@pikaa-ai/pikaa 0.3.1 → 0.3.5
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/dist/cli.js +1181 -600
- package/dist/index.js +525 -204
- package/package.json +5 -3
- package/skills/adaptyv/references/api-endpoints.md +0 -690
- package/skills/aeon/references/anomaly_detection.md +0 -154
- package/skills/aeon/references/classification.md +0 -144
- package/skills/aeon/references/clustering.md +0 -123
- package/skills/aeon/references/datasets_benchmarking.md +0 -392
- package/skills/aeon/references/distances.md +0 -256
- package/skills/aeon/references/forecasting.md +0 -109
- package/skills/aeon/references/networks.md +0 -289
- package/skills/aeon/references/regression.md +0 -118
- package/skills/aeon/references/segmentation.md +0 -163
- package/skills/aeon/references/similarity_search.md +0 -187
- package/skills/aeon/references/transformations.md +0 -246
- package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
- package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
- package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
- package/skills/analytical-method-validation/references/framework-selection.md +0 -87
- package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
- package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
- package/skills/analytical-method-validation/references/source-ledger.md +0 -125
- package/skills/analytical-method-validation/references/statistics.md +0 -209
- package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
- package/skills/analytical-method-validation/scripts/_common.py +0 -955
- package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
- package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
- package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
- package/skills/analytical-method-validation/scripts/check_response.py +0 -243
- package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
- package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
- package/skills/anndata/references/best_practices.md +0 -532
- package/skills/anndata/references/concatenation.md +0 -399
- package/skills/anndata/references/data_structure.md +0 -314
- package/skills/anndata/references/io_operations.md +0 -466
- package/skills/anndata/references/manipulation.md +0 -516
- package/skills/arbor/references/arbor-upstream.md +0 -91
- package/skills/arbor/references/executor-brief.md +0 -68
- package/skills/arbor/references/htr-methodology.md +0 -177
- package/skills/arbor/references/report-template.md +0 -39
- package/skills/arbor/scripts/tree.py +0 -564
- package/skills/arboreto/references/algorithms.md +0 -152
- package/skills/arboreto/references/basic_inference.md +0 -181
- package/skills/arboreto/references/distributed_computing.md +0 -242
- package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
- package/skills/astropy/references/coordinates.md +0 -280
- package/skills/astropy/references/cosmology.md +0 -309
- package/skills/astropy/references/fits.md +0 -398
- package/skills/astropy/references/tables.md +0 -495
- package/skills/astropy/references/time.md +0 -412
- package/skills/astropy/references/units.md +0 -178
- package/skills/astropy/references/wcs_and_other_modules.md +0 -377
- package/skills/autoskill/config.yaml +0 -53
- package/skills/autoskill/references/https-proxy.md +0 -62
- package/skills/autoskill/references/screenpipe-config.yaml +0 -61
- package/skills/autoskill/scripts/autoskill.py +0 -35
- package/skills/autoskill/scripts/backends.py +0 -116
- package/skills/autoskill/scripts/cluster.py +0 -54
- package/skills/autoskill/scripts/doctor.py +0 -108
- package/skills/autoskill/scripts/fetch_window.py +0 -33
- package/skills/autoskill/scripts/match_skills.py +0 -46
- package/skills/autoskill/scripts/promote.py +0 -58
- package/skills/autoskill/scripts/redact.py +0 -40
- package/skills/autoskill/scripts/run.py +0 -194
- package/skills/autoskill/scripts/synthesize.py +0 -72
- package/skills/benchling-integration/references/api_endpoints.md +0 -883
- package/skills/benchling-integration/references/authentication.md +0 -390
- package/skills/benchling-integration/references/core_capabilities.md +0 -355
- package/skills/benchling-integration/references/eventbridge.md +0 -255
- package/skills/benchling-integration/references/sdk_reference.md +0 -772
- package/skills/bids/references/beps.yml +0 -637
- package/skills/bids/references/bids_schema.json +0 -21015
- package/skills/bids/references/bids_specification.md +0 -165
- package/skills/bids/references/conversion_tools.md +0 -475
- package/skills/bids/references/core_workflows.md +0 -552
- package/skills/bids/references/metadata_fields.md +0 -365
- package/skills/bids/scripts/update_schema.py +0 -89
- package/skills/biopython/references/advanced.md +0 -580
- package/skills/biopython/references/alignment.md +0 -377
- package/skills/biopython/references/blast.md +0 -463
- package/skills/biopython/references/databases.md +0 -492
- package/skills/biopython/references/phylogenetics.md +0 -566
- package/skills/biopython/references/sequence_io.md +0 -289
- package/skills/biopython/references/structure.md +0 -564
- package/skills/bioservices/references/identifier_mapping.md +0 -685
- package/skills/bioservices/references/services_reference.md +0 -638
- package/skills/bioservices/references/workflow_patterns.md +0 -813
- package/skills/bioservices/scripts/batch_id_converter.py +0 -347
- package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
- package/skills/bioservices/scripts/pathway_analysis.py +0 -309
- package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
- package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
- package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
- package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
- package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
- package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
- package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
- package/skills/cellxgene-census/references/census_schema.md +0 -218
- package/skills/cellxgene-census/references/common_patterns.md +0 -368
- package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
- package/skills/cirq/references/building.md +0 -307
- package/skills/cirq/references/experiments.md +0 -572
- package/skills/cirq/references/hardware.md +0 -527
- package/skills/cirq/references/noise.md +0 -514
- package/skills/cirq/references/simulation.md +0 -353
- package/skills/cirq/references/transformation.md +0 -416
- package/skills/citation-management/assets/bibtex_template.bib +0 -264
- package/skills/citation-management/assets/citation_checklist.md +0 -386
