scitex 2.14.0__py3-none-any.whl → 2.15.2__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.
- scitex/__init__.py +71 -17
- scitex/_env_loader.py +156 -0
- scitex/_mcp_resources/__init__.py +37 -0
- scitex/_mcp_resources/_cheatsheet.py +135 -0
- scitex/_mcp_resources/_figrecipe.py +138 -0
- scitex/_mcp_resources/_formats.py +102 -0
- scitex/_mcp_resources/_modules.py +337 -0
- scitex/_mcp_resources/_session.py +149 -0
- scitex/_mcp_tools/__init__.py +4 -0
- scitex/_mcp_tools/audio.py +66 -0
- scitex/_mcp_tools/diagram.py +11 -95
- scitex/_mcp_tools/introspect.py +210 -0
- scitex/_mcp_tools/plt.py +260 -305
- scitex/_mcp_tools/scholar.py +74 -0
- scitex/_mcp_tools/social.py +244 -0
- scitex/_mcp_tools/template.py +24 -0
- scitex/_mcp_tools/writer.py +21 -204
- scitex/ai/_gen_ai/_PARAMS.py +10 -7
- scitex/ai/classification/reporters/_SingleClassificationReporter.py +45 -1603
- scitex/ai/classification/reporters/_mixins/__init__.py +36 -0
- scitex/ai/classification/reporters/_mixins/_constants.py +67 -0
- scitex/ai/classification/reporters/_mixins/_cv_summary.py +387 -0
- scitex/ai/classification/reporters/_mixins/_feature_importance.py +119 -0
- scitex/ai/classification/reporters/_mixins/_metrics.py +275 -0
- scitex/ai/classification/reporters/_mixins/_plotting.py +179 -0
- scitex/ai/classification/reporters/_mixins/_reports.py +153 -0
- scitex/ai/classification/reporters/_mixins/_storage.py +160 -0
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +30 -1550
- scitex/ai/classification/timeseries/_sliding_window_core.py +467 -0
- scitex/ai/classification/timeseries/_sliding_window_plotting.py +369 -0
- scitex/audio/README.md +40 -36
- scitex/audio/__init__.py +129 -61
- scitex/audio/_branding.py +185 -0
- scitex/audio/_mcp/__init__.py +32 -0
- scitex/audio/_mcp/handlers.py +59 -6
- scitex/audio/_mcp/speak_handlers.py +238 -0
- scitex/audio/_relay.py +225 -0
- scitex/audio/_tts.py +18 -10
- scitex/audio/engines/base.py +17 -10
- scitex/audio/engines/elevenlabs_engine.py +7 -2
- scitex/audio/mcp_server.py +228 -75
- scitex/canvas/README.md +1 -1
- scitex/canvas/editor/_dearpygui/__init__.py +25 -0
- scitex/canvas/editor/_dearpygui/_editor.py +147 -0
- scitex/canvas/editor/_dearpygui/_handlers.py +476 -0
- scitex/canvas/editor/_dearpygui/_panels/__init__.py +17 -0
- scitex/canvas/editor/_dearpygui/_panels/_control.py +119 -0
- scitex/canvas/editor/_dearpygui/_panels/_element_controls.py +190 -0
- scitex/canvas/editor/_dearpygui/_panels/_preview.py +43 -0
- scitex/canvas/editor/_dearpygui/_panels/_sections.py +390 -0
- scitex/canvas/editor/_dearpygui/_plotting.py +187 -0
- scitex/canvas/editor/_dearpygui/_rendering.py +504 -0
- scitex/canvas/editor/_dearpygui/_selection.py +295 -0
- scitex/canvas/editor/_dearpygui/_state.py +93 -0
- scitex/canvas/editor/_dearpygui/_utils.py +61 -0
- scitex/canvas/editor/flask_editor/_core/__init__.py +27 -0
- scitex/canvas/editor/flask_editor/_core/_bbox_extraction.py +200 -0
- scitex/canvas/editor/flask_editor/_core/_editor.py +173 -0
- scitex/canvas/editor/flask_editor/_core/_export_helpers.py +353 -0
- scitex/canvas/editor/flask_editor/_core/_routes_basic.py +190 -0
- scitex/canvas/editor/flask_editor/_core/_routes_export.py +332 -0
- scitex/canvas/editor/flask_editor/_core/_routes_panels.py +252 -0
- scitex/canvas/editor/flask_editor/_core/_routes_save.py +218 -0
- scitex/canvas/editor/flask_editor/_core.py +25 -1684
- scitex/canvas/editor/flask_editor/templates/__init__.py +32 -70
- scitex/cli/__init__.py +38 -43
- scitex/cli/audio.py +76 -27
- scitex/cli/capture.py +13 -20
- scitex/cli/introspect.py +481 -0
- scitex/cli/main.py +200 -109
- scitex/cli/mcp.py +60 -34
- scitex/cli/plt.py +357 -0
