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Shellcheck fixes

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This commit is contained in:
Nicola Soranzo
2025-10-29 18:45:26 +00:00
parent 6cf9d49c8a
commit f20306b03b
6 changed files with 87 additions and 64 deletions
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lib/galaxy/dependencies/update.sh
+4
View File
@@ -47,7 +47,11 @@ fi
# Update pinned requirements files.
UV_EXPORT_OPTIONS='--frozen --no-annotate --no-hashes'
# shellcheck disable=SC2086
${uv} export ${UV_EXPORT_OPTIONS} --no-dev > "$this_directory/pinned-requirements.txt"
# shellcheck disable=SC2086
${uv} export ${UV_EXPORT_OPTIONS} --only-group=test > "$this_directory/pinned-test-requirements.txt"
# shellcheck disable=SC2086
${uv} export ${UV_EXPORT_OPTIONS} --only-group=dev > "$this_directory/dev-requirements.txt"
# shellcheck disable=SC2086
${uv} export ${UV_EXPORT_OPTIONS} --only-group=typecheck > "$this_directory/pinned-typecheck-requirements.txt"
packages/package-build-install.sh
+29 -25
View File
@@ -7,8 +7,8 @@
#
set -euo pipefail
: ${PACKAGE_LIST_FILE:=packages_by_dep_dag.txt}
: ${PIP_EXTRA_ARGS:=--extra-index-url https://wheels.galaxyproject.org}
: "${PACKAGE_LIST_FILE:=packages_by_dep_dag.txt}"
: "${PIP_EXTRA_ARGS:=--extra-index-url https://wheels.galaxyproject.org}"
#: ${SETUP_VENV:=true}
INSTALL=true
@@ -26,7 +26,7 @@ fi
# Prevent making a venv for build deps for each package, Used inside the package dir, so refers to
# <source_root>/packages/.venv
: ${VENV=../.venv}
: "${VENV=../.venv}"
export VENV
trap_handler() {
@@ -36,42 +36,45 @@ trap_handler() {
}
trap trap_handler EXIT
usage() {
echo "usage: $0 [-bem] [up_to_package]"
echo " -b build only, no install"
echo " -e install packages in \"editable\" mode (pip install -e)"
echo " -m install galaxy metapackage, installing pinned deps in meta/requirements.txt"
}
while getopts ':bhem' OPTION
do
case $OPTION in
b)
INSTALL=false
;;
h)
echo "usage: $0 [-bem] [up_to_package]"
echo " -b build only, no install"
echo " -e install packages in \"editable\" mode (pip install -e)"
echo " -m install galaxy metapackage, installing pinned deps in meta/requirements.txt"
exit 0
;;
e)
EDITABLE=true
INSTALL=true
;;
m)
META=true
;;
b) INSTALL=false
;;
h) usage
exit 0
;;
e) EDITABLE=true
INSTALL=true
;;
m) META=true
;;
?) usage
exit 2
;;
esac
done
shift $((OPTIND - 1))
up_to="${1:-}"
if [ -n "$up_to" -a ! -d "$up_to" ]; then
if [ -n "$up_to" ] && [ ! -d "$up_to" ]; then
echo "ERROR: package does not exist: $up_to"
exit 1
fi
while read package; do
while read -r package; do
[ -n "$package" ] || continue
if $INSTALL && [[ $package == meta ]] && ! $META; then continue; fi
printf "\n========= PACKAGE %s =========\n\n" "$package"
pushd $package
pushd "$package"
if $EDITABLE; then
${PIP_CMD} install -e .
else
@@ -90,6 +93,7 @@ done < "$PACKAGE_LIST_FILE"
if $INSTALL && $META && ! $EDITABLE; then
WHEELHOUSE=$(mktemp -d -t gxpkgwheelhouseXXXXXX)
cp */dist/*.whl "$WHEELHOUSE"
${PIP_CMD} install $PIP_EXTRA_ARGS --find-links "$WHEELHOUSE" meta/dist/*.whl
cp ./*/dist/*.whl "$WHEELHOUSE"
# shellcheck disable=SC2086
${PIP_CMD} install ${PIP_EXTRA_ARGS} --find-links "$WHEELHOUSE" meta/dist/*.whl
fi
packages/test.sh
+2 -2
View File
@@ -11,8 +11,8 @@ SKIP_PACKAGES=(
should_skip_package() {
local pkg
for pkg in ${SKIP_PACKAGES[@]}; do
[[ $1 == $pkg ]] && return 0
for pkg in "${SKIP_PACKAGES[@]}"; do
[ "$1" = "$pkg" ] && return 0
done
return 1
}
scripts/common_startup.sh
+1 -1
View File
@@ -267,7 +267,7 @@ if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
# Set plugin path
GALAXY_PLUGIN_PATH=$(python scripts/config_parse.py --setting=plugin_path --config-file="$GALAXY_CONFIG_FILE")
