@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.
Files changed (1870) hide show
  1. package/dist/cli.js +1169 -601
  2. package/dist/index.js +525 -204
  3. package/package.json +5 -3
  4. package/skills/adaptyv/references/api-endpoints.md +0 -690
  5. package/skills/aeon/references/anomaly_detection.md +0 -154
  6. package/skills/aeon/references/classification.md +0 -144
  7. package/skills/aeon/references/clustering.md +0 -123
  8. package/skills/aeon/references/datasets_benchmarking.md +0 -392
  9. package/skills/aeon/references/distances.md +0 -256
  10. package/skills/aeon/references/forecasting.md +0 -109
  11. package/skills/aeon/references/networks.md +0 -289
  12. package/skills/aeon/references/regression.md +0 -118
  13. package/skills/aeon/references/segmentation.md +0 -163
  14. package/skills/aeon/references/similarity_search.md +0 -187
  15. package/skills/aeon/references/transformations.md +0 -246
  16. package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
  17. package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
  18. package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
  19. package/skills/analytical-method-validation/references/framework-selection.md +0 -87
  20. package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
  21. package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
  22. package/skills/analytical-method-validation/references/source-ledger.md +0 -125
  23. package/skills/analytical-method-validation/references/statistics.md +0 -209
  24. package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
  25. package/skills/analytical-method-validation/scripts/_common.py +0 -955
  26. package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
  27. package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
  28. package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
  29. package/skills/analytical-method-validation/scripts/check_response.py +0 -243
  30. package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
  31. package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
  32. package/skills/anndata/references/best_practices.md +0 -532
  33. package/skills/anndata/references/concatenation.md +0 -399
  34. package/skills/anndata/references/data_structure.md +0 -314
  35. package/skills/anndata/references/io_operations.md +0 -466
  36. package/skills/anndata/references/manipulation.md +0 -516
  37. package/skills/arbor/references/arbor-upstream.md +0 -91
  38. package/skills/arbor/references/executor-brief.md +0 -68
  39. package/skills/arbor/references/htr-methodology.md +0 -177
  40. package/skills/arbor/references/report-template.md +0 -39
  41. package/skills/arbor/scripts/tree.py +0 -564
  42. package/skills/arboreto/references/algorithms.md +0 -152
  43. package/skills/arboreto/references/basic_inference.md +0 -181
  44. package/skills/arboreto/references/distributed_computing.md +0 -242
  45. package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
  46. package/skills/astropy/references/coordinates.md +0 -280
  47. package/skills/astropy/references/cosmology.md +0 -309
  48. package/skills/astropy/references/fits.md +0 -398
  49. package/skills/astropy/references/tables.md +0 -495
  50. package/skills/astropy/references/time.md +0 -412
  51. package/skills/astropy/references/units.md +0 -178
  52. package/skills/astropy/references/wcs_and_other_modules.md +0 -377
  53. package/skills/autoskill/config.yaml +0 -53
  54. package/skills/autoskill/references/https-proxy.md +0 -62
  55. package/skills/autoskill/references/screenpipe-config.yaml +0 -61
  56. package/skills/autoskill/scripts/autoskill.py +0 -35
  57. package/skills/autoskill/scripts/backends.py +0 -116
  58. package/skills/autoskill/scripts/cluster.py +0 -54
  59. package/skills/autoskill/scripts/doctor.py +0 -108
  60. package/skills/autoskill/scripts/fetch_window.py +0 -33
  61. package/skills/autoskill/scripts/match_skills.py +0 -46
  62. package/skills/autoskill/scripts/promote.py +0 -58
  63. package/skills/autoskill/scripts/redact.py +0 -40
  64. package/skills/autoskill/scripts/run.py +0 -194
  65. package/skills/autoskill/scripts/synthesize.py +0 -72
  66. package/skills/benchling-integration/references/api_endpoints.md +0 -883
  67. package/skills/benchling-integration/references/authentication.md +0 -390
  68. package/skills/benchling-integration/references/core_capabilities.md +0 -355
  69. package/skills/benchling-integration/references/eventbridge.md +0 -255
  70. package/skills/benchling-integration/references/sdk_reference.md +0 -772
  71. package/skills/bids/references/beps.yml +0 -637
  72. package/skills/bids/references/bids_schema.json +0 -21015
  73. package/skills/bids/references/bids_specification.md +0 -165
  74. package/skills/bids/references/conversion_tools.md +0 -475
  75. package/skills/bids/references/core_workflows.md +0 -552
  76. package/skills/bids/references/metadata_fields.md +0 -365
  77. package/skills/bids/scripts/update_schema.py +0 -89
  78. package/skills/biopython/references/advanced.md +0 -580
  79. package/skills/biopython/references/alignment.md +0 -377
  80. package/skills/biopython/references/blast.md +0 -463
  81. package/skills/biopython/references/databases.md +0 -492
  82. package/skills/biopython/references/phylogenetics.md +0 -566
  83. package/skills/biopython/references/sequence_io.md +0 -289
  84. package/skills/biopython/references/structure.md +0 -564