- scitex/cli/repro.py +15 -8
- scitex/cli/resource.py +15 -8
- scitex/cli/scholar/__init__.py +23 -8
- scitex/cli/scholar/_crossref_scitex.py +296 -0
- scitex/cli/scholar/_fetch.py +25 -3
- scitex/cli/social.py +314 -0
- scitex/cli/stats.py +15 -8
- scitex/cli/template.py +129 -12
- scitex/cli/tex.py +15 -8
- scitex/cli/writer.py +132 -8
- scitex/cloud/__init__.py +41 -2
- scitex/config/README.md +1 -1
- scitex/config/__init__.py +16 -2
- scitex/config/_env_registry.py +256 -0
- scitex/context/__init__.py +22 -0
- scitex/dev/__init__.py +20 -1
- scitex/diagram/__init__.py +42 -19
- scitex/diagram/mcp_server.py +13 -125
- scitex/gen/__init__.py +50 -14
- scitex/gen/_list_packages.py +4 -4
- scitex/introspect/__init__.py +82 -0
- scitex/introspect/_call_graph.py +303 -0
- scitex/introspect/_class_hierarchy.py +163 -0
- scitex/introspect/_core.py +41 -0
- scitex/introspect/_docstring.py +131 -0
- scitex/introspect/_examples.py +113 -0
- scitex/introspect/_imports.py +271 -0
- scitex/{gen/_inspect_module.py → introspect/_list_api.py} +43 -54
- scitex/introspect/_mcp/__init__.py +41 -0
- scitex/introspect/_mcp/handlers.py +233 -0
- scitex/introspect/_members.py +155 -0
- scitex/introspect/_resolve.py +89 -0
- scitex/introspect/_signature.py +131 -0
- scitex/introspect/_source.py +80 -0
- scitex/introspect/_type_hints.py +172 -0
- scitex/io/_save.py +1 -2
- scitex/io/bundle/README.md +1 -1
- scitex/logging/_formatters.py +19 -9
- scitex/mcp_server.py +98 -5
- scitex/os/__init__.py +4 -0
- scitex/{gen → os}/_check_host.py +4 -5
- scitex/plt/__init__.py +245 -550
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin/_wrappers.py +5 -10
- scitex/plt/docs/EXTERNAL_PACKAGE_BRANDING.md +149 -0
- scitex/plt/gallery/README.md +1 -1
- scitex/plt/utils/_hitmap/__init__.py +82 -0
- scitex/plt/utils/_hitmap/_artist_extraction.py +343 -0
- scitex/plt/utils/_hitmap/_color_application.py +346 -0
- scitex/plt/utils/_hitmap/_color_conversion.py +121 -0
- scitex/plt/utils/_hitmap/_constants.py +40 -0
- scitex/plt/utils/_hitmap/_hitmap_core.py +334 -0
- scitex/plt/utils/_hitmap/_path_extraction.py +357 -0
- scitex/plt/utils/_hitmap/_query.py +113 -0
- scitex/plt/utils/_hitmap.py +46 -1616
- scitex/plt/utils/_metadata/__init__.py +80 -0
- scitex/plt/utils/_metadata/_artists/__init__.py +25 -0
- scitex/plt/utils/_metadata/_artists/_base.py +195 -0
- scitex/plt/utils/_metadata/_artists/_collections.py +356 -0
- scitex/plt/utils/_metadata/_artists/_extract.py +57 -0
- scitex/plt/utils/_metadata/_artists/_images.py +80 -0
- scitex/plt/utils/_metadata/_artists/_lines.py +261 -0
- scitex/plt/utils/_metadata/_artists/_patches.py +247 -0
- scitex/plt/utils/_metadata/_artists/_text.py +106 -0
- scitex/plt/utils/_metadata/_csv.py +416 -0
- scitex/plt/utils/_metadata/_detect.py +225 -0
- scitex/plt/utils/_metadata/_legend.py +127 -0
- scitex/plt/utils/_metadata/_rounding.py +117 -0
- scitex/plt/utils/_metadata/_verification.py +202 -0
- scitex/schema/README.md +1 -1
- scitex/scholar/__init__.py +8 -0
- scitex/scholar/_mcp/crossref_handlers.py +265 -0
- scitex/scholar/core/Scholar.py +63 -1700
- scitex/scholar/core/_mixins/__init__.py +36 -0
- scitex/scholar/core/_mixins/_enrichers.py +270 -0
- scitex/scholar/core/_mixins/_library_handlers.py +100 -0
- scitex/scholar/core/_mixins/_loaders.py +103 -0
- scitex/scholar/core/_mixins/_pdf_download.py +375 -0
- scitex/scholar/core/_mixins/_pipeline.py +312 -0
- scitex/scholar/core/_mixins/_project_handlers.py +125 -0
- scitex/scholar/core/_mixins/_savers.py +69 -0
- scitex/scholar/core/_mixins/_search.py +103 -0
- scitex/scholar/core/_mixins/_services.py +88 -0
- scitex/scholar/core/_mixins/_url_finding.py +105 -0
- scitex/scholar/crossref_scitex.py +367 -0
