@synsci/cli-darwin-x64 1.1.76 → 1.1.78
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/bin/skills/adaptyv/SKILL.md +114 -0
- package/bin/skills/adaptyv/reference/api_reference.md +308 -0
- package/bin/skills/adaptyv/reference/examples.md +913 -0
- package/bin/skills/adaptyv/reference/experiments.md +360 -0
- package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
- package/bin/skills/aeon/SKILL.md +374 -0
- package/bin/skills/aeon/references/anomaly_detection.md +154 -0
- package/bin/skills/aeon/references/classification.md +144 -0
- package/bin/skills/aeon/references/clustering.md +123 -0
- package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
- package/bin/skills/aeon/references/distances.md +256 -0
- package/bin/skills/aeon/references/forecasting.md +140 -0
- package/bin/skills/aeon/references/networks.md +289 -0
- package/bin/skills/aeon/references/regression.md +118 -0
- package/bin/skills/aeon/references/segmentation.md +163 -0
- package/bin/skills/aeon/references/similarity_search.md +187 -0
- package/bin/skills/aeon/references/transformations.md +246 -0
- package/bin/skills/alphafold-database/SKILL.md +513 -0
- package/bin/skills/alphafold-database/references/api_reference.md +423 -0
- package/bin/skills/anndata/SKILL.md +400 -0
- package/bin/skills/anndata/references/best_practices.md +525 -0
- package/bin/skills/anndata/references/concatenation.md +396 -0
- package/bin/skills/anndata/references/data_structure.md +314 -0
- package/bin/skills/anndata/references/io_operations.md +404 -0
- package/bin/skills/anndata/references/manipulation.md +516 -0
- package/bin/skills/arboreto/SKILL.md +243 -0
- package/bin/skills/arboreto/references/algorithms.md +138 -0
- package/bin/skills/arboreto/references/basic_inference.md +151 -0
- package/bin/skills/arboreto/references/distributed_computing.md +242 -0
- package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
- package/bin/skills/astropy/SKILL.md +331 -0
- package/bin/skills/astropy/references/coordinates.md +273 -0
- package/bin/skills/astropy/references/cosmology.md +307 -0
- package/bin/skills/astropy/references/fits.md +396 -0
- package/bin/skills/astropy/references/tables.md +489 -0
- package/bin/skills/astropy/references/time.md +404 -0
- package/bin/skills/astropy/references/units.md +178 -0
- package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
- package/bin/skills/benchling-integration/SKILL.md +480 -0
- package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/bin/skills/benchling-integration/references/authentication.md +379 -0
- package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
- package/bin/skills/biopython/SKILL.md +443 -0
- package/bin/skills/biopython/references/advanced.md +577 -0
- package/bin/skills/biopython/references/alignment.md +362 -0
- package/bin/skills/biopython/references/blast.md +455 -0
- package/bin/skills/biopython/references/databases.md +484 -0
- package/bin/skills/biopython/references/phylogenetics.md +566 -0
- package/bin/skills/biopython/references/sequence_io.md +285 -0
- package/bin/skills/biopython/references/structure.md +564 -0
- package/bin/skills/biorxiv-database/SKILL.md +483 -0
- package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
- package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
- package/bin/skills/bioservices/SKILL.md +361 -0
- package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
- package/bin/skills/bioservices/references/services_reference.md +636 -0
- package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
- package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
- package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
- package/bin/skills/brenda-database/SKILL.md +719 -0
- package/bin/skills/brenda-database/references/api_reference.md +537 -0
- package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
- package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
- package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
- package/bin/skills/cellxgene-census/SKILL.md +511 -0
