From 120a9b862c15adc4d0c60d45e3e589c6d0e0d7e7 Mon Sep 17 00:00:00 2001
From: Yusuke Watanabe <ywatanabe@scitex.ai>
Date: Sun, 15 Mar 2026 10:03:31 +1100
Subject: [PATCH 1/5] docs: auto-generate RST stubs for all 66 public modules

Previously only 20 modules had manual RST stubs. Updated
generate_api_docs.py to auto-discover all public modules from
the package directory and generate missing stubs.

47 new module stubs created covering: app, audio, audit, benchmark,
browser, canvas, capture, cli, cloud, container, cv, dataset, etc.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 docs/sphinx/generate_api_docs.py  | 267 ++++++++++++++++++++++++------
 docs/sphinx/modules/app.rst       |   7 +
 docs/sphinx/modules/audio.rst     |   7 +
 docs/sphinx/modules/audit.rst     |   7 +
 docs/sphinx/modules/benchmark.rst |   7 +
 docs/sphinx/modules/bridge.rst    |   7 +
 docs/sphinx/modules/browser.rst   |   7 +
 docs/sphinx/modules/canvas.rst    |   7 +
 docs/sphinx/modules/capture.rst   |   7 +
 docs/sphinx/modules/cli.rst       |   7 +
 docs/sphinx/modules/cloud.rst     |   7 +
 docs/sphinx/modules/compat.rst    |   7 +
 docs/sphinx/modules/container.rst |   7 +
 docs/sphinx/modules/context.rst   |   7 +
 docs/sphinx/modules/cv.rst        |   7 +
 docs/sphinx/modules/dataset.rst   |   7 +
 docs/sphinx/modules/datetime.rst  |   7 +
 docs/sphinx/modules/db.rst        |   7 +
 docs/sphinx/modules/dev.rst       |   7 +
 docs/sphinx/modules/dict.rst      |   7 +
 docs/sphinx/modules/etc.rst       |   7 +
 docs/sphinx/modules/events.rst    |   7 +
 docs/sphinx/modules/gists.rst     |   7 +
 docs/sphinx/modules/git.rst       |   7 +
 docs/sphinx/modules/index.rst     | 190 ++++++++-------------
 docs/sphinx/modules/linalg.rst    |   7 +
 docs/sphinx/modules/media.rst     |   7 +
 docs/sphinx/modules/module.rst    |   7 +
 docs/sphinx/modules/msword.rst    |   7 +
 docs/sphinx/modules/notebook.rst  |   7 +
 docs/sphinx/modules/notify.rst    |   7 +
 docs/sphinx/modules/os.rst        |   7 +
 docs/sphinx/modules/parallel.rst  |   7 +
 docs/sphinx/modules/path.rst      |   7 +
 docs/sphinx/modules/project.rst   |   7 +
 docs/sphinx/modules/resource.rst  |   7 +
 docs/sphinx/modules/rng.rst       |   7 +
 docs/sphinx/modules/schema.rst    |   7 +
 docs/sphinx/modules/security.rst  |   7 +
 docs/sphinx/modules/sh.rst        |   7 +
 docs/sphinx/modules/social.rst    |   7 +
 docs/sphinx/modules/str.rst       |   7 +
 docs/sphinx/modules/tex.rst       |   7 +
 docs/sphinx/modules/torch.rst     |   7 +
 docs/sphinx/modules/tunnel.rst    |   7 +
 docs/sphinx/modules/types.rst     |   7 +
 docs/sphinx/modules/ui.rst        |   7 +
 docs/sphinx/modules/utils.rst     |   7 +
 docs/sphinx/modules/web.rst       |   7 +
 49 files changed, 615 insertions(+), 171 deletions(-)
 mode change 100644 => 100755 docs/sphinx/generate_api_docs.py
 create mode 100644 docs/sphinx/modules/app.rst
 create mode 100644 docs/sphinx/modules/audio.rst
 create mode 100644 docs/sphinx/modules/audit.rst
 create mode 100644 docs/sphinx/modules/benchmark.rst
 create mode 100644 docs/sphinx/modules/bridge.rst
 create mode 100644 docs/sphinx/modules/browser.rst
 create mode 100644 docs/sphinx/modules/canvas.rst
 create mode 100644 docs/sphinx/modules/capture.rst
 create mode 100644 docs/sphinx/modules/cli.rst
 create mode 100644 docs/sphinx/modules/cloud.rst
 create mode 100644 docs/sphinx/modules/compat.rst
 create mode 100644 docs/sphinx/modules/container.rst
 create mode 100644 docs/sphinx/modules/context.rst
 create mode 100644 docs/sphinx/modules/cv.rst
 create mode 100644 docs/sphinx/modules/dataset.rst
 create mode 100644 docs/sphinx/modules/datetime.rst
 create mode 100644 docs/sphinx/modules/db.rst
 create mode 100644 docs/sphinx/modules/dev.rst
 create mode 100644 docs/sphinx/modules/dict.rst
 create mode 100644 docs/sphinx/modules/etc.rst
 create mode 100644 docs/sphinx/modules/events.rst
 create mode 100644 docs/sphinx/modules/gists.rst
 create mode 100644 docs/sphinx/modules/git.rst
 create mode 100644 docs/sphinx/modules/linalg.rst
 create mode 100644 docs/sphinx/modules/media.rst
 create mode 100644 docs/sphinx/modules/module.rst
 create mode 100644 docs/sphinx/modules/msword.rst
 create mode 100644 docs/sphinx/modules/notebook.rst
 create mode 100644 docs/sphinx/modules/notify.rst
 create mode 100644 docs/sphinx/modules/os.rst
 create mode 100644 docs/sphinx/modules/parallel.rst
 create mode 100644 docs/sphinx/modules/path.rst
 create mode 100644 docs/sphinx/modules/project.rst
 create mode 100644 docs/sphinx/modules/resource.rst
 create mode 100644 docs/sphinx/modules/rng.rst
 create mode 100644 docs/sphinx/modules/schema.rst
 create mode 100644 docs/sphinx/modules/security.rst
 create mode 100644 docs/sphinx/modules/sh.rst
 create mode 100644 docs/sphinx/modules/social.rst
 create mode 100644 docs/sphinx/modules/str.rst
 create mode 100644 docs/sphinx/modules/tex.rst
 create mode 100644 docs/sphinx/modules/torch.rst
 create mode 100644 docs/sphinx/modules/tunnel.rst
 create mode 100644 docs/sphinx/modules/types.rst
 create mode 100644 docs/sphinx/modules/ui.rst
 create mode 100644 docs/sphinx/modules/utils.rst
 create mode 100644 docs/sphinx/modules/web.rst

diff --git a/docs/sphinx/generate_api_docs.py b/docs/sphinx/generate_api_docs.py
old mode 100644
new mode 100755
index ed42de709..9f411f8ae
--- a/docs/sphinx/generate_api_docs.py
+++ b/docs/sphinx/generate_api_docs.py
@@ -1,69 +1,242 @@
 #!/usr/bin/env python3
-"""Generate API documentation files for SciTeX modules."""
+# noqa: STX-S001 — build utility, not a research script
+"""Generate API documentation stubs for all SciTeX public modules.
 