- scitex/scholar/docs/EXTERNAL_PACKAGE_BRANDING.md +149 -0
- scitex/scholar/examples/00_run_all.sh +120 -0
- scitex/scholar/jobs/_executors.py +27 -3
- scitex/scholar/pdf_download/ScholarPDFDownloader.py +38 -416
- scitex/scholar/pdf_download/_cli.py +154 -0
- scitex/scholar/pdf_download/strategies/__init__.py +11 -8
- scitex/scholar/pdf_download/strategies/manual_download_fallback.py +80 -3
- scitex/scholar/pipelines/ScholarPipelineBibTeX.py +73 -121
- scitex/scholar/pipelines/ScholarPipelineParallel.py +80 -138
- scitex/scholar/pipelines/ScholarPipelineSingle.py +43 -63
- scitex/scholar/pipelines/_single_steps.py +71 -36
- scitex/scholar/storage/_LibraryManager.py +97 -1695
- scitex/scholar/storage/_mixins/__init__.py +30 -0
- scitex/scholar/storage/_mixins/_bibtex_handlers.py +128 -0
- scitex/scholar/storage/_mixins/_library_operations.py +218 -0
- scitex/scholar/storage/_mixins/_metadata_conversion.py +226 -0
- scitex/scholar/storage/_mixins/_paper_saving.py +456 -0
- scitex/scholar/storage/_mixins/_resolution.py +376 -0
- scitex/scholar/storage/_mixins/_storage_helpers.py +121 -0
- scitex/scholar/storage/_mixins/_symlink_handlers.py +226 -0
- scitex/scholar/url_finder/.tmp/open_url/KNOWN_RESOLVERS.py +462 -0
- scitex/scholar/url_finder/.tmp/open_url/README.md +223 -0
- scitex/scholar/url_finder/.tmp/open_url/_DOIToURLResolver.py +694 -0
- scitex/scholar/url_finder/.tmp/open_url/_OpenURLResolver.py +1160 -0
- scitex/scholar/url_finder/.tmp/open_url/_ResolverLinkFinder.py +344 -0
- scitex/scholar/url_finder/.tmp/open_url/__init__.py +24 -0
- scitex/security/README.md +3 -3
- scitex/session/README.md +1 -1
- scitex/session/__init__.py +26 -7
- scitex/session/_decorator.py +1 -1
- scitex/sh/README.md +1 -1
- scitex/sh/__init__.py +7 -4
- scitex/social/__init__.py +155 -0
- scitex/social/docs/EXTERNAL_PACKAGE_BRANDING.md +149 -0
- scitex/stats/_mcp/_handlers/__init__.py +31 -0
- scitex/stats/_mcp/_handlers/_corrections.py +113 -0
- scitex/stats/_mcp/_handlers/_descriptive.py +78 -0
- scitex/stats/_mcp/_handlers/_effect_size.py +106 -0
- scitex/stats/_mcp/_handlers/_format.py +94 -0
- scitex/stats/_mcp/_handlers/_normality.py +110 -0
- scitex/stats/_mcp/_handlers/_posthoc.py +224 -0
- scitex/stats/_mcp/_handlers/_power.py +247 -0
- scitex/stats/_mcp/_handlers/_recommend.py +102 -0
- scitex/stats/_mcp/_handlers/_run_test.py +279 -0
- scitex/stats/_mcp/_handlers/_stars.py +48 -0
- scitex/stats/_mcp/handlers.py +19 -1171
- scitex/stats/auto/_stat_style.py +175 -0
- scitex/stats/auto/_style_definitions.py +411 -0
- scitex/stats/auto/_styles.py +22 -620
- scitex/stats/descriptive/__init__.py +11 -8
- scitex/stats/descriptive/_ci.py +39 -0
- scitex/stats/power/_power.py +15 -4
- scitex/str/__init__.py +2 -1
- scitex/str/_title_case.py +63 -0
- scitex/template/README.md +1 -1
- scitex/template/__init__.py +25 -10
- scitex/template/_code_templates.py +147 -0
- scitex/template/_mcp/handlers.py +81 -0
- scitex/template/_mcp/tool_schemas.py +55 -0
- scitex/template/_templates/__init__.py +51 -0
- scitex/template/_templates/audio.py +233 -0
- scitex/template/_templates/canvas.py +312 -0
- scitex/template/_templates/capture.py +268 -0
- scitex/template/_templates/config.py +43 -0
- scitex/template/_templates/diagram.py +294 -0
- scitex/template/_templates/io.py +107 -0
- scitex/template/_templates/module.py +53 -0
- scitex/template/_templates/plt.py +202 -0
- scitex/template/_templates/scholar.py +267 -0
- scitex/template/_templates/session.py +130 -0
- scitex/template/_templates/session_minimal.py +43 -0
- scitex/template/_templates/session_plot.py +67 -0
- scitex/template/_templates/session_stats.py +77 -0
- scitex/template/_templates/stats.py +323 -0
