@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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# Domain conversions and dimensional blind spots
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Values below were produced with pint 0.25.3 and SciPy 1.18.0 (CODATA 2022). Anything
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marked *exact* is fixed by definition and carries zero uncertainty.
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## Dimensional analysis does not catch these
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Two quantities with the same dimensions convert freely, whether or not the conversion
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means anything.
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| Pair | Shared dimension | What pint does | Why it matters |
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| --- | --- | --- | --- |
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| gray and sievert | L²T⁻² | converts 1:1, silently | Sv includes a radiation weighting factor; the numbers coincide only for photons and electrons |
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| newton-metre and joule | ML²T⁻² | converts 1:1, silently | torque is a vector product, energy a scalar; adding them is meaningless |
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| hertz and becquerel | T⁻¹ | converts 1:1, silently | one is periodic, the other stochastic |
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| radian and dimensionless | none | radians vanish | `sin(x)` needs radians; a degrees value that lost its unit is silently wrong |
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| mol/L and mol/kg | different | raises | molarity and molality are genuinely different quantities |
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| mg/L and ppm | different | raises | equal only for dilute aqueous solutions near 1 g/mL |
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The last two raise because they *are* dimensionally distinct. The first four are the
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dangerous ones: no tool will warn you.
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## Energy ladder
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Molecular science quotes the same energy in at least six units, three of which are
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per-mole and therefore need the Avogadro constant.
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| From | To | Factor |
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| --- | --- | --- |
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| 1 eV | kJ/mol | 96.48533212331002 |
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| 1 hartree | eV | 27.21138624598103 |
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| 1 hartree | kcal/mol | 627.5094740628942 |
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| 1 cm⁻¹ | eV | 1.2398419843320026e-4 |
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| 1 cm⁻¹ | K (as E/k_B) | 1.4387768775039336 |
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| k_B T at 298.15 K | eV | 0.02569257912108585 |
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| k_B T at 298.15 K | kJ/mol | 2.478957029602389 |
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| 1 cal (thermochemical) | J | 4.184 (exact) |
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| 1 cal_IT | J | 4.1868 (exact) |
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Two traps. First, **per-mole and per-particle units are not dimensionally
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interchangeable**: eV is an energy, kJ/mol is an energy per amount of substance, and the
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conversion needs N_A. Pint will refuse `Q(1, "eV").to("kJ/mol")` and accept
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`Q(1, "eV * N_A").to("kJ/mol")`. Second, **there are two calories** and a factor of
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1.00067 between them; thermochemical is the default in chemistry, IT in engineering.
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```python
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Q(1, "eV * N_A").to("kJ/mol") # 96.48533212331002 kilojoule / mole
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Q(1, "1/cm").to("eV", "sp") # 0.00012398419843320026 electron_volt
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Q(298.15, "K").to("eV", "boltzmann") # 0.02569257912108585 electron_volt
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```
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## Spectroscopy
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Wavelength, frequency, wavenumber, and photon energy are related by physics, not by
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dimensional analysis, and the relations are *reciprocal* — an uncertainty does not
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convert by the same factor as the value.
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```python
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Q(532, "nm").to("THz", "sp") # 563.5196578947367 terahertz
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Q(532, "nm").to("1/cm", "sp") # 18796.992481203004 / centimeter
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Q(532, "nm").to("eV", "sp") # 2.3305300457368467 electron_volt
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```
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Because E = hc/λ, a constant wavelength uncertainty becomes an energy uncertainty that
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scales as 1/λ². Propagate through the relation, do not scale the uncertainty by the
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value's conversion factor. `scripts/convert_units.py --uncertainty` does this with the
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conversion's local derivative.
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The `sp` context assumes vacuum unless given a refractive index: `n=1.33` for water
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shifts a 532 nm frequency from 563.5 THz to 423.7 THz.
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## Concentration
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| Quantity | Unit | Depends on |
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| --- | --- | --- |
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| Molarity | mol/L | temperature, through solution volume |
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| Molality | mol/kg solvent | nothing — preferred for thermodynamics |
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| Mole fraction | dimensionless | nothing |
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| Mass fraction, ppm(m/m) | dimensionless | nothing |
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| Volume fraction, ppm(v/v) | dimensionless | temperature |
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| Mass concentration | mg/L, g/L | temperature |
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"ppm" alone is ambiguous: mass/mass, volume/volume, and mol/mol differ by the ratio of
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densities or molar masses. In environmental water chemistry ppm conventionally means
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mg/L, which equals mg/kg only because dilute water is close to 1 kg/L. In gas analysis
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it conventionally means volume/volume. State which.
