@delta-infra/cli 1.1.19 → 1.1.23

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (77) hide show
  1. package/README.md +511 -520
  2. package/checksums.txt +5 -5
  3. package/package.json +1 -1
  4. package/scripts/install-wizard.js +689 -688
  5. package/scripts/install.js +442 -442
  6. package/scripts/run.js +65 -65
  7. package/skills/delta-protein/AGENTS.md +72 -72
  8. package/skills/delta-protein/SKILL.md +388 -388
  9. package/skills/delta-protein/agents/openai.yaml +3 -3
  10. package/skills/delta-protein/references/bfitter.md +63 -63
  11. package/skills/delta-protein/references/catapro_predict.md +62 -62
  12. package/skills/delta-protein/references/catpred_predict.md +64 -64
  13. package/skills/delta-protein/references/caver_tunnel_analyze.md +62 -62
  14. package/skills/delta-protein/references/consensus_mutation.md +60 -60
  15. package/skills/delta-protein/references/consurf_predict.md +66 -66
  16. package/skills/delta-protein/references/crop_sequence.md +68 -68
  17. package/skills/delta-protein/references/dock.md +81 -81
  18. package/skills/delta-protein/references/dock_score.md +69 -69
  19. package/skills/delta-protein/references/easifa_predict_active_site.md +69 -69
  20. package/skills/delta-protein/references/ephod_predict_mutation.md +65 -65
  21. package/skills/delta-protein/references/ephod_predict_protein.md +60 -60
  22. package/skills/delta-protein/references/esmfold2_predict.md +66 -66
  23. package/skills/delta-protein/references/evcouplings_mutation.md +63 -63
  24. package/skills/delta-protein/references/fasta_to_sequence.md +58 -58
  25. package/skills/delta-protein/references/foldseek.md +60 -60
  26. package/skills/delta-protein/references/generate_msa.md +60 -60
  27. package/skills/delta-protein/references/interpro_analyze.md +62 -62
  28. package/skills/delta-protein/references/mpnn_design_sequence.md +70 -70
  29. package/skills/delta-protein/references/multievolve.md +72 -72
  30. package/skills/delta-protein/references/pisa_query.md +69 -69
  31. package/skills/delta-protein/references/plip_analyze.md +64 -64
  32. package/skills/delta-protein/references/pocket_prediction.md +62 -62
  33. package/skills/delta-protein/references/protein_design.md +64 -64
  34. package/skills/delta-protein/references/protein_evolution.md +76 -76
  35. package/skills/delta-protein/references/protein_sol_predict_mutation.md +65 -65
  36. package/skills/delta-protein/references/protein_sol_predict_protein.md +60 -60
  37. package/skills/delta-protein/references/protenix.md +65 -65
  38. package/skills/delta-protein/references/protrek_search.md +89 -89
  39. package/skills/delta-protein/references/pubchem_search.md +67 -67
  40. package/skills/delta-protein/references/pubmed_search.md +78 -78
  41. package/skills/delta-protein/references/reap_design_primer.md +68 -68
  42. package/skills/delta-protein/references/rfd3_design.md +64 -64
  43. package/skills/delta-protein/references/structure_to_sequence.md +60 -60
  44. package/skills/delta-protein/references/summarize_result.md +67 -67
  45. package/skills/delta-protein/references/surface_charge.md +83 -83
  46. package/skills/delta-protein/references/uniprot_batch_query.md +62 -62
  47. package/skills/delta-protein/references/uniprot_query.md +63 -63
  48. package/skills/delta-protein/references/zero_shot_mutant_candidates.md +75 -75
  49. package/skills/delta-protein/scripts/gen_references.py +166 -166
  50. package/skills/delta-protein/scripts/output_metadata.json +274 -274
  51. package/skills/delta-sandbox/SKILL.md +388 -388
  52. package/skills/delta-sandbox/agents/openai.yaml +4 -4
  53. package/skills/delta-sandbox/references/commands.md +71 -58
  54. package/skills/delta-sandbox/references/lifecycle.md +101 -100
  55. package/skills/delta-sandbox/references/recipes.md +138 -138
  56. package/skills/delta-science/AGENTS.md +47 -47
  57. package/skills/delta-science/SKILL.md +227 -227
  58. package/skills/delta-science/agents/openai.yaml +4 -4
  59. package/skills/delta-science/references/antbo.md +105 -105
  60. package/skills/delta-science/references/delta-bo.md +92 -92
  61. package/skills/delta-science/references/gsasii.md +118 -118
  62. package/skills/delta-science/references/lammps.md +68 -68
  63. package/skills/delta-science/references/ldm-bo.md +132 -132
  64. package/skills/delta-science/references/materials-design.md +130 -130
  65. package/skills/delta-science/references/pubchem.md +128 -128
  66. package/skills/delta-science/references/pymatgen.md +69 -69
  67. package/skills/delta-science/references/qe.md +134 -134
  68. package/skills/delta-science/references/rdkit.md +141 -141
  69. package/skills/delta-science/references/strbo.md +95 -95
  70. package/skills/delta-science/references/synbo.md +201 -201
  71. package/skills/delta-science/references/xrd.md +154 -170
  72. package/skills/delta-science/scripts/catalog.py +92 -92
  73. package/skills/delta-science/scripts/generated_catalog.py +69 -69
  74. package/skills/delta-science/scripts/invoke.py +346 -346
  75. package/skills/delta-shared/SKILL.md +115 -113
  76. package/skills/delta-shared/agents/openai.yaml +4 -4
  77. package/skills/manifest.json +20 -20
package/checksums.txt CHANGED
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package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@delta-infra/cli",
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- "version": "1.1.19",
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+ "version": "1.1.23",
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  "description": "Delta Agent Cloud CLI for sandbox compute and science tools.",
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  "bin": {
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  "delta-cli": "scripts/run.js"