scitex 2.14.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

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 (218) hide show
  1. scitex/__init__.py +47 -0
  2. scitex/_env_loader.py +156 -0
  3. scitex/_mcp_resources/__init__.py +37 -0
  4. scitex/_mcp_resources/_cheatsheet.py +135 -0
  5. scitex/_mcp_resources/_figrecipe.py +138 -0
  6. scitex/_mcp_resources/_formats.py +102 -0
  7. scitex/_mcp_resources/_modules.py +337 -0
  8. scitex/_mcp_resources/_session.py +149 -0
  9. scitex/_mcp_tools/__init__.py +4 -0
  10. scitex/_mcp_tools/audio.py +66 -0
  11. scitex/_mcp_tools/diagram.py +11 -95
  12. scitex/_mcp_tools/introspect.py +191 -0
  13. scitex/_mcp_tools/plt.py +260 -305
  14. scitex/_mcp_tools/scholar.py +74 -0
  15. scitex/_mcp_tools/social.py +244 -0
  16. scitex/_mcp_tools/writer.py +21 -204
  17. scitex/ai/_gen_ai/_PARAMS.py +10 -7
  18. scitex/ai/classification/reporters/_SingleClassificationReporter.py +45 -1603
  19. scitex/ai/classification/reporters/_mixins/__init__.py +36 -0
  20. scitex/ai/classification/reporters/_mixins/_constants.py +67 -0
  21. scitex/ai/classification/reporters/_mixins/_cv_summary.py +387 -0
  22. scitex/ai/classification/reporters/_mixins/_feature_importance.py +119 -0
  23. scitex/ai/classification/reporters/_mixins/_metrics.py +275 -0
  24. scitex/ai/classification/reporters/_mixins/_plotting.py +179 -0
  25. scitex/ai/classification/reporters/_mixins/_reports.py +153 -0
  26. scitex/ai/classification/reporters/_mixins/_storage.py +160 -0
  27. scitex/audio/README.md +40 -36
  28. scitex/audio/__init__.py +127 -59
  29. scitex/audio/_branding.py +185 -0
  30. scitex/audio/_mcp/__init__.py +32 -0
  31. scitex/audio/_mcp/handlers.py +59 -6
  32. scitex/audio/_mcp/speak_handlers.py +238 -0
  33. scitex/audio/_relay.py +225 -0
  34. scitex/audio/engines/elevenlabs_engine.py +6 -1
  35. scitex/audio/mcp_server.py +228 -75
  36. scitex/canvas/README.md +1 -1
  37. scitex/canvas/editor/_dearpygui/__init__.py +25 -0
  38. scitex/canvas/editor/_dearpygui/_editor.py +147 -0
  39. scitex/canvas/editor/_dearpygui/_handlers.py +476 -0
  40. scitex/canvas/editor/_dearpygui/_panels/__init__.py +17 -0
  41. scitex/canvas/editor/_dearpygui/_panels/_control.py +119 -0
  42. scitex/canvas/editor/_dearpygui/_panels/_element_controls.py +190 -0
  43. scitex/canvas/editor/_dearpygui/_panels/_preview.py +43 -0
  44. scitex/canvas/editor/_dearpygui/_panels/_sections.py +390 -0
  45. scitex/canvas/editor/_dearpygui/_plotting.py +187 -0
  46. scitex/canvas/editor/_dearpygui/_rendering.py +504 -0
  47. scitex/canvas/editor/_dearpygui/_selection.py +295 -0
  48. scitex/canvas/editor/_dearpygui/_state.py +93 -0
  49. scitex/canvas/editor/_dearpygui/_utils.py +61 -0
  50. scitex/canvas/editor/flask_editor/templates/__init__.py +32 -70
  51. scitex/cli/__init__.py +38 -43
  52. scitex/cli/audio.py +76 -27
  53. scitex/cli/capture.py +13 -20
  54. scitex/cli/introspect.py +443 -0
  55. scitex/cli/main.py +198 -109
  56. scitex/cli/mcp.py +60 -34
  57. scitex/cli/scholar/__init__.py +8 -0
  58. scitex/cli/scholar/_crossref_scitex.py +296 -0
  59. scitex/cli/scholar/_fetch.py +25 -3
  60. scitex/cli/social.py +314 -0
  61. scitex/cli/writer.py +117 -0
  62. scitex/config/README.md +1 -1
  63. scitex/config/__init__.py +16 -2
  64. scitex/config/_env_registry.py +191 -0
  65. scitex/diagram/__init__.py +42 -19
  66. scitex/diagram/mcp_server.py +13 -125
  67. scitex/introspect/__init__.py +75 -0
  68. scitex/introspect/_call_graph.py +303 -0
  69. scitex/introspect/_class_hierarchy.py +163 -0
  70. scitex/introspect/_core.py +42 -0
  71. scitex/introspect/_docstring.py +131 -0
  72. scitex/introspect/_examples.py +113 -0
  73. scitex/introspect/_imports.py +271 -0
  74. scitex/introspect/_mcp/__init__.py +37 -0