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Pint treats `ppm` and `percent` as plain dimensionless scale factors (1e-6 and 0.01),
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which is right for arithmetic and gives no protection against mixing the three senses.
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Defining `ureg.define("ppm_v = 1e-6 = ppmv")` as a distinct unit does give protection.
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Mass and amount of substance need the `chemistry` context and a molar mass:
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```python
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Q(1, "g").to("mol", "chemistry", mw=Q(180.156, "g/mol")) # 0.005550744909966918 mole
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```
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## Pressure
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| 1 atm | 101325 | exact |
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| 1 bar | 100000 | exact |
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| 1 torr | 133.32236842105263 | atm/760, exact by definition |
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| 1 psi | 6894.7572931683635 | |
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| 1 mmHg | 133.322387415 | *not* identical to torr, differs in the 8th digit |
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**Gauge and absolute pressure are different quantities and no unit library models the
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difference.** "psig" and "psia" have the same dimensions; a gauge reading needs the
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ambient pressure added before it can be used in a gas law. Vacuum work, autoclave
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protocols, and chromatography backpressures are where this bites.
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## Radiation, magnetism, rotation
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```python
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Q(1, "Ci").to("Bq") # 37000000000.0 becquerel (exact by definition)
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Q(1, "gauss").to("T", "Gaussian") # 9.999999999338245e-05 tesla
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Q(1, "rpm").to("rad/s") # 0.10471975511965977 radian / second
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```
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Gauss fails *without* the Gaussian context: CGS electromagnetic units have different
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dimensions from SI ones, not merely different scales. Magnetic field strength H (A/m,
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oersted) and magnetic flux density B (T, gauss) are distinct quantities that literature
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routinely calls "the field".
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## Mass spectrometry
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The unified atomic mass unit and the dalton are the same thing:
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1 Da = 1.66053906892e-27 kg (CODATA 2022, relative standard uncertainty 3.1e-10).
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m/z is conventionally reported as a dimensionless number: the ratio of mass in daltons
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to charge number. The thomson (Th) exists but is not SI and is rarely used. Treating m/z
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as a mass is wrong for any ion with z > 1, which is most of a protein spectrum.
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## Logarithmic quantities
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pH, pKa, dB, and magnitudes are logarithms of ratios. They do not add, average, or
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propagate like ordinary quantities:
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- the mean of pH 5 and pH 7 is not pH 6 — averaging requires converting to
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concentration, averaging, and converting back;
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- a standard deviation in pH units is a *relative* standard deviation in concentration;
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- adding two dB quantities multiplies the underlying linear quantities (see
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`pint-recipes.md`);
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- decibel scales differ by reference: dBm references 1 mW, dBW references 1 W, dBV
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references 1 V, and dB alone references nothing until you say so.
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## Temperature
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Kelvin and rankine are ratio scales and behave normally. Celsius and Fahrenheit are
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interval scales: 20 degC is not "twice" 10 degC, and their differences live in
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`delta_degC` / `delta_degF`. See `pint-recipes.md` for what pint permits.
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Absolute zero is exactly 273.15 K below 0 degC — `scipy.constants.zero_Celsius`.
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## Constants: which values, and which uncertainties
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The 2019 SI redefinition fixed several constants **exactly**, so their relative standard
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uncertainty is zero and no future CODATA release will change them:
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| Constant | Exact value |
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| --- | --- |
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| speed of light in vacuum, c | 299792458 m/s |
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| Planck constant, h | 6.62607015e-34 J/Hz |
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| elementary charge, e | 1.602176634e-19 C |
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| Boltzmann constant, k | 1.380649e-23 J/K |
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| Avogadro constant, N_A | 6.02214076e23 /mol |
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Everything else is a measured recommended value that moves between CODATA releases —
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electron mass, the gravitational constant, the fine-structure constant, the Rydberg
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constant, and every derived quantity built from them.
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```python
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import scipy.constants as constants
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constants.value("electron mass") # 9.1093837139e-31
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constants.unit("electron mass") # kg
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constants.precision("electron mass") # 3.07e-10 relative standard uncertainty
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constants.precision("Planck constant") # 0.0 exact by definition
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```
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`scipy.constants` in SciPy 1.18.0 defaults to **CODATA 2022**; SciPy 1.11 and earlier
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served CODATA 2018. Hard-coding a constant pins you to whichever release you copied it
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from and discards its uncertainty entirely. `scripts/audit_units.py` flags literals that
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match a known constant (`CONST001`).