+Discovers modules automatically from the package directory.
+Generates both modules/*.rst stubs and updates modules/index.rst toctree.
+
+Usage:
+    python generate_api_docs.py           # Generate missing stubs only
+    python generate_api_docs.py --force   # Regenerate all stubs
+"""
+
+import sys
 from pathlib import Path
 
-# API documentation template
-API_TEMPLATE = """{module_name} API Reference
+# Template for module RST stub (minimal — Sphinx autodoc fills in the rest)
+MODULE_TEMPLATE = """{title}
 {underline}
 
-.. automodule:: {module_path}
+.. automodule:: scitex.{module_name}
    :members:
    :undoc-members:
    :show-inheritance:
-   :inherited-members:
+"""
 
-Submodules
-----------
+# Modules to skip (internal, private, or aliases)
+SKIP_MODULES = {
+    "_dev",
+    "_docs",
+    "_mcp_resources",
+    "_mcp_tools",
+    "__pycache__",
+    ".claude",
+    "fig",  # alias for plt
+    "ml",  # alias for ai
+    "dt",  # alias for datetime
+    "reproduce",  # alias for repro
+    "verify",  # alias for clew
+    "fts",  # internal bundle schemas
+    "errors",  # deprecated, use logging
+    "units",  # internal
+}
+
+# Module categories for the index (ordered)
+MODULE_CATEGORIES = {
+    "Core": [
+        "session",
+        "io",
+        "config",
+        "logging",
+        "repro",
+        "clew",
+    ],
+    "Science & Analysis": [
+        "stats",
+        "plt",
+        "dsp",
+        "diagram",
+        "canvas",
+    ],
+    "Literature & Writing": [
+        "scholar",
+        "writer",
+        "linter",
+        "notebook",
+    ],
+    "Machine Learning": [
+        "ai",
+        "nn",
+        "torch",
+        "cv",
+        "benchmark",
+    ],
+    "Data & I/O": [
+        "pd",
+        "db",
+        "dataset",
+        "schema",
+    ],
+    "Infrastructure": [
+        "app",
+        "cloud",
+        "container",
+        "tunnel",
+        "cli",
+        "browser",
+        "capture",
+        "audio",
+        "notify",
+        "social",
+    ],
+    "Utilities": [
+        "gen",
+        "template",
+        "decorators",
+        "introspect",
+        "str",
+        "dict",
+        "path",
+        "os",
+        "sh",
+        "git",
+        "parallel",
+        "linalg",
+        "datetime",
+        "types",
+        "rng",
+        "context",
+        "resource",
+        "utils",
+        "etc",
+        "web",
+        "msword",
+        "tex",
+        "bridge",
+        "compat",
+        "module",
+        "gists",
+        "media",
+        "security",
+        "ui",
+        "usage",
+        "dev",
+        "audit",
+    ],
+}
+
+
+def discover_modules(src_dir: Path) -> list[str]:
+    """Discover all public submodule directories."""
+    modules = []
+    for child in sorted(src_dir.iterdir()):
+        if not child.is_dir():
+            continue
+        name = child.name
+        if name.startswith("_") or name in SKIP_MODULES:
+            continue
+        if (child / "__init__.py").exists():
+            modules.append(name)
+    return modules
+
+
+def generate_stub(module_name: str, output_path: Path, force: bool = False):
+    """Generate a single RST stub file."""
+    if output_path.exists() and not force:
+        return False
+
+    title = f"{module_name} Module (``stx.{module_name}``)"
+    underline = "=" * len(title)
+
+    content = MODULE_TEMPLATE.format(
+        title=title,
+        underline=underline,
+        module_name=module_name,
+    )
 
-.. autosummary::
-   :toctree: generated
-   :recursive:
+    output_path.write_text(content)
+    return True
 
-   {module_path}
-"""
 
+def generate_index(modules_dir: Path, all_modules: list[str]):
+    """Generate modules/index.rst with all modules in categorized toctrees."""
+    # Collect categorized and uncategorized modules
+    categorized = set()
+    for mods in MODULE_CATEGORIES.values():
+        categorized.update(mods)
 
-def create_api_doc(module_name, module_path, output_file):
-    """Create an API documentation file for a module."""
-    title = f"scitex.{module_name}"
-    underline = "=" * len(title + " API Reference")
+    uncategorized = [m for m in all_modules if m not in categorized]
 
-    content = API_TEMPLATE.format(
-        module_name=title, module_path=module_path, underline=underline
-    )
+    # Build index content
+    lines = [
+        "Module Overview",
+        "===============",
+        "",
+        "SciTeX is organized into focused modules.",
+        "All modules are accessible via ``import scitex as stx`` followed by ``stx.<module>``.",
+        "",
+    ]
 
-    with open(output_file, "w") as f:
-        f.write(content)
-    print(f"Created: {output_file}")
+    for category, mods in MODULE_CATEGORIES.items():
+        # Only include modules that actually exist
+        existing = [m for m in mods if m in all_modules]
+        if not existing:
+            continue
 
+        lines.append(f".. toctree::")
+        lines.append(f"   :maxdepth: 2")
+        lines.append(f"   :caption: {category}")
+        lines.append(f"")
+        for m in existing:
+            lines.append(f"   {m}")
+        lines.append("")
 