- package/skills/citation-management/references/best_practices.md +0 -91
- package/skills/citation-management/references/bibtex_formatting.md +0 -908
- package/skills/citation-management/references/citation_validation.md +0 -835
- package/skills/citation-management/references/core_workflow.md +0 -569
- package/skills/citation-management/references/example_workflows.md +0 -126
- package/skills/citation-management/references/google_scholar_search.md +0 -732
- package/skills/citation-management/references/metadata_extraction.md +0 -870
- package/skills/citation-management/references/pubmed_search.md +0 -839
- package/skills/citation-management/references/script_reference.md +0 -250
- package/skills/citation-management/references/search_strategies.md +0 -110
- package/skills/citation-management/scripts/_common.py +0 -331
- package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
- package/skills/citation-management/scripts/extract_metadata.py +0 -690
- package/skills/citation-management/scripts/format_bibtex.py +0 -356
- package/skills/citation-management/scripts/search_google_scholar.py +0 -268
- package/skills/citation-management/scripts/search_openalex.py +0 -297
- package/skills/citation-management/scripts/search_pubmed.py +0 -419
- package/skills/citation-management/scripts/validate_citations.py +0 -688
- package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
- package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
- package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
- package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
- package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
- package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
- package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
- package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
- package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
- package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
- package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
- package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
- package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
- package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
- package/skills/clinical-decision-support/references/security_validation.md +0 -60
- package/skills/clinical-decision-support/references/sources.md +0 -119
- package/skills/clinical-decision-support/references/study_reporting.md +0 -134
- package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
- package/skills/clinical-decision-support/scripts/_common.py +0 -223
- package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
- package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
- package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
- package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
- package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
- package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
- package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
- package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
- package/skills/clinical-reports/assets/case_report_template.json +0 -43
- package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
- package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
- package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
- package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
- package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
- package/skills/clinical-reports/assets/lab_report_template.json +0 -36
- package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
- package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
- package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
- package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
- package/skills/clinical-reports/assets/research_summary_template.json +0 -36
- package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
- package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
- package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
- package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
- package/skills/clinical-reports/references/data_presentation.md +0 -92
- package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
- package/skills/clinical-reports/references/medical_terminology.md +0 -84
- package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
- package/skills/clinical-reports/references/professional_review.md +0 -78
- package/skills/clinical-reports/references/report_type_routing.md +0 -57
- package/skills/clinical-reports/references/safety_reporting.md +0 -109
- package/skills/clinical-reports/references/sources.md +0 -75
- package/skills/clinical-reports/scripts/_common.py +0 -263
- package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
- package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
- package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
- package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
- package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
- package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
- package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
- package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
- package/skills/cobrapy/references/api_quick_reference.md +0 -665
- package/skills/cobrapy/references/workflows.md +0 -600
- package/skills/consciousness-council/references/advanced-configurations.md +0 -96
- package/skills/dask/references/arrays.md +0 -495
- package/skills/dask/references/bags.md +0 -468
- package/skills/dask/references/best-practices.md +0 -277
- package/skills/dask/references/dataframes.md +0 -370
- package/skills/dask/references/futures.md +0 -541
- package/skills/dask/references/schedulers.md +0 -517
- package/skills/database-lookup/references/addgene.md +0 -38
- package/skills/database-lookup/references/alphafold.md +0 -52
- package/skills/database-lookup/references/alphavantage.md +0 -261
- package/skills/database-lookup/references/bea.md +0 -409
- package/skills/database-lookup/references/bindingdb.md +0 -85
- package/skills/database-lookup/references/biogrid.md +0 -110
- package/skills/database-lookup/references/bls.md +0 -235
- package/skills/database-lookup/references/brenda.md +0 -71
- package/skills/database-lookup/references/cbioportal.md +0 -206
- package/skills/database-lookup/references/census.md +0 -251
- package/skills/database-lookup/references/chebi.md +0 -103
- package/skills/database-lookup/references/chembl.md +0 -80
- package/skills/database-lookup/references/clinicaltrials.md +0 -86