- scitex/template/_templates/writer.py +296 -0
- scitex/template/clone_writer_directory.py +5 -5
- scitex/ui/_backends/_email.py +10 -2
- scitex/ui/_backends/_webhook.py +5 -1
- scitex/web/_search_pubmed.py +10 -6
- scitex/writer/README.md +1 -1
- scitex/writer/_mcp/handlers.py +11 -744
- scitex/writer/_mcp/tool_schemas.py +5 -335
- scitex-2.15.2.dist-info/METADATA +648 -0
- {scitex-2.14.0.dist-info → scitex-2.15.2.dist-info}/RECORD +246 -150
- scitex/canvas/editor/flask_editor/templates/_scripts.py +0 -4933
- scitex/canvas/editor/flask_editor/templates/_styles.py +0 -1658
- scitex/dev/plt/data/mpl/PLOTTING_FUNCTIONS.yaml +0 -90
- scitex/dev/plt/data/mpl/PLOTTING_SIGNATURES.yaml +0 -1571
- scitex/dev/plt/data/mpl/PLOTTING_SIGNATURES_DETAILED.yaml +0 -6262
- scitex/dev/plt/data/mpl/SIGNATURES_FLATTENED.yaml +0 -1274
- scitex/dev/plt/data/mpl/dir_ax.txt +0 -459
- scitex/diagram/_compile.py +0 -312
- scitex/diagram/_diagram.py +0 -355
- scitex/diagram/_mcp/__init__.py +0 -4
- scitex/diagram/_mcp/handlers.py +0 -400
- scitex/diagram/_mcp/tool_schemas.py +0 -157
- scitex/diagram/_presets.py +0 -173
- scitex/diagram/_schema.py +0 -182
- scitex/diagram/_split.py +0 -278
- scitex/gen/_ci.py +0 -12
- scitex/gen/_title_case.py +0 -89
- scitex/plt/_mcp/__init__.py +0 -4
- scitex/plt/_mcp/_handlers_annotation.py +0 -102
- scitex/plt/_mcp/_handlers_figure.py +0 -195
- scitex/plt/_mcp/_handlers_plot.py +0 -252
- scitex/plt/_mcp/_handlers_style.py +0 -219
- scitex/plt/_mcp/handlers.py +0 -74
- scitex/plt/_mcp/tool_schemas.py +0 -497
- scitex/plt/mcp_server.py +0 -231
- scitex/scholar/data/.gitkeep +0 -0
- scitex/scholar/data/README.md +0 -44
- scitex/scholar/data/bib_files/bibliography.bib +0 -1952
- scitex/scholar/data/bib_files/neurovista.bib +0 -277
- scitex/scholar/data/bib_files/neurovista_enriched.bib +0 -441
- scitex/scholar/data/bib_files/neurovista_enriched_enriched.bib +0 -441
- scitex/scholar/data/bib_files/neurovista_processed.bib +0 -338
- scitex/scholar/data/bib_files/openaccess.bib +0 -89
- scitex/scholar/data/bib_files/pac-seizure_prediction_enriched.bib +0 -2178
- scitex/scholar/data/bib_files/pac.bib +0 -698
- scitex/scholar/data/bib_files/pac_enriched.bib +0 -1061
- scitex/scholar/data/bib_files/pac_processed.bib +0 -0
- scitex/scholar/data/bib_files/pac_titles.txt +0 -75
- scitex/scholar/data/bib_files/paywalled.bib +0 -98
- scitex/scholar/data/bib_files/related-papers-by-coauthors.bib +0 -58
- scitex/scholar/data/bib_files/related-papers-by-coauthors_enriched.bib +0 -87
- scitex/scholar/data/bib_files/seizure_prediction.bib +0 -694
- scitex/scholar/data/bib_files/seizure_prediction_processed.bib +0 -0
- scitex/scholar/data/bib_files/test_complete_enriched.bib +0 -437
- scitex/scholar/data/bib_files/test_final_enriched.bib +0 -437
- scitex/scholar/data/bib_files/test_seizure.bib +0 -46
- scitex/scholar/data/impact_factor/JCR_IF_2022.xlsx +0 -0
- scitex/scholar/data/impact_factor/JCR_IF_2024.db +0 -0
- scitex/scholar/data/impact_factor/JCR_IF_2024.xlsx +0 -0
- scitex/scholar/data/impact_factor/JCR_IF_2024_v01.db +0 -0
- scitex/scholar/data/impact_factor.db +0 -0
- scitex/scholar/examples/SUGGESTIONS.md +0 -865
- scitex/scholar/examples/dev.py +0 -38
- scitex-2.14.0.dist-info/METADATA +0 -1238
- /scitex/{gen → context}/_detect_environment.py +0 -0
- /scitex/{gen → context}/_get_notebook_path.py +0 -0
- /scitex/{gen/_shell.py → sh/_shell_legacy.py} +0 -0
- {scitex-2.14.0.dist-info → scitex-2.15.2.dist-info}/WHEEL +0 -0
- {scitex-2.14.0.dist-info → scitex-2.15.2.dist-info}/entry_points.txt +0 -0
- {scitex-2.14.0.dist-info → scitex-2.15.2.dist-info}/licenses/LICENSE +0 -0
scitex/plt/_mcp/tool_schemas.py
