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Update Python dependencies #19123

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Nov 12, 2024
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Update Python dependencies #19123

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4145833
Update Python dependencies
galaxybot Nov 9, 2024
94593bd
Pin scipy to >=1.14.1 for Python 3.13 support
nsoranzo Nov 10, 2024
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18 changes: 9 additions & 9 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ black==24.8.0
boto3==1.35.36
botocore==1.35.36
build==1.2.2.post1
cachecontrol==0.14.0
cachecontrol==0.14.1
certifi==2024.8.30
cffi==1.17.1
charset-normalizer==3.4.0
Expand Down Expand Up @@ -83,10 +83,10 @@ myst-parser==3.0.1
nh3==0.2.18
numpy==1.24.4 ; python_full_version < '3.9'
numpy==2.0.2 ; python_full_version == '3.9.*'
numpy==2.1.2 ; python_full_version >= '3.10'
numpy==2.1.3 ; python_full_version >= '3.10'
onedatafilerestclient==21.2.5.2
outcome==1.3.0.post0
packaging==24.1
packaging==24.2
pathspec==0.12.1
pbr==6.1.0 ; python_full_version >= '3.9'
pillow==10.4.0
Expand All @@ -103,7 +103,7 @@ psutil==6.1.0 ; sys_platform != 'cygwin'
psycopg==3.2.3
pycparser==2.22
pyee==12.0.0
pygithub==2.4.0
pygithub==2.5.0
pygments==2.18.0
pyjwt==2.9.0
pynacl==1.5.0
Expand Down Expand Up @@ -135,20 +135,20 @@ requests==2.32.3
requests-toolbelt==1.0.0
responses==0.25.3
rfc3986==2.0.0
rich==13.9.3
rpds-py==0.20.0 ; python_full_version >= '3.9'
rich==13.9.4
rpds-py==0.20.1 ; python_full_version >= '3.9'
ruamel-yaml==0.18.6
ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
rucio-clients==35.4.1 ; python_full_version >= '3.9'
rucio-clients==35.5.0 ; python_full_version >= '3.9'
s3transfer==0.10.3
schema-salad==8.7.20241010092723
scipy==1.10.1 ; python_full_version < '3.9'
scipy==1.13.1 ; python_full_version == '3.9.*'
scipy==1.14.1 ; python_full_version >= '3.10'
secretstorage==3.3.3 ; sys_platform == 'linux'
selenium==4.25.0
selenium==4.26.1
seletools==1.5.0
setuptools==75.2.0
setuptools==75.3.0
six==1.16.0
sniffio==1.3.1
snowballstemmer==2.2.0
Expand Down
4 changes: 2 additions & 2 deletions lib/galaxy/dependencies/pinned-lint-requirements.txt
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@@ -1,7 +1,7 @@
attrs==24.2.0
flake8==7.1.1
flake8-bugbear==24.8.19
flake8-bugbear==24.10.31
mccabe==0.7.0
pycodestyle==2.12.1
pyflakes==3.2.0
ruff==0.7.1
ruff==0.7.3
32 changes: 17 additions & 15 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Expand Up @@ -9,7 +9,7 @@ aiohappyeyeballs==2.4.3
aiohttp==3.10.10
aioitertools==0.12.0
aiosignal==1.3.1
alembic==1.13.3
alembic==1.14.0
amqp==5.2.0
annotated-types==0.7.0
anyio==4.5.2
Expand All @@ -28,13 +28,13 @@ bcrypt==4.2.0
bdbag==1.7.3
beaker==1.13.0
billiard==4.2.1
bioblend==1.3.0
bioblend==1.4.0
bleach==6.1.0
boltons==24.0.0
boltons==24.1.0
boto==2.49.0
botocore==1.35.36
bx-python==0.13.0
cachecontrol==0.14.0
cachecontrol==0.14.1
celery==5.4.0
certifi==2024.8.30
cffi==1.17.1
Expand All @@ -60,7 +60,7 @@ dictobj==0.4