- package/skills/database-lookup/references/clinpgx.md +0 -64
- package/skills/database-lookup/references/clinvar.md +0 -91
- package/skills/database-lookup/references/cod.md +0 -121
- package/skills/database-lookup/references/cosmic.md +0 -59
- package/skills/database-lookup/references/dailymed.md +0 -65
- package/skills/database-lookup/references/database_selection_guide.md +0 -166
- package/skills/database-lookup/references/datacommons.md +0 -237
- package/skills/database-lookup/references/dbsnp.md +0 -143
- package/skills/database-lookup/references/disgenet.md +0 -52
- package/skills/database-lookup/references/drugbank.md +0 -54
- package/skills/database-lookup/references/ecb.md +0 -191
- package/skills/database-lookup/references/emdb.md +0 -37
- package/skills/database-lookup/references/ena.md +0 -372
- package/skills/database-lookup/references/encode.md +0 -47
- package/skills/database-lookup/references/ensembl.md +0 -539
- package/skills/database-lookup/references/epa.md +0 -232
- package/skills/database-lookup/references/eurostat.md +0 -237
- package/skills/database-lookup/references/fda.md +0 -64
- package/skills/database-lookup/references/federal-reserve.md +0 -216
- package/skills/database-lookup/references/fred.md +0 -297
- package/skills/database-lookup/references/gene-ontology.md +0 -147
- package/skills/database-lookup/references/geo.md +0 -130
- package/skills/database-lookup/references/gnomad.md +0 -93
- package/skills/database-lookup/references/gtex.md +0 -136
- package/skills/database-lookup/references/gwas-catalog.md +0 -46
- package/skills/database-lookup/references/hca.md +0 -35
- package/skills/database-lookup/references/hpo.md +0 -48
- package/skills/database-lookup/references/human-protein-atlas.md +0 -57
- package/skills/database-lookup/references/interpro.md +0 -120
- package/skills/database-lookup/references/jaspar.md +0 -50
- package/skills/database-lookup/references/kegg.md +0 -78
- package/skills/database-lookup/references/lincs-l1000.md +0 -68
- package/skills/database-lookup/references/materials-project.md +0 -123
- package/skills/database-lookup/references/metabolomics-workbench.md +0 -98
- package/skills/database-lookup/references/monarch.md +0 -46
- package/skills/database-lookup/references/mousemine.md +0 -40
- package/skills/database-lookup/references/nasa-exoplanet-archive.md +0 -112
- package/skills/database-lookup/references/nasa.md +0 -121
- package/skills/database-lookup/references/ncbi-gene.md +0 -64
- package/skills/database-lookup/references/ncbi-protein.md +0 -104
- package/skills/database-lookup/references/ncbi-taxonomy.md +0 -121
- package/skills/database-lookup/references/nist.md +0 -105
- package/skills/database-lookup/references/noaa.md +0 -199
- package/skills/database-lookup/references/omim.md +0 -114
- package/skills/database-lookup/references/opentargets.md +0 -459
- package/skills/database-lookup/references/openweathermap.md +0 -255
- package/skills/database-lookup/references/pdb.md +0 -121
- package/skills/database-lookup/references/pride.md +0 -74
- package/skills/database-lookup/references/pubchem.md +0 -145
- package/skills/database-lookup/references/quickgo.md +0 -45
- package/skills/database-lookup/references/reactome.md +0 -140
- package/skills/database-lookup/references/retrieval-contract.md +0 -123
- package/skills/database-lookup/references/rummageo.md +0 -32
- package/skills/database-lookup/references/sdss.md +0 -130
- package/skills/database-lookup/references/sec-edgar.md +0 -315
- package/skills/database-lookup/references/simbad.md +0 -405
- package/skills/database-lookup/references/sra.md +0 -149
- package/skills/database-lookup/references/string.md +0 -283
- package/skills/database-lookup/references/tcga-gdc.md +0 -58
- package/skills/database-lookup/references/treasury.md +0 -215
- package/skills/database-lookup/references/ucsc-genome.md +0 -135
- package/skills/database-lookup/references/uniprot.md +0 -283
- package/skills/database-lookup/references/usgs.md +0 -260
- package/skills/database-lookup/references/uspto.md +0 -130
- package/skills/database-lookup/references/who.md +0 -283
- package/skills/database-lookup/references/worldbank.md +0 -239
- package/skills/database-lookup/references/zinc.md +0 -202
- package/skills/datamol/references/conformers_module.md +0 -131
- package/skills/datamol/references/core_api.md +0 -136
- package/skills/datamol/references/core_workflows.md +0 -451
- package/skills/datamol/references/descriptors_viz.md +0 -195
- package/skills/datamol/references/fragments_scaffolds.md +0 -174
- package/skills/datamol/references/io_module.md +0 -112
- package/skills/datamol/references/reactions_data.md +0 -218
- package/skills/datamol/references/workflow_patterns.md +0 -104
- package/skills/deepchem/references/api_reference.md +0 -305
- package/skills/deepchem/references/core_capabilities.md +0 -276
- package/skills/deepchem/references/typical_workflows.md +0 -109
- package/skills/deepchem/references/workflows.md +0 -491
- package/skills/deepchem/scripts/graph_neural_network.py +0 -350
- package/skills/deepchem/scripts/predict_solubility.py +0 -223
- package/skills/deepchem/scripts/transfer_learning.py +0 -443
- package/skills/deepspot-m/references/api.md +0 -186
- package/skills/deepspot-m/references/whole_slide.md +0 -174
- package/skills/deeptools/assets/quick_reference.md +0 -65
- package/skills/deeptools/references/core_workflows.md +0 -134
- package/skills/deeptools/references/effective_genome_sizes.md +0 -118
- package/skills/deeptools/references/normalization_methods.md +0 -424
- package/skills/deeptools/references/tools_reference.md +0 -569
- package/skills/deeptools/references/workflows.md +0 -476
- package/skills/deeptools/scripts/validate_files.py +0 -195
- package/skills/deeptools/scripts/workflow_generator.py +0 -520
- package/skills/depmap/references/dependency_analysis.md +0 -178
- package/skills/dhdna-profiler/references/advanced-profiling.md +0 -72
- package/skills/diffdock/assets/batch_template.csv +0 -4
- package/skills/diffdock/assets/custom_inference_config.yaml +0 -94
- package/skills/diffdock/references/confidence_and_limitations.md +0 -182
- package/skills/diffdock/references/parameters_reference.md +0 -173
- package/skills/diffdock/references/workflows_examples.md +0 -401
- package/skills/diffdock/scripts/analyze_results.py +0 -346
- package/skills/diffdock/scripts/prepare_batch_csv.py +0 -257
- package/skills/diffdock/scripts/setup_check.py +0 -283
- package/skills/dnanexus-integration/references/app-development.md +0 -371
- package/skills/dnanexus-integration/references/authentication.md +0 -226