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"description": "Top margin in millimeters (default: 20)",
|
|
61
|
-
},
|
|
62
|
-
"margin_bottom_mm": {
|
|
63
|
-
"type": "number",
|
|
64
|
-
"description": "Bottom margin in millimeters (default: 20)",
|
|
65
|
-
},
|
|
66
|
-
"dpi": {
|
|
67
|
-
"type": "integer",
|
|
68
|
-
"description": "Output resolution in DPI (default: 300)",
|
|
69
|
-
},
|
|
70
|
-
"axis_font_size_pt": {
|
|
71
|
-
"type": "number",
|
|
72
|
-
"description": "Axis label font size in points (default: 7)",
|
|
73
|
-
},
|
|
74
|
-
"tick_font_size_pt": {
|
|
75
|
-
"type": "number",
|
|
76
|
-
"description": "Tick label font size in points (default: 7)",
|
|
77
|
-
},
|
|
78
|
-
"title_font_size_pt": {
|
|
79
|
-
"type": "number",
|
|
80
|
-
"description": "Title font size in points (default: 8)",
|
|
81
|
-
},
|
|
82
|
-
"legend_font_size_pt": {
|
|
83
|
-
"type": "number",
|
|
84
|
-
"description": "Legend font size in points (default: 6)",
|
|
85
|
-
},
|
|
86
|
-
"trace_thickness_mm": {
|
|
87
|
-
"type": "number",
|
|
88
|
-
"description": "Line trace thickness in mm (default: 0.2)",
|
|
89
|
-
},
|
|
90
|
-
"reset": {
|
|
91
|
-
"type": "boolean",
|
|
92
|
-
"description": "If true, reset style to defaults before applying",
|
|
93
|
-
},
|
|
94
|
-
},
|
|
95
|
-
"required": [],
|
|
96
|
-
},
|
|
97
|
-
),
|
|
98
|
-
# List presets
|
|
99
|
-
types.Tool(
|
|
100
|
-
name="list_presets",
|
|
101
|
-
description="List available publication style presets (e.g., Nature, Science journal styles)",
|
|
102
|
-
inputSchema={
|
|
103
|
-
"type": "object",
|
|
104
|
-
"properties": {},
|
|
105
|
-
"required": [],
|
|
106
|
-
},
|
|
107
|
-
),
|
|
108
|
-
# Crop figure
|
|
109
|
-
types.Tool(
|
|
110
|
-
name="crop_figure",
|
|
111
|
-
description="Auto-crop whitespace from a saved figure image",
|
|
112
|
-
inputSchema={
|
|
113
|
-
"type": "object",
|
|
114
|
-
"properties": {
|
|
115
|
-
"input_path": {
|
|
116
|
-
"type": "string",
|
|
117
|
-
"description": "Path to the input figure image",
|
|
118
|
-
},
|
|
119
|
-
"output_path": {
|
|
120
|
-
"type": "string",
|
|
121
|
-
"description": "Output path (optional, adds '_cropped' suffix if not provided)",
|
|
122
|
-
},
|
|
123
|
-
"margin": {
|
|
124
|
-
"type": "integer",
|
|
125
|
-
"description": "Margin in pixels around content (default: 12, ~1mm at 300 DPI)",
|
|
126
|
-
"default": 12,
|
|
127
|
-
},
|
|
128
|
-
"overwrite": {
|
|
129
|
-
"type": "boolean",
|
|
130
|
-
"description": "Overwrite input file (default: false)",
|
|
131
|
-
"default": False,
|
|
132
|
-
},
|
|
133
|
-
},
|
|
134
|
-
"required": ["input_path"],
|
|
135
|
-
},
|
|
136
|
-
),
|
|
137
|
-
# Get DPI settings
|
|
138
|
-
types.Tool(
|
|
139
|
-
name="get_dpi_settings",
|
|
140
|
-
description="Get DPI settings for different output contexts (save, display, preview)",
|
|
141
|
-
inputSchema={
|
|
142
|
-
"type": "object",
|
|
143
|
-
"properties": {},
|
|
144
|
-
"required": [],
|
|
145
|
-
},
|
|
146
|
-
),
|
|
147
|
-
# Get color palette
|
|
148
|
-
types.Tool(
|
|
149
|
-
name="get_color_palette",
|
|
150
|
-
description="Get the SciTeX color palette for consistent figure colors",
|
|
151
|
-
inputSchema={
|
|
152
|
-
"type": "object",
|
|
153
|
-
"properties": {
|
|
154
|
-
"format": {
|
|
155
|
-
"type": "string",
|
|
156
|
-
"description": "Color format to return",
|
|
157
|
-
"enum": ["hex", "rgb", "rgba"],
|
|
158
|
-
"default": "hex",
|
|
159
|
-
},
|
|
160
|
-
},
|
|
161
|
-
"required": [],
|
|
162
|
-
},
|
|
163
|
-
),
|
|
164
|
-
# =================================================================
|
|
165
|
-
# PLOTTING TOOLS - Create publication figures via MCP
|
|
166
|
-
# =================================================================
|
