@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.
Files changed (830) hide show
  1. package/bin/skills/adaptyv/SKILL.md +114 -0
  2. package/bin/skills/adaptyv/reference/api_reference.md +308 -0
  3. package/bin/skills/adaptyv/reference/examples.md +913 -0
  4. package/bin/skills/adaptyv/reference/experiments.md +360 -0
  5. package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
  6. package/bin/skills/aeon/SKILL.md +374 -0
  7. package/bin/skills/aeon/references/anomaly_detection.md +154 -0
  8. package/bin/skills/aeon/references/classification.md +144 -0
  9. package/bin/skills/aeon/references/clustering.md +123 -0
  10. package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
  11. package/bin/skills/aeon/references/distances.md +256 -0
  12. package/bin/skills/aeon/references/forecasting.md +140 -0
  13. package/bin/skills/aeon/references/networks.md +289 -0
  14. package/bin/skills/aeon/references/regression.md +118 -0
  15. package/bin/skills/aeon/references/segmentation.md +163 -0
  16. package/bin/skills/aeon/references/similarity_search.md +187 -0
  17. package/bin/skills/aeon/references/transformations.md +246 -0
  18. package/bin/skills/alphafold-database/SKILL.md +513 -0
  19. package/bin/skills/alphafold-database/references/api_reference.md +423 -0
  20. package/bin/skills/anndata/SKILL.md +400 -0
  21. package/bin/skills/anndata/references/best_practices.md +525 -0
  22. package/bin/skills/anndata/references/concatenation.md +396 -0
  23. package/bin/skills/anndata/references/data_structure.md +314 -0
  24. package/bin/skills/anndata/references/io_operations.md +404 -0
  25. package/bin/skills/anndata/references/manipulation.md +516 -0
  26. package/bin/skills/arboreto/SKILL.md +243 -0
  27. package/bin/skills/arboreto/references/algorithms.md +138 -0
  28. package/bin/skills/arboreto/references/basic_inference.md +151 -0
  29. package/bin/skills/arboreto/references/distributed_computing.md +242 -0
  30. package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
  31. package/bin/skills/astropy/SKILL.md +331 -0
  32. package/bin/skills/astropy/references/coordinates.md +273 -0
  33. package/bin/skills/astropy/references/cosmology.md +307 -0
  34. package/bin/skills/astropy/references/fits.md +396 -0
  35. package/bin/skills/astropy/references/tables.md +489 -0
  36. package/bin/skills/astropy/references/time.md +404 -0
  37. package/bin/skills/astropy/references/units.md +178 -0
  38. package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
  39. package/bin/skills/benchling-integration/SKILL.md +480 -0
  40. package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
  41. package/bin/skills/benchling-integration/references/authentication.md +379 -0
  42. package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
  43. package/bin/skills/biopython/SKILL.md +443 -0
  44. package/bin/skills/biopython/references/advanced.md +577 -0
  45. package/bin/skills/biopython/references/alignment.md +362 -0
  46. package/bin/skills/biopython/references/blast.md +455 -0
  47. package/bin/skills/biopython/references/databases.md +484 -0
  48. package/bin/skills/biopython/references/phylogenetics.md +566 -0
  49. package/bin/skills/biopython/references/sequence_io.md +285 -0
  50. package/bin/skills/biopython/references/structure.md +564 -0
  51. package/bin/skills/biorxiv-database/SKILL.md +483 -0
  52. package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
  53. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
  54. package/bin/skills/bioservices/SKILL.md +361 -0
  55. package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
  56. package/bin/skills/bioservices/references/services_reference.md +636 -0
  57. package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
  58. package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
  59. package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
  60. package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
  61. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
  62. package/bin/skills/brenda-database/SKILL.md +719 -0
  63. package/bin/skills/brenda-database/references/api_reference.md +537 -0
  64. package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
  65. package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
  66. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
  67. package/bin/skills/cellxgene-census/SKILL.md +511 -0
  68. package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
  69. package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
  70. package/bin/skills/chembl-database/SKILL.md +389 -0
  71. package/bin/skills/chembl-database/references/api_reference.md +272 -0
  72. package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
  73. package/bin/skills/cirq/SKILL.md +346 -0
  74. package/bin/skills/cirq/references/building.md +307 -0
  75. package/bin/skills/cirq/references/experiments.md +572 -0
  76. package/bin/skills/cirq/references/hardware.md +515 -0
  77. package/bin/skills/cirq/references/noise.md +515 -0
  78. package/bin/skills/cirq/references/simulation.md +350 -0
  79. package/bin/skills/cirq/references/transformation.md +416 -0
  80. package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
  81. package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
  82. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
  83. package/bin/skills/clinpgx-database/SKILL.md +638 -0
  84. package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
  85. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
  86. package/bin/skills/clinvar-database/SKILL.md +362 -0
  87. package/bin/skills/clinvar-database/references/api_reference.md +227 -0
  88. package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
  89. package/bin/skills/clinvar-database/references/data_formats.md +358 -0
  90. package/bin/skills/cobrapy/SKILL.md +463 -0
  91. package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
  92. package/bin/skills/cobrapy/references/workflows.md +593 -0
  93. package/bin/skills/cosmic-database/SKILL.md +336 -0