- package/skills/dnanexus-integration/references/configuration.md +0 -444
- package/skills/dnanexus-integration/references/data-operations.md +0 -474
- package/skills/dnanexus-integration/references/job-execution.md +0 -482
- package/skills/dnanexus-integration/references/operations-and-troubleshooting.md +0 -506
- package/skills/dnanexus-integration/references/python-sdk.md +0 -548
- package/skills/dnanexus-integration/references/sources.md +0 -168
- package/skills/dnanexus-integration/references/workflow-languages.md +0 -292
- package/skills/dnanexus-integration/scripts/inspect_dxpy.py +0 -366
- package/skills/dnanexus-integration/scripts/validate_dxapp.py +0 -796
- package/skills/docx/LICENSE.txt +0 -30
- package/skills/docx/scripts/__init__.py +0 -1
- package/skills/docx/scripts/accept_changes.py +0 -135
- package/skills/docx/scripts/comment.py +0 -368
- package/skills/docx/scripts/merge_runs.py +0 -310
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- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/xlsx/scripts/office/soffice.py +0 -232
- package/skills/xlsx/scripts/office/validate.py +0 -173
- package/skills/xlsx/scripts/office/validators/__init__.py +0 -15
- package/skills/xlsx/scripts/office/validators/base.py +0 -875
- package/skills/xlsx/scripts/office/validators/docx.py +0 -466
- package/skills/xlsx/scripts/office/validators/pptx.py +0 -441
- package/skills/xlsx/scripts/office/validators/redlining.py +0 -299
- package/skills/xlsx/scripts/recalc.py +0 -308
- package/skills/zarr-python/references/api_reference.md +0 -162
- package/skills/zarr-python/references/chunking_and_compression.md +0 -138
- package/skills/zarr-python/references/integration.md +0 -147
- package/skills/zarr-python/references/performance_and_patterns.md +0 -198
- package/skills/zarr-python/references/storage_backends.md +0 -91
- package/skills/zarr-python/references/v3_migration.md +0 -127
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# Integration, Security, and Migration Guide
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| Gymnasium instance adaptation | `pufferlib.emulation.GymnasiumPufferEnv` | Removed from current source |
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| Native Python `PufferEnv` | Supported | Replaced by current C/Ocean interface |
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| Trainer | `pufferlib.pufferl.PuffeRL` | Native backend or `pufferlib.torch_pufferl.PuffeRL` |
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| Primary config | merged INI sections | different INI schema |
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| Checkpoints | Torch state dict plus trainer state | native `.bin`; Torch fallback state dict |
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## Correct stable adaptation patterns
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### Gymnasium
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make_env,
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try:
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observations, rewards, terminals, truncations, infos = vecenv.step(actions)
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finally:
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vecenv.close()
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```
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`CartPole-v1` or another plug-in. Review the exact environment and dependencies
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first.
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### PettingZoo
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this adapter. Convert explicitly with PettingZoo's supported utilities only
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when the environment's turn semantics permit it, then test action ordering,
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interfaces; do not return Gym's scalar four-tuple.
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| `pufferlib.emulate(...)` | Stable: instantiate `GymnasiumPufferEnv` or `PettingZooPufferEnv` explicitly |
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| `pufferlib.vectorization.Serial` | Stable module is `pufferlib.vector.Serial` |
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| arbitrary dotted `entry_point` registration | Import an audited callable directly; bundled tools reject dotted paths |
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baselines. Attribute behavior changes; do not compare headline SPS alone.
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## Third-party environments and native code
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PufferLib optional extra is not a security or license endorsement.
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network after required artifacts are staged.
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until separately trusted.
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External tracking is disabled by default. The stable logger implementations can
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injection or secret manager;
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locally and how later sync behaves.
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acceptable; reading or logging its value is not.
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## Integration acceptance test
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For each reviewed environment/profile:
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5. Close and confirm no child processes/resources remain.
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7. Compare a same-seed trace.
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## Sources
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published 2025-06-23; accessed 2026-07-23.
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- [PufferLib 3.0 emulation source](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/emulation.py)
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— stable adapters; accessed 2026-07-23.
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- [PufferLib 3.0 vector source](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/vector.py)
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— stable vector API; accessed 2026-07-23.
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- [PufferLib 3.0 trainer source](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/pufferl.py)
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— stable logger/checkpoint behavior; accessed 2026-07-23.