|
167
|
-
# Create multi-panel figure
|
|
168
|
-
types.Tool(
|
|
169
|
-
name="create_figure",
|
|
170
|
-
description="Create a multi-panel figure canvas with SciTeX style. Returns figure_id for subsequent plotting.",
|
|
171
|
-
inputSchema={
|
|
172
|
-
"type": "object",
|
|
173
|
-
"properties": {
|
|
174
|
-
"nrows": {
|
|
175
|
-
"type": "integer",
|
|
176
|
-
"description": "Number of rows (default: 1)",
|
|
177
|
-
"default": 1,
|
|
178
|
-
},
|
|
179
|
-
"ncols": {
|
|
180
|
-
"type": "integer",
|
|
181
|
-
"description": "Number of columns (default: 1)",
|
|
182
|
-
"default": 1,
|
|
183
|
-
},
|
|
184
|
-
"axes_width_mm": {
|
|
185
|
-
"type": "number",
|
|
186
|
-
"description": "Width of each axes in mm (default: 40)",
|
|
187
|
-
"default": 40,
|
|
188
|
-
},
|
|
189
|
-
"axes_height_mm": {
|
|
190
|
-
"type": "number",
|
|
191
|
-
"description": "Height of each axes in mm (default: 28)",
|
|
192
|
-
"default": 28,
|
|
193
|
-
},
|
|
194
|
-
"space_w_mm": {
|
|
195
|
-
"type": "number",
|
|
196
|
-
"description": "Horizontal spacing between panels in mm (default: 8 from style)",
|
|
197
|
-
},
|
|
198
|
-
"space_h_mm": {
|
|
199
|
-
"type": "number",
|
|
200
|
-
"description": "Vertical spacing between panels in mm (default: 10 from style)",
|
|
201
|
-
},
|
|
202
|
-
},
|
|
203
|
-
"required": [],
|
|
204
|
-
},
|
|
205
|
-
),
|
|
206
|
-
# Bar plot
|
|
207
|
-
types.Tool(
|
|
208
|
-
name="plot_bar",
|
|
209
|
-
description="Create a bar plot on specified panel",
|
|
210
|
-
inputSchema={
|
|
211
|
-
"type": "object",
|
|
212
|
-
"properties": {
|
|
213
|
-
"figure_id": {
|
|
214
|
-
"type": "string",
|
|
215
|
-
"description": "Figure ID from create_figure (uses current if not specified)",
|
|
216
|
-
},
|
|
217
|
-
"panel": {
|
|
218
|
-
"type": "string",
|
|
219
|
-
"description": "Panel index as 'row,col' e.g. '0,0' or panel label e.g. 'A' (default: '0,0')",
|
|
220
|
-
"default": "0,0",
|
|
221
|
-
},
|
|
222
|
-
"x": {
|
|
223
|
-
"type": "array",
|
|
224
|
-
"items": {"type": "string"},
|
|
225
|
-
"description": "X-axis labels/categories",
|
|
226
|
-
},
|
|
227
|
-
"y": {
|
|
228
|
-
"type": "array",
|
|
229
|
-
"items": {"type": "number"},
|
|
230
|
-
"description": "Y-axis values (heights)",
|
|
231
|
-
},
|
|
232
|
-
"yerr": {
|
|
233
|
-
"type": "array",
|
|
234
|
-
"items": {"type": "number"},
|
|
235
|
-
"description": "Error bar values (optional)",
|
|
236
|
-
},
|
|
237
|
-
"colors": {
|
|
238
|
-
"type": "array",
|
|
239
|
-
"items": {"type": "string"},
|
|
240
|
-
"description": "Bar colors (optional, uses palette)",
|
|
241
|
-
},
|
|
242
|
-
"xlabel": {"type": "string", "description": "X-axis label"},
|
|
243
|
-
"ylabel": {"type": "string", "description": "Y-axis label"},
|
|
244
|
-
"title": {"type": "string", "description": "Panel title"},
|
|
245
|
-
},
|
|
246
|
-
"required": ["x", "y"],
|
|
247
|
-
},
|
|
248
|
-
),
|
|
249
|
-
# Scatter plot
|
|
250
|
-
types.Tool(
|
|
251
|
-
name="plot_scatter",
|
|
252
|
-
description="Create a scatter plot on specified panel",
|
|
253
|
-
inputSchema={
|
|
254
|
-
"type": "object",
|
|
255
|
-
"properties": {
|
|
256
|
-
"figure_id": {"type": "string", "description": "Figure ID"},
|
|
257
|
-
"panel": {"type": "string", "default": "0,0"},
|
|
258
|
-
"x": {
|
|
259
|
-
"type": "array",
|
|
260
|
-
"items": {"type": "number"},
|
|
261
|
-
"description": "X values",
|
|
262
|
-
},
|
|
263
|
-
"y": {
|
|
264
|
-
"type": "array",
|
|
265
|
-
"items": {"type": "number"},
|
|
266
|
-
"description": "Y values",
|
|
267
|
-
},
|
|
268
|
-
"color": {"type": "string", "description": "Point color"},
|
|
269
|
-
"size": {"type": "number", "description": "Point size in mm"},
