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richard-burhans/galaxy-tool-refactor

https://github.com/richard-burhans/galaxy-tool-refactor · scanned 2026-06-15 23:51 UTC (2 months, 3 weeks ago)

141 raw signals (0 security + 141 graph)

File as issue Image

UNIFIED Repobility · multi-layer engine · AI coders

Complete repo analysis

Last scanned 2 months, 3 weeks ago · v1 · 119 actionable findings from 1 signal source. 22 repeated signals grouped for readability. Security checks, system graph analysis, and verified AI-agent feedback are merged into one review queue.

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88.9% cov · 119 findings

Severity distribution — click a segment to filter

Active filters: excluding tests × Reset all

Severity: Critical 0 High 2 Medium 16 Low 71 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 119 Crowd 0 Layer: Software 11 Frontend 1 Cicd 4 Quality 101 Security 2

Exclude dismissed / FP Exclude test files

All 7614 nodes from the latest scan, grouped by kind. Each node is a unit the engine identified (file, function, endpoint, table…). Most users won't need this view — it's primarily for debugging the engine's graph extraction or for AI agents that want to enumerate the project structure.

Label	Layer	Status	Path
`TransformOutcome`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/cli_support.py:29`
`Action`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/cli_support.py:45`
`RunOptions`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/cli_support.py:58`
`Counts`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/cli_support.py:84`
`CanonicalIndent`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/rule_indent.py:53`
`NoOp`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/edits.py:29`
`SetText`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/edits.py:34`
`SetTail`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/edits.py:47`
`ClearText`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/edits.py:55`
`EmptyElementShorthand`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/rule_empty_element.py:48`
`BlankLineBetweenSections`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/rule_blank_line.py:31`
`Rule`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/rules.py:40`
`Suggestion`	software	healthy	`galaxy-tool-refactor-cli/src/galaxy_tool_refactor_cli/gate_…`
`SuggestResult`	software	healthy	`galaxy-tool-refactor-cli/src/galaxy_tool_refactor_cli/gate_…`
`DetectCoincidence`	software	healthy	`scripts/pr_impact.py:124`
`FixCoincidence`	software	healthy	`scripts/pr_impact.py:135`
`PrImpactResult`	software	healthy	`scripts/pr_impact.py:148`
`PrSetComposition`	software	healthy	`scripts/pr_impact.py:372`
`_LenientTextFieldsResult`	software	healthy	`scripts/measure.py:169`
`_ValidityDistributionResult`	software	healthy	`scripts/measure.py:179`
`_ExpansionFailedIdsResult`	software	healthy	`scripts/measure.py:192`
`_MacroPlaceholderProfileResult`	software	healthy	`scripts/measure.py:199`
`_ToolIdVsPathResult`	software	healthy	`scripts/measure.py:206`
`_CorpusSizeSourceMixResult`	software	healthy	`scripts/measure.py:215`
`_NoValidProfileTaxonomyResult`	software	healthy	`scripts/measure.py:228`
`_MacroUsageResult`	software	healthy	`scripts/measure.py:236`
`_CrossSourcePresenceResult`	software	healthy	`scripts/measure.py:244`
`_CorrectionsResult`	software	healthy	`scripts/measure.py:261`
`_ParamTypesResult`	software	healthy	`scripts/measure.py:271`
`_CollectionTypeNormalizationResult`	software	healthy	`scripts/measure.py:278`
`_MacroProfileTokensResult`	software	healthy	`scripts/measure.py:823`
`_MacroFileFacts`	software	healthy	`scripts/measure.py:947`
`_MacroTopologyResult`	software	healthy	`scripts/measure.py:955`
`_ProfileOwnershipResult`	software	healthy	`scripts/measure.py:1474`
`_CommandIucHeuristicsResult`	software	healthy	`scripts/measure.py:1799`
`_LoneAmpResult`	software	healthy	`scripts/measure.py:1908`
`_UnquotedVarResult`	software	healthy	`scripts/measure.py:2032`
`_Iuc011FixabilityResult`	software	healthy	`scripts/measure.py:2108`
`_CommandQuotingKindsResult`	software	healthy	`scripts/measure.py:2232`
`_TextParamQuotableResult`	software	healthy	`scripts/measure.py:2551`
`_SelectQuotingResult`	software	healthy	`scripts/measure.py:2698`
`_ShellOracleQuotingResult`	software	healthy	`scripts/measure.py:2814`
`_VersionTokenizationResult`	software	healthy	`scripts/measure.py:2923`
`_MacroFmtIdempotenceResult`	software	healthy	`scripts/measure.py:3042`
`_UpgradeHeadroomResult`	software	healthy	`scripts/measure.py:3610`
`_SemanticBoundariesResult`	software	healthy	`scripts/measure.py:3723`
`_ApplicabilityResult`	software	healthy	`scripts/measure.py:3879`
`_SetETighteningResult`	software	healthy	`scripts/measure.py:4047`
`_ExpansionGapResult`	software	healthy	`scripts/measure.py:4133`
`_ProfileShiftResult`	software	healthy	`scripts/measure.py:4306`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`test_all_rules_returns_expected_rule_classes`	software	healthy	`galaxy-tool-fmt/tests/test_framework.py:30`
`test_all_rules_is_sorted_by_order`	software	healthy	`galaxy-tool-fmt/tests/test_framework.py:36`
`test_apply_edits_dispatches_noop_without_changing_tree`	software	healthy	`galaxy-tool-fmt/tests/test_framework.py:42`
`test_format_tool_document_is_identity_with_empty_rules`	software	healthy	`galaxy-tool-fmt/tests/test_framework.py:52`
`test_format_tool_document_does_not_import_codemod_package`	software	healthy	`galaxy-tool-fmt/tests/test_framework.py:67`
`test_format_preserves_structure_and_attributes`	software	healthy	`galaxy-tool-fmt/tests/test_framework.py:116`
`make_doc`	software	healthy	`galaxy-tool-fmt/tests/conftest.py:13`
`_build`	software	healthy	`galaxy-tool-fmt/tests/conftest.py:22`
`test_subset_with_all_rules_equals_whole_pipeline`	software	healthy	`galaxy-tool-fmt/tests/test_subset.py:41`