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- [PufferLib 4.0 package tree](https://github.com/PufferAI/PufferLib/tree/4.0/pufferlib)
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— current modules; accessed 2026-07-23.
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- [PufferLib 4.0 docs](https://puffer.ai/docs.html) — current architecture and
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removal note; accessed 2026-07-23.
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- [PufferLib releases](https://github.com/PufferAI/PufferLib/releases) —
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checked for source releases on 2026-07-23.
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- [Gymnasium Env API](https://gymnasium.farama.org/api/env/) — current
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single-agent contract; accessed 2026-07-23.
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- [PyTorch security policy](https://github.com/pytorch/pytorch/security) —
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model/native-package safety; accessed 2026-07-23.
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# Policies and Model Contracts
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Research snapshot: **2026-07-23**. Policy APIs changed substantially between
|
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published PufferLib 3.0.0 and current 4.0 source.
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## Published 3.0.0
|
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PufferLib 3.0 policies are ordinary `torch.nn.Module` objects. The environment
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exposes `single_observation_space` and `single_action_space`; size heads from
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those single-agent spaces, not from the batched spaces.
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### Minimal feed-forward policy
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Build an `nn.Module` with an encoder sized from
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`env.single_observation_space.shape`, an action head sized from
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`env.single_action_space`, and a one-value critic head. The official stable
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example defines a rollout method named `forward_eval(observations, state=None)`
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and makes the normal `forward` method use the same contract. Here, `forward_eval`
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is a PufferLib/PyTorch method name; it does **not** invoke Python's dangerous
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`eval()` builtin.
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For a discrete action space, the first output contains action logits and the
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second is the value estimate. Preserve the leading agent-batch dimension.
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### Recurrent composition
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The stable `pufferlib.models.LSTMWrapper` expects a base policy with:
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```python
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def encode_observations(self, observations, state=None):
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...
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def decode_actions(self, hidden):
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...
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```
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The wrapper uses an `LSTMCell` during rollout inference and an `LSTM` over
|
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time-batched data during training. Do not manually reshape recurrent state
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without checking the source's batch/time convention. Reset hidden state on
|
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actual terminations and truncations according to the trainer's mask behavior.
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|
|
42
|
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### Structured observations
|
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|
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44
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Stable emulation flattens `Dict` and `Tuple` spaces into a homogeneous array.
|
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The byte layout is described by `env.emulated`. In policy setup:
|
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|
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47
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```python
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native_dtype = pufferlib.pytorch.nativize_dtype(env.emulated)
|
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```
|
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|
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In the forward pass:
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|
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```python
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structured = pufferlib.pytorch.nativize_tensor(observations, native_dtype)
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```
|
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Keep the original flattened dtype. Constructing a new float tensor before
|
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unflattening can destroy the packed representation. Validate every recovered
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leaf shape and dtype before training.
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### Action spaces
|
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The 3.0 source handles:
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- `Discrete`: one categorical logits tensor.
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- `MultiDiscrete`: one logits tensor per action branch.
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- `Box`: a Normal distribution path for continuous actions.
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Do not infer support from the 2024 paper's limitations section; that paper
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describes an earlier release. Test clipping/scaling against the environment's
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actual `Box.low`, `Box.high`, shape, and dtype. A `tanh` output is not a general
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substitute for affine mapping to arbitrary bounds.
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### Stable model utilities
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Useful 3.0 symbols include:
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- `pufferlib.pytorch.layer_init`
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- `pufferlib.pytorch.nativize_dtype`
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- `pufferlib.pytorch.nativize_tensor`
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- `pufferlib.models.Default`
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- `pufferlib.models.LSTMWrapper`
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- `pufferlib.models.Convolutional`
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- `pufferlib.models.ProcgenResnet`
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Inspect the exact 3.0 source before copying signatures. Do not use top-level
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`pufferlib.pufferl.PuffeRL`.
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## Current 4.0 source
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The current PyTorch fallback composes a policy from three modules:
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Torch fallback components:
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hidden_size = 128
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Run these checks before a long job:
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that masks reset state at episode boundaries.
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behavior. Record PyTorch, CUDA, compiler mode, precision, and deterministic
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settings. Do not claim determinism solely because seeds are fixed.
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## Checkpoint-safe policy workflow
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fallback use `torch.load` for model paths; provenance review is therefore a
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precondition, not an optional cleanup.
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Torch or deserializes.
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operation in a disposable sandbox with no credentials, network, host mounts,
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or sensitive data. PyTorch warns that models are programs and that even
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inspection tools may execute model code.
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## Sources
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— stable implementation; accessed 2026-07-23.
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- [PufferLib 3.0 models](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/models.py)
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— stable model classes; accessed 2026-07-23.
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- [PufferLib 4.0 models](https://github.com/PufferAI/PufferLib/blob/4.0/pufferlib/models.py)
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— current source model contract; accessed 2026-07-23.
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- [PufferLib 4.0 Torch trainer](https://github.com/PufferAI/PufferLib/blob/4.0/pufferlib/torch_pufferl.py)
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— current fallback and checkpoint loading; accessed 2026-07-23.
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- [PyTorch security policy](https://github.com/pytorch/pytorch/security) —
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untrusted-model guidance; accessed 2026-07-23.
