scitex 2.11.0__py3-none-any.whl → 2.13.0__py3-none-any.whl

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Files changed (148) hide show
  1. scitex/__main__.py +24 -5
  2. scitex/__version__.py +1 -1
  3. scitex/_optional_deps.py +33 -0
  4. scitex/ai/classification/reporters/_ClassificationReporter.py +1 -1
  5. scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +2 -2
  6. scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +2 -2
  7. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +2 -2
  8. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +2 -2
  9. scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +2 -2
  10. scitex/ai/classification/timeseries/_normalize_timestamp.py +1 -1
  11. scitex/ai/metrics/_calc_seizure_prediction_metrics.py +1 -1
  12. scitex/ai/plt/_plot_feature_importance.py +1 -1
  13. scitex/ai/plt/_plot_learning_curve.py +1 -1
  14. scitex/ai/plt/_plot_optuna_study.py +1 -1
  15. scitex/ai/plt/_plot_pre_rec_curve.py +1 -1
  16. scitex/ai/plt/_plot_roc_curve.py +1 -1
  17. scitex/ai/plt/_stx_conf_mat.py +1 -1
  18. scitex/ai/training/_LearningCurveLogger.py +1 -1
  19. scitex/audio/mcp_server.py +38 -8
  20. scitex/browser/automation/CookieHandler.py +1 -1
  21. scitex/browser/core/BrowserMixin.py +1 -1
  22. scitex/browser/core/ChromeProfileManager.py +1 -1
  23. scitex/browser/debugging/_browser_logger.py +1 -1
  24. scitex/browser/debugging/_highlight_element.py +1 -1
  25. scitex/browser/debugging/_show_grid.py +1 -1
  26. scitex/browser/interaction/click_center.py +1 -1
  27. scitex/browser/interaction/click_with_fallbacks.py +1 -1
  28. scitex/browser/interaction/close_popups.py +1 -1
  29. scitex/browser/interaction/fill_with_fallbacks.py +1 -1
  30. scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +1 -1
  31. scitex/browser/pdf/detect_chrome_pdf_viewer.py +1 -1
  32. scitex/browser/stealth/HumanBehavior.py +1 -1
  33. scitex/browser/stealth/StealthManager.py +1 -1
  34. scitex/canvas/_mcp_handlers.py +372 -0
  35. scitex/canvas/_mcp_tool_schemas.py +219 -0
  36. scitex/canvas/mcp_server.py +151 -0
  37. scitex/capture/mcp_server.py +41 -12
  38. scitex/cli/audio.py +233 -0
  39. scitex/cli/capture.py +307 -0
  40. scitex/cli/main.py +27 -4
  41. scitex/cli/repro.py +233 -0
  42. scitex/cli/resource.py +240 -0
  43. scitex/cli/stats.py +325 -0
  44. scitex/cli/template.py +236 -0
  45. scitex/cli/tex.py +286 -0
  46. scitex/cli/web.py +11 -12
  47. scitex/dev/__init__.py +3 -0
  48. scitex/dev/_pyproject.py +405 -0
  49. scitex/dev/plt/__init__.py +2 -2
  50. scitex/dev/plt/mpl/get_dir_ax.py +1 -1
  51. scitex/dev/plt/mpl/get_signatures.py +1 -1
  52. scitex/dev/plt/mpl/get_signatures_details.py +1 -1
  53. scitex/diagram/_mcp_handlers.py +400 -0
  54. scitex/diagram/_mcp_tool_schemas.py +157 -0
  55. scitex/diagram/mcp_server.py +151 -0
  56. scitex/dsp/_demo_sig.py +51 -5
  57. scitex/dsp/_mne.py +13 -2
  58. scitex/dsp/_modulation_index.py +15 -3
  59. scitex/dsp/_pac.py +23 -5
  60. scitex/dsp/_psd.py +16 -4
  61. scitex/dsp/_resample.py +24 -4
  62. scitex/dsp/_transform.py +16 -3
  63. scitex/dsp/add_noise.py +15 -1
  64. scitex/dsp/norm.py +17 -2
  65. scitex/dsp/reference.py +17 -1
  66. scitex/dsp/utils/_differential_bandpass_filters.py +20 -2
  67. scitex/dsp/utils/_zero_pad.py +18 -4
  68. scitex/dt/_normalize_timestamp.py +1 -1
  69. scitex/git/_session.py +1 -1
  70. scitex/io/_load_modules/_con.py +12 -1
  71. scitex/io/_load_modules/_eeg.py +12 -1
  72. scitex/io/_load_modules/_optuna.py +21 -63
  73. scitex/io/_load_modules/_torch.py +11 -3
  74. scitex/io/_save_modules/_optuna_study_as_csv_and_pngs.py +13 -2
  75. scitex/io/_save_modules/_torch.py +11 -3
  76. scitex/mcp_server.py +159 -0
  77. scitex/plt/_mcp_handlers.py +361 -0
