@pikaa-ai/pikaa 0.2.5 → 0.3.1
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.
- package/LICENSE +21 -0
- package/README.md +153 -104
- package/assets/frames/blocks/frame_1.txt +17 -0
- package/assets/frames/blocks/frame_10.txt +17 -0
- package/assets/frames/blocks/frame_11.txt +17 -0
- package/assets/frames/blocks/frame_12.txt +17 -0
- package/assets/frames/blocks/frame_13.txt +17 -0
- package/assets/frames/blocks/frame_14.txt +17 -0
- package/assets/frames/blocks/frame_15.txt +17 -0
- package/assets/frames/blocks/frame_16.txt +17 -0
- package/assets/frames/blocks/frame_17.txt +17 -0
- package/assets/frames/blocks/frame_18.txt +17 -0
- package/assets/frames/blocks/frame_19.txt +17 -0
- package/assets/frames/blocks/frame_2.txt +17 -0
- package/assets/frames/blocks/frame_20.txt +17 -0
- package/assets/frames/blocks/frame_21.txt +17 -0
- package/assets/frames/blocks/frame_22.txt +17 -0
- package/assets/frames/blocks/frame_23.txt +17 -0
- package/assets/frames/blocks/frame_24.txt +17 -0
- package/assets/frames/blocks/frame_25.txt +17 -0
- package/assets/frames/blocks/frame_26.txt +17 -0
- package/assets/frames/blocks/frame_27.txt +17 -0
- package/assets/frames/blocks/frame_28.txt +17 -0
- package/assets/frames/blocks/frame_29.txt +17 -0
- package/assets/frames/blocks/frame_3.txt +17 -0
- package/assets/frames/blocks/frame_30.txt +17 -0
- package/assets/frames/blocks/frame_31.txt +17 -0
- package/assets/frames/blocks/frame_32.txt +17 -0
- package/assets/frames/blocks/frame_33.txt +17 -0
- package/assets/frames/blocks/frame_34.txt +17 -0
- package/assets/frames/blocks/frame_35.txt +17 -0
- package/assets/frames/blocks/frame_36.txt +17 -0
- package/assets/frames/blocks/frame_4.txt +17 -0
- package/assets/frames/blocks/frame_5.txt +17 -0
- package/assets/frames/blocks/frame_6.txt +17 -0
- package/assets/frames/blocks/frame_7.txt +17 -0
- package/assets/frames/blocks/frame_8.txt +17 -0
- package/assets/frames/blocks/frame_9.txt +17 -0
- package/assets/frames/default/frame_1.txt +17 -0
- package/assets/frames/default/frame_10.txt +17 -0
- package/assets/frames/default/frame_11.txt +17 -0
- package/assets/frames/default/frame_12.txt +17 -0
- package/assets/frames/default/frame_13.txt +17 -0
- package/assets/frames/default/frame_14.txt +17 -0
- package/assets/frames/default/frame_15.txt +17 -0
- package/assets/frames/default/frame_16.txt +17 -0
- package/assets/frames/default/frame_17.txt +17 -0
- package/assets/frames/default/frame_18.txt +17 -0
- package/assets/frames/default/frame_19.txt +17 -0
- package/assets/frames/default/frame_2.txt +17 -0
- package/assets/frames/default/frame_20.txt +17 -0
- package/assets/frames/default/frame_21.txt +17 -0
- package/assets/frames/default/frame_22.txt +17 -0
- package/assets/frames/default/frame_23.txt +17 -0
- package/assets/frames/default/frame_24.txt +17 -0
- package/assets/frames/default/frame_25.txt +17 -0
- package/assets/frames/default/frame_26.txt +17 -0
- package/assets/frames/default/frame_27.txt +17 -0
- package/assets/frames/default/frame_28.txt +17 -0
- package/assets/frames/default/frame_29.txt +17 -0
- package/assets/frames/default/frame_3.txt +17 -0
- package/assets/frames/default/frame_30.txt +17 -0
- package/assets/frames/default/frame_31.txt +17 -0
- package/assets/frames/default/frame_32.txt +17 -0
- package/assets/frames/default/frame_33.txt +17 -0
- package/assets/frames/default/frame_34.txt +17 -0
- package/assets/frames/default/frame_35.txt +17 -0
- package/assets/frames/default/frame_36.txt +17 -0
- package/assets/frames/default/frame_4.txt +17 -0
- package/assets/frames/default/frame_5.txt +17 -0
- package/assets/frames/default/frame_6.txt +17 -0
- package/assets/frames/default/frame_7.txt +17 -0
- package/assets/frames/default/frame_8.txt +17 -0
- package/assets/frames/default/frame_9.txt +17 -0
- package/assets/frames/dots/frame_1.txt +17 -0
- package/assets/frames/dots/frame_10.txt +17 -0
- package/assets/frames/dots/frame_11.txt +17 -0
- package/assets/frames/dots/frame_12.txt +17 -0
- package/assets/frames/dots/frame_13.txt +17 -0
- package/assets/frames/dots/frame_14.txt +17 -0
- package/assets/frames/dots/frame_15.txt +17 -0
- package/assets/frames/dots/frame_16.txt +17 -0
- package/assets/frames/dots/frame_17.txt +17 -0
- package/assets/frames/dots/frame_18.txt +17 -0
- package/assets/frames/dots/frame_19.txt +17 -0
- package/assets/frames/dots/frame_2.txt +17 -0
- package/assets/frames/dots/frame_20.txt +17 -0
- package/assets/frames/dots/frame_21.txt +17 -0
- package/assets/frames/dots/frame_22.txt +17 -0
- package/assets/frames/dots/frame_23.txt +17 -0
- package/assets/frames/dots/frame_24.txt +17 -0
- package/assets/frames/dots/frame_25.txt +17 -0
- package/assets/frames/dots/frame_26.txt +17 -0
- package/assets/frames/dots/frame_27.txt +17 -0
- package/assets/frames/dots/frame_28.txt +17 -0
- package/assets/frames/dots/frame_29.txt +17 -0
- package/assets/frames/dots/frame_3.txt +17 -0
- package/assets/frames/dots/frame_30.txt +17 -0
- package/assets/frames/dots/frame_31.txt +17 -0
- package/assets/frames/dots/frame_32.txt +17 -0
- package/assets/frames/dots/frame_33.txt +17 -0
- package/assets/frames/dots/frame_34.txt +17 -0
- package/assets/frames/dots/frame_35.txt +17 -0
- package/assets/frames/dots/frame_36.txt +17 -0
- package/assets/frames/dots/frame_4.txt +17 -0
- package/assets/frames/dots/frame_5.txt +17 -0
- package/assets/frames/dots/frame_6.txt +17 -0
- package/assets/frames/dots/frame_7.txt +17 -0
- package/assets/frames/dots/frame_8.txt +17 -0
- package/assets/frames/dots/frame_9.txt +17 -0
- package/assets/frames/groupy/frame_1.txt +17 -0
- package/assets/frames/groupy/frame_10.txt +17 -0
- package/assets/frames/groupy/frame_11.txt +17 -0
- package/assets/frames/groupy/frame_12.txt +17 -0
- package/assets/frames/groupy/frame_13.txt +17 -0
- package/assets/frames/groupy/frame_14.txt +17 -0
- package/assets/frames/groupy/frame_15.txt +17 -0
- package/assets/frames/groupy/frame_16.txt +17 -0
- package/assets/frames/groupy/frame_17.txt +17 -0
- package/assets/frames/groupy/frame_18.txt +17 -0
- package/assets/frames/groupy/frame_19.txt +17 -0
- package/assets/frames/groupy/frame_2.txt +17 -0
- package/assets/frames/groupy/frame_20.txt +17 -0
- package/assets/frames/groupy/frame_21.txt +17 -0
- package/assets/frames/groupy/frame_22.txt +17 -0
- package/assets/frames/groupy/frame_23.txt +17 -0
- package/assets/frames/groupy/frame_24.txt +17 -0
- package/assets/frames/groupy/frame_25.txt +17 -0
- package/assets/frames/groupy/frame_26.txt +17 -0
- package/assets/frames/groupy/frame_27.txt +17 -0
- package/assets/frames/groupy/frame_28.txt +17 -0
- package/assets/frames/groupy/frame_29.txt +17 -0
- package/assets/frames/groupy/frame_3.txt +17 -0
- package/assets/frames/groupy/frame_30.txt +17 -0
- package/assets/frames/groupy/frame_31.txt +17 -0
- package/assets/frames/groupy/frame_32.txt +17 -0
- package/assets/frames/groupy/frame_33.txt +17 -0
- package/assets/frames/groupy/frame_34.txt +17 -0
- package/assets/frames/groupy/frame_35.txt +17 -0
- package/assets/frames/groupy/frame_36.txt +17 -0
- package/assets/frames/groupy/frame_4.txt +17 -0
- package/assets/frames/groupy/frame_5.txt +17 -0
- package/assets/frames/groupy/frame_6.txt +17 -0
- package/assets/frames/groupy/frame_7.txt +17 -0
- package/assets/frames/groupy/frame_8.txt +17 -0
- package/assets/frames/groupy/frame_9.txt +17 -0
- package/assets/frames/hash/frame_1.txt +17 -0
- package/assets/frames/hash/frame_10.txt +17 -0
- package/assets/frames/hash/frame_11.txt +17 -0
- package/assets/frames/hash/frame_12.txt +17 -0
- package/assets/frames/hash/frame_13.txt +17 -0
- package/assets/frames/hash/frame_14.txt +17 -0
- package/assets/frames/hash/frame_15.txt +17 -0
- package/assets/frames/hash/frame_16.txt +17 -0
- package/assets/frames/hash/frame_17.txt +17 -0
- package/assets/frames/hash/frame_18.txt +17 -0
- package/assets/frames/hash/frame_19.txt +17 -0
- package/assets/frames/hash/frame_2.txt +17 -0
- package/assets/frames/hash/frame_20.txt +17 -0
- package/assets/frames/hash/frame_21.txt +17 -0
- package/assets/frames/hash/frame_22.txt +17 -0
- package/assets/frames/hash/frame_23.txt +17 -0
- package/assets/frames/hash/frame_24.txt +17 -0
- package/assets/frames/hash/frame_25.txt +17 -0
- package/assets/frames/hash/frame_26.txt +17 -0
- package/assets/frames/hash/frame_27.txt +17 -0
- package/assets/frames/hash/frame_28.txt +17 -0
- package/assets/frames/hash/frame_29.txt +17 -0
- package/assets/frames/hash/frame_3.txt +17 -0
- package/assets/frames/hash/frame_30.txt +17 -0
- package/assets/frames/hash/frame_31.txt +17 -0
- package/assets/frames/hash/frame_32.txt +17 -0
- package/assets/frames/hash/frame_33.txt +17 -0
- package/assets/frames/hash/frame_34.txt +17 -0
- package/assets/frames/hash/frame_35.txt +17 -0
- package/assets/frames/hash/frame_36.txt +17 -0
- package/assets/frames/hash/frame_4.txt +17 -0
- package/assets/frames/hash/frame_5.txt +17 -0
- package/assets/frames/hash/frame_6.txt +17 -0
- package/assets/frames/hash/frame_7.txt +17 -0
- package/assets/frames/hash/frame_8.txt +17 -0
- package/assets/frames/hash/frame_9.txt +17 -0
- package/assets/frames/hbars/frame_1.txt +17 -0
- package/assets/frames/hbars/frame_10.txt +17 -0
- package/assets/frames/hbars/frame_11.txt +17 -0
- package/assets/frames/hbars/frame_12.txt +17 -0
- package/assets/frames/hbars/frame_13.txt +17 -0
- package/assets/frames/hbars/frame_14.txt +17 -0
- package/assets/frames/hbars/frame_15.txt +17 -0
- package/assets/frames/hbars/frame_16.txt +17 -0
- package/assets/frames/hbars/frame_17.txt +17 -0
- package/assets/frames/hbars/frame_18.txt +17 -0
- package/assets/frames/hbars/frame_19.txt +17 -0
- package/assets/frames/hbars/frame_2.txt +17 -0
- package/assets/frames/hbars/frame_20.txt +17 -0
- package/assets/frames/hbars/frame_21.txt +17 -0
- package/assets/frames/hbars/frame_22.txt +17 -0
- package/assets/frames/hbars/frame_23.txt +17 -0
- package/assets/frames/hbars/frame_24.txt +17 -0
- package/assets/frames/hbars/frame_25.txt +17 -0
- package/assets/frames/hbars/frame_26.txt +17 -0
- package/assets/frames/hbars/frame_27.txt +17 -0
- package/assets/frames/hbars/frame_28.txt +17 -0
- package/assets/frames/hbars/frame_29.txt +17 -0
- package/assets/frames/hbars/frame_3.txt +17 -0
- package/assets/frames/hbars/frame_30.txt +17 -0
- package/assets/frames/hbars/frame_31.txt +17 -0
- package/assets/frames/hbars/frame_32.txt +17 -0
- package/assets/frames/hbars/frame_33.txt +17 -0
- package/assets/frames/hbars/frame_34.txt +17 -0
- package/assets/frames/hbars/frame_35.txt +17 -0
- package/assets/frames/hbars/frame_36.txt +17 -0
- package/assets/frames/hbars/frame_4.txt +17 -0
- package/assets/frames/hbars/frame_5.txt +17 -0
- package/assets/frames/hbars/frame_6.txt +17 -0
- package/assets/frames/hbars/frame_7.txt +17 -0
- package/assets/frames/hbars/frame_8.txt +17 -0
- package/assets/frames/hbars/frame_9.txt +17 -0
- package/assets/frames/mesosfer/frame_1.txt +17 -0
- package/assets/frames/mesosfer/frame_10.txt +17 -0
- package/assets/frames/mesosfer/frame_11.txt +17 -0
- package/assets/frames/mesosfer/frame_12.txt +17 -0
- package/assets/frames/mesosfer/frame_13.txt +17 -0
- package/assets/frames/mesosfer/frame_14.txt +17 -0
- package/assets/frames/mesosfer/frame_15.txt +17 -0
- package/assets/frames/mesosfer/frame_16.txt +17 -0
- package/assets/frames/mesosfer/frame_17.txt +17 -0
- package/assets/frames/mesosfer/frame_18.txt +17 -0
- package/assets/frames/mesosfer/frame_19.txt +17 -0
- package/assets/frames/mesosfer/frame_2.txt +17 -0
- package/assets/frames/mesosfer/frame_20.txt +17 -0
- package/assets/frames/mesosfer/frame_21.txt +17 -0
- package/assets/frames/mesosfer/frame_22.txt +17 -0
- package/assets/frames/mesosfer/frame_23.txt +17 -0
- package/assets/frames/mesosfer/frame_24.txt +17 -0
- package/assets/frames/mesosfer/frame_25.txt +17 -0
- package/assets/frames/mesosfer/frame_26.txt +17 -0
- package/assets/frames/mesosfer/frame_27.txt +17 -0
- package/assets/frames/mesosfer/frame_28.txt +17 -0
- package/assets/frames/mesosfer/frame_29.txt +17 -0
- package/assets/frames/mesosfer/frame_3.txt +17 -0
- package/assets/frames/mesosfer/frame_30.txt +17 -0
- package/assets/frames/mesosfer/frame_31.txt +17 -0
- package/assets/frames/mesosfer/frame_32.txt +17 -0
- package/assets/frames/mesosfer/frame_33.txt +17 -0
- package/assets/frames/mesosfer/frame_34.txt +17 -0
- package/assets/frames/mesosfer/frame_35.txt +17 -0
- package/assets/frames/mesosfer/frame_36.txt +17 -0
- package/assets/frames/mesosfer/frame_4.txt +17 -0
- package/assets/frames/mesosfer/frame_5.txt +17 -0
- package/assets/frames/mesosfer/frame_6.txt +17 -0
- package/assets/frames/mesosfer/frame_7.txt +17 -0
- package/assets/frames/mesosfer/frame_8.txt +17 -0
- package/assets/frames/mesosfer/frame_9.txt +17 -0
- package/assets/frames/shapes/frame_1.txt +17 -0
- package/assets/frames/shapes/frame_10.txt +17 -0
- package/assets/frames/shapes/frame_11.txt +17 -0
- package/assets/frames/shapes/frame_12.txt +17 -0
- package/assets/frames/shapes/frame_13.txt +17 -0
- package/assets/frames/shapes/frame_14.txt +17 -0
- package/assets/frames/shapes/frame_15.txt +17 -0
- package/assets/frames/shapes/frame_16.txt +17 -0
- package/assets/frames/shapes/frame_17.txt +17 -0
- package/assets/frames/shapes/frame_18.txt +17 -0
- package/assets/frames/shapes/frame_19.txt +17 -0
- package/assets/frames/shapes/frame_2.txt +17 -0
- package/assets/frames/shapes/frame_20.txt +17 -0
- package/assets/frames/shapes/frame_21.txt +17 -0
- package/assets/frames/shapes/frame_22.txt +17 -0
- package/assets/frames/shapes/frame_23.txt +17 -0
- package/assets/frames/shapes/frame_24.txt +17 -0
- package/assets/frames/shapes/frame_25.txt +17 -0
- package/assets/frames/shapes/frame_26.txt +17 -0
- package/assets/frames/shapes/frame_27.txt +17 -0
- package/assets/frames/shapes/frame_28.txt +17 -0
- package/assets/frames/shapes/frame_29.txt +17 -0
- package/assets/frames/shapes/frame_3.txt +17 -0
- package/assets/frames/shapes/frame_30.txt +17 -0
- package/assets/frames/shapes/frame_31.txt +17 -0
- package/assets/frames/shapes/frame_32.txt +17 -0
- package/assets/frames/shapes/frame_33.txt +17 -0
- package/assets/frames/shapes/frame_34.txt +17 -0
- package/assets/frames/shapes/frame_35.txt +17 -0
- package/assets/frames/shapes/frame_36.txt +17 -0
- package/assets/frames/shapes/frame_4.txt +17 -0
- package/assets/frames/shapes/frame_5.txt +17 -0
- package/assets/frames/shapes/frame_6.txt +17 -0
- package/assets/frames/shapes/frame_7.txt +17 -0
- package/assets/frames/shapes/frame_8.txt +17 -0
- package/assets/frames/shapes/frame_9.txt +17 -0
- package/assets/frames/slug/frame_1.txt +17 -0
- package/assets/frames/slug/frame_10.txt +17 -0
- package/assets/frames/slug/frame_11.txt +17 -0
- package/assets/frames/slug/frame_12.txt +17 -0
- package/assets/frames/slug/frame_13.txt +17 -0
- package/assets/frames/slug/frame_14.txt +17 -0
- package/assets/frames/slug/frame_15.txt +17 -0
- package/assets/frames/slug/frame_16.txt +17 -0
- package/assets/frames/slug/frame_17.txt +17 -0
- package/assets/frames/slug/frame_18.txt +17 -0
- package/assets/frames/slug/frame_19.txt +17 -0
- package/assets/frames/slug/frame_2.txt +17 -0
- package/assets/frames/slug/frame_20.txt +17 -0
- package/assets/frames/slug/frame_21.txt +17 -0
- package/assets/frames/slug/frame_22.txt +17 -0
- package/assets/frames/slug/frame_23.txt +17 -0
- package/assets/frames/slug/frame_24.txt +17 -0
- package/assets/frames/slug/frame_25.txt +17 -0
- package/assets/frames/slug/frame_26.txt +17 -0
- package/assets/frames/slug/frame_27.txt +17 -0
- package/assets/frames/slug/frame_28.txt +17 -0
- package/assets/frames/slug/frame_29.txt +17 -0
- package/assets/frames/slug/frame_3.txt +17 -0
- package/assets/frames/slug/frame_30.txt +17 -0
- package/assets/frames/slug/frame_31.txt +17 -0
- package/assets/frames/slug/frame_32.txt +17 -0
- package/assets/frames/slug/frame_33.txt +17 -0
- package/assets/frames/slug/frame_34.txt +17 -0
- package/assets/frames/slug/frame_35.txt +17 -0
- package/assets/frames/slug/frame_36.txt +17 -0
- package/assets/frames/slug/frame_4.txt +17 -0
- package/assets/frames/slug/frame_5.txt +17 -0
- package/assets/frames/slug/frame_6.txt +17 -0
- package/assets/frames/slug/frame_7.txt +17 -0
- package/assets/frames/slug/frame_8.txt +17 -0
- package/assets/frames/slug/frame_9.txt +17 -0
- package/assets/frames/vbars/frame_1.txt +17 -0
- package/assets/frames/vbars/frame_10.txt +17 -0
- package/assets/frames/vbars/frame_11.txt +17 -0
- package/assets/frames/vbars/frame_12.txt +17 -0
- package/assets/frames/vbars/frame_13.txt +17 -0
- package/assets/frames/vbars/frame_14.txt +17 -0
- package/assets/frames/vbars/frame_15.txt +17 -0
- package/assets/frames/vbars/frame_16.txt +17 -0
- package/assets/frames/vbars/frame_17.txt +17 -0
- package/assets/frames/vbars/frame_18.txt +17 -0
- package/assets/frames/vbars/frame_19.txt +17 -0
- package/assets/frames/vbars/frame_2.txt +17 -0
- package/assets/frames/vbars/frame_20.txt +17 -0
- package/assets/frames/vbars/frame_21.txt +17 -0
- package/assets/frames/vbars/frame_22.txt +17 -0
- package/assets/frames/vbars/frame_23.txt +17 -0
- package/assets/frames/vbars/frame_24.txt +17 -0
- package/assets/frames/vbars/frame_25.txt +17 -0
- package/assets/frames/vbars/frame_26.txt +17 -0
- package/assets/frames/vbars/frame_27.txt +17 -0
- package/assets/frames/vbars/frame_28.txt +17 -0
- package/assets/frames/vbars/frame_29.txt +17 -0
- package/assets/frames/vbars/frame_3.txt +17 -0
- package/assets/frames/vbars/frame_30.txt +17 -0
- package/assets/frames/vbars/frame_31.txt +17 -0
- package/assets/frames/vbars/frame_32.txt +17 -0
- package/assets/frames/vbars/frame_33.txt +17 -0
- package/assets/frames/vbars/frame_34.txt +17 -0
- package/assets/frames/vbars/frame_35.txt +17 -0
- package/assets/frames/vbars/frame_36.txt +17 -0
- package/assets/frames/vbars/frame_4.txt +17 -0
- package/assets/frames/vbars/frame_5.txt +17 -0
- package/assets/frames/vbars/frame_6.txt +17 -0
- package/assets/frames/vbars/frame_7.txt +17 -0
- package/assets/frames/vbars/frame_8.txt +17 -0
- package/assets/frames/vbars/frame_9.txt +17 -0
- package/bin/pikaa.js +1 -0
- package/dist/cli.js +3484 -879
- package/dist/index.js +6835 -437
- package/package.json +6 -1
- package/skills/adaptyv/SKILL.md +240 -0
- package/skills/adaptyv/references/api-endpoints.md +690 -0
- package/skills/aeon/SKILL.md +402 -0
- package/skills/aeon/references/anomaly_detection.md +154 -0
- package/skills/aeon/references/classification.md +144 -0
- package/skills/aeon/references/clustering.md +123 -0
- package/skills/aeon/references/datasets_benchmarking.md +392 -0
- package/skills/aeon/references/distances.md +256 -0
- package/skills/aeon/references/forecasting.md +109 -0
- package/skills/aeon/references/networks.md +289 -0
- package/skills/aeon/references/regression.md +118 -0
- package/skills/aeon/references/segmentation.md +163 -0
- package/skills/aeon/references/similarity_search.md +187 -0
- package/skills/aeon/references/transformations.md +246 -0
- package/skills/analytical-method-validation/SKILL.md +299 -0
- package/skills/analytical-method-validation/assets/validation-protocol-template.md +106 -0
- package/skills/analytical-method-validation/assets/validation-report-template.md +116 -0
- package/skills/analytical-method-validation/references/compendial-and-clsi.md +96 -0
- package/skills/analytical-method-validation/references/framework-selection.md +87 -0
- package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +123 -0
- package/skills/analytical-method-validation/references/ich-q2r2.md +229 -0
- package/skills/analytical-method-validation/references/source-ledger.md +125 -0
- package/skills/analytical-method-validation/references/statistics.md +209 -0
- package/skills/analytical-method-validation/scripts/_catalog.py +499 -0
- package/skills/analytical-method-validation/scripts/_common.py +955 -0
- package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +328 -0
- package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +293 -0
- package/skills/analytical-method-validation/scripts/check_detection_limits.py +310 -0
- package/skills/analytical-method-validation/scripts/check_response.py +243 -0
- package/skills/analytical-method-validation/scripts/compare_methods.py +215 -0
- package/skills/analytical-method-validation/scripts/plan_validation.py +381 -0
- package/skills/anndata/SKILL.md +431 -0
- package/skills/anndata/references/best_practices.md +532 -0
- package/skills/anndata/references/concatenation.md +399 -0
- package/skills/anndata/references/data_structure.md +314 -0
- package/skills/anndata/references/io_operations.md +466 -0
- package/skills/anndata/references/manipulation.md +516 -0
- package/skills/arbor/SKILL.md +152 -0
- package/skills/arbor/references/arbor-upstream.md +91 -0
- package/skills/arbor/references/executor-brief.md +68 -0
- package/skills/arbor/references/htr-methodology.md +177 -0
- package/skills/arbor/references/report-template.md +39 -0
- package/skills/arbor/scripts/tree.py +564 -0
- package/skills/arboreto/SKILL.md +267 -0
- package/skills/arboreto/references/algorithms.md +152 -0
- package/skills/arboreto/references/basic_inference.md +181 -0
- package/skills/arboreto/references/distributed_computing.md +242 -0
- package/skills/arboreto/scripts/basic_grn_inference.py +107 -0
- package/skills/astropy/SKILL.md +353 -0
- package/skills/astropy/references/coordinates.md +280 -0
- package/skills/astropy/references/cosmology.md +309 -0
- package/skills/astropy/references/fits.md +398 -0
- package/skills/astropy/references/tables.md +495 -0
- package/skills/astropy/references/time.md +412 -0
- package/skills/astropy/references/units.md +178 -0
- package/skills/astropy/references/wcs_and_other_modules.md +377 -0
- package/skills/autoskill/SKILL.md +233 -0
- package/skills/autoskill/config.yaml +53 -0
- package/skills/autoskill/references/https-proxy.md +62 -0
- package/skills/autoskill/references/screenpipe-config.yaml +61 -0
- package/skills/autoskill/scripts/autoskill.py +35 -0
- package/skills/autoskill/scripts/backends.py +116 -0
- package/skills/autoskill/scripts/cluster.py +54 -0
- package/skills/autoskill/scripts/doctor.py +108 -0
- package/skills/autoskill/scripts/fetch_window.py +33 -0
- package/skills/autoskill/scripts/match_skills.py +46 -0
- package/skills/autoskill/scripts/promote.py +58 -0
- package/skills/autoskill/scripts/redact.py +40 -0
- package/skills/autoskill/scripts/run.py +194 -0
- package/skills/autoskill/scripts/synthesize.py +72 -0
- package/skills/benchling-integration/SKILL.md +229 -0