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- [PyTorch `torch.load` documentation](https://docs.pytorch.org/docs/stable/generated/torch.load.html)
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— deserialization warning; accessed 2026-07-23.
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@@ -1,287 +0,0 @@
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# Training, Evaluation, Configuration, and Logging
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Research snapshot: **2026-07-23**.
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## Choose a version profile first
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### Published stable package
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PyPI's latest stable `pufferlib` release is **3.0.0**, published
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**2025-06-23**. It declares Python `>=3.9` and is distributed only as a
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60.7 MB source archive:
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```text
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pufferlib-3.0.0.tar.gz
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sha256: 7df3a3e3f5f894d78d2a1f5374097890aec01473183e748abefe4f3faa10eaa9
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```
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The uploaded metadata depends on NumPy `<2.0`, Gym `<=0.23`, Gymnasium
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`<=0.29.1`, PettingZoo `<=1.24.1`, Shimmy, Torch, Neptune, W&B, and other
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packages without a complete transitive lock. It does not declare a CUDA
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version or a minimum Torch version. Do not invent compatibility guarantees.
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### Current source line
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The upstream default branch is `4.0`; its `pyproject.toml` says version `4.0.0`,
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Python `>=3.10`, and Torch `>=2.9`. As of the research date, this source line
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is not the latest stable PyPI artifact.
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The current PufferTank Dockerfile uses:
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- Ubuntu 24.04
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- NVIDIA CUDA `13.0.2` cuDNN development image
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- Python 3.12
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- Nsight Systems `2025.6.3`
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The Dockerfile does **not** pin an exact Torch wheel, uv version, PufferLib
|
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commit, or every apt package. It is an upstream convenience environment, not a
|
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complete reproducibility lock.
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|
|
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|
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## Reproducible uv workflow
|
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|
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Do not use an unpinned `uv pip install pufferlib`. Work in a disposable,
|
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project-specific environment and commit `pyproject.toml` plus `uv.lock`.
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For the published profile, after reviewing the source archive and build:
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-
|
|
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```bash
|
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uv venv --python 3.11
|
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uv add --exact --no-sync "pufferlib==3.0.0"
|
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uv lock
|
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uv sync --frozen
|
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```
|
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|
|
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Confirm the lock records the published SHA-256 above and review every resolved
|
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dependency. The 3.0.0 source build can compile native code and may fetch build
|
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assets. Resolve and build in a sandbox with no credentials or sensitive mounts.
|
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|
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Do not treat a successful resolver run as a security review.
|
|
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|
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|
|
60
|
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For 4.0 source work, pin an immutable revision rather than branch `4.0`:
|
|
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|
|
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|
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```bash
|
|
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|
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uv add --no-sync \
|
|
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|
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"pufferlib @ git+https://github.com/PufferAI/PufferLib.git@25647630e1b15330bb3153a5a0d3ff8d234c3acf"
|
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uv lock
|
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```
|
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|
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The commit above is the reviewed 4.0 branch head on 2026-07-23. Re-review before
|
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updating it. Native training still requires an audited build of a specific
|
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environment; uv locking does not lock compilers, CUDA, NCCL, cuDNN, Raylib, or
|
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system libraries.
|
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Never run remote install scripts directly from a pipe. Download, inspect, pin,
|
|
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|
-
verify, and execute only in an appropriate sandbox.
|
|
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|
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|
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## Published 3.0.0 training
|
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|
|
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|
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### CLI
|
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|
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|
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The 3.0 console entry point is `puffer = pufferlib.pufferl:main`:
|
|
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|
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|
|
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|
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```bash
|
|
83
|
-
puffer train ENV_NAME [OPTIONS]
|
|
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puffer eval ENV_NAME [OPTIONS]
|
|
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puffer sweep ENV_NAME [OPTIONS]
|
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puffer autotune ENV_NAME [OPTIONS]
|
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puffer profile ENV_NAME [OPTIONS]
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|
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|
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puffer export ENV_NAME [OPTIONS]
|
|
89
|
-
```
|
|
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|
-
|
|
91
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Environment, vector, policy, recurrent, training, and sweep values come from
|
|
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|
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INI sections. Overrides use section-qualified flags:
|
|
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|
|
94
|
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```bash
|
|
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|
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puffer train puffer_breakout \
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--train.device cpu \
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--train.total-timesteps 100000 \
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--vec.backend Serial \
|
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--vec.num-envs 2
|
|
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```
|
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|
|
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Run `puffer train ENV_NAME --help` against the exact locked environment because
|
|
103
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available options are generated from merged INI files.
|
|
104
|
-
|
|
105
|
-
### Python API
|
|
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|
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|
|
107
|
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The stable trainer is `pufferlib.pufferl.PuffeRL`, not a top-level
|
|
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|
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`pufferlib.PuffeRL`:
|
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|
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|
|
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|
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```python
|
|
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|
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from pufferlib import pufferl
|
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|
|
113
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args = pufferl.load_config("puffer_breakout")
|
|
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vecenv = pufferl.load_env("puffer_breakout", args)
|
|
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|
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policy = pufferl.load_policy(args, vecenv, "puffer_breakout")
|
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|
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trainer = pufferl.PuffeRL(args["train"], vecenv, policy)
|
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|
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|
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|
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try:
|
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|
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while trainer.epoch < trainer.total_epochs:
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trainer.evaluate()
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trainer.train()
|
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trainer.mean_and_log()
|
|
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|
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finally:
|
|
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|
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trainer.close()
|
|
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|
-
```
|
|
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|
-
|
|
127
|
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The exact public methods include `evaluate`, `train`, `mean_and_log`,
|
|
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`save_checkpoint`, `print_dashboard`, and `close`. Use the CLI when possible;
|
|
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the Python trainer is a relatively low-level implementation surface.