-def main():
-    # Create API directory
-    api_dir = Path(__file__).parent / "api"
-    api_dir.mkdir(exist_ok=True)
-
-    # Define modules
-    modules = [
-        ("gen", "scitex.gen"),
-        ("io", "scitex.io"),
-        ("plt", "scitex.plt"),
-        ("dsp", "scitex.dsp"),
-        ("stats", "scitex.stats"),
-        ("pd", "scitex.pd"),
-        ("ai", "scitex.ai"),
-        ("nn", "scitex.nn"),
-        ("db", "scitex.db"),
-        ("decorators", "scitex.decorators"),
-        ("path", "scitex.path"),
-        ("str", "scitex.str"),
-        ("dict", "scitex.dict"),
-    ]
+    if uncategorized:
+        lines.append(".. toctree::")
+        lines.append("   :maxdepth: 2")
+        lines.append("   :caption: Other")
+        lines.append("")
+        for m in sorted(uncategorized):
+            lines.append(f"   {m}")
+        lines.append("")
 
-    # Create API documentation files
-    for module_name, module_path in modules:
-        output_file = api_dir / f"scitex.{module_name}.rst"
-        create_api_doc(module_name, module_path, output_file)
+    (modules_dir / "index.rst").write_text("\n".join(lines))
+
+
+def main():
+    force = "--force" in sys.argv
+
+    # Paths
+    script_dir = Path(__file__).parent
+    src_dir = script_dir.parent.parent / "src" / "scitex"
+    modules_dir = script_dir / "modules"
+    modules_dir.mkdir(exist_ok=True)
+
+    if not src_dir.exists():
+        print(f"Error: Source directory not found: {src_dir}")
+        sys.exit(1)
+
+    # Discover all public modules
+    all_modules = discover_modules(src_dir)
+    print(f"Discovered {len(all_modules)} public modules")
+
+    # Generate stubs
+    created = 0
+    skipped = 0
+    for module_name in all_modules:
+        output_path = modules_dir / f"{module_name}.rst"
+        if generate_stub(module_name, output_path, force=force):
+            created += 1
+            print(f"  Created: {module_name}.rst")
+        else:
+            skipped += 1
+
+    # Generate index
+    generate_index(modules_dir, all_modules)
+    print(f"  Updated: index.rst")
+
+    print(f"\nDone: {created} created, {skipped} existing (skipped)")
+    print(f"Total modules documented: {len(all_modules)}")
 
 
 if __name__ == "__main__":
diff --git a/docs/sphinx/modules/app.rst b/docs/sphinx/modules/app.rst
new file mode 100644
index 000000000..a8374c34d
--- /dev/null
+++ b/docs/sphinx/modules/app.rst
@@ -0,0 +1,7 @@
+app Module (``stx.app``)
+========================
+
+.. automodule:: scitex.app
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/audio.rst b/docs/sphinx/modules/audio.rst
new file mode 100644
index 000000000..ab835cbfe
--- /dev/null
+++ b/docs/sphinx/modules/audio.rst
@@ -0,0 +1,7 @@
+audio Module (``stx.audio``)
+============================
+
+.. automodule:: scitex.audio
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/audit.rst b/docs/sphinx/modules/audit.rst
new file mode 100644
index 000000000..e7f92881e
--- /dev/null
+++ b/docs/sphinx/modules/audit.rst
@@ -0,0 +1,7 @@
+audit Module (``stx.audit``)
+============================
+
+.. automodule:: scitex.audit
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/benchmark.rst b/docs/sphinx/modules/benchmark.rst
new file mode 100644
index 000000000..014b80120
--- /dev/null
+++ b/docs/sphinx/modules/benchmark.rst
@@ -0,0 +1,7 @@
+benchmark Module (``stx.benchmark``)
+====================================
+
+.. automodule:: scitex.benchmark
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/bridge.rst b/docs/sphinx/modules/bridge.rst
new file mode 100644
index 000000000..8028c570b
--- /dev/null
+++ b/docs/sphinx/modules/bridge.rst
@@ -0,0 +1,7 @@
+bridge Module (``stx.bridge``)
+==============================
+
+.. automodule:: scitex.bridge
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/browser.rst b/docs/sphinx/modules/browser.rst
new file mode 100644
index 000000000..c91604cc8
--- /dev/null
+++ b/docs/sphinx/modules/browser.rst
@@ -0,0 +1,7 @@
+browser Module (``stx.browser``)
+================================
+
+.. automodule:: scitex.browser
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/canvas.rst b/docs/sphinx/modules/canvas.rst
new file mode 100644
index 000000000..210c63590
--- /dev/null
+++ b/docs/sphinx/modules/canvas.rst
@@ -0,0 +1,7 @@
+canvas Module (``stx.canvas``)
+==============================
+
+.. automodule:: scitex.canvas
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/capture.rst b/docs/sphinx/modules/capture.rst
new file mode 100644
index 000000000..7e0855faf
--- /dev/null
+++ b/docs/sphinx/modules/capture.rst
@@ -0,0 +1,7 @@
+capture Module (``stx.capture``)
+================================
+
+.. automodule:: scitex.capture