- package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
- package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
- package/bin/skills/chembl-database/SKILL.md +389 -0
- package/bin/skills/chembl-database/references/api_reference.md +272 -0
- package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
- package/bin/skills/cirq/SKILL.md +346 -0
- package/bin/skills/cirq/references/building.md +307 -0
- package/bin/skills/cirq/references/experiments.md +572 -0
- package/bin/skills/cirq/references/hardware.md +515 -0
- package/bin/skills/cirq/references/noise.md +515 -0
- package/bin/skills/cirq/references/simulation.md +350 -0
- package/bin/skills/cirq/references/transformation.md +416 -0
- package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
- package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
- package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
- package/bin/skills/clinpgx-database/SKILL.md +638 -0
- package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
- package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
- package/bin/skills/clinvar-database/SKILL.md +362 -0
- package/bin/skills/clinvar-database/references/api_reference.md +227 -0
- package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
- package/bin/skills/clinvar-database/references/data_formats.md +358 -0
- package/bin/skills/cobrapy/SKILL.md +463 -0
- package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
- package/bin/skills/cobrapy/references/workflows.md +593 -0
- package/bin/skills/cosmic-database/SKILL.md +336 -0
- package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
- package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
- package/bin/skills/dask/SKILL.md +456 -0
- package/bin/skills/dask/references/arrays.md +497 -0
- package/bin/skills/dask/references/bags.md +468 -0
- package/bin/skills/dask/references/best-practices.md +277 -0
- package/bin/skills/dask/references/dataframes.md +368 -0
- package/bin/skills/dask/references/futures.md +541 -0
- package/bin/skills/dask/references/schedulers.md +504 -0
- package/bin/skills/datacommons-client/SKILL.md +255 -0
- package/bin/skills/datacommons-client/references/getting_started.md +417 -0
- package/bin/skills/datacommons-client/references/node.md +250 -0
- package/bin/skills/datacommons-client/references/observation.md +185 -0
- package/bin/skills/datacommons-client/references/resolve.md +246 -0
- package/bin/skills/datamol/SKILL.md +706 -0
- package/bin/skills/datamol/references/conformers_module.md +131 -0
- package/bin/skills/datamol/references/core_api.md +130 -0
- package/bin/skills/datamol/references/descriptors_viz.md +195 -0
- package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
- package/bin/skills/datamol/references/io_module.md +109 -0
- package/bin/skills/datamol/references/reactions_data.md +218 -0
- package/bin/skills/deepchem/SKILL.md +597 -0
- package/bin/skills/deepchem/references/api_reference.md +303 -0
- package/bin/skills/deepchem/references/workflows.md +491 -0
- package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
- package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
- package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
- package/bin/skills/deeptools/SKILL.md +531 -0
- package/bin/skills/deeptools/assets/quick_reference.md +58 -0
- package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
- package/bin/skills/deeptools/references/normalization_methods.md +410 -0
- package/bin/skills/deeptools/references/tools_reference.md +533 -0
- package/bin/skills/deeptools/references/workflows.md +474 -0
- package/bin/skills/deeptools/scripts/validate_files.py +195 -0
- package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
- package/bin/skills/denario/SKILL.md +215 -0
- package/bin/skills/denario/references/examples.md +494 -0
- package/bin/skills/denario/references/installation.md +213 -0
- package/bin/skills/denario/references/llm_configuration.md +265 -0
- package/bin/skills/denario/references/research_pipeline.md +471 -0
