Reduce command duplications

lib/galaxy/dependencies/update_lint_requirements.sh

@@ -8,22 +8,26 @@ set -e
 
 THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
 
+if command -v uv >/dev/null; then
+    VENV_CMD="$(command -v uv) venv --python python3.9"
+    PIP_CMD="$(command -v uv) pip"
+    FREEZE_OPTIONS=''
+else
+    VENV_CMD='python3.9 -m venv'
+    PIP_CMD='python -m pip'
+    FREEZE_OPTIONS='-l'
+fi
+
 update_pinned_reqs() {
     VENV=$(mktemp -d "${TMPDIR:-/tmp}/$1_venv.XXXXXXXXXX")
-    if command -v uv >/dev/null; then
-        uv self update
-        uv venv "${VENV}" --python python3.9
-        . "${VENV}/bin/activate"
-        uv pip install -r "${THIS_DIRECTORY}/$1-requirements.txt"
-        uv pip freeze | grep -v 'pkg_resources==0.0.0' > "${THIS_DIRECTORY}/pinned-$1-requirements.txt"
-    else
-        python3.9 -m venv "${VENV}"
-        . "${VENV}/bin/activate"
-        pip install --upgrade pip setuptools
-        pip install -r "${THIS_DIRECTORY}/$1-requirements.txt"
-        # The grep below is needed to workaround https://github.com/pypa/pip/issues/8331
-        pip freeze -l | grep -v 'pkg_resources==0.0.0' > "${THIS_DIRECTORY}/pinned-$1-requirements.txt"
+    ${VENV_CMD} "${VENV}"
+    . "${VENV}/bin/activate"
+    if [ "${PIP_CMD}" = 'python -m pip' ]; then
+        ${PIP_CMD} install --upgrade pip setuptools
     fi
+    ${PIP_CMD} install -r "${THIS_DIRECTORY}/$1-requirements.txt"
+    # The grep below is needed to workaround https://github.com/pypa/pip/issues/8331
+    ${PIP_CMD} freeze ${FREEZE_OPTIONS} | grep -v 'pkg_resources==0.0.0' > "${THIS_DIRECTORY}/pinned-$1-requirements.txt"
     rm -rf "${VENV}"
 }
 

packages/package-build-install.sh

@@ -16,6 +16,14 @@ EDITABLE=false
 META=false
 WHEELHOUSE=
 
+if command -v uv >/dev/null; then
+    VENV_CMD="$(command -v uv) venv"
+    PIP_CMD="$(command -v uv) pip"
+else
+    VENV_CMD='python3 -m venv'
+    PIP_CMD='pip'
+fi
+
 # Prevent making a venv for build deps for each package, Used inside the package dir, so refers to
 # <source_root>/packages/.venv
 : ${VENV=../.venv}
@@ -65,28 +73,15 @@ while read package; do
     printf "\n========= PACKAGE %s =========\n\n" "$package"
     pushd $package
     if $EDITABLE; then
-        if command -v uv >/dev/null; then
-            uv pip install -e .
-        else
-            pip install -e .
-        fi
+        ${PIP_CMD} install -e .
     else
         if [ ! -d "$VENV" ]; then
-            if command -v uv >/dev/null; then
-                uv venv "$VENV"
-                VIRTUAL_ENV="${VENV}" uv pip install -r dev-requirements.txt
-            else
-                python3 -m venv "$VENV"
-                "${VENV}/bin/pip" install -r dev-requirements.txt
-            fi
+            ${VENV_CMD} "$VENV"
+            VIRTUAL_ENV="${VENV}" ${PIP_CMD} install -r dev-requirements.txt
         fi
         make dist
         if $INSTALL && ! $META; then
-            if command -v uv >/dev/null; then
-                uv pip install dist/*.whl
-            else
-                pip install dist/*.whl
-            fi
+            ${PIP_CMD} install dist/*.whl
         fi
     fi
     popd
@@ -96,9 +91,5 @@ done < "$PACKAGE_LIST_FILE"
 if $INSTALL && $META && ! $EDITABLE; then
     WHEELHOUSE=$(mktemp -d -t gxpkgwheelhouseXXXXXX)
     cp */dist/*.whl "$WHEELHOUSE"
-    if command -v uv >/dev/null; then
-        uv pip install $PIP_EXTRA_ARGS --find-links "$WHEELHOUSE" meta/dist/*.whl
-    else
-        pip install $PIP_EXTRA_ARGS --find-links "$WHEELHOUSE" meta/dist/*.whl
-    fi
+    ${PIP_CMD} install $PIP_EXTRA_ARGS --find-links "$WHEELHOUSE" meta/dist/*.whl
 fi

