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 +1,265 @@
1
+ #!/usr/bin/env python3
2
+ # Timestamp: 2026-01-24
3
+ # File: src/scitex/scholar/_mcp/crossref_handlers.py
4
+ """CrossRef-SciTeX handler implementations via crossref-local delegation.
5
+
6
+ These handlers delegate to crossref-local for fast access to 167M+ papers.
7
+ Branded as crossref-scitex to distinguish from official CrossRef API.
8
+ """
9
+
10
+ from __future__ import annotations
11
+
12
+ import asyncio
13
+ from datetime import datetime
14
+
15
+ __all__ = [
16
+ "crossref_search_handler",
17
+ "crossref_get_handler",
18
+ "crossref_count_handler",
19
+ "crossref_citations_handler",
20
+ "crossref_info_handler",
21
+ ]
22
+
23
+
24
+ def _ensure_crossref():
25
+ """Ensure crossref_scitex module is available."""
26
+ try:
27
+ from scitex.scholar import crossref_scitex
28
+
29
+ return crossref_scitex
30
+ except ImportError as e:
31
+ raise RuntimeError(
32
+ "crossref-local not installed. Install with: pip install crossref-local"
33
+ ) from e
34
+
35
+
36
+ async def crossref_search_handler(
37
+ query: str,
38
+ limit: int = 20,
39
+ offset: int = 0,
40
+ year_min: int | None = None,
41
+ year_max: int | None = None,
42
+ enrich: bool = False,
43
+ ) -> dict:
44
+ """Search CrossRef database (167M+ papers) via crossref-local.
45
+
46
+ Args:
47
+ query: Search query string (full-text search)
48
+ limit: Maximum number of results (default: 20)
49
+ offset: Number of results to skip for pagination
50
+ year_min: Minimum publication year filter
51
+ year_max: Maximum publication year filter
52
+ enrich: If True, add citation counts and references
53
+ """
54
+ try:
55
+ crossref = _ensure_crossref()
56
+ loop = asyncio.get_running_loop()
57
+
58
+ def do_search():
59
+ # Fetch more results for filtering
60
+ fetch_limit = limit * 2 if (year_min or year_max) else limit
61
+ results = crossref.search(query, limit=fetch_limit, offset=offset)
62
+
63
+ if enrich:
64
+ results = crossref.enrich(results)
65
+
66
+ papers = []
67
+ for work in results:
68
+ # Apply year filters
69
+ if year_min and work.year and work.year < year_min:
70
+ continue
71
+ if year_max and work.year and work.year > year_max:
72
+ continue
73
+
74
+ papers.append(
75
+ {
76
+ "doi": work.doi,
77
+ "title": work.title,
78
+ "authors": work.authors[:10] if work.authors else [],
79
+ "year": work.year,
80
+ "journal": work.journal,
81
+ "abstract": (
82
+ work.abstract[:500] + "..."
83
+ if work.abstract and len(work.abstract) > 500
84
+ else work.abstract
85
+ ),
86
+ "citation_count": work.citation_count,
87
+ "reference_count": work.reference_count,
88
+ "type": work.type,
89
+ }
90
+ )
91
+ if len(papers) >= limit:
92
+ break
93
+
94
+ return papers, results.total
95
+
96
+ papers, total = await loop.run_in_executor(None, do_search)
97
+
98
+ return {
99
+ "success": True,
100
+ "query": query,
101
+ "total": total,
102
+ "count": len(papers),
103
+ "offset": offset,
104
+ "limit": limit,
105
+ "papers": papers,
106
+ "source": "crossref_local",
107
+ "timestamp": datetime.now().isoformat(),
108
+ }
109
+
110
+ except Exception as e:
111
+ return {"success": False, "error": str(e)}
112
+
113
+
114
+ async def crossref_get_handler(
115
+ doi: str,
116
+ include_citations: bool = False,
117
+ include_references: bool = False,
118
+ ) -> dict:
119
+ """Get a paper by DOI from CrossRef database.
