@pikaa-ai/pikaa 0.3.1 → 0.3.4
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 +1169 -601
- 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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# Events, environments, and scheduling
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Verified 2026-07-23 against SimPy 4.1.2 documentation and tagged source.
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## Scheduler model
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`Environment` owns a single event queue and processes one event at a time. Tagged
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4.1.2 stores queue entries as `(time, priority, event_id, event)`:
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1. smallest simulation time first;
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2. smallest numeric priority first (`URGENT=0`, `NORMAL=1` in public event APIs);
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3. smallest strictly increasing event ID first.
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Thus same-time, same-priority events are FIFO by scheduling order. This is
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deterministic sequential execution, even when model processes represent concurrent
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activities. Floating-point discretization can collapse physically distinct times
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onto the same value, so test tie behavior explicitly.
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## Event lifecycle
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An `Event` moves once through:
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1. **not triggered** — not scheduled and no value;
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2. **triggered** — outcome/value fixed and scheduled; `event.triggered` is true;
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3. **processed** — removed for callback execution; `event.processed` is true when
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`event.callbacks is None`.
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```python
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import simpy
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env = simpy.Environment()
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event = env.event()
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assert not event.triggered and not event.processed
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event.succeed("ready")
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assert event.triggered and not event.processed
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env.step()
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assert event.processed and event.value == "ready"
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```
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`event.succeed(value)` and `event.fail(exception)` return that event and may be
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called only once. In 4.1.2 `fail()` requires an `Exception`. `event.trigger(other)`
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copies the other event's success/failure and value, and returns `None`.
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A failed event throws its exception into a waiting process. If no process or
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callback defuses it, `Environment.step()` raises it. Treat private `_ok`, `_value`,
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and `_defused` as implementation details.
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## Callbacks
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Before processing, `event.callbacks` is a mutable list of one-argument callables.
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Yielding an event adds the waiting process's resume method. Processing executes
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callbacks in list order. Once fully processed, callbacks becomes `None`; appending
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then is invalid.
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```python
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log = []
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timeout = env.timeout(2, value=7)
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timeout.callbacks.append(lambda completed: log.append(completed.value))
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env.run()
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assert log == [7]
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```
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Keep callbacks short and non-blocking. A callback runs synchronously inside
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`Environment.step()` and can affect scheduler latency.
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## Timeout
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`env.timeout(delay, value=None)` creates a `Timeout`, immediately triggers it, and
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schedules it at `env.now + delay`. Because it is already triggered at construction,
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do not call `succeed()` or `fail()` on it.
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```python
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def timer(env):
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result = yield env.timeout(3, value="elapsed")
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assert result == "elapsed"
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```
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Reject negative delay. Use a consistent numeric time unit; SimPy does not attach
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units or protect against incompatible scales.
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## Process
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`env.process(generator)` requires a **generator object**, not an ordinary function
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result. It schedules an urgent `Initialize` event. Each yielded event suspends the
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generator; after the event's outcome, SimPy sends its value back or throws its
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failure into the generator.
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```python
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def child(env):
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yield env.timeout(1)
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return 42
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def parent(env):
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child_process = env.process(child(env))
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result = yield child_process
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assert result == 42
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env = simpy.Environment()
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env.process(parent(env))
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env.run()
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```
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A `Process` is itself an event. It succeeds with the generator's return value or
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fails with an uncaught exception. `process.is_alive`, `process.target`, and
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`process.name` expose its current status.
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Common mistakes:
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- `env.process(worker)` instead of `env.process(worker(env))`;
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- a function without any reachable `yield`, which is not a generator;
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- performing blocking I/O or `time.sleep()` inside a normal Environment process;
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- yielding a number rather than an Event.
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## Condition events
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`AnyOf(env, events)` / `a | b` and `AllOf(env, events)` / `a & b` return a
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`Condition`. Yielding one produces a `ConditionValue`, an ordered dict-like mapping
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whose keys are the original Event objects and whose values are their values.
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```python
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def coordinate(env):
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fast = env.timeout(1, value="fast")
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slow = env.timeout(2, value="slow")
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first = yield fast | slow
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assert fast in first
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assert first[fast] == "fast"
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both = yield fast & slow
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assert list(both.items()) == [(fast, "fast"), (slow, "slow")]
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```
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For `AllOf`, all input events appear. For `AnyOf`, all target events that occurred
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before the condition itself is processed can appear; do not assume exactly one
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winner when events tie. Input order determines result order.