  85. package/skills/bioservices/references/identifier_mapping.md +0 -685
  86. package/skills/bioservices/references/services_reference.md +0 -638
  87. package/skills/bioservices/references/workflow_patterns.md +0 -813
  88. package/skills/bioservices/scripts/batch_id_converter.py +0 -347
  89. package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
  90. package/skills/bioservices/scripts/pathway_analysis.py +0 -309
  91. package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
  92. package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
  93. package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
  94. package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
  95. package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
  96. package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
  97. package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
  98. package/skills/cellxgene-census/references/census_schema.md +0 -218
  99. package/skills/cellxgene-census/references/common_patterns.md +0 -368
  100. package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
  101. package/skills/cirq/references/building.md +0 -307
  102. package/skills/cirq/references/experiments.md +0 -572
  103. package/skills/cirq/references/hardware.md +0 -527
  104. package/skills/cirq/references/noise.md +0 -514
  105. package/skills/cirq/references/simulation.md +0 -353
  106. package/skills/cirq/references/transformation.md +0 -416
  107. package/skills/citation-management/assets/bibtex_template.bib +0 -264
  108. package/skills/citation-management/assets/citation_checklist.md +0 -386
  109. package/skills/citation-management/references/best_practices.md +0 -91
  110. package/skills/citation-management/references/bibtex_formatting.md +0 -908
  111. package/skills/citation-management/references/citation_validation.md +0 -835
  112. package/skills/citation-management/references/core_workflow.md +0 -569
  113. package/skills/citation-management/references/example_workflows.md +0 -126
  114. package/skills/citation-management/references/google_scholar_search.md +0 -732
  115. package/skills/citation-management/references/metadata_extraction.md +0 -870
  116. package/skills/citation-management/references/pubmed_search.md +0 -839
  117. package/skills/citation-management/references/script_reference.md +0 -250
  118. package/skills/citation-management/references/search_strategies.md +0 -110
  119. package/skills/citation-management/scripts/_common.py +0 -331
  120. package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  121. package/skills/citation-management/scripts/extract_metadata.py +0 -690
  122. package/skills/citation-management/scripts/format_bibtex.py +0 -356
  123. package/skills/citation-management/scripts/search_google_scholar.py +0 -268
  124. package/skills/citation-management/scripts/search_openalex.py +0 -297
  125. package/skills/citation-management/scripts/search_pubmed.py +0 -419
  126. package/skills/citation-management/scripts/validate_citations.py +0 -688
  127. package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
  128. package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
  129. package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
  130. package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
  131. package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
  132. package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
  133. package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
  134. package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
  135. package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
  136. package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
  137. package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
  138. package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
  139. package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
  140. package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
  141. package/skills/clinical-decision-support/references/security_validation.md +0 -60
  142. package/skills/clinical-decision-support/references/sources.md +0 -119
  143. package/skills/clinical-decision-support/references/study_reporting.md +0 -134
  144. package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
  145. package/skills/clinical-decision-support/scripts/_common.py +0 -223
  146. package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
  147. package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
  148. package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
  149. package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
  150. package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
  151. package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
  152. package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
  153. package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
  154. package/skills/clinical-reports/assets/case_report_template.json +0 -43
  155. package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
  156. package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
  157. package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
  158. package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
  159. package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
  160. package/skills/clinical-reports/assets/lab_report_template.json +0 -36
