@delta-infra/cli 1.1.18 → 1.1.21

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 +507 -513
  2. package/checksums.txt +5 -5
  3. package/package.json +3 -2
  4. package/scripts/install-wizard.js +689 -701
  5. package/scripts/install.js +442 -442
  6. package/scripts/run.js +65 -65
  7. package/skills/delta-protein/AGENTS.md +73 -0
  8. package/skills/delta-protein/SKILL.md +389 -0
  9. package/skills/delta-protein/agents/openai.yaml +4 -0
  10. package/skills/delta-protein/references/bfitter.md +64 -0
  11. package/skills/delta-protein/references/catapro_predict.md +63 -0
  12. package/skills/delta-protein/references/catpred_predict.md +65 -0
  13. package/skills/delta-protein/references/caver_tunnel_analyze.md +63 -0
  14. package/skills/delta-protein/references/consensus_mutation.md +61 -0
  15. package/skills/delta-protein/references/consurf_predict.md +67 -0
  16. package/skills/delta-protein/references/crop_sequence.md +69 -0
  17. package/skills/delta-protein/references/dock.md +82 -0
  18. package/skills/delta-protein/references/dock_score.md +70 -0
  19. package/skills/delta-protein/references/easifa_predict_active_site.md +70 -0
  20. package/skills/delta-protein/references/ephod_predict_mutation.md +66 -0
  21. package/skills/delta-protein/references/ephod_predict_protein.md +61 -0
  22. package/skills/delta-protein/references/esmfold2_predict.md +67 -0
  23. package/skills/delta-protein/references/evcouplings_mutation.md +64 -0
  24. package/skills/delta-protein/references/fasta_to_sequence.md +59 -0
  25. package/skills/delta-protein/references/foldseek.md +61 -0
  26. package/skills/delta-protein/references/generate_msa.md +61 -0
  27. package/skills/delta-protein/references/interpro_analyze.md +63 -0
  28. package/skills/delta-protein/references/mpnn_design_sequence.md +71 -0
  29. package/skills/delta-protein/references/multievolve.md +73 -0
  30. package/skills/delta-protein/references/pisa_query.md +70 -0
  31. package/skills/delta-protein/references/plip_analyze.md +65 -0
  32. package/skills/delta-protein/references/pocket_prediction.md +63 -0
  33. package/skills/delta-protein/references/protein_design.md +65 -0
  34. package/skills/delta-protein/references/protein_evolution.md +77 -0
  35. package/skills/delta-protein/references/protein_sol_predict_mutation.md +66 -0
  36. package/skills/delta-protein/references/protein_sol_predict_protein.md +61 -0
  37. package/skills/delta-protein/references/protenix.md +66 -0
  38. package/skills/delta-protein/references/protrek_search.md +90 -0
  39. package/skills/delta-protein/references/pubchem_search.md +68 -0
  40. package/skills/delta-protein/references/pubmed_search.md +79 -0
  41. package/skills/delta-protein/references/reap_design_primer.md +69 -0
  42. package/skills/delta-protein/references/rfd3_design.md +65 -0
  43. package/skills/delta-protein/references/structure_to_sequence.md +61 -0
  44. package/skills/delta-protein/references/summarize_result.md +68 -0
  45. package/skills/delta-protein/references/surface_charge.md +84 -0
  46. package/skills/delta-protein/references/uniprot_batch_query.md +63 -0
  47. package/skills/delta-protein/references/uniprot_query.md +64 -0
  48. package/skills/delta-protein/references/zero_shot_mutant_candidates.md +76 -0
  49. package/skills/delta-protein/scripts/gen_references.py +167 -0
  50. package/skills/delta-protein/scripts/output_metadata.json +275 -0
  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 +58 -58
  54. package/skills/delta-sandbox/references/lifecycle.md +100 -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 +688 -197
  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 +113 -113
  76. package/skills/delta-shared/agents/openai.yaml +4 -4
  77. package/skills/manifest.json +20 -19
package/checksums.txt CHANGED
@@ -1,5 +1,5 @@
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- 3fd24fd43adacb420e155e3e636beb43af693112b6b3c70b92de706f74fd85c6 *delta-cli-darwin-amd64.tar.gz
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- c134129e704633f45108b03dcdcd40bf3c60eab0b29ef0227ca5b75d11da2a06 *delta-cli-darwin-arm64.tar.gz
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- 4e1a7f8d4aea6e1c49390ccdba84b9dae8b20d39eababcb7b01a8d1d6789f310 *delta-cli-linux-amd64.tar.gz
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- b609bace1814405a3eceb0f298e95056d27630e92b9b489c90bc48890ea52eaa *delta-cli-linux-arm64.tar.gz
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- 06bddaa9d5733720b61985e2552036f660ebc2076afece1a1674d5c56a4f8b6b *delta-cli-windows-amd64.zip
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+ 146e95ba3dca9f41c4e7751244178ce461c2aa428a6057212d7e7065be17f5ff delta-cli-darwin-amd64.tar.gz
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+ 6d339b78e509d215a0e25042d42d806ae7f9a22cb54fbb66ebd26bbf374ced76 delta-cli-darwin-arm64.tar.gz
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+ d65dacbc85b09a775403407d0779f0c040f5f17b84eb0a6e19f3c5985b7dc952 delta-cli-linux-amd64.tar.gz
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+ 68f6aa27e13b3cd5168fe48f1ab810ad0d203a70553d881f21d584593a7114fc delta-cli-linux-arm64.tar.gz
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+ 9fe0d9ad21ba47792caee7ebf60a423db1fbb24f142f6cd9430c125a0381eb74 delta-cli-windows-amd64.zip
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
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  {
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  "name": "@delta-infra/cli",
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- "version": "1.1.18",
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+ "version": "1.1.21",
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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"
@@ -16,7 +16,8 @@
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  "skills/manifest.json",
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  "skills/delta-sandbox/",
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  "skills/delta-shared/",
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- "skills/delta-science/"
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+ "skills/delta-science/",
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+ "skills/delta-protein/"
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  ],
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  "os": [
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  "darwin",