|
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|
|
131
|
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### Stable configuration checks
|
|
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|
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|
|
133
|
-
- Make rollout/batch relationships explicit; do not rely on `auto` in a
|
|
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|
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published experiment.
|
|
135
|
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- Record environment, vector, policy, recurrent, and train sections verbatim.
|
|
136
|
-
- Fix `seed` in both `[vec]` and `[train]`, then run multiple independent seeds.
|
|
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|
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- Record `torch_deterministic`, precision, compile settings, optimizer, horizon,
|
|
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|
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minibatch, and total timesteps.
|
|
139
|
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- Keep evaluation seeds, instances, and metrics separate from training.
|
|
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|
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|
|
141
|
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## Current 4.0 training
|
|
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|
-
|
|
143
|
-
Build one audited environment, then use:
|
|
144
|
-
|
|
145
|
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```bash
|
|
146
|
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puffer train breakout
|
|
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puffer eval breakout --load-model-path checkpoints/.../weights.bin
|
|
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|
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puffer sweep breakout
|
|
149
|
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puffer match breakout \
|
|
150
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--load-model-path trusted-a.bin \
|
|
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|
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--load-enemy-model-path trusted-b.bin
|
|
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|
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```
|
|
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|
-
|
|
154
|
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Current modes are `train`, `eval`, `sweep`, `paretosweep`, and `match`.
|
|
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|
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Native training is the default. `--slowly` selects the Torch fallback.
|
|
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Configuration uses sections such as:
|
|
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|
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|
|
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|
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```ini
|
|
159
|
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[vec]
|
|
160
|
-
total_agents = 4096
|
|
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|
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num_buffers = 2
|
|
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|
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num_threads = 16
|
|
163
|
-
|
|
164
|
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[train]
|
|
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|
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total_timesteps = 10_000_000
|
|
166
|
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minibatch_size = 8192
|
|
167
|
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horizon = 64
|
|
168
|
-
|
|
169
|
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[torch]
|
|
170
|
-
network = MinGRU
|
|
171
|
-
encoder = DefaultEncoder
|
|
172
|
-
decoder = DefaultDecoder
|
|
173
|
-
```
|
|
174
|
-
|
|
175
|
-
Current source validates that `minibatch_size` is divisible by `horizon` and
|
|
176
|
-
does not exceed `horizon * total_agents`. Multi-GPU launch uses spawn. Do a
|
|
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|
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small CPU/local build and contract test before CUDA training.
|
|
178
|
-
|
|
179
|
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## Held-out evaluation
|
|
180
|
-
|
|
181
|
-
Training rollouts are not evaluation. For every reported result:
|
|
182
|
-
|
|
183
|
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1. Freeze one checkpoint-selection rule before inspecting held-out scores.
|
|
184
|
-
2. Construct fresh evaluation environment instances.
|
|
185
|
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3. Use evaluation seeds disjoint from training seeds.
|
|
186
|
-
4. Disable optimizer updates, exploration noise unless explicitly measuring it,
|
|
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|
-
curriculum updates, normalization-stat updates, and reward shaping used only
|
|
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|
-
for training.
|
|
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|
-
5. Report deterministic and stochastic policy protocols separately.
|
|
190
|
-
6. Run enough episodes for uncertainty; report per-seed results and aggregate
|
|
191
|
-
intervals, not only a best run.
|
|
192
|
-
7. Preserve terminated versus truncated semantics in return/length accounting.
|
|
193
|
-
8. Record wrappers, frame skip, autoreset mode, opponent pool, policy state
|
|
194
|
-
reset, and rendering state.
|
|
195
|
-
|
|
196
|
-
Generate a starting plan:
|
|
197
|
-
|
|
198
|
-
```bash
|
|
199
|
-
python3 scripts/repro_plan.py --environment synthetic
|
|
200
|
-
```
|
|
201
|
-
|
|
202
|
-
## Checkpoints
|
|
203
|
-
|
|
204
|
-
PufferLib 3.0 saves a policy `state_dict` with `torch.save` and a separate
|
|
205
|
-
trainer state containing optimizer state, global step, epoch, and run ID. Its
|
|
206
|
-
loading paths call `torch.load`. The 4.0 native backend writes `.bin` weight
|
|
207
|
-
files; the 4.0 Torch fallback also uses `torch.save`/`torch.load`.
|
|
208
|
-
|
|
209
|
-
Rules:
|
|
210
|
-
|
|
211
|
-
- Never load an untrusted checkpoint, even to “inspect” it.
|
|
212
|
-
- Record SHA-256, size, source URL, immutable revision, license, environment,
|
|
213
|
-
policy architecture, package lock, and training config in a strict JSON
|
|
214
|
-
sidecar.
|
|
215
|
-
- Do not use `latest` in a reproducible run; resolve and record the exact path
|
|
216
|
-
and digest.
|
|
217
|
-
- Do not auto-download a run artifact by ID.
|
|
218
|
-
- Test restore and evaluation in a disposable environment before a long resume.
|
|
219
|
-
- A model-only checkpoint is not a bitwise resume; optimizer, scheduler,
|
|
220
|
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normalizer, RNG, environment, and recurrent state may also matter.