  161. package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
  162. package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
  163. package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
  164. package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
  165. package/skills/clinical-reports/assets/research_summary_template.json +0 -36
  166. package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
  167. package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
  168. package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
  169. package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
  170. package/skills/clinical-reports/references/data_presentation.md +0 -92
  171. package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
  172. package/skills/clinical-reports/references/medical_terminology.md +0 -84
  173. package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
  174. package/skills/clinical-reports/references/professional_review.md +0 -78
  175. package/skills/clinical-reports/references/report_type_routing.md +0 -57
  176. package/skills/clinical-reports/references/safety_reporting.md +0 -109
  177. package/skills/clinical-reports/references/sources.md +0 -75
  178. package/skills/clinical-reports/scripts/_common.py +0 -263
  179. package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
  180. package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
  181. package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
  182. package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
  183. package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
  184. package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
  185. package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
  186. package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
  187. package/skills/cobrapy/references/api_quick_reference.md +0 -665
  188. package/skills/cobrapy/references/workflows.md +0 -600
  189. package/skills/consciousness-council/references/advanced-configurations.md +0 -96
  190. package/skills/dask/references/arrays.md +0 -495
  191. package/skills/dask/references/bags.md +0 -468
  192. package/skills/dask/references/best-practices.md +0 -277
  193. package/skills/dask/references/dataframes.md +0 -370
  194. package/skills/dask/references/futures.md +0 -541
  195. package/skills/dask/references/schedulers.md +0 -517
  196. package/skills/database-lookup/references/addgene.md +0 -38
  197. package/skills/database-lookup/references/alphafold.md +0 -52
  198. package/skills/database-lookup/references/alphavantage.md +0 -261
  199. package/skills/database-lookup/references/bea.md +0 -409
  200. package/skills/database-lookup/references/bindingdb.md +0 -85
  201. package/skills/database-lookup/references/biogrid.md +0 -110
  202. package/skills/database-lookup/references/bls.md +0 -235
  203. package/skills/database-lookup/references/brenda.md +0 -71
  204. package/skills/database-lookup/references/cbioportal.md +0 -206
  205. package/skills/database-lookup/references/census.md +0 -251
  206. package/skills/database-lookup/references/chebi.md +0 -103
  207. package/skills/database-lookup/references/chembl.md +0 -80
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  210. package/skills/database-lookup/references/clinvar.md +0 -91
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  212. package/skills/database-lookup/references/cosmic.md +0 -59
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  218. package/skills/database-lookup/references/drugbank.md +0 -54
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  229. package/skills/database-lookup/references/gene-ontology.md +0 -147
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  236. package/skills/database-lookup/references/human-protein-atlas.md +0 -57
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@@ -1,188 +0,0 @@
1
- # Domain conversions and dimensional blind spots
2
-
3
- Values below were produced with pint 0.25.3 and SciPy 1.18.0 (CODATA 2022). Anything
4
- marked *exact* is fixed by definition and carries zero uncertainty.
5
-
6
- ## Dimensional analysis does not catch these
7
-
8
- Two quantities with the same dimensions convert freely, whether or not the conversion
9
- means anything.
10
-
11
- | Pair | Shared dimension | What pint does | Why it matters |
12
- | --- | --- | --- | --- |
13
- | gray and sievert | L²T⁻² | converts 1:1, silently | Sv includes a radiation weighting factor; the numbers coincide only for photons and electrons |
14
- | newton-metre and joule | ML²T⁻² | converts 1:1, silently | torque is a vector product, energy a scalar; adding them is meaningless |
15
- | hertz and becquerel | T⁻¹ | converts 1:1, silently | one is periodic, the other stochastic |
16
- | radian and dimensionless | none | radians vanish | `sin(x)` needs radians; a degrees value that lost its unit is silently wrong |
17
- | mol/L and mol/kg | different | raises | molarity and molality are genuinely different quantities |
18
- | mg/L and ppm | different | raises | equal only for dilute aqueous solutions near 1 g/mL |
19
-
20
- The last two raise because they *are* dimensionally distinct. The first four are the
21
- dangerous ones: no tool will warn you.
22
-
23
- ## Energy ladder
24
-
25
- Molecular science quotes the same energy in at least six units, three of which are
26
- per-mole and therefore need the Avogadro constant.