`test_empty_subset_serialises_unchanged`	software	healthy	`galaxy-tool-fmt/tests/test_subset.py:50`
`test_subset_runs_in_meta_order_regardless_of_input_order`	software	healthy	`galaxy-tool-fmt/tests/test_subset.py:61`
`test_detect_subset_with_all_rules_equals_whole_pipeline`	software	healthy	`galaxy-tool-fmt/tests/test_subset.py:74`
`test_detect_single_rule_subset_reports_only_that_code`	software	healthy	`galaxy-tool-fmt/tests/test_subset.py:83`
`test_rules_for_kind_filters_by_applies_to`	software	healthy	`galaxy-tool-fmt/tests/test_subset.py:94`
`test_format_macro_document_indents_and_shorthands`	software	healthy	`galaxy-tool-fmt/tests/test_subset.py:102`
`test_multiline_attributes_collapse_to_one_line`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_line_layout.py:20`
`test_many_attributes_stay_on_one_line`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_line_layout.py:38`
`test_newline_inside_attribute_value_preserved_as_entity`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_line_layout.py:55`
`test_no_newline_appears_inside_a_start_tag`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_line_layout.py:71`
`test_package_imports`	software	healthy	`galaxy-tool-fmt/tests/test_smoke.py:6`
`test_canonical_document_reports_no_violations`	software	healthy	`galaxy-tool-fmt/tests/test_detect.py:28`
`test_flat_document_reports_indent_violations`	software	healthy	`galaxy-tool-fmt/tests/test_detect.py:41`
`test_whitespace_only_leaf_reports_gtx004`	software	healthy	`galaxy-tool-fmt/tests/test_detect.py:58`
`test_detect_does_not_mutate_the_input`	software	healthy	`galaxy-tool-fmt/tests/test_detect.py:72`
`test_violation_message_is_the_owning_rules_summary`	software	healthy	`galaxy-tool-fmt/tests/test_detect.py:82`
`test_canonical_document_with_comment_reports_no_violations`	software	healthy	`galaxy-tool-fmt/tests/test_detect.py:91`
`_fixture_paths`	software	healthy	`galaxy-tool-fmt/tests/test_regressions.py:27`
`test_regression_fixture_is_idempotent`	software	healthy	`galaxy-tool-fmt/tests/test_regressions.py:43`
`test_simple_attribute_values_are_double_quoted`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_quoting.py:20`
`test_single_quoted_input_serializes_double_quoted`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_quoting.py:30`
`test_double_quote_inside_value_is_escaped_as_entity`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_quoting.py:39`
`test_single_quote_inside_value_stays_unescaped`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_quoting.py:52`
`_tree`	software	healthy	`galaxy-tool-fmt/tests/test_serializer.py:17`
`test_to_bytes_emits_no_xml_declaration`	software	healthy	`galaxy-tool-fmt/tests/test_serializer.py:21`
`test_to_bytes_drops_a_declaration_present_on_input`	software	healthy	`galaxy-tool-fmt/tests/test_serializer.py:28`
`test_to_bytes_round_trips_without_a_declaration`	software	healthy	`galaxy-tool-fmt/tests/test_serializer.py:34`
`test_to_bytes_ends_with_exactly_one_trailing_newline`	software	healthy	`galaxy-tool-fmt/tests/test_serializer.py:42`
`test_to_bytes_trailing_newline_is_idempotent`	software	healthy	`galaxy-tool-fmt/tests/test_serializer.py:50`
`test_parsed_empty_long_form_serializes_short`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:13`
`test_whitespace_only_text_collapses_to_short_form`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:22`
`test_text_content_is_preserved`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:30`
`test_element_with_children_is_not_collapsed`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:42`
`test_cdata_with_real_content_is_preserved`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:55`
`test_empty_element_shorthand_is_idempotent`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:67`
`test_whitespace_only_xml_comment_is_preserved`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:76`
`test_whitespace_only_content_bearing_text_is_preserved`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:96`
`test_whitespace_only_help_still_collapses`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:113`
`test_schema_derived_text_bearing_leaves_are_preserved`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:128`
`test_configfiles_inputs_text_is_preserved_tool_inputs_still…`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:146`
`test_macros_whitespace_still_collapses`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py:163`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`ARCHITECTURE.md`	software	healthy	`ARCHITECTURE.md`
`README.md`	software	healthy	`README.md`
`CLAUDE.md`	software	healthy	`CLAUDE.md`
`corpus_sources.json`	software	healthy	`corpus_sources.json`
`CONTRIBUTING.md`	software	healthy	`CONTRIBUTING.md`
`.readthedocs.yaml`	software	healthy	`.readthedocs.yaml`
`pyproject.toml`	software	healthy	`pyproject.toml`
`Makefile`	software	healthy	`Makefile`
`SECURITY.md`	software	healthy	`SECURITY.md`
`CHANGELOG.md`	software	healthy	`CHANGELOG.md`
`README.md`	software	healthy	`galaxy-tool-fmt/README.md`
`CLAUDE.md`	software	healthy	`galaxy-tool-fmt/CLAUDE.md`
`pyproject.toml`	software	healthy	`galaxy-tool-fmt/pyproject.toml`
`LICENSE`	software	healthy	`galaxy-tool-fmt/LICENSE`
`PLAN.md`	software	healthy	`galaxy-tool-fmt/PLAN.md`
`test_framework.py`	software	healthy	`galaxy-tool-fmt/tests/test_framework.py`
`conftest.py`	software	healthy	`galaxy-tool-fmt/tests/conftest.py`
`test_subset.py`	software	healthy	`galaxy-tool-fmt/tests/test_subset.py`
`test_attribute_line_layout.py`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_line_layout.py`
`test_smoke.py`	software	healthy	`galaxy-tool-fmt/tests/test_smoke.py`
`test_detect.py`	software	healthy	`galaxy-tool-fmt/tests/test_detect.py`
`test_regressions.py`	software	healthy	`galaxy-tool-fmt/tests/test_regressions.py`