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Note also that `constants.precision` returns a *relative* standard uncertainty. The
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absolute standard uncertainty is `value * precision`.
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# GUM methodology
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The *Guide to the Expression of Uncertainty in Measurement* (JCGM 100:2008, "the GUM")
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and its Supplement 1 (JCGM 101:2008, the Monte Carlo method) define how an uncertainty
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is evaluated, combined, and reported. This file covers the parts that decide whether a
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number is defensible.
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## Vocabulary that has to stay straight
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| Term | Symbol | Meaning |
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| --- | --- | --- |
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| Measurand | Y | the quantity intended to be measured |
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| Estimate | y | the value obtained for it |
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| Standard uncertainty | u(x) | uncertainty of an input, expressed as a standard deviation |
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| Combined standard uncertainty | u_c(y) | standard uncertainty of the result |
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| Expanded uncertainty | U | k * u_c(y) |
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| Coverage factor | k | multiplier chosen for a stated coverage probability |
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| Coverage probability | p | probability that the interval contains the measurand |
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"Error" and "uncertainty" are not synonyms. An error is a single unknowable difference
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from the true value; an uncertainty is a dispersion. "Accuracy" and "precision" are
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qualitative words in the GUM's vocabulary and never carry a number.
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## Type A and Type B are methods, not qualities
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The distinction is only about *how the uncertainty was evaluated*. Neither is more
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reliable than the other, and both produce a standard uncertainty on the same footing.
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**Type A** — evaluated from a statistical analysis of repeated observations.
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For n independent readings with experimental standard deviation s(q):
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```text
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u(q_bar) = s(q) / sqrt(n) degrees of freedom: nu = n - 1
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```
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The standard uncertainty of the *mean* is what enters the budget when the reported
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value is a mean. Using s(q) itself overstates it by sqrt(n); using `numpy.std` without
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`ddof=1` understates s(q) itself. Both mistakes are common and neither is visible in
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the output.
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Pooling repeatability across several runs raises the degrees of freedom and is worth
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doing when the same instrument and procedure produced them.
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**Type B** — evaluated by any other means: a calibration certificate, a manufacturer's
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specification, a handbook value, a previous measurement, or documented judgement.
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The stated quantity is converted to a standard uncertainty by dividing by a factor that
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depends on what the statement means:
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| What the source states | Assumed density | Divisor | u |
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| --- | --- | --- | --- |
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| Expanded uncertainty U with coverage factor k | normal | k | U / k |
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| 95% confidence interval, no k given | normal | 1.96 | half-width / 1.96 |
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| A standard uncertainty | normal | 1 | as stated |
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| Limits ±a, any value equally likely | rectangular | sqrt(3) | a / sqrt(3) |
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| Limits ±a, centre far more likely | triangular | sqrt(6) | a / sqrt(6) |
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| Limits ±a, extremes more likely (sinusoidal drift, cyclic error) | arcsine | sqrt(2) | a / sqrt(2) |
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Rectangular is the default when a specification gives limits and says nothing about the
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distribution inside them. Digital resolution of one least significant digit d gives
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half-width a = d/2, so u = d / (2 sqrt(3)).
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The most frequent Type B error is treating a certificate's expanded uncertainty as a
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standard uncertainty: it silently doubles the reported interval.
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## Law of propagation of uncertainty
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For a model Y = f(X_1, ..., X_N) with uncorrelated inputs (JCGM 100:2008 equation 10):
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```text
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u_c(y)^2 = sum_i ( df/dx_i )^2 * u(x_i)^2
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```
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with correlated inputs (equation 13):
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```text
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u_c(y)^2 = sum_i ( df/dx_i )^2 u(x_i)^2
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+ 2 * sum_i sum_{j>i} (df/dx_i)(df/dx_j) u(x_i) u(x_j) r(x_i, x_j)
|
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```
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|
-
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82
|
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The partial derivatives are the **sensitivity coefficients** c_i. They carry units, and
|
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83
|
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`c_i * u(x_i)` is the contribution of that input expressed in the units of the result.
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Comparing contributions, not raw uncertainties, is what tells you where to spend effort.
