orthogroups: deep README+AI_GUIDE evaluation pass — bring to phylonam… #86
000specificci.yml
on: push
Validate YAML files
17s
Validate Python syntax
25s
Validate shell scripts
19s
Check project structure
5s
Check documentation
4s
Test demo (placeholder)
5s
Annotations
2 errors and 16 warnings
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Check project structure
Process completed with exit code 1.
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Validate YAML files:
./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_orthofinder/workflow-COPYME-run_orthofinder/START_HERE-user_config.yaml#L49
49:1 [key-duplicates] duplication of key "cpus" in mapping
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Check documentation
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Check project structure
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Test demo (placeholder)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Validate YAML files
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Validate YAML files:
./gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/conda_environment.yml#L41
41:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-snap_family/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/conda_environment.yml#L41
41:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_orthohmm_GIGANTIC/workflow-COPYME-run_orthohmm_GIGANTIC/ai/conda_environment.yml#L47
47:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_broccoli/workflow-COPYME-run_broccoli/ai/conda_environment.yml#L52
52:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_orthohmm/workflow-COPYME-run_orthohmm/ai/conda_environment.yml#L47
47:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/annotations_hmms/BLOCK_metapredict/workflow-COPYME-run_metapredict/ai/conda_environment.yml#L43
43:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/annotations_hmms/BLOCK_tmbed/workflow-COPYME-run_tmbed/ai/conda_environment.yml#L57
57:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/trees_species/BLOCK_user_requests/workflow-COPYME-select_structures/ai/conda_environment.yml#L42
42:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/trees_gene_families/gene_family_COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/conda_environment.yml#L41
41:5 [indentation] wrong indentation: expected 6 but found 4
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Validate YAML files:
./gigantic_project-COPYME/subprojects/homolog_counts/BLOCK_homolog_counts/workflow-COPYME-homolog_counts/START_HERE-user_config.yaml#L39
39:27 [colons] too many spaces after colon
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Validate shell scripts
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Validate Python syntax
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/setup-python@v5. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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