@synsci/cli-darwin-x64 1.1.70 → 1.1.72

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 (339) hide show
  1. package/bin/skills/citation-management/SKILL.md +1109 -0
  2. package/bin/skills/citation-management/assets/bibtex_template.bib +264 -0
  3. package/bin/skills/citation-management/assets/citation_checklist.md +386 -0
  4. package/bin/skills/citation-management/references/bibtex_formatting.md +908 -0
  5. package/bin/skills/citation-management/references/citation_validation.md +794 -0
  6. package/bin/skills/citation-management/references/google_scholar_search.md +725 -0
  7. package/bin/skills/citation-management/references/metadata_extraction.md +870 -0
  8. package/bin/skills/citation-management/references/pubmed_search.md +839 -0
  9. package/bin/skills/citation-management/scripts/doi_to_bibtex.py +182 -0
  10. package/bin/skills/citation-management/scripts/extract_metadata.py +570 -0
  11. package/bin/skills/citation-management/scripts/format_bibtex.py +349 -0
  12. package/bin/skills/citation-management/scripts/search_google_scholar.py +251 -0
  13. package/bin/skills/citation-management/scripts/search_pubmed.py +348 -0
  14. package/bin/skills/citation-management/scripts/validate_citations.py +494 -0
  15. package/bin/skills/clinical-decision-support/README.md +129 -0
  16. package/bin/skills/clinical-decision-support/SKILL.md +506 -0
  17. package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
  18. package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
  19. package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
  20. package/bin/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
  21. package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
  22. package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
  23. package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
  24. package/bin/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
  25. package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
  26. package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
  27. package/bin/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
  28. package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
  29. package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
  30. package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +383 -0
  31. package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +417 -0
  32. package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +509 -0
  33. package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +441 -0
  34. package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +326 -0
  35. package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  36. package/bin/skills/clinical-reports/README.md +236 -0
  37. package/bin/skills/clinical-reports/SKILL.md +1127 -0
  38. package/bin/skills/clinical-reports/assets/case_report_template.md +352 -0
  39. package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  40. package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  41. package/bin/skills/clinical-reports/assets/consult_note_template.md +305 -0
  42. package/bin/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  43. package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  44. package/bin/skills/clinical-reports/assets/history_physical_template.md +305 -0
  45. package/bin/skills/clinical-reports/assets/lab_report_template.md +309 -0
  46. package/bin/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  47. package/bin/skills/clinical-reports/assets/quality_checklist.md +338 -0
  48. package/bin/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  49. package/bin/skills/clinical-reports/assets/soap_note_template.md +253 -0
  50. package/bin/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  51. package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  52. package/bin/skills/clinical-reports/references/data_presentation.md +530 -0
  53. package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  54. package/bin/skills/clinical-reports/references/medical_terminology.md +588 -0
  55. package/bin/skills/clinical-reports/references/patient_documentation.md +744 -0
  56. package/bin/skills/clinical-reports/references/peer_review_standards.md +585 -0
  57. package/bin/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  58. package/bin/skills/clinical-reports/scripts/check_deidentification.py +332 -0
  59. package/bin/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  60. package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +97 -0
  61. package/bin/skills/clinical-reports/scripts/format_adverse_events.py +97 -0
  62. package/bin/skills/clinical-reports/scripts/generate_report_template.py +149 -0
  63. package/bin/skills/clinical-reports/scripts/terminology_validator.py +126 -0
  64. package/bin/skills/clinical-reports/scripts/validate_case_report.py +323 -0
  65. package/bin/skills/clinical-reports/scripts/validate_trial_report.py +88 -0
  66. package/bin/skills/fireworks-ai/SKILL.md +665 -0
  67. package/bin/skills/generate-image/SKILL.md +178 -0
  68. package/bin/skills/generate-image/scripts/generate_image.py +254 -0
  69. package/bin/skills/groq/SKILL.md +347 -0
  70. package/bin/skills/hypothesis-generation/SKILL.md +293 -0
  71. package/bin/skills/hypothesis-generation/assets/FORMATTING_GUIDE.md +672 -0
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  73. package/bin/skills/hypothesis-generation/assets/hypothesis_report_template.tex +572 -0
  74. package/bin/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
  75. package/bin/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
  76. package/bin/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
  77. package/bin/skills/latex-posters/README.md +417 -0
  78. package/bin/skills/latex-posters/SKILL.md +1602 -0
  79. package/bin/skills/latex-posters/assets/baposter_template.tex +257 -0
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  81. package/bin/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
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  83. package/bin/skills/latex-posters/references/latex_poster_packages.md +745 -0