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/cli.rst b/docs/sphinx/modules/cli.rst
new file mode 100644
index 000000000..c6054e8fd
--- /dev/null
+++ b/docs/sphinx/modules/cli.rst
@@ -0,0 +1,7 @@
+cli Module (``stx.cli``)
+========================
+
+.. automodule:: scitex.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/cloud.rst b/docs/sphinx/modules/cloud.rst
new file mode 100644
index 000000000..6980fd71e
--- /dev/null
+++ b/docs/sphinx/modules/cloud.rst
@@ -0,0 +1,7 @@
+cloud Module (``stx.cloud``)
+============================
+
+.. automodule:: scitex.cloud
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/compat.rst b/docs/sphinx/modules/compat.rst
new file mode 100644
index 000000000..7438ae6ca
--- /dev/null
+++ b/docs/sphinx/modules/compat.rst
@@ -0,0 +1,7 @@
+compat Module (``stx.compat``)
+==============================
+
+.. automodule:: scitex.compat
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/container.rst b/docs/sphinx/modules/container.rst
new file mode 100644
index 000000000..6ac42573b
--- /dev/null
+++ b/docs/sphinx/modules/container.rst
@@ -0,0 +1,7 @@
+container Module (``stx.container``)
+====================================
+
+.. automodule:: scitex.container
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/context.rst b/docs/sphinx/modules/context.rst
new file mode 100644
index 000000000..7a7f5b8ff
--- /dev/null
+++ b/docs/sphinx/modules/context.rst
@@ -0,0 +1,7 @@
+context Module (``stx.context``)
+================================
+
+.. automodule:: scitex.context
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/cv.rst b/docs/sphinx/modules/cv.rst
new file mode 100644
index 000000000..e4b53ed96
--- /dev/null
+++ b/docs/sphinx/modules/cv.rst
@@ -0,0 +1,7 @@
+cv Module (``stx.cv``)
+======================
+
+.. automodule:: scitex.cv
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/dataset.rst b/docs/sphinx/modules/dataset.rst
new file mode 100644
index 000000000..8f600181a
--- /dev/null
+++ b/docs/sphinx/modules/dataset.rst
@@ -0,0 +1,7 @@
+dataset Module (``stx.dataset``)
+================================
+
+.. automodule:: scitex.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/datetime.rst b/docs/sphinx/modules/datetime.rst
new file mode 100644
index 000000000..78541bb81
--- /dev/null
+++ b/docs/sphinx/modules/datetime.rst
@@ -0,0 +1,7 @@
+datetime Module (``stx.datetime``)
+==================================
+
+.. automodule:: scitex.datetime
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/db.rst b/docs/sphinx/modules/db.rst
new file mode 100644
index 000000000..5945aa66d
--- /dev/null
+++ b/docs/sphinx/modules/db.rst
@@ -0,0 +1,7 @@
+db Module (``stx.db``)
+======================
+
+.. automodule:: scitex.db
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/dev.rst b/docs/sphinx/modules/dev.rst
new file mode 100644
index 000000000..de05c5990
--- /dev/null
+++ b/docs/sphinx/modules/dev.rst
@@ -0,0 +1,7 @@
+dev Module (``stx.dev``)
+========================
+
+.. automodule:: scitex.dev
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/dict.rst b/docs/sphinx/modules/dict.rst
new file mode 100644
index 000000000..7157aba95
--- /dev/null
+++ b/docs/sphinx/modules/dict.rst
@@ -0,0 +1,7 @@
+dict Module (``stx.dict``)
+==========================
+
+.. automodule:: scitex.dict
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/etc.rst b/docs/sphinx/modules/etc.rst
new file mode 100644
index 000000000..b10d3a1f4
--- /dev/null
+++ b/docs/sphinx/modules/etc.rst
@@ -0,0 +1,7 @@
+etc Module (``stx.etc``)
+========================
+
+.. automodule:: scitex.etc
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/events.rst b/docs/sphinx/modules/events.rst
new file mode 100644
index 000000000..2039cfecd
--- /dev/null
+++ b/docs/sphinx/modules/events.rst
@@ -0,0 +1,7 @@
+events Module (``stx.events``)
+==============================
+
+.. automodule:: scitex.events
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/gists.rst b/docs/sphinx/modules/gists.rst
new file mode 100644
index 000000000..b77c7eaf9
--- /dev/null
+++ b/docs/sphinx/modules/gists.rst
@@ -0,0 +1,7 @@
+gists Module (``stx.gists``)
+============================
+
+.. automodule:: scitex.gists
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/git.rst b/docs/sphinx/modules/git.rst
new file mode 100644
index 000000000..fcec156e3
--- /dev/null
+++ b/docs/sphinx/modules/git.rst
@@ -0,0 +1,7 @@
+git Module (``stx.git``)
+========================
+
+.. automodule:: scitex.git
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/index.rst b/docs/sphinx/modules/index.rst
index a1dd72f1f..0c60cea18 100644
--- a/docs/sphinx/modules/index.rst
+++ b/docs/sphinx/modules/index.rst
@@ -1,127 +1,12 @@
 Module Overview
 ===============
 