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|
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Correlation is not exotic. It appears whenever two inputs were calibrated against the
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same standard, corrected with the same reference value, measured with the same
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|
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instrument, or derived from a common fit. Ignoring a positive correlation understates
|
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u_c; ignoring a negative one overstates it. In a difference of two similar quantities
|
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measured the same way, the correlation is the whole point — it is what makes the
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difference more precise than either term.
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## Degrees of freedom and the coverage factor
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-
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95
|
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k = 2 is a convention, not a law. It corresponds to p ≈ 95% only when the effective
|
|
96
|
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degrees of freedom are large. The Welch-Satterthwaite formula (JCGM 100:2008 G.2b)
|
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|
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gives them:
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|
|
99
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```text
|
|
100
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nu_eff = u_c(y)^4 / sum_i ( (c_i u(x_i))^4 / nu_i )
|
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```
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Components evaluated as Type B from a specification are conventionally assigned
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infinite degrees of freedom and drop out of the denominator. A single Type A component
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from a handful of readings can pull nu_eff low enough that k rises well above 2:
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| nu_eff | k for p = 95% |
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| --- | --- |
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| 2 | 4.30 |
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| 5 | 2.57 |
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| 10 | 2.23 |
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| 20 | 2.09 |
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| 50 | 2.01 |
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| infinite | 1.96 |
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If the dominant component came from five readings, reporting k = 2 understates the
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interval by about a quarter. The formula assumes uncorrelated inputs; with correlation
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it is an approximation with no established validity.
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## When the GUM framework is not applicable
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The framework linearizes f about the estimates. That is fine when the model is close to
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linear across the input uncertainties, and wrong when it is not. Specifically, it
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breaks down when:
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- the model is significantly nonlinear over ±2u of an input — squares, reciprocals,
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ratios of comparable quantities, exponentials;
|
|
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- a single non-normal component dominates, so the output is not approximately normal
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and k from a t-distribution does not deliver the claimed coverage;
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- the output distribution is asymmetric, which the symmetric interval y ± U cannot
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represent;
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- an input's relative uncertainty is large (above roughly 20-30%), where the second-order
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terms the expansion drops are no longer negligible;
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- the model has a bound the interval crosses — a variance, a concentration, or a
|
|
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squared quantity whose GUM interval extends below zero.
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-
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|
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## Monte Carlo propagation (JCGM 101:2008)
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|
138
|
-
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|
139
|
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The supplement propagates the input distributions rather than their standard
|
|
140
|
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deviations. The procedure is:
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|
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-
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|
142
|
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1. assign a probability density to each input, not merely a standard uncertainty;
|
|
143
|
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2. draw M samples from the joint density, respecting any correlation;
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|
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3. evaluate the model for each draw;
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|
145
|
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4. take the mean as the estimate and the standard deviation as u_c;
|
|
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|
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5. take a coverage interval from the sorted output.
|
|
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|
-
|
|
148
|
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Two intervals are defined and they differ for an asymmetric output. The
|
|
149
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**probabilistically symmetric** interval cuts (1-p)/2 from each tail. The **shortest**
|
|
150
|
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interval is the narrowest one containing the fraction p; it is the honest choice when
|
|
151
|
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the output is skewed, and identical to the other when it is not.
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|
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|
|
153
|
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M = 10^6 is the usual starting point for a 95% interval; JCGM 101 also defines an
|
|
154
|
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adaptive procedure that keeps drawing until the results are stable to within the
|
|
155
|
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numerical tolerance below. Fewer than 10^4 trials cannot resolve a 95% interval's
|
|
156
|
-
endpoints reliably.
|
|
157
|
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|
|
158
|
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## The validation test that decides which answer to report
|
|
159
|
-
|
|
160
|
-
JCGM 101 clause 8 is the reason to run both methods rather than choosing one. Write u_c
|
|
161
|
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from the GUM framework to n_dig significant digits (1 or 2) as c × 10^L. The numerical
|
|
162
|
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tolerance is half of that last digit:
|
|
163
|
-
|
|
164
|
-
```text
|
|
165
|
-
delta = 0.5 * 10^L
|
|
166
|
-
```
|
|
167
|
-
|
|
168
|
-
Compare the endpoints of the two coverage intervals:
|
|
169
|
-
|
|
170
|
-
```text
|
|
171
|
-
d_low = | (y - U) - y_low_MC |
|
|
172
|
-
d_high = | (y + U) - y_high_MC |
|
|
173
|
-
```
|
|
174
|
-
|
|
175
|
-
If both are at or below delta, the linearization is validated and the GUM framework
|
|
176
|
-
result may be reported. If either exceeds delta, the framework is not validated for
|
|
177
|
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this model, and the Monte Carlo result is what should be reported.