- package/bin/skills/diffdock/SKILL.md +483 -0
- package/bin/skills/diffdock/assets/batch_template.csv +4 -0
- package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
- package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
- package/bin/skills/diffdock/references/parameters_reference.md +163 -0
- package/bin/skills/diffdock/references/workflows_examples.md +392 -0
- package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
- package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
- package/bin/skills/diffdock/scripts/setup_check.py +278 -0
- package/bin/skills/dnanexus-integration/SKILL.md +383 -0
- package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
- package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
- package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
- package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
- package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
- package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/docx/SKILL.md +233 -0
- package/bin/skills/document-skills/docx/docx-js.md +350 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
- package/bin/skills/document-skills/docx/ooxml.md +610 -0
- package/bin/skills/document-skills/docx/scripts/__init__.py +1 -0
- package/bin/skills/document-skills/docx/scripts/document.py +1276 -0
- package/bin/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/people.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/utilities.py +374 -0
- package/bin/skills/document-skills/pdf/LICENSE.txt +30 -0
- package/bin/skills/document-skills/pdf/SKILL.md +330 -0
- package/bin/skills/document-skills/pdf/forms.md +205 -0
- package/bin/skills/document-skills/pdf/reference.md +612 -0
- package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
- package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
- package/bin/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
- package/bin/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
- package/bin/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
- package/bin/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
- package/bin/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
- package/bin/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
- package/bin/skills/document-skills/pptx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/pptx/SKILL.md +520 -0
- package/bin/skills/document-skills/pptx/html2pptx.md +625 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
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- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
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# Time Handling (astropy.time)
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times = Time(['2023-01-01', '2023-06-01', '2023-12-31'])
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```
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```python
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# ISO 8601
|
|
48
|
+
t = Time('2023-01-15 12:30:45', format='iso')
|
|
49
|
+
t = Time('2023-01-15T12:30:45.123', format='isot')
|
|
50
|
+
|
|
51
|
+
# Julian dates
|
|
52
|
+
t = Time(2460000.0, format='jd') # Julian Date
|
|
53
|
+
t = Time(59945.0, format='mjd') # Modified Julian Date
|
|
54
|
+
|
|
55
|
+
# Decimal year
|
|
56
|
+
t = Time(2023.5, format='decimalyear')
|
|
57
|
+
t = Time(2023.5, format='jyear') # Julian year
|
|
58
|
+
t = Time(2023.5, format='byear') # Besselian year
|
|
59
|
+
|
|
60
|
+
# Year and day-of-year
|
|
61
|
+
t = Time('2023:046', format='yday') # 46th day of 2023
|
|
62
|
+
|
|
63
|
+
# FITS format
|
|
64
|
+
t = Time('2023-01-15T12:30:45', format='fits')
|
|
65
|
+
|
|
66
|
+
# GPS seconds
|
|
67
|
+
t = Time(1000000000.0, format='gps')
|
|
68
|
+
|
|
69
|
+
# Unix time
|
|
70
|
+
t = Time(1673785845.0, format='unix')
|
|
71
|
+
|
|
72
|
+
# Matplotlib dates
|
|
73
|
+
t = Time(738521.0, format='plot_date')
|
|
74
|
+
|
|
75
|
+
# datetime objects
|
|
76
|
+
from datetime import datetime
|
|
77
|
+
dt = datetime(2023, 1, 15, 12, 30, 45)
