.11.9
|
||||
packaging==26.2
|
||||
packaging==26.3
|
||||
paramiko==5.0.0
|
||||
parsley==1.3
|
||||
paste==3.10.1
|
||||
pathable==0.6.0
|
||||
pebble==5.2.0
|
||||
pillow==12.3.0
|
||||
platformdirs==4.11.0
|
||||
platformdirs==4.11.1
|
||||
prompt-toolkit==3.0.53
|
||||
propcache==0.5.2
|
||||
proto-plus==1.28.2
|
||||
proto-plus==1.28.3
|
||||
protobuf==7.35.1
|
||||
prov==1.5.1
|
||||
psutil==7.2.2
|
||||
@@ -193,13 +194,13 @@ pyasn1-modules==0.4.2
|
||||
pycparser==3.0 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
|
||||
pycryptodome==3.23.0
|
||||
pydantic==2.13.4
|
||||
pydantic-ai==2.22.0
|
||||
pydantic-ai-slim==2.22.0
|
||||
pydantic-ai==2.26.0
|
||||
pydantic-ai-slim==2.26.0
|
||||
pydantic-core==2.46.4
|
||||
pydantic-evals==2.22.0
|
||||
pydantic-evals==2.26.0
|
||||
pydantic-extra-types==2.11.1
|
||||
pydantic-graph==2.22.0
|
||||
pydantic-settings==2.14.2
|
||||
pydantic-graph==2.26.0
|
||||
pydantic-settings==2.15.0
|
||||
pydantic-tes==0.4.0
|
||||
pydicom==3.0.2
|
||||
pydot==4.0.1
|
||||
@@ -249,13 +250,13 @@ setuptools==81.0.0
|
||||
six==1.17.0
|
||||
slowapi==0.1.10
|
||||
sniffio==1.3.1
|
||||
social-auth-core==5.0.2
|
||||
social-auth-core==5.1.0
|
||||
sortedcontainers==2.4.0
|
||||
spython==0.3.14
|
||||
sqlalchemy==2.0.51
|
||||
sqlparse==0.5.5
|
||||
sse-starlette==3.4.6
|
||||
starlette==1.3.1
|
||||
sse-starlette==3.4.8
|
||||
starlette==1.4.1
|
||||
starlette-context==0.5.1
|
||||
supervisor==4.3.0
|
||||
svgwrite==1.4.3
|
||||
@@ -265,13 +266,13 @@ tifffile==2025.5.10 ; python_full_version < '3.11'
|
||||
tifffile==2026.3.3 ; python_full_version == '3.11.*'
|
||||
tifffile==2026.7.31 ; python_full_version >= '3.12'
|
||||
tiktoken==0.13.0
|
||||
tinydb==4.8.2
|
||||
tinydb==4.9.0
|
||||
tomli==2.4.1 ; python_full_version < '3.11'
|
||||
tornado==6.5.7
|
||||
tornado==6.5.8
|
||||
tqdm==4.70.0
|
||||
truststore==0.10.4
|
||||
tuspy==1.1.0
|
||||
tuspyserver==4.2.12
|
||||
tuspyserver==4.2.13
|
||||
typing-extensions==4.16.0
|
||||
typing-inspection==0.4.2
|
||||
tzdata==2026.3
|
||||
@@ -279,13 +280,13 @@ tzlocal==5.4.4
|
||||
ubiquerg==0.9.3
|
||||
uncalled-for==0.3.2
|
||||
urllib3==2.7.0
|
||||
uvicorn==0.52.0
|
||||
uvicorn==0.52.1
|
||||
uvloop==0.22.1
|
||||
vine==5.1.0
|
||||
watchfiles==1.2.0
|
||||
wcwidth==0.8.2
|
||||
webencodings==0.5.1
|
||||
webob==1.8.10
|
||||
webob==1.8.11
|
||||
websockets==16.1.1
|
||||
whoosh==2.7.4
|
||||
wrapt==2.3.0
|
||||
|
||||
@@ -6,27 +6,27 @@ aiohttp==3.14.3
|
||||
aiosignal==1.4.0
|
||||
annotated-types==0.8.0
|
||||
ase==3.29.0
|
||||
ast-serialize==0.6.0
|
||||
ast-serialize==0.8.0
|
||||
async-timeout==5.0.1 ; python_full_version < '3.11'
|
||||
attrs==26.1.0
|
||||