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If any input event fails before the condition succeeds, `AnyOf` and `AllOf` fail.
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Conditions can be nested. `AnyOf` does **not** cancel losing events:
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```python
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with resource.request() as request:
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patience = env.timeout(5)
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result = yield request | patience
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if request not in result:
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# Context-manager exit cancels the still-pending request.
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return
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yield env.timeout(2)
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```
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An ordinary losing timeout remains scheduled. This is usually harmless but matters
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for event counts and traces.
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## `Environment.run()` boundaries
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### No criterion
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`env.run()` stops only when the event queue is empty. An endless generator such as
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`while True: yield env.timeout(1)` makes it nonterminating.
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### Numeric criterion
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`env.run(until=10)` creates an internal urgent stop event at time 10. It advances
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`env.now` to 10 but does **not** process ordinary events scheduled exactly at 10:
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```python
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env = simpy.Environment()
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boundary = env.timeout(10)
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env.run(until=10)
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assert env.now == 10
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assert not boundary.processed
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```
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The numeric target must be strictly greater than `env.now`.
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### Event criterion
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`env.run(until=event)` attaches a stop callback and returns the event value when
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that callback fires. It raises `RuntimeError` if the schedule empties before the
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criterion is triggered.
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Important 4.1.2 implementation detail: `Environment.step()` catches
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`StopSimulation`, preserves callbacks after the stopping callback, and reschedules
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the event at priority `-1`. Since `processed` means callbacks is `None`, the target
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can still report `processed == False` immediately after `run()` returns:
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```python
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env = simpy.Environment()
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target = env.timeout(5, value="done")
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assert env.run(until=target) == "done"
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assert target.triggered
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assert not target.processed
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env.step()
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assert target.processed
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```
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This behavior follows tagged 4.1.2 `simpy/core.py`; the topical guide's informal
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"processed" wording is not a safe postcondition. Depend on the returned value and
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your model state, not solely on `processed`.
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A timeout event and a numeric time can reach the same clock value but differ in
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same-time ordering. Numeric stopping is the clearer half-open horizon.
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## Manual stepping
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```python
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until = 10
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steps = 0
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max_steps = 100_000
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while env.peek() < until and steps < max_steps:
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env.step()
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steps += 1
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if steps == max_steps:
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raise RuntimeError("event budget reached")
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```
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`peek()` returns infinity when empty; `step()` raises `simpy.core.EmptySchedule`
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when no event remains. Explicit step/event caps prevent a zero-delay loop from
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hanging diagnostics.
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## Sources
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See `sources.md` for versioned environment/event guides, API references, tagged
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`core.py`, and the scheduling guide.
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@@ -1,260 +0,0 @@
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# Monitoring, tracing, and stepping
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Verified 2026-07-23 against SimPy 4.1.2.
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Monitoring is model instrumentation, not an automatic statistical analysis. Define:
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1. the estimand/state (queue waiting only, users in service, total in system);
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2. the observation instant (before request, after request, grant, release, final);
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3. the aggregation rule (time average, entity average, count, quantile);
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4. the analysis window and warm-up;
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5. memory/trace caps.
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## Prefer explicit domain observations
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Record domain events where their meaning is unambiguous:
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```python
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def customer(env, resource, log):
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arrival = env.now
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log.append({"event": "arrival", "time": env.now})
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with resource.request() as request:
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yield request
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log.append(
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{
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"event": "service_start",
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"queue_wait": env.now - arrival,
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"time": env.now,
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}
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)
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yield env.timeout(2)
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log.append({"event": "departure", "time": env.now})
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```
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Entity-average wait and time-average queue length are different estimands.
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## Why queue samples are timing-sensitive
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For `Resource.request()`:
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- before the method: the new request is absent;
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- immediately after: an available slot may already be allocated, or the request is
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in `queue`;
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- when the request Event is processed: waiting Process callbacks run;
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- during release: a queued request may be granted synchronously before the release
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Event's callbacks finish.
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Several states may therefore exist at the same simulation timestamp. Label sample
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phase. Equal-time samples contribute zero duration to a time integral but affect an
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unweighted sample average.
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`len(resource.queue)` counts pending requests, not users in service. Total number in
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the congestion point is normally `resource.count + len(resource.queue)`.
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For Container/Store, distinguish `level`/`len(items)` from pending
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`put_queue`/`get_queue`.
