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Switch galaxyproject package index to `--extra-index-url`

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so that `uv pip install` treats it with higher priority:

https://docs.astral.sh/uv/concepts/indexes/#-index-url-and-extra-index-url

Note that `pip` treats all indexes with the same priority:

https://pip.pypa.io/en/stable/cli/pip_install/#finding-packages

Allows uv to install the Python 3.14 wheel of pysam==0.23.3 from
wheels.galaxyproject.org instead of trying to build it from the source
package from PyPI.
This commit is contained in:
Nicola Soranzo
2025-12-09 19:36:16 +00:00
parent 0de53df7b8
commit fc7d1dee35
1 changed files with 2 additions and 3 deletions
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scripts/common_startup.sh
+2 -3
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@@ -185,7 +185,6 @@ if [ $SET_VENV -eq 1 ] && [ -z "$VIRTUAL_ENV" ]; then
fi
: "${GALAXY_WHEELS_INDEX_URL:=https://wheels.galaxyproject.org/simple}"
: "${PYPI_INDEX_URL:=https://pypi.python.org/simple}"
: "${GALAXY_DEV_REQUIREMENTS:=./lib/galaxy/dependencies/dev-requirements.txt}"
requirement_args="-r requirements.txt"
@@ -203,7 +202,7 @@ if [ $FETCH_WHEELS -eq 1 ]; then
${PIP_CMD} install "pip>=${MIN_PIP_VERSION}" wheel
fi
# shellcheck disable=SC2086
${PIP_CMD} install $requirement_args --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
${PIP_CMD} install $requirement_args --extra-index-url "${GALAXY_WHEELS_INDEX_URL}"
set_galaxy_config_file_var
GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "from __future__ import print_function; import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))")
if [ -n "$GALAXY_CONDITIONAL_DEPENDENCIES" ]; then
@@ -211,7 +210,7 @@ if [ $FETCH_WHEELS -eq 1 ]; then
echo "An older version of psycopg2 (non-binary, version 2.7.3) has been detected. Galaxy now uses psycopg2-binary, which will be installed after removing psycopg2."
${PIP_CMD} uninstall ${UNINSTALL_OPTIONS} psycopg2 psycopg2-binary
fi
echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | ${PIP_CMD} install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | ${PIP_CMD} install -r /dev/stdin --extra-index-url "${GALAXY_WHEELS_INDEX_URL}"
fi
fi