- package/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/skills/benchling-integration/references/authentication.md +390 -0
- package/skills/benchling-integration/references/core_capabilities.md +355 -0
- package/skills/benchling-integration/references/eventbridge.md +255 -0
- package/skills/benchling-integration/references/sdk_reference.md +772 -0
- package/skills/bgpt-paper-search/SKILL.md +75 -0
- package/skills/bids/SKILL.md +237 -0
- package/skills/bids/references/beps.yml +637 -0
- package/skills/bids/references/bids_schema.json +21015 -0
- package/skills/bids/references/bids_specification.md +165 -0
- package/skills/bids/references/conversion_tools.md +475 -0
- package/skills/bids/references/core_workflows.md +552 -0
- package/skills/bids/references/metadata_fields.md +365 -0
- package/skills/bids/scripts/update_schema.py +89 -0
- package/skills/biopython/SKILL.md +472 -0
- package/skills/biopython/references/advanced.md +580 -0
- package/skills/biopython/references/alignment.md +377 -0
- package/skills/biopython/references/blast.md +463 -0
- package/skills/biopython/references/databases.md +492 -0
- package/skills/biopython/references/phylogenetics.md +566 -0
- package/skills/biopython/references/sequence_io.md +289 -0
- package/skills/biopython/references/structure.md +564 -0
- package/skills/bioservices/SKILL.md +399 -0
- package/skills/bioservices/references/identifier_mapping.md +685 -0
- package/skills/bioservices/references/services_reference.md +638 -0
- package/skills/bioservices/references/workflow_patterns.md +813 -0
- package/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/skills/bioservices/scripts/compound_cross_reference.py +387 -0
- package/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/skills/bioservices/scripts/protein_analysis_workflow.py +441 -0
- package/skills/bulk-rnaseq/SKILL.md +198 -0
- package/skills/bulk-rnaseq/references/counts-and-handoff.md +91 -0
- package/skills/bulk-rnaseq/references/design-and-qc.md +68 -0
- package/skills/bulk-rnaseq/references/upstream-manual.md +128 -0
- package/skills/bulk-rnaseq/references/upstream-nfcore.md +108 -0
- package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +203 -0
- package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +206 -0
- package/skills/cellxgene-census/SKILL.md +283 -0
- package/skills/cellxgene-census/references/census_schema.md +218 -0
- package/skills/cellxgene-census/references/common_patterns.md +368 -0
- package/skills/cellxgene-census/references/core_workflow_patterns.md +297 -0
- package/skills/cirq/SKILL.md +370 -0
- package/skills/cirq/references/building.md +307 -0
- package/skills/cirq/references/experiments.md +572 -0
- package/skills/cirq/references/hardware.md +527 -0
- package/skills/cirq/references/noise.md +514 -0
- package/skills/cirq/references/simulation.md +353 -0
- package/skills/cirq/references/transformation.md +416 -0
- package/skills/citation-management/SKILL.md +329 -0
- package/skills/citation-management/assets/bibtex_template.bib +264 -0
- package/skills/citation-management/assets/citation_checklist.md +386 -0
- package/skills/citation-management/references/best_practices.md +91 -0
- package/skills/citation-management/references/bibtex_formatting.md +908 -0
- package/skills/citation-management/references/citation_validation.md +835 -0
- package/skills/citation-management/references/core_workflow.md +569 -0
- package/skills/citation-management/references/example_workflows.md +126 -0
- package/skills/citation-management/references/google_scholar_search.md +732 -0
- package/skills/citation-management/references/metadata_extraction.md +870 -0
- package/skills/citation-management/references/pubmed_search.md +839 -0
- package/skills/citation-management/references/script_reference.md +250 -0
- package/skills/citation-management/references/search_strategies.md +110 -0
- package/skills/citation-management/scripts/_common.py +331 -0
- package/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- package/skills/citation-management/scripts/extract_metadata.py +690 -0
- package/skills/citation-management/scripts/format_bibtex.py +356 -0
- package/skills/citation-management/scripts/search_google_scholar.py +268 -0
- package/skills/citation-management/scripts/search_openalex.py +297 -0
- package/skills/citation-management/scripts/search_pubmed.py +419 -0
- package/skills/citation-management/scripts/validate_citations.py +688 -0
- package/skills/clinical-decision-support/SKILL.md +238 -0
- package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +114 -0
- package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +115 -0
- package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +81 -0
- package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +108 -0
- package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +176 -0
- package/skills/clinical-decision-support/assets/evidence_profile_template.json +139 -0
- package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +134 -0
- package/skills/clinical-decision-support/references/README.md +62 -0
- package/skills/clinical-decision-support/references/cohort_evaluation.md +142 -0
- package/skills/clinical-decision-support/references/decision_logic_traceability.md +146 -0
- package/skills/clinical-decision-support/references/evidence_profiles.md +153 -0
- package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +152 -0
- package/skills/clinical-decision-support/references/privacy_and_disclosure.md +144 -0
- package/skills/clinical-decision-support/references/regulatory_and_governance.md +104 -0
- package/skills/clinical-decision-support/references/safety_and_scope.md +103 -0
- package/skills/clinical-decision-support/references/security_validation.md +60 -0
- package/skills/clinical-decision-support/references/sources.md +119 -0
- package/skills/clinical-decision-support/references/study_reporting.md +134 -0
- package/skills/clinical-decision-support/references/survival_analysis.md +156 -0
- package/skills/clinical-decision-support/scripts/_common.py +223 -0
- package/skills/clinical-decision-support/scripts/cohort_table_generator.py +288 -0
- package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +313 -0
- package/skills/clinical-decision-support/scripts/deidentification_checklist.py +260 -0
- package/skills/clinical-decision-support/scripts/evidence_profile_check.py +259 -0
- package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +345 -0
- package/skills/clinical-decision-support/scripts/survival_plan_validator.py +294 -0
- package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +269 -0
- package/skills/clinical-reports/SKILL.md +248 -0
- package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +1 -0
- package/skills/clinical-reports/assets/case_report_template.json +43 -0
- package/skills/clinical-reports/assets/clinical_trial_csr_template.json +51 -0
- package/skills/clinical-reports/assets/clinical_trial_results_template.json +66 -0
- package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +49 -0
- package/skills/clinical-reports/assets/consistency_manifest_template.json +15 -0
- package/skills/clinical-reports/assets/deidentification_process_checklist.json +56 -0
- package/skills/clinical-reports/assets/lab_report_template.json +36 -0
- package/skills/clinical-reports/assets/pathology_report_template.json +36 -0
- package/skills/clinical-reports/assets/provenance_manifest_template.json +17 -0
- package/skills/clinical-reports/assets/quality_review_checklist.json +34 -0
- package/skills/clinical-reports/assets/radiology_report_template.json +34 -0
- package/skills/clinical-reports/assets/research_summary_template.json +36 -0
- package/skills/clinical-reports/assets/terminology_manifest_template.json +11 -0
- package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +70 -0
- package/skills/clinical-reports/references/README.md +34 -0
- package/skills/clinical-reports/references/case_report_guidelines.md +72 -0
- package/skills/clinical-reports/references/clinical_trial_reporting.md +97 -0
- package/skills/clinical-reports/references/data_presentation.md +92 -0
- package/skills/clinical-reports/references/diagnostic_reports_standards.md +76 -0
- package/skills/clinical-reports/references/medical_terminology.md +84 -0
- package/skills/clinical-reports/references/privacy_and_deidentification.md +84 -0
- package/skills/clinical-reports/references/professional_review.md +78 -0
- package/skills/clinical-reports/references/report_type_routing.md +57 -0
- package/skills/clinical-reports/references/safety_reporting.md +109 -0
- package/skills/clinical-reports/references/sources.md +75 -0
- package/skills/clinical-reports/scripts/_common.py +263 -0
- package/skills/clinical-reports/scripts/check_deidentification.py +298 -0
- package/skills/clinical-reports/scripts/consistency_checker.py +390 -0
- package/skills/clinical-reports/scripts/format_adverse_events.py +455 -0
- package/skills/clinical-reports/scripts/generate_report_template.py +115 -0
- package/skills/clinical-reports/scripts/provenance_validator.py +263 -0
- package/skills/clinical-reports/scripts/terminology_validator.py +277 -0
- package/skills/clinical-reports/scripts/validate_case_report.py +278 -0
- package/skills/clinical-reports/scripts/validate_trial_report.py +534 -0
- package/skills/cobrapy/SKILL.md +496 -0
- package/skills/cobrapy/references/api_quick_reference.md +665 -0
- package/skills/cobrapy/references/workflows.md +600 -0
- package/skills/consciousness-council/SKILL.md +151 -0
- package/skills/consciousness-council/references/advanced-configurations.md +96 -0
- package/skills/dask/SKILL.md +482 -0
- package/skills/dask/references/arrays.md +495 -0
- package/skills/dask/references/bags.md +468 -0
- package/skills/dask/references/best-practices.md +277 -0
- package/skills/dask/references/dataframes.md +370 -0
- package/skills/dask/references/futures.md +541 -0
- package/skills/dask/references/schedulers.md +517 -0
- package/skills/database-lookup/SKILL.md +386 -0
- package/skills/database-lookup/references/addgene.md +38 -0
- package/skills/database-lookup/references/alphafold.md +52 -0
- package/skills/database-lookup/references/alphavantage.md +261 -0
- package/skills/database-lookup/references/bea.md +409 -0
- package/skills/database-lookup/references/bindingdb.md +85 -0
- package/skills/database-lookup/references/biogrid.md +110 -0
- package/skills/database-lookup/references/bls.md +235 -0
- package/skills/database-lookup/references/brenda.md +71 -0
- package/skills/database-lookup/references/cbioportal.md +206 -0
- package/skills/database-lookup/references/census.md +251 -0
- package/skills/database-lookup/references/chebi.md +103 -0
- package/skills/database-lookup/references/chembl.md +80 -0
- package/skills/database-lookup/references/clinicaltrials.md +86 -0
- package/skills/database-lookup/references/clinpgx.md +64 -0
- package/skills/database-lookup/references/clinvar.md +91 -0
- package/skills/database-lookup/references/cod.md +121 -0
- package/skills/database-lookup/references/cosmic.md +59 -0
- package/skills/database-lookup/references/dailymed.md +65 -0
- package/skills/database-lookup/references/database_selection_guide.md +166 -0
- package/skills/database-lookup/references/datacommons.md +237 -0
- package/skills/database-lookup/references/dbsnp.md +143 -0
- package/skills/database-lookup/references/disgenet.md +52 -0
- package/skills/database-lookup/references/drugbank.md +54 -0
- package/skills/database-lookup/references/ecb.md +191 -0
- package/skills/database-lookup/references/emdb.md +37 -0
- package/skills/database-lookup/references/ena.md +372 -0
- package/skills/database-lookup/references/encode.md +47 -0
- package/skills/database-lookup/references/ensembl.md +539 -0
- package/skills/database-lookup/references/epa.md +232 -0
- package/skills/database-lookup/references/eurostat.md +237 -0
- package/skills/database-lookup/references/fda.md +64 -0
- package/skills/database-lookup/references/federal-reserve.md +216 -0
- package/skills/database-lookup/references/fred.md +297 -0
- package/skills/database-lookup/references/gene-ontology.md +147 -0
- package/skills/database-lookup/references/geo.md +130 -0
- package/skills/database-lookup/references/gnomad.md +93 -0
- package/skills/database-lookup/references/gtex.md +136 -0
- package/skills/database-lookup/references/gwas-catalog.md +46 -0
- package/skills/database-lookup/references/hca.md +35 -0
- package/skills/database-lookup/references/hpo.md +48 -0
- package/skills/database-lookup/references/human-protein-atlas.md +57 -0
- package/skills/database-lookup/references/interpro.md +120 -0
- package/skills/database-lookup/references/jaspar.md +50 -0
- package/skills/database-lookup/references/kegg.md +78 -0
- package/skills/database-lookup/references/lincs-l1000.md +68 -0
- package/skills/database-lookup/references/materials-project.md +123 -0
- package/skills/database-lookup/references/metabolomics-workbench.md +98 -0
- package/skills/database-lookup/references/monarch.md +46 -0
- package/skills/database-lookup/references/mousemine.md +40 -0
- package/skills/database-lookup/references/nasa-exoplanet-archive.md +112 -0
- package/skills/database-lookup/references/nasa.md +121 -0
- package/skills/database-lookup/references/ncbi-gene.md +64 -0
- package/skills/database-lookup/references/ncbi-protein.md +104 -0
- package/skills/database-lookup/references/ncbi-taxonomy.md +121 -0
- package/skills/database-lookup/references/nist.md +105 -0
- package/skills/database-lookup/references/noaa.md +199 -0
- package/skills/database-lookup/references/omim.md +114 -0
- package/skills/database-lookup/references/opentargets.md +459 -0
- package/skills/database-lookup/references/openweathermap.md +255 -0
- package/skills/database-lookup/references/pdb.md +121 -0
- package/skills/database-lookup/references/pride.md +74 -0
- package/skills/database-lookup/references/pubchem.md +145 -0
- package/skills/database-lookup/references/quickgo.md +45 -0
- package/skills/database-lookup/references/reactome.md +140 -0
- package/skills/database-lookup/references/retrieval-contract.md +123 -0
- package/skills/database-lookup/references/rummageo.md +32 -0
- package/skills/database-lookup/references/sdss.md +130 -0
- package/skills/database-lookup/references/sec-edgar.md +315 -0
- package/skills/database-lookup/references/simbad.md +405 -0
- package/skills/database-lookup/references/sra.md +149 -0
- package/skills/database-lookup/references/string.md +283 -0
- package/skills/database-lookup/references/tcga-gdc.md +58 -0
- package/skills/database-lookup/references/treasury.md +215 -0
- package/skills/database-lookup/references/ucsc-genome.md +135 -0
- package/skills/database-lookup/references/uniprot.md +283 -0
- package/skills/database-lookup/references/usgs.md +260 -0
- package/skills/database-lookup/references/uspto.md +130 -0
- package/skills/database-lookup/references/who.md +283 -0
- package/skills/database-lookup/references/worldbank.md +239 -0
- package/skills/database-lookup/references/zinc.md +202 -0
- package/skills/datamol/SKILL.md +200 -0
- package/skills/datamol/references/conformers_module.md +131 -0
- package/skills/datamol/references/core_api.md +136 -0
- package/skills/datamol/references/core_workflows.md +451 -0
- package/skills/datamol/references/descriptors_viz.md +195 -0
- package/skills/datamol/references/fragments_scaffolds.md +174 -0
- package/skills/datamol/references/io_module.md +112 -0
- package/skills/datamol/references/reactions_data.md +218 -0
- package/skills/datamol/references/workflow_patterns.md +104 -0
- package/skills/deepchem/SKILL.md +244 -0
- package/skills/deepchem/references/api_reference.md +305 -0
- package/skills/deepchem/references/core_capabilities.md +276 -0
- package/skills/deepchem/references/typical_workflows.md +109 -0
- package/skills/deepchem/references/workflows.md +491 -0
- package/skills/deepchem/scripts/graph_neural_network.py +350 -0
- package/skills/deepchem/scripts/predict_solubility.py +223 -0
- package/skills/deepchem/scripts/transfer_learning.py +443 -0
- package/skills/deepspot-m/SKILL.md +175 -0
- package/skills/deepspot-m/references/api.md +186 -0
- package/skills/deepspot-m/references/whole_slide.md +174 -0
- package/skills/deeptools/SKILL.md +412 -0
- package/skills/deeptools/assets/quick_reference.md +65 -0
- package/skills/deeptools/references/core_workflows.md +134 -0
- package/skills/deeptools/references/effective_genome_sizes.md +118 -0
- package/skills/deeptools/references/normalization_methods.md +424 -0
- package/skills/deeptools/references/tools_reference.md +569 -0
- package/skills/deeptools/references/workflows.md +476 -0
- package/skills/deeptools/scripts/validate_files.py +195 -0
- package/skills/deeptools/scripts/workflow_generator.py +520 -0
- package/skills/depmap/SKILL.md +301 -0
- package/skills/depmap/references/dependency_analysis.md +178 -0
- package/skills/dhdna-profiler/SKILL.md +184 -0
- package/skills/dhdna-profiler/references/advanced-profiling.md +72 -0
- package/skills/diffdock/SKILL.md +488 -0
- package/skills/diffdock/assets/batch_template.csv +4 -0
- package/skills/diffdock/assets/custom_inference_config.yaml +94 -0
- package/skills/diffdock/references/confidence_and_limitations.md +182 -0
- package/skills/diffdock/references/parameters_reference.md +173 -0
- package/skills/diffdock/references/workflows_examples.md +401 -0
- package/skills/diffdock/scripts/analyze_results.py +346 -0
- package/skills/diffdock/scripts/prepare_batch_csv.py +257 -0
- package/skills/diffdock/scripts/setup_check.py +283 -0
- package/skills/dnanexus-integration/SKILL.md +325 -0
- package/skills/dnanexus-integration/references/app-development.md +371 -0
- package/skills/dnanexus-integration/references/authentication.md +226 -0
- package/skills/dnanexus-integration/references/configuration.md +444 -0
- package/skills/dnanexus-integration/references/data-operations.md +474 -0
- package/skills/dnanexus-integration/references/job-execution.md +482 -0
- package/skills/dnanexus-integration/references/operations-and-troubleshooting.md +506 -0
- package/skills/dnanexus-integration/references/python-sdk.md +548 -0
- package/skills/dnanexus-integration/references/sources.md +168 -0
- package/skills/dnanexus-integration/references/workflow-languages.md +292 -0
- package/skills/dnanexus-integration/scripts/inspect_dxpy.py +366 -0
- package/skills/dnanexus-integration/scripts/validate_dxapp.py +796 -0
- package/skills/docx/LICENSE.txt +30 -0
- package/skills/docx/SKILL.md +99 -0
- package/skills/docx/scripts/__init__.py +1 -0
- package/skills/docx/scripts/accept_changes.py +135 -0
- package/skills/docx/scripts/comment.py +368 -0
- package/skills/docx/scripts/merge_runs.py +310 -0
- package/skills/docx/scripts/office/helpers/__init__.py +111 -0
- package/skills/docx/scripts/office/helpers/pptx_chart.py +170 -0
- package/skills/docx/scripts/office/helpers/pptx_slide.py +60 -0
- package/skills/docx/scripts/office/helpers/pptx_theme.py +114 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/skills/docx/scripts/office/schemas/mce/mc.xsd +75 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/skills/docx/scripts/office/soffice.py +232 -0
- package/skills/docx/scripts/office/validate.py +173 -0
- package/skills/docx/scripts/office/validators/__init__.py +15 -0
- package/skills/docx/scripts/office/validators/base.py +875 -0
- package/skills/docx/scripts/office/validators/docx.py +466 -0
- package/skills/docx/scripts/office/validators/pptx.py +441 -0
- package/skills/docx/scripts/office/validators/redlining.py +299 -0
- package/skills/docx/scripts/templates/comments.xml +3 -0
- package/skills/docx/scripts/templates/commentsExtended.xml +3 -0
- package/skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- package/skills/docx/scripts/templates/commentsIds.xml +3 -0
- package/skills/docx/scripts/templates/people.xml +3 -0
- package/skills/esm/SKILL.md +334 -0
- package/skills/esm/references/biohub-platform.md +111 -0
- package/skills/esm/references/esm-c-api.md +609 -0
- package/skills/esm/references/esm3-api.md +462 -0
- package/skills/esm/references/forge-api.md +675 -0
- package/skills/esm/references/workflows.md +685 -0
- package/skills/etetoolkit/SKILL.md +327 -0
- package/skills/etetoolkit/references/api_reference.md +546 -0
- package/skills/etetoolkit/references/migration-ete3-to-ete4.md +579 -0
- package/skills/etetoolkit/references/taxonomy.md +362 -0
- package/skills/etetoolkit/references/visualization.md +516 -0
- package/skills/etetoolkit/references/workflows.md +537 -0
- package/skills/etetoolkit/scripts/quick_visualize.py +455 -0
- package/skills/etetoolkit/scripts/tree_operations.py +446 -0
- package/skills/exa-search/SKILL.md +102 -0
- package/skills/exa-search/references/web-extract.md +53 -0
- package/skills/exa-search/references/web-search.md +119 -0
- package/skills/exa-search/scripts/exa_extract.py +117 -0
- package/skills/exa-search/scripts/exa_search.py +179 -0
- package/skills/executing-plans/SKILL.md +14 -0
- package/skills/experimental-design/SKILL.md +234 -0
- package/skills/experimental-design/references/design_types.md +129 -0
- package/skills/experimental-design/references/factorial_and_doe.md +130 -0
- package/skills/experimental-design/references/randomization_and_blocking.md +116 -0
- package/skills/experimental-design/references/sequential_and_adaptive.md +97 -0
- package/skills/experimental-design/scripts/doe_designs.py +183 -0
- package/skills/experimental-design/scripts/randomization.py +171 -0
- package/skills/exploratory-data-analysis/SKILL.md +280 -0
- package/skills/exploratory-data-analysis/assets/report_template.md +202 -0
- package/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +192 -0
- package/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +183 -0
- package/skills/exploratory-data-analysis/references/general_scientific_formats.md +259 -0
- package/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +189 -0
- package/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +217 -0
- package/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +191 -0
- package/skills/exploratory-data-analysis/scripts/__init__.py +1 -0
- package/skills/exploratory-data-analysis/scripts/_capabilities.py +576 -0
- package/skills/exploratory-data-analysis/scripts/_common.py +460 -0
- package/skills/exploratory-data-analysis/scripts/_structured.py +391 -0
- package/skills/exploratory-data-analysis/scripts/_tabular.py +905 -0
- package/skills/exploratory-data-analysis/scripts/capability_manifest.py +184 -0
- package/skills/exploratory-data-analysis/scripts/distribution_sensitivity.py +117 -0