|
|
270
|
-
"alpha": {"type": "number", "description": "Transparency (0-1)"},
|
|
271
|
-
"add_regression": {
|
|
272
|
-
"type": "boolean",
|
|
273
|
-
"description": "Add regression line",
|
|
274
|
-
"default": False,
|
|
275
|
-
},
|
|
276
|
-
"xlabel": {"type": "string"},
|
|
277
|
-
"ylabel": {"type": "string"},
|
|
278
|
-
"title": {"type": "string"},
|
|
279
|
-
},
|
|
280
|
-
"required": ["x", "y"],
|
|
281
|
-
},
|
|
282
|
-
),
|
|
283
|
-
# Line plot
|
|
284
|
-
types.Tool(
|
|
285
|
-
name="plot_line",
|
|
286
|
-
description="Create a line plot on specified panel",
|
|
287
|
-
inputSchema={
|
|
288
|
-
"type": "object",
|
|
289
|
-
"properties": {
|
|
290
|
-
"figure_id": {"type": "string"},
|
|
291
|
-
"panel": {"type": "string", "default": "0,0"},
|
|
292
|
-
"x": {
|
|
293
|
-
"type": "array",
|
|
294
|
-
"items": {"type": "number"},
|
|
295
|
-
"description": "X values",
|
|
296
|
-
},
|
|
297
|
-
"y": {
|
|
298
|
-
"type": "array",
|
|
299
|
-
"items": {"type": "number"},
|
|
300
|
-
"description": "Y values",
|
|
301
|
-
},
|
|
302
|
-
"yerr": {
|
|
303
|
-
"type": "array",
|
|
304
|
-
"items": {"type": "number"},
|
|
305
|
-
"description": "Y error values for shaded region",
|
|
306
|
-
},
|
|
307
|
-
"color": {"type": "string"},
|
|
308
|
-
"label": {"type": "string", "description": "Legend label"},
|
|
309
|
-
"linestyle": {
|
|
310
|
-
"type": "string",
|
|
311
|
-
"enum": ["-", "--", ":", "-."],
|
|
312
|
-
"default": "-",
|
|
313
|
-
},
|
|
314
|
-
"xlabel": {"type": "string"},
|
|
315
|
-
"ylabel": {"type": "string"},
|
|
316
|
-
"title": {"type": "string"},
|
|
317
|
-
},
|
|
318
|
-
"required": ["x", "y"],
|
|
319
|
-
},
|
|
320
|
-
),
|
|
321
|
-
# Box plot
|
|
322
|
-
types.Tool(
|
|
323
|
-
name="plot_box",
|
|
324
|
-
description="Create a box plot on specified panel",
|
|
325
|
-
inputSchema={
|
|
326
|
-
"type": "object",
|
|
327
|
-
"properties": {
|
|
328
|
-
"figure_id": {"type": "string"},
|
|
329
|
-
"panel": {"type": "string", "default": "0,0"},
|
|
330
|
-
"data": {
|
|
331
|
-
"type": "array",
|
|
332
|
-
"items": {"type": "array", "items": {"type": "number"}},
|
|
333
|
-
"description": "List of data arrays, one per group",
|
|
334
|
-
},
|
|
335
|
-
"labels": {
|
|
336
|
-
"type": "array",
|
|
337
|
-
"items": {"type": "string"},
|
|
338
|
-
"description": "Group labels",
|
|
339
|
-
},
|
|
340
|
-
"colors": {
|
|
341
|
-
"type": "array",
|
|
342
|
-
"items": {"type": "string"},
|
|
343
|
-
"description": "Box colors",
|
|
344
|
-
},
|
|
345
|
-
"xlabel": {"type": "string"},
|
|
346
|
-
"ylabel": {"type": "string"},
|
|
347
|
-
"title": {"type": "string"},
|
|
348
|
-
},
|
|
349
|
-
"required": ["data"],
|
|
350
|
-
},
|
|
351
|
-
),
|
|
352
|
-
# Violin plot
|
|
353
|
-
types.Tool(
|
|
354
|
-
name="plot_violin",
|
|
355
|
-
description="Create a violin plot on specified panel",
|
|
356
|
-
inputSchema={
|
|
357
|
-
"type": "object",
|
|
358
|
-
"properties": {
|
|
359
|
-
"figure_id": {"type": "string"},
|
|
360
|
-
"panel": {"type": "string", "default": "0,0"},
|
|
361
|
-
"data": {
|
|
362
|
-
"type": "array",
|
|
363
|
-
"items": {"type": "array", "items": {"type": "number"}},
|
|
364
|
-
"description": "List of data arrays, one per group",
|
|
365
|
-
},
|
|
366
|
-
"labels": {
|
|
367
|
-
"type": "array",
|
|
368
|
-
"items": {"type": "string"},
|
|
369
|
-
},
|
|
370
|
-
"colors": {
|
|
371
|
-
"type": "array",
|
|
372
|
-
"items": {"type": "string"},
|
|
373
|
-
},
|
|
374
|
-
"xlabel": {"type": "string"},
|
|
375
|
-
"ylabel": {"type": "string"},
|
|
376
|
-
"title": {"type": "string"},
|
|
377
|
-
},
|
|
378
|
-
"required": ["data"],
|
|
379
|
-
},
|
|
380
|