|
|
178
|
-
|
|
179
|
-
`scripts/propagate_uncertainty.py` runs both methods and applies this test. Two
|
|
180
|
-
outcomes worth understanding:
|
|
181
|
-
|
|
182
|
-
**Rectangular inputs, linear model.** A model dominated by rectangular contributions
|
|
183
|
-
fails validation even though it is perfectly linear: the true output distribution is
|
|
184
|
-
closer to trapezoidal than normal, and k = 1.96 over-covers. The GUM value and u_c are
|
|
185
|
-
right; the interval is too wide.
|
|
186
|
-
|
|
187
|
-
**Nonlinear model.** For y = x^2 with x = 1.0 ± 0.5, the framework gives y = 1.0,
|
|
188
|
-
u_c = 1.0, and a 95% interval of [-0.96, 2.96] — an interval that is largely negative
|
|
189
|
-
for a squared quantity. Monte Carlo gives a mean of 1.25, u_c = 1.06, and a shortest
|
|
190
|
-
95% interval of [0, 3.32]. The framework result is not merely imprecise; it is outside
|
|
191
|
-
the range the model can produce.
|
|
192
|
-
|
|
193
|
-
## Order of operations
|
|
194
|
-
|
|
195
|
-
1. Write the measurement model explicitly, including every correction, even those whose
|
|
196
|
-
value is zero. A correction with an estimated value of zero still has an uncertainty,
|
|
197
|
-
and leaving it out of the model leaves its uncertainty out of the budget.
|
|
198
|
-
2. Assign each input an estimate, a standard uncertainty, a distribution, and degrees of
|
|
199
|
-
freedom.
|
|
200
|
-
3. Identify correlations before combining anything.
|
|
201
|
-
4. Compute sensitivity coefficients and the budget.
|
|
202
|
-
5. Combine, and check the linearization against Monte Carlo.
|
|
203
|
-
6. Choose k from nu_eff, not by habit.
|
|
204
|
-
7. Round the uncertainty first, then the value (see `reporting-rules.md`).
|
|
205
|
-
|
|
206
|
-
## Recurring defects
|
|
207
|
-
|
|
208
|
-
- Reporting a standard deviation of readings as the uncertainty of their mean.
|
|
209
|
-
- Dividing a certificate's expanded uncertainty by nothing, or by 2 when the certificate
|
|
210
|
-
states a different k.
|
|
211
|
-
- Omitting a correction from the model because its value is negligible, thereby omitting
|
|
212
|
-
its uncertainty too.
|
|
213
|
-
- Combining relative and absolute uncertainties without converting.
|
|
214
|
-
- Treating resolution and repeatability as independent when the resolution is what
|
|
215
|
-
limits the repeatability — double counting.
|
|
216
|
-
- Quoting k = 2 with an effective degrees of freedom below 10.
|
|
217
|
-
- Applying the framework to a strongly nonlinear model and never checking.
|
|
218
|
-
- Propagating uncertainty through a fitted model without using the fit's covariance
|
|
219
|
-
matrix, which discards the correlation between the fitted parameters.
|
|
@@ -1,228 +0,0 @@
|
|
|
1
|
-
# Pint recipes
|
|
2
|
-
|
|
3
|
-
Verified against pint 0.25.3 with NumPy 2.5.1. Every output below was produced by
|
|
4
|
-
running the snippet.
|
|
5
|
-
|
|
6
|
-
## One registry per process
|
|
7
|
-
|
|
8
|
-
A `Quantity` belongs to the registry that created it. Two registries produce quantities
|
|
9
|
-
that cannot interact, and the failure is a bare `ValueError` far from the cause:
|
|
10
|
-
|
|
11
|
-
```python
|
|
12
|
-
import pint
|
|
13
|
-
|
|
14
|
-
first = pint.UnitRegistry()
|
|
15
|
-
second = pint.UnitRegistry()
|
|
16
|
-
first.Quantity(1, "m") + second.Quantity(1, "m")
|
|
17
|
-
# ValueError: Cannot operate with Quantity and Quantity of different registries.
|
|
18
|
-
```
|
|
19
|
-
|
|
20
|
-
This bites hardest across module boundaries, where each module innocently creates its
|
|
21
|
-
own registry at import time, and after unpickling, because a pickled quantity is
|
|
22
|
-
restored against the *application* registry rather than the one that created it.