-SciTeX is organized into focused modules across five categories,
-ordered from core infrastructure to higher-level tools.
-
-.. image:: ../_static/architecture.png
-   :width: 100%
-   :alt: Module architecture: Experiment (session, config, io, logging, repro), Analysis & Visualization (stats, dsp, plt, diagram), Publication (scholar, writer, clew)
-
-Core
-----
-
-The essential workflow: session management, file I/O, configuration,
-logging, reproducibility, and provenance tracking.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 25 75
-
-   * - Module
-     - Description
-   * - :doc:`@stx.session <session>`
-     - **Entry point** -- decorator providing CLI generation, output directories, config injection, and provenance tracking
-   * - :doc:`stx.io <io>`
-     - Universal file I/O -- save/load for 30+ formats (CSV, NumPy, pickle, HDF5, images, YAML, JSON, ...)
-   * - :doc:`stx.config <config>`
-     - YAML configuration with priority resolution (CLI > config files > defaults)
-   * - :doc:`stx.logging <logging>`
-     - Logging, warnings, exception hierarchy, and stream redirection
-   * - :doc:`stx.repro <repro>`
-     - Reproducibility: ``fix_seeds()``, ``gen_id()``, ``gen_timestamp()``, ``RandomStateManager``
-   * - :doc:`stx.clew <clew>`
-     - Hash-based provenance tracking -- verify runs, trace dependency chains
-
-Science & Analysis
-------------------
-
-Statistical tests, publication-ready figures, signal processing,
-and diagrams.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 25 75
-
-   * - Module
-     - Description
-   * - :doc:`stx.stats <stats>`
-     - 23 statistical tests with effect sizes, confidence intervals, and APA formatting
-   * - :doc:`stx.plt <plt>`
-     - Publication figures via figrecipe: 47 plot types, mm-based layout, auto CSV export
-   * - :doc:`stx.dsp <dsp>`
-     - Signal processing: bandpass/lowpass/highpass filters, PSD, Hilbert, wavelet, PAC
-   * - :doc:`stx.diagram <diagram>`
-     - Paper-optimized diagrams with Mermaid and Graphviz backends
-
-Literature & Writing
---------------------
-
-Research, write, and validate scientific manuscripts.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 25 75
-
-   * - Module
-     - Description
-   * - :doc:`stx.scholar <scholar>`
-     - Literature management: search, download PDFs, enrich BibTeX, organize library
-   * - :doc:`stx.writer <writer>`
-     - LaTeX manuscript compilation, table/figure management, IMRAD guidelines
-   * - :doc:`stx.linter <linter>`
-     - AST-based Python linter enforcing SciTeX conventions (45 rules)
-
-Machine Learning
-----------------
-
-Training utilities, classification pipelines, and PyTorch layers.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 25 75
-
-   * - Module
-     - Description
-   * - :doc:`stx.ai <ai>`
-     - ML utilities: ``LearningCurveLogger``, ``EarlyStopping``, ``ClassificationReporter``, metrics
-   * - :doc:`stx.nn <nn>`
-     - PyTorch layers: signal processing, attention, 1D ResNet, PAC
-
-Utilities
----------
-
-Templates, decorators, introspection, and data helpers.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 25 75
-
-   * - Module
-     - Description
-   * - :doc:`stx.template <template>`
-     - Project scaffolding and code snippet templates
-   * - :doc:`stx.decorators <decorators>`
-     - Type conversion (``@torch_fn``), batching (``@batch_fn``), caching, timeout
-   * - :doc:`stx.introspect <introspect>`
-     - IPython-like code inspection: ``q()``, ``qq()``, ``dir()``, call graphs
-   * - :doc:`stx.pd <pd>`
-     - Pandas helpers: ``find_indi``, ``melt_cols``, ``merge_cols``, ``to_xyz``
-   * - ``stx.gen``
-     - General utilities: ``mk_spath()``, ``run()``, ``copy()/paste()``
-   * - ``stx.str``
-     - LaTeX formatting, axis labels, ``color_text()``, ``to_latex_style()``
-   * - ``stx.dict``
-     - ``DotDict``, ``flatten()``, ``safe_merge()``, ``listed_dict()``
-   * - ``stx.db``
-     - SQLite3 and PostgreSQL wrappers with batch operations
-   * - ``stx.social``
-     - Social media posting and Google Analytics
+SciTeX is organized into focused modules.
+All modules are accessible via ``import scitex as stx`` followed by ``stx.<module>``.
 