- package/skills/exploratory-data-analysis/scripts/eda_analyzer.py +345 -0
- package/skills/exploratory-data-analysis/scripts/image_inspector.py +214 -0
- package/skills/exploratory-data-analysis/scripts/missingness_leakage_audit.py +130 -0
- package/skills/exploratory-data-analysis/scripts/report_scaffold.py +143 -0
- package/skills/exploratory-data-analysis/scripts/sequence_inspector.py +255 -0
- package/skills/exploratory-data-analysis/scripts/tabular_profile.py +109 -0
- package/skills/flowio/SKILL.md +310 -0
- package/skills/flowio/references/api_reference.md +355 -0
- package/skills/flowio/references/fcs_semantics.md +315 -0
- package/skills/flowio/references/sources.md +89 -0
- package/skills/flowio/references/troubleshooting.md +399 -0
- package/skills/flowio/references/workflows.md +368 -0
- package/skills/flowio/scripts/inspect_fcs.py +439 -0
- package/skills/fluidsim/SKILL.md +279 -0
- package/skills/fluidsim/references/advanced_features.md +347 -0
- package/skills/fluidsim/references/installation.md +263 -0
- package/skills/fluidsim/references/output_analysis.md +314 -0
- package/skills/fluidsim/references/parameters.md +322 -0
- package/skills/fluidsim/references/simulation_workflow.md +329 -0
- package/skills/fluidsim/references/solvers.md +191 -0
- package/skills/fluidsim/scripts/__init__.py +1 -0
- package/skills/fluidsim/scripts/_common.py +491 -0
- package/skills/fluidsim/scripts/_schema.py +872 -0
- package/skills/fluidsim/scripts/budget_summary.py +396 -0
- package/skills/fluidsim/scripts/grid_resource_estimator.py +286 -0
- package/skills/fluidsim/scripts/output_inventory.py +353 -0
- package/skills/fluidsim/scripts/restart_compatibility.py +424 -0
- package/skills/fluidsim/scripts/simulation_dry_run.py +246 -0
- package/skills/fluidsim/scripts/solver_config_validator.py +70 -0
- package/skills/frontend-design/SKILL.md +99 -0
- package/skills/generate-image/SKILL.md +304 -0
- package/skills/generate-image/references/models.md +173 -0
- package/skills/generate-image/scripts/generate_image.py +752 -0
- package/skills/geniml/SKILL.md +310 -0
- package/skills/geniml/references/bedspace.md +267 -0
- package/skills/geniml/references/consensus_peaks.md +334 -0
- package/skills/geniml/references/region2vec.md +289 -0
- package/skills/geniml/references/scembed.md +307 -0
- package/skills/geniml/references/utilities.md +385 -0
- package/skills/geniml/scripts/__init__.py +1 -0
- package/skills/geniml/scripts/_common.py +399 -0
- package/skills/geniml/scripts/bed_validator.py +363 -0
- package/skills/geniml/scripts/consensus_plan.py +416 -0
- package/skills/geniml/scripts/corpus_auditor.py +304 -0
- package/skills/geniml/scripts/embedding_plan.py +476 -0
- package/skills/geniml/scripts/model_artifact_inspector.py +358 -0
- package/skills/geniml/scripts/tokenizer_compatibility.py +321 -0
- package/skills/genomic-coordinates/SKILL.md +189 -0
- package/skills/genomic-coordinates/references/format-conventions.md +205 -0
- package/skills/genomic-coordinates/references/reference-builds.md +154 -0
- package/skills/genomic-coordinates/references/transcript-coordinates.md +141 -0
- package/skills/genomic-coordinates/references/variant-representation.md +155 -0
- package/skills/genomic-coordinates/scripts/_common.py +335 -0
- package/skills/genomic-coordinates/scripts/audit_intervals.py +511 -0
- package/skills/genomic-coordinates/scripts/check_contigs.py +382 -0
- package/skills/genomic-coordinates/scripts/convert_coords.py +180 -0
- package/skills/genomic-coordinates/scripts/normalize_variant.py +290 -0
- package/skills/genomic-intelligence/SKILL.md +243 -0
- package/skills/genomic-intelligence/references/api-and-auth.md +45 -0
- package/skills/genomic-intelligence/references/mcp.md +94 -0
- package/skills/genomic-intelligence/references/sequence-acquisition.md +52 -0
- package/skills/genomic-intelligence/references/tasks.md +75 -0
- package/skills/geomaster/README.md +105 -0
- package/skills/geomaster/SKILL.md +366 -0
- package/skills/geomaster/references/advanced-gis.md +376 -0
- package/skills/geomaster/references/big-data.md +363 -0
- package/skills/geomaster/references/code-examples.md +531 -0
- package/skills/geomaster/references/coordinate-systems.md +364 -0
- package/skills/geomaster/references/core-libraries.md +273 -0
- package/skills/geomaster/references/data-sources.md +330 -0
- package/skills/geomaster/references/gis-software.md +369 -0
- package/skills/geomaster/references/industry-applications.md +420 -0
- package/skills/geomaster/references/machine-learning.md +462 -0
- package/skills/geomaster/references/programming-languages.md +456 -0
- package/skills/geomaster/references/remote-sensing.md +370 -0
- package/skills/geomaster/references/scientific-domains.md +416 -0
- package/skills/geomaster/references/specialized-topics.md +428 -0
- package/skills/geomaster/references/troubleshooting.md +439 -0
- package/skills/geopandas/SKILL.md +250 -0
- package/skills/geopandas/references/crs-management.md +231 -0
- package/skills/geopandas/references/data-io.md +323 -0
- package/skills/geopandas/references/data-structures.md +207 -0
- package/skills/geopandas/references/geometric-operations.md +262 -0
- package/skills/geopandas/references/spatial-analysis.md +294 -0
- package/skills/geopandas/references/visualization.md +230 -0
- package/skills/geopandas/scripts/_common.py +605 -0
- package/skills/geopandas/scripts/crs_reprojection_plan.py +210 -0
- package/skills/geopandas/scripts/export_plan.py +305 -0
- package/skills/geopandas/scripts/geometry_validity_report.py +227 -0
- package/skills/geopandas/scripts/sensitive_coordinates_checklist.py +230 -0
- package/skills/geopandas/scripts/spatial_join_audit.py +368 -0
- package/skills/geopandas/scripts/vector_inventory.py +140 -0
- package/skills/get-available-resources/SKILL.md +260 -0
- package/skills/get-available-resources/references/resource_semantics.md +206 -0
- package/skills/get-available-resources/references/snapshot_schema.md +172 -0
- package/skills/get-available-resources/references/sources.md +124 -0
- package/skills/get-available-resources/scripts/_common.py +190 -0
- package/skills/get-available-resources/scripts/accelerator_diagnostics.py +151 -0
- package/skills/get-available-resources/scripts/detect_resources.py +1767 -0
- package/skills/get-available-resources/scripts/plan_workload.py +311 -0
- package/skills/get-available-resources/scripts/snapshot_tools.py +486 -0
- package/skills/gget/SKILL.md +153 -0
- package/skills/gget/references/common_workflows.md +120 -0
- package/skills/gget/references/database_info.md +336 -0
- package/skills/gget/references/module_catalog.md +733 -0
- package/skills/gget/references/module_reference.md +526 -0
- package/skills/gget/references/workflows.md +815 -0
- package/skills/gget/scripts/batch_sequence_analysis.py +192 -0
- package/skills/gget/scripts/enrichment_pipeline.py +235 -0
- package/skills/gget/scripts/gene_analysis.py +175 -0
- package/skills/ginkgo-cloud-lab/SKILL.md +106 -0
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-hibit.md +53 -0
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md +85 -0
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md +71 -0
- package/skills/ginkgo-cloud-lab/references/cfps-expression-purification-quantification.md +60 -0
- package/skills/ginkgo-cloud-lab/references/cfps-strep-purification-thermal-shift.md +63 -0
- package/skills/ginkgo-cloud-lab/references/cfps-strep-tag-purification-a280.md +55 -0
- package/skills/ginkgo-cloud-lab/references/echo-ms-cfps-detection.md +49 -0
- package/skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md +56 -0
- package/skills/ginkgo-cloud-lab/references/ecoli-expression-purification-quantification.md +49 -0
- package/skills/ginkgo-cloud-lab/references/ecoli-minibinder-expression-histag-a280.md +62 -0
- package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-hibit.md +44 -0
- package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-histag-a280.md +47 -0
- package/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md +73 -0
- package/skills/ginkgo-cloud-lab/references/ivt-rna-synthesis-qpcr.md +67 -0
- package/skills/ginkgo-cloud-lab/references/minibinder-strep-tag-a280.md +58 -0
- package/skills/ginkgo-cloud-lab/references/pichia-protein-expression-labchip.md +43 -0
- package/skills/ginkgo-cloud-lab/references/spr-target-onboarding.md +58 -0
- package/skills/glycoengineering/SKILL.md +339 -0
- package/skills/glycoengineering/references/glycan_databases.md +165 -0
- package/skills/gtars/SKILL.md +282 -0
- package/skills/gtars/references/cli.md +334 -0
- package/skills/gtars/references/coverage.md +224 -0
- package/skills/gtars/references/overlap.md +220 -0
- package/skills/gtars/references/python-api.md +280 -0
- package/skills/gtars/references/refget.md +318 -0
- package/skills/gtars/references/tokenizers.md +256 -0
- package/skills/gtars/scripts/__init__.py +1 -0
- package/skills/gtars/scripts/_common.py +461 -0
- package/skills/gtars/scripts/artifact_inspector.py +328 -0
- package/skills/gtars/scripts/bed_validator.py +183 -0
- package/skills/gtars/scripts/coverage_preflight.py +256 -0
- package/skills/gtars/scripts/execution_plan.py +365 -0
- package/skills/gtars/scripts/refget_digest_plan.py +311 -0
- package/skills/gtars/scripts/tokenizer_manifest.py +238 -0
- package/skills/histolab/SKILL.md +243 -0
- package/skills/histolab/references/core_capabilities.md +305 -0
- package/skills/histolab/references/filters_preprocessing.md +537 -0
- package/skills/histolab/references/slide_management.md +184 -0
- package/skills/histolab/references/tile_extraction.md +421 -0
- package/skills/histolab/references/tissue_masks.md +251 -0
- package/skills/histolab/references/typical_workflows.md +196 -0
- package/skills/histolab/references/visualization.md +548 -0
- package/skills/hugging-science/SKILL.md +132 -0
- package/skills/hugging-science/references/flagship-resources.md +81 -0
- package/skills/hugging-science/references/topics-and-slugs.md +82 -0
- package/skills/hugging-science/references/using-datasets.md +107 -0
- package/skills/hugging-science/references/using-models.md +122 -0
- package/skills/hugging-science/references/using-spaces.md +119 -0
- package/skills/hugging-science/scripts/fetch_catalog.py +358 -0
- package/skills/hypogenic/SKILL.md +290 -0
- package/skills/hypogenic/assets/dataset_manifest.example.json +30 -0
- package/skills/hypogenic/assets/result.example.json +18 -0
- package/skills/hypogenic/assets/run_config.example.json +46 -0
- package/skills/hypogenic/assets/task_config.example.yaml +38 -0
- package/skills/hypogenic/references/configuration.md +136 -0
- package/skills/hypogenic/references/datasets.md +146 -0
- package/skills/hypogenic/references/evaluation.md +155 -0
- package/skills/hypogenic/references/security.md +167 -0
- package/skills/hypogenic/references/sources.md +113 -0
- package/skills/hypogenic/references/upstream.md +188 -0
- package/skills/hypogenic/scripts/__init__.py +1 -0
- package/skills/hypogenic/scripts/_common.py +1312 -0
- package/skills/hypogenic/scripts/audit_dataset.py +410 -0
- package/skills/hypogenic/scripts/evaluate_local.py +250 -0
- package/skills/hypogenic/scripts/inspect_outputs.py +166 -0
- package/skills/hypogenic/scripts/plan_run.py +247 -0
- package/skills/hypogenic/scripts/validate_config.py +192 -0
- package/skills/hypothesis-generation/SKILL.md +264 -0
- package/skills/hypothesis-generation/assets/evidence_ledger_template.csv +2 -0
- package/skills/hypothesis-generation/assets/falsification_controls_template.json +116 -0
- package/skills/hypothesis-generation/assets/hypothesis_record_template.json +331 -0
- package/skills/hypothesis-generation/assets/operationalization_template.json +56 -0
- package/skills/hypothesis-generation/assets/prediction_rival_matrix_template.csv +3 -0
- package/skills/hypothesis-generation/assets/preregistration_scaffold_template.md +137 -0
- package/skills/hypothesis-generation/assets/search_boundary_template.json +23 -0
- package/skills/hypothesis-generation/assets/source_ledger.csv +37 -0
- package/skills/hypothesis-generation/references/causal_inference_and_claims.md +190 -0
- package/skills/hypothesis-generation/references/concepts_and_workflow.md +173 -0
- package/skills/hypothesis-generation/references/ethics_safety_and_ai.md +216 -0
- package/skills/hypothesis-generation/references/experimental_design_patterns.md +301 -0
- package/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +203 -0
- package/skills/hypothesis-generation/references/literature_search_strategies.md +208 -0
- package/skills/hypothesis-generation/references/preregistration_and_open_science.md +205 -0
- package/skills/hypothesis-generation/references/security_validation.md +74 -0
- package/skills/hypothesis-generation/references/source_ledger.md +116 -0
- package/skills/hypothesis-generation/references/tool_reference.md +246 -0
- package/skills/hypothesis-generation/scripts/_common.py +412 -0
- package/skills/hypothesis-generation/scripts/audit_evidence_ledger.py +337 -0
- package/skills/hypothesis-generation/scripts/check_falsification_controls.py +455 -0
- package/skills/hypothesis-generation/scripts/check_operationalization.py +237 -0
- package/skills/hypothesis-generation/scripts/generate_preregistration_scaffold.py +384 -0
- package/skills/hypothesis-generation/scripts/lint_causal_claims.py +189 -0
- package/skills/hypothesis-generation/scripts/validate_hypothesis_schema.py +1078 -0
- package/skills/hypothesis-generation/scripts/validate_prediction_matrix.py +286 -0
- package/skills/imaging-data-commons/SKILL.md +496 -0
- package/skills/imaging-data-commons/references/bigquery_guide.md +858 -0
- package/skills/imaging-data-commons/references/cli_guide.md +287 -0
- package/skills/imaging-data-commons/references/clinical_data_guide.md +328 -0
- package/skills/imaging-data-commons/references/cloud_storage_guide.md +333 -0
- package/skills/imaging-data-commons/references/dicomweb_guide.md +399 -0
- package/skills/imaging-data-commons/references/digital_pathology_guide.md +403 -0
- package/skills/imaging-data-commons/references/index_tables_guide.md +203 -0
- package/skills/imaging-data-commons/references/licensing_and_citation.md +230 -0
- package/skills/imaging-data-commons/references/mcp_guide.md +181 -0
- package/skills/imaging-data-commons/references/parquet_access_guide.md +200 -0
- package/skills/imaging-data-commons/references/rest_api_guide.md +612 -0
- package/skills/imaging-data-commons/references/sql_patterns.md +462 -0
- package/skills/imaging-data-commons/references/use_cases.md +277 -0
- package/skills/imaging-data-commons/scripts/check_version.py +132 -0
- package/skills/infographics/SKILL.md +315 -0
- package/skills/infographics/references/color_palettes.md +496 -0
- package/skills/infographics/references/design_principles.md +636 -0
- package/skills/infographics/references/infographic_type_catalog.md +158 -0
- package/skills/infographics/references/infographic_types.md +907 -0
- package/skills/infographics/references/iterative_refinement.md +119 -0
- package/skills/infographics/scripts/generate_infographic.py +291 -0
- package/skills/infographics/scripts/generate_infographic_ai.py +1446 -0
- package/skills/iso-standards-readiness/SKILL.md +352 -0
- package/skills/iso-standards-readiness/assets/templates/capa-record-template.json +99 -0
- package/skills/iso-standards-readiness/assets/templates/document-register-template.json +75 -0
- package/skills/iso-standards-readiness/assets/templates/evidence-manifest-template.json +65 -0
- package/skills/iso-standards-readiness/assets/templates/laboratory-scope-intake-template.json +111 -0
- package/skills/iso-standards-readiness/assets/templates/medical-laboratory-scope-intake-template.json +111 -0
- package/skills/iso-standards-readiness/assets/templates/procedures/CAPA-procedure-template.md +148 -0
- package/skills/iso-standards-readiness/assets/templates/procedures/document-control-procedure-template.md +132 -0
- package/skills/iso-standards-readiness/assets/templates/qmsr-transition-template.json +181 -0
- package/skills/iso-standards-readiness/assets/templates/quality-manual-template.md +182 -0
- package/skills/iso-standards-readiness/assets/templates/scope-intake-template.json +109 -0
- package/skills/iso-standards-readiness/assets/templates/supplier-controls-template.json +119 -0
- package/skills/iso-standards-readiness/assets/templates/traceability-matrix-template.json +154 -0
- package/skills/iso-standards-readiness/references/assurance-lanes.md +116 -0
- package/skills/iso-standards-readiness/references/evidence-architecture.md +282 -0
- package/skills/iso-standards-readiness/references/gap-analysis-checklist.md +346 -0
- package/skills/iso-standards-readiness/references/iso-13485.md +236 -0
- package/skills/iso-standards-readiness/references/iso-14971.md +172 -0
- package/skills/iso-standards-readiness/references/iso-15189.md +219 -0
- package/skills/iso-standards-readiness/references/iso-17025.md +208 -0
- package/skills/iso-standards-readiness/references/quality-manual-guide.md +282 -0
- package/skills/iso-standards-readiness/references/source-ledger.md +357 -0
- package/skills/iso-standards-readiness/scripts/_catalog.py +248 -0
- package/skills/iso-standards-readiness/scripts/_common.py +558 -0
- package/skills/iso-standards-readiness/scripts/audit_document_records.py +148 -0
- package/skills/iso-standards-readiness/scripts/check_capa.py +240 -0
- package/skills/iso-standards-readiness/scripts/check_qmsr_transition.py +164 -0
- package/skills/iso-standards-readiness/scripts/check_supplier_controls.py +166 -0
- package/skills/iso-standards-readiness/scripts/check_traceability.py +171 -0
- package/skills/iso-standards-readiness/scripts/gap_analyzer.py +167 -0
- package/skills/iso-standards-readiness/scripts/validate_evidence_manifest.py +246 -0
- package/skills/iso-standards-readiness/scripts/validate_scope_intake.py +209 -0
- package/skills/lab-hardware-cad/SKILL.md +372 -0
- package/skills/lab-hardware-cad/assets/standards.json +198 -0
- package/skills/lab-hardware-cad/references/behavior-rigs.md +136 -0
- package/skills/lab-hardware-cad/references/build123d-patterns.md +363 -0
- package/skills/lab-hardware-cad/references/fabrication-limits.md +156 -0
- package/skills/lab-hardware-cad/references/labware-adapters.md +190 -0
- package/skills/lab-hardware-cad/references/microfluidics.md +157 -0
- package/skills/lab-hardware-cad/references/optomechanics.md +148 -0
- package/skills/lab-hardware-cad/references/validation.md +132 -0
- package/skills/lab-hardware-cad/scripts/_common.py +650 -0
- package/skills/lab-hardware-cad/scripts/check.py +645 -0
- package/skills/lab-hardware-cad/scripts/gen.py +264 -0
- package/skills/lab-hardware-cad/scripts/snapshot.py +278 -0
- package/skills/labarchive-integration/SKILL.md +216 -0
- package/skills/labarchive-integration/references/api_reference.md +250 -0
- package/skills/labarchive-integration/references/authentication_guide.md +191 -0
- package/skills/labarchive-integration/references/integrations.md +162 -0
- package/skills/labarchive-integration/references/sources.md +213 -0
- package/skills/labarchive-integration/scripts/entry_operations.py +381 -0
- package/skills/labarchive-integration/scripts/notebook_operations.py +451 -0
- package/skills/labarchive-integration/scripts/setup_config.py +258 -0
- package/skills/lamindb/SKILL.md +408 -0
- package/skills/lamindb/references/annotation-validation.md +510 -0
- package/skills/lamindb/references/core-concepts.md +383 -0
- package/skills/lamindb/references/data-management.md +432 -0
- package/skills/lamindb/references/integrations.md +663 -0
- package/skills/lamindb/references/ontologies.md +498 -0
- package/skills/lamindb/references/setup-deployment.md +755 -0
- package/skills/latchbio-integration/SKILL.md +227 -0
- package/skills/latchbio-integration/references/data-management.md +257 -0
- package/skills/latchbio-integration/references/latch-mcp.md +158 -0
- package/skills/latchbio-integration/references/nextflow-snakemake.md +258 -0
- package/skills/latchbio-integration/references/operations-and-debugging.md +320 -0
- package/skills/latchbio-integration/references/registry.md +275 -0
- package/skills/latchbio-integration/references/resource-configuration.md +274 -0
- package/skills/latchbio-integration/references/ui-and-automation.md +355 -0
- package/skills/latchbio-integration/references/verified-workflows.md +226 -0
- package/skills/latchbio-integration/references/workflow-creation.md +275 -0
- package/skills/latchbio-integration/scripts/inspect_latch_sdk.py +290 -0
- package/skills/latex-posters/SKILL.md +369 -0
- package/skills/latex-posters/assets/baposter_template.tex +257 -0
- package/skills/latex-posters/assets/beamerposter_template.tex +244 -0
- package/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
- package/skills/latex-posters/assets/tikzposter_template.tex +251 -0
- package/skills/latex-posters/references/README.md +439 -0
- package/skills/latex-posters/references/ai_graphics_for_posters.md +524 -0
- package/skills/latex-posters/references/compilation_and_quality_control.md +467 -0
- package/skills/latex-posters/references/latex_poster_packages.md +745 -0
- package/skills/latex-posters/references/latex_poster_reference.md +241 -0
- package/skills/latex-posters/references/poster_content_guide.md +748 -0
- package/skills/latex-posters/references/poster_design_principles.md +806 -0
- package/skills/latex-posters/references/poster_layout_design.md +900 -0
- package/skills/latex-posters/references/poster_patterns_and_presentation.md +81 -0
- package/skills/latex-posters/scripts/generate_schematic.py +198 -0
- package/skills/latex-posters/scripts/generate_schematic_ai.py +950 -0
- package/skills/latex-posters/scripts/review_poster.sh +214 -0
- package/skills/liteparse/SKILL.md +295 -0
- package/skills/liteparse/references/api_reference.md +169 -0
- package/skills/liteparse/references/choosing_a_parser.md +70 -0
- package/skills/liteparse/references/cli_reference.md +118 -0
- package/skills/liteparse/references/ocr_and_formats.md +143 -0
- package/skills/liteparse/references/output_formats.md +146 -0
- package/skills/liteparse/scripts/batch_parse_dir.py +163 -0
- package/skills/literature-review/SKILL.md +263 -0
- package/skills/literature-review/assets/review_template.md +412 -0
- package/skills/literature-review/references/citation_styles.md +166 -0
- package/skills/literature-review/references/core_workflow.md +260 -0
- package/skills/literature-review/references/database_strategies.md +455 -0