dnspython==2.6.1
docopt==0.6.2
docutils==0.20.1
dparse==0.6.3
dparse==0.6.4
edam-ontology==1.25.2
email-validator==2.2.0
exceptiongroup==1.2.2 ; python_full_version < '3.11'
Expand All @@ -72,7 +72,7 @@ fs==2.4.16
fsspec==2024.10.0
future==1.0.0
galaxy2cwl==0.1.4
graphene==3.4.1
graphene==3.4.3
graphene-sqlalchemy==3.0.0rc1
graphql-core==3.2.5
graphql-relay==3.2.0
Expand Down Expand Up @@ -116,11 +116,11 @@ networkx==3.1
nodeenv==1.9.1
numpy==1.24.4 ; python_full_version < '3.9'
numpy==2.0.2 ; python_full_version == '3.9.*'
numpy==2.1.2 ; python_full_version >= '3.10'
numpy==2.1.3 ; python_full_version >= '3.10'
oauthlib==3.2.2
orjson==3.10.10
orjson==3.10.11
oyaml==1.0
packaging==24.1
packaging==24.2
paramiko==3.5.0
parsley==1.3
paste==3.10.1
Expand Down Expand Up @@ -152,29 +152,30 @@ pyreadline3==3.5.4 ; sys_platform == 'win32'
pysam==0.22.1
python-dateutil==2.9.0.post0
python-magic==0.4.27
python-multipart==0.0.16
python-multipart==0.0.17
python-slugify==8.0.4
python3-openid==3.2.0
pytz==2024.2
pyyaml==6.0.2
pyzmq==26.2.0
rdflib==6.3.2
referencing==0.35.1
refgenconf==0.12.2
regex==2024.9.11
regex==2024.11.6
repoze-lru==0.7
requests==2.32.3
requests-oauthlib==2.0.0
requests-toolbelt==1.0.0
requests-unixsocket==0.3.0
rich==13.9.3
rich==13.9.4
rocrate==0.11.0
routes==2.5.1
rpds-py==0.20.0
rpds-py==0.20.1
ruamel-yaml==0.18.6
ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
s3fs==2024.10.0
schema-salad==8.7.20241010092723
setuptools==75.2.0
setuptools==75.3.0
setuptools-scm==5.0.2
six==1.16.0
sniffio==1.3.1
Expand All @@ -190,11 +191,12 @@ starlette-graphene3==0.6.0
supervisor==4.2.5
svgwrite==1.4.3
tenacity==9.0.0
text-unidecode==1.3
tifffile==2023.7.10
tinydb==4.8.2
tomli==2.0.2 ; python_full_version < '3.11'
tornado==6.4.1
tqdm==4.66.6
tqdm==4.67.0
tuspy==1.0.3
tuswsgi==0.5.5
typing-extensions==4.12.2
Expand Down
8 changes: 4 additions & 4 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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@@ -1,8 +1,8 @@
# This file was autogenerated by uv via the following command:
# uv export --frozen --no-hashes --only-group=typecheck
annotated-types==0.7.0
boto3-stubs==1.35.49
botocore-stubs==1.35.49
boto3-stubs==1.35.57
botocore-stubs==1.35.57
cffi==1.17.1 ; platform_python_implementation != 'PyPy'
cryptography==43.0.3
lxml-stubs==0.5.1
Expand All @@ -27,7 +27,7 @@ types-python-slugify==8.0.2.20240310
types-pyyaml==6.0.12.20240917
types-requests==2.31.0.6
types-s3transfer==0.10.3
types-setuptools==75.2.0.20241025
types-six==1.16.21.20241009
types-setuptools==75.3.0.20241107
types-six==1.16.21.20241105
types-urllib3==1.26.25.14
typing-extensions==4.12.2
1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -149,6 +149,7 @@ dev = [
"pytest-shard",
"responses",
"rucio-clients>=33.6.0 ; python_version>='3.9'", # https://github.com/galaxyproject/galaxy/pull/17156
"scipy>=1.14.1; python_version>='3.10'", # ase dependency, Python 3.13 support
"selenium",
"seletools",
"Sphinx>=4.0", # support docutils 0.17
Expand Down
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