  84. package/bin/skills/latex-posters/references/poster_content_guide.md +748 -0
  85. package/bin/skills/latex-posters/references/poster_design_principles.md +806 -0
  86. package/bin/skills/latex-posters/references/poster_layout_design.md +900 -0
  87. package/bin/skills/latex-posters/scripts/review_poster.sh +214 -0
  88. package/bin/skills/literature-review/SKILL.md +641 -0
  89. package/bin/skills/literature-review/assets/review_template.md +412 -0
  90. package/bin/skills/literature-review/references/citation_styles.md +166 -0
  91. package/bin/skills/literature-review/references/database_strategies.md +455 -0
  92. package/bin/skills/literature-review/scripts/generate_pdf.py +184 -0
  93. package/bin/skills/literature-review/scripts/search_databases.py +310 -0
  94. package/bin/skills/literature-review/scripts/verify_citations.py +218 -0
  95. package/bin/skills/market-research-reports/SKILL.md +904 -0
  96. package/bin/skills/market-research-reports/assets/FORMATTING_GUIDE.md +428 -0
  97. package/bin/skills/market-research-reports/assets/market_report_template.tex +1380 -0
  98. package/bin/skills/market-research-reports/assets/market_research.sty +564 -0
  99. package/bin/skills/market-research-reports/references/data_analysis_patterns.md +548 -0
  100. package/bin/skills/market-research-reports/references/report_structure_guide.md +999 -0
  101. package/bin/skills/market-research-reports/references/visual_generation_guide.md +1077 -0
  102. package/bin/skills/market-research-reports/scripts/generate_market_visuals.py +472 -0
  103. package/bin/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  104. package/bin/skills/markitdown/LICENSE.txt +22 -0
  105. package/bin/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  106. package/bin/skills/markitdown/QUICK_REFERENCE.md +309 -0
  107. package/bin/skills/markitdown/README.md +184 -0
  108. package/bin/skills/markitdown/SKILL.md +486 -0
  109. package/bin/skills/markitdown/SKILL_SUMMARY.md +307 -0
  110. package/bin/skills/markitdown/assets/example_usage.md +463 -0
  111. package/bin/skills/markitdown/references/api_reference.md +399 -0
  112. package/bin/skills/markitdown/references/file_formats.md +542 -0
  113. package/bin/skills/markitdown/scripts/batch_convert.py +195 -0
  114. package/bin/skills/markitdown/scripts/convert_literature.py +262 -0
  115. package/bin/skills/markitdown/scripts/convert_with_ai.py +224 -0
  116. package/bin/skills/ml-paper-writing/SKILL.md +937 -0
  117. package/bin/skills/ml-paper-writing/references/checklists.md +361 -0
  118. package/bin/skills/ml-paper-writing/references/citation-workflow.md +562 -0
  119. package/bin/skills/ml-paper-writing/references/reviewer-guidelines.md +367 -0
  120. package/bin/skills/ml-paper-writing/references/sources.md +159 -0
  121. package/bin/skills/ml-paper-writing/references/writing-guide.md +476 -0
  122. package/bin/skills/ml-paper-writing/templates/README.md +251 -0
  123. package/bin/skills/ml-paper-writing/templates/aaai2026/README.md +534 -0
  124. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026-unified-supp.tex +144 -0
  125. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026-unified-template.tex +952 -0
  126. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.bib +111 -0
  127. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.bst +1493 -0
  128. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.sty +315 -0
  129. package/bin/skills/ml-paper-writing/templates/acl/README.md +50 -0
  130. package/bin/skills/ml-paper-writing/templates/acl/acl.sty +312 -0
  131. package/bin/skills/ml-paper-writing/templates/acl/acl_latex.tex +377 -0
  132. package/bin/skills/ml-paper-writing/templates/acl/acl_lualatex.tex +101 -0
  133. package/bin/skills/ml-paper-writing/templates/acl/acl_natbib.bst +1940 -0
  134. package/bin/skills/ml-paper-writing/templates/acl/anthology.bib.txt +26 -0
  135. package/bin/skills/ml-paper-writing/templates/acl/custom.bib +70 -0
  136. package/bin/skills/ml-paper-writing/templates/acl/formatting.md +326 -0
  137. package/bin/skills/ml-paper-writing/templates/colm2025/README.md +3 -0
  138. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.bib +11 -0
  139. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.bst +1440 -0
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  142. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.tex +305 -0
  143. package/bin/skills/ml-paper-writing/templates/colm2025/fancyhdr.sty +485 -0
  144. package/bin/skills/ml-paper-writing/templates/colm2025/math_commands.tex +508 -0
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  146. package/bin/skills/ml-paper-writing/templates/iclr2026/fancyhdr.sty +485 -0
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  167. package/bin/skills/paper-2-web/SKILL.md +491 -0
  168. package/bin/skills/paper-2-web/references/installation.md +141 -0
  169. package/bin/skills/paper-2-web/references/paper2poster.md +346 -0
  170. package/bin/skills/paper-2-web/references/paper2video.md +305 -0
  171. package/bin/skills/paper-2-web/references/paper2web.md +187 -0
  172. package/bin/skills/paper-2-web/references/usage_examples.md +436 -0
  173. package/bin/skills/peer-review/SKILL.md +702 -0
  174. package/bin/skills/peer-review/references/calibration_guidelines.md +196 -0
  175. package/bin/skills/peer-review/references/common_issues.md +552 -0
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  177. package/bin/skills/peer-review/references/reporting_standards.md +290 -0
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  179. package/bin/skills/pptx-posters/SKILL.md +410 -0
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  185. package/bin/skills/research-grants/README.md +285 -0
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  187. package/bin/skills/research-grants/assets/budget_justification_template.md +453 -0
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  191. package/bin/skills/research-grants/references/darpa_guidelines.md +636 -0
  192. package/bin/skills/research-grants/references/doe_guidelines.md +586 -0