- package/skills/literature-review/references/example_workflow.md +68 -0
- package/skills/literature-review/references/search_and_citation.md +157 -0
- package/skills/literature-review/scripts/generate_pdf.py +176 -0
- package/skills/literature-review/scripts/generate_schematic.py +198 -0
- package/skills/literature-review/scripts/generate_schematic_ai.py +950 -0
- package/skills/literature-review/scripts/search_databases.py +303 -0
- package/skills/literature-review/scripts/verify_citations.py +222 -0
- package/skills/markdown-mermaid-writing/SKILL.md +322 -0
- package/skills/markdown-mermaid-writing/assets/examples/example-research-report.md +221 -0
- package/skills/markdown-mermaid-writing/references/diagrams/architecture.md +108 -0
- package/skills/markdown-mermaid-writing/references/diagrams/block.md +177 -0
- package/skills/markdown-mermaid-writing/references/diagrams/c4.md +136 -0
- package/skills/markdown-mermaid-writing/references/diagrams/class.md +246 -0
- package/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +384 -0
- package/skills/markdown-mermaid-writing/references/diagrams/er.md +222 -0
- package/skills/markdown-mermaid-writing/references/diagrams/flowchart.md +177 -0
- package/skills/markdown-mermaid-writing/references/diagrams/gantt.md +138 -0
- package/skills/markdown-mermaid-writing/references/diagrams/git_graph.md +74 -0
- package/skills/markdown-mermaid-writing/references/diagrams/kanban.md +107 -0
- package/skills/markdown-mermaid-writing/references/diagrams/mindmap.md +74 -0
- package/skills/markdown-mermaid-writing/references/diagrams/packet.md +55 -0
- package/skills/markdown-mermaid-writing/references/diagrams/pie.md +52 -0
- package/skills/markdown-mermaid-writing/references/diagrams/quadrant.md +66 -0
- package/skills/markdown-mermaid-writing/references/diagrams/radar.md +59 -0
- package/skills/markdown-mermaid-writing/references/diagrams/requirement.md +88 -0
- package/skills/markdown-mermaid-writing/references/diagrams/sankey.md +71 -0
- package/skills/markdown-mermaid-writing/references/diagrams/sequence.md +174 -0
- package/skills/markdown-mermaid-writing/references/diagrams/state.md +150 -0
- package/skills/markdown-mermaid-writing/references/diagrams/timeline.md +96 -0
- package/skills/markdown-mermaid-writing/references/diagrams/treemap.md +66 -0
- package/skills/markdown-mermaid-writing/references/diagrams/user_journey.md +108 -0
- package/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +53 -0
- package/skills/markdown-mermaid-writing/references/diagrams/zenuml.md +71 -0
- package/skills/markdown-mermaid-writing/references/markdown_style_guide.md +733 -0
- package/skills/markdown-mermaid-writing/references/mermaid_style_guide.md +458 -0
- package/skills/markdown-mermaid-writing/templates/decision_record.md +211 -0
- package/skills/markdown-mermaid-writing/templates/how_to_guide.md +275 -0
- package/skills/markdown-mermaid-writing/templates/issue.md +303 -0
- package/skills/markdown-mermaid-writing/templates/kanban.md +223 -0
- package/skills/markdown-mermaid-writing/templates/presentation.md +312 -0
- package/skills/markdown-mermaid-writing/templates/project_documentation.md +412 -0
- package/skills/markdown-mermaid-writing/templates/pull_request.md +319 -0
- package/skills/markdown-mermaid-writing/templates/research_paper.md +304 -0
- package/skills/markdown-mermaid-writing/templates/status_report.md +185 -0
- package/skills/market-research-reports/SKILL.md +337 -0
- package/skills/market-research-reports/assets/FORMATTING_GUIDE.md +149 -0
- package/skills/market-research-reports/assets/claims_ledger_template.csv +4 -0
- package/skills/market-research-reports/assets/competitor_feature_matrix_template.csv +5 -0
- package/skills/market-research-reports/assets/consistency_check_template.csv +3 -0
- package/skills/market-research-reports/assets/forecast_sensitivity_template.json +90 -0
- package/skills/market-research-reports/assets/market_report_template.tex +279 -0
- package/skills/market-research-reports/assets/market_research.sty +241 -0
- package/skills/market-research-reports/assets/market_sizing_scenarios_template.json +129 -0
- package/skills/market-research-reports/assets/report_manifest_template.json +27 -0
- package/skills/market-research-reports/assets/source_ledger_template.csv +4 -0
- package/skills/market-research-reports/references/data_analysis_patterns.md +290 -0
- package/skills/market-research-reports/references/evidence_model.md +148 -0
- package/skills/market-research-reports/references/methods_and_ethics.md +162 -0
- package/skills/market-research-reports/references/official_data_sources.md +196 -0
- package/skills/market-research-reports/references/report_structure_guide.md +283 -0
- package/skills/market-research-reports/references/sources.md +73 -0
- package/skills/market-research-reports/references/visual_generation_guide.md +158 -0
- package/skills/market-research-reports/scripts/_common.py +312 -0
- package/skills/market-research-reports/scripts/audit_claim_citations.py +326 -0
- package/skills/market-research-reports/scripts/calculate_market_sizing.py +389 -0
- package/skills/market-research-reports/scripts/check_unit_consistency.py +217 -0
- package/skills/market-research-reports/scripts/forecast_sensitivity.py +326 -0
- package/skills/market-research-reports/scripts/generate_report_scaffold.py +444 -0
- package/skills/market-research-reports/scripts/validate_competitor_matrix.py +223 -0
- package/skills/market-research-reports/scripts/validate_evidence_ledger.py +291 -0
- package/skills/markitdown/SKILL.md +264 -0
- package/skills/markitdown/references/api_reference.md +418 -0
- package/skills/markitdown/references/cloud_and_ocr.md +320 -0
- package/skills/markitdown/references/file_formats.md +281 -0
- package/skills/markitdown/references/mcp_and_plugins.md +243 -0
- package/skills/markitdown/references/migration.md +356 -0
- package/skills/markitdown/references/security.md +246 -0
- package/skills/markitdown/references/workflows.md +309 -0
- package/skills/markitdown/scripts/batch_convert.py +354 -0
- package/skills/markitdown/scripts/convert_literature.py +405 -0
- package/skills/markitdown/scripts/inspect_installation.py +162 -0
- package/skills/matchms/SKILL.md +276 -0
- package/skills/matchms/references/filtering.md +299 -0
- package/skills/matchms/references/importing_exporting.md +323 -0
- package/skills/matchms/references/migration.md +387 -0
- package/skills/matchms/references/similarity.md +413 -0
- package/skills/matchms/references/sources.md +113 -0
- package/skills/matchms/references/workflows.md +451 -0
- package/skills/matchms/scripts/library_search.py +593 -0
- package/skills/matlab/SKILL.md +274 -0
- package/skills/matlab/assets/project_manifest_template.json +33 -0
- package/skills/matlab/assets/python_compatibility_r2026a.json +27 -0
- package/skills/matlab/assets/reproducibility_manifest_template.json +32 -0
- package/skills/matlab/references/data-import-export.md +221 -0
- package/skills/matlab/references/executing-scripts.md +213 -0
- package/skills/matlab/references/graphics-visualization.md +181 -0
- package/skills/matlab/references/mathematics.md +208 -0
- package/skills/matlab/references/matrices-arrays.md +228 -0
- package/skills/matlab/references/octave-compatibility.md +212 -0
- package/skills/matlab/references/programming.md +225 -0
- package/skills/matlab/references/python-integration.md +248 -0
- package/skills/matlab/scripts/_common.py +263 -0
- package/skills/matlab/scripts/generate_function_scaffold.py +165 -0
- package/skills/matlab/scripts/inventory_mat_file.py +351 -0
- package/skills/matlab/scripts/plan_batch_command.py +257 -0
- package/skills/matlab/scripts/plan_python_compatibility.py +176 -0
- package/skills/matlab/scripts/reproducibility_report.py +233 -0
- package/skills/matlab/scripts/scan_m_code.py +433 -0
- package/skills/matlab/scripts/validate_project_manifest.py +348 -0
- package/skills/matplotlib/SKILL.md +378 -0
- package/skills/matplotlib/references/api_reference.md +409 -0
- package/skills/matplotlib/references/common_issues.md +562 -0
- package/skills/matplotlib/references/plot_types.md +469 -0
- package/skills/matplotlib/references/styling_guide.md +600 -0
- package/skills/matplotlib/scripts/plot_template.py +406 -0
- package/skills/matplotlib/scripts/style_configurator.py +412 -0
- package/skills/medchem/SKILL.md +321 -0
- package/skills/medchem/references/api_guide.md +331 -0
- package/skills/medchem/references/rules_catalog.md +328 -0
- package/skills/medchem/scripts/filter_molecules.py +302 -0
- package/skills/modal/SKILL.md +468 -0
- package/skills/modal/references/api_reference.md +225 -0
- package/skills/modal/references/examples.md +276 -0
- package/skills/modal/references/functions.md +260 -0
- package/skills/modal/references/getting-started.md +171 -0
- package/skills/modal/references/gpu.md +177 -0
- package/skills/modal/references/images.md +266 -0
- package/skills/modal/references/resources.md +117 -0
- package/skills/modal/references/scaling.md +173 -0
- package/skills/modal/references/scheduled-jobs.md +147 -0
- package/skills/modal/references/secrets.md +119 -0
- package/skills/modal/references/volumes.md +247 -0
- package/skills/modal/references/web-endpoints.md +259 -0
- package/skills/molecular-dynamics/SKILL.md +458 -0
- package/skills/molecular-dynamics/references/mdanalysis_analysis.md +208 -0
- package/skills/molfeat/SKILL.md +348 -0
- package/skills/molfeat/references/api_reference.md +429 -0
- package/skills/molfeat/references/available_featurizers.md +335 -0
- package/skills/molfeat/references/choosing_a_featurizer.md +192 -0
- package/skills/molfeat/references/examples.md +720 -0
- package/skills/ncats-arax/SKILL.md +178 -0
- package/skills/ncats-arax/references/output-schema.md +186 -0
- package/skills/ncats-arax/references/query-contract.md +140 -0
- package/skills/ncats-arax/scripts/arax_client.py +2087 -0
- package/skills/networkx/SKILL.md +440 -0
- package/skills/networkx/references/algorithms.md +384 -0
- package/skills/networkx/references/generators.md +385 -0
- package/skills/networkx/references/graph-basics.md +284 -0
- package/skills/networkx/references/io.md +457 -0
- package/skills/networkx/references/visualization.md +531 -0
- package/skills/neurokit2/SKILL.md +323 -0
- package/skills/neurokit2/references/bio_module.md +244 -0
- package/skills/neurokit2/references/complexity.md +212 -0
- package/skills/neurokit2/references/ecg_cardiac.md +193 -0
- package/skills/neurokit2/references/eda.md +185 -0
- package/skills/neurokit2/references/eeg.md +204 -0
- package/skills/neurokit2/references/emg.md +157 -0
- package/skills/neurokit2/references/eog.md +154 -0
- package/skills/neurokit2/references/epochs_events.md +199 -0
- package/skills/neurokit2/references/hrv.md +205 -0
- package/skills/neurokit2/references/ppg.md +191 -0
- package/skills/neurokit2/references/rsp.md +212 -0
- package/skills/neurokit2/references/signal_processing.md +160 -0
- package/skills/neurokit2/scripts/_common.py +567 -0
- package/skills/neurokit2/scripts/ecg_hrv_pipeline.py +303 -0
- package/skills/neurokit2/scripts/eda_pipeline.py +288 -0
- package/skills/neurokit2/scripts/generate_synthetic.py +221 -0
- package/skills/neurokit2/scripts/inspect_signal.py +362 -0
- package/skills/neurokit2/scripts/plan_epochs.py +281 -0
- package/skills/neurokit2/scripts/validate_multimodal.py +350 -0
- package/skills/neuropixels-analysis/SKILL.md +412 -0
- package/skills/neuropixels-analysis/assets/analysis_template.py +271 -0
- package/skills/neuropixels-analysis/references/AI_CURATION.md +164 -0
- package/skills/neuropixels-analysis/references/ANALYSIS.md +392 -0
- package/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +435 -0
- package/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +323 -0
- package/skills/neuropixels-analysis/references/PREPROCESSING.md +273 -0
- package/skills/neuropixels-analysis/references/QUALITY_METRICS.md +359 -0
- package/skills/neuropixels-analysis/references/SPIKE_SORTING.md +339 -0
- package/skills/neuropixels-analysis/references/api_reference.md +229 -0
- package/skills/neuropixels-analysis/references/plotting_guide.md +454 -0
- package/skills/neuropixels-analysis/references/standard_workflow.md +305 -0
- package/skills/neuropixels-analysis/scripts/compute_metrics.py +182 -0
- package/skills/neuropixels-analysis/scripts/explore_recording.py +168 -0
- package/skills/neuropixels-analysis/scripts/export_to_phy.py +79 -0
- package/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +442 -0
- package/skills/neuropixels-analysis/scripts/preprocess_recording.py +122 -0
- package/skills/neuropixels-analysis/scripts/run_sorting.py +98 -0
- package/skills/nextflow/SKILL.md +195 -0
- package/skills/nextflow/references/configuration.md +276 -0
- package/skills/nextflow/references/containers.md +92 -0
- package/skills/nextflow/references/developing.md +301 -0
- package/skills/nextflow/references/language.md +327 -0
- package/skills/nextflow/references/nf-core-tools.md +130 -0
- package/skills/nextflow/references/running-pipelines.md +131 -0
- package/skills/nextflow/references/testing.md +189 -0
- package/skills/omero-integration/SKILL.md +222 -0
- package/skills/omero-integration/references/advanced.md +273 -0
- package/skills/omero-integration/references/connection.md +293 -0
- package/skills/omero-integration/references/data_access.md +359 -0
- package/skills/omero-integration/references/image_processing.md +286 -0
- package/skills/omero-integration/references/metadata.md +313 -0
- package/skills/omero-integration/references/rois.md +291 -0
- package/skills/omero-integration/references/scripts.md +304 -0
- package/skills/omero-integration/references/sources.md +194 -0
- package/skills/omero-integration/references/tables.md +269 -0
- package/skills/omero-integration/scripts/export_image_metadata.py +560 -0
- package/skills/omero-integration/scripts/inventory.py +302 -0
- package/skills/omero-integration/scripts/omero_common.py +490 -0
- package/skills/omero-integration/scripts/plan_transfer.py +393 -0
- package/skills/omero-integration/scripts/validate_config.py +140 -0
- package/skills/onekgpd/SKILL.md +371 -0
- package/skills/onekgpd/assets/kgpe.json +48032 -0
- package/skills/onekgpd/references/annotation_vocabularies.md +187 -0
- package/skills/onekgpd/references/onekgpd_commands.md +296 -0
- package/skills/onekgpd/scripts/onekgpd_api.py +794 -0
- package/skills/onekgpd/scripts/onekgpd_meta.py +485 -0
- package/skills/ontology-term-resolution/SKILL.md +147 -0
- package/skills/ontology-term-resolution/references/curation-rules.md +110 -0
- package/skills/ontology-term-resolution/references/ols4-api.md +135 -0
- package/skills/ontology-term-resolution/references/ontology-registry.md +110 -0
- package/skills/ontology-term-resolution/scripts/ols_client.py +341 -0
- package/skills/ontology-term-resolution/scripts/resolve_terms.py +255 -0
- package/skills/ontology-term-resolution/scripts/validate_terms.py +297 -0
- package/skills/open-notebook/SKILL.md +297 -0
- package/skills/open-notebook/references/api_reference.md +715 -0
- package/skills/open-notebook/references/architecture.md +163 -0
- package/skills/open-notebook/references/configuration.md +226 -0
- package/skills/open-notebook/references/examples.md +290 -0
- package/skills/open-notebook/scripts/chat_interaction.py +190 -0
- package/skills/open-notebook/scripts/notebook_management.py +142 -0
- package/skills/open-notebook/scripts/source_ingestion.py +160 -0
- package/skills/openpiv/SKILL.md +469 -0
- package/skills/openpiv/references/advanced_algorithms.md +233 -0
- package/skills/openpiv/scripts/__init__.py +1 -0
- package/skills/openpiv/scripts/analyze.py +143 -0
- package/skills/openpiv/scripts/run_example.py +78 -0
- package/skills/openpiv/scripts/runner.py +214 -0
- package/skills/opentrons-integration/SKILL.md +322 -0
- package/skills/opentrons-integration/references/api_reference.md +382 -0
- package/skills/opentrons-integration/references/liquid_handling.md +387 -0
- package/skills/opentrons-integration/references/migration-api-2-19-to-2-29.md +328 -0
- package/skills/opentrons-integration/references/modules_and_deck.md +409 -0
- package/skills/opentrons-integration/references/protocol_authoring.md +352 -0
- package/skills/opentrons-integration/references/sources.md +151 -0
- package/skills/opentrons-integration/references/validation_and_operations.md +314 -0
- package/skills/opentrons-integration/requirements-flex.txt +1 -0
- package/skills/opentrons-integration/requirements-ot2.txt +1 -0
- package/skills/opentrons-integration/scripts/absorbance_reader_template.py +82 -0
- package/skills/opentrons-integration/scripts/basic_protocol_template.py +68 -0
- package/skills/opentrons-integration/scripts/ot2_basic_protocol_template.py +63 -0
- package/skills/opentrons-integration/scripts/pcr_setup_template.py +146 -0
- package/skills/opentrons-integration/scripts/runtime_parameters_template.py +110 -0
- package/skills/opentrons-integration/scripts/serial_dilution_template.py +113 -0
- package/skills/optimize-for-gpu/SKILL.md +176 -0
- package/skills/optimize-for-gpu/references/code_transformation_patterns.md +301 -0
- package/skills/optimize-for-gpu/references/cucim.md +679 -0
- package/skills/optimize-for-gpu/references/cudf.md +762 -0
- package/skills/optimize-for-gpu/references/cugraph.md +733 -0
- package/skills/optimize-for-gpu/references/cuml.md +710 -0
- package/skills/optimize-for-gpu/references/cupy.md +668 -0
- package/skills/optimize-for-gpu/references/cuspatial.md +420 -0
- package/skills/optimize-for-gpu/references/cuvs.md +671 -0
- package/skills/optimize-for-gpu/references/cuxfilter.md +600 -0
- package/skills/optimize-for-gpu/references/decision_framework.md +234 -0
- package/skills/optimize-for-gpu/references/installation.md +121 -0
- package/skills/optimize-for-gpu/references/kvikio.md +612 -0
- package/skills/optimize-for-gpu/references/numba.md +808 -0
- package/skills/optimize-for-gpu/references/raft.md +312 -0
- package/skills/optimize-for-gpu/references/warp.md +623 -0
- package/skills/owasp-top10/SKILL.md +48 -0
- package/skills/pacsomatic/LICENSE +21 -0
- package/skills/pacsomatic/SKILL.md +150 -0
- package/skills/pacsomatic/config.yaml +42 -0
- package/skills/pacsomatic/references/agent-playbook.md +73 -0
- package/skills/pacsomatic/references/config-and-output.md +100 -0
- package/skills/pacsomatic/references/pacsomatic_guide.md +254 -0
- package/skills/pacsomatic/scripts/run_pacsomatic.py +794 -0
- package/skills/paper-lookup/SKILL.md +263 -0
- package/skills/paper-lookup/references/arxiv.md +275 -0
- package/skills/paper-lookup/references/biorxiv.md +163 -0
- package/skills/paper-lookup/references/core.md +150 -0
- package/skills/paper-lookup/references/crossref.md +181 -0
- package/skills/paper-lookup/references/europepmc.md +226 -0
- package/skills/paper-lookup/references/medrxiv.md +126 -0
- package/skills/paper-lookup/references/openalex.md +174 -0
- package/skills/paper-lookup/references/pmc.md +228 -0
- package/skills/paper-lookup/references/pubmed.md +124 -0
- package/skills/paper-lookup/references/semantic-scholar.md +203 -0
- package/skills/paper-lookup/references/unpaywall.md +127 -0
- package/skills/paper-lookup/scripts/_common.py +227 -0
- package/skills/paper-lookup/scripts/arxiv_atom.py +200 -0
- package/skills/paper-lookup/scripts/jats_to_text.py +324 -0
- package/skills/paper-lookup/scripts/openalex_abstract.py +163 -0
- package/skills/paper-lookup/scripts/paginate.py +490 -0
- package/skills/paperclip/SKILL.md +413 -0
- package/skills/paperclip/references/cli-reference.md +389 -0
- package/skills/paperclip/references/installation.md +341 -0
- package/skills/paperclip/references/map-reduce.md +252 -0
- package/skills/paperclip/references/python-sdk.md +323 -0
- package/skills/paperclip/references/repos-and-workspace.md +271 -0
- package/skills/paperclip/references/search-and-retrieval.md +281 -0
- package/skills/paperzilla/SKILL.md +159 -0
- package/skills/parallel-web/SKILL.md +128 -0
- package/skills/parallel-web/references/data-enrichment.md +104 -0
- package/skills/parallel-web/references/deep-research.md +91 -0
- package/skills/parallel-web/references/findall.md +81 -0
- package/skills/parallel-web/references/monitor.md +83 -0
- package/skills/parallel-web/references/web-extract.md +59 -0
- package/skills/parallel-web/references/web-search.md +100 -0
- package/skills/pathml/SKILL.md +222 -0
- package/skills/pathml/references/data_management.md +357 -0
- package/skills/pathml/references/graphs.md +335 -0
- package/skills/pathml/references/image_loading.md +301 -0
- package/skills/pathml/references/machine_learning.md +408 -0
- package/skills/pathml/references/multiparametric.md +352 -0
- package/skills/pathml/references/preprocessing.md +371 -0
- package/skills/pathml/scripts/_common.py +385 -0
- package/skills/pathml/scripts/image_qc.py +325 -0
- package/skills/pathml/scripts/plan_inference.py +282 -0
- package/skills/pathml/scripts/plan_pipeline.py +239 -0
- package/skills/pathml/scripts/slide_manifest.py +405 -0
- package/skills/pathml/scripts/validate_spatial_schema.py +420 -0
- package/skills/pathogen-variant-surveillance/SKILL.md +208 -0
- package/skills/pathogen-variant-surveillance/references/lapis-api.md +209 -0
- package/skills/pathogen-variant-surveillance/references/lineage-nomenclature.md +126 -0
- package/skills/pathogen-variant-surveillance/references/surveillance-caveats.md +149 -0
- package/skills/pathogen-variant-surveillance/scripts/lapis_client.py +776 -0
- package/skills/pathogen-variant-surveillance/scripts/lineage_prevalence.py +310 -0
- package/skills/pathogen-variant-surveillance/scripts/mutation_profile.py +215 -0
- package/skills/pathogen-variant-surveillance/scripts/reporting_lag.py +217 -0
- package/skills/pathogen-variant-surveillance/scripts/resolve_lineage.py +198 -0
- package/skills/pathway-enrichment/SKILL.md +194 -0
- package/skills/pathway-enrichment/references/databases-and-gene-sets.md +140 -0
- package/skills/pathway-enrichment/references/gseapy.md +189 -0
- package/skills/pathway-enrichment/references/interpretation.md +118 -0
- package/skills/pathway-enrichment/scripts/run_enrichment.py +231 -0
- package/skills/pdf/LICENSE.txt +30 -0
- package/skills/pdf/SKILL.md +322 -0
- package/skills/pdf/forms.md +294 -0
- package/skills/pdf/reference.md +612 -0
- package/skills/pdf/scripts/check_bounding_boxes.py +65 -0
- package/skills/pdf/scripts/check_fillable_fields.py +11 -0
- package/skills/pdf/scripts/convert_pdf_to_images.py +33 -0
