Replace poetry with uv

for lightning-fast Python dependency updates.

To update all dependencies (as done by the GitHub action):

$ make update-dependencies

To update only one package:

./lib/galaxy/dependencies/update.sh -p <PKG>

.github/workflows/dependencies.yaml

@@ -17,9 +17,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Update dependencies
-        run: | 
-          python -m venv .venv
-          make update-dependencies
+        run: make update-dependencies
       - name: Create pull request
         uses: peter-evans/create-pull-request@v6
         with:

doc/source/admin/framework_dependencies.rst

@@ -185,7 +185,7 @@ Adding additional Galaxy dependencies
 -------------------------------------
 
 New packages can be added to Galaxy, or the versions of existing packages can be
-updated, using `poetry`_ and `Wheelforge`_.
+updated, using `uv`_ and `Wheelforge`_.
 
 If wheels already exist on PyPI for all platforms and Python versions supported
 by Galaxy, you can skip to step 3 in the process below.
@@ -195,11 +195,13 @@ by Galaxy, you can skip to step 3 in the process below.
 
 2. Submit a pull request to `Wheelforge`_.
 
-3. Add the new dependency to the `[tool.poetry.dependencies]` (or to `[tool.poetry.group.dev.dependencies]` if only needed for Galaxy development) section of `pyproject.toml` .
-4. Run `make update-dependencies` to update the requirements file in `lib/galaxy/dependencies`_.
+3. Add the new dependency to the ``dependencies`` list in the ``[project]``
+   section (or to ``dev`` list in the ``[dependency-groups]`` section if only
+   needed for Galaxy development) of `pyproject.toml`_ .
+4. Run ``make update-dependencies`` to update the requirements files in `lib/galaxy/dependencies`_.
 5. Submit a pull request to Galaxy with your changes.
 
-.. _poetry: https://python-poetry.org/
+.. _uv: https://docs.astral.sh/uv/
 .. _Wheelforge: https://github.com/galaxyproject/wheelforge/
-.. _Pull Request #4891: https://github.com/galaxyproject/galaxy/pull/4891
+.. _pyproject.toml: https://github.com/galaxyproject/galaxy/blob/dev/pyproject.toml
 .. _lib/galaxy/dependencies: https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/dependencies

lib/galaxy/dependencies/pinned-typecheck-requirements.txt

@@ -1,30 +1,32 @@
-annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3-stubs[s3]==1.35.49 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.35.49 ; python_version >= "3.8" and python_version < "3.13"
-cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-cryptography==43.0.3 ; python_version >= "3.8" and python_version < "3.13"
-lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
-mypy-boto3-s3==1.35.46 ; python_version >= "3.8" and python_version < "3.13"
-mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-mypy==1.13.0 ; python_version >= "3.8" and python_version < "3.13"
-pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-pydantic-core==2.23.4 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13"
-tomli==2.0.2 ; python_version >= "3.8" and python_version < "3.11"
-types-awscrt==0.23.0 ; python_version >= "3.8" and python_version < "3.13"
-types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
-types-boto==2.49.18.20241019 ; python_version >= "3.8" and python_version < "3.13"
-types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
-types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
-types-docutils==0.21.0.20241005 ; python_version >= "3.8" and python_version < "3.13"
-types-html5lib==1.1.11.20241018 ; python_version >= "3.8" and python_version < "3.13"
-types-markdown==3.7.0.20240822 ; python_version >= "3.8" and python_version < "3.13"
-types-paramiko==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3.13"
-types-python-dateutil==2.9.0.20241003 ; python_version >= "3.8" and python_version < "3.13"
-types-pyyaml==6.0.12.20240917 ; python_version >= "3.8" and python_version < "3.13"
-types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
-types-s3transfer==0.10.3 ; python_version >= "3.8" and python_version < "3.13"
-types-setuptools==75.2.0.20241025 ; python_version >= "3.8" and python_version < "3.13"
-types-six==1.16.21.20241009 ; python_version >= "3.8" and python_version < "3.13"
-types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
+# This file was autogenerated by uv via the following command:
+#    uv export --no-hashes --only-group=typecheck
+annotated-types==0.7.0
+boto3-stubs==1.35.49
+botocore-stubs==1.35.49
+cffi==1.17.1 ; platform_python_implementation != 'PyPy'
+cryptography==43.0.3
+lxml-stubs==0.5.1
+mypy==1.13.0
+mypy-boto3-s3==1.35.46
+mypy-extensions==1.0.0
+pycparser==2.22 ; platform_python_implementation != 'PyPy'
+pydantic==2.9.2
+pydantic-core==2.23.4
+tomli==2.0.2 ; python_full_version < '3.11'
+types-awscrt==0.23.0
+types-bleach==6.1.0.20240331
+types-boto==2.49.18.20241019
+types-contextvars==2.4.7.3
+types-dataclasses==0.6.6
+types-docutils==0.21.0.20241005
+types-html5lib==1.1.11.20241018
+types-markdown==3.7.0.20240822
+types-paramiko==3.5.0.20240928
+types-python-dateutil==2.9.0.20241003
+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-urllib3==1.26.25.14
+typing-extensions==4.12.2

lib/galaxy/dependencies/update.sh

@@ -1,25 +1,25 @@
 #!/bin/sh
 
-# This script installs poetry if it's not already installed in the user account.
-# It then runs poetry inside Galaxy's root directory, potentially updating 
-# pyproject.toml and poetry.lock, and the pinned and dev requirements files.
+# This script installs uv if it's not already installed in the user account.
+# It then runs uv inside Galaxy's root directory, potentially updating
+# pyproject.toml and uv.lock, and the pinned requirements files.
 
