@delta-infra/cli 1.1.17 → 1.1.19

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 +520 -506
  2. package/checksums.txt +5 -5
  3. package/package.json +3 -2
  4. package/scripts/install-wizard.js +688 -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 -185
  58. package/skills/delta-science/agents/openai.yaml +4 -4
  59. package/skills/delta-science/references/antbo.md +105 -100
  60. package/skills/delta-science/references/delta-bo.md +92 -89
  61. package/skills/delta-science/references/gsasii.md +118 -116
  62. package/skills/delta-science/references/lammps.md +68 -66
  63. package/skills/delta-science/references/ldm-bo.md +132 -129
  64. package/skills/delta-science/references/materials-design.md +130 -118
  65. package/skills/delta-science/references/pubchem.md +128 -126
  66. package/skills/delta-science/references/pymatgen.md +69 -68
  67. package/skills/delta-science/references/qe.md +134 -125
  68. package/skills/delta-science/references/rdkit.md +141 -138
  69. package/skills/delta-science/references/strbo.md +95 -87
  70. package/skills/delta-science/references/synbo.md +201 -198
  71. package/skills/delta-science/references/xrd.md +619 -101
  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 -111
  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 @@
1
- 835c80605c32d1d4556f59d1881999ef2f8b09726a3698681702b86680556687 delta-cli-darwin-amd64.tar.gz
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- 56bf86cb914402d0ed38289fce1f04cdfcf59c87f3864226f0923bf4d0c534c4 delta-cli-darwin-arm64.tar.gz
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- 97d5804293f0e915ee66de6cbbacc60eade7063f6b34c508da5a193b03516b3f delta-cli-linux-amd64.tar.gz
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- bf065a9be705a484bafc7a8ce1b0dcf01f196cb0a314a9dfac4002d7feb03dc6 delta-cli-linux-arm64.tar.gz
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- ddc6f3bf99735f5ef5b1ab8de8a2b49592fd2c2921920eca3592ae90b47ef380 delta-cli-windows-amd64.zip
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+ a85ffee5fb646cc77fc8d5afe4d34e3b6ed713b1f7abc3987fe3c7f43f5ab1da *delta-cli-darwin-amd64.tar.gz
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+ 9f0656be23adce565aeec0ae3db6bbae4fee484f8b784323ad13041219af7dd3 *delta-cli-linux-amd64.tar.gz
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+ 354c1a28dc0f6d47797276098efbd09bc0ae2394a74ac6eb07ed1e341c3111fc *delta-cli-linux-arm64.tar.gz
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+ 20656d7fbfe7d36d656bbb6a12b09a3b8fe789c2c1b716e4ed8c2096109f1fd0 *delta-cli-windows-amd64.zip
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": "1.1.17",
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+ "version": "1.1.19",
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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",