  78. scitex/plt/_mcp_tool_schemas.py +169 -0
  79. scitex/plt/mcp_server.py +205 -0
  80. scitex/repro/README_RandomStateManager.md +3 -3
  81. scitex/repro/_RandomStateManager.py +14 -14
  82. scitex/repro/_gen_ID.py +1 -1
  83. scitex/repro/_gen_timestamp.py +1 -1
  84. scitex/repro/_hash_array.py +4 -4
  85. scitex/scholar/__main__.py +24 -2
  86. scitex/scholar/_mcp_handlers.py +685 -0
  87. scitex/scholar/_mcp_tool_schemas.py +339 -0
  88. scitex/scholar/docs/template.py +1 -1
  89. scitex/scholar/examples/07_storage_integration.py +1 -1
  90. scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py +1 -1
  91. scitex/scholar/impact_factor/jcr/build_database.py +1 -1
  92. scitex/scholar/mcp_server.py +315 -0
  93. scitex/scholar/pdf_download/ScholarPDFDownloader.py +1 -1
  94. scitex/scholar/pipelines/ScholarPipelineBibTeX.py +1 -1
  95. scitex/scholar/pipelines/ScholarPipelineParallel.py +1 -1
  96. scitex/scholar/pipelines/ScholarPipelineSingle.py +1 -1
  97. scitex/scholar/storage/PaperIO.py +1 -1
  98. scitex/session/README.md +4 -4
  99. scitex/session/__init__.py +1 -1
  100. scitex/session/_decorator.py +9 -9
  101. scitex/session/_lifecycle.py +5 -5
  102. scitex/session/template.py +1 -1
  103. scitex/stats/__main__.py +281 -0
  104. scitex/stats/_mcp_handlers.py +1191 -0
  105. scitex/stats/_mcp_tool_schemas.py +384 -0
  106. scitex/stats/correct/_correct_bonferroni.py +1 -1
  107. scitex/stats/correct/_correct_fdr.py +1 -1
  108. scitex/stats/correct/_correct_fdr_.py +1 -1
  109. scitex/stats/correct/_correct_holm.py +1 -1
  110. scitex/stats/correct/_correct_sidak.py +1 -1
  111. scitex/stats/effect_sizes/_cliffs_delta.py +1 -1
  112. scitex/stats/effect_sizes/_cohens_d.py +1 -1
  113. scitex/stats/effect_sizes/_epsilon_squared.py +1 -1
  114. scitex/stats/effect_sizes/_eta_squared.py +1 -1
  115. scitex/stats/effect_sizes/_prob_superiority.py +1 -1
  116. scitex/stats/mcp_server.py +405 -0
  117. scitex/stats/posthoc/_dunnett.py +1 -1
  118. scitex/stats/posthoc/_games_howell.py +1 -1
  119. scitex/stats/posthoc/_tukey_hsd.py +1 -1
  120. scitex/stats/power/_power.py +1 -1
  121. scitex/stats/utils/_effect_size.py +1 -1
  122. scitex/stats/utils/_formatters.py +1 -1
  123. scitex/stats/utils/_power.py +1 -1
  124. scitex/template/_mcp_handlers.py +259 -0
  125. scitex/template/_mcp_tool_schemas.py +112 -0
  126. scitex/template/mcp_server.py +186 -0
  127. scitex/utils/_verify_scitex_format.py +2 -2
  128. scitex/utils/template.py +1 -1
  129. scitex/web/__init__.py +12 -11
  130. scitex/web/_scraping.py +26 -265
  131. scitex/web/download_images.py +316 -0
  132. scitex/writer/Writer.py +1 -1
  133. scitex/writer/_clone_writer_project.py +1 -1
  134. scitex/writer/_validate_tree_structures.py +1 -1
  135. scitex/writer/dataclasses/config/_WriterConfig.py +1 -1
  136. scitex/writer/dataclasses/contents/_ManuscriptContents.py +1 -1
  137. scitex/writer/dataclasses/core/_Document.py +1 -1
  138. scitex/writer/dataclasses/core/_DocumentSection.py +1 -1
  139. scitex/writer/dataclasses/results/_CompilationResult.py +1 -1
  140. scitex/writer/dataclasses/results/_LaTeXIssue.py +1 -1
  141. scitex/writer/utils/.legacy_git_retry.py +7 -5
  142. scitex/writer/utils/_parse_latex_logs.py +1 -1
  143. {scitex-2.11.0.dist-info → scitex-2.13.0.dist-info}/METADATA +431 -269
  144. {scitex-2.11.0.dist-info → scitex-2.13.0.dist-info}/RECORD +147 -118
  145. scitex-2.13.0.dist-info/entry_points.txt +11 -0
  146. scitex-2.11.0.dist-info/entry_points.txt +0 -2
  147. {scitex-2.11.0.dist-info → scitex-2.13.0.dist-info}/WHEEL +0 -0
  148. {scitex-2.11.0.dist-info → scitex-2.13.0.dist-info}/licenses/LICENSE +0 -0
scitex/writer/Writer.py CHANGED
@@ -363,7 +363,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/_clone_writer_project.py CHANGED
