@synsci/cli-darwin-arm64 1.1.77 → 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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  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
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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
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  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
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  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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+ # Dask Schedulers
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+
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+ ## Overview
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+
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+ Dask provides multiple task schedulers, each suited to different workloads. The scheduler determines how tasks are executed: sequentially, in parallel threads, in parallel processes, or distributed across a cluster.
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+
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+ ## Scheduler Types
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+
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+ ### Single-Machine Schedulers
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+
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+ #### 1. Local Threads (Default)
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+
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+ **Description**: The threaded scheduler executes computations with a local `concurrent.futures.ThreadPoolExecutor`.
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+
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+ **When to Use**:
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+ - Numeric computations in NumPy, Pandas, scikit-learn
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+ - Libraries that release the GIL (Global Interpreter Lock)
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+ - Operations benefit from shared memory access
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+ - Default for Dask Arrays and DataFrames
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+
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+ **Characteristics**:
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+ - Low overhead
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+ - Shared memory between threads
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+ - Best for GIL-releasing operations
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+ - Poor for pure Python code (GIL contention)
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+
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+ **Example**:
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+ ```python
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+ import dask.array as da
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+
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+ # Uses threads by default
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+ x = da.random.random((10000, 10000), chunks=(1000, 1000))
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+ result = x.mean().compute() # Computed with threads
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+ ```
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+
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+ **Explicit Configuration**:
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+ ```python
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+ import dask
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+
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+ # Set globally
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+ dask.config.set(scheduler='threads')
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+
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+ # Or per-compute
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+ result = x.mean().compute(scheduler='threads')
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+ ```
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+
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+ #### 2. Local Processes
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+
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+ **Description**: Multiprocessing scheduler that uses `concurrent.futures.ProcessPoolExecutor`.
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+
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+ **When to Use**:
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+ - Pure Python code with GIL contention
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+ - Text processing and Python collections
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+ - Operations that benefit from process isolation
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+ - CPU-bound Python code
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+
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+ **Characteristics**:
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+ - Bypasses GIL limitations
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+ - Incurs data transfer costs between processes
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+ - Higher overhead than threads
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+ - Ideal for linear workflows with small inputs/outputs
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+
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+ **Example**:
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+ ```python
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+ import dask.bag as db
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+
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+ # Good for Python object processing
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+ bag = db.read_text('data/*.txt')
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+ result = bag.map(complex_python_function).compute(scheduler='processes')
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+ ```
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+
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+ **Explicit Configuration**:
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+ ```python
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+ import dask
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+
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+ # Set globally
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+ dask.config.set(scheduler='processes')
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+
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+ # Or per-compute
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+ result = computation.compute(scheduler='processes')
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+ ```
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+
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+ **Limitations**:
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+ - Data must be serializable (pickle)
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+ - Overhead from process creation
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+ - Memory overhead from data copying
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+
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+ #### 3. Single Thread (Synchronous)
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+
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+ **Description**: The single-threaded synchronous scheduler executes all computations in the local thread with no parallelism at all.
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+
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+ **When to Use**:
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+ - Debugging with pdb
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+ - Profiling with standard Python tools
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+ - Understanding errors in detail
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+ - Development and testing
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+
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+ **Characteristics**:
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+ - No parallelism
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+ - Easy debugging
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+ - No overhead
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+ - Deterministic execution
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+
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+ **Example**:
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+ ```python
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+ import dask
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+
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+ # Enable for debugging
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+ dask.config.set(scheduler='synchronous')
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+
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+ # Now can use pdb
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+ result = computation.compute() # Runs in single thread
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+ ```
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+
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+ **Debugging with IPython**:
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+ ```python
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+ # In IPython/Jupyter
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+ %pdb on
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+
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+ dask.config.set(scheduler='synchronous')
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+ result = problematic_computation.compute() # Drops into debugger on error
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+ ```
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+
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+ ### Distributed Schedulers
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+
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+ #### 4. Local Distributed
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+
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+ **Description**: Despite its name, this scheduler runs effectively on personal machines using the distributed scheduler infrastructure.
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+
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+ **When to Use**:
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+ - Need diagnostic dashboard
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+ - Asynchronous APIs
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+ - Better data locality handling than multiprocessing
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+ - Development before scaling to cluster
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+ - Want distributed features on single machine
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+
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+ **Characteristics**:
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+ - Provides dashboard for monitoring
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+ - Better memory management
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+ - More overhead than threads/processes
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+ - Can scale to cluster later
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+
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+ **Example**:
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+ ```python
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+ from dask.distributed import Client
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+ import dask.dataframe as dd
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+
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+ # Create local cluster
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+ client = Client() # Automatically uses all cores
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+
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+ # Use distributed scheduler
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+ ddf = dd.read_csv('data.csv')
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+ result = ddf.groupby('category').mean().compute()
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+
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+ # View dashboard
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+ print(client.dashboard_link)
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+
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+ # Clean up
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+ client.close()
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+ ```
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+
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+ **Configuration Options**:
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+ ```python
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+ # Control resources
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+ client = Client(
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+ n_workers=4,
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+ threads_per_worker=2,
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+ memory_limit='4GB'
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+ )
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+ ```
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+
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+ #### 5. Cluster Distributed
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+
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+ **Description**: For scaling across multiple machines using the distributed scheduler.