 .. toctree::
    :maxdepth: 2
    :caption: Core
-   :hidden:
 
    session
    io
@@ -133,37 +18,94 @@ Templates, decorators, introspection, and data helpers.
 .. toctree::
    :maxdepth: 2
    :caption: Science & Analysis
-   :hidden:
 
    stats
    plt
    dsp
    diagram
+   canvas
 
 .. toctree::
    :maxdepth: 2
    :caption: Literature & Writing
-   :hidden:
 
    scholar
    writer
-   linter
+   notebook
 
 .. toctree::
    :maxdepth: 2
    :caption: Machine Learning
-   :hidden:
 
    ai
    nn
+   torch
+   cv
+   benchmark
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Data & I/O
+
+   pd
+   db
+   dataset
+   schema
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Infrastructure
+
+   app
+   cloud
+   container
+   tunnel
+   cli
+   browser
+   capture
+   audio
+   notify
+   social
 
 .. toctree::
    :maxdepth: 2
    :caption: Utilities
-   :hidden:
 
+   gen
    template
    decorators
    introspect
-   pd
-   gen
+   str
+   dict
+   path
+   os
+   sh
+   git
+   parallel
+   linalg
+   datetime
+   types
+   rng
+   context
+   resource
+   utils
+   etc
+   web
+   msword
+   tex
+   bridge
+   compat
+   module
+   gists
+   media
+   security
+   ui
+   dev
+   audit
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Other
+
+   events
+   project
diff --git a/docs/sphinx/modules/linalg.rst b/docs/sphinx/modules/linalg.rst
new file mode 100644
index 000000000..2f7ce9a85
--- /dev/null
+++ b/docs/sphinx/modules/linalg.rst
@@ -0,0 +1,7 @@
+linalg Module (``stx.linalg``)
+==============================
+
+.. automodule:: scitex.linalg
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/media.rst b/docs/sphinx/modules/media.rst
new file mode 100644
index 000000000..34e386c28
--- /dev/null
+++ b/docs/sphinx/modules/media.rst
@@ -0,0 +1,7 @@
+media Module (``stx.media``)
+============================
+
+.. automodule:: scitex.media
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/module.rst b/docs/sphinx/modules/module.rst
new file mode 100644
index 000000000..6ba06a686
--- /dev/null
+++ b/docs/sphinx/modules/module.rst
@@ -0,0 +1,7 @@
+module Module (``stx.module``)
+==============================
+
+.. automodule:: scitex.module
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/msword.rst b/docs/sphinx/modules/msword.rst
new file mode 100644
index 000000000..a48391fae
--- /dev/null
+++ b/docs/sphinx/modules/msword.rst
@@ -0,0 +1,7 @@
+msword Module (``stx.msword``)
+==============================
+
+.. automodule:: scitex.msword
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/notebook.rst b/docs/sphinx/modules/notebook.rst
new file mode 100644
index 000000000..b66a0a1c0
--- /dev/null
+++ b/docs/sphinx/modules/notebook.rst
@@ -0,0 +1,7 @@
+notebook Module (``stx.notebook``)
+==================================
+
+.. automodule:: scitex.notebook
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/notify.rst b/docs/sphinx/modules/notify.rst
new file mode 100644
index 000000000..4dfc60e3a
--- /dev/null
+++ b/docs/sphinx/modules/notify.rst
@@ -0,0 +1,7 @@
+notify Module (``stx.notify``)
+==============================
+
+.. automodule:: scitex.notify
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/os.rst b/docs/sphinx/modules/os.rst
new file mode 100644
index 000000000..be2fda313
--- /dev/null
+++ b/docs/sphinx/modules/os.rst
@@ -0,0 +1,7 @@
+os Module (``stx.os``)
+======================
+
+.. automodule:: scitex.os
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/parallel.rst b/docs/sphinx/modules/parallel.rst
new file mode 100644
index 000000000..620d8333d
--- /dev/null
+++ b/docs/sphinx/modules/parallel.rst
@@ -0,0 +1,7 @@
+parallel Module (``stx.parallel``)
+==================================
+
+.. automodule:: scitex.parallel
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/path.rst b/docs/sphinx/modules/path.rst
new file mode 100644
index 000000000..672ff6967
--- /dev/null
+++ b/docs/sphinx/modules/path.rst
@@ -0,0 +1,7 @@
+path Module (``stx.path``)
+==========================
+
+.. automodule:: scitex.path
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/project.rst b/docs/sphinx/modules/project.rst
new file mode 100644
index 000000000..b0440a59f
--- /dev/null
+++ b/docs/sphinx/modules/project.rst
@@ -0,0 +1,7 @@
+project Module (``stx.project``)
+================================
+
+.. automodule:: scitex.project
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/resource.rst b/docs/sphinx/modules/resource.rst
new file mode 100644
index 000000000..d4fbcc001
--- /dev/null
+++ b/docs/sphinx/modules/resource.rst
@@ -0,0 +1,7 @@
+resource Module (``stx.resource``)
+==================================
+
+.. automodule:: scitex.resource
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/rng.rst b/docs/sphinx/modules/rng.rst
new file mode 100644
index 000000000..a6ab74def
--- /dev/null
+++ b/docs/sphinx/modules/rng.rst
@@ -0,0 +1,7 @@
+rng Module (``stx.rng``)
+========================
+
+.. automodule:: scitex.rng
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/schema.rst b/docs/sphinx/modules/schema.rst
new file mode 100644
index 000000000..919582dbf
--- /dev/null
+++ b/docs/sphinx/modules/schema.rst
@@ -0,0 +1,7 @@
+schema Module (``stx.schema``)
+==============================
+
+.. automodule:: scitex.schema
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/security.rst b/docs/sphinx/modules/security.rst
new file mode 100644
index 000000000..232a5da7f
--- /dev/null
+++ b/docs/sphinx/modules/security.rst
@@ -0,0 +1,7 @@
+security Module (``stx.security``)
+==================================
+
+.. automodule:: scitex.security
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/sh.rst b/docs/sphinx/modules/sh.rst
new file mode 100644
index 000000000..7c4694af6
--- /dev/null
+++ b/docs/sphinx/modules/sh.rst
@@ -0,0 +1,7 @@
+sh Module (``stx.sh``)
+======================
+
+.. automodule:: scitex.sh
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/social.rst b/docs/sphinx/modules/social.rst
new file mode 100644
index 000000000..cc82af401
--- /dev/null
+++ b/docs/sphinx/modules/social.rst
@@ -0,0 +1,7 @@
+social Module (``stx.social``)
+==============================
+
+.. automodule:: scitex.social
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/str.rst b/docs/sphinx/modules/str.rst
new file mode 100644
index 000000000..b29b4f485
--- /dev/null
+++ b/docs/sphinx/modules/str.rst
@@ -0,0 +1,7 @@
+str Module (``stx.str``)
+========================
+
+.. automodule:: scitex.str
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/tex.rst b/docs/sphinx/modules/tex.rst
new file mode 100644
index 000000000..e0f775bd9
--- /dev/null
+++ b/docs/sphinx/modules/tex.rst
@@ -0,0 +1,7 @@
+tex Module (``stx.tex``)
+========================
+
+.. automodule:: scitex.tex
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/torch.rst b/docs/sphinx/modules/torch.rst
new file mode 100644
index 000000000..1a11fe241
--- /dev/null
+++ b/docs/sphinx/modules/torch.rst
@@ -0,0 +1,7 @@
+torch Module (``stx.torch``)
+============================
+
+.. automodule:: scitex.torch
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/tunnel.rst b/docs/sphinx/modules/tunnel.rst
new file mode 100644
index 000000000..e28928527
--- /dev/null
+++ b/docs/sphinx/modules/tunnel.rst
@@ -0,0 +1,7 @@
+tunnel Module (``stx.tunnel``)
+==============================
+
+.. automodule:: scitex.tunnel
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/types.rst b/docs/sphinx/modules/types.rst
new file mode 100644
index 000000000..f4f1e1031
--- /dev/null
+++ b/docs/sphinx/modules/types.rst
@@ -0,0 +1,7 @@
+types Module (``stx.types``)
+============================
+
+.. automodule:: scitex.types
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/ui.rst b/docs/sphinx/modules/ui.rst
new file mode 100644
index 000000000..2a8a65a64
--- /dev/null
+++ b/docs/sphinx/modules/ui.rst
@@ -0,0 +1,7 @@
+ui Module (``stx.ui``)
+======================
+
+.. automodule:: scitex.ui
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/utils.rst b/docs/sphinx/modules/utils.rst
new file mode 100644
index 000000000..9b893ac20
--- /dev/null
+++ b/docs/sphinx/modules/utils.rst
@@ -0,0 +1,7 @@
+utils Module (``stx.utils``)
+============================
+
+.. automodule:: scitex.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/modules/web.rst b/docs/sphinx/modules/web.rst
new file mode 100644
index 000000000..5b6589d9d
--- /dev/null
+++ b/docs/sphinx/modules/web.rst
@@ -0,0 +1,7 @@
+web Module (``stx.web``)
+========================
+
+.. automodule:: scitex.web
+   :members:
+   :undoc-members:
+   :show-inheritance:

From b0a4937281a6a97f6f5b42b7de6cdd1f5842f096 Mon Sep 17 00:00:00 2001
From: Yusuke Watanabe <ywatanabe@scitex.ai>
Date: Sun, 15 Mar 2026 10:13:37 +1100
Subject: [PATCH 2/5] fix(docs): generate RST stubs into correct Sphinx source
 directory