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+ # Deploying models to LM Studio
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+
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+ You can run and deploy your fine-tuned LLM directly in LM Studio. [LM Studio](https://lmstudio.ai/) enables easy running and deployment of **GGUF** models (llama.cpp format).
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+
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+ You can use our [LM Studio notebook](https://colab.research.google.com/github/unslothai/notebooks/blob/main/nb/FunctionGemma_(270M)-LMStudio.ipynb) or follow the instructions below:
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+
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+ 1. **Export your Unsloth fine-tuned model to `.gguf`**
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+ 2. **Import / download the GGUF into LM Studio**
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+ 3. **Load it in Chat** (or run it behind an OpenAI-compatible local API)
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+
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+ ### 1) Export to GGUF (from Unsloth)
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+
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+ If you already exported a `.gguf`, skip to **Importing into LM Studio**.
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+
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+ ```python
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+ # Save locally (creates GGUF artifacts in the folder)
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+ model.save_pretrained_gguf("my_model_gguf", tokenizer, quantization_method = "q4_k_m")
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+ # model.save_pretrained_gguf("my_model_gguf", tokenizer, quantization_method = "q8_0")
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+ # model.save_pretrained_gguf("my_model_gguf", tokenizer, quantization_method = "f16")
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+
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+ # Or push GGUF to the Hugging Face Hub
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+ model.push_to_hub_gguf("hf_username/my_model_gguf", tokenizer, quantization_method = "q4_k_m")
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+ ```
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+
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+ > `q4_k_m` is usually the default for local runs.
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+ > `q8_0` is the optimum for near full precision quality.
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+ > `f16` is largest / slowest, but original unquantized precision.
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+
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+ ### 2) Import the GGUF into LM Studio
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+
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+ #### CLI Import (lms import)
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+
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+ LM Studio provides a CLI called `lms` that can import a local `.gguf` into LM Studio's models folder.
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+
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+ **Import a GGUF file:**
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+
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+ ```bash
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+ lms import /path/to/model.gguf
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+ ```
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+
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+ **Keep the original file (copy instead of move):**
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+
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+ ```bash
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+ lms import /path/to/model.gguf --copy
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+ ```
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+
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+ **Keep the model where it is (symlink):**
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+
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+ This is helpful for large models stored on a dedicated drive.
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+
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+ ```bash
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+ lms import /path/to/model.gguf --symbolic-link
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+ ```
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+
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+ **Skip prompts and choose the target namespace yourself:**
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+
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+ ```bash
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+ lms import /path/to/model.gguf --user-repo my-user/my-finetuned-models
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+ ```
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+
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+ **Dry-run (shows what will happen):**
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+
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+ ```bash
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+ lms import /path/to/model.gguf --dry-run
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+ ```
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+
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+ After importing, the model should appear in LM Studio under **My Models**.
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+
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+ #### From Hugging Face
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+
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+ If you pushed your GGUF repo to Hugging Face, you can download it directly from within LM Studio.