120
+
121
+ Args:
122
+ doi: DOI of the paper
123
+ include_citations: Include list of citing DOIs
124
+ include_references: Include list of referenced DOIs
125
+ """
126
+ try:
127
+ crossref = _ensure_crossref()
128
+ loop = asyncio.get_running_loop()
129
+
130
+ def do_get():
131
+ work = crossref.get(doi)
132
+ if not work:
133
+ return None
134
+
135
+ result = {
136
+ "doi": work.doi,
137
+ "title": work.title,
138
+ "authors": work.authors,
139
+ "year": work.year,
140
+ "journal": work.journal,
141
+ "abstract": work.abstract,
142
+ "citation_count": work.citation_count,
143
+ "reference_count": work.reference_count,
144
+ "type": work.type,
145
+ "publisher": work.publisher,
146
+ "url": work.url,
147
+ }
148
+
149
+ if include_citations:
150
+ result["citing_dois"] = crossref.get_citing(doi)
151
+
152
+ if include_references:
153
+ result["referenced_dois"] = crossref.get_cited(doi)
154
+
155
+ return result
156
+
157
+ result = await loop.run_in_executor(None, do_get)
158
+
159
+ if result is None:
160
+ return {
161
+ "success": False,
162
+ "error": f"DOI not found: {doi}",
163
+ "doi": doi,
164
+ }
165
+
166
+ return {
167
+ "success": True,
168
+ "paper": result,
169
+ "source": "crossref_local",
170
+ "timestamp": datetime.now().isoformat(),
171
+ }
172
+
173
+ except Exception as e:
174
+ return {"success": False, "error": str(e)}
175
+
176
+
177
+ async def crossref_count_handler(query: str) -> dict:
178
+ """Count papers matching a search query.
179
+
180
+ Args:
181
+ query: Search query string
182
+ """
183
+ try:
184
+ crossref = _ensure_crossref()
185
+ loop = asyncio.get_running_loop()
186
+
187
+ count = await loop.run_in_executor(None, crossref.count, query)
188
+
189
+ return {
190
+ "success": True,
191
+ "query": query,
192
+ "count": count,
193
+ "source": "crossref_local",
194
+ "timestamp": datetime.now().isoformat(),
195
+ }
196
+
197
+ except Exception as e:
198
+ return {"success": False, "error": str(e)}
199
+
200
+
201
+ async def crossref_citations_handler(
202
+ doi: str,
203
+ direction: str = "citing", # "citing", "cited", or "both"
204
+ limit: int = 100,
205
+ ) -> dict:
206
+ """Get citation relationships for a paper.
207
+
208
+ Args:
209
+ doi: DOI of the paper
210
+ direction: "citing" (papers that cite this), "cited" (references), or "both"
211
+ limit: Maximum number of results per direction
212
+ """
213
+ try:
214
+ crossref = _ensure_crossref()
215
+ loop = asyncio.get_running_loop()
216
+
217
+ def do_citations():
218
+ result = {"doi": doi}
219
+
220
+ if direction in ("citing", "both"):
221
+ citing = crossref.get_citing(doi)
222
+ result["citing_dois"] = citing[:limit]
223
+ result["citing_count"] = len(citing)
224
+
225
+ if direction in ("cited", "both"):
226
+ cited = crossref.get_cited(doi)
227
+ result["cited_dois"] = cited[:limit]
228
+ result["cited_count"] = len(cited)
229
+
230
+ return result
231
+
232
+ result = await loop.run_in_executor(None, do_citations)
233
+
234
+ return {
235
+ "success": True,
236
+ **result,
237
+ "direction": direction,
238
+ "source": "crossref_local",
239
+ "timestamp": datetime.now().isoformat(),
240
+ }
241
+
242
+ except Exception as e:
243
+ return {"success": False, "error": str(e)}
244
+
245
+
246
+ async def crossref_info_handler() -> dict:
247
+ """Get information about CrossRef database configuration and status."""
248
+ try:
249
+ crossref = _ensure_crossref()
250
+ loop = asyncio.get_running_loop()
251
+
252
+ info = await loop.run_in_executor(None, crossref.info)
253
+
254
+ return {
255
+ "success": True,
256
+ "info": info,
257
+ "mode": crossref.get_mode(),
258
+ "timestamp": datetime.now().isoformat(),
259
+ }
260
+
261
+ except Exception as e:
262
+ return {"success": False, "error": str(e)}
263
+
264
+
265
+ # EOF