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Fix lint job stopping early after first failure #55

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merged 5 commits into from
Dec 16, 2023
Merged

Fix lint job stopping early after first failure #55

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f54763c
test commit
bernt-matthias Dec 15, 2023
da9a8bc
set fail level warn in linter test
bernt-matthias Dec 15, 2023
fcc0286
lint: do not exit on first failing tool
bernt-matthias Dec 15, 2023
0fd5575
fix for pipefail
bernt-matthias Dec 15, 2023
0f832f1
Reduce magic
bernt-matthias Dec 16, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/tools.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ jobs:
with:
mode: lint
report-level: all
fail-level: error
fail-level: warn
repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }}
tool-list: ${{ needs.setup-ci-tools.outputs.tool-list }}
additional-planemo-options: --report_level all
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11 changes: 7 additions & 4 deletions planemo_ci_actions.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -109,24 +109,27 @@ fi
# - call `planemo lint` for each repo
# - check if each tool is in a repo (i.e. if `.shed.yml` is present)
if [ "$MODE" == "lint" ]; then
lint_fail=false
mapfile -t REPO_ARRAY < repository_list.txt
for DIR in "${REPO_ARRAY[@]}"; do
if [ "$WORKFLOWS" != "true" ]; then
planemo shed_lint --tools --ensure_metadata --urls --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" --recursive "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt
(planemo shed_lint --tools --ensure_metadata --urls --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" --recursive "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt) || lint_fail=true
else
planemo workflow_lint --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt
(planemo workflow_lint --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt) || lint_fail=true
fi
done

# Check if each changed tool is in the list of changed repositories
mapfile -t TOOL_ARRAY < tool_list.txt
for TOOL in "${TOOL_ARRAY[@]}"; do
# Check if any changed repo dir is a substring of $TOOL
if ! echo "$TOOL" | grep -qf repository_list.txt; then
echo "Tool $TOOL not in changed repositories list: .shed.yml file missing" >&2
exit 1
lint_fail=true
fi
done
if [ "$lint_fail" = "true" ]; then
exit 1
fi
fi

# test mode
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