27
-
28
- | From | To | Factor |
29
- | --- | --- | --- |
30
- | 1 eV | kJ/mol | 96.48533212331002 |
31
- | 1 hartree | eV | 27.21138624598103 |
32
- | 1 hartree | kcal/mol | 627.5094740628942 |
33
- | 1 cm⁻¹ | eV | 1.2398419843320026e-4 |
34
- | 1 cm⁻¹ | K (as E/k_B) | 1.4387768775039336 |
35
- | k_B T at 298.15 K | eV | 0.02569257912108585 |
36
- | k_B T at 298.15 K | kJ/mol | 2.478957029602389 |
37
- | 1 cal (thermochemical) | J | 4.184 (exact) |
38
- | 1 cal_IT | J | 4.1868 (exact) |
39
-
40
- Two traps. First, **per-mole and per-particle units are not dimensionally
41
- interchangeable**: eV is an energy, kJ/mol is an energy per amount of substance, and the
42
- conversion needs N_A. Pint will refuse `Q(1, "eV").to("kJ/mol")` and accept
43
- `Q(1, "eV * N_A").to("kJ/mol")`. Second, **there are two calories** and a factor of
44
- 1.00067 between them; thermochemical is the default in chemistry, IT in engineering.
45
-
46
- ```python
47
- Q(1, "eV * N_A").to("kJ/mol") # 96.48533212331002 kilojoule / mole
48
- Q(1, "1/cm").to("eV", "sp") # 0.00012398419843320026 electron_volt
49
- Q(298.15, "K").to("eV", "boltzmann") # 0.02569257912108585 electron_volt
50
- ```
51
-
52
- ## Spectroscopy
53
-
54
- Wavelength, frequency, wavenumber, and photon energy are related by physics, not by
55
- dimensional analysis, and the relations are *reciprocal* — an uncertainty does not
56
- convert by the same factor as the value.
57
-
58
- ```python
59
- Q(532, "nm").to("THz", "sp") # 563.5196578947367 terahertz
60
- Q(532, "nm").to("1/cm", "sp") # 18796.992481203004 / centimeter
61
- Q(532, "nm").to("eV", "sp") # 2.3305300457368467 electron_volt
62
- ```
63
-
64
- Because E = hc/λ, a constant wavelength uncertainty becomes an energy uncertainty that
65
- scales as 1/λ². Propagate through the relation, do not scale the uncertainty by the
66
- value's conversion factor. `scripts/convert_units.py --uncertainty` does this with the
67
- conversion's local derivative.
68
-
69
- The `sp` context assumes vacuum unless given a refractive index: `n=1.33` for water
70
- shifts a 532 nm frequency from 563.5 THz to 423.7 THz.
71
-
72
- ## Concentration
73
-
74
- | Quantity | Unit | Depends on |
75
- | --- | --- | --- |
76
- | Molarity | mol/L | temperature, through solution volume |
77
- | Molality | mol/kg solvent | nothing — preferred for thermodynamics |
78
- | Mole fraction | dimensionless | nothing |
79
- | Mass fraction, ppm(m/m) | dimensionless | nothing |
80
- | Volume fraction, ppm(v/v) | dimensionless | temperature |
81
- | Mass concentration | mg/L, g/L | temperature |
82
-
83
- "ppm" alone is ambiguous: mass/mass, volume/volume, and mol/mol differ by the ratio of
84
- densities or molar masses. In environmental water chemistry ppm conventionally means
85
- mg/L, which equals mg/kg only because dilute water is close to 1 kg/L. In gas analysis
86
- it conventionally means volume/volume. State which.
87
-
88
- Pint treats `ppm` and `percent` as plain dimensionless scale factors (1e-6 and 0.01),
89
- which is right for arithmetic and gives no protection against mixing the three senses.
90
- Defining `ureg.define("ppm_v = 1e-6 = ppmv")` as a distinct unit does give protection.