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## Time-weighted state
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For a left-continuous piecewise-constant state `q(t)`, compute:
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`average = sum(q_i * (t_{i+1} - t_i)) / (end - start)`.
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Requirements:
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- initial sample at monitoring start;
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- every relevant state transition;
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- final sample exactly at the reporting horizon;
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- warm-up window clipping;
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- nondecreasing timestamps.
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Do not use `sum(queue_samples) / len(queue_samples)` as time-average queue length;
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busy periods typically generate more events and become overrepresented.
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## Bundled ResourceMonitor
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`scripts/resource_monitor.py` wraps one Resource-like instance, records request,
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grant, cancellation, release, and final states, and calculates time-weighted
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utilization/queue length.
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```python
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import simpy
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82
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from resource_monitor import ResourceMonitor
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env = simpy.Environment()
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resource = simpy.Resource(env, capacity=2)
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monitor = ResourceMonitor(env, resource, "server")
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# Register bounded processes, then run.
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env.run(until=100)
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monitor.finalize(at=100)
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summary = monitor.summary(start=20, end=100)
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```
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The warm-up sample state is reconstructed from the last transition at or before
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`start`; the final sample closes the interval. `export_csv()` writes local private
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CSV atomically and refuses overwrite unless requested.
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Monkey-patching changes method identity and can interact with other wrappers. Attach
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one monitor per instance, patch before processes obtain method references, and call
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`detach()` before another instrumentation layer.
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## Generic resource wrappers
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The official guide demonstrates pre/post method wrappers:
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```python
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from functools import wraps
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def patch_resource(resource, pre=None, post=None):
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def wrap(operation):
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@wraps(operation)
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def wrapper(*args, **kwargs):
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if pre is not None:
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pre(resource)
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event = operation(*args, **kwargs)
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if post is not None:
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post(resource)
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return event
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return wrapper
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121
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for name in ("put", "get", "request", "release"):
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if hasattr(resource, name):
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setattr(resource, name, wrap(getattr(resource, name)))
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```
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126
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Here "post" means after the method call, not necessarily after the returned Event
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is processed. To observe completion, append a callback while `event.callbacks` is
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still a list. Handle immediately triggered events before the environment steps.
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Subclassing can be clearer for one stable use case, but it still depends on
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protected `_env` in common examples. Prefer an explicit `env` reference.
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## Event tracing
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135
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The official guide identifies:
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136
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-
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137
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- `Environment.schedule()` — event enters the queue;
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- `Environment.step()` — next queued event is processed.
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|
139
|
-
|
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140
|
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The bundled `EventTraceRecorder` wraps `step()`, reads the next queue tuple, and
|
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141
|
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records only:
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142
|
-
|
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143
|
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- simulation time;
|
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144
|
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- priority;
|
|
145
|
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- event ID;
|
|
146
|
-
- event class name;
|
|
147
|
-
- queue size before the step.
|
|
148
|
-
|
|
149
|
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It avoids `repr(event)`, which can contain nondeterministic memory addresses. It
|
|
150
|
-
caps records and writes JSON Lines.
|
|
151
|
-
|
|
152
|
-
```python
|
|
153
|
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from resource_monitor import EventTraceRecorder
|
|
154
|
-
|
|
155
|
-
trace = EventTraceRecorder(env, max_records=10_000)
|
|
156
|
-
env.run(until=100)
|
|
157
|
-
trace.detach()
|
|
158
|
-
trace.export_jsonl("trace.jsonl")
|
|
159
|
-
```
|
|
160
|
-
|
|
161
|
-
This intentionally accesses `env._queue`, a private implementation detail. Pin
|
|
162
|
-
SimPy and regression-test the tuple shape after upgrades. Full tracing increases
|
|
163
|
-
runtime and memory; use a small deterministic diagnostic scenario.
|
|
164
|
-
|
|
165
|
-
Summarize without executing model code:
|
|
166
|
-
|
|
167
|
-
```bash
|
|
168
|
-
python skills/simpy/scripts/event_trace_summary.py trace.jsonl
|
|
169
|
-
python skills/simpy/scripts/event_trace_summary.py resource_samples.csv
|
|
170
|
-
```
|
|
171
|
-
|
|
172
|
-
The summarizer validates fixed schemas, file size, record count, numeric finiteness,
|
|
173
|
-
and ordering.