- package/skills/pdf/scripts/create_validation_image.py +37 -0
- package/skills/pdf/scripts/extract_form_field_info.py +122 -0
- package/skills/pdf/scripts/extract_form_structure.py +115 -0
- package/skills/pdf/scripts/fill_fillable_fields.py +98 -0
- package/skills/pdf/scripts/fill_pdf_form_with_annotations.py +107 -0
- package/skills/peer-review/SKILL.md +288 -0
- package/skills/peer-review/assets/citation_references_template.csv +2 -0
- package/skills/peer-review/assets/claim_evidence_matrix_template.csv +4 -0
- package/skills/peer-review/assets/reporting_checklist_template.csv +31 -0
- package/skills/peer-review/assets/reporting_guidelines.json +466 -0
- package/skills/peer-review/assets/review_intake_template.json +52 -0
- package/skills/peer-review/assets/review_scaffold_template.md +68 -0
- package/skills/peer-review/assets/source_ledger.csv +32 -0
- package/skills/peer-review/assets/statistical_reproducibility_template.json +210 -0
- package/skills/peer-review/assets/study_profile_template.json +12 -0
- package/skills/peer-review/references/common_issues.md +257 -0
- package/skills/peer-review/references/ethical_review_practice.md +233 -0
- package/skills/peer-review/references/reporting_standards.md +249 -0
- package/skills/peer-review/references/security_validation.md +75 -0
- package/skills/peer-review/references/statistical_reproducibility.md +329 -0
- package/skills/peer-review/references/tool_reference.md +253 -0
- package/skills/peer-review/scripts/_common.py +398 -0
- package/skills/peer-review/scripts/audit_citations.py +207 -0
- package/skills/peer-review/scripts/audit_statistics_reproducibility.py +305 -0
- package/skills/peer-review/scripts/generate_review_scaffold.py +81 -0
- package/skills/peer-review/scripts/lint_review.py +254 -0
- package/skills/peer-review/scripts/select_reporting_guidelines.py +383 -0
- package/skills/peer-review/scripts/validate_claim_evidence.py +221 -0
- package/skills/peer-review/scripts/validate_review_intake.py +452 -0
- package/skills/penetration-testing/SKILL.md +31 -0
- package/skills/pennylane/SKILL.md +240 -0
- package/skills/pennylane/references/advanced_features.md +667 -0
- package/skills/pennylane/references/devices_backends.md +562 -0
- package/skills/pennylane/references/getting_started.md +232 -0
- package/skills/pennylane/references/optimization.md +670 -0
- package/skills/pennylane/references/quantum_chemistry.md +576 -0
- package/skills/pennylane/references/quantum_circuits.md +443 -0
- package/skills/pennylane/references/quantum_ml.md +555 -0
- package/skills/phylogenetics/SKILL.md +409 -0
- package/skills/phylogenetics/references/iqtree_inference.md +181 -0
- package/skills/phylogenetics/scripts/phylogenetic_analysis.py +272 -0
- package/skills/pi-agent/SKILL.md +83 -0
- package/skills/pi-agent/references/compaction.md +76 -0
- package/skills/pi-agent/references/containerization.md +80 -0
- package/skills/pi-agent/references/custom-provider.md +131 -0
- package/skills/pi-agent/references/development.md +61 -0
- package/skills/pi-agent/references/environment-variables.md +57 -0
- package/skills/pi-agent/references/extensions.md +185 -0
- package/skills/pi-agent/references/json.md +69 -0
- package/skills/pi-agent/references/keybindings.md +58 -0
- package/skills/pi-agent/references/llama-cpp.md +69 -0
- package/skills/pi-agent/references/models.md +114 -0
- package/skills/pi-agent/references/overview.md +37 -0
- package/skills/pi-agent/references/packages.md +103 -0
- package/skills/pi-agent/references/pi-interview.md +123 -0
- package/skills/pi-agent/references/pi-mcp-adapter.md +191 -0
- package/skills/pi-agent/references/pi-subagents.md +371 -0
- package/skills/pi-agent/references/pi-web-access.md +243 -0
- package/skills/pi-agent/references/prompt-templates.md +48 -0
- package/skills/pi-agent/references/providers.md +122 -0
- package/skills/pi-agent/references/quickstart.md +73 -0
- package/skills/pi-agent/references/rpc.md +95 -0
- package/skills/pi-agent/references/sdk.md +151 -0
- package/skills/pi-agent/references/security.md +52 -0
- package/skills/pi-agent/references/session-format.md +90 -0
- package/skills/pi-agent/references/sessions.md +56 -0
- package/skills/pi-agent/references/settings.md +102 -0
- package/skills/pi-agent/references/shell-aliases.md +15 -0
- package/skills/pi-agent/references/skills.md +83 -0
- package/skills/pi-agent/references/terminal-setup.md +87 -0
- package/skills/pi-agent/references/termux.md +31 -0
- package/skills/pi-agent/references/themes.md +69 -0
- package/skills/pi-agent/references/tmux.md +44 -0
- package/skills/pi-agent/references/tui.md +97 -0
- package/skills/pi-agent/references/usage.md +129 -0
- package/skills/pi-agent/references/windows.md +23 -0
- package/skills/pkpd-modeling/SKILL.md +381 -0
- package/skills/pkpd-modeling/assets/nca-reporting-checklist.md +72 -0
- package/skills/pkpd-modeling/assets/popk-analysis-plan.md +136 -0
- package/skills/pkpd-modeling/references/antimicrobial-and-tdm.md +110 -0
- package/skills/pkpd-modeling/references/bioequivalence.md +132 -0
- package/skills/pkpd-modeling/references/dataset-standards.md +103 -0
- package/skills/pkpd-modeling/references/ddi-and-qt.md +132 -0
- package/skills/pkpd-modeling/references/nca-conventions.md +128 -0
- package/skills/pkpd-modeling/references/pbpk.md +103 -0
- package/skills/pkpd-modeling/references/pd-and-exposure-response.md +149 -0
- package/skills/pkpd-modeling/references/population-pk.md +133 -0
- package/skills/pkpd-modeling/references/regulatory-guidance.md +82 -0
- package/skills/pkpd-modeling/references/software-ecosystem.md +123 -0
- package/skills/pkpd-modeling/references/source-ledger.md +89 -0
- package/skills/pkpd-modeling/references/special-populations.md +126 -0
- package/skills/pkpd-modeling/references/structural-models.md +140 -0
- package/skills/pkpd-modeling/references/tmdd-and-biologics.md +115 -0
- package/skills/pkpd-modeling/scripts/_common.py +327 -0
- package/skills/pkpd-modeling/scripts/_models.py +673 -0
- package/skills/pkpd-modeling/scripts/allometry_and_fih.py +346 -0
- package/skills/pkpd-modeling/scripts/bioequivalence.py +480 -0
- package/skills/pkpd-modeling/scripts/check_popk_dataset.py +400 -0
- package/skills/pkpd-modeling/scripts/ddi_static.py +346 -0
- package/skills/pkpd-modeling/scripts/exposure_response.py +328 -0
- package/skills/pkpd-modeling/scripts/fit_compartmental.py +558 -0
- package/skills/pkpd-modeling/scripts/nca.py +587 -0
- package/skills/pkpd-modeling/scripts/simulate_regimen.py +323 -0
- package/skills/pkpd-modeling/scripts/tdm_bayes.py +312 -0
- package/skills/polars/SKILL.md +393 -0
- package/skills/polars/references/best_practices.md +651 -0
- package/skills/polars/references/core_concepts.md +380 -0
- package/skills/polars/references/io_guide.md +564 -0
- package/skills/polars/references/operations.md +602 -0
- package/skills/polars/references/pandas_migration.md +417 -0
- package/skills/polars/references/transformations.md +549 -0
- package/skills/polars-bio/SKILL.md +379 -0
- package/skills/polars-bio/references/bioframe_migration.md +250 -0
- package/skills/polars-bio/references/configuration.md +187 -0
- package/skills/polars-bio/references/file_io.md +469 -0
- package/skills/polars-bio/references/interval_operations.md +370 -0
- package/skills/polars-bio/references/pileup_operations.md +176 -0
- package/skills/polars-bio/references/sql_processing.md +224 -0
- package/skills/ponytail/SKILL.md +31 -0
- package/skills/ponytail-audit/SKILL.md +18 -0
- package/skills/pptx/LICENSE.txt +30 -0
- package/skills/pptx/SKILL.md +246 -0
- package/skills/pptx/scripts/__init__.py +0 -0
- package/skills/pptx/scripts/add_slide.py +367 -0
- package/skills/pptx/scripts/clean.py +309 -0
- package/skills/pptx/scripts/office/helpers/__init__.py +111 -0
- package/skills/pptx/scripts/office/helpers/pptx_chart.py +170 -0
- package/skills/pptx/scripts/office/helpers/pptx_slide.py +60 -0
- package/skills/pptx/scripts/office/helpers/pptx_theme.py +114 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/skills/pptx/scripts/office/schemas/mce/mc.xsd +75 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/skills/pptx/scripts/office/soffice.py +232 -0
- package/skills/pptx/scripts/office/validate.py +173 -0
- package/skills/pptx/scripts/office/validators/__init__.py +15 -0
- package/skills/pptx/scripts/office/validators/base.py +875 -0
- package/skills/pptx/scripts/office/validators/docx.py +466 -0
- package/skills/pptx/scripts/office/validators/pptx.py +441 -0
- package/skills/pptx/scripts/office/validators/redlining.py +299 -0
- package/skills/pptx/scripts/thumbnail.py +311 -0
- package/skills/pptx-posters/SKILL.md +258 -0
- package/skills/pptx-posters/assets/generation_dependencies.json +5 -0
- package/skills/pptx-posters/assets/poster_manifest_template.json +154 -0
- package/skills/pptx-posters/assets/poster_quality_checklist.md +192 -0
- package/skills/pptx-posters/references/manifest_spec.md +297 -0
- package/skills/pptx-posters/references/poster_content_guide.md +176 -0
- package/skills/pptx-posters/references/poster_design_principles.md +226 -0
- package/skills/pptx-posters/references/poster_layout_design.md +189 -0
- package/skills/pptx-posters/references/pptx_security.md +202 -0
- package/skills/pptx-posters/references/security_validation.md +90 -0
- package/skills/pptx-posters/references/source_ledger.md +256 -0
- package/skills/pptx-posters/scripts/_common.py +396 -0
- package/skills/pptx-posters/scripts/_manifest.py +1318 -0
- package/skills/pptx-posters/scripts/_pptx.py +1484 -0
- package/skills/pptx-posters/scripts/check_layout.py +179 -0
- package/skills/pptx-posters/scripts/check_palette.py +142 -0
- package/skills/pptx-posters/scripts/generate_poster.py +427 -0
- package/skills/pptx-posters/scripts/inspect_pptx.py +40 -0
- package/skills/pptx-posters/scripts/inventory_images.py +252 -0
- package/skills/pptx-posters/scripts/plan_export.py +201 -0
- package/skills/pptx-posters/scripts/validate_manifest.py +55 -0
- package/skills/primekg/SKILL.md +99 -0
- package/skills/primekg/scripts/query_primekg.py +128 -0
- package/skills/protocolsio-integration/SKILL.md +236 -0
- package/skills/protocolsio-integration/assets/protocol-snapshot.schema.json +179 -0
- package/skills/protocolsio-integration/references/additional_features.md +202 -0
- package/skills/protocolsio-integration/references/authentication.md +135 -0
- package/skills/protocolsio-integration/references/discussions.md +192 -0
- package/skills/protocolsio-integration/references/file_manager.md +256 -0
- package/skills/protocolsio-integration/references/protocols_api.md +256 -0
- package/skills/protocolsio-integration/references/workspaces.md +192 -0
- package/skills/protocolsio-integration/scripts/__init__.py +1 -0
- package/skills/protocolsio-integration/scripts/_common.py +613 -0
- package/skills/protocolsio-integration/scripts/pagination_helper.py +248 -0
- package/skills/protocolsio-integration/scripts/plan_write_request.py +657 -0
- package/skills/protocolsio-integration/scripts/protocols_read.py +493 -0
- package/skills/protocolsio-integration/scripts/validate_auth_config.py +128 -0
- package/skills/protocolsio-integration/scripts/validate_protocol_json.py +358 -0
- package/skills/pufferlib/SKILL.md +328 -0
- package/skills/pufferlib/references/environments.md +260 -0
- package/skills/pufferlib/references/integration.md +192 -0
- package/skills/pufferlib/references/policies.md +181 -0
- package/skills/pufferlib/references/training.md +287 -0
- package/skills/pufferlib/references/vectorization.md +210 -0
- package/skills/pufferlib/scripts/__init__.py +1 -0
- package/skills/pufferlib/scripts/_common.py +199 -0
- package/skills/pufferlib/scripts/benchmark_vectorization.py +244 -0
- package/skills/pufferlib/scripts/env_contract_validator.py +198 -0
- package/skills/pufferlib/scripts/env_template.py +210 -0
- package/skills/pufferlib/scripts/inspect_checkpoint.py +225 -0
- package/skills/pufferlib/scripts/repro_plan.py +177 -0
- package/skills/pufferlib/scripts/train_template.py +282 -0
- package/skills/pufferlib/scripts/validate_plan.py +570 -0
- package/skills/pydeseq2/SKILL.md +369 -0
- package/skills/pydeseq2/references/analysis_patterns.md +70 -0
- package/skills/pydeseq2/references/api_reference.md +256 -0
- package/skills/pydeseq2/references/core_workflow_steps.md +162 -0
- package/skills/pydeseq2/references/workflow_guide.md +603 -0
- package/skills/pydeseq2/scripts/run_deseq2_analysis.py +388 -0
- package/skills/pydicom/SKILL.md +381 -0
- package/skills/pydicom/references/common_tags.md +277 -0
- package/skills/pydicom/references/transfer_syntaxes.md +348 -0
- package/skills/pydicom/scripts/__init__.py +1 -0
- package/skills/pydicom/scripts/_common.py +916 -0
- package/skills/pydicom/scripts/anonymize_dicom.py +713 -0
- package/skills/pydicom/scripts/deidentification_audit.py +380 -0
- package/skills/pydicom/scripts/dicom_inventory.py +402 -0
- package/skills/pydicom/scripts/dicom_to_image.py +459 -0
- package/skills/pydicom/scripts/extract_metadata.py +330 -0
- package/skills/pydicom/scripts/pixel_frame_planner.py +303 -0
- package/skills/pydicom/scripts/transfer_syntax_inspector.py +245 -0
- package/skills/pydicom/scripts/uid_mapping_validator.py +240 -0
- package/skills/pyhealth/SKILL.md +124 -0
- package/skills/pyhealth/assets/starter_pipeline.py +58 -0
- package/skills/pyhealth/references/datasets.md +126 -0
- package/skills/pyhealth/references/examples.md +237 -0
- package/skills/pyhealth/references/installation.md +112 -0
- package/skills/pyhealth/references/medcode.md +94 -0
- package/skills/pyhealth/references/models.md +114 -0
- package/skills/pyhealth/references/tasks.md +143 -0
- package/skills/pylabrobot/SKILL.md +216 -0
- package/skills/pylabrobot/assets/protocol-manifest.schema.json +367 -0
- package/skills/pylabrobot/references/analytical-equipment.md +200 -0
- package/skills/pylabrobot/references/hardware-backends.md +215 -0
- package/skills/pylabrobot/references/liquid-handling.md +223 -0
- package/skills/pylabrobot/references/material-handling.md +229 -0
- package/skills/pylabrobot/references/resources.md +238 -0
- package/skills/pylabrobot/references/visualization.md +187 -0
- package/skills/pylabrobot/scripts/__init__.py +1 -0
- package/skills/pylabrobot/scripts/_common.py +718 -0
- package/skills/pylabrobot/scripts/check_deck_geometry.py +52 -0
- package/skills/pylabrobot/scripts/generate_simulation_plan.py +140 -0
- package/skills/pylabrobot/scripts/inspect_backends.py +216 -0
- package/skills/pylabrobot/scripts/plan_transfers.py +59 -0
- package/skills/pylabrobot/scripts/validate_manifest.py +47 -0
- package/skills/pymatgen/SKILL.md +404 -0
- package/skills/pymatgen/references/analysis_modules.md +352 -0
- package/skills/pymatgen/references/core_classes.md +290 -0
- package/skills/pymatgen/references/io_formats.md +323 -0
- package/skills/pymatgen/references/materials_project_api.md +406 -0
- package/skills/pymatgen/references/transformations_workflows.md +385 -0
- package/skills/pymatgen/scripts/_common.py +316 -0
- package/skills/pymatgen/scripts/artifact_manifest.py +172 -0
- package/skills/pymatgen/scripts/composition_structure_validator.py +300 -0
- package/skills/pymatgen/scripts/io_conversion_plan.py +204 -0
- package/skills/pymatgen/scripts/mp_query.py +416 -0
- package/skills/pymatgen/scripts/phase_diagram_generator.py +415 -0
- package/skills/pymatgen/scripts/structure_analyzer.py +293 -0
- package/skills/pymatgen/scripts/structure_converter.py +219 -0
- package/skills/pymatgen/scripts/symmetry_sensitivity_report.py +212 -0
- package/skills/pymc/SKILL.md +310 -0
- package/skills/pymc/assets/hierarchical_model_template.py +332 -0
- package/skills/pymc/assets/linear_regression_template.py +244 -0
- package/skills/pymc/references/distributions.md +345 -0
- package/skills/pymc/references/model_patterns.md +130 -0
- package/skills/pymc/references/sampling_inference.md +432 -0
- package/skills/pymc/references/standard_workflow.md +176 -0
- package/skills/pymc/references/workflows.md +530 -0
- package/skills/pymc/scripts/model_comparison.py +409 -0
- package/skills/pymc/scripts/model_diagnostics.py +328 -0
- package/skills/pymoo/SKILL.md +276 -0
- package/skills/pymoo/references/algorithms.md +232 -0
- package/skills/pymoo/references/constraints_mcdm.md +417 -0
- package/skills/pymoo/references/operators.md +345 -0
- package/skills/pymoo/references/parallelization.md +80 -0
- package/skills/pymoo/references/problems.md +265 -0
- package/skills/pymoo/references/quick_start_workflows.md +404 -0
- package/skills/pymoo/references/visualization.md +353 -0
- package/skills/pymoo/scripts/custom_problem_example.py +181 -0
- package/skills/pymoo/scripts/decision_making_example.py +161 -0
- package/skills/pymoo/scripts/many_objective_example.py +74 -0
- package/skills/pymoo/scripts/multi_objective_example.py +63 -0
- package/skills/pymoo/scripts/single_objective_example.py +59 -0
- package/skills/pyopenms/SKILL.md +179 -0
- package/skills/pyopenms/references/data_structures.md +498 -0
- package/skills/pyopenms/references/feature_detection.md +495 -0
- package/skills/pyopenms/references/file_io.md +359 -0
- package/skills/pyopenms/references/identification.md +431 -0
- package/skills/pyopenms/references/metabolomics.md +548 -0
- package/skills/pyopenms/references/signal_processing.md +444 -0
- package/skills/pyopenms/scripts/accurate_mass_search.py +111 -0
- package/skills/pyopenms/scripts/align_link_quantify.py +140 -0
- package/skills/pyopenms/scripts/consensus_to_matrix.py +70 -0
- package/skills/pyopenms/scripts/convert_format.py +95 -0
- package/skills/pyopenms/scripts/detect_adducts.py +90 -0
- package/skills/pyopenms/scripts/detect_features_centroided.py +80 -0
- package/skills/pyopenms/scripts/detect_features_metabo.py +110 -0
- package/skills/pyopenms/scripts/digest_protein.py +102 -0
- package/skills/pyopenms/scripts/export_gnps_sirius.py +90 -0
- package/skills/pyopenms/scripts/extract_chromatograms.py +105 -0
- package/skills/pyopenms/scripts/inspect_ms_data.py +167 -0
- package/skills/pyopenms/scripts/mass_calculator.py +92 -0
- package/skills/pyopenms/scripts/plot_ms_data.py +129 -0
- package/skills/pyopenms/scripts/process_identifications.py +111 -0
- package/skills/pyopenms/scripts/process_spectra.py +124 -0
- package/skills/pyopenms/scripts/theoretical_spectrum.py +75 -0
- package/skills/pysam/SKILL.md +330 -0
- package/skills/pysam/references/alignment_files.md +374 -0
- package/skills/pysam/references/api_reference.md +421 -0
- package/skills/pysam/references/common_workflows.md +442 -0
- package/skills/pysam/references/coordinates_and_indexing.md +318 -0
- package/skills/pysam/references/cram_and_performance.md +314 -0
- package/skills/pysam/references/migration_to_0_24.md +177 -0
- package/skills/pysam/references/sequence_files.md +316 -0
- package/skills/pysam/references/sources.md +132 -0
- package/skills/pysam/references/variant_files.md +396 -0
- package/skills/pysam/scripts/alignment_qc.py +326 -0
- package/skills/pysam/scripts/filter_alignments.py +359 -0
- package/skills/pysam/scripts/inspect_hts.py +485 -0
- package/skills/pysam/scripts/variant_summary.py +362 -0
- package/skills/pytdc/SKILL.md +297 -0
- package/skills/pytdc/references/datasets.md +242 -0
- package/skills/pytdc/references/oracles.md +273 -0
- package/skills/pytdc/references/sources.md +165 -0
- package/skills/pytdc/references/utilities.md +364 -0
- package/skills/pytdc/scripts/_common.py +205 -0
- package/skills/pytdc/scripts/benchmark_evaluation.py +367 -0
- package/skills/pytdc/scripts/cache_audit.py +146 -0
- package/skills/pytdc/scripts/discover_metadata.py +174 -0
- package/skills/pytdc/scripts/load_and_split_data.py +374 -0
- package/skills/pytdc/scripts/molecular_generation.py +417 -0
- package/skills/pytorch-lightning/SKILL.md +191 -0
- package/skills/pytorch-lightning/references/best_practices.md +724 -0
- package/skills/pytorch-lightning/references/callbacks.md +564 -0
- package/skills/pytorch-lightning/references/data_module.md +565 -0
- package/skills/pytorch-lightning/references/distributed_training.md +644 -0
- package/skills/pytorch-lightning/references/lightning_module.md +487 -0
- package/skills/pytorch-lightning/references/logging.md +636 -0
- package/skills/pytorch-lightning/references/trainer.md +641 -0
- package/skills/pytorch-lightning/scripts/quick_trainer_setup.py +473 -0
- package/skills/pytorch-lightning/scripts/template_datamodule.py +328 -0
- package/skills/pytorch-lightning/scripts/template_lightning_module.py +220 -0
- package/skills/pyzotero/SKILL.md +137 -0
- package/skills/pyzotero/references/authentication.md +105 -0
- package/skills/pyzotero/references/cli.md +102 -0
- package/skills/pyzotero/references/collections.md +113 -0
- package/skills/pyzotero/references/error-handling.md +108 -0
- package/skills/pyzotero/references/exports.md +102 -0
- package/skills/pyzotero/references/files-attachments.md +97 -0
- package/skills/pyzotero/references/full-text.md +68 -0
- package/skills/pyzotero/references/mcp.md +90 -0
- package/skills/pyzotero/references/pagination.md +79 -0
- package/skills/pyzotero/references/read-api.md +137 -0
- package/skills/pyzotero/references/saved-searches.md +77 -0
- package/skills/pyzotero/references/search-params.md +90 -0
- package/skills/pyzotero/references/tags.md +87 -0
- package/skills/pyzotero/references/write-api.md +123 -0
- package/skills/qiskit/SKILL.md +259 -0
- package/skills/qiskit/references/algorithms.md +311 -0
- package/skills/qiskit/references/backends.md +382 -0
- package/skills/qiskit/references/circuits.md +319 -0
- package/skills/qiskit/references/migration.md +338 -0
- package/skills/qiskit/references/patterns.md +386 -0
- package/skills/qiskit/references/primitives.md +400 -0
- package/skills/qiskit/references/setup.md +253 -0
- package/skills/qiskit/references/sources.md +156 -0
- package/skills/qiskit/references/testing.md +428 -0
- package/skills/qiskit/references/transpilation.md +333 -0
- package/skills/qiskit/references/visualization.md +361 -0
- package/skills/qiskit/scripts/check_environment.py +260 -0
- package/skills/qiskit/scripts/inspect_runtime.py +224 -0
- package/skills/qiskit/scripts/run_local_primitives.py +200 -0
- package/skills/qutip/SKILL.md +317 -0
- package/skills/qutip/references/advanced.md +413 -0
- package/skills/qutip/references/analysis.md +319 -0
- package/skills/qutip/references/core_concepts.md +300 -0
- package/skills/qutip/references/time_evolution.md +373 -0
- package/skills/qutip/references/visualization.md +334 -0
- package/skills/qutip/scripts/_common.py +370 -0