RST module stubs were being generated into docs/sphinx/modules/ but
Sphinx reads from docs/sphinx/source/api/. This caused only 2 modules
(io, plt) to appear in built docs. Now all 68 modules have API docs.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 docs/sphinx/generate_api_docs.py      |   5 +-
 docs/sphinx/source/api/ai.rst         |  82 ++++++++++
 docs/sphinx/source/api/app.rst        |   7 +
 docs/sphinx/source/api/audio.rst      |   7 +
 docs/sphinx/source/api/audit.rst      |   7 +
 docs/sphinx/source/api/benchmark.rst  |   7 +
 docs/sphinx/source/api/bridge.rst     |   7 +
 docs/sphinx/source/api/browser.rst    |   7 +
 docs/sphinx/source/api/canvas.rst     |   7 +
 docs/sphinx/source/api/capture.rst    |   7 +
 docs/sphinx/source/api/clew.rst       |  94 ++++++++++++
 docs/sphinx/source/api/cli.rst        |   7 +
 docs/sphinx/source/api/cloud.rst      |   7 +
 docs/sphinx/source/api/compat.rst     |   7 +
 docs/sphinx/source/api/config.rst     |  88 +++++++++++
 docs/sphinx/source/api/container.rst  |   7 +
 docs/sphinx/source/api/context.rst    |   7 +
 docs/sphinx/source/api/cv.rst         |   7 +
 docs/sphinx/source/api/dataset.rst    |   7 +
 docs/sphinx/source/api/datetime.rst   |   7 +
 docs/sphinx/source/api/db.rst         |   7 +
 docs/sphinx/source/api/decorators.rst |  80 ++++++++++
 docs/sphinx/source/api/dev.rst        |   7 +
 docs/sphinx/source/api/diagram.rst    |  99 ++++++++++++
 docs/sphinx/source/api/dict.rst       |   7 +
 docs/sphinx/source/api/dsp.rst        |  75 +++++++++
 docs/sphinx/source/api/etc.rst        |   7 +
 docs/sphinx/source/api/events.rst     |   7 +
 docs/sphinx/source/api/gen.rst        |  38 +++++
 docs/sphinx/source/api/gists.rst      |   7 +
 docs/sphinx/source/api/git.rst        |   7 +
 docs/sphinx/source/api/index.rst      | 107 ++++++++++++-
 docs/sphinx/source/api/introspect.rst |  71 +++++++++
 docs/sphinx/source/api/linalg.rst     |   7 +
 docs/sphinx/source/api/linter.rst     | 133 ++++++++++++++++
 docs/sphinx/source/api/logging.rst    | 108 +++++++++++++
 docs/sphinx/source/api/media.rst      |   7 +
 docs/sphinx/source/api/module.rst     |   7 +
 docs/sphinx/source/api/msword.rst     |   7 +
 docs/sphinx/source/api/nn.rst         |  80 ++++++++++
 docs/sphinx/source/api/notebook.rst   |   7 +
 docs/sphinx/source/api/notify.rst     |   7 +
 docs/sphinx/source/api/os.rst         |   7 +
 docs/sphinx/source/api/parallel.rst   |   7 +
 docs/sphinx/source/api/path.rst       |   7 +
 docs/sphinx/source/api/pd.rst         |  46 ++++++
 docs/sphinx/source/api/project.rst    |   7 +
 docs/sphinx/source/api/repro.rst      |  71 +++++++++
 docs/sphinx/source/api/resource.rst   |   7 +
 docs/sphinx/source/api/rng.rst        |   7 +
 docs/sphinx/source/api/schema.rst     |   7 +
 docs/sphinx/source/api/scholar.rst    | 133 ++++++++++++++++
 docs/sphinx/source/api/security.rst   |   7 +
 docs/sphinx/source/api/session.rst    | 213 ++++++++++++++++++++++++++
 docs/sphinx/source/api/sh.rst         |   7 +
 docs/sphinx/source/api/social.rst     |   7 +
 docs/sphinx/source/api/stats.rst      | 153 ++++++++++++++++++
 docs/sphinx/source/api/str.rst        |   7 +
 docs/sphinx/source/api/template.rst   |  86 +++++++++++
 docs/sphinx/source/api/tex.rst        |   7 +
 docs/sphinx/source/api/torch.rst      |   7 +
 docs/sphinx/source/api/tunnel.rst     |   7 +
 docs/sphinx/source/api/types.rst      |   7 +
 docs/sphinx/source/api/ui.rst         |   7 +
 docs/sphinx/source/api/utils.rst      |   7 +
 docs/sphinx/source/api/web.rst        |   7 +
 docs/sphinx/source/api/writer.rst     | 166 ++++++++++++++++++++
 67 files changed, 2254 insertions(+), 3 deletions(-)
 create mode 100644 docs/sphinx/source/api/ai.rst
 create mode 100644 docs/sphinx/source/api/app.rst
 create mode 100644 docs/sphinx/source/api/audio.rst
 create mode 100644 docs/sphinx/source/api/audit.rst
 create mode 100644 docs/sphinx/source/api/benchmark.rst
 create mode 100644 docs/sphinx/source/api/bridge.rst
 create mode 100644 docs/sphinx/source/api/browser.rst
 create mode 100644 docs/sphinx/source/api/canvas.rst
 create mode 100644 docs/sphinx/source/api/capture.rst
 create mode 100644 docs/sphinx/source/api/clew.rst
 create mode 100644 docs/sphinx/source/api/cli.rst
 create mode 100644 docs/sphinx/source/api/cloud.rst
 create mode 100644 docs/sphinx/source/api/compat.rst
 create mode 100644 docs/sphinx/source/api/config.rst
 create mode 100644 docs/sphinx/source/api/container.rst
 create mode 100644 docs/sphinx/source/api/context.rst
 create mode 100644 docs/sphinx/source/api/cv.rst
 create mode 100644 docs/sphinx/source/api/dataset.rst
 create mode 100644 docs/sphinx/source/api/datetime.rst
 create mode 100644 docs/sphinx/source/api/db.rst
 create mode 100644 docs/sphinx/source/api/decorators.rst
 create mode 100644 docs/sphinx/source/api/dev.rst
 create mode 100644 docs/sphinx/source/api/diagram.rst
 create mode 100644 docs/sphinx/source/api/dict.rst
 create mode 100644 docs/sphinx/source/api/dsp.rst
 create mode 100644 docs/sphinx/source/api/etc.rst
 create mode 100644 docs/sphinx/source/api/events.rst
 create mode 100644 docs/sphinx/source/api/gen.rst
 create mode 100644 docs/sphinx/source/api/gists.rst
 create mode 100644 docs/sphinx/source/api/git.rst
 create mode 100644 docs/sphinx/source/api/introspect.rst
 create mode 100644 docs/sphinx/source/api/linalg.rst
 create mode 100644 docs/sphinx/source/api/linter.rst
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 create mode 100644 docs/sphinx/source/api/parallel.rst
 create mode 100644 docs/sphinx/source/api/path.rst
 create mode 100644 docs/sphinx/source/api/pd.rst
 create mode 100644 docs/sphinx/source/api/project.rst
 create mode 100644 docs/sphinx/source/api/repro.rst
 create mode 100644 docs/sphinx/source/api/resource.rst
 create mode 100644 docs/sphinx/source/api/rng.rst
 create mode 100644 docs/sphinx/source/api/schema.rst
 create mode 100644 docs/sphinx/source/api/scholar.rst
 create mode 100644 docs/sphinx/source/api/security.rst
 create mode 100644 docs/sphinx/source/api/session.rst
 create mode 100644 docs/sphinx/source/api/sh.rst
 create mode 100644 docs/sphinx/source/api/social.rst
 create mode 100644 docs/sphinx/source/api/stats.rst
 create mode 100644 docs/sphinx/source/api/str.rst
 create mode 100644 docs/sphinx/source/api/template.rst
 create mode 100644 docs/sphinx/source/api/tex.rst
 create mode 100644 docs/sphinx/source/api/torch.rst
 create mode 100644 docs/sphinx/source/api/tunnel.rst
 create mode 100644 docs/sphinx/source/api/types.rst
 create mode 100644 docs/sphinx/source/api/ui.rst
 create mode 100644 docs/sphinx/source/api/utils.rst
 create mode 100644 docs/sphinx/source/api/web.rst
 create mode 100644 docs/sphinx/source/api/writer.rst