 set -e
 
-SUPPORTED_PYTHON_VERSIONS="3.8 3.9 3.10 3.11 3.12"
-NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.13"
-
 this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)"
 
 usage() {
-    printf "Usage: %s: [-a] [pkg_spec...]\n" "${0##*/}" >&2
+    printf "Usage: %s: [-p pkg]\n" "${0##*/}" >&2
 }
 
-add=
-while getopts 'a' OPTION
+pkg=
+while getopts 'p:h' OPTION
 do
     case $OPTION in
-        a) add=1
+        p) pkg="$OPTARG"
+           ;;
+        h) usage
+           exit 0
            ;;
         ?) usage
            exit 2
@@ -28,68 +28,20 @@ do
 done
 shift $((OPTIND - 1))
 
-if [ -n "$add" ] && [ $# -eq 0 ]; then
-    printf "When adding (-a), you must provide at least one package specification.\n" >&2
-    usage
-    exit 2
-fi
-
-# Install the latest version of poetry into the user account
-curl -sSL https://install.python-poetry.org | python3 -
-poetry self add 'poetry-plugin-export!=1.7.0'  # https://github.com/python-poetry/poetry-plugin-export/issues/269
+# Create a virtual environment in a tmp directory and install uv into it
+uv_venv=$(mktemp -d "${TMPDIR:-/tmp}/uv_venv.XXXXXXXXXX")
+python3 -m venv "${uv_venv}"
+"${uv_venv}/bin/python" -m pip install uv
+uv="${uv_venv}/bin/uv"
 
-# Run poetry (this may update pyproject.toml and poetry.lock).
-if [ -z "$add" ]; then
-    poetry update -vv --lock "$@"
+# Run uv (this may update pyproject.toml and uv.lock).
+if [ -n "$pkg" ]; then
+    ${uv} lock --upgrade-package "$pkg"
 else
-    poetry add -vv --lock "$@"
+    ${uv} lock
 fi
 
 # Update pinned requirements files.
-PINNED_REQUIREMENTS_FILE=$this_directory/pinned-requirements.txt
-PINNED_DEV_REQUIREMENTS_FILE=$this_directory/dev-requirements.txt
-poetry export -f requirements.txt --without-hashes --output "$PINNED_REQUIREMENTS_FILE"
-poetry export --only dev -f requirements.txt --without-hashes --output "$PINNED_DEV_REQUIREMENTS_FILE"
-poetry export --only typecheck -f requirements.txt --without-hashes --output "$this_directory/pinned-typecheck-requirements.txt"
-
-# Fix requirements
-
-latest_package_version_for_python_version () {
-    PIP_INDEX_OUT=$(pip index versions --python-version "$2" "$1")
-    echo "$PIP_INDEX_OUT" | head -n 1 | sed -e 's/.* (\(.*\)).*/\1/'
-}
-
-split_requirement () {
-    PACKAGE_NAME=$1
-
-    if ! pip index version --help >/dev/null; then
-        echo "pip >= 21.2.1 required for the 'index' command"
-        exit 1
-    fi
-
-    NEW_REQUIREMENTS=
-    PREVIOUS_LATEST_PACKAGE_VERSION=
-    for PYTHON_VERSION in $SUPPORTED_PYTHON_VERSIONS; do
-        LATEST_PACKAGE_VERSION=$(latest_package_version_for_python_version "$PACKAGE_NAME" "$PYTHON_VERSION")
-        if [ -z "$NEW_REQUIREMENTS" ]; then
-            NEW_REQUIREMENTS="$PACKAGE_NAME==$LATEST_PACKAGE_VERSION ; python_version >= \"$PYTHON_VERSION\""
-        elif [ "$LATEST_PACKAGE_VERSION" != "$PREVIOUS_LATEST_PACKAGE_VERSION" ]; then
-            NEW_REQUIREMENTS="$NEW_REQUIREMENTS and python_version < \"$PYTHON_VERSION\"\n$PACKAGE_NAME==$LATEST_PACKAGE_VERSION ; python_version >= \"$PYTHON_VERSION\""
-        fi
-        PREVIOUS_LATEST_PACKAGE_VERSION=$LATEST_PACKAGE_VERSION
-    done
-    if [ -n "$NOT_SUPPORTED_NEXT_PYTHON_VERSION" ]; then
-        NEW_REQUIREMENTS="$NEW_REQUIREMENTS and python_version < \"$NOT_SUPPORTED_NEXT_PYTHON_VERSION\""
-    fi
-
-    sed -i.orig -e "s/^$PACKAGE_NAME==.*/$NEW_REQUIREMENTS/" "$PINNED_REQUIREMENTS_FILE" "$PINNED_DEV_REQUIREMENTS_FILE"
-}
-
-# For some packages there is no recent version that works on all Python versions
-# supported by Galaxy, so Poetry resorts to an old version. Here we replace any
-# such requirement with multiple Python-version-specific requirements.
-split_requirement contourpy
-split_requirement h5py
-split_requirement matplotlib
-split_requirement numpy
-split_requirement scipy
+${uv} export --no-hashes --no-dev > "$this_directory/pinned-requirements.txt"
+${uv} export --no-hashes --only-group=dev > "$this_directory/dev-requirements.txt"
+${uv} export --no-hashes --only-group=typecheck > "$this_directory/pinned-typecheck-requirements.txt"