  94. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
  95. package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
  96. package/bin/skills/dask/SKILL.md +456 -0
  97. package/bin/skills/dask/references/arrays.md +497 -0
  98. package/bin/skills/dask/references/bags.md +468 -0
  99. package/bin/skills/dask/references/best-practices.md +277 -0
  100. package/bin/skills/dask/references/dataframes.md +368 -0
  101. package/bin/skills/dask/references/futures.md +541 -0
  102. package/bin/skills/dask/references/schedulers.md +504 -0
  103. package/bin/skills/datacommons-client/SKILL.md +255 -0
  104. package/bin/skills/datacommons-client/references/getting_started.md +417 -0
  105. package/bin/skills/datacommons-client/references/node.md +250 -0
  106. package/bin/skills/datacommons-client/references/observation.md +185 -0
  107. package/bin/skills/datacommons-client/references/resolve.md +246 -0
  108. package/bin/skills/datamol/SKILL.md +706 -0
  109. package/bin/skills/datamol/references/conformers_module.md +131 -0
  110. package/bin/skills/datamol/references/core_api.md +130 -0
  111. package/bin/skills/datamol/references/descriptors_viz.md +195 -0
  112. package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
  113. package/bin/skills/datamol/references/io_module.md +109 -0
  114. package/bin/skills/datamol/references/reactions_data.md +218 -0
  115. package/bin/skills/deepchem/SKILL.md +597 -0
  116. package/bin/skills/deepchem/references/api_reference.md +303 -0
  117. package/bin/skills/deepchem/references/workflows.md +491 -0
  118. package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
  119. package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
  120. package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
  121. package/bin/skills/deeptools/SKILL.md +531 -0
  122. package/bin/skills/deeptools/assets/quick_reference.md +58 -0
  123. package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
  124. package/bin/skills/deeptools/references/normalization_methods.md +410 -0
  125. package/bin/skills/deeptools/references/tools_reference.md +533 -0
  126. package/bin/skills/deeptools/references/workflows.md +474 -0
  127. package/bin/skills/deeptools/scripts/validate_files.py +195 -0
  128. package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
  129. package/bin/skills/denario/SKILL.md +215 -0
  130. package/bin/skills/denario/references/examples.md +494 -0
  131. package/bin/skills/denario/references/installation.md +213 -0
  132. package/bin/skills/denario/references/llm_configuration.md +265 -0
  133. package/bin/skills/denario/references/research_pipeline.md +471 -0
  134. package/bin/skills/diffdock/SKILL.md +483 -0
  135. package/bin/skills/diffdock/assets/batch_template.csv +4 -0
  136. package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
  137. package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
  138. package/bin/skills/diffdock/references/parameters_reference.md +163 -0
  139. package/bin/skills/diffdock/references/workflows_examples.md +392 -0
  140. package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
  141. package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
  142. package/bin/skills/diffdock/scripts/setup_check.py +278 -0
  143. package/bin/skills/dnanexus-integration/SKILL.md +383 -0
  144. package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
  145. package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
  146. package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
  147. package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
  148. package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
  149. package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
  150. package/bin/skills/document-skills/docx/SKILL.md +233 -0
  151. package/bin/skills/document-skills/docx/docx-js.md +350 -0
  152. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  153. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  154. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  155. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  156. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  157. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  158. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  159. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  160. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  161. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  162. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  163. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
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  165. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  166. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  167. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  168. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
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  170. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  171. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  172. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  173. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  174. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  175. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  176. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  177. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  178. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  179. package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  180. package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  181. package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  182. package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  183. package/bin/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  184. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