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222
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Safe metadata inspection:
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-
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```bash
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python3 scripts/inspect_checkpoint.py trusted/model.pt \
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|
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--expected-sha256 EXPECTED_DIGEST
|
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227
|
-
```
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228
|
-
|
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229
|
-
The helper hashes and classifies bytes only. It never imports Torch, invokes
|
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|
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pickle, opens archive members, or extracts files.
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231
|
-
|
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232
|
-
## External logging
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233
|
-
|
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234
|
-
Local logging is the default. W&B and Neptune are optional network services
|
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235
|
-
that may transmit configuration, metrics, source metadata, hardware telemetry,
|
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236
|
-
stdout/stderr, and explicitly uploaded checkpoints/artifacts. They can create
|
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237
|
-
storage, seat, compute, or retention costs and are subject to vendor privacy,
|
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238
|
-
access, and retention policies.
|
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239
|
-
|
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240
|
-
Credential rules:
|
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241
|
-
|
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242
|
-
- W&B: use the named environment variable `WANDB_API_KEY` or an approved secret
|
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|
-
manager.
|
|
244
|
-
- Neptune: use `NEPTUNE_API_TOKEN` or an approved secret manager.
|
|
245
|
-
- Never pass either secret as a CLI argument, INI/JSON value, logger config,
|
|
246
|
-
tag, run name, or chat/tool input.
|
|
247
|
-
- Never print the value or include it in a broad environment dump.
|
|
248
|
-
- Do not recursively search for `.env` files. If policy permits a local secret
|
|
249
|
-
file, read only the explicitly named key from the explicitly named file.
|
|
250
|
-
- Sanitize configuration before logging; reject keys containing token, secret,
|
|
251
|
-
password, credential, authorization, private key, or API key.
|
|
252
|
-
- Disable checkpoint/source upload unless separately approved.
|
|
253
|
-
|
|
254
|
-
PufferLib 3.0 supports both `--wandb` and `--neptune`; its sweep mode requires
|
|
255
|
-
one. Current 4.0 source exposes W&B but no Neptune CLI integration. In either
|
|
256
|
-
profile, require explicit logging opt-in and disclosure acknowledgment. The
|
|
257
|
-
bundled training planner enforces this without reading credential values:
|
|
258
|
-
|
|
259
|
-
```bash
|
|
260
|
-
python3 scripts/train_template.py \
|
|
261
|
-
--logger wandb \
|
|
262
|
-
--enable-external-logging \
|
|
263
|
-
--acknowledge-external-disclosure
|
|
264
|
-
```
|
|
265
|
-
|
|
266
|
-
## Sources
|
|
267
|
-
|
|
268
|
-
- [PyPI: pufferlib 3.0.0](https://pypi.org/project/pufferlib/3.0.0/) —
|
|
269
|
-
released 2025-06-23; accessed 2026-07-23.
|
|
270
|
-
- [PyPI 3.0.0 JSON metadata](https://pypi.org/pypi/pufferlib/3.0.0/json) —
|
|
271
|
-
package requirements and digest; accessed 2026-07-23.
|
|
272
|
-
- [PufferLib 3.0 trainer](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/pufferl.py)
|
|
273
|
-
— stable CLI, logger, and checkpoint source; accessed 2026-07-23.
|
|
274
|
-
- [PufferLib 3.0 default config](https://github.com/PufferAI/PufferLib/blob/3.0/pufferlib/config/default.ini)
|
|
275
|
-
— stable parameters; accessed 2026-07-23.
|
|
276
|
-
- [PufferLib 4.0 docs](https://puffer.ai/docs.html) — current CLI and
|
|
277
|
-
architecture; accessed 2026-07-23.
|
|
278
|
-
- [PufferLib 4.0 trainer](https://github.com/PufferAI/PufferLib/blob/4.0/pufferlib/pufferl.py)
|
|
279
|
-
— current modes/config/checkpoints; accessed 2026-07-23.
|
|
280
|
-
- [PufferLib 4.0 package metadata](https://github.com/PufferAI/PufferLib/blob/4.0/pyproject.toml)
|
|
281
|
-
— current Python/Torch requirements; accessed 2026-07-23.
|
|
282
|
-
- [PufferTank 4.0 Dockerfile](https://github.com/PufferAI/PufferTank/blob/4.0/puffertank.dockerfile)
|
|
283
|
-
— CUDA/Python reference environment; accessed 2026-07-23.
|
|
284
|
-
- [Neptune Run API](https://docs.neptune.ai/run) — token and offline-mode
|
|
285
|
-
guidance; accessed 2026-07-23.
|
|
286
|
-
- [W&B documentation](https://docs.wandb.ai/) — logging and credential
|
|
287
|
-
guidance; accessed 2026-07-23.
|