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Pin minimum package versions for Python 3.13 support
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Also:
- Cheetah3 package on PyPI has been renamed to CT3 since 3.3.0, see
  https://cheetahtemplate.org/news.html
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nsoranzo committed Oct 29, 2024
1 parent fe2c01d commit 4d67df6
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Showing 10 changed files with 21 additions and 23 deletions.
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/conditional-requirements.txt
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# These dependencies are only required when certain config options are set
psycopg2-binary==2.9.9
psycopg2-binary==2.9.10
mysqlclient
fluent-logger
sentry-sdk[fastapi]
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4 changes: 2 additions & 2 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Expand Up @@ -40,7 +40,6 @@ celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13"
charset-normalizer==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
circus==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13"
click-plugins==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -52,6 +51,7 @@ colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platfo
coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
conda-package-streaming==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
cryptography==43.0.3 ; python_version >= "3.8" and python_version < "3.13"
ct3==3.3.3.post1 ; 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==0.35 ; python_version >= "3.8" and python_version < "3.13"
cwltool==3.1.20241007082533 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -104,7 +104,7 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
markdown==3.7 ; python_version >= "3.8" and python_version < "3.13"
markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
mercurial==6.8.1 ; python_version >= "3.8" and python_version < "3.13"
mercurial==6.8.2 ; python_version >= "3.8" and python_version < "3.13"
mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
mrcfile==1.5.3 ; python_version >= "3.8" and python_version < "3.13"
msal==1.31.0 ; python_version >= "3.8" and python_version < "3.13"
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4 changes: 2 additions & 2 deletions packages/app/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ install_requires =
Mako
Markdown
MarkupSafe
mercurial
mercurial>=6.8.2
packaging
paramiko!=2.9.0,!=2.9.1
pebble
Expand All @@ -74,7 +74,7 @@ install_requires =
starlette
svgwrite
typing-extensions
WebOb
WebOb>=1.8.9
Whoosh
packages = find:
python_requires = >=3.8
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3 changes: 1 addition & 2 deletions packages/data/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ install_requires =
h5grove>=1.2.1
h5py
isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master
isal
isal>=1.7.0
MarkupSafe
msal
mrcfile
Expand All @@ -62,7 +62,6 @@ install_requires =
SQLAlchemy>=2.0,<2.1,!=2.0.36
tifffile
typing-extensions
WebOb
packages = find:
python_requires = >=3.8

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1 change: 0 additions & 1 deletion packages/files/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ include_package_data = True
install_requires =
galaxy-util[config_template]
fs
isal
typing-extensions
packages = find:
python_requires = >=3.8
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2 changes: 1 addition & 1 deletion packages/test_base/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ install_requires =
galaxy-tool-util
galaxy-util
bioblend
cwltest
cwltest>=2.5.20240906231108
gxformat2
pytest
PyYAML
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2 changes: 1 addition & 1 deletion packages/tool_shed/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ install_requires =
graphql-core
Mako
MarkupSafe
mercurial
mercurial>=6.8.2
Paste
pydantic>=2.7.4
Routes
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2 changes: 1 addition & 1 deletion packages/util/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ python_requires = >=3.7
jstree =
dictobj
template =
Cheetah3
CT3>=3.3.3
future>=1.0.0
config_template =
Jinja2
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6 changes: 3 additions & 3 deletions packages/web_apps/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ install_requires =
a2wsgi
apispec
Babel
Cheetah3
CT3>=3.3.3
fastapi>=0.101.0
gunicorn
gxformat2
Expand All @@ -63,8 +63,8 @@ install_requires =
tuswsgi
typing-extensions
uvicorn
uvloop
WebOb
uvloop>=0.21.0
WebOb>=1.8.9
packages = find:
python_requires = >=3.8

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18 changes: 9 additions & 9 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -46,10 +46,10 @@ boltons = "*"
boto = "*"
bx-python = "*"
celery = "*"
Cheetah3 = "*"
cloudauthz = "==0.6.0"
cloudbridge = "*"
circus = "*"
CT3 = ">=3.3.3" # Python 3.13 support
cwltool = ">=3.1.20230624081518" # save time, minimum needed by cwl-1.0 branch
conda-package-streaming = "*"
dictobj = "*"
Expand All @@ -72,12 +72,12 @@ importlib-resources = { version = "*", python = "<3.9" } # for importlib.{abc.T
isa-rwval = { git = "https://github.com/nsoranzo/isa-rwval.git", branch = "master" } # https://github.com/ISA-tools/isa-rwval/pull/17
jinja2 = "*"
kombu = ">=5.3" # for importlib-metadata fix
isal = "*"
isal = ">=1.7.0" # Python 3.13 support
lagom = "*"
Mako = "*"
Markdown = "*"
MarkupSafe = "*"
Mercurial = "*"
mercurial = ">=6.8.2" # Python 3.13 support
mrcfile = "*"
msal = "*"
nodeenv = "*"
Expand Down Expand Up @@ -107,7 +107,7 @@ regex = "*"
requests = "*"
rocrate = "*"
Routes = "*"
schema-salad = "!=8.3.20220721194857" # https://github.com/common-workflow-language/schema_salad/issues/575
schema-salad = ">=8.7.20240905150001" # Python 3.13 support
social-auth-core = ">=4.5.0" # to drop dependency on abandoned python-jose
sortedcontainers = "*"
SQLAlchemy = ">=2.0,<2.1,!=2.0.36" # https://github.com/sqlalchemy/sqlalchemy/issues/12019
Expand All @@ -121,8 +121,8 @@ tifffile = "*"
tuswsgi = "*"
typing-extensions = "*"
uvicorn = "!=0.28.0" # https://github.com/galaxyproject/galaxy/issues/17669
uvloop = "*"
WebOb = "*"
uvloop = ">=0.21.0" # Python 3.13 support
WebOb = ">=1.8.9" # Python 3.13 support
Whoosh = "*"
zipstream-new = "*"
s3fs = ">=2023.1.0"
Expand All @@ -133,7 +133,7 @@ axe-selenium-python = "*"
black = "*"
boto3 = "*"
codespell = "*"
cwltest = "*"
cwltest = ">=2.5.20240906231108" # Python 3.13 support
darker = "*"
fluent-logger = "*"
galaxy-release-util = "*"
Expand All @@ -144,7 +144,7 @@ markdown-it-reporter = "*"
myst-parser = "*"
onedatafilerestclient = "==21.2.5.2"
pkce = "*"
playwright = "*"
playwright = ">=1.48.0" # Python 3.13 support
pytest = "*"
pytest-asyncio = "*"
pytest-cov = "*"
Expand All @@ -166,7 +166,7 @@ sphinx-rtd-theme = "*"
statsd = "*"
testfixtures = "*"
tuspy = "*"
twill = ">=3.2.1" # https://github.com/twill-tools/twill/issues/18
twill = ">=3.2.5" # Python 3.13 support
watchdog = "*"
Werkzeug = "*"

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