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+
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+ **When to Use**:
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+ - Data exceeds single machine capacity
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+ - Need computational power beyond one machine
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+ - Production deployments
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+ - Cluster computing environments (HPC, cloud)
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+
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+ **Characteristics**:
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+ - Scales to hundreds of machines
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+ - Requires cluster setup
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+ - Network communication overhead
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+ - Advanced features (adaptive scaling, task prioritization)
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+
188
+ **Example with Dask-Jobqueue (HPC)**:
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+ ```python
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+ from dask_jobqueue import SLURMCluster
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+ from dask.distributed import Client
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+
193
+ # Create cluster on HPC with SLURM
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+ cluster = SLURMCluster(
195
+ cores=24,
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+ memory='100GB',
197
+ walltime='02:00:00',
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+ queue='regular'
199
+ )
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+
201
+ # Scale to 10 jobs
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+ cluster.scale(jobs=10)
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+
204
+ # Connect client
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+ client = Client(cluster)
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+
207
+ # Run computation
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+ result = computation.compute()
209
+
210
+ client.close()
211
+ ```
212
+
213
+ **Example with Dask on Kubernetes**:
214
+ ```python
215
+ from dask_kubernetes import KubeCluster
216
+ from dask.distributed import Client
217
+
218
+ cluster = KubeCluster()
219
+ cluster.scale(20) # 20 workers
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+
221
+ client = Client(cluster)
222
+ result = computation.compute()
223
+
224
+ client.close()
225
+ ```
226
+
227
+ ## Scheduler Configuration
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+
229
+ ### Global Configuration
230
+
231
+ ```python
232
+ import dask
233
+
234
+ # Set scheduler globally for session
235
+ dask.config.set(scheduler='threads')
236
+ dask.config.set(scheduler='processes')
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+ dask.config.set(scheduler='synchronous')
238
+ ```
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+
240
+ ### Context Manager
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+
242
+ ```python
243
+ import dask
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+
245
+ # Temporarily use different scheduler
246
+ with dask.config.set(scheduler='processes'):
247
+ result = computation.compute()
248
+
249
+ # Back to default scheduler
250
+ result2 = computation2.compute()
251
+ ```
252
+
253
+ ### Per-Compute
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+
255
+ ```python
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+ # Specify scheduler per compute call
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+ result = computation.compute(scheduler='threads')
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+ result = computation.compute(scheduler='processes')
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+ result = computation.compute(scheduler='synchronous')
260
+ ```
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+
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+ ### Distributed Client
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+
264
+ ```python
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+ from dask.distributed import Client
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+
267
+ # Using client automatically sets distributed scheduler
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+ client = Client()
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+
270
+ # All computations use distributed scheduler
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+ result = computation.compute()
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+
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+ client.close()
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+ ```
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+
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+ ## Choosing the Right Scheduler
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+
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+ ### Decision Matrix
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+
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+ | Workload Type | Recommended Scheduler | Rationale |
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+ |--------------|----------------------|-----------|
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+ | NumPy/Pandas operations | Threads (default) | GIL-releasing, shared memory |
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+ | Pure Python objects | Processes | Avoids GIL contention |
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+ | Text/log processing | Processes | Python-heavy operations |
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+ | Debugging | Synchronous | Easy debugging, deterministic |
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+ | Need dashboard | Local Distributed | Monitoring and diagnostics |
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+ | Multi-machine | Cluster Distributed | Exceeds single machine capacity |
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+ | Small data, quick tasks | Threads | Lowest overhead |
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+ | Large data, single machine | Local Distributed | Better memory management |
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+
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+ ### Performance Considerations
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+
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+ **Threads**:
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+ - Overhead: ~10 µs per task
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+ - Best for: Numeric operations
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+ - Memory: Shared
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+ - GIL: Affected by GIL
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+
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+ **Processes**:
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+ - Overhead: ~10 ms per task
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+ - Best for: Python operations
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+ - Memory: Copied between processes
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+ - GIL: Not affected
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+
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+ **Synchronous**:
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+ - Overhead: ~1 µs per task
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+ - Best for: Debugging
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+ - Memory: No parallelism
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+ - GIL: Not relevant