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  188. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  189. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  190. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  191. package/bin/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  192. package/bin/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  193. package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  194. package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  195. package/bin/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  196. package/bin/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  197. package/bin/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  198. package/bin/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  199. package/bin/skills/document-skills/docx/ooxml.md +610 -0
  200. package/bin/skills/document-skills/docx/scripts/__init__.py +1 -0
  201. package/bin/skills/document-skills/docx/scripts/document.py +1276 -0
  202. package/bin/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  203. package/bin/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  204. package/bin/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  205. package/bin/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  206. package/bin/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  207. package/bin/skills/document-skills/docx/scripts/utilities.py +374 -0
  208. package/bin/skills/document-skills/pdf/LICENSE.txt +30 -0
  209. package/bin/skills/document-skills/pdf/SKILL.md +330 -0
  210. package/bin/skills/document-skills/pdf/forms.md +205 -0
  211. package/bin/skills/document-skills/pdf/reference.md +612 -0
  212. package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  213. package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  214. package/bin/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  215. package/bin/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  216. package/bin/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  217. package/bin/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
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  219. package/bin/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  220. package/bin/skills/document-skills/pptx/LICENSE.txt +30 -0
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  805. package/bin/skills/uniprot-database/references/api_examples.md +413 -0
  806. package/bin/skills/uniprot-database/references/api_fields.md +275 -0
  807. package/bin/skills/uniprot-database/references/id_mapping_databases.md +285 -0
  808. package/bin/skills/uniprot-database/references/query_syntax.md +256 -0
  809. package/bin/skills/uniprot-database/scripts/uniprot_client.py +341 -0
  810. package/bin/skills/uspto-database/SKILL.md +607 -0
  811. package/bin/skills/uspto-database/references/additional_apis.md +394 -0
  812. package/bin/skills/uspto-database/references/patentsearch_api.md +266 -0
  813. package/bin/skills/uspto-database/references/peds_api.md +212 -0
  814. package/bin/skills/uspto-database/references/trademark_api.md +358 -0
  815. package/bin/skills/uspto-database/scripts/patent_search.py +290 -0
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  817. package/bin/skills/uspto-database/scripts/trademark_client.py +311 -0
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  819. package/bin/skills/vaex/references/core_dataframes.md +367 -0
  820. package/bin/skills/vaex/references/data_processing.md +555 -0
  821. package/bin/skills/vaex/references/io_operations.md +703 -0
  822. package/bin/skills/vaex/references/machine_learning.md +728 -0
  823. package/bin/skills/vaex/references/performance.md +571 -0
  824. package/bin/skills/vaex/references/visualization.md +613 -0
  825. package/bin/skills/zarr-python/SKILL.md +779 -0
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  827. package/bin/skills/zinc-database/SKILL.md +404 -0
  828. package/bin/skills/zinc-database/references/api_reference.md +692 -0
  829. package/bin/synsc +0 -0
  830. package/package.json +1 -1
@@ -0,0 +1,404 @@
1
+ # Time Handling (astropy.time)
2
+
3
+ The `astropy.time` module provides robust tools for manipulating times and dates with support for various time scales and formats.
4
+
5
+ ## Creating Time Objects
6
+
7
+ ### Basic Creation
8
+
9
+ ```python
10
+ from astropy.time import Time
11
+ import astropy.units as u
12
+
13
+ # ISO format (automatically detected)
14
+ t = Time('2023-01-15 12:30:45')
15
+ t = Time('2023-01-15T12:30:45')
16
+
17
+ # Specify format explicitly
18
+ t = Time('2023-01-15 12:30:45', format='iso', scale='utc')
19
+
20
+ # Julian Date
21
+ t = Time(2460000.0, format='jd')
22
+
23
+ # Modified Julian Date
24
+ t = Time(59945.0, format='mjd')
25
+
26
+ # Unix time (seconds since 1970-01-01)
27
+ t = Time(1673785845.0, format='unix')
28
+ ```
29
+
30
+ ### Array of Times
31
+
32
+ ```python
33
+ # Multiple times
34
+ times = Time(['2023-01-01', '2023-06-01', '2023-12-31'])
35
+
36
+ # From arrays
37
+ import numpy as np
38
+ jd_array = np.linspace(2460000, 2460100, 100)
39
+ times = Time(jd_array, format='jd')
40
+ ```
41
+
42
+ ## Time Formats
43
+
44
+ ### Supported Formats
45
+
46
+ ```python
47
+ # 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
+ # For radial velocity correction
396
+ rv_correction = ltt_bary.to(u.km, equivalencies=u.dimensionless_angles())
397
+ ```
398
+
399
+ ## Performance Considerations
400
+
401
+ 1. **Array operations are fast**: Process multiple times as arrays
402
+ 2. **Format conversions are cached**: Repeated access is efficient
403
+ 3. **Scale conversions may require IERS data**: Downloads automatically
404
+ 4. **High precision maintained**: Sub-nanosecond accuracy across astronomical timescales
@@ -0,0 +1,178 @@
1
+ # Units and Quantities (astropy.units)
2
+
3
+ The `astropy.units` module handles defining, converting between, and performing arithmetic with physical quantities.
4
+
5
+ ## Creating Quantities
6
+
7
+ Multiply or divide numeric values by built-in units to create Quantity objects:
8
+
9
+ ```python
10
+ from astropy import units as u
11
+ import numpy as np
12
+
13
+ # Scalar quantities
14
+ distance = 42.0 * u.meter
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
+ ```