- package/skills/qutip/scripts/convergence_sweep.py +358 -0
- package/skills/qutip/scripts/qobj_model_validator.py +327 -0
- package/skills/qutip/scripts/result_audit.py +395 -0
- package/skills/qutip/scripts/solver_config_planner.py +297 -0
- package/skills/qutip/scripts/steady_state_spectrum_planner.py +245 -0
- package/skills/qutip/scripts/two_level_simulation.py +394 -0
- package/skills/rdkit/SKILL.md +94 -0
- package/skills/rdkit/references/api_reference.md +443 -0
- package/skills/rdkit/references/core_capabilities.md +604 -0
- package/skills/rdkit/references/descriptors_reference.md +595 -0
- package/skills/rdkit/references/smarts_patterns.md +668 -0
- package/skills/rdkit/references/workflows_and_best_practices.md +169 -0
- package/skills/rdkit/scripts/molecular_properties.py +243 -0
- package/skills/rdkit/scripts/similarity_search.py +297 -0
- package/skills/rdkit/scripts/substructure_filter.py +386 -0
- package/skills/relsa-severity-assessment/SKILL.md +354 -0
- package/skills/relsa-severity-assessment/assets/example_cohort.csv +55 -0
- package/skills/relsa-severity-assessment/references/forecasting.md +155 -0
- package/skills/relsa-severity-assessment/references/relsa-method.md +175 -0
- package/skills/relsa-severity-assessment/references/thresholds-and-zones.md +154 -0
- package/skills/relsa-severity-assessment/scripts/_common.py +287 -0
- package/skills/relsa-severity-assessment/scripts/forecast_relsa.py +757 -0
- package/skills/relsa-severity-assessment/scripts/kde_thresholds.py +369 -0
- package/skills/relsa-severity-assessment/scripts/relsa_score.py +488 -0
- package/skills/research-grants/SKILL.md +296 -0
- package/skills/research-grants/assets/budget_justification_template.md +453 -0
- package/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
- package/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
- package/skills/research-grants/references/README.md +287 -0
- package/skills/research-grants/references/broader_impacts.md +392 -0
- package/skills/research-grants/references/core_components.md +397 -0
- package/skills/research-grants/references/darpa_guidelines.md +636 -0
- package/skills/research-grants/references/doe_guidelines.md +586 -0
- package/skills/research-grants/references/nih_guidelines.md +853 -0
- package/skills/research-grants/references/nsf_guidelines.md +570 -0
- package/skills/research-grants/references/nstc_guidelines.md +733 -0
- package/skills/research-grants/references/proposal_types_and_resubmission.md +81 -0
- package/skills/research-grants/references/review_criteria.md +93 -0
- package/skills/research-grants/references/specific_aims_guide.md +458 -0
- package/skills/research-grants/references/writing_principles.md +94 -0
- package/skills/research-lookup/README.md +106 -0
- package/skills/research-lookup/SKILL.md +338 -0
- package/skills/research-lookup/scripts/manuscript_packet.py +754 -0
- package/skills/research-lookup/scripts/research_lookup.py +1204 -0
- package/skills/rowan/SKILL.md +398 -0
- package/skills/rowan/references/access_and_pricing.md +37 -0
- package/skills/rowan/references/batch_and_webhooks.md +255 -0
- package/skills/rowan/references/end_to_end_example.md +119 -0
- package/skills/rowan/references/troubleshooting.md +106 -0
- package/skills/rowan/references/workflow_catalog.md +308 -0
- package/skills/scanpy/SKILL.md +303 -0
- package/skills/scanpy/assets/analysis_template.py +301 -0
- package/skills/scanpy/assets/celltype_mapping.json +10 -0
- package/skills/scanpy/assets/gene_signatures.json +9 -0
- package/skills/scanpy/assets/pipeline_config.json +19 -0
- package/skills/scanpy/references/analysis_workflow.md +236 -0
- package/skills/scanpy/references/api_reference.md +267 -0
- package/skills/scanpy/references/plotting_guide.md +365 -0
- package/skills/scanpy/references/r_interop.md +292 -0
- package/skills/scanpy/references/standard_workflow.md +223 -0
- package/skills/scanpy/scripts/_common.py +127 -0
- package/skills/scanpy/scripts/annotate.py +84 -0
- package/skills/scanpy/scripts/batch_correct.py +65 -0
- package/skills/scanpy/scripts/cluster.py +63 -0
- package/skills/scanpy/scripts/convert.py +43 -0
- package/skills/scanpy/scripts/find_markers.py +75 -0
- package/skills/scanpy/scripts/inspect_data.py +81 -0
- package/skills/scanpy/scripts/plot.py +78 -0
- package/skills/scanpy/scripts/preprocess.py +88 -0
- package/skills/scanpy/scripts/pseudobulk.py +74 -0
- package/skills/scanpy/scripts/qc_analysis.py +104 -0
- package/skills/scanpy/scripts/reduce_dimensions.py +64 -0
- package/skills/scanpy/scripts/run_pipeline.py +182 -0
- package/skills/scanpy/scripts/score_genes.py +82 -0
- package/skills/scanpy/scripts/subset.py +64 -0
- package/skills/scholar-evaluation/SKILL.md +296 -0
- package/skills/scholar-evaluation/assets/evaluation_template.json +50 -0
- package/skills/scholar-evaluation/assets/evidence_manifest_template.json +63 -0
- package/skills/scholar-evaluation/assets/process_checklist_template.json +70 -0
- package/skills/scholar-evaluation/assets/ratings_template.csv +21 -0
- package/skills/scholar-evaluation/assets/rubric_template.json +301 -0
- package/skills/scholar-evaluation/references/evaluation_framework.md +264 -0
- package/skills/scholar-evaluation/references/local_tooling.md +232 -0
- package/skills/scholar-evaluation/references/responsible_assessment.md +196 -0
- package/skills/scholar-evaluation/references/security_validation.md +95 -0
- package/skills/scholar-evaluation/references/source_ledger.md +222 -0
- package/skills/scholar-evaluation/scripts/_common.py +986 -0
- package/skills/scholar-evaluation/scripts/calculate_scores.py +57 -0
- package/skills/scholar-evaluation/scripts/check_process.py +231 -0
- package/skills/scholar-evaluation/scripts/check_traceability.py +233 -0
- package/skills/scholar-evaluation/scripts/generate_report_scaffold.py +231 -0
- package/skills/scholar-evaluation/scripts/summarize_agreement.py +235 -0
- package/skills/scholar-evaluation/scripts/validate_rubric.py +54 -0
- package/skills/scholar-evaluation/scripts/weight_sensitivity.py +251 -0
- package/skills/scientific-brainstorming/SKILL.md +282 -0
- package/skills/scientific-brainstorming/references/brainstorming_methods.md +292 -0
- package/skills/scientific-brainstorming/references/facilitation_workflows.md +284 -0
- package/skills/scientific-brainstorming/references/idea_evaluation.md +268 -0
- package/skills/scientific-brainstorming/references/responsible_ai.md +220 -0
- package/skills/scientific-brainstorming/references/sources.md +364 -0
- package/skills/scientific-brainstorming/scripts/_common.py +307 -0
- package/skills/scientific-brainstorming/scripts/evaluate_matrix.py +518 -0
- package/skills/scientific-brainstorming/scripts/session_scaffold.py +248 -0
- package/skills/scientific-brainstorming/scripts/validate_register.py +654 -0
- package/skills/scientific-critical-thinking/SKILL.md +180 -0
- package/skills/scientific-critical-thinking/references/common_biases.md +364 -0
- package/skills/scientific-critical-thinking/references/core_capabilities.md +407 -0
- package/skills/scientific-critical-thinking/references/evidence_hierarchy.md +485 -0
- package/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
- package/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
- package/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
- package/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
- package/skills/scientific-schematics/SKILL.md +370 -0
- package/skills/scientific-schematics/references/best_practices.md +574 -0
- package/skills/scientific-schematics/references/iterative_refinement.md +315 -0
- package/skills/scientific-schematics/scripts/example_usage.sh +92 -0
- package/skills/scientific-schematics/scripts/generate_schematic.py +198 -0
- package/skills/scientific-schematics/scripts/generate_schematic_ai.py +950 -0
- package/skills/scientific-slides/SKILL.md +379 -0
- package/skills/scientific-slides/assets/beamer_template_conference.tex +407 -0
- package/skills/scientific-slides/assets/beamer_template_defense.tex +906 -0
- package/skills/scientific-slides/assets/beamer_template_seminar.tex +870 -0
- package/skills/scientific-slides/assets/powerpoint_design_guide.md +662 -0
- package/skills/scientific-slides/assets/timing_guidelines.md +597 -0
- package/skills/scientific-slides/references/beamer_guide.md +1019 -0
- package/skills/scientific-slides/references/common_pitfalls.md +85 -0
- package/skills/scientific-slides/references/data_visualization_slides.md +708 -0
- package/skills/scientific-slides/references/presentation_structure.md +642 -0
- package/skills/scientific-slides/references/presentation_workflow.md +196 -0
- package/skills/scientific-slides/references/prompt_writing.md +42 -0
- package/skills/scientific-slides/references/script_reference.md +143 -0
- package/skills/scientific-slides/references/slide_capabilities.md +360 -0
- package/skills/scientific-slides/references/slide_design_principles.md +849 -0
- package/skills/scientific-slides/references/talk_types_guide.md +687 -0
- package/skills/scientific-slides/references/visual_review_workflow.md +775 -0
- package/skills/scientific-slides/scripts/generate_schematic.py +198 -0
- package/skills/scientific-slides/scripts/generate_schematic_ai.py +950 -0
- package/skills/scientific-slides/scripts/generate_slide_image.py +197 -0
- package/skills/scientific-slides/scripts/generate_slide_image_ai.py +877 -0
- package/skills/scientific-slides/scripts/pdf_to_images.py +221 -0
- package/skills/scientific-slides/scripts/slides_to_pdf.py +235 -0
- package/skills/scientific-slides/scripts/validate_presentation.py +408 -0
- package/skills/scientific-visualization/SKILL.md +285 -0
- package/skills/scientific-visualization/assets/color_palettes.py +263 -0
- package/skills/scientific-visualization/assets/nature.mplstyle +68 -0
- package/skills/scientific-visualization/assets/presentation.mplstyle +68 -0
- package/skills/scientific-visualization/assets/publication.mplstyle +77 -0
- package/skills/scientific-visualization/assets/publisher_profiles.json +269 -0
- package/skills/scientific-visualization/references/color_palettes.md +227 -0
- package/skills/scientific-visualization/references/journal_requirements.md +169 -0
- package/skills/scientific-visualization/references/matplotlib_examples.md +336 -0
- package/skills/scientific-visualization/references/publication_guidelines.md +196 -0
- package/skills/scientific-visualization/references/sources.md +76 -0
- package/skills/scientific-visualization/scripts/_common.py +136 -0
- package/skills/scientific-visualization/scripts/export_plan.py +493 -0
- package/skills/scientific-visualization/scripts/figure_export.py +642 -0
- package/skills/scientific-visualization/scripts/image_metadata.py +731 -0
- package/skills/scientific-visualization/scripts/palette_audit.py +327 -0
- package/skills/scientific-visualization/scripts/style_presets.py +501 -0
- package/skills/scientific-visualization/scripts/style_preview.py +232 -0
- package/skills/scientific-writing/SKILL.md +356 -0
- package/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md +60 -0
- package/skills/scientific-writing/assets/authorship_template.json +56 -0
- package/skills/scientific-writing/assets/claim_evidence_template.csv +2 -0
- package/skills/scientific-writing/assets/consistency_manifest_template.json +43 -0
- package/skills/scientific-writing/assets/manuscript_manifest_template.json +37 -0
- package/skills/scientific-writing/assets/manuscript_scaffold.md +65 -0
- package/skills/scientific-writing/assets/reporting_coverage_template.json +6 -0
- package/skills/scientific-writing/assets/reporting_guidelines.json +529 -0
- package/skills/scientific-writing/assets/source_manifest_template.json +27 -0
- package/skills/scientific-writing/references/authorship_ai_confidentiality.md +111 -0
- package/skills/scientific-writing/references/citation_styles.md +92 -0
- package/skills/scientific-writing/references/cli_reference.md +113 -0
- package/skills/scientific-writing/references/evidence_workflow.md +94 -0
- package/skills/scientific-writing/references/figures_tables.md +94 -0
- package/skills/scientific-writing/references/imrad_structure.md +114 -0
- package/skills/scientific-writing/references/journal_policies.md +56 -0
- package/skills/scientific-writing/references/professional_report_formatting.md +82 -0
- package/skills/scientific-writing/references/reporting_guidelines.md +107 -0
- package/skills/scientific-writing/references/research_integrity_open_science.md +97 -0
- package/skills/scientific-writing/references/source_ledger.md +268 -0
- package/skills/scientific-writing/references/writing_principles.md +97 -0
- package/skills/scientific-writing/scripts/_common.py +240 -0
- package/skills/scientific-writing/scripts/audit_claims.py +241 -0
- package/skills/scientific-writing/scripts/check_consistency.py +408 -0
- package/skills/scientific-writing/scripts/check_references.py +219 -0
- package/skills/scientific-writing/scripts/lint_manuscript.py +171 -0
- package/skills/scientific-writing/scripts/scaffold_manuscript.py +143 -0
- package/skills/scientific-writing/scripts/select_reporting_guidelines.py +214 -0
- package/skills/scientific-writing/scripts/validate_authorship.py +322 -0
- package/skills/scientific-writing/scripts/validate_manifest.py +460 -0
- package/skills/scikit-bio/SKILL.md +470 -0
- package/skills/scikit-bio/references/api_reference.md +766 -0
- package/skills/scikit-learn/SKILL.md +324 -0
- package/skills/scikit-learn/references/common_workflows.md +107 -0
- package/skills/scikit-learn/references/core_capabilities.md +133 -0
- package/skills/scikit-learn/references/model_evaluation.md +592 -0
- package/skills/scikit-learn/references/pipelines_and_composition.md +612 -0
- package/skills/scikit-learn/references/preprocessing.md +606 -0
- package/skills/scikit-learn/references/quick_reference.md +436 -0
- package/skills/scikit-learn/references/supervised_learning.md +379 -0
- package/skills/scikit-learn/references/unsupervised_learning.md +517 -0
- package/skills/scikit-learn/scripts/classification_pipeline.py +257 -0
- package/skills/scikit-learn/scripts/clustering_analysis.py +386 -0
- package/skills/scikit-survival/SKILL.md +313 -0
- package/skills/scikit-survival/references/competing-risks.md +302 -0
- package/skills/scikit-survival/references/cox-models.md +252 -0
- package/skills/scikit-survival/references/data-handling.md +278 -0
- package/skills/scikit-survival/references/ensemble-models.md +287 -0
- package/skills/scikit-survival/references/evaluation-metrics.md +391 -0
- package/skills/scikit-survival/references/svm-models.md +277 -0
- package/skills/scikit-survival/scripts/_common.py +456 -0
- package/skills/scikit-survival/scripts/competing_risk_cif.py +286 -0
- package/skills/scikit-survival/scripts/evaluate_survival_metrics.py +296 -0
- package/skills/scikit-survival/scripts/model_report.py +297 -0
- package/skills/scikit-survival/scripts/train_survival_model.py +583 -0
- package/skills/scikit-survival/scripts/validate_survival_csv.py +172 -0
- package/skills/scvelo/SKILL.md +328 -0
- package/skills/scvelo/references/velocity_models.md +168 -0
- package/skills/scvelo/scripts/rna_velocity_workflow.py +240 -0
- package/skills/scvi-tools/SKILL.md +201 -0
- package/skills/scvi-tools/references/differential-expression.md +597 -0
- package/skills/scvi-tools/references/models-atac-seq.md +329 -0
- package/skills/scvi-tools/references/models-multimodal.md +400 -0
- package/skills/scvi-tools/references/models-scrna-seq.md +333 -0
- package/skills/scvi-tools/references/models-spatial.md +432 -0
- package/skills/scvi-tools/references/models-specialized.md +376 -0
- package/skills/scvi-tools/references/theoretical-foundations.md +438 -0
- package/skills/scvi-tools/references/workflows.md +559 -0
- package/skills/seaborn/SKILL.md +254 -0
- package/skills/seaborn/references/examples.md +824 -0
- package/skills/seaborn/references/function_reference.md +772 -0
- package/skills/seaborn/references/grids_and_levels.md +85 -0
- package/skills/seaborn/references/objects_interface.md +963 -0
- package/skills/seaborn/references/palettes_and_theming.md +110 -0
- package/skills/seaborn/references/patterns_and_troubleshooting.md +114 -0
- package/skills/seaborn/references/plotting_functions.md +178 -0
- package/skills/security-auditor/SKILL.md +37 -0
- package/skills/shap/SKILL.md +282 -0
- package/skills/shap/references/data-maskers.md +287 -0
- package/skills/shap/references/explainers.md +376 -0
- package/skills/shap/references/migration.md +415 -0
- package/skills/shap/references/modalities.md +353 -0
- package/skills/shap/references/plots.md +406 -0
- package/skills/shap/references/theory.md +352 -0
- package/skills/shap/references/troubleshooting.md +442 -0
- package/skills/shap/references/workflows.md +565 -0
- package/skills/shap/scripts/tabular_report.py +326 -0
- package/skills/simpy/SKILL.md +283 -0
- package/skills/simpy/references/cli-guide.md +266 -0
- package/skills/simpy/references/events.md +225 -0
- package/skills/simpy/references/monitoring.md +260 -0
- package/skills/simpy/references/process-interaction.md +269 -0
- package/skills/simpy/references/real-time.md +174 -0
- package/skills/simpy/references/resources.md +274 -0
- package/skills/simpy/references/simulation-methodology.md +293 -0
- package/skills/simpy/references/sources.md +167 -0
- package/skills/simpy/scripts/_common.py +473 -0
- package/skills/simpy/scripts/basic_simulation_template.py +415 -0
- package/skills/simpy/scripts/bounded_queue_scenario.py +126 -0
- package/skills/simpy/scripts/event_trace_summary.py +296 -0
- package/skills/simpy/scripts/replication_runner.py +194 -0
- package/skills/simpy/scripts/resource_monitor.py +474 -0
- package/skills/simpy/scripts/validate_simulation_config.py +111 -0
- package/skills/stable-baselines3/SKILL.md +325 -0
- package/skills/stable-baselines3/references/algorithms.md +348 -0
- package/skills/stable-baselines3/references/callbacks.md +571 -0
- package/skills/stable-baselines3/references/custom_environments.md +528 -0
- package/skills/stable-baselines3/references/vectorized_envs.md +580 -0
- package/skills/stable-baselines3/scripts/custom_env_template.py +314 -0
- package/skills/stable-baselines3/scripts/evaluate_agent.py +245 -0
- package/skills/stable-baselines3/scripts/train_rl_agent.py +165 -0
- package/skills/statistical-analysis/SKILL.md +446 -0
- package/skills/statistical-analysis/references/assumptions_and_diagnostics.md +379 -0
- package/skills/statistical-analysis/references/bayesian_statistics.md +686 -0
- package/skills/statistical-analysis/references/effect_sizes_and_power.md +649 -0
- package/skills/statistical-analysis/references/reporting_standards.md +482 -0
- package/skills/statistical-analysis/references/test_selection_guide.md +129 -0
- package/skills/statistical-analysis/scripts/assumption_checks.py +652 -0
- package/skills/statistical-power/SKILL.md +200 -0
- package/skills/statistical-power/references/closed_form_recipes.md +174 -0
- package/skills/statistical-power/references/effect_sizes.md +121 -0
- package/skills/statistical-power/references/simulation_based_power.md +101 -0
- package/skills/statistical-power/scripts/power.py +320 -0
- package/skills/statistical-power/scripts/simulate_power.py +217 -0
- package/skills/statsmodels/SKILL.md +238 -0
- package/skills/statsmodels/references/discrete_choice.md +669 -0
- package/skills/statsmodels/references/glm.md +619 -0
- package/skills/statsmodels/references/linear_models.md +447 -0
- package/skills/statsmodels/references/model_selection.md +99 -0
- package/skills/statsmodels/references/modeling_capabilities.md +168 -0
- package/skills/statsmodels/references/quick_start_guide.md +154 -0
- package/skills/statsmodels/references/stats_diagnostics.md +859 -0
- package/skills/statsmodels/references/time_series.md +723 -0
- package/skills/sympy/SKILL.md +354 -0
- package/skills/sympy/references/advanced-topics.md +635 -0
- package/skills/sympy/references/code-generation-printing.md +628 -0
- package/skills/sympy/references/core-capabilities.md +348 -0
- package/skills/sympy/references/core_capabilities.md +190 -0
- package/skills/sympy/references/matrices-linear-algebra.md +526 -0
- package/skills/sympy/references/physics-mechanics.md +592 -0
- package/skills/systematic-debugging/SKILL.md +35 -0
- package/skills/tamarind/SKILL.md +285 -0
- package/skills/tamarind/references/api_reference.md +165 -0
- package/skills/tamarind/references/examples.md +132 -0
- package/skills/tamarind/references/tool_catalog.md +66 -0
- package/skills/tamarind/references/workflows.md +263 -0
- package/skills/tdd/SKILL.md +26 -0
- package/skills/tiledbvcf/SKILL.md +456 -0
- package/skills/timesfm-forecasting/SKILL.md +408 -0
- package/skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py +524 -0
- package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.json +448 -0
- package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png +0 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py +568 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png +0 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_metadata.json +59 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/sales_with_covariates.csv +109 -0
- package/skills/timesfm-forecasting/examples/global-temperature/README.md +178 -0
- package/skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py +147 -0
- package/skills/timesfm-forecasting/examples/global-temperature/generate_gif.py +248 -0
- package/skills/timesfm-forecasting/examples/global-temperature/generate_html.py +544 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/animation_data.json +5441 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif +0 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.csv +13 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.json +188 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png +0 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html +5939 -0
- package/skills/timesfm-forecasting/examples/global-temperature/run_example.sh +53 -0
- package/skills/timesfm-forecasting/examples/global-temperature/run_forecast.py +167 -0
- package/skills/timesfm-forecasting/examples/global-temperature/temperature_anomaly.csv +37 -0
- package/skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py +123 -0
- package/skills/timesfm-forecasting/references/api_reference.md +231 -0
- package/skills/timesfm-forecasting/references/data_preparation.md +272 -0
- package/skills/timesfm-forecasting/references/examples_and_validation.md +103 -0