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+
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+ **Distributed**:
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+ - Overhead: ~1 ms per task
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+ - Best for: Complex workflows, monitoring
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+ - Memory: Managed by scheduler
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+ - GIL: Workers can use threads or processes
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+
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+ ## Thread Configuration for Distributed Scheduler
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+
319
+ ### Setting Thread Count
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+
321
+ ```python
322
+ from dask.distributed import Client
323
+
324
+ # Control thread/worker configuration
325
+ client = Client(
326
+ n_workers=4, # Number of worker processes
327
+ threads_per_worker=2 # Threads per worker process
328
+ )
329
+ ```
330
+
331
+ ### Recommended Configuration
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+
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+ **For Numeric Workloads**:
334
+ - Aim for roughly 4 threads per process
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+ - Balance between parallelism and overhead
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+ - Example: 8 cores → 2 workers with 4 threads each
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+
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+ **For Python Workloads**:
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+ - Use more workers with fewer threads
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+ - Example: 8 cores → 8 workers with 1 thread each
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+
342
+ ### Environment Variables
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+
344
+ ```bash
345
+ # Set thread count via environment
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+ export DASK_NUM_WORKERS=4
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+ export DASK_THREADS_PER_WORKER=2
348
+
349
+ # Or via config file
350
+ ```
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+
352
+ ## Common Patterns
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+
354
+ ### Development to Production
355
+
356
+ ```python
357
+ # Development: Use local distributed for testing
358
+ from dask.distributed import Client
359
+ client = Client(processes=False) # In-process for debugging
360
+
361
+ # Production: Scale to cluster
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+ from dask.distributed import Client
363
+ client = Client('scheduler-address:8786')
364
+ ```
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+
366
+ ### Mixed Workloads
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+
368
+ ```python
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+ import dask
370
+ import dask.dataframe as dd
371
+
372
+ # Use threads for DataFrame operations
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+ ddf = dd.read_parquet('data.parquet')
374
+ result1 = ddf.mean().compute(scheduler='threads')
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+
376
+ # Use processes for Python code
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+ import dask.bag as db
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+ bag = db.read_text('logs/*.txt')
379
+ result2 = bag.map(parse_log).compute(scheduler='processes')
380
+ ```
381
+
382
+ ### Debugging Workflow
383
+
384
+ ```python
385
+ import dask
386
+
387
+ # Step 1: Debug with synchronous scheduler
388
+ dask.config.set(scheduler='synchronous')
389
+ result = problematic_computation.compute()
390
+
391
+ # Step 2: Test with threads
392
+ dask.config.set(scheduler='threads')
393
+ result = computation.compute()
394
+
395
+ # Step 3: Scale with distributed
396
+ from dask.distributed import Client
397
+ client = Client()
398
+ result = computation.compute()
399
+ ```
400
+
401
+ ## Monitoring and Diagnostics
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+
403
+ ### Dashboard Access (Distributed Only)
404
+
405
+ ```python
406
+ from dask.distributed import Client
407
+
408
+ client = Client()
409
+
410
+ # Get dashboard URL
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+ print(client.dashboard_link)
412
+ # Opens dashboard in browser showing:
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+ # - Task progress
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+ # - Worker status
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+ # - Memory usage
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+ # - Task stream
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+ # - Resource utilization
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+ ```
419
+
420
+ ### Performance Profiling
421
+
422
+ ```python
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+ # Profile computation
424
+ from dask.distributed import Client
425
+
426
+ client = Client()
427
+ result = computation.compute()
428
+
429
+ # Get performance report
430
+ client.profile(filename='profile.html')
431
+ ```
432
+
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+ ### Resource Monitoring
434
+
435
+ ```python
436
+ # Check worker info
437
+ client.scheduler_info()
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+
439
+ # Get current tasks
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+ client.who_has()
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+
442
+ # Memory usage
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+ client.run(lambda: psutil.virtual_memory().percent)
444
+ ```
445
+
446
+ ## Advanced Configuration
447
+
448
+ ### Custom Executors
449
+
450
+ ```python
451
+ from concurrent.futures import ThreadPoolExecutor
452
+ import dask
453
+
454
+ # Use custom thread pool
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+ with ThreadPoolExecutor(max_workers=4) as executor:
456
+ dask.config.set(pool=executor)
457
+ result = computation.compute(scheduler='threads')
458
+ ```
459
+
460
+ ### Adaptive Scaling (Distributed)
461
+
462
+ ```python
463
+ from dask.distributed import Client
464
+
465
+ client = Client()
466
+
467
+ # Enable adaptive scaling
468
+ client.cluster.adapt(minimum=2, maximum=10)
469
+
470
+ # Cluster scales based on workload
471
+ result = computation.compute()
472
+ ```
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+
474
+ ### Worker Plugins
475
+
476
+ ```python
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+ from dask.distributed import Client, WorkerPlugin
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+
479
+ class CustomPlugin(WorkerPlugin):
480
+ def setup(self, worker):
481
+ # Initialize worker-specific resources
482
+ worker.custom_resource = initialize_resource()
483
+
484
+ client = Client()
485
+ client.register_worker_plugin(CustomPlugin())
486
+ ```
487
+
488
+ ## Troubleshooting
489
+
490
+ ### Slow Performance with Threads
491
+ **Problem**: Pure Python code slow with threaded scheduler
492
+ **Solution**: Switch to processes or distributed scheduler
493
+
494
+ ### Memory Errors with Processes
495
+ **Problem**: Data too large to pickle/copy between processes
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+ **Solution**: Use threaded or distributed scheduler
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+
498
+ ### Debugging Difficult
499
+ **Problem**: Can't use pdb with parallel schedulers
500
+ **Solution**: Use synchronous scheduler for debugging
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+
502
+ ### Task Overhead High
503
+ **Problem**: Many tiny tasks causing overhead
504
+ **Solution**: Use threaded scheduler (lowest overhead) or increase chunk sizes