  75. scitex/introspect/_mcp/handlers.py +208 -0
  76. scitex/introspect/_members.py +151 -0
  77. scitex/introspect/_resolve.py +89 -0
  78. scitex/introspect/_signature.py +131 -0
  79. scitex/introspect/_source.py +80 -0
  80. scitex/introspect/_type_hints.py +172 -0
  81. scitex/io/bundle/README.md +1 -1
  82. scitex/mcp_server.py +98 -5
  83. scitex/plt/__init__.py +248 -550
  84. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin/_wrappers.py +5 -10
  85. scitex/plt/docs/EXTERNAL_PACKAGE_BRANDING.md +149 -0
  86. scitex/plt/gallery/README.md +1 -1
  87. scitex/plt/utils/_hitmap/__init__.py +82 -0
  88. scitex/plt/utils/_hitmap/_artist_extraction.py +343 -0
  89. scitex/plt/utils/_hitmap/_color_application.py +346 -0
  90. scitex/plt/utils/_hitmap/_color_conversion.py +121 -0
  91. scitex/plt/utils/_hitmap/_constants.py +40 -0
  92. scitex/plt/utils/_hitmap/_hitmap_core.py +334 -0
  93. scitex/plt/utils/_hitmap/_path_extraction.py +357 -0
  94. scitex/plt/utils/_hitmap/_query.py +113 -0
  95. scitex/plt/utils/_hitmap.py +46 -1616
  96. scitex/plt/utils/_metadata/__init__.py +80 -0
  97. scitex/plt/utils/_metadata/_artists/__init__.py +25 -0
  98. scitex/plt/utils/_metadata/_artists/_base.py +195 -0
  99. scitex/plt/utils/_metadata/_artists/_collections.py +356 -0
  100. scitex/plt/utils/_metadata/_artists/_extract.py +57 -0
  101. scitex/plt/utils/_metadata/_artists/_images.py +80 -0
  102. scitex/plt/utils/_metadata/_artists/_lines.py +261 -0
  103. scitex/plt/utils/_metadata/_artists/_patches.py +247 -0
  104. scitex/plt/utils/_metadata/_artists/_text.py +106 -0
  105. scitex/plt/utils/_metadata/_csv.py +416 -0
  106. scitex/plt/utils/_metadata/_detect.py +225 -0
  107. scitex/plt/utils/_metadata/_legend.py +127 -0
  108. scitex/plt/utils/_metadata/_rounding.py +117 -0
  109. scitex/plt/utils/_metadata/_verification.py +202 -0
  110. scitex/schema/README.md +1 -1
  111. scitex/scholar/__init__.py +8 -0
  112. scitex/scholar/_mcp/crossref_handlers.py +265 -0
  113. scitex/scholar/core/Scholar.py +63 -1700
  114. scitex/scholar/core/_mixins/__init__.py +36 -0
  115. scitex/scholar/core/_mixins/_enrichers.py +270 -0
  116. scitex/scholar/core/_mixins/_library_handlers.py +100 -0
  117. scitex/scholar/core/_mixins/_loaders.py +103 -0
  118. scitex/scholar/core/_mixins/_pdf_download.py +375 -0
  119. scitex/scholar/core/_mixins/_pipeline.py +312 -0
  120. scitex/scholar/core/_mixins/_project_handlers.py +125 -0
  121. scitex/scholar/core/_mixins/_savers.py +69 -0
  122. scitex/scholar/core/_mixins/_search.py +103 -0
  123. scitex/scholar/core/_mixins/_services.py +88 -0
  124. scitex/scholar/core/_mixins/_url_finding.py +105 -0
  125. scitex/scholar/crossref_scitex.py +367 -0
  126. scitex/scholar/docs/EXTERNAL_PACKAGE_BRANDING.md +149 -0
  127. scitex/scholar/examples/00_run_all.sh +120 -0
  128. scitex/scholar/jobs/_executors.py +27 -3
  129. scitex/scholar/pdf_download/ScholarPDFDownloader.py +38 -416
  130. scitex/scholar/pdf_download/_cli.py +154 -0
  131. scitex/scholar/pdf_download/strategies/__init__.py +11 -8
  132. scitex/scholar/pdf_download/strategies/manual_download_fallback.py +80 -3
  133. scitex/scholar/pipelines/ScholarPipelineBibTeX.py +73 -121
  134. scitex/scholar/pipelines/ScholarPipelineParallel.py +80 -138
  135. scitex/scholar/pipelines/ScholarPipelineSingle.py +43 -63
  136. scitex/scholar/pipelines/_single_steps.py +71 -36
  137. scitex/scholar/storage/_LibraryManager.py +97 -1695
  138. scitex/scholar/storage/_mixins/__init__.py +30 -0
  139. scitex/scholar/storage/_mixins/_bibtex_handlers.py +128 -0
  140. scitex/scholar/storage/_mixins/_library_operations.py +218 -0
  141. scitex/scholar/storage/_mixins/_metadata_conversion.py +226 -0