-
),
|
|
381
|
-
# Add significance bracket
|
|
382
|
-
types.Tool(
|
|
383
|
-
name="add_significance",
|
|
384
|
-
description="Add significance bracket between two groups",
|
|
385
|
-
inputSchema={
|
|
386
|
-
"type": "object",
|
|
387
|
-
"properties": {
|
|
388
|
-
"figure_id": {"type": "string"},
|
|
389
|
-
"panel": {"type": "string", "default": "0,0"},
|
|
390
|
-
"x1": {
|
|
391
|
-
"type": "number",
|
|
392
|
-
"description": "X position of first group (0-indexed)",
|
|
393
|
-
},
|
|
394
|
-
"x2": {
|
|
395
|
-
"type": "number",
|
|
396
|
-
"description": "X position of second group",
|
|
397
|
-
},
|
|
398
|
-
"y": {
|
|
399
|
-
"type": "number",
|
|
400
|
-
"description": "Y position of bracket base",
|
|
401
|
-
},
|
|
402
|
-
"text": {
|
|
403
|
-
"type": "string",
|
|
404
|
-
"description": "Significance text: '*', '**', '***', 'n.s.', or p-value",
|
|
405
|
-
},
|
|
406
|
-
"height": {
|
|
407
|
-
"type": "number",
|
|
408
|
-
"description": "Bracket height (auto if not specified)",
|
|
409
|
-
},
|
|
410
|
-
},
|
|
411
|
-
"required": ["x1", "x2", "y", "text"],
|
|
412
|
-
},
|
|
413
|
-
),
|
|
414
|
-
# Add panel label
|
|
415
|
-
types.Tool(
|
|
416
|
-
name="add_panel_label",
|
|
417
|
-
description="Add panel label (A, B, C, etc.) to a panel",
|
|
418
|
-
inputSchema={
|
|
419
|
-
"type": "object",
|
|
420
|
-
"properties": {
|
|
421
|
-
"figure_id": {"type": "string"},
|
|
422
|
-
"panel": {"type": "string", "default": "0,0"},
|
|
423
|
-
"label": {
|
|
424
|
-
"type": "string",
|
|
425
|
-
"description": "Label text (e.g., 'A', 'B')",
|
|
426
|
-
},
|
|
427
|
-
"x": {
|
|
428
|
-
"type": "number",
|
|
429
|
-
"description": "X position in axes coordinates (default: -0.15)",
|
|
430
|
-
"default": -0.15,
|
|
431
|
-
},
|
|
432
|
-
"y": {
|
|
433
|
-
"type": "number",
|
|
434
|
-
"description": "Y position in axes coordinates (default: 1.1)",
|
|
435
|
-
"default": 1.1,
|
|
436
|
-
},
|
|
437
|
-
"fontsize": {
|
|
438
|
-
"type": "number",
|
|
439
|
-
"description": "Font size in points (default: 10)",
|
|
440
|
-
"default": 10,
|
|
441
|
-
},
|
|
442
|
-
"fontweight": {
|
|
443
|
-
"type": "string",
|
|
444
|
-
"enum": ["normal", "bold"],
|
|
445
|
-
"default": "bold",
|
|
446
|
-
},
|
|
447
|
-
},
|
|
448
|
-
"required": ["label"],
|
|
449
|
-
},
|
|
450
|
-
),
|
|
451
|
-
# Save figure
|
|
452
|
-
types.Tool(
|
|
453
|
-
name="save_figure",
|
|
454
|
-
description="Save the current figure to file",
|
|
455
|
-
inputSchema={
|
|
456
|
-
"type": "object",
|
|
457
|
-
"properties": {
|
|
458
|
-
"figure_id": {"type": "string"},
|
|
459
|
-
"output_path": {
|
|
460
|
-
"type": "string",
|
|
461
|
-
"description": "Output file path (supports .png, .pdf, .svg)",
|
|
462
|
-
},
|
|
463
|
-
"dpi": {
|
|
464
|
-
"type": "integer",
|
|
465
|
-
"description": "Resolution (default: 300)",
|
|
466
|
-
"default": 300,
|
|
467
|
-
},
|
|
468
|
-
"crop": {
|
|
469
|
-
"type": "boolean",
|
|
470
|
-
"description": "Auto-crop whitespace (default: true)",
|
|
471
|
-
"default": True,
|
|
472
|
-
},
|
|
473
|
-
},
|
|
474
|
-
"required": ["output_path"],
|
|
475
|
-
},
|
|
476
|
-
),
|
|
477
|
-
# Close figure
|
|
478
|
-
types.Tool(
|
|
479
|
-
name="close_figure",
|
|
480
|
-
description="Close a figure and free memory",
|
|
481
|
-
inputSchema={
|
|
482
|
-
"type": "object",
|
|
483
|
-
"properties": {
|
|
484
|
-
"figure_id": {
|
|
485
|
-
"type": "string",
|
|
486
|
-
"description": "Figure ID to close (closes current if not specified)",
|
|
487
|
-
},
|
|
488
|
-
},
|
|
489
|
-
"required": [],
|
|
490
|
-
},
|
|
491
|
-
),
|
|
492
|
-
]
|
|
493
|
-
|
|
494
|
-
|
|
495
|
-
__all__ = ["get_tool_schemas"]
|
|
496
|
-
|
|
497
|
-
# EOF
|