|
|
174
|
-
|
|
175
|
-
## Manual stepping
|
|
176
|
-
|
|
177
|
-
Stepping is useful for debuggers, GUI integration, invariants, and hard event caps:
|
|
178
|
-
|
|
179
|
-
```python
|
|
180
|
-
from simpy.core import EmptySchedule
|
|
181
|
-
|
|
182
|
-
max_events = 100_000
|
|
183
|
-
processed = 0
|
|
184
|
-
while env.peek() < 100 and processed < max_events:
|
|
185
|
-
env.step()
|
|
186
|
-
processed += 1
|
|
187
|
-
|
|
188
|
-
if processed == max_events:
|
|
189
|
-
raise RuntimeError("event budget exhausted")
|
|
190
|
-
if env.peek() == float("inf"):
|
|
191
|
-
# Empty schedule; verify intended completion instead of assuming success.
|
|
192
|
-
pass
|
|
193
|
-
```
|
|
194
|
-
|
|
195
|
-
`env.peek() < horizon` gives the same half-open boundary policy as numeric
|
|
196
|
-
`run(until=horizon)`. `<=` processes events at the boundary and is a different
|
|
197
|
-
estimand/termination convention.
|
|
198
|
-
|
|
199
|
-
If a stop callback fires during `step()` in 4.1.2, SimPy may reschedule the Event to
|
|
200
|
-
preserve remaining callbacks. See `events.md`.
|
|
201
|
-
|
|
202
|
-
## Periodic polling
|
|
203
|
-
|
|
204
|
-
Polling is simple but approximates the state path and adds events:
|
|
205
|
-
|
|
206
|
-
```python
|
|
207
|
-
def poll(env, resource, interval, end, samples):
|
|
208
|
-
while env.now < end:
|
|
209
|
-
samples.append((env.now, resource.count, len(resource.queue)))
|
|
210
|
-
delay = min(interval, end - env.now)
|
|
211
|
-
if delay <= 0:
|
|
212
|
-
return
|
|
213
|
-
yield env.timeout(delay)
|
|
214
|
-
```
|
|
215
|
-
|
|
216
|
-
Never use a zero/negative interval. Polling can miss short peaks. It is suitable
|
|
217
|
-
for visualization at a declared resolution, not exact time integrals.
|
|
218
|
-
|
|
219
|
-
## Measurement windows and censoring
|
|
220
|
-
|
|
221
|
-
At a finite horizon:
|
|
222
|
-
|
|
223
|
-
- an entity may arrive but remain queued;
|
|
224
|
-
- service may start but not finish;
|
|
225
|
-
- a future timeout may remain scheduled;
|
|
226
|
-
- numeric `run(until=horizon)` excludes ordinary events exactly at the horizon.
|
|
227
|
-
|
|
228
|
-
Report arrived, admitted, rejected, completed, and unfinished counts. A
|
|
229
|
-
completed-only customer mean can be biased when long waits/services are more likely
|
|
230
|
-
to be unfinished. Consider a terminating design that drains the system, a
|
|
231
|
-
right-censoring-aware estimand, or sensitivity to a longer horizon.
|
|
232
|
-
|
|
233
|
-
For steady-state replication/deletion, define whether an observation enters the
|
|
234
|
-
analysis by arrival time, service-start time, departure time, or time-integral
|
|
235
|
-
window. Do not choose after seeing favorable results.
|
|
236
|
-
|
|
237
|
-
## Monitor non-interference tests
|
|
238
|
-
|
|
239
|
-
For a deterministic miniature model, compare monitored and unmonitored runs:
|
|
240
|
-
|
|
241
|
-
- same completion order and timestamps;
|
|
242
|
-
- same resource counts and outputs;
|
|
243
|
-
- same random draws/seed manifest;
|
|
244
|
-
- no pending monitor bookkeeping after completion;
|
|
245
|
-
- identical exception/interrupt behavior.
|
|
246
|
-
|
|
247
|
-
Also test:
|
|
248
|
-
|
|
249
|
-
- simultaneous request/release;
|
|
250
|
-
- cancellation while queued;
|
|
251
|
-
- preemption;
|
|
252
|
-
- zero queue capacity;
|
|
253
|
-
- final interval closure;
|
|
254
|
-
- warm-up starting between transitions;
|
|
255
|
-
- trace-cap behavior.
|
|
256
|
-
|
|
257
|
-
## Sources
|
|
258
|
-
|
|
259
|
-
See `sources.md` for the official monitoring, environment, time/scheduling, and
|
|
260
|
-
tagged core source links.
|