|
|
23
|
-
|
|
24
|
-
Build one registry and share it, or use the application registry everywhere:
|
|
25
|
-
|
|
26
|
-
```python
|
|
27
|
-
import pint
|
|
28
|
-
|
|
29
|
-
ureg = pint.UnitRegistry()
|
|
30
|
-
pint.set_application_registry(ureg)
|
|
31
|
-
|
|
32
|
-
# in every other module
|
|
33
|
-
ureg = pint.get_application_registry()
|
|
34
|
-
```
|
|
35
|
-
|
|
36
|
-
## Offset units
|
|
37
|
-
|
|
38
|
-
Degrees Celsius and Fahrenheit measure a point on a scale, not an amount, so
|
|
39
|
-
multiplication and addition are undefined for them. Pint refuses rather than guessing:
|
|
40
|
-
|
|
41
|
-
```python
|
|
42
|
-
Q = ureg.Quantity
|
|
43
|
-
Q(20, "degC") * 2
|
|
44
|
-
# OffsetUnitCalculusError: Ambiguous operation with offset unit (degree_Celsius).
|
|
45
|
-
Q(20, "degC") + Q(5, "degC")
|
|
46
|
-
# OffsetUnitCalculusError: Ambiguous operation with offset unit (...).
|
|
47
|
-
```
|
|
48
|
-
|
|
49
|
-
The delta units carry temperature *differences*, and mixed arithmetic works:
|
|
50
|
-
|
|
51
|
-
```python
|
|
52
|
-
Q(20, "degC") + Q(5, "delta_degC") # 25 degree_Celsius
|
|
53
|
-
Q(25, "degC") - Q(20, "degC") # 5 delta_degree_Celsius
|
|
54
|
-
```
|
|
55
|
-
|
|
56
|
-
Note the second line: subtracting two absolute temperatures yields a delta unit
|
|
57
|
-
automatically, which is correct and often surprising downstream.
|
|
58
|
-
|
|
59
|
-
An uncertainty on a temperature is always a difference. `u = 0.5 degC` means
|
|
60
|
-
`0.5 delta_degC`; converting it to Fahrenheit multiplies by 9/5 and applies no offset,
|
|
61
|
-
giving `0.9 delta_degF`. Converting the *value* 20 degC to Fahrenheit applies the
|
|
62
|
-
offset and gives 68 degF. Two different conversions on the same line of a report.
|
|
63
|
-
|
|
64
|
-
`pint.UnitRegistry(autoconvert_offset_to_baseunit=True)` makes arithmetic proceed by
|
|
65
|
-
converting to kelvin first. It removes the exception, not the ambiguity; enable it
|
|
66
|
-
deliberately, not to silence an error.
|
|
67
|
-
|
|
68
|
-
## Logarithmic units
|
|
69
|
-
|
|
70
|
-
Pint models dB, dBm, and friends as non-multiplicative units, and `+` on them means
|
|
71
|
-
what it means in log space — multiplication of the underlying linear quantities:
|
|
72
|
-
|
|
73
|
-
```python
|
|
74
|
-
Q(10, "dBm").to("mW") # 10.000000000000002 milliwatt
|
|
75
|
-
Q(10, "dBm") + Q(10, "dBm") # 0.00010000000000000005 kilogram**2 * meter**4 / second**6
|
|
76
|
-
```
|
|
77
|
-
|
|
78
|
-
The second line is 10 mW × 10 mW = 10^-4 W², not 20 mW and not 13 dBm. Nothing raises.
|
|
79
|
-
Convert to a linear unit, do the arithmetic, convert back.
|
|
80
|
-
|
|
81
|
-
## Contexts
|
|
82
|
-
|
|
83
|
-
Some conversions are physical relations rather than dimensional identities. Pint
|
|
84
|
-
performs them only inside a named context, which is a feature: it forces the physics to
|
|
85
|
-
be stated.