|
|
78
|
+
t = Time(dt)
|
|
79
|
+
```
|
|
80
|
+
|
|
81
|
+
## Time Scales
|
|
82
|
+
|
|
83
|
+
### Available Time Scales
|
|
84
|
+
|
|
85
|
+
```python
|
|
86
|
+
# UTC - Coordinated Universal Time (default)
|
|
87
|
+
t = Time('2023-01-15 12:00:00', scale='utc')
|
|
88
|
+
|
|
89
|
+
# TAI - International Atomic Time
|
|
90
|
+
t = Time('2023-01-15 12:00:00', scale='tai')
|
|
91
|
+
|
|
92
|
+
# TT - Terrestrial Time
|
|
93
|
+
t = Time('2023-01-15 12:00:00', scale='tt')
|
|
94
|
+
|
|
95
|
+
# TDB - Barycentric Dynamical Time
|
|
96
|
+
t = Time('2023-01-15 12:00:00', scale='tdb')
|
|
97
|
+
|
|
98
|
+
# TCG - Geocentric Coordinate Time
|
|
99
|
+
t = Time('2023-01-15 12:00:00', scale='tcg')
|
|
100
|
+
|
|
101
|
+
# TCB - Barycentric Coordinate Time
|
|
102
|
+
t = Time('2023-01-15 12:00:00', scale='tcb')
|
|
103
|
+
|
|
104
|
+
# UT1 - Universal Time
|
|
105
|
+
t = Time('2023-01-15 12:00:00', scale='ut1')
|
|
106
|
+
```
|
|
107
|
+
|
|
108
|
+
### Converting Time Scales
|
|
109
|
+
|
|
110
|
+
```python
|
|
111
|
+
t = Time('2023-01-15 12:00:00', scale='utc')
|
|
112
|
+
|
|
113
|
+
# Convert to different scales
|
|
114
|
+
t_tai = t.tai
|
|
115
|
+
t_tt = t.tt
|
|
116
|
+
t_tdb = t.tdb
|
|
117
|
+
t_ut1 = t.ut1
|
|
118
|
+
|
|
119
|
+
# Check offset
|
|
120
|
+
print(f"TAI - UTC = {(t.tai - t.utc).sec} seconds")
|
|
121
|
+
# TAI - UTC = 37 seconds (leap seconds)
|
|
122
|
+
```
|
|
123
|
+
|
|
124
|
+
## Format Conversions
|
|
125
|
+
|
|
126
|
+
### Change Output Format
|
|
127
|
+
|
|
128
|
+
```python
|
|
129
|
+
t = Time('2023-01-15 12:30:45')
|
|
130
|
+
|
|
131
|
+
# Access in different formats
|
|
132
|
+
print(t.jd) # Julian Date
|
|
133
|
+
print(t.mjd) # Modified Julian Date
|
|
134
|
+
print(t.iso) # ISO format
|
|
135
|
+
print(t.isot) # ISO with 'T'
|
|
136
|
+
print(t.unix) # Unix time
|
|
137
|
+
print(t.decimalyear) # Decimal year
|
|
138
|
+
|
|
139
|
+
# Change default format
|
|
140
|
+
t.format = 'mjd'
|
|
141
|
+
print(t) # Displays as MJD
|
|
142
|
+
```
|
|
143
|
+
|
|
144
|
+
### High-Precision Output
|
|
145
|
+
|
|
146
|
+
```python
|
|
147
|
+
# Use subfmt for precision control
|
|
148
|
+
t.to_value('mjd', subfmt='float') # Standard float
|
|
149
|
+
t.to_value('mjd', subfmt='long') # Extended precision
|
|
150
|
+
t.to_value('mjd', subfmt='decimal') # Decimal (highest precision)
|
|
151
|
+
t.to_value('mjd', subfmt='str') # String representation
|
|
152
|
+
```
|
|
153
|
+
|
|
154
|
+
## Time Arithmetic
|
|
155
|
+
|
|
156
|
+
### TimeDelta Objects
|
|
157
|
+
|
|
158
|
+
```python
|
|
159
|
+
from astropy.time import TimeDelta
|
|
160
|
+
|
|
161
|
+
# Create time difference
|
|
162
|
+
dt = TimeDelta(1.0, format='jd') # 1 day
|
|
163
|
+
dt = TimeDelta(3600.0, format='sec') # 1 hour
|
|
164
|
+
|
|
165
|
+
# Subtract times
|
|
166
|
+
t1 = Time('2023-01-15')
|
|
167
|
+
t2 = Time('2023-02-15')
|
|
168
|
+
dt = t2 - t1
|
|
169
|
+
print(dt.jd) # 31 days
|
|
170
|
+
print(dt.sec) # 2678400 seconds
|
|
171
|
+
```
|
|
172
|
+
|
|
173
|
+
### Adding/Subtracting Time
|
|
174
|
+
|
|
175
|
+
```python
|
|
176
|
+
t = Time('2023-01-15 12:00:00')
|
|
177
|
+
|
|
178
|
+
# Add TimeDelta
|
|
179
|
+
t_future = t + TimeDelta(7, format='jd') # Add 7 days
|
|
180
|
+
|
|
181
|
+
# Add Quantity
|
|
182
|
+
t_future = t + 1*u.hour
|
|
183
|
+
t_future = t + 30*u.day
|
|
184
|
+
t_future = t + 1*u.year
|
|
185
|
+
|
|
186
|
+
# Subtract
|
|
187
|
+
t_past = t - 1*u.week
|
|
188
|
+
```
|
|
189
|
+
|
|
190
|
+
### Time Ranges
|
|
191
|
+
|
|
192
|
+
```python
|
|
193
|
+
# Create range of times
|
|
194
|
+
start = Time('2023-01-01')
|
|
195
|
+
end = Time('2023-12-31')
|
|
196
|
+
times = start + np.linspace(0, 365, 100) * u.day
|
|
197
|
+
|
|
198
|
+
# Or using TimeDelta
|
|
199
|
+
times = start + TimeDelta(np.linspace(0, 365, 100), format='jd')
|
|
200
|
+
```
|
|
201
|
+
|
|
202
|
+
## Observing-Related Features
|
|
203
|
+
|
|
204
|
+
### Sidereal Time
|
|
205
|
+
|
|
206
|
+
```python
|
|
207
|
+
from astropy.coordinates import EarthLocation