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+
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+ **Option A: Use LM Studio's in-app downloader**
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+
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+ 1. Open LM Studio
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+ 2. Go to the **Discover** tab
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+ 3. Search for `hf_username/repo_name` (or paste the Hugging Face URL)
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+ 4. Download the quant you want (e.g. `Q4_K_M`)
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+
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+ **Option B: Use the CLI downloader**
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+
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+ ```bash
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+ # Download from HF by repo name
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+ lms get hf_username/my_model_gguf
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+
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+ # Pick a quantization with @
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+ lms get hf_username/my_model_gguf@Q4_K_M
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+ ```
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+
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+ #### Manual Import (folder structure)
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+
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+ If you don't want to use the CLI, you can place the `.gguf` file into LM Studio's expected model directory structure.
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+
94
+ LM Studio expects models to look like this:
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+
96
+ ```
97
+ ~/.lmstudio/models/
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+ └── publisher/
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+ └── model/
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+ └── model-file.gguf
101
+ ```
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+
103
+ Example:
104
+
105
+ ```
106
+ ~/.lmstudio/models/
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+ └── my-name/
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+ └── my-finetune/
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+ └── my-finetune-Q4_K_M.gguf
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+ ```
111
+
112
+ Then open LM Studio and check **My Models**.
113
+
114
+ ### 3) Load and chat in LM Studio
115
+
116
+ 1. Open LM Studio -> **Chat**
117
+ 2. Open the **model loader**
118
+ 3. Select your imported model
119
+ 4. (Optional) adjust load settings (GPU offload, context length, etc.)
120
+ 5. Chat normally in the UI
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+
122
+ ### 4) Serve your fine-tuned model as a local API (OpenAI-compatible)
123
+
124
+ LM Studio can serve your loaded model behind an OpenAI-compatible API (handy for apps like Open WebUI, custom agents, scripts, etc.).
125
+
126
+ #### GUI (Developer tab)
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+
128
+ 1. Load your model in LM Studio
129
+ 2. Go to the **Developer** tab
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+ 3. Start the local server
131
+ 4. Use the shown base URL (default is typically `http://localhost:1234`)
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+
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+ #### CLI (lms load + lms server start)
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+
135
+ **1) List available models:**
136
+
137
+ ```bash
138
+ lms ls
139
+ ```
140
+
141
+ **2) Load your model (optional flags):**
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+
143
+ ```bash
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+ lms load <model-identifier> --gpu=auto --context-length=8192
145
+ ```
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+
147
+ Notes:
148
+ * `--gpu=1.0` means "try to offload 100% to GPU"
149
+ * You can set a stable identifier:
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+
151
+ ```bash
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+ lms load <model-identifier> --identifier="my-finetuned-model"
153
+ ```
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+
155
+ **3) Start the server:**
156
+
157
+ ```bash
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+ lms server start --port 1234
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+ ```
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+
161
+ **Quick test: list models**
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+
163
+ ```bash
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+ curl http://localhost:1234/v1/models
165
+ ```
166
+
167
+ **Python example (OpenAI SDK):**
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+
169
+ ```python
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+ from openai import OpenAI
171
+
172
+ client = OpenAI(
173
+ base_url="http://localhost:1234/v1",
174
+ api_key="lm-studio", # LM Studio may not require a real key; this is a common placeholder
175
+ )
176
+
177
+ resp = client.chat.completions.create(
178
+ model="model-identifier-from-lm-studio",
179
+ messages=[
180
+ {"role": "system", "content": "You are a helpful assistant."},
181
+ {"role": "user", "content": "Hello! What did I fine-tune you to do?"},
182
+ ],
183
+ temperature=0.7,
184
+ )
185
+
186
+ print(resp.choices[0].message.content)
187
+ ```
188
+
189
+ **cURL example (chat completions):**
190
+
191
+ ```bash
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+ curl http://localhost:1234/v1/chat/completions \
193
+ -H "Content-Type: application/json" \
194
+ -d '{
195
+ "model": "model-identifier-from-lm-studio",
196
+ "messages": [
197
+ {"role": "user", "content": "Say this is a test!"}
198
+ ],
199
+ "temperature": 0.7
200
+ }'
201
+ ```
202
+
203
+ > **Debugging tip:** If you're troubleshooting formatting/templates, you can inspect the raw prompt LM Studio sends to the model by running: `lms log stream`
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+
205
+ ### Troubleshooting
206
+
207
+ #### Model runs in Unsloth, but LM Studio output is gibberish / repeats
208
+
209
+ This is almost always a **prompt template / chat template mismatch**.