|
|
86
|
-
|
|
87
|
-
```python
|
|
88
|
-
Q(532, "nm").to("THz", "sp") # 563.5196578947367 terahertz
|
|
89
|
-
Q(532, "nm").to("1/cm", "sp") # 18796.992481203004 / centimeter
|
|
90
|
-
Q(532, "nm").to("eV", "sp") # 2.3305300457368467 electron_volt
|
|
91
|
-
Q(532, "nm").to("THz") # DimensionalityError
|
|
92
|
-
|
|
93
|
-
Q(1, "g").to("mol", "chemistry", mw=Q(180.156, "g/mol")) # 0.005550744909966918 mole
|
|
94
|
-
Q(298.15, "K").to("eV", "boltzmann") # 0.02569257912108585 electron_volt
|
|
95
|
-
Q(1, "gauss").to("T", "Gaussian") # 9.999999999338245e-05 tesla
|
|
96
|
-
```
|
|
97
|
-
|
|
98
|
-
The registry ships `spectroscopy` (`sp`), `chemistry` (`chem`), `boltzmann`, `energy`,
|
|
99
|
-
`textile`, `Gaussian` (`Gau`), and `ESU` (`esu`). `ureg.enable_contexts("sp")` turns one
|
|
100
|
-
on for every subsequent conversion and `ureg.disable_contexts()` turns it off again;
|
|
101
|
-
prefer passing the context per call so the assumption stays visible at the point of use.
|
|
102
|
-
|
|
103
|
-
The spectroscopy context accepts a refractive index `n`, defaulting to 1 (vacuum). It
|
|
104
|
-
matters more than it looks:
|
|
105
|
-
|
|
106
|
-
```python
|
|
107
|
-
Q(532, "nm").to("THz", "sp") # 563.5196578947367 terahertz
|
|
108
|
-
Q(532, "nm").to("THz", "sp", n=1.33) # 423.69899089829823 terahertz
|
|
109
|
-
```
|
|
110
|
-
|
|
111
|
-
Note that `gauss` fails without the Gaussian context: CGS electromagnetic units have
|
|
112
|
-
different *dimensions* from SI ones, not merely different scales.
|
|
113
|
-
|
|
114
|
-
## Stripping the unit
|
|
115
|
-
|
|
116
|
-
`.magnitude` returns whatever number the quantity happens to be carrying, in whatever
|
|
117
|
-
unit it happens to be in. That is the single most common way a unit error enters a
|
|
118
|
-
correct-looking program:
|
|
119
|
-
|
|
120
|
-
```python
|
|
121
|
-
length = (12.7 * ureg.mm).magnitude # 12.7 -- but of what?
|
|
122
|
-
length = (12.7 * ureg.mm).to("m").magnitude # 0.0127 metres, stated
|
|
123
|
-
length = (12.7 * ureg.mm).m_as("m") # same, shorter
|
|
124
|
-
```
|
|
125
|
-
|
|
126
|
-
Always name the unit at the point of extraction. `m_as` exists precisely so there is no
|
|
127
|
-
excuse.
|
|
128
|
-
|
|
129
|
-
## Boundary enforcement
|
|
130
|
-
|
|
131
|
-
Rather than sprinkling conversions through a function, convert once at its boundary:
|
|
132
|
-
|
|
133
|
-
```python
|
|
134
|
-
@ureg.wraps("J", ("N", "m"))
|
|
135
|
-
def work(force, distance):
|
|
136
|
-
return force * distance
|
|
137
|
-
|
|
138
|
-
work(ureg.Quantity(2, "N"), ureg.Quantity(300, "cm")) # 6.0 joule
|
|
139
|
-
```
|
|
140
|
-
|
|
141
|
-
`wraps` strips the declared units on the way in and reattaches the result unit on the
|
|
142
|
-
way out, so the body is plain floats and stays fast. It defaults to `strict=True`,
|
|
143
|
-
which rejects bare numbers:
|
|
144
|
-
|
|
145
|
-
```python
|
|
146
|
-
work(2.0, 3.0)
|
|
147
|
-
# ValueError: A wrapped function using strict=True requires quantity or a string
|
|
148
|
-
# for all arguments with not None units.
|
|
149
|
-
```
|
|
150
|
-
|
|
151
|
-
`strict=False` accepts bare numbers and assumes they are already in the declared units.
|
|
152
|
-
That is convenient and it is also exactly the assumption that unit tracking exists to
|
|
153
|
-
avoid; use it only at an edge you control.