|
|
208
|
+
|
|
209
|
+
# Define observer location
|
|
210
|
+
location = EarthLocation(lat=40*u.deg, lon=-120*u.deg, height=1000*u.m)
|
|
211
|
+
|
|
212
|
+
# Create time with location
|
|
213
|
+
t = Time('2023-06-15 23:00:00', location=location)
|
|
214
|
+
|
|
215
|
+
# Calculate sidereal time
|
|
216
|
+
lst_apparent = t.sidereal_time('apparent')
|
|
217
|
+
lst_mean = t.sidereal_time('mean')
|
|
218
|
+
|
|
219
|
+
print(f"Local Sidereal Time: {lst_apparent}")
|
|
220
|
+
```
|
|
221
|
+
|
|
222
|
+
### Light Travel Time Corrections
|
|
223
|
+
|
|
224
|
+
```python
|
|
225
|
+
from astropy.coordinates import SkyCoord, EarthLocation
|
|
226
|
+
|
|
227
|
+
# Define target and observer
|
|
228
|
+
target = SkyCoord(ra=10*u.deg, dec=20*u.deg)
|
|
229
|
+
location = EarthLocation.of_site('Keck Observatory')
|
|
230
|
+
|
|
231
|
+
# Observation times
|
|
232
|
+
times = Time(['2023-01-01', '2023-06-01', '2023-12-31'],
|
|
233
|
+
location=location)
|
|
234
|
+
|
|
235
|
+
# Calculate light travel time to solar system barycenter
|
|
236
|
+
ltt_bary = times.light_travel_time(target, kind='barycentric')
|
|
237
|
+
ltt_helio = times.light_travel_time(target, kind='heliocentric')
|
|
238
|
+
|
|
239
|
+
# Apply correction
|
|
240
|
+
times_barycentric = times.tdb + ltt_bary
|
|
241
|
+
```
|
|
242
|
+
|
|
243
|
+
### Earth Rotation Angle
|
|
244
|
+
|
|
245
|
+
```python
|
|
246
|
+
# Earth rotation angle (for celestial to terrestrial transformations)
|
|
247
|
+
era = t.earth_rotation_angle()
|
|
248
|
+
```
|
|
249
|
+
|
|
250
|
+
## Handling Missing or Invalid Times
|
|
251
|
+
|
|
252
|
+
### Masked Times
|
|
253
|
+
|
|
254
|
+
```python
|
|
255
|
+
import numpy as np
|
|
256
|
+
|
|
257
|
+
# Create times with missing values
|
|
258
|
+
times = Time(['2023-01-01', '2023-06-01', '2023-12-31'])
|
|
259
|
+
times[1] = np.ma.masked # Mark as missing
|
|
260
|
+
|
|
261
|
+
# Check for masks
|
|
262
|
+
print(times.mask) # [False True False]
|
|
263
|
+
|
|
264
|
+
# Get unmasked version
|
|
265
|
+
times_clean = times.unmasked
|
|
266
|
+
|
|
267
|
+
# Fill masked values
|
|
268
|
+
times_filled = times.filled(Time('2000-01-01'))
|
|
269
|
+
```
|
|
270
|
+
|
|
271
|
+
## Time Precision and Representation
|
|
272
|
+
|
|
273
|
+
### Internal Representation
|
|
274
|
+
|
|
275
|
+
Time objects use two 64-bit floats (jd1, jd2) for high precision:
|
|
276
|
+
|
|
277
|
+
```python
|
|
278
|
+
t = Time('2023-01-15 12:30:45.123456789', format='iso', scale='utc')
|
|
279
|
+
|
|
280
|
+
# Access internal representation
|
|
281
|
+
print(t.jd1, t.jd2) # Integer and fractional parts
|
|
282
|
+
|
|
283
|
+
# This allows sub-nanosecond precision over astronomical timescales
|
|
284
|
+
```
|
|
285
|
+
|
|
286
|
+
### Precision
|
|
287
|
+
|
|
288
|
+
```python
|
|
289
|
+
# High precision for long time intervals
|
|
290
|
+
t1 = Time('1900-01-01')
|
|
291
|
+
t2 = Time('2100-01-01')
|
|
292
|
+
dt = t2 - t1
|
|
293
|
+
print(f"Time span: {dt.sec / (365.25 * 86400)} years")
|
|
294
|
+
# Maintains precision throughout
|
|
295
|
+
```
|
|
296
|
+
|
|
297
|
+
## Time Formatting
|
|
298
|
+
|
|
299
|
+
### Custom String Format
|
|
300
|
+
|
|
301
|
+
```python
|
|
302
|
+
t = Time('2023-01-15 12:30:45')
|
|
303
|
+
|
|
304
|
+
# Strftime-style formatting
|
|
305
|
+
t.strftime('%Y-%m-%d %H:%M:%S') # '2023-01-15 12:30:45'
|
|
306
|
+
t.strftime('%B %d, %Y') # 'January 15, 2023'
|
|
307
|
+
|
|
308
|
+
# ISO format subformats
|
|
309
|
+
t.iso # '2023-01-15 12:30:45.000'
|
|
310
|
+
t.isot # '2023-01-15T12:30:45.000'
|
|
311
|
+
t.to_value('iso', subfmt='date_hms') # '2023-01-15 12:30:45.000'
|
|
312
|
+
```
|
|
313
|
+
|
|
314
|
+
## Common Use Cases
|
|
315
|
+
|
|
316
|
+
### Converting Between Formats
|
|
317
|
+
|
|
318
|
+
```python
|
|
319
|
+
# MJD to ISO
|
|
320
|
+
t_mjd = Time(59945.0, format='mjd')
|
|
321
|
+
iso_string = t_mjd.iso
|
|
322
|
+
|
|
323
|
+
# ISO to JD
|
|
324
|
+
t_iso = Time('2023-01-15 12:00:00')
|
|
325
|
+
jd_value = t_iso.jd