  142. scitex/scholar/storage/_mixins/_paper_saving.py +456 -0
  143. scitex/scholar/storage/_mixins/_resolution.py +376 -0
  144. scitex/scholar/storage/_mixins/_storage_helpers.py +121 -0
  145. scitex/scholar/storage/_mixins/_symlink_handlers.py +226 -0
  146. scitex/scholar/url_finder/.tmp/open_url/KNOWN_RESOLVERS.py +462 -0
  147. scitex/scholar/url_finder/.tmp/open_url/README.md +223 -0
  148. scitex/scholar/url_finder/.tmp/open_url/_DOIToURLResolver.py +694 -0
  149. scitex/scholar/url_finder/.tmp/open_url/_OpenURLResolver.py +1160 -0
  150. scitex/scholar/url_finder/.tmp/open_url/_ResolverLinkFinder.py +344 -0
  151. scitex/scholar/url_finder/.tmp/open_url/__init__.py +24 -0
  152. scitex/security/README.md +3 -3
  153. scitex/session/README.md +1 -1
  154. scitex/sh/README.md +1 -1
  155. scitex/social/__init__.py +153 -0
  156. scitex/social/docs/EXTERNAL_PACKAGE_BRANDING.md +149 -0
  157. scitex/template/README.md +1 -1
  158. scitex/template/clone_writer_directory.py +5 -5
  159. scitex/writer/README.md +1 -1
  160. scitex/writer/_mcp/handlers.py +11 -744
  161. scitex/writer/_mcp/tool_schemas.py +5 -335
  162. scitex-2.15.1.dist-info/METADATA +648 -0
  163. {scitex-2.14.0.dist-info → scitex-2.15.1.dist-info}/RECORD +166 -111
  164. scitex/canvas/editor/flask_editor/templates/_scripts.py +0 -4933
  165. scitex/canvas/editor/flask_editor/templates/_styles.py +0 -1658
  166. scitex/dev/plt/data/mpl/PLOTTING_FUNCTIONS.yaml +0 -90
  167. scitex/dev/plt/data/mpl/PLOTTING_SIGNATURES.yaml +0 -1571
  168. scitex/dev/plt/data/mpl/PLOTTING_SIGNATURES_DETAILED.yaml +0 -6262
  169. scitex/dev/plt/data/mpl/SIGNATURES_FLATTENED.yaml +0 -1274
  170. scitex/dev/plt/data/mpl/dir_ax.txt +0 -459
  171. scitex/diagram/_compile.py +0 -312
  172. scitex/diagram/_diagram.py +0 -355
  173. scitex/diagram/_mcp/__init__.py +0 -4
  174. scitex/diagram/_mcp/handlers.py +0 -400
  175. scitex/diagram/_mcp/tool_schemas.py +0 -157
  176. scitex/diagram/_presets.py +0 -173
  177. scitex/diagram/_schema.py +0 -182
  178. scitex/diagram/_split.py +0 -278
  179. scitex/plt/_mcp/__init__.py +0 -4
  180. scitex/plt/_mcp/_handlers_annotation.py +0 -102
  181. scitex/plt/_mcp/_handlers_figure.py +0 -195
  182. scitex/plt/_mcp/_handlers_plot.py +0 -252
  183. scitex/plt/_mcp/_handlers_style.py +0 -219
  184. scitex/plt/_mcp/handlers.py +0 -74
  185. scitex/plt/_mcp/tool_schemas.py +0 -497
  186. scitex/plt/mcp_server.py +0 -231
  187. scitex/scholar/data/.gitkeep +0 -0
  188. scitex/scholar/data/README.md +0 -44
  189. scitex/scholar/data/bib_files/bibliography.bib +0 -1952
  190. scitex/scholar/data/bib_files/neurovista.bib +0 -277
  191. scitex/scholar/data/bib_files/neurovista_enriched.bib +0 -441
  192. scitex/scholar/data/bib_files/neurovista_enriched_enriched.bib +0 -441
  193. scitex/scholar/data/bib_files/neurovista_processed.bib +0 -338
  194. scitex/scholar/data/bib_files/openaccess.bib +0 -89
  195. scitex/scholar/data/bib_files/pac-seizure_prediction_enriched.bib +0 -2178
  196. scitex/scholar/data/bib_files/pac.bib +0 -698
  197. scitex/scholar/data/bib_files/pac_enriched.bib +0 -1061
  198. scitex/scholar/data/bib_files/pac_processed.bib +0 -0
  199. scitex/scholar/data/bib_files/pac_titles.txt +0 -75
  200. scitex/scholar/data/bib_files/paywalled.bib +0 -98
  201. scitex/scholar/data/bib_files/related-papers-by-coauthors.bib +0 -58
  202. scitex/scholar/data/bib_files/related-papers-by-coauthors_enriched.bib +0 -87
  203. scitex/scholar/data/bib_files/seizure_prediction.bib +0 -694
  204. scitex/scholar/data/bib_files/seizure_prediction_processed.bib +0 -0
  205. scitex/scholar/data/bib_files/test_complete_enriched.bib +0 -437
  206. scitex/scholar/data/bib_files/test_final_enriched.bib +0 -437
  207. scitex/scholar/data/bib_files/test_seizure.bib +0 -46