`test_attribute_quoting.py`	software	healthy	`galaxy-tool-fmt/tests/test_attribute_quoting.py`
`test_serializer.py`	software	healthy	`galaxy-tool-fmt/tests/test_serializer.py`
`test_rule_empty_element.py`	software	healthy	`galaxy-tool-fmt/tests/test_rule_empty_element.py`
`test_rule_blank_line.py`	software	healthy	`galaxy-tool-fmt/tests/test_rule_blank_line.py`
`test_cli.py`	software	healthy	`galaxy-tool-fmt/tests/test_cli.py`
`test_rule_indent.py`	software	healthy	`galaxy-tool-fmt/tests/test_rule_indent.py`
`test_corpus_check.py`	software	healthy	`galaxy-tool-fmt/tests/test_corpus_check.py`
`decisions.md`	software	healthy	`galaxy-tool-fmt/docs/decisions.md`
`serializer.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/serializer.py`
`cli_support.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/cli_support.py`
`__init__.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/__init__.py`
`rule_indent.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/rule_indent.py`
`edits.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/edits.py`
`format.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/format.py`
`cli.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/cli.py`
`rule_empty_element.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/rule_empty_element.py`
`rule_blank_line.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/rule_blank_line.py`
`rules.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/rules.py`
`payload.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/payload.py`
`detect.py`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt/detect.py`
`galaxy_server_versions.json`	software	healthy	`docs/galaxy_server_versions.json`
`data_sources.md`	software	healthy	`docs/data_sources.md`
`architecture_audit.md`	software	healthy	`docs/architecture_audit.md`
`galaxy_reimplementations.md`	software	healthy	`docs/galaxy_reimplementations.md`
`macro_format_residual_stats.md`	software	healthy	`docs/macro_format_residual_stats.md`
`deferred_fix_opportunities.md`	software	healthy	`docs/deferred_fix_opportunities.md`
`iuc_conference_talking_points.md`	software	healthy	`docs/iuc_conference_talking_points.md`
`interpreter_bucket_stats.md`	software	healthy	`docs/interpreter_bucket_stats.md`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`galaxy-tool-fmt`	software	healthy	`galaxy-tool-fmt`
`tests`	software	healthy	`galaxy-tool-fmt/tests`
`docs`	software	healthy	`galaxy-tool-fmt/docs`
`src`	software	healthy	`galaxy-tool-fmt/src`
`galaxy_tool_fmt`	software	healthy	`galaxy-tool-fmt/src/galaxy_tool_fmt`
`docs`	software	healthy	`docs`
`blog`	software	healthy	`docs/blog`
`2026-06-11-a-repository-for-both-humans-and-ai-agents`	software	healthy	`docs/blog/2026-06-11-a-repository-for-both-humans-and-ai-ag…`
`2026-06-14-what-galaxy-tool-refactor-does-for-your-tools`	software	healthy	`docs/blog/2026-06-14-what-galaxy-tool-refactor-does-for-you…`
`2026-06-15-fixing-galaxy-tools-at-scale`	software	healthy	`docs/blog/2026-06-15-fixing-galaxy-tools-at-scale`
`upgrade_research`	software	healthy	`docs/upgrade_research`
`examples`	software	healthy	`docs/examples`
`proofs`	software	healthy	`docs/proofs`
`corpus_data`	software	healthy	`docs/corpus_data`
`failures`	software	healthy	`docs/corpus_data/failures`
`guide`	software	healthy	`docs/guide`
`usage`	software	healthy	`docs/guide/usage`
`galaxy-tool-refactor-cli`	software	healthy	`galaxy-tool-refactor-cli`
`tests`	software	healthy	`galaxy-tool-refactor-cli/tests`
`docs`	software	healthy	`galaxy-tool-refactor-cli/docs`
`src`	software	healthy	`galaxy-tool-refactor-cli/src`
`galaxy_tool_refactor_cli`	software	healthy	`galaxy-tool-refactor-cli/src/galaxy_tool_refactor_cli`
`scripts`	software	healthy	`scripts`
`galaxy-tool-source`	software	healthy	`galaxy-tool-source`
`tests`	software	healthy	`galaxy-tool-source/tests`
`docs`	software	healthy	`galaxy-tool-source/docs`
`src`	software	healthy	`galaxy-tool-source/src`
`galaxy_tool_source`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source`
`models`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models`
`v20_09`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v20_09`
`v25_0`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v25_0`
`v24_2`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v24_2`
`v24_0`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v24_0`
`v20_05`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v20_05`
`v19_09`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v19_09`
`v22_05`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v22_05`
`v18_05`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v18_05`
`v26_0`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v26_0`
`v17_01`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v17_01`
`v21_09`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v21_09`
`v21_05`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v21_05`
`v23_0`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v23_0`
`v23_2`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v23_2`
`v21_01`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v21_01`
`v18_09`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v18_09`
`v16_10`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v16_10`
`v24_1`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v24_1`
`v23_1`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v23_1`
`v17_05`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v17_05`
`v18_01`	software	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v18_01`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`qa`	cicd	healthy	`.github/workflows/ci.yml`
`ci`	cicd	healthy	`.github/workflows/ci.yml`
`refresh`	cicd	healthy	`.github/workflows/corpus-stats.yml`
`build`	cicd	healthy	`.github/workflows/release.yml`
`publish`	cicd	healthy	`.github/workflows/release.yml`