axe-selenium-python==2.1.6 ; python_full_version < '3.12'
|
||||
axe-selenium-python==3.0.0 ; python_full_version >= '3.12'
|
||||
backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
|
||||
boto3==1.43.46
|
||||
botocore==1.43.46
|
||||
boto3==1.43.56
|
||||
botocore==1.43.56
|
||||
cachecontrol==0.14.4
|
||||
cachetools==7.1.6
|
||||
cachetools==7.1.7
|
||||
cattrs==26.1.0
|
||||
certifi==2026.7.22
|
||||
cffi==2.1.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
|
||||
cffi==2.1.1 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
|
||||
charset-normalizer==3.4.9
|
||||
click==8.4.2
|
||||
cloudbridge==4.3.0
|
||||
cloudbridge==4.3.1
|
||||
colorama==0.4.6 ; sys_platform == 'win32'
|
||||
colorlog==6.12.0
|
||||
contourpy==1.3.2 ; python_full_version < '3.11'
|
||||
contourpy==1.3.3 ; python_full_version >= '3.11'
|
||||
coverage==7.15.2
|
||||
coverage==7.15.4
|
||||
cryptography==50.0.0
|
||||
cwltest==2.6.20251216093331
|
||||
cycler==0.12.1
|
||||
@@ -41,17 +41,17 @@ fonttools==4.63.0
|
||||
frozenlist==1.8.0
|
||||
fsspec==2026.7.0
|
||||
gcsfs==2026.7.0
|
||||
google-api-core==2.33.0
|
||||
google-auth==2.56.2
|
||||
google-api-core==2.34.0
|
||||
google-auth==2.56.3
|
||||
google-auth-oauthlib==1.4.0
|
||||
google-cloud-core==2.6.0
|
||||
google-cloud-storage==3.13.0
|
||||
google-cloud-storage-control==1.12.0
|
||||
google-cloud-core==2.6.1
|
||||
google-cloud-storage==3.13.1
|
||||
google-cloud-storage-control==1.13.0
|
||||
google-crc32c==1.8.0
|
||||
google-resumable-media==2.10.0
|
||||
googleapis-common-protos==1.75.0
|
||||
google-resumable-media==2.10.1
|
||||
googleapis-common-protos==1.75.1
|
||||
greenlet==3.5.4
|
||||
grpc-google-iam-v1==0.14.4
|
||||
grpc-google-iam-v1==0.14.5
|
||||
grpcio==1.83.0
|
||||
grpcio-status==1.83.0
|
||||
h11==0.16.0
|
||||
@@ -70,7 +70,7 @@ jsonschema==4.26.0
|
||||
jsonschema-specifications==2025.9.1
|
||||
junit-xml==1.9
|
||||
kiwisolver==1.5.0
|
||||
librt==0.13.0 ; platform_python_implementation != 'PyPy'
|
||||
librt==0.15.0 ; platform_python_implementation != 'PyPy'
|
||||
lxml==6.1.1
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
markdown-it-py==4.2.0 ; python_full_version >= '3.11'
|
||||
@@ -91,19 +91,19 @@ oauthlib==3.3.1
|
||||
onedatafilerestclient==21.2.5.2
|
||||
outcome==1.3.0.post0
|
||||
owlrl==7.6.2
|
||||
packaging==26.2
|
||||
packaging==26.3
|
||||
pathspec==1.1.1
|
||||
pfzy==0.3.4
|
||||
pillow==12.3.0
|
||||
pkce==1.0.3
|
||||
platformdirs==4.11.0
|
||||
platformdirs==4.11.1
|
||||
playwright==1.62.0
|
||||
pluggy==1.6.0
|
||||
port-for==1.0.0
|
||||
prettytable==3.18.0
|
||||
prompt-toolkit==3.0.53
|
||||
propcache==0.5.2
|
||||
proto-plus==1.28.2
|
||||
proto-plus==1.28.3