  208. scitex/scholar/data/impact_factor/JCR_IF_2022.xlsx +0 -0
  209. scitex/scholar/data/impact_factor/JCR_IF_2024.db +0 -0
  210. scitex/scholar/data/impact_factor/JCR_IF_2024.xlsx +0 -0
  211. scitex/scholar/data/impact_factor/JCR_IF_2024_v01.db +0 -0
  212. scitex/scholar/data/impact_factor.db +0 -0
  213. scitex/scholar/examples/SUGGESTIONS.md +0 -865
  214. scitex/scholar/examples/dev.py +0 -38
  215. scitex-2.14.0.dist-info/METADATA +0 -1238
  216. {scitex-2.14.0.dist-info → scitex-2.15.1.dist-info}/WHEEL +0 -0
  217. {scitex-2.14.0.dist-info → scitex-2.15.1.dist-info}/entry_points.txt +0 -0
  218. {scitex-2.14.0.dist-info → scitex-2.15.1.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,191 @@
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+ #!/usr/bin/env python3
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+ # Timestamp: 2025-01-20
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+ # File: /home/ywatanabe/proj/scitex-code/src/scitex/_mcp_tools/introspect.py
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+
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+ """Introspection module tools for FastMCP unified server."""
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+
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+ from __future__ import annotations
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+
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+ import json
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+ from typing import Optional
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+
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+
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+ def _json(data: dict) -> str:
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+ return json.dumps(data, indent=2, default=str)
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+
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+
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+ def register_introspect_tools(mcp) -> None:
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+ """Register introspection tools with FastMCP server."""
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+
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+ @mcp.tool()
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+ async def introspect_signature(
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+ dotted_path: str,
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+ include_defaults: bool = True,
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+ include_annotations: bool = True,
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+ ) -> str:
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+ """[introspect] Get function/class signature (like IPython's func?)."""
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+ from scitex.introspect._mcp.handlers import signature_handler
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+
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+ result = await signature_handler(
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+ dotted_path=dotted_path,
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+ include_defaults=include_defaults,
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+ include_annotations=include_annotations,
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+ )
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_docstring(
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+ dotted_path: str,
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+ format: str = "raw",
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+ ) -> str:
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+ """[introspect] Get docstring of a Python object. format: raw|parsed|summary."""