|
|
326
|
+
|
|
327
|
+
# Unix to ISO
|
|
328
|
+
t_unix = Time(1673785845.0, format='unix')
|
|
329
|
+
iso_string = t_unix.iso
|
|
330
|
+
```
|
|
331
|
+
|
|
332
|
+
### Time Differences in Various Units
|
|
333
|
+
|
|
334
|
+
```python
|
|
335
|
+
t1 = Time('2023-01-01')
|
|
336
|
+
t2 = Time('2023-12-31')
|
|
337
|
+
|
|
338
|
+
dt = t2 - t1
|
|
339
|
+
print(f"Days: {dt.to(u.day)}")
|
|
340
|
+
print(f"Hours: {dt.to(u.hour)}")
|
|
341
|
+
print(f"Seconds: {dt.sec}")
|
|
342
|
+
print(f"Years: {dt.to(u.year)}")
|
|
343
|
+
```
|
|
344
|
+
|
|
345
|
+
### Creating Regular Time Series
|
|
346
|
+
|
|
347
|
+
```python
|
|
348
|
+
# Daily observations for a year
|
|
349
|
+
start = Time('2023-01-01')
|
|
350
|
+
times = start + np.arange(365) * u.day
|
|
351
|
+
|
|
352
|
+
# Hourly observations for a day
|
|
353
|
+
start = Time('2023-01-15 00:00:00')
|
|
354
|
+
times = start + np.arange(24) * u.hour
|
|
355
|
+
|
|
356
|
+
# Observations every 30 seconds
|
|
357
|
+
start = Time('2023-01-15 12:00:00')
|
|
358
|
+
times = start + np.arange(1000) * 30 * u.second
|
|
359
|
+
```
|
|
360
|
+
|
|
361
|
+
### Time Zone Handling
|
|
362
|
+
|
|
363
|
+
```python
|
|
364
|
+
# UTC to local time (requires datetime)
|
|
365
|
+
t = Time('2023-01-15 12:00:00', scale='utc')
|
|
366
|
+
dt_utc = t.to_datetime()
|
|
367
|
+
|
|
368
|
+
# Convert to specific timezone using pytz
|
|
369
|
+
import pytz
|
|
370
|
+
eastern = pytz.timezone('US/Eastern')
|
|
371
|
+
dt_eastern = dt_utc.replace(tzinfo=pytz.utc).astimezone(eastern)
|
|
372
|
+
```
|
|
373
|
+
|
|
374
|
+
### Barycentric Correction Example
|
|
375
|
+
|
|
376
|
+
```python
|
|
377
|
+
from astropy.coordinates import SkyCoord, EarthLocation
|
|
378
|
+
|
|
379
|
+
# Target coordinates
|
|
380
|
+
target = SkyCoord(ra='23h23m08.55s', dec='+18d24m59.3s')
|
|
381
|
+
|
|
382
|
+
# Observatory location
|
|
383
|
+
location = EarthLocation.of_site('Keck Observatory')
|
|
384
|
+
|
|
385
|
+
# Observation times (must include location)
|
|
386
|
+
times = Time(['2023-01-15 08:30:00', '2023-01-16 08:30:00'],
|
|
387
|
+
location=location)
|
|
388
|
+
|
|
389
|
+
# Calculate barycentric correction
|
|
390
|
+
ltt_bary = times.light_travel_time(target, kind='barycentric')
|
|
391
|
+
|
|
392
|
+
# Apply correction to get barycentric times
|
|
393
|
+
times_bary = times.tdb + ltt_bary
|
|
394
|
+
|
|
395
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# For radial velocity correction
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396
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rv_correction = ltt_bary.to(u.km, equivalencies=u.dimensionless_angles())
|
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397
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+
```
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398
|
+
|
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399
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+
## Performance Considerations
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400
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+
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401
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+
1. **Array operations are fast**: Process multiple times as arrays
|
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402
|
+
2. **Format conversions are cached**: Repeated access is efficient
|
|
403
|
+
3. **Scale conversions may require IERS data**: Downloads automatically
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404
|
+
4. **High precision maintained**: Sub-nanosecond accuracy across astronomical timescales
|
|
@@ -0,0 +1,178 @@
|
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1
|
+
# Units and Quantities (astropy.units)
|
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2
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+
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3
|
+
The `astropy.units` module handles defining, converting between, and performing arithmetic with physical quantities.