if [ $INSTALL_PREBUILT_CLIENT -eq 0 ]; then
if [ "${INSTALL_PREBUILT_CLIENT}" -eq 0 ]; then
# If we have not opted to use a prebuilt client, then build client.
cd client
# shellcheck disable=SC2086
scripts/release.sh
+40 -28
View File
@@ -5,27 +5,27 @@ shopt -s extglob
# TODO: upload packages
# TODO: set dev version in 21.01 (+ 20.09?) branches
: ${VENV:=.venv}
: ${FORK_REMOTE:=origin}
: ${UPSTREAM_REMOTE:=upstream}
: ${UPSTREAM_REMOTE_URL:=git@github.com:galaxyproject/galaxy.git}
: ${DEV_BRANCH:=dev}
: ${STABLE_BRANCH:=master}
: "${VENV:=.venv}"
: "${FORK_REMOTE:=origin}"
: "${UPSTREAM_REMOTE:=upstream}"
: "${UPSTREAM_REMOTE_URL:=git@github.com:galaxyproject/galaxy.git}"
: "${DEV_BRANCH:=dev}"
: "${STABLE_BRANCH:=master}"
# Vars for local releases
: ${RELEASE_LOCAL_TAG:=local}
: ${RELEASE_LOCAL_COMMIT:=$(git rev-parse --short HEAD)}
: ${RELEASE_LOCAL_VERSION:=${RELEASE_LOCAL_TAG}$(date -u +%Y%m%dT%H%M%SZ).${RELEASE_LOCAL_COMMIT}}
: "${RELEASE_LOCAL_TAG:=local}"
: "${RELEASE_LOCAL_COMMIT:=$(git rev-parse --short HEAD)}"
: "${RELEASE_LOCAL_VERSION:=${RELEASE_LOCAL_TAG}$(date -u +%Y%m%dT%H%M%SZ).${RELEASE_LOCAL_COMMIT}}"
# Only use this for dev/testing/CI to ignore forward merge conflicts, skip confirmation and package builds, etc.
: ${TEST_MODE:=false}
: "${TEST_MODE:=false}"
$TEST_MODE && MERGE_STRATEGY_OPTIONS='-X ours' || MERGE_STRATEGY_OPTIONS=
VERIFY_PACKAGES=(wheel packaging)
BRANCH_CURR=$(git branch --show-current)
: ${RELEASE_CURR:=$(grep '^VERSION_MAJOR' lib/galaxy/version.py | sed -E -e "s/^[^'\"]*['\"]([^'\"]*)['\"]$/\1/")}
: "${RELEASE_CURR:=$(grep '^VERSION_MAJOR' lib/galaxy/version.py | sed -E -e "s/^[^'\"]*['\"]([^'\"]*)['\"]$/\1/")}"
RELEASE_NEXT=
RELEASE_CURR_MINOR=
RELEASE_CURR_MINOR_NEXT=
@@ -70,7 +70,6 @@ done
function trap_handler() {
{ set +x; } 2>/dev/null
local file
$ERROR && log_func=log_error || log_func=log
$log_func "Cleaning up..."