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+ from scitex.introspect._mcp.handlers import docstring_handler
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+
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+ result = await docstring_handler(
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+ dotted_path=dotted_path,
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+ format=format,
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+ )
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_source(
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+ dotted_path: str,
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+ max_lines: Optional[int] = None,
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+ include_decorators: bool = True,
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+ ) -> str:
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+ """[introspect] Get source code of a Python object (like IPython's func??)."""
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+ from scitex.introspect._mcp.handlers import source_handler
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+
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+ result = await source_handler(
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+ dotted_path=dotted_path,
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+ max_lines=max_lines,
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+ include_decorators=include_decorators,
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+ )
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_members(
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+ dotted_path: str,
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+ filter: str = "public",
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+ kind: Optional[str] = None,
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+ include_inherited: bool = False,
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+ ) -> str:
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+ """[introspect] List members of module/class (like dir()). filter: all|public|private|dunder."""
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+ from scitex.introspect._mcp.handlers import members_handler
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+
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+ result = await members_handler(
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+ dotted_path=dotted_path,
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+ filter=filter,
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+ kind=kind,
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+ include_inherited=include_inherited,
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+ )
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_exports(dotted_path: str) -> str:
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+ """[introspect] Get __all__ exports of a module."""
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+ from scitex.introspect._mcp.handlers import exports_handler
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+
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+ result = await exports_handler(dotted_path=dotted_path)
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_examples(
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+ dotted_path: str,
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+ search_paths: Optional[str] = None,
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+ max_results: int = 10,
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+ ) -> str:
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+ """[introspect] Find usage examples in tests/examples directories."""
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+ from scitex.introspect._mcp.handlers import examples_handler
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+
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+ # Parse search_paths if provided as comma-separated string
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+ paths_list = None
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+ if search_paths:
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+ paths_list = [p.strip() for p in search_paths.split(",")]
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+
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+ result = await examples_handler(
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+ dotted_path=dotted_path,
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+ search_paths=paths_list,
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+ max_results=max_results,
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+ )
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+ return _json(result)
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+
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+ # Advanced introspection tools
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+
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+ @mcp.tool()
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+ async def introspect_class_hierarchy(
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+ dotted_path: str,
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+ include_builtins: bool = False,
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+ max_depth: int = 10,
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+ ) -> str:
121
+ """[introspect] Get class inheritance hierarchy (MRO + subclasses)."""
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+ from scitex.introspect._mcp.handlers import class_hierarchy_handler
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+
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+ result = await class_hierarchy_handler(
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+ dotted_path=dotted_path,
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+ include_builtins=include_builtins,
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+ max_depth=max_depth,
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+ )
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_type_hints(
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+ dotted_path: str,
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+ include_extras: bool = True,
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+ ) -> str:
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+ """[introspect] Get detailed type hint analysis for function/class."""
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+ from scitex.introspect._mcp.handlers import type_hints_handler
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+
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+ result = await type_hints_handler(
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+ dotted_path=dotted_path,
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+ include_extras=include_extras,
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+ )
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_imports(
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+ dotted_path: str,
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+ categorize: bool = True,
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+ ) -> str:
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+ """[introspect] Get all imports from a module (AST-based static analysis)."""
151
+ from scitex.introspect._mcp.handlers import imports_handler
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+
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+ result = await imports_handler(
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+ dotted_path=dotted_path,
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+ categorize=categorize,
156
+ )
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_dependencies(
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+ dotted_path: str,
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+ recursive: bool = False,
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+ max_depth: int = 3,
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+ ) -> str:
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+ """[introspect] Get module dependencies (what it imports)."""
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+ from scitex.introspect._mcp.handlers import dependencies_handler
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+
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+ result = await dependencies_handler(
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+ dotted_path=dotted_path,
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+ recursive=recursive,
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+ max_depth=max_depth,
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+ )
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+ return _json(result)
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+
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+ @mcp.tool()
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+ async def introspect_call_graph(
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+ dotted_path: str,
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+ max_depth: int = 2,
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+ timeout_seconds: int = 10,
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+ internal_only: bool = True,
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+ ) -> str:
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+ """[introspect] Get function call graph (with timeout protection)."""
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+ from scitex.introspect._mcp.handlers import call_graph_handler
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+
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+ result = await call_graph_handler(
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+ dotted_path=dotted_path,
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+ max_depth=max_depth,
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+ timeout_seconds=timeout_seconds,
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+ internal_only=internal_only,
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+ )
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+ return _json(result)