|
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4
|
+
|
|
5
|
+
## Creating Quantities
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6
|
+
|
|
7
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+
Multiply or divide numeric values by built-in units to create Quantity objects:
|
|
8
|
+
|
|
9
|
+
```python
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|
10
|
+
from astropy import units as u
|
|
11
|
+
import numpy as np
|
|
12
|
+
|
|
13
|
+
# Scalar quantities
|
|
14
|
+
distance = 42.0 * u.meter
|
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15
|
+
velocity = 100 * u.km / u.s
|
|
16
|
+
|
|
17
|
+
# Array quantities
|
|
18
|
+
distances = np.array([1., 2., 3.]) * u.m
|
|
19
|
+
wavelengths = [500, 600, 700] * u.nm
|
|
20
|
+
```
|
|
21
|
+
|
|
22
|
+
Access components via `.value` and `.unit` attributes:
|
|
23
|
+
```python
|
|
24
|
+
distance.value # 42.0
|
|
25
|
+
distance.unit # Unit("m")
|
|
26
|
+
```
|
|
27
|
+
|
|
28
|
+
## Unit Conversions
|
|
29
|
+
|
|
30
|
+
Use `.to()` method for conversions:
|
|
31
|
+
|
|
32
|
+
```python
|
|
33
|
+
distance = 1.0 * u.parsec
|
|
34
|
+
distance.to(u.km) # <Quantity 30856775814671.914 km>
|
|
35
|
+
|
|
36
|
+
wavelength = 500 * u.nm
|
|
37
|
+
wavelength.to(u.angstrom) # <Quantity 5000. Angstrom>
|
|
38
|
+
```
|
|
39
|
+
|
|
40
|
+
## Arithmetic Operations
|
|
41
|
+
|
|
42
|
+
Quantities support standard arithmetic with automatic unit management:
|
|
43
|
+
|
|
44
|
+
```python
|
|
45
|
+
# Basic operations
|
|
46
|
+
speed = 15.1 * u.meter / (32.0 * u.second) # <Quantity 0.471875 m / s>
|
|
47
|
+
area = (5 * u.m) * (3 * u.m) # <Quantity 15. m2>
|
|
48
|
+
|
|
49
|
+
# Units cancel when appropriate
|
|
50
|
+
ratio = (10 * u.m) / (5 * u.m) # <Quantity 2. (dimensionless)>
|
|
51
|
+
|
|
52
|
+
# Decompose complex units
|
|
53
|
+
time = (3.0 * u.kilometer / (130.51 * u.meter / u.second))
|
|
54
|
+
time.decompose() # <Quantity 22.986744310780782 s>
|
|
55
|
+
```
|
|
56
|
+
|
|
57
|
+
## Unit Systems
|
|
58
|
+
|
|
59
|
+
Convert between major unit systems:
|
|
60
|
+
|
|
61
|
+
```python
|
|
62
|
+
# SI to CGS
|
|
63
|
+
pressure = 1.0 * u.Pa
|
|
64
|
+
pressure.cgs # <Quantity 10. Ba>
|
|
65
|
+
|
|
66
|
+
# Find equivalent representations
|
|
67
|
+
(u.s ** -1).compose() # [Unit("Bq"), Unit("Hz"), ...]