|
|
154
|
-
|
|
155
|
-
`check` validates dimensionality without converting:
|
|
156
|
-
|
|
157
|
-
```python
|
|
158
|
-
@ureg.check("[length]", "[time]")
|
|
159
|
-
def speed(distance, elapsed):
|
|
160
|
-
return distance / elapsed
|
|
161
|
-
|
|
162
|
-
speed(ureg.Quantity(10, "kg"), ureg.Quantity(2, "s"))
|
|
163
|
-
# DimensionalityError: Cannot convert from '10 kilogram' ([mass]) to 'a quantity of' ([length])
|
|
164
|
-
```
|
|
165
|
-
|
|
166
|
-
## NumPy interoperability
|
|
167
|
-
|
|
168
|
-
A quantity can wrap an array, and most ufuncs and many array functions are supported:
|
|
169
|
-
|
|
170
|
-
```python
|
|
171
|
-
import numpy as np
|
|
172
|
-
|
|
173
|
-
a = ureg.Quantity(np.array([1.0, 2.0, 3.0]), "m")
|
|
174
|
-
np.mean(a) # 2.0 meter
|
|
175
|
-
np.concatenate([a, ureg.Quantity(np.array([100.0]), "cm")]) # [1.0 2.0 3.0 1.0] meter
|
|
176
|
-
np.concatenate([a, np.array([1.0])])
|
|
177
|
-
# DimensionalityError: Cannot convert from 'dimensionless' to 'meter'
|
|
178
|
-
```
|
|
179
|
-
|
|
180
|
-
Note that the mixed concatenation converted centimetres to metres correctly, and the
|
|
181
|
-
bare array was rejected rather than assumed. Both behaviours are what you want.
|
|
182
|
-
|
|
183
|
-
Wrapped arrays carry per-operation overhead. In an inner loop, convert at the boundary
|
|
184
|
-
with `wraps` or `m_as` and compute on raw arrays.
|
|
185
|
-
|
|
186
|
-
## Custom units and definitions
|
|
187
|
-
|
|
188
|
-
```python
|
|
189
|
-
ureg.define("cell = [cell_count] = cells")
|
|
190
|
-
ureg.define("od600 = [optical_density]")
|
|
191
|
-
ureg.define("percent_v_v = 0.01 = %v/v")
|
|
192
|
-
```
|
|
193
|
-
|
|
194
|
-
Defining a new base dimension in square brackets makes it dimensionally distinct from
|
|
195
|
-
everything else, which is the point: `cells / mL` will then refuse to be added to
|
|
196
|
-
`particles / mL`. Load a whole file of them with `ureg.load_definitions("units.txt")`.
|
|
197
|
-
|
|
198
|
-
## Formatting
|
|
199
|
-
|
|
200
|
-
```python
|
|
201
|
-
q = ureg.Quantity(1.2345, "kg*m/s**2")
|
|
202
|
-
f"{q}" # 1.2345 kilogram * meter / second ** 2
|
|
203
|
-
f"{q:~}" # 1.2345 kg * m / s ** 2
|
|
204
|
-
f"{q:.3f~P}" # 1.234 kg·m/s²
|
|
205
|
-
f"{q:~L}" # 1.2345\ \frac{\mathrm{kg} \cdot \mathrm{m}}{\mathrm{s}^{2}}
|
|
206
|
-
```
|
|
207
|
-
|
|
208
|
-
`~` gives short unit symbols, `P` pretty Unicode, `L` LaTeX, `C` compact ASCII. Numeric
|
|
209
|
-
format specs come first and behave as usual.
|
|
210
|
-
|
|
211
|
-
## With uncertainties
|
|
212
|
-
|
|
213
|
-
The two libraries compose: a `ufloat` magnitude inside a pint quantity converts and
|
|
214
|
-
formats correctly.
|
|
215
|
-
|
|
216
|
-
```python
|
|
217
|
-
from uncertainties import ufloat
|
|
218
|
-
|
|
219
|
-
q = ufloat(2.5, 0.1) * ureg.meter
|
|
220
|
-
q.to("cm") # 250+/-10 centimeter
|
|
221
|
-
f"{q:.2uS}" # 2.50(10) meter
|
|
222
|
-
```
|
|
223
|
-
|
|
224
|
-
## Related packages
|
|
225
|
-
|
|
226
|
-
`pint-pandas` provides a pandas extension dtype so a DataFrame column carries a unit;
|
|
227
|
-
`pint-xarray` does the same for xarray. Both are separate installs and both inherit the
|
|
228
|
-
one-registry rule.
|