- package/skills/timesfm-forecasting/references/output_and_config.md +93 -0
- package/skills/timesfm-forecasting/references/performance_tuning.md +80 -0
- package/skills/timesfm-forecasting/references/system_requirements.md +201 -0
- package/skills/timesfm-forecasting/references/workflows.md +126 -0
- package/skills/timesfm-forecasting/scripts/check_system.py +521 -0
- package/skills/timesfm-forecasting/scripts/forecast_csv.py +269 -0
- package/skills/torch-geometric/SKILL.md +458 -0
- package/skills/torch-geometric/references/custom_datasets.md +239 -0
- package/skills/torch-geometric/references/explainability.md +208 -0
- package/skills/torch-geometric/references/heterogeneous.md +241 -0
- package/skills/torch-geometric/references/link_prediction.md +226 -0
- package/skills/torch-geometric/references/message_passing.md +121 -0
- package/skills/torch-geometric/references/scaling.md +269 -0
- package/skills/torchdrug/SKILL.md +241 -0
- package/skills/torchdrug/references/core_concepts.md +241 -0
- package/skills/torchdrug/references/datasets.md +179 -0
- package/skills/torchdrug/references/knowledge_graphs.md +226 -0
- package/skills/torchdrug/references/models_architectures.md +223 -0
- package/skills/torchdrug/references/molecular_generation.md +246 -0
- package/skills/torchdrug/references/molecular_property_prediction.md +239 -0
- package/skills/torchdrug/references/protein_modeling.md +221 -0
- package/skills/torchdrug/references/retrosynthesis.md +247 -0
- package/skills/transformers/SKILL.md +195 -0
- package/skills/transformers/references/generation.md +473 -0
- package/skills/transformers/references/models.md +371 -0
- package/skills/transformers/references/pipelines.md +334 -0
- package/skills/transformers/references/tokenizers.md +449 -0
- package/skills/transformers/references/training.md +504 -0
- package/skills/treatment-plans/SKILL.md +174 -0
- package/skills/treatment-plans/assets/clinician_authored_intervention_template.json +11 -0
- package/skills/treatment-plans/assets/goals_monitoring_checkpoint_template.json +13 -0
- package/skills/treatment-plans/assets/informed_preference_shared_decision_template.json +11 -0
- package/skills/treatment-plans/assets/intended_use_handoff_template.json +83 -0
- package/skills/treatment-plans/assets/source_fact_manifest_template.json +11 -0
- package/skills/treatment-plans/assets/transition_reconciliation_template.json +27 -0
- package/skills/treatment-plans/references/README.md +19 -0
- package/skills/treatment-plans/references/documentation_workflow.md +165 -0
- package/skills/treatment-plans/references/privacy_governance.md +119 -0
- package/skills/treatment-plans/references/safety_scope.md +101 -0
- package/skills/treatment-plans/references/security_validation.md +68 -0
- package/skills/treatment-plans/references/shared_decision_handoff.md +138 -0
- package/skills/treatment-plans/references/source_boundaries.md +127 -0
- package/skills/treatment-plans/references/source_ledger.md +131 -0
- package/skills/treatment-plans/scripts/_common.py +1160 -0
- package/skills/treatment-plans/scripts/check_completeness.py +572 -0
- package/skills/treatment-plans/scripts/check_consistency.py +386 -0
- package/skills/treatment-plans/scripts/generate_template.py +133 -0
- package/skills/treatment-plans/scripts/privacy_process_check.py +213 -0
- package/skills/treatment-plans/scripts/timeline_generator.py +260 -0
- package/skills/treatment-plans/scripts/validate_traceability.py +147 -0
- package/skills/treatment-plans/scripts/validate_treatment_plan.py +95 -0
- package/skills/umap-learn/SKILL.md +488 -0
- package/skills/umap-learn/references/api_reference.md +574 -0
- package/skills/uncertainty-and-units/SKILL.md +384 -0
- package/skills/uncertainty-and-units/references/domain-conversions.md +188 -0
- package/skills/uncertainty-and-units/references/gum-methodology.md +219 -0
- package/skills/uncertainty-and-units/references/pint-recipes.md +228 -0
- package/skills/uncertainty-and-units/references/plausibility-scales.md +168 -0
- package/skills/uncertainty-and-units/references/reporting-rules.md +133 -0
- package/skills/uncertainty-and-units/references/uncertainties-recipes.md +167 -0
- package/skills/uncertainty-and-units/scripts/_common.py +666 -0
- package/skills/uncertainty-and-units/scripts/audit_units.py +575 -0
- package/skills/uncertainty-and-units/scripts/check_plausibility.py +894 -0
- package/skills/uncertainty-and-units/scripts/convert_units.py +280 -0
- package/skills/uncertainty-and-units/scripts/format_result.py +326 -0
- package/skills/uncertainty-and-units/scripts/propagate_uncertainty.py +662 -0
- package/skills/uncertainty-and-units/scripts/uncertainty_budget.py +363 -0
- package/skills/usfiscaldata/SKILL.md +171 -0
- package/skills/usfiscaldata/references/api-basics.md +105 -0
- package/skills/usfiscaldata/references/datasets-debt.md +166 -0
- package/skills/usfiscaldata/references/datasets-fiscal.md +212 -0
- package/skills/usfiscaldata/references/datasets-interest-rates.md +188 -0
- package/skills/usfiscaldata/references/datasets-securities.md +238 -0
- package/skills/usfiscaldata/references/examples.md +258 -0
- package/skills/usfiscaldata/references/parameters.md +182 -0
- package/skills/usfiscaldata/references/response-format.md +178 -0
- package/skills/vaex/SKILL.md +204 -0
- package/skills/vaex/references/core_dataframes.md +373 -0
- package/skills/vaex/references/data_processing.md +555 -0
- package/skills/vaex/references/io_operations.md +718 -0
- package/skills/vaex/references/machine_learning.md +728 -0
- package/skills/vaex/references/performance.md +571 -0
- package/skills/vaex/references/visualization.md +644 -0
- package/skills/venue-templates/SKILL.md +269 -0
- package/skills/venue-templates/assets/examples/cell_summary_example.md +247 -0
- package/skills/venue-templates/assets/examples/medical_structured_abstract.md +313 -0
- package/skills/venue-templates/assets/examples/nature_abstract_examples.md +213 -0
- package/skills/venue-templates/assets/examples/neurips_introduction_example.md +245 -0
- package/skills/venue-templates/assets/grants/nih_specific_aims.tex +237 -0
- package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +384 -0
- package/skills/venue-templates/assets/journals/elsarticle-harv.bst +1598 -0
- package/skills/venue-templates/assets/journals/elsarticle-num-names.bst +1535 -0
- package/skills/venue-templates/assets/journals/elsarticle-num.bst +1509 -0
- package/skills/venue-templates/assets/journals/elsarticle-template-harv.tex +286 -0
- package/skills/venue-templates/assets/journals/elsarticle-template-num-names.tex +284 -0
- package/skills/venue-templates/assets/journals/elsarticle-template-num.tex +286 -0
- package/skills/venue-templates/assets/journals/nature_article.tex +174 -0
- package/skills/venue-templates/assets/journals/neurips_article.tex +292 -0
- package/skills/venue-templates/assets/journals/plos_one.tex +320 -0
- package/skills/venue-templates/assets/posters/beamerposter_academic.tex +312 -0
- package/skills/venue-templates/references/cell_press_style.md +486 -0
- package/skills/venue-templates/references/conferences_formatting.md +175 -0
- package/skills/venue-templates/references/cs_conference_style.md +465 -0
- package/skills/venue-templates/references/grants_requirements.md +267 -0
- package/skills/venue-templates/references/journals_formatting.md +200 -0
- package/skills/venue-templates/references/medical_journal_styles.md +536 -0
- package/skills/venue-templates/references/ml_conference_style.md +562 -0
- package/skills/venue-templates/references/nature_science_style.md +407 -0
- package/skills/venue-templates/references/posters_guidelines.md +630 -0
- package/skills/venue-templates/references/reviewer_expectations.md +422 -0
- package/skills/venue-templates/references/venue_writing_styles.md +323 -0
- package/skills/venue-templates/scripts/customize_template.py +206 -0
- package/skills/venue-templates/scripts/query_template.py +202 -0
- package/skills/venue-templates/scripts/validate_format.py +321 -0
- package/skills/verification-before-completion/SKILL.md +21 -0
- package/skills/waypoint-bio/SKILL.md +273 -0
- package/skills/waypoint-bio/references/cli-reference.md +210 -0
- package/skills/waypoint-bio/references/compass-benchmark.md +124 -0
- package/skills/waypoint-bio/references/data-preparation.md +200 -0
- package/skills/waypoint-bio/references/python-api.md +219 -0
- package/skills/waypoint-bio/scripts/profiler_to_waypoint.py +481 -0
- package/skills/waypoint-bio/scripts/vocab_coverage.py +235 -0
- package/skills/what-if-oracle/SKILL.md +184 -0
- package/skills/what-if-oracle/references/scenario-templates.md +137 -0
- package/skills/writing-plans/SKILL.md +15 -0
- package/skills/xlsx/LICENSE.txt +30 -0
- package/skills/xlsx/SKILL.md +110 -0
- package/skills/xlsx/scripts/office/helpers/__init__.py +111 -0
- package/skills/xlsx/scripts/office/helpers/pptx_chart.py +170 -0
- package/skills/xlsx/scripts/office/helpers/pptx_slide.py +60 -0
- package/skills/xlsx/scripts/office/helpers/pptx_theme.py +114 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +75 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/skills/xlsx/scripts/office/soffice.py +232 -0
- package/skills/xlsx/scripts/office/validate.py +173 -0
- package/skills/xlsx/scripts/office/validators/__init__.py +15 -0
- package/skills/xlsx/scripts/office/validators/base.py +875 -0
- package/skills/xlsx/scripts/office/validators/docx.py +466 -0
- package/skills/xlsx/scripts/office/validators/pptx.py +441 -0
- package/skills/xlsx/scripts/office/validators/redlining.py +299 -0
- package/skills/xlsx/scripts/recalc.py +308 -0
- package/skills/zarr-python/SKILL.md +241 -0
- package/skills/zarr-python/references/api_reference.md +162 -0
- package/skills/zarr-python/references/chunking_and_compression.md +138 -0
- package/skills/zarr-python/references/integration.md +147 -0
- package/skills/zarr-python/references/performance_and_patterns.md +198 -0
- package/skills/zarr-python/references/storage_backends.md +91 -0
- package/skills/zarr-python/references/v3_migration.md +127 -0
- package/templates/agents/orchestrator.md +37 -0
- package/templates/base/groupy_prompt.md +92 -0
- package/templates/compact/prompt.md +9 -0
- package/templates/compact/summary_prefix.md +1 -0
- package/templates/modes/default.md +19 -0
- package/templates/modes/plan.md +128 -0
- package/templates/modes/review.md +60 -0
- package/templates/permissions/approval_policy/never.md +1 -0
- package/templates/permissions/approval_policy/on_request.md +23 -0
- package/templates/permissions/sandbox_mode/danger_full_access.md +1 -0
- package/templates/permissions/sandbox_mode/read_only.md +1 -0
- package/templates/permissions/sandbox_mode/workspace_write.md +1 -0
- package/templates/personalities/friendly.md +19 -0
- package/templates/personalities/pragmatic.md +17 -0
|
@@ -0,0 +1,260 @@
|
|
|
1
|
+
# Environment Contracts and Native Environments
|
|
2
|
+
|
|
3
|
+
Research snapshot: **2026-07-23**.
|
|
4
|
+
|
|
5
|
+
## Start from the Gymnasium contract
|
|
6
|
+
|
|
7
|
+
A current single-agent Gymnasium environment defines `observation_space` and
|
|
8
|
+
`action_space`, then implements:
|
|
9
|
+
|
|
10
|
+
```python
|
|
11
|
+
def reset(self, *, seed=None, options=None):
|
|
12
|
+
super().reset(seed=seed)
|
|
13
|
+
return observation, info
|
|
14
|
+
|
|
15
|
+
def step(self, action):
|
|
16
|
+
return observation, reward, terminated, truncated, info
|
|
17
|
+
```
|
|
18
|
+
|
|
19
|
+
Contract requirements:
|
|
20
|
+
|
|
21
|
+
- `observation` must be contained in `observation_space` after reset and every
|
|
22
|
+
step, with the documented shape and dtype.
|
|
23
|
+
- `action` must be contained in `action_space`.
|
|
24
|
+
- `reward` is a finite scalar for ordinary single-agent tasks.
|
|
25
|
+
- `terminated` means the task's MDP reached a terminal state.
|
|
26
|
+
- `truncated` means an external limit ended the episode, commonly a time limit.
|
|
27
|
+
- `info` is a dictionary; never hide the only termination signal in it.
|
|
28
|
+
- Call `reset()` after either `terminated` or `truncated`.
|
|
29
|
+
- Seed the environment through `reset(seed=...)`. Seed the action space
|
|
30
|
+
separately when sampled actions must be reproducible.
|
|
31
|
+
- Always call `close()`.
|
|
32
|
+
|
|
33
|
+
Do not collapse `terminated` and `truncated` during learning. A time-limit
|
|
34
|
+
truncation can still permit value bootstrapping; a true terminal state does not.
|
|
35
|
+
|
|
36
|
+
Run the local contract tool before involving PufferLib:
|
|
37
|
+
|
|
38
|
+
```bash
|
|
39
|
+
python3 scripts/env_contract_validator.py
|
|
40
|
+
```
|
|
41
|
+
|
|
42
|
+
It validates only the bundled synthetic environment. It intentionally has no
|
|
43
|
+
module-path option, so it cannot dynamically import an untrusted package.
|
|
44
|
+
|
|
45
|
+
## Published PufferLib 3.0.0 native contract
|
|
46
|
+
|
|
47
|
+
For a native Python `PufferEnv`, assign these attributes **before** calling
|
|
48
|
+
`super().__init__(buf)`:
|
|
49
|
+
|
|
50
|
+
```python
|
|
51
|
+
import gymnasium
|
|
52
|
+
import numpy as np
|
|
53
|
+
import pufferlib
|
|
54
|
+
|
|
55
|
+
|
|
56
|
+
class ReviewedEnv(pufferlib.PufferEnv):
|
|
57
|
+
def __init__(self, buf=None, seed=0):
|
|
58
|
+
self.single_observation_space = gymnasium.spaces.Box(
|
|
59
|
+
low=-1.0, high=1.0, shape=(4,), dtype=np.float32
|
|
60
|
+
)
|
|
61
|
+
self.single_action_space = gymnasium.spaces.Discrete(3)
|
|
62
|
+
self.num_agents = 2
|
|
63
|
+
super().__init__(buf)
|
|
64
|
+
```
|
|
65
|
+
|
|
66
|
+
The stable base accepts a Box observation space and Discrete, MultiDiscrete, or
|
|
67
|
+
Box action space. It allocates or attaches:
|
|
68
|
+
|
|
69
|
+
- `observations`
|
|
70
|
+
- `actions`
|
|
71
|
+
- `rewards`
|
|
72
|
+
- `terminals`
|
|
73
|
+
- `truncations`
|
|
74
|
+
- `masks`
|
|
75
|
+
|
|
76
|
+
Native methods operate on those buffers:
|
|
77
|
+
|
|
78
|
+
```python
|
|
79
|
+
def reset(self, seed=None):
|
|
80
|
+
# update self.observations in place
|
|
81
|
+
return self.observations, []
|
|
82
|
+
|
|
83
|
+
def step(self, actions):
|
|
84
|
+
# update all buffers in place
|
|
85
|
+
return (
|
|
86
|
+
self.observations,
|
|
87
|
+
self.rewards,
|
|
88
|
+
self.terminals,
|
|
89
|
+
self.truncations,
|
|
90
|
+
[],
|
|
91
|
+
)
|
|
92
|
+
```
|
|
93
|
+
|
|
94
|
+
The `infos` value for native Puffer environments is a list of dictionaries.
|
|
95
|
+
PufferLib's native interface expects vector rows for agents, even when there is
|
|
96
|
+
one agent. Native environments handle their own resets; clear rewards,
|
|
97
|
+
terminals, truncations, masks, and partially written observations explicitly.
|
|
98
|
+
Never leave a previous step's buffer values in place.
|
|
99
|
+
|
|
100
|
+
### Native shape checklist
|
|
101
|
+
|
|
102
|
+
For `A = num_agents` and single observation shape `S`:
|
|
103
|
+
|
|
104
|
+
- observations: `(A, *S)`
|
|
105
|
+
- rewards: `(A,)`
|
|
106
|
+
- terminals: `(A,)`
|
|
107
|
+
- truncations: `(A,)`
|
|
108
|
+
- masks: `(A,)`
|
|
109
|
+
- actions: joint shape derived from the single action space and `A`
|
|
110
|
+
|
|
111
|
+
Validate the exact allocated action shape rather than assuming `(A,)`, especially
|
|
112
|
+
for MultiDiscrete and Box actions.
|
|
113
|
+
|
|
114
|
+
## Stable Gymnasium and PettingZoo adaptation
|
|
115
|
+
|
|
116
|
+
PufferLib 3.0 uses explicit adapters:
|
|
117
|
+
|
|
118
|
+
```python
|
|
119
|
+
import pufferlib.emulation
|
|
120
|
+
|
|
121
|
+
wrapped = pufferlib.emulation.GymnasiumPufferEnv(reviewed_gymnasium_instance)
|
|
122
|
+
```
|
|
123
|
+
|
|
124
|
+
or:
|
|
125
|
+
|
|
126
|
+
```python
|
|
127
|
+
wrapped = pufferlib.emulation.PettingZooPufferEnv(reviewed_parallel_instance)
|
|
128
|
+
```
|
|
129
|
+
|
|
130
|
+
There is no supported 3.0 `pufferlib.emulate(...)` convenience function matching
|
|
131
|
+
the old skill examples. Pass either an `env` instance or an `env_creator`
|
|
132
|
+
callable according to the class signature; do not pass both.
|
|
133
|
+
|
|
134
|
+
The Gymnasium adapter:
|
|
135
|
+
|
|
136
|
+
- maps structured observation/action spaces to flat arrays;
|
|
137
|
+
- checks the first observation and action against the original spaces;
|
|
138
|
+
- returns separate terminal and truncation values;
|
|
139
|
+
- requires reset before step and reset after episode end.
|
|
140
|
+
|
|
141
|
+
The PettingZoo adapter:
|
|
142
|
+
|
|
143
|
+
- targets the Parallel API;
|
|
144
|
+
- uses `possible_agents` as the fixed slot set;
|
|
145
|
+
- pads missing agents and exposes masks;
|
|
146
|
+
- canonicalizes per-agent spaces and flattened buffers.
|
|
147
|
+
|
|
148
|
+
Validate heterogeneous-agent spaces before use. The adapter derives its single
|
|
149
|
+
spaces from the first possible agent, so environments with incompatible spaces
|
|
150
|
+
need an explicit reviewed transformation.
|
|
151
|
+
|
|
152
|
+
### Structured spaces
|
|
153
|
+
|
|
154
|
+
Stable emulation supports Box, Discrete, MultiDiscrete, Tuple, and Dict patterns
|
|
155
|
+
through a packed NumPy dtype. This is byte-layout conversion, not semantic
|
|
156
|
+
feature engineering. Check:
|
|
157
|
+
|
|
158
|
+
- deterministic Dict key order;
|
|
159
|
+
- leaf shape and dtype;
|
|
160
|
+
- finite numeric values;
|
|
161
|
+
- lossless action reconstruction;
|
|
162
|
+
- policy-side unflattening;
|
|
163
|
+
- padding/mask handling for variable populations.
|
|
164
|
+
|
|
165
|
+
## Current 4.0 Ocean contract
|
|
166
|
+
|
|
167
|
+
The 4.0 default branch focuses on first-party C environments. It no longer
|
|
168
|
+
provides the 3.0 Python emulation/vector modules. The official starting points
|
|
169
|
+
are:
|
|
170
|
+
|
|
171
|
+
- `ocean/squared`: commented single-agent template
|
|
172
|
+
- `ocean/target`: commented multi-agent template
|
|
173
|
+
|
|
174
|
+
A binding defines compile-time metadata such as:
|
|
175
|
+
|
|
176
|
+
```c
|
|
177
|
+
#define OBS_SIZE 121
|
|
178
|
+
#define NUM_ATNS 1
|
|
179
|
+
#define ACT_SIZES {5}
|
|
180
|
+
#define OBS_TENSOR_T ByteTensor
|
|
181
|
+
|
|
182
|
+
#define Env Squared
|
|
183
|
+
#include "vecenv.h"
|
|
184
|
+
```
|
|
185
|
+
|
|
186
|
+
The environment struct must include pointers for observations, actions,
|
|
187
|
+
rewards, and terminals, plus `num_agents` and a log struct. It implements
|
|
188
|
+
`c_reset`, `c_step`, `c_render`, and `c_close`; `binding.c` supplies `my_init`
|
|
189
|
+
and `my_log`.
|
|
190
|
+
|
|
191
|
+
Security and correctness rules:
|
|
192
|
+
|
|
193
|
+
1. Treat the C environment and every linked library as native code.
|
|
194
|
+
2. Verify repository/commit, license, asset rights, and checksums before build.
|
|
195
|
+
3. Build only the selected environment in a disposable container or VM.
|
|
196
|
+
4. Start with the local/address-sanitizer build described by upstream.
|
|
197
|
+
5. Match `OBS_SIZE`, tensor dtype, action branch count/sizes, and actual writes.
|
|
198
|
+
6. Bounds-check every index and allocation; use checked arithmetic for sizes.
|
|
199
|
+
7. Initialize every output element each step. Reset reward/terminal buffers
|
|
200
|
+
before early returns.
|
|
201
|
+
8. Use an environment-owned RNG seeded per instance; do not use global RNG
|
|
202
|
+
state for reproducibility.
|
|
203
|
+
9. Free only memory owned by the environment. Do not free framework buffers.
|
|
204
|
+
10. Fuzz reset/step/action boundaries before optimization.
|
|
205
|
+
|
|
206
|
+
`c_step` may reset immediately after marking a terminal. Record this autoreset
|
|
207
|
+
behavior when interpreting terminal observations.
|
|
208
|
+
|
|
209
|
+
## Environment provenance
|
|
210
|
+
|
|
211
|
+
An environment package may execute arbitrary Python/native code and may fetch
|
|
212
|
+
assets at import, build, reset, or render time. Before execution:
|
|
213
|
+
|
|
214
|
+
- use the official repository and immutable revision;
|
|
215
|
+
- inspect package/build scripts and transitive dependencies;
|
|
216
|
+
- verify artifact hashes or attestations;
|
|
217
|
+
- review license compatibility for code, datasets, media, ROMs, maps, and model
|
|
218
|
+
opponents separately;
|
|
219
|
+
- reject unlicensed ROMs or “accept ROM license” automation without proof of
|
|
220
|
+
rights;
|
|
221
|
+
- disable network and credentials in the first-run sandbox;
|
|
222
|
+
- cap disk, memory, processes, threads, episode length, agents, and render size;
|
|
223
|
+
- do not load bundled checkpoints or pickle files during environment import.
|
|
224
|
+
|
|
225
|
+
An entry in Ocean/config is not a blanket security, quality, or licensing
|
|
226
|
+
approval.
|
|
227
|
+
|
|
228
|
+
## Testing ladder
|
|
229
|
+
|
|
230
|
+
1. Built-in synthetic contract validator.
|
|
231
|
+
2. One environment, one seed, serial, tens of steps.
|
|
232
|
+
3. Boundary actions and intentionally invalid actions.
|
|
233
|
+
4. Termination and time-limit truncation tests.
|
|
234
|
+
5. Same-seed trace comparison.
|
|
235
|
+
6. Independent-seed diversity check.
|
|
236
|
+
7. Structured-space round trip.
|
|
237
|
+
8. Multi-agent join/leave and mask tests.
|
|
238
|
+
9. Serial versus vectorized trace equivalence where ordering permits.
|
|
239
|
+
10. Bounded throughput benchmark only after correctness passes.
|
|
240
|
+
|
|
241
|
+
## Sources
|
|
242
|
+
|
|
243
|
+
- [Gymnasium Env API](https://gymnasium.farama.org/api/env/) — current reset,
|
|
244
|
+
step, spaces, and seeding contract; accessed 2026-07-23.
|
|
245
|
+
- [Gymnasium terminated/truncated explanation](https://farama.org/Gymnasium-Terminated-Truncated-Step-API)
|
|
246
|
+
— published 2023-10-27; accessed 2026-07-23.
|
|
247
|
+
- [PufferLib 3.0 core environment source](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/pufferlib.py)
|
|
248
|
+
— stable native contract; accessed 2026-07-23.
|
|
249
|
+
- [PufferLib 3.0 emulation source](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/emulation.py)
|
|
250
|
+
— stable adapters; accessed 2026-07-23.
|
|
251
|
+
- [PufferLib 3.0 Gymnasium example](https://github.com/PufferAI/PufferLib/blob/3.0/examples/gymnasium_env.py)
|
|
252
|
+
— stable example; accessed 2026-07-23.
|
|
253
|
+
- [PufferLib 3.0 PettingZoo example](https://github.com/PufferAI/PufferLib/blob/3.0/examples/pettingzoo_env.py)
|
|
254
|
+
— stable example; accessed 2026-07-23.
|
|
255
|
+
- [PufferLib 4.0 Squared template](https://github.com/PufferAI/PufferLib/tree/4.0/ocean/squared)
|
|
256
|
+
— current single-agent native template; accessed 2026-07-23.