|
|
68
|
+
```
|
|
69
|
+
|
|
70
|
+
## Equivalencies
|
|
71
|
+
|
|
72
|
+
Domain-specific conversions require equivalencies:
|
|
73
|
+
|
|
74
|
+
```python
|
|
75
|
+
# Spectral equivalency (wavelength ↔ frequency)
|
|
76
|
+
wavelength = 1000 * u.nm
|
|
77
|
+
wavelength.to(u.Hz, equivalencies=u.spectral())
|
|
78
|
+
# <Quantity 2.99792458e+14 Hz>
|
|
79
|
+
|
|
80
|
+
# Doppler equivalencies
|
|
81
|
+
velocity = 1000 * u.km / u.s
|
|
82
|
+
velocity.to(u.Hz, equivalencies=u.doppler_optical(500*u.nm))
|
|
83
|
+
|
|
84
|
+
# Other equivalencies
|
|
85
|
+
u.brightness_temperature(500*u.GHz)
|
|
86
|
+
u.doppler_radio(1.4*u.GHz)
|
|
87
|
+
u.mass_energy()
|
|
88
|
+
u.parallax()
|
|
89
|
+
```
|
|
90
|
+
|
|
91
|
+
## Logarithmic Units
|
|
92
|
+
|
|
93
|
+
Special units for magnitudes, decibels, and dex:
|
|
94
|
+
|
|
95
|
+
```python
|
|
96
|
+
# Magnitudes
|
|
97
|
+
flux = -2.5 * u.mag(u.ct / u.s)
|
|
98
|
+
|
|
99
|
+
# Decibels
|
|
100
|
+
power_ratio = 3 * u.dB(u.W)
|
|
101
|
+
|
|
102
|
+
# Dex (base-10 logarithm)
|
|
103
|
+
abundance = 8.5 * u.dex(u.cm**-3)
|
|
104
|
+
```
|
|
105
|
+
|
|
106
|
+
## Common Units
|
|
107
|
+
|
|
108
|
+
### Length
|
|
109
|
+
`u.m, u.km, u.cm, u.mm, u.micron, u.angstrom, u.au, u.pc, u.kpc, u.Mpc, u.lyr`
|
|
110
|
+
|
|
111
|
+
### Time
|
|
112
|
+
`u.s, u.min, u.hour, u.day, u.year, u.Myr, u.Gyr`
|
|
113
|
+
|
|
114
|
+
### Mass
|
|
115
|
+
`u.kg, u.g, u.M_sun, u.M_earth, u.M_jup`
|
|
116
|
+
|
|
117
|
+
### Temperature
|
|
118
|
+
`u.K, u.deg_C`
|
|
119
|
+
|
|
120
|
+
### Angle
|
|
121
|
+
`u.deg, u.arcmin, u.arcsec, u.rad, u.hourangle, u.mas`
|
|
122
|
+
|
|
123
|
+
### Energy/Power
|
|
124
|
+
`u.J, u.erg, u.eV, u.keV, u.MeV, u.GeV, u.W, u.L_sun`
|
|
125
|
+
|
|
126
|
+
### Frequency
|
|
127
|
+
`u.Hz, u.kHz, u.MHz, u.GHz`
|
|
128
|
+
|
|
129
|
+
### Flux
|
|
130
|
+
`u.Jy, u.mJy, u.erg / u.s / u.cm**2`
|
|
131
|
+
|
|
132
|
+
## Performance Optimization
|
|
133
|
+
|
|
134
|
+
Pre-compute composite units for array operations:
|
|
135
|
+
|
|
136
|
+
```python
|
|
137
|
+
# Slow (creates intermediate quantities)
|
|
138
|
+
result = array * u.m / u.s / u.kg / u.sr
|
|
139
|
+
|
|
140
|
+
# Fast (pre-computed composite unit)
|
|
141
|
+
UNIT_COMPOSITE = u.m / u.s / u.kg / u.sr
|
|
142
|
+
result = array * UNIT_COMPOSITE
|
|
143
|
+
|
|
144
|
+
# Fastest (avoid copying with <<)
|
|
145
|
+
result = array << UNIT_COMPOSITE # 10000x faster
|
|
146
|
+
```
|
|
147
|
+
|
|
148
|
+
## String Formatting
|
|
149
|
+
|
|
150
|
+
Format quantities with standard Python syntax:
|
|
151
|
+
|
|
152
|
+
```python
|
|
153
|
+
velocity = 15.1 * u.meter / (32.0 * u.second)
|
|
154
|
+
f"{velocity:0.03f}" # '0.472 m / s'
|
|
155
|
+
f"{velocity:.2e}" # '4.72e-01 m / s'
|
|
156
|
+
f"{velocity.unit:FITS}" # 'm s-1'
|
|
157
|
+
```
|
|
158
|
+
|
|
159
|
+
## Defining Custom Units
|
|
160
|
+
|
|
161
|
+
```python
|
|
162
|
+
# Create new unit
|
|
163
|
+
bakers_fortnight = u.def_unit('bakers_fortnight', 13 * u.day)
|
|
164
|
+
|
|
165
|
+
# Enable in string parsing
|
|
166
|
+
u.add_enabled_units([bakers_fortnight])
|
|
167
|
+
```
|
|
168
|
+
|
|
169
|
+
## Constants
|
|
170
|
+
|
|
171
|
+
Access physical constants with units:
|
|
172
|
+
|
|
173
|
+
```python
|
|
174
|
+
from astropy.constants import c, G, M_sun, h, k_B
|
|
175
|
+
|
|
176
|
+
speed_of_light = c.to(u.km/u.s)
|
|
177
|
+
gravitational_constant = G.to(u.m**3 / u.kg / u.s**2)
|
|
178
|
+
```
|