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+
211
+ LM Studio will **auto-detect** the prompt template from the GGUF metadata when possible, but custom or incorrectly-tagged models may need a manual override.
212
+
213
+ **Fix:**
214
+
215
+ 1. Go to **My Models** -> click the gear next to your model
216
+ 2. Find **Prompt Template** and set it to match the template you trained with
217
+ 3. Alternatively, in the Chat sidebar: enable the **Prompt Template** box (you can force it to always show)
218
+
219
+ #### LM Studio doesn't show my model in "My Models"
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+
221
+ * Prefer `lms import /path/to/model.gguf`
222
+ * Or confirm the file is in the correct folder structure: `~/.lmstudio/models/publisher/model/model-file.gguf`
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+
224
+ #### OOM / slow performance
225
+
226
+ * Use a smaller quant (ex: `Q4_K_M`)
227
+ * Reduce context length
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+ * Adjust GPU offload (LM Studio "Per-model defaults" / load settings)
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+
230
+ ### More resources
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+
232
+ * [LM Studio + Unsloth blog post](https://lmstudio.ai/blog/functiongemma-unsloth) (FunctionGemma walkthrough)
233
+ * LM Studio [Import Models docs](https://lmstudio.ai/docs/app/advanced/import-model)
234
+ * LM Studio [Prompt Template docs](https://lmstudio.ai/docs/app/advanced)
235
+ * LM Studio [OpenAI-compatible API docs](https://lmstudio.ai/docs/developer/openai-compat)
@@ -0,0 +1,75 @@
1
+ # LoRA Hot Swapping Guide
2
+
3
+ ### vLLM LoRA Hot Swapping / Dynamic LoRAs
4
+
5
+ To enable LoRA serving for at most 4 LoRAs at 1 time (these are hot swapped / changed), first set the environment flag to allow hot swapping:
6
+
7
+ ```bash
8
+ export VLLM_ALLOW_RUNTIME_LORA_UPDATING=True
9
+ ```
10
+
11
+ Then, serve it with LoRA support:
12
+
13
+ ```bash
14
+ export VLLM_ALLOW_RUNTIME_LORA_UPDATING=True
15
+ vllm serve unsloth/Llama-3.1-8B-Instruct \
16
+ --quantization fp8 \
17
+ --kv-cache-dtype fp8
18
+ --gpu-memory-utilization 0.8 \
19
+ --max-model-len 65536 \
20
+ --enable-lora \
21
+ --max-loras 4 \
22
+ --max-lora-rank 64
23
+ ```
24
+
25
+ To load a LoRA dynamically (set the lora name as well), do:
26
+
27
+ ```bash
28
+ curl -X POST http://localhost:8000/v1/load_lora_adapter \
29
+ -H "Content-Type: application/json" \
30
+ -d '{
31
+ "lora_name": "LORA_NAME",
32
+ "lora_path": "/path/to/LORA"
33
+ }'
34
+ ```
35
+
36
+ To remove it from the pool:
37
+
38
+ ```bash
39
+ curl -X POST http://localhost:8000/v1/unload_lora_adapter \
40
+ -H "Content-Type: application/json" \
41
+ -d '{
42
+ "lora_name": "LORA_NAME"
43
+ }'
44
+ ```
45
+
46
+ For example when finetuning with Unsloth:
47
+
48
+ ```python
49
+ from unsloth import FastLanguageModel
50
+ import torch
51
+ model, tokenizer = FastLanguageModel.from_pretrained(
52
+ model_name = "unsloth/Llama-3.1-8B-Instruct",
53
+ max_seq_length = 2048,
54
+ load_in_4bit = True,
55
+ )
56
+ model = FastLanguageModel.get_peft_model(model)
57
+ ```
58
+
59
+ Then after training, we save the LoRAs:
60
+
61
+ ```python
62
+ model.save_pretrained("finetuned_lora")
63
+ tokenizer.save_pretrained("finetuned_lora")
64
+ ```
65
+
66
+ We can then load the LoRA:
67
+
68
+ ```bash
69
+ curl -X POST http://localhost:8000/v1/load_lora_adapter \
70
+ -H "Content-Type: application/json" \
71
+ -d '{
72
+ "lora_name": "LORA_NAME_finetuned_lora",
73
+ "lora_path": "finetuned_lora"
74
+ }'
75
+ ```