if $WORKING_DIR_CLEAN; then
@@ -140,7 +139,8 @@ function sed_inplace() {
function fork_owner() {
local url=$(git remote get-url "$FORK_REMOTE")
local url
url=$(git remote get-url "$FORK_REMOTE")
case "$url" in
https://github.com/*)
echo "$url" | awk -F/ '{print $4}'
@@ -182,7 +182,7 @@ function ensure_prereqs() {
else
pip_list=$(log_exec "${VENV}/bin/pip" list)
fi
for package in ${VERIFY_PACKAGES[@]}; do
for package in "${VERIFY_PACKAGES[@]}"; do
echo "$pip_list" | grep -E "^${package}\s+" || { log_error "Package '${package}' missing from venv: ${VENV}" ; exit 1; }
done
}
@@ -257,7 +257,8 @@ function branch_exists() {
function _test_forward_merge() {
local curr="$1"
local next="$(release_next "$curr")"
local next
next=$(release_next "$curr")
local curr_branch="${UPSTREAM_REMOTE}/release_${curr}"
local next_branch="${UPSTREAM_REMOTE}/release_${next}"
local curr_local_branch="__release_merge_test_${curr}"
@@ -274,6 +275,7 @@ function _test_forward_merge() {
fi
git_checkout_temp "$next_local_branch" "$next_branch"
# Test the merge even if ignoring just to test the code path
# shellcheck disable=SC2086
log_exec git merge $MERGE_STRATEGY_OPTIONS -m 'test merge; please ignore' "$curr_local_branch" || {
log_error "Merging unmodified ${curr} to ${next} failed, resolve upstream first!"; exit 1; }
if $recurse; then
@@ -283,21 +285,27 @@ function _test_forward_merge() {
function test_forward_merge() {
local branch_curr=$(git branch --show-current)
local branch_curr
branch_curr=$(git branch --show-current)
_test_forward_merge "$@"
git checkout "$branch_curr"
}
function perform_stable_merge() {
[ "$RELEASE_TYPE" == 'initial' -o "$RELEASE_TYPE" == 'point' ] || return 0
local branch_curr=$(git branch --show-current)
[ "$RELEASE_TYPE" == 'initial' ] || [ "$RELEASE_TYPE" == 'point' ] || return 0
local branch_curr
branch_curr=$(git branch --show-current)
git_checkout_temp '__stable' "${UPSTREAM_REMOTE}/${STABLE_BRANCH}"
local stable=$(get_version_major)
local curr_int=$(echo "$RELEASE_CURR" | tr -d .)
local stable_int=$(echo "$stable" | tr -d .)
local stable
stable=$(get_version_major)
local curr_int
curr_int=$(echo "$RELEASE_CURR" | tr -d .)
local stable_int
stable_int=$(echo "$stable" | tr -d .)
if [ "$curr_int" -ge "$stable_int" ]; then
log "Release '${RELEASE_CURR}' >= stable branch release '${stable}', merging 'release_${RELEASE_CURR}' to '${STABLE_BRANCH}'"
# shellcheck disable=SC2086
log_exec git merge $MERGE_STRATEGY_OPTIONS -m "Merge branch 'release_${RELEASE_CURR}' into '${STABLE_BRANCH}'" "__release_${RELEASE_CURR}"
PUSH_BRANCHES+=("__stable:${STABLE_BRANCH}")
else
@@ -309,7 +317,8 @@ function perform_stable_merge() {
function _perform_forward_merge() {
local curr="$1"
local next="$(release_next "$curr")"
local next
next="$(release_next "$curr")"
local curr_branch="${UPSTREAM_REMOTE}/release_${curr}"
local next_branch="${UPSTREAM_REMOTE}/release_${next}"
local curr_local_branch="__release_${curr}"
@@ -335,7 +344,8 @@ function _perform_forward_merge() {
function perform_forward_merge() {
local curr="$1"
local branch_curr=$(git branch --show-current)
local branch_curr
branch_curr=$(git branch --show-current)
_perform_forward_merge "$@"
declare -p PUSH_BRANCHES
git checkout "$branch_curr"
@@ -348,7 +358,7 @@ function push_merged() {
log "Pushing '${branch}' to remote '${UPSTREAM_REMOTE}'"
log_exec git push "$UPSTREAM_REMOTE" "$branch"
done
if [ "$RELEASE_TYPE" == 'initial' -o "$RELEASE_TYPE" == 'point' ]; then
if [ "$RELEASE_TYPE" == 'initial' ] || [ "$RELEASE_TYPE" == 'point' ]; then
log_exec git push --tags "$UPSTREAM_REMOTE"
fi
}
@@ -448,7 +458,7 @@ function packages_make_all() {
(
cd packages/
for dir in *; do