91
-
92
- Mass and amount of substance need the `chemistry` context and a molar mass:
93
-
94
- ```python
95
- Q(1, "g").to("mol", "chemistry", mw=Q(180.156, "g/mol")) # 0.005550744909966918 mole
96
- ```
97
-
98
- ## Pressure
99
-
100
- | From | To Pa | Note |
101
- | --- | --- | --- |
102
- | 1 atm | 101325 | exact |
103
- | 1 bar | 100000 | exact |
104
- | 1 torr | 133.32236842105263 | atm/760, exact by definition |
105
- | 1 psi | 6894.7572931683635 | |
106
- | 1 mmHg | 133.322387415 | *not* identical to torr, differs in the 8th digit |
107
-
108
- **Gauge and absolute pressure are different quantities and no unit library models the
109
- difference.** "psig" and "psia" have the same dimensions; a gauge reading needs the
110
- ambient pressure added before it can be used in a gas law. Vacuum work, autoclave
111
- protocols, and chromatography backpressures are where this bites.
112
-
113
- ## Radiation, magnetism, rotation
114
-
115
- ```python
116
- Q(1, "Ci").to("Bq") # 37000000000.0 becquerel (exact by definition)
117
- Q(1, "gauss").to("T", "Gaussian") # 9.999999999338245e-05 tesla
118
- Q(1, "rpm").to("rad/s") # 0.10471975511965977 radian / second
119
- ```
120
-
121
- Gauss fails *without* the Gaussian context: CGS electromagnetic units have different
122
- dimensions from SI ones, not merely different scales. Magnetic field strength H (A/m,
123
- oersted) and magnetic flux density B (T, gauss) are distinct quantities that literature
124
- routinely calls "the field".
125
-
126
- ## Mass spectrometry
127
-
128
- The unified atomic mass unit and the dalton are the same thing:
129
- 1 Da = 1.66053906892e-27 kg (CODATA 2022, relative standard uncertainty 3.1e-10).
130
-
131
- m/z is conventionally reported as a dimensionless number: the ratio of mass in daltons
132
- to charge number. The thomson (Th) exists but is not SI and is rarely used. Treating m/z
133
- as a mass is wrong for any ion with z > 1, which is most of a protein spectrum.
134
-
135
- ## Logarithmic quantities
136
-
137
- pH, pKa, dB, and magnitudes are logarithms of ratios. They do not add, average, or
138
- propagate like ordinary quantities:
139
-
140
- - the mean of pH 5 and pH 7 is not pH 6 — averaging requires converting to
141
- concentration, averaging, and converting back;
142
- - a standard deviation in pH units is a *relative* standard deviation in concentration;
143
- - adding two dB quantities multiplies the underlying linear quantities (see
144
- `pint-recipes.md`);
145
- - decibel scales differ by reference: dBm references 1 mW, dBW references 1 W, dBV
146
- references 1 V, and dB alone references nothing until you say so.
147
-
148
- ## Temperature
149
-
150
- Kelvin and rankine are ratio scales and behave normally. Celsius and Fahrenheit are
151
- interval scales: 20 degC is not "twice" 10 degC, and their differences live in
152
- `delta_degC` / `delta_degF`. See `pint-recipes.md` for what pint permits.
153
-
154
- Absolute zero is exactly 273.15 K below 0 degC — `scipy.constants.zero_Celsius`.
155
-
156
- ## Constants: which values, and which uncertainties
157
-
158
- The 2019 SI redefinition fixed several constants **exactly**, so their relative standard
159
- uncertainty is zero and no future CODATA release will change them:
160
-
161
- | Constant | Exact value |
162
- | --- | --- |
163
- | speed of light in vacuum, c | 299792458 m/s |
164
- | Planck constant, h | 6.62607015e-34 J/Hz |
165
- | elementary charge, e | 1.602176634e-19 C |
166
- | Boltzmann constant, k | 1.380649e-23 J/K |
167
- | Avogadro constant, N_A | 6.02214076e23 /mol |
168
-
169
- Everything else is a measured recommended value that moves between CODATA releases —
170
- electron mass, the gravitational constant, the fine-structure constant, the Rydberg
171
- constant, and every derived quantity built from them.
172
-
173
- ```python
174
- import scipy.constants as constants
175
-
176
- constants.value("electron mass") # 9.1093837139e-31
177
- constants.unit("electron mass") # kg
178
- constants.precision("electron mass") # 3.07e-10 relative standard uncertainty
179
- constants.precision("Planck constant") # 0.0 exact by definition
180
- ```
181
-
182
- `scipy.constants` in SciPy 1.18.0 defaults to **CODATA 2022**; SciPy 1.11 and earlier
183
- served CODATA 2018. Hard-coding a constant pins you to whichever release you copied it
184
- from and discards its uncertainty entirely. `scripts/audit_units.py` flags literals that
185
- match a known constant (`CONST001`).