Label	Layer	Status	Path
`gha::ci`	cicd	healthy	`.github/workflows/ci.yml`
`gha::corpus-stats`	cicd	healthy	`.github/workflows/corpus-stats.yml`
`gha::release`	cicd	healthy	`.github/workflows/release.yml`

Label	Layer	Status	Path
`repobility-clone-bstr3e1g`	software	healthy	`/tmp/repobility-clone-bstr3e1g`

Label	Layer	Status	Path
`postgres`	data	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v26_0/gala…`

Label	Layer	Status	Path
`nginx`	network	healthy	`galaxy-tool-source/tests/test_corpus_check.py`

Label	Layer	Status	Path
`port:06`	network	healthy	`.github/workflows/corpus-stats.yml`

Label	Layer	Status	Path
`gpu (detected)`	hardware	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v25_0/gala…`

Label	Layer	Status	Path
`vps::aws`	hardware	healthy	`galaxy-tool-source/src/galaxy_tool_source/models/v26_0/gala…`

Label	Layer	Status	Path
`auth::.github/workflows/release.yml`	security	healthy	`.github/workflows/release.yml`

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richard-burhans/galaxy-tool-refactor

Complete repo analysis

class 50+

function 50+

file 50+

directory 50+

job 5

pipeline 3

repo 1

database 1

load_balancer 1

port 1

gpu 1

vps 1

auth 1