packages/test.sh

@@ -37,20 +37,20 @@ TEST_PYTHON=${TEST_PYTHON:-"python3"}
 TEST_ENV_DIR=${TEST_ENV_DIR:-$(mktemp -d -t gxpkgtestenvXXXXXX)}
 
 if command -v uv >/dev/null; then
-    uv venv "$TEST_ENV_DIR" --python "$TEST_PYTHON"
-    PIP="$(command -v uv) pip"
+    uv venv --python "$TEST_PYTHON" "$TEST_ENV_DIR"
+    PIP_CMD="$(command -v uv) pip"
 else
     "$TEST_PYTHON" -m venv "$TEST_ENV_DIR"
-    PIP="pip"
+    PIP_CMD='python -m pip'
 fi
 
 # shellcheck disable=SC1091
 . "${TEST_ENV_DIR}/bin/activate"
-if ! command -v uv >/dev/null; then
-    pip install --upgrade pip setuptools wheel
+if [ "${PIP_CMD}" = 'python -m pip' ]; then
+    ${PIP_CMD} install --upgrade pip setuptools wheel
 fi
 if [ $FOR_PULSAR -eq 0 ]; then
-    ${PIP} install -r ../lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+    ${PIP_CMD} install -r ../lib/galaxy/dependencies/pinned-typecheck-requirements.txt
 fi
 
 # Ensure ordered by dependency DAG
@@ -74,13 +74,13 @@ while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.
 
     # Install extras (if needed)
     if [ "$package_dir" = "util" ]; then
-        ${PIP} install '.[image-util,template,jstree,config-template,test]'
+        ${PIP_CMD} install '.[image-util,template,jstree,config-template,test]'
     elif [ "$package_dir" = "tool_util" ]; then
-        ${PIP} install '.[cwl,mulled,edam,extended-assertions,test]'
+        ${PIP_CMD} install '.[cwl,mulled,edam,extended-assertions,test]'
     elif grep -q 'test =' setup.cfg 2>/dev/null; then
-        ${PIP} install '.[test]'
+        ${PIP_CMD} install '.[test]'
     else
-        ${PIP} install .
+        ${PIP_CMD} install .
     fi
 
     if [ $FOR_PULSAR -eq 0 ]; then

scripts/common_startup.sh

@@ -133,7 +133,7 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
             echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_VIRTUAL_ENV to an"
             echo "existing environment before starting Galaxy."
             if command -v uv >/dev/null; then
-                uv venv "$GALAXY_VIRTUAL_ENV" --python "$GALAXY_PYTHON"
+                uv venv --python "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
             else
                 # First try to use the venv standard library module, although it is
                 # not always installed by default on Linux distributions.
@@ -168,6 +168,14 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
     fi
 fi
 
+if command -v uv >/dev/null; then
+    PIP_CMD="$(command -v uv) pip"
+    UNINSTALL_OPTIONS=''
+else
+    PIP_CMD='python -m pip'
+    UNINSTALL_OPTIONS='--yes'
+fi
+
 # activate virtualenv or conda env, sets $GALAXY_VIRTUAL_ENV and $GALAXY_CONDA_ENV
 setup_python
 
@@ -188,32 +196,19 @@ fi
 [ "$CI" = 'true' ] && export PIP_PROGRESS_BAR=off
 
 if [ $FETCH_WHEELS -eq 1 ]; then
-    if command -v uv >/dev/null; then
-        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 uv pip list --format=columns | 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."
-                uv pip uninstall psycopg2 psycopg2-binary
-            fi
-            echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | uv pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
-        fi
-    else
-        python -m pip install "pip>=$MIN_PIP_VERSION" wheel
-        # shellcheck disable=SC2086
-        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
-                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
-            fi
-            echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
+    if [ "${PIP_CMD}" = 'python -m pip' ]; 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 "${PYPI_INDEX_URL}"
+    set_galaxy_config_file_var
+    GALAXY_CONDITIONAL_DEPENDENCIES=$(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_CMD} list --format=columns | 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_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}"
     fi
 fi