186
-
187
- Note also that `constants.precision` returns a *relative* standard uncertainty. The
188
- absolute standard uncertainty is `value * precision`.
@@ -1,219 +0,0 @@
1
- # GUM methodology
2
-
3
- The *Guide to the Expression of Uncertainty in Measurement* (JCGM 100:2008, "the GUM")
4
- and its Supplement 1 (JCGM 101:2008, the Monte Carlo method) define how an uncertainty
5
- is evaluated, combined, and reported. This file covers the parts that decide whether a
6
- number is defensible.
7
-
8
- ## Vocabulary that has to stay straight
9
-
10
- | Term | Symbol | Meaning |
11
- | --- | --- | --- |
12
- | Measurand | Y | the quantity intended to be measured |
13
- | Estimate | y | the value obtained for it |
14
- | Standard uncertainty | u(x) | uncertainty of an input, expressed as a standard deviation |
15
- | Combined standard uncertainty | u_c(y) | standard uncertainty of the result |
16
- | Expanded uncertainty | U | k * u_c(y) |
17
- | Coverage factor | k | multiplier chosen for a stated coverage probability |
18
- | Coverage probability | p | probability that the interval contains the measurand |
19
-
20
- "Error" and "uncertainty" are not synonyms. An error is a single unknowable difference
21
- from the true value; an uncertainty is a dispersion. "Accuracy" and "precision" are
22
- qualitative words in the GUM's vocabulary and never carry a number.
23
-
24
- ## Type A and Type B are methods, not qualities
25
-
26
- The distinction is only about *how the uncertainty was evaluated*. Neither is more
27
- reliable than the other, and both produce a standard uncertainty on the same footing.
28
-
29
- **Type A** — evaluated from a statistical analysis of repeated observations.
30
-
31
- For n independent readings with experimental standard deviation s(q):
32
-
33
- ```text
34
- u(q_bar) = s(q) / sqrt(n) degrees of freedom: nu = n - 1
35
- ```
36
-
37
- The standard uncertainty of the *mean* is what enters the budget when the reported
38
- value is a mean. Using s(q) itself overstates it by sqrt(n); using `numpy.std` without
39
- `ddof=1` understates s(q) itself. Both mistakes are common and neither is visible in
40
- the output.
41
-
42
- Pooling repeatability across several runs raises the degrees of freedom and is worth
43
- doing when the same instrument and procedure produced them.
44
-
45
- **Type B** — evaluated by any other means: a calibration certificate, a manufacturer's
46
- specification, a handbook value, a previous measurement, or documented judgement.
47
-
48
- The stated quantity is converted to a standard uncertainty by dividing by a factor that
49
- depends on what the statement means:
50
-
51
- | What the source states | Assumed density | Divisor | u |
52
- | --- | --- | --- | --- |
53
- | Expanded uncertainty U with coverage factor k | normal | k | U / k |
54
- | 95% confidence interval, no k given | normal | 1.96 | half-width / 1.96 |
55
- | A standard uncertainty | normal | 1 | as stated |
56
- | Limits ±a, any value equally likely | rectangular | sqrt(3) | a / sqrt(3) |
57
- | Limits ±a, centre far more likely | triangular | sqrt(6) | a / sqrt(6) |
58
- | Limits ±a, extremes more likely (sinusoidal drift, cyclic error) | arcsine | sqrt(2) | a / sqrt(2) |
59
-
60
- Rectangular is the default when a specification gives limits and says nothing about the
61
- distribution inside them. Digital resolution of one least significant digit d gives
62
- half-width a = d/2, so u = d / (2 sqrt(3)).
63
-
64
- The most frequent Type B error is treating a certificate's expanded uncertainty as a
65
- standard uncertainty: it silently doubles the reported interval.
