Enhance package management by integrating 'uv' for faster installation and virtual environment creation across scripts

scripts/common_startup.sh

@@ -4,6 +4,22 @@ set -e
 # The caller may do this as well, but since common_startup.sh can be called independently, we need to do it here
 . ./scripts/common_startup_functions.sh
 
+# Ensure uv is installed (used throughout this script)
+ensure_uv() {
+    if ! command -v uv >/dev/null; then
+        echo "Installing uv..."
+        local python_cmd="${1:-python3}"
+        if command -v curl >/dev/null; then
+            curl -LsSf https://astral.sh/uv/install.sh | sh || "$python_cmd" -m pip install "uv>=${MIN_UV_VERSION}"
+        elif command -v wget >/dev/null; then
+            wget -qO- https://astral.sh/uv/install.sh | sh || "$python_cmd" -m pip install "uv>=${MIN_UV_VERSION}"
+        else
+            "$python_cmd" -m pip install "uv>=${MIN_UV_VERSION}"
+        fi
+        export PATH="$HOME/.local/bin:$PATH"
+    fi
+}
+
 DEV_WHEELS=0
 FETCH_WHEELS=1
 CREATE_VENV=1
@@ -38,7 +54,7 @@ RMFILES="
 "
 
 MIN_PYTHON_VERSION=3.9
-MIN_PIP_VERSION=20.3
+MIN_UV_VERSION=0.5.0
 
 # return true if $1 is in $2 else false
 in_dir() {
@@ -112,12 +128,15 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
                     echo "Creating Conda environment for Galaxy: $GALAXY_CONDA_ENV"
                     echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_CONDA_ENV to an"
                     echo "existing environment before starting Galaxy."
-                    $CONDA_EXE create --yes --override-channels --channel conda-forge --name "$GALAXY_CONDA_ENV" "python=${GALAXY_CONDA_PYTHON_VERSION}" "pip>=${MIN_PIP_VERSION}"
+                    # Note: uv will be installed via standalone installer, not conda
+                    $CONDA_EXE create --yes --override-channels --channel conda-forge --name "$GALAXY_CONDA_ENV" "python=${GALAXY_CONDA_PYTHON_VERSION}"
                     unset __CONDA_INFO
                 fi
                 conda_activate
             fi
-            python3 -m venv "$GALAXY_VIRTUAL_ENV"
+            # Install uv first if not available, then use uv venv for fast virtual environment creation
+            ensure_uv python
+            uv venv "$GALAXY_VIRTUAL_ENV" --python python3
         else
             # If $GALAXY_VIRTUAL_ENV does not exist, and there is no conda available, attempt to create it.
 
@@ -128,15 +147,18 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
             echo "using Python: $GALAXY_PYTHON"
             echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_VIRTUAL_ENV to an"
             echo "existing environment before starting Galaxy."
-            # First try to use the venv standard library module, although it is
-            # not always installed by default on Linux distributions.
-            if ! "$GALAXY_PYTHON" -m venv "$GALAXY_VIRTUAL_ENV"; then
-                echo "Creating the Python virtual environment using the venv standard library module failed."
-                echo "Trying with virtualenv now."
+            
+            # Install uv first if not available, then use uv venv for fast virtual environment creation
+            ensure_uv "$GALAXY_PYTHON"
+            
+            # Use uv venv for much faster virtual environment creation
+            if ! uv venv "$GALAXY_VIRTUAL_ENV" --python "$GALAXY_PYTHON"; then
+                echo "Creating the Python virtual environment using uv failed."
+                echo "Trying with virtualenv now as fallback."
                 if command -v virtualenv >/dev/null; then
                     virtualenv -p "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
                 else
-                    # Download virtualenv zipapp
+                    # Download virtualenv zipapp as last resort
                     vurl="https://bootstrap.pypa.io/virtualenv/${MIN_PYTHON_VERSION}/virtualenv.pyz"
                     vtmp=$(mktemp -d -t galaxy-virtualenv-XXXXXX)
                     vsrc="$vtmp/$(basename $vurl)"
@@ -180,18 +202,22 @@ fi
 [ "$CI" = 'true' ] && export PIP_PROGRESS_BAR=off
 
 if [ $FETCH_WHEELS -eq 1 ]; then
-    python -m pip install "pip>=$MIN_PIP_VERSION" wheel
+    # Ensure uv is installed - uv is much faster than pip (10-100x)
+    ensure_uv python
+    
+    # Use uv pip install for fast package installation
+    # Note: uv pip install is significantly faster than pip install
     # shellcheck disable=SC2086
-    pip install $requirement_args --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
+    uv pip install $requirement_args --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_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
-        if pip list --format=columns | grep "psycopg2[\(\ ]*2.7.3" > /dev/null; then
+        if uv pip list | grep "psycopg2[\(\ ]*2.7.3" > /dev/null; 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 uninstall -y psycopg2 psycopg2-binary
+            uv pip uninstall psycopg2 psycopg2-binary
         fi
-        echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
+        echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | uv pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
     fi
 fi