|
||||
protobuf==7.35.1
|
||||
psutil==7.2.2 ; sys_platform != 'cygwin'
|
||||
psycopg==3.3.4
|
||||
@@ -166,7 +166,7 @@ tenacity==9.1.4
|
||||
testfixtures==8.3.0 ; python_full_version < '3.11'
|
||||
testfixtures==12.3.0 ; python_full_version >= '3.11'
|
||||
text-unidecode==1.3
|
||||
tinydb==4.8.2
|
||||
tinydb==4.9.0
|
||||
toml==0.10.2
|
||||
tomli==2.4.1 ; python_full_version <= '3.11'
|
||||
total-perspective-vortex==3.2.1
|
||||
|
||||
@@ -1,15 +1,15 @@
|
||||
# This file was autogenerated by uv via the following command:
|
||||
# uv export --frozen --no-annotate --no-hashes --only-group=typecheck
|
||||
annotated-types==0.8.0
|
||||
ast-serialize==0.6.0
|
||||
boto3-stubs==1.43.62
|
||||
ast-serialize==0.8.0
|
||||
boto3-stubs==1.43.67
|
||||
botocore-stubs==1.43.14
|
||||
cffi==2.1.0 ; platform_python_implementation != 'PyPy'
|
||||
cffi==2.1.1 ; platform_python_implementation != 'PyPy'
|
||||
cryptography==50.0.0
|
||||
librt==0.13.0 ; platform_python_implementation != 'PyPy'
|
||||
librt==0.15.0 ; platform_python_implementation != 'PyPy'
|
||||
lxml-stubs==0.5.1
|
||||
mypy==2.3.0
|
||||
mypy-boto3-s3==1.43.50
|
||||
mypy-boto3-s3==1.43.66
|
||||
mypy-extensions==1.1.0
|
||||
pathspec==1.1.1
|
||||
pycparser==3.0 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
|
||||
@@ -26,12 +26,12 @@ types-docutils==0.22.3.20260724
|
||||
types-html5lib==1.1.11.20260518
|
||||
types-markdown==3.10.2.20260712
|
||||
types-paramiko==5.0.0.20260724
|
||||
types-python-dateutil==2.9.0.20260716
|
||||
types-python-dateutil==2.9.0.20260807
|
||||
types-python-slugify==8.0.2.20240310
|
||||
types-pyyaml==6.0.12.20260724
|
||||
types-requests==2.33.0.20260712
|
||||
types-s3transfer==0.16.0
|
||||
types-setuptools==83.0.0.20260724
|
||||
types-setuptools==83.0.0.20260807
|
||||
types-six==1.17.0.20260724
|
||||
types-webencodings==0.5.0.20260408
|
||||
typing-extensions==4.16.0
|
||||
|
||||
@@ -2267,7 +2267,11 @@ class JobSubmitter:
|
||||
# API dataset materialization is immutable and produces new datasets
|
||||
# here we just created the datasets - lets just materialize them in place
|
||||
# and avoid extra and confusing input copies
|
||||
self.hda_manager.materialize(materialize_request, sa_session(), in_place=True)
|
||||
materialized = self.hda_manager.materialize(materialize_request, sa_session(), in_place=True)
|
||||
if not materialized:
|
||||
raise RequestParameterInvalidException(
|
||||
f"Failed to fetch dataset from '{to_materialize.request.url}'"
|
||||
)
|
||||
if request.data_manager_mode:
|
||||
tool_request.request["__data_manager_mode"] = request.data_manager_mode
|
||||
credentials_context = (
|
||||
|
||||
Reference in New Issue
Block a user