@@ -72,7 +72,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/_validate_tree_structures.py CHANGED
@@ -147,7 +147,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/dataclasses/config/_WriterConfig.py CHANGED
@@ -104,7 +104,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/dataclasses/contents/_ManuscriptContents.py CHANGED
@@ -148,7 +148,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/dataclasses/core/_Document.py CHANGED
@@ -80,7 +80,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/dataclasses/core/_DocumentSection.py CHANGED
@@ -462,7 +462,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/dataclasses/results/_CompilationResult.py CHANGED
@@ -80,7 +80,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/dataclasses/results/_LaTeXIssue.py CHANGED
@@ -38,7 +38,7 @@ def run_session() -> None:
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,
scitex/writer/utils/.legacy_git_retry.py CHANGED
@@ -1,9 +1,9 @@
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  #!/usr/bin/env python3
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- # -*- coding: utf-8 -*-
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  # Timestamp: "2025-10-28 17:10:52 (ywatanabe)"
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  # File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/git_utils.py
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  # ----------------------------------------
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  from __future__ import annotations
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+
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  import os
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  __FILE__ = "./src/scitex/writer/git_utils.py"
@@ -16,10 +16,10 @@ Git utilities for Writer.
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  """
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- import time
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  import subprocess
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- from typing import Callable
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- from typing import TypeVar
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+ import time
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+ from typing import Callable, TypeVar
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+
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  from scitex.logging import getLogger
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@@ -99,12 +99,14 @@ def run_session() -> None:
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  """Initialize scitex framework, run main function, and cleanup."""
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  global CONFIG, CC, sys, plt, rng
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  import sys
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+
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  import matplotlib.pyplot as plt
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+
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  import scitex as stx
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  args = parse_args()
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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scitex/writer/utils/_parse_latex_logs.py CHANGED
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- CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
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+ CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
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  sys,
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  plt,
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  args=args,