66
-
67
- ## Law of propagation of uncertainty
68
-
69
- For a model Y = f(X_1, ..., X_N) with uncorrelated inputs (JCGM 100:2008 equation 10):
70
-
71
- ```text
72
- u_c(y)^2 = sum_i ( df/dx_i )^2 * u(x_i)^2
73
- ```
74
-
75
- with correlated inputs (equation 13):
76
-
77
- ```text
78
- u_c(y)^2 = sum_i ( df/dx_i )^2 u(x_i)^2
79
- + 2 * sum_i sum_{j>i} (df/dx_i)(df/dx_j) u(x_i) u(x_j) r(x_i, x_j)
80
- ```
81
-
82
- The partial derivatives are the **sensitivity coefficients** c_i. They carry units, and
83
- `c_i * u(x_i)` is the contribution of that input expressed in the units of the result.
84
- Comparing contributions, not raw uncertainties, is what tells you where to spend effort.
85
-
86
- Correlation is not exotic. It appears whenever two inputs were calibrated against the
87
- same standard, corrected with the same reference value, measured with the same
88
- instrument, or derived from a common fit. Ignoring a positive correlation understates
89
- u_c; ignoring a negative one overstates it. In a difference of two similar quantities
90
- measured the same way, the correlation is the whole point — it is what makes the
91
- difference more precise than either term.
92
-
93
- ## Degrees of freedom and the coverage factor
94
-
95
- k = 2 is a convention, not a law. It corresponds to p ≈ 95% only when the effective
96
- degrees of freedom are large. The Welch-Satterthwaite formula (JCGM 100:2008 G.2b)
97
- gives them:
98
-
99
- ```text
100
- nu_eff = u_c(y)^4 / sum_i ( (c_i u(x_i))^4 / nu_i )
101
- ```
102
-
103
- Components evaluated as Type B from a specification are conventionally assigned
104
- infinite degrees of freedom and drop out of the denominator. A single Type A component
105
- from a handful of readings can pull nu_eff low enough that k rises well above 2:
106
-
107
- | nu_eff | k for p = 95% |
108
- | --- | --- |
109
- | 2 | 4.30 |
110
- | 5 | 2.57 |
111
- | 10 | 2.23 |
112
- | 20 | 2.09 |
113
- | 50 | 2.01 |
114
- | infinite | 1.96 |
115
-
116
- If the dominant component came from five readings, reporting k = 2 understates the
117
- interval by about a quarter. The formula assumes uncorrelated inputs; with correlation
118
- it is an approximation with no established validity.
119
-
120
- ## When the GUM framework is not applicable
121
-
122
- The framework linearizes f about the estimates. That is fine when the model is close to
123
- linear across the input uncertainties, and wrong when it is not. Specifically, it
124
- breaks down when:
125
-
126
- - the model is significantly nonlinear over ±2u of an input — squares, reciprocals,
127
- ratios of comparable quantities, exponentials;
128
- - a single non-normal component dominates, so the output is not approximately normal
129
- and k from a t-distribution does not deliver the claimed coverage;
130
- - the output distribution is asymmetric, which the symmetric interval y ± U cannot
131
- represent;
132
- - an input's relative uncertainty is large (above roughly 20-30%), where the second-order
133
- terms the expansion drops are no longer negligible;
134
- - the model has a bound the interval crosses — a variance, a concentration, or a
135
- squared quantity whose GUM interval extends below zero.
136
-
137
- ## Monte Carlo propagation (JCGM 101:2008)
138
-
139
- The supplement propagates the input distributions rather than their standard
140
- deviations. The procedure is:
141
-
142
- 1. assign a probability density to each input, not merely a standard uncertainty;
143
- 2. draw M samples from the joint density, respecting any correlation;
144
- 3. evaluate the model for each draw;
145
- 4. take the mean as the estimate and the standard deviation as u_c;
146
- 5. take a coverage interval from the sorted output.
147
-
148
- Two intervals are defined and they differ for an asymmetric output. The
149
- **probabilistically symmetric** interval cuts (1-p)/2 from each tail. The **shortest**
150
- interval is the narrowest one containing the fraction p; it is the honest choice when
151
- the output is skewed, and identical to the other when it is not.
152
-
153
- M = 10^6 is the usual starting point for a 95% interval; JCGM 101 also defines an
154
- adaptive procedure that keeps drawing until the results are stable to within the
155
- numerical tolerance below. Fewer than 10^4 trials cannot resolve a 95% interval's
156
- endpoints reliably.
157
-
158
- ## 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
- from the GUM framework to n_dig significant digits (1 or 2) as c × 10^L. The numerical
162
- 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
- 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.