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Merge branch 'release_24.0' into release_24.1
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nsoranzo committed Jul 29, 2024
2 parents 9c507f2 + 9191eee commit 90b5251
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Showing 3 changed files with 11 additions and 2 deletions.
4 changes: 4 additions & 0 deletions lib/galaxy/dependencies/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -294,6 +294,10 @@ def check_weasyprint(self):
# See notes in ./conditional-requirements.txt for more information.
return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"

def check_pydyf(self):
# See notes in ./conditional-requirements.txt for more information.
return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"

def check_custos_sdk(self):
return "custos" == self.vault_type

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7 changes: 6 additions & 1 deletion lib/galaxy/dependencies/conditional-requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,12 @@ tensorflow==2.9.3
# xref https://github.com/galaxyproject/galaxy/pull/9651
# Run run.sh or common_startup script with GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT=1
# to install weasyprint as part of Galaxy's conditonal dependency instalation process.
weasyprint
weasyprint>=61.2
# We pin the transitive weasyprint dependency pydyf here because newer versions are
# not compatible with the last weasyprint version that still supports python 3.8.
# This dependency is ignored on python >= 3.9 and should be removed when deprecating
# support for python 3.8.
pydyf<0.11; python_version<"3.9"

# AWS Batch runner
boto3
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2 changes: 1 addition & 1 deletion lib/galaxy/tools/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -379,7 +379,7 @@ def __init__(self, app):

def reset_tags(self):
log.info(
f"removing all tool tag associations ({str(self.sa_session.scalar(select(func.count(self.app.model.ToolTagAssociation))))})"
f"removing all tool tag associations ({str(self.sa_session.scalar(select(func.count(self.app.model.ToolTagAssociation.id))))})"
)
self.sa_session.execute(delete(self.app.model.ToolTagAssociation))
with transaction(self.sa_session):
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