[ ! -d "$dir" -o ! -f "${dir}/setup.cfg" ] && continue
[ ! -d "$dir" ] || [ ! -f "${dir}/setup.cfg" ] && continue
# can't use log_exec here because we want to capture output
echo + make -C "$dir" "$@" 1>&2
make -C "$dir" "$@" >"${dir}/make-${1}.log" 2>&1
@@ -504,7 +514,7 @@ function perform_version_update() {
function perform_version_update_dev() {
[ "$RELEASE_TYPE" == 'initial' -o "$RELEASE_TYPE" == 'point' ] || return 0
[ "$RELEASE_TYPE" == 'initial' ] || [ "$RELEASE_TYPE" == 'point' ] || return 0
log "Incrementing release version to '${RELEASE_CURR}.${RELEASE_CURR_MINOR_NEXT_DEV}' for development of next point release"
update_galaxy_version 'VERSION_MINOR' "$RELEASE_CURR_MINOR_NEXT_DEV"
log_exec git diff --exit-code && { log_error 'Missing expected version.py changes'; exit 1; } || true
@@ -542,7 +552,8 @@ function create_release_rc_initial() {
sed_inplace -e "s/^RELEASE_CURR:=.*/RELEASE_CURR:=${RELEASE_NEXT}/" Makefile
log_exec git diff --exit-code && { log_error 'Missing expected Makefile changes'; exit 1; } || true
git add -- Makefile
local package_version=$(packaging_version "${RELEASE_NEXT}.0dev0" "true")
local package_version
package_version=$(packaging_version "${RELEASE_NEXT}.0dev0" "true")
update_package_versions "$package_version"
git add -- packages/
log_exec git commit -m "Update version to ${RELEASE_NEXT}.dev0"
@@ -551,7 +562,8 @@ function create_release_rc_initial() {
log_exec git merge -X ours -m "Merge branch 'release_${RELEASE_CURR}' into 'dev'" "__release_${RELEASE_CURR}"
# Push branches for PR
local owner=$(fork_owner)
local owner
owner=$(fork_owner)
local curr_remote_branch="version-${RELEASE_CURR}.${RELEASE_CURR_MINOR_NEXT}"
local next_remote_branch="version-${RELEASE_NEXT}.dev"
log_exec git push "$FORK_REMOTE" "__release_${RELEASE_CURR}:${curr_remote_branch}"
test/release.sh
+11 -8
View File
@@ -4,8 +4,8 @@ set -euo pipefail
# Necessary for testing the release script
export TEST_MODE=true
: ${ORIGIN:=origin}
: ${STABLE_BRANCH:=master}
: "${ORIGIN:=origin}"
: "${STABLE_BRANCH:=master}"
REPO_ROOT=
FORK_ROOT=$(mktemp -d -t galaxy_release_test_XXXXXXXX)
@@ -16,7 +16,7 @@ TEST_RELEASE_CURR='99.0'
TEST_RELEASE_NEXT='99.1'
TEST_RELEASE_NEXT_NEXT='99.2'
: ${VENV:=${FORK_ROOT}/venv}
: "${VENV:=${FORK_ROOT}/venv}"
export VENV
@@ -60,7 +60,8 @@ function get_stable_version() {
local part="$1"
(
cd_fork work
local restore_branch="$(git branch --show-current)"
local restore_branch
restore_branch="$(git branch --show-current)"
git checkout -q --no-track -b __stable_version_check "upstream/${STABLE_BRANCH}"
grep "^VERSION_${part}" lib/galaxy/version.py | sed -E -e "s/^[^'\"]*['\"]([^'\"]*)['\"]$/\1/"
git checkout -q "$restore_branch"
@@ -148,8 +149,9 @@ function verify_version() {
local minor="$2"
local ref="$3"
local _ref="$3"
local restore_branch="$(git branch --show-current)"
[ -n "$(git tag -l $ref)" ] || _ref="upstream/${ref}"
local restore_branch
restore_branch="$(git branch --show-current)"
[ -n "$(git tag -l "$ref")" ] || _ref="upstream/${ref}"
log_exec git checkout --no-track -b "__${ref}" "$_ref"
if grep -q "^VERSION_MAJOR = \"${major}\"$" lib/galaxy/version.py; then
log "**** Major version '${major}' is correct at ref '${ref}'"
@@ -174,8 +176,9 @@ function verify_makefile_version() {
local major="$1"
local ref="$2"
local _ref="$2"
local restore_branch="$(git branch --show-current)"
[ -n "$(git tag -l $ref)" ] || _ref="upstream/${ref}"
local restore_branch
restore_branch="$(git branch --show-current)"
[ -n "$(git tag -l "$ref")" ] || _ref="upstream/${ref}"
log_exec git checkout --no-track -b "__${ref}" "$_ref"
if grep -q "^RELEASE_CURR:=${major}$" Makefile; then
log "**** RELEASE_CURR '${major}' is correct in Makefile at ref '${ref}'"