|
|
257
|
+
- [PufferLib 4.0 Target template](https://github.com/PufferAI/PufferLib/tree/4.0/ocean/target)
|
|
258
|
+
— current multi-agent native template; accessed 2026-07-23.
|
|
259
|
+
- [PufferLib Ocean](https://puffer.ai/ocean.html) — current first-party
|
|
260
|
+
collection; accessed 2026-07-23.
|
|
@@ -0,0 +1,192 @@
|
|
|
1
|
+
# Integration, Security, and Migration Guide
|
|
2
|
+
|
|
3
|
+
Research snapshot: **2026-07-23**.
|
|
4
|
+
|
|
5
|
+
## Compatibility matrix
|
|
6
|
+
|
|
7
|
+
| Need | Published `pufferlib==3.0.0` | Current `4.0` source |
|
|
8
|
+
|---|---|---|
|
|
9
|
+
| Gymnasium instance adaptation | `pufferlib.emulation.GymnasiumPufferEnv` | Removed from current source |
|
|
10
|
+
| PettingZoo Parallel adaptation | `pufferlib.emulation.PettingZooPufferEnv` | Removed from current source |
|
|
11
|
+
| Python vector backends | `pufferlib.vector` | Removed from current source |
|
|
12
|
+
| Native Python `PufferEnv` | Supported | Replaced by current C/Ocean interface |
|
|
13
|
+
| Trainer | `pufferlib.pufferl.PuffeRL` | Native backend or `pufferlib.torch_pufferl.PuffeRL` |
|
|
14
|
+
| External logging | W&B and Neptune | W&B in current CLI |
|
|
15
|
+
| Primary config | merged INI sections | different INI schema |
|
|
16
|
+
| Checkpoints | Torch state dict plus trainer state | native `.bin`; Torch fallback state dict |
|
|
17
|
+
|
|
18
|
+
Pin a profile. Do not import from a floating branch or blend examples across
|
|
19
|
+
columns.
|
|
20
|
+
|
|
21
|
+
## Correct stable adaptation patterns
|
|
22
|
+
|
|
23
|
+
### Gymnasium
|
|
24
|
+
|
|
25
|
+
```python
|
|
26
|
+
import gymnasium
|
|
27
|
+
import pufferlib.emulation
|
|
28
|
+
import pufferlib.vector
|
|
29
|
+
|
|
30
|
+
|
|
31
|
+
def make_env():
|
|
32
|
+
raw = gymnasium.make("CartPole-v1")
|
|
33
|
+
return pufferlib.emulation.GymnasiumPufferEnv(raw)
|
|
34
|
+
|
|
35
|
+
|
|
36
|
+
vecenv = pufferlib.vector.make(
|
|
37
|
+
make_env,
|
|
38
|
+
backend=pufferlib.vector.Serial,
|
|
39
|
+
num_envs=2,
|
|
40
|
+
seed=42,
|
|
41
|
+
)
|
|
42
|
+
try:
|
|
43
|
+
observations, infos = vecenv.reset(seed=42)
|
|
44
|
+
actions = vecenv.action_space.sample()
|
|
45
|
+
observations, rewards, terminals, truncations, infos = vecenv.step(actions)
|
|
46
|
+
finally:
|
|
47
|
+
vecenv.close()
|
|
48
|
+
```
|
|
49
|
+
|
|
50
|
+
This example is an API pattern, not authorization to install or execute
|
|
51
|
+
`CartPole-v1` or another plug-in. Review the exact environment and dependencies
|
|
52
|
+
first.
|
|
53
|
+
|
|
54
|
+
### PettingZoo
|
|
55
|
+
|
|
56
|
+
Use a reviewed Parallel environment instance:
|
|
57
|
+
|
|
58
|
+
```python
|
|
59
|
+
wrapped = pufferlib.emulation.PettingZooPufferEnv(reviewed_parallel_env)
|
|
60
|
+
```
|
|
61
|
+
|
|
62
|
+
The stable source does not document automatic AEC-to-Parallel conversion in
|
|
63
|
+
this adapter. Convert explicitly with PettingZoo's supported utilities only
|
|
64
|
+
when the environment's turn semantics permit it, then test action ordering,
|
|
65
|
+
dead-agent handling, masks, and termination/truncation dictionaries.
|
|
66
|
+
|
|
67
|
+
### Native stable environment
|
|
68
|
+
|
|
69
|
+
Subclass `pufferlib.PufferEnv`, define `single_observation_space`,
|
|
70
|
+
`single_action_space`, and `num_agents` before `super().__init__`, then update
|
|
71
|
+
the provided arrays in place. Native Puffer environments are already vector
|
|
72
|
+
interfaces; do not return Gym's scalar four-tuple.
|
|
73
|
+
|
|
74
|
+
## Unsupported shortcuts from the old skill
|
|
75
|
+
|
|
76
|
+
Remove or migrate these historical patterns:
|
|
77
|
+
|
|
78
|
+
| Historical pattern | Current guidance |
|
|
79
|
+
|---|---|
|
|
80
|
+
| `pufferlib.make("name", ...)` | Stable: import an audited creator and use `pufferlib.vector.make`; 4.0: build/configure a named native environment |
|
|
81
|
+
| `pufferlib.emulate(...)` | Stable: instantiate `GymnasiumPufferEnv` or `PettingZooPufferEnv` explicitly |
|
|
82
|
+
| `pufferlib.vectorization.Serial` | Stable module is `pufferlib.vector.Serial` |
|
|
83
|
+
| `from pufferlib import PuffeRL` | Stable trainer is `pufferlib.pufferl.PuffeRL`; 4.0 fallback is in `torch_pufferl` |
|
|
84
|
+
| define native `observation_space`/`action_space` | Stable native class requires `single_observation_space`/`single_action_space` before `super()` |
|
|
85
|
+
| return `(obs, reward, done, info)` | Return separate termination and truncation values |
|
|
86
|
+
| native multi-agent dictionaries and `dones["__all__"]` | Use stable vector buffers or a reviewed PettingZoo Parallel adapter |
|
|
87
|
+
| arbitrary dotted `entry_point` registration | Import an audited callable directly; bundled tools reject dotted paths |
|
|
88
|
+
| top-level `WandbLogger`/`NeptuneLogger` | Stable logger classes live in `pufferlib.pufferl`; prefer the CLI and sanitized config |
|
|
89
|
+
| assume Atari/Procgen/NetHack names exist everywhere | Verify the chosen version's config/source and install the separately reviewed environment |
|
|
90
|
+
|
|
91
|
+
## Migrating 3.0 to 4.0
|
|
92
|
+
|
|
93
|
+
This is a redesign, not a drop-in upgrade:
|
|
94
|
+
|
|
95
|
+
1. Preserve the 3.0 lock, source digest, config, checkpoint hashes, and baseline
|
|
96
|
+
evaluation before changing anything.
|
|
97
|
+
2. Inventory use of `emulation`, `vector`, `PufferEnv`, third-party environments,
|
|
98
|
+
policy wrappers, INI keys, logger flags, and Torch checkpoints.
|
|
99
|
+
3. Decide whether the application should stay on published 3.0.0 or port to a
|
|
100
|
+
native 4.0 C environment. The current docs say the Python/third-party layer
|
|
101
|
+
was removed from 4.0.
|
|
102
|
+
4. Port environment logic to the reviewed Squared/Target C binding contract.
|
|
103
|
+
5. Recreate configuration using 4.0 `[vec]`, `[policy]`, `[torch]`, and `[train]`
|
|
104
|
+
keys. Do not mechanically rename old keys.
|
|
105
|
+
6. Rebuild policy composition around 4.0 encoder/decoder/network modules or the
|
|
106
|
+
native backend.
|
|
107
|
+
7. Treat old `.pt` and new `.bin` files as incompatible unless an official,
|
|
108
|
+
tested converter says otherwise. Do not improvise binary conversion.
|
|
109
|
+
8. Re-run contract, same-seed trace, throughput, and held-out learning
|
|
110
|
+
baselines. Attribute behavior changes; do not compare headline SPS alone.
|
|
111
|
+
|
|
112
|
+
The default branch contains some stale 3.0-style examples even though the
|
|
113
|
+
corresponding modules are absent. Prefer current implementation and docs over
|
|
114
|
+
those copied examples.
|
|
115
|
+
|
|
116
|
+
## Third-party environments and native code
|
|
117
|
+
|
|
118
|
+
Environment extras can pull old Gym versions, native libraries, renderers,
|
|
119
|
+
emulators, datasets, model opponents, and ROM tooling. A package name in a
|
|
120
|
+
PufferLib optional extra is not a security or license endorsement.
|
|
121
|
+
|
|
122
|
+
Before install/import/build:
|
|
123
|
+
|
|
124
|
+
1. Identify the official repository and immutable revision.
|
|
125
|
+
2. Read build/install hooks and all network downloads.
|
|
126
|
+
3. Verify licenses for code and assets separately.
|
|
127
|
+
4. Verify hashes/attestations; record missing provenance.
|
|
128
|
+
5. Use a disposable sandbox without credentials, home-directory mounts, or
|
|
129
|
+
network after required artifacts are staged.
|
|
130
|
+
6. Cap processes, threads, memory, disk, render resolution, agents, and steps.
|
|
131
|
+
7. Do not execute bundled native extensions, ROMs, checkpoints, or pickle files
|
|
132
|
+
until separately trusted.
|
|
133
|
+
|
|
134
|
+
For Atari and similar systems, the user must supply legally obtained assets.
|
|
135
|
+
Never download ROM sets or auto-accept a license on the user's behalf.
|
|
136
|
+
|
|
137
|
+
## Logging integration
|
|
138
|
+
|
|
139
|
+
External tracking is disabled by default. The stable logger implementations can
|
|
140
|
+
log the full argument mapping and can upload model artifacts. Therefore:
|
|
141
|
+
|
|
142
|
+
- sanitize arguments before logger construction;
|
|
143
|
+
- keep `WANDB_API_KEY` and `NEPTUNE_API_TOKEN` only in an approved environment
|
|
144
|
+
injection or secret manager;
|
|
145
|
+
- never add credential keys to nested INI/JSON/config objects;
|
|
146
|
+
- do not pass a token on the command line;
|
|
147
|
+
- disable model/source upload unless explicitly approved;
|
|
148
|
+
- review project visibility, retention, residency, access controls, and cost;
|
|
149
|
+
- use vendor offline/disabled modes only after confirming what is written
|
|
150
|
+
locally and how later sync behaves.
|
|
151
|
+
|
|
152
|
+
Do not print all environment variables or recursively discover `.env` files.
|
|
153
|
+
Checking whether one explicitly named credential variable exists can be
|
|
154
|
+
acceptable; reading or logging its value is not.
|
|
155
|
+
|
|
156
|
+
## Integration acceptance test
|
|
157
|
+
|
|
158
|
+
For each reviewed environment/profile:
|
|
159
|
+
|
|
160
|
+
1. Create one instance without network or GPU.
|
|
161
|
+
2. Validate spaces and reset return.
|
|
162
|
+
3. Step a fixed action trace until both ordinary and episode-end paths run.
|
|
163
|
+
4. Verify terminated/truncated semantics and final observation behavior.
|
|
164
|
+
5. Close and confirm no child processes/resources remain.
|
|
165
|
+
6. Run stable Serial or one 4.0 local native instance.
|
|
166
|
+
7. Compare a same-seed trace.
|
|
167
|
+
8. Scale to two workers/threads with small caps.
|
|
168
|
+
9. Run policy shape and finite-value checks.
|
|
169
|
+
10. Run held-out evaluation with logging still disabled.
|
|
170
|
+
|
|
171
|
+
Only then consider GPU training, external logging, or larger parallelism.
|
|
172
|
+
|
|
173
|
+
## Sources
|
|
174
|
+
|
|
175
|
+
- [PufferLib PyPI 3.0.0](https://pypi.org/project/pufferlib/3.0.0/) —
|
|
176
|
+
published 2025-06-23; accessed 2026-07-23.
|
|
177
|
+
- [PufferLib 3.0 emulation source](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/emulation.py)
|
|
178
|
+
— stable adapters; accessed 2026-07-23.
|
|
179
|
+
- [PufferLib 3.0 vector source](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/vector.py)
|
|
180
|
+
— stable vector API; accessed 2026-07-23.
|
|
181
|
+
- [PufferLib 3.0 trainer source](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/pufferl.py)
|
|
182
|
+
— stable logger/checkpoint behavior; accessed 2026-07-23.
|
|
183
|
+
- [PufferLib 4.0 package tree](https://github.com/PufferAI/PufferLib/tree/4.0/pufferlib)
|
|
184
|
+
— current modules; accessed 2026-07-23.
|
|
185
|
+
- [PufferLib 4.0 docs](https://puffer.ai/docs.html) — current architecture and
|
|
186
|
+
removal note; accessed 2026-07-23.
|
|
187
|
+
- [PufferLib releases](https://github.com/PufferAI/PufferLib/releases) —
|
|
188
|
+
checked for source releases on 2026-07-23.
|
|
189
|
+
- [Gymnasium Env API](https://gymnasium.farama.org/api/env/) — current
|
|
190
|
+
single-agent contract; accessed 2026-07-23.
|
|
191
|
+
- [PyTorch security policy](https://github.com/pytorch/pytorch/security) —
|
|
192
|
+
model/native-package safety; accessed 2026-07-23.
|
|
@@ -0,0 +1,181 @@
|
|
|
1
|
+
# Policies and Model Contracts
|
|
2
|
+
|
|
3
|
+
Research snapshot: **2026-07-23**. Policy APIs changed substantially between
|
|
4
|
+
published PufferLib 3.0.0 and current 4.0 source.
|
|
5
|
+
|
|
6
|
+
## Published 3.0.0
|
|
7
|
+
|
|
8
|
+
PufferLib 3.0 policies are ordinary `torch.nn.Module` objects. The environment
|
|
9
|
+
exposes `single_observation_space` and `single_action_space`; size heads from
|
|
10
|
+
those single-agent spaces, not from the batched spaces.
|
|
11
|
+
|
|
12
|
+
### Minimal feed-forward policy
|
|
13
|
+
|
|
14
|
+
Build an `nn.Module` with an encoder sized from
|
|
15
|
+
`env.single_observation_space.shape`, an action head sized from
|
|
16
|
+
`env.single_action_space`, and a one-value critic head. The official stable
|
|
17
|
+
example defines a rollout method named `forward_eval(observations, state=None)`
|
|
18
|
+
and makes the normal `forward` method use the same contract. Here, `forward_eval`
|
|
19
|
+
is a PufferLib/PyTorch method name; it does **not** invoke Python's dangerous
|
|
20
|
+
`eval()` builtin.
|
|
21
|
+
|
|
22
|
+
For a discrete action space, the first output contains action logits and the
|
|
23
|
+
second is the value estimate. Preserve the leading agent-batch dimension.
|
|
24
|
+
|
|
25
|
+
### Recurrent composition
|
|
26
|
+
|
|
27
|
+
The stable `pufferlib.models.LSTMWrapper` expects a base policy with:
|
|
28
|
+
|
|
29
|
+
```python
|
|
30
|
+
def encode_observations(self, observations, state=None):
|
|
31
|
+
...
|
|
32
|
+
|
|
33
|
+
def decode_actions(self, hidden):
|
|
34
|
+
...
|
|
35
|
+
```
|
|
36
|
+
|
|
37
|
+
The wrapper uses an `LSTMCell` during rollout inference and an `LSTM` over
|
|
38
|
+
time-batched data during training. Do not manually reshape recurrent state
|
|
39
|
+
without checking the source's batch/time convention. Reset hidden state on
|
|
40
|
+
actual terminations and truncations according to the trainer's mask behavior.
|
|
41
|
+
|
|
42
|
+
### Structured observations
|
|
43
|
+
|
|
44
|
+
Stable emulation flattens `Dict` and `Tuple` spaces into a homogeneous array.
|
|
45
|
+
The byte layout is described by `env.emulated`. In policy setup:
|
|
46
|
+
|
|
47
|
+
```python
|
|
48
|
+
native_dtype = pufferlib.pytorch.nativize_dtype(env.emulated)
|
|
49
|
+
```
|
|
50
|
+
|
|
51
|
+
In the forward pass:
|
|
52
|
+
|
|
53
|
+
```python
|
|
54
|
+
structured = pufferlib.pytorch.nativize_tensor(observations, native_dtype)
|
|
55
|
+
```
|
|
56
|
+
|
|
57
|
+
Keep the original flattened dtype. Constructing a new float tensor before
|
|
58
|
+
unflattening can destroy the packed representation. Validate every recovered
|
|
59
|
+
leaf shape and dtype before training.
|
|
60
|
+
|
|
61
|
+
### Action spaces
|
|
62
|
+
|
|
63
|
+
The 3.0 source handles:
|
|
64
|
+
|
|
65
|
+
- `Discrete`: one categorical logits tensor.
|
|
66
|
+
- `MultiDiscrete`: one logits tensor per action branch.
|
|
67
|
+
- `Box`: a Normal distribution path for continuous actions.
|
|
68
|
+
|
|
69
|
+
Do not infer support from the 2024 paper's limitations section; that paper
|
|
70
|
+
describes an earlier release. Test clipping/scaling against the environment's
|
|
71
|
+
actual `Box.low`, `Box.high`, shape, and dtype. A `tanh` output is not a general
|
|
72
|
+
substitute for affine mapping to arbitrary bounds.
|
|
73
|
+
|
|
74
|
+
### Stable model utilities
|
|
75
|
+
|
|
76
|
+
Useful 3.0 symbols include:
|
|
77
|
+
|
|
78
|
+
- `pufferlib.pytorch.layer_init`
|
|
79
|
+
- `pufferlib.pytorch.nativize_dtype`
|
|
80
|
+
- `pufferlib.pytorch.nativize_tensor`
|
|
81
|
+
- `pufferlib.models.Default`
|
|
82
|
+
- `pufferlib.models.LSTMWrapper`
|
|
83
|
+
- `pufferlib.models.Convolutional`
|
|
84
|
+
- `pufferlib.models.ProcgenResnet`
|
|
85
|
+
|
|
86
|
+
Inspect the exact 3.0 source before copying signatures. Do not use top-level
|
|
87
|
+
`from pufferlib import PuffeRL`; the trainer is
|
|
88
|
+
`pufferlib.pufferl.PuffeRL`.
|
|
89
|
+
|
|
90
|
+
## Current 4.0 source
|
|
91
|
+
|
|
92
|
+
The current PyTorch fallback composes a policy from three modules:
|
|
93
|
+
|
|
94
|
+
```python
|
|
95
|
+
policy = pufferlib.models.Policy(
|
|
96
|
+
encoder=encoder,
|
|
97
|
+
decoder=decoder,
|
|
98
|
+
network=network,
|
|
99
|
+
)
|
|
100
|
+
```
|
|
101
|
+
|
|
102
|
+
The source contract is:
|
|
103
|
+
|
|
104
|
+
- `Policy.initial_state(batch_size, device)`
|
|
105
|
+
- `Policy.forward_eval(x, state)` for rollout inference
|
|
106
|
+
- `Policy.forward(x)` for time-batched training
|
|
107
|
+
- encoder maps observations to hidden vectors
|
|
108
|
+
- recurrent/network module maps hidden vectors and state
|
|
109
|
+
- decoder maps hidden vectors to action logits and values
|
|
110
|
+
|
|
111
|
+
Current built-ins include `DefaultEncoder`, `DefaultDecoder`, `MLP`, `MinGRU`,
|
|
112
|
+
`LSTM`, `GRU`, `NatureEncoder`, and `ImpalaEncoder`. INI config selects the
|
|
113
|
+
Torch fallback components:
|
|
114
|
+
|
|
115
|
+
```ini
|
|
116
|
+
[torch]
|
|
117
|
+
network = MinGRU
|
|
118
|
+
encoder = DefaultEncoder
|
|
119
|
+
decoder = DefaultDecoder
|
|
120
|
+
|
|
121
|
+
[policy]
|
|
122
|
+
hidden_size = 128
|
|
123
|
+
num_layers = 4
|
|
124
|
+
```
|
|
125
|
+
|
|
126
|
+
The default 4.0 backend is the native implementation, not this Torch fallback.
|
|
127
|
+
The CLI flag `--slowly` selects the fallback.
|
|
128
|
+
|
|
129
|
+
## Shape and numerical checks
|
|
130
|
+
|
|
131
|
+
Run these checks before a long job:
|
|
132
|
+
|
|
133
|
+
1. Reset the reviewed environment and record observation shape/dtype/range.
|
|
134
|
+
2. Run one policy inference under `torch.no_grad()`.
|
|
135
|
+
3. For discrete actions, require logits shape
|
|
136
|
+
`(agent_batch, action_space.n)`.
|
|
137
|
+
4. Require values to represent one scalar per active agent.
|
|
138
|
+
5. For `MultiDiscrete`, verify branch count and each branch width.
|
|
139
|
+
6. For recurrent policies, verify state batch matches active agent rows and
|
|
140
|
+
that masks reset state at episode boundaries.
|
|
141
|
+
7. Reject NaN/Infinity in observations, logits, values, losses, and gradients.
|
|
142
|
+
8. Confirm inactive/padded multi-agent rows do not contribute to loss.
|
|
143
|
+
9. Run backward once and verify finite, non-missing gradients.
|
|
144
|
+
10. Compare eager and compiled outputs before enabling compilation.
|
|
145
|
+
|
|
146
|
+
`torch.compile` and reduced precision can alter performance and numerical
|
|
147
|
+
behavior. Record PyTorch, CUDA, compiler mode, precision, and deterministic
|
|
148
|
+
settings. Do not claim determinism solely because seeds are fixed.
|
|
149
|
+
|
|
150
|
+
## Checkpoint-safe policy workflow
|
|
151
|
+
|
|
152
|
+
- Save weights/state dictionaries, architecture config, environment revision,
|
|
153
|
+
package lock, seed, and checksum separately.
|
|
154
|
+
- Do not serialize arbitrary policy objects.
|
|
155
|
+
- Never call `torch.load` on an untrusted file. PufferLib 3.0 and the 4.0 Torch
|
|
156
|
+
fallback use `torch.load` for model paths; provenance review is therefore a
|
|
157
|
+
precondition, not an optional cleanup.
|
|
158
|
+
- Inspect metadata first with `scripts/inspect_checkpoint.py`; it never imports
|
|
159
|
+
Torch or deserializes.
|
|
160
|
+
- Verify an expected SHA-256 and license before loading.
|
|
161
|
+
- If business requirements force inspection of an untrusted model, isolate the
|
|
162
|
+
operation in a disposable sandbox with no credentials, network, host mounts,
|
|
163
|
+
or sensitive data. PyTorch warns that models are programs and that even
|
|
164
|
+
inspection tools may execute model code.
|
|
165
|
+
|
|
166
|
+
## Sources
|
|
167
|
+
|
|
168
|
+
- [PufferLib 3.0 policy example](https://github.com/PufferAI/PufferLib/blob/3.0/examples/pufferl.py)
|
|
169
|
+
— stable example; accessed 2026-07-23.
|
|
170
|
+
- [PufferLib 3.0 PyTorch utilities](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/pytorch.py)
|
|
171
|
+
— stable implementation; accessed 2026-07-23.
|
|
172
|
+
- [PufferLib 3.0 models](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/models.py)
|
|
173
|
+
— stable model classes; accessed 2026-07-23.
|
|
174
|
+
- [PufferLib 4.0 models](https://github.com/PufferAI/PufferLib/blob/4.0/pufferlib/models.py)
|
|
175
|
+
— current source model contract; accessed 2026-07-23.
|
|
176
|
+
- [PufferLib 4.0 Torch trainer](https://github.com/PufferAI/PufferLib/blob/4.0/pufferlib/torch_pufferl.py)
|
|
177
|
+
— current fallback and checkpoint loading; accessed 2026-07-23.
|
|
178
|
+
- [PyTorch security policy](https://github.com/pytorch/pytorch/security) —
|
|
179
|
+
untrusted-model guidance; accessed 2026-07-23.
|
|
180
|
+
- [PyTorch `torch.load` documentation](https://docs.pytorch.org/docs/stable/generated/torch.load.html)
|
|
181
|
+
— deserialization warning; accessed 2026-07-23.
|