diff --git a/docs/sphinx/generate_api_docs.py b/docs/sphinx/generate_api_docs.py
index 9f411f8ae..5c7c6fa1b 100755
--- a/docs/sphinx/generate_api_docs.py
+++ b/docs/sphinx/generate_api_docs.py
@@ -209,8 +209,9 @@ def main():
     # Paths
     script_dir = Path(__file__).parent
     src_dir = script_dir.parent.parent / "src" / "scitex"
-    modules_dir = script_dir / "modules"
-    modules_dir.mkdir(exist_ok=True)
+    # Output to source/api/ (where Sphinx actually reads from)
+    modules_dir = script_dir / "source" / "api"
+    modules_dir.mkdir(parents=True, exist_ok=True)
 
     if not src_dir.exists():
         print(f"Error: Source directory not found: {src_dir}")
diff --git a/docs/sphinx/source/api/ai.rst b/docs/sphinx/source/api/ai.rst
new file mode 100644
index 000000000..e5fb03cee
--- /dev/null
+++ b/docs/sphinx/source/api/ai.rst
@@ -0,0 +1,82 @@
+AI Module (``stx.ai``)
+======================
+
+Machine learning utilities for training, classification, and metrics
+with PyTorch and scikit-learn.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   import scitex as stx
+
+   # Training utilities
+   from scitex.ai import LearningCurveLogger, EarlyStopping
+
+   logger = LearningCurveLogger()
+   stopper = EarlyStopping(patience=10, direction="minimize")
+
+   for epoch in range(100):
+       # ... training loop ...
+       logger({"loss": loss, "acc": acc}, step="Training")
+       if stopper(val_loss, {"model": model_path}, epoch):
+           break
+
+   logger.plot_learning_curves(spath="curves.png")
+
+   # Classification
+   from scitex.ai import ClassificationReporter, Classifier
+
+   clf = Classifier()("SVC")
+   reporter = ClassificationReporter(output_dir="./results")
+   reporter.calculate_metrics(y_true, y_pred, y_proba)
+   reporter.save_summary()
+
+Training
+--------
+
+- ``LearningCurveLogger`` -- Track and visualize training/validation/test metrics across epochs
+- ``EarlyStopping`` -- Monitor validation metrics and stop when improvement plateaus
+
+Classification
+--------------
+
+- ``ClassificationReporter`` -- Unified reporter for single/multi-task classification (balanced accuracy, MCC, ROC-AUC, confusion matrices)
+- ``Classifier`` -- Factory for scikit-learn classifiers (SVC, KNN, Logistic Regression, AdaBoost, ...)
+- ``CrossValidationExperiment`` -- Cross-validation framework
+
+Metrics
+-------
+
+Standardized ``calc_*`` functions:
+
+- ``calc_bacc`` -- Balanced accuracy
+- ``calc_mcc`` -- Matthews Correlation Coefficient
+- ``calc_conf_mat`` -- Confusion matrix
+- ``calc_roc_auc`` -- ROC-AUC score
+- ``calc_pre_rec_auc`` -- Precision-Recall AUC
+- ``calc_feature_importance`` -- Feature importance scores
+
+Visualization
+-------------
+
+- ``plot_learning_curve`` -- Training/validation curves
+- ``stx_conf_mat`` -- Confusion matrix heatmap
+- ``plot_roc_curve`` -- ROC curve
+- ``plot_pre_rec_curve`` -- Precision-Recall curve
+- ``plot_feature_importance`` -- Feature importance bar plots
+
+Other
+-----
+
+- ``MultiTaskLoss`` -- Multi-task learning loss weighting
+- ``get_optimizer`` / ``set_optimizer`` -- Optimizer management
+- ``GenAI`` -- Generative AI wrapper (lazy-loaded)
+- Clustering: ``pca``, ``umap``
+
+API Reference
+-------------
+
+.. automodule:: scitex.ai
+   :members:
diff --git a/docs/sphinx/source/api/app.rst b/docs/sphinx/source/api/app.rst
new file mode 100644
index 000000000..a8374c34d
--- /dev/null
+++ b/docs/sphinx/source/api/app.rst
@@ -0,0 +1,7 @@
+app Module (``stx.app``)
+========================
+
+.. automodule:: scitex.app
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/audio.rst b/docs/sphinx/source/api/audio.rst
new file mode 100644
index 000000000..ab835cbfe
--- /dev/null
+++ b/docs/sphinx/source/api/audio.rst
@@ -0,0 +1,7 @@
+audio Module (``stx.audio``)
+============================
+
+.. automodule:: scitex.audio
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/audit.rst b/docs/sphinx/source/api/audit.rst
new file mode 100644
index 000000000..e7f92881e
--- /dev/null
+++ b/docs/sphinx/source/api/audit.rst
@@ -0,0 +1,7 @@
+audit Module (``stx.audit``)
+============================
+
+.. automodule:: scitex.audit
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/benchmark.rst b/docs/sphinx/source/api/benchmark.rst
new file mode 100644
index 000000000..014b80120
--- /dev/null
+++ b/docs/sphinx/source/api/benchmark.rst
@@ -0,0 +1,7 @@
+benchmark Module (``stx.benchmark``)
+====================================
+
+.. automodule:: scitex.benchmark
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/bridge.rst b/docs/sphinx/source/api/bridge.rst
new file mode 100644
index 000000000..8028c570b
--- /dev/null
+++ b/docs/sphinx/source/api/bridge.rst
@@ -0,0 +1,7 @@
+bridge Module (``stx.bridge``)
+==============================
+
+.. automodule:: scitex.bridge
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/browser.rst b/docs/sphinx/source/api/browser.rst
new file mode 100644
index 000000000..c91604cc8
--- /dev/null
+++ b/docs/sphinx/source/api/browser.rst
@@ -0,0 +1,7 @@
+browser Module (``stx.browser``)
+================================
+
+.. automodule:: scitex.browser
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/canvas.rst b/docs/sphinx/source/api/canvas.rst
new file mode 100644
index 000000000..210c63590
--- /dev/null
+++ b/docs/sphinx/source/api/canvas.rst
@@ -0,0 +1,7 @@
+canvas Module (``stx.canvas``)
+==============================
+
+.. automodule:: scitex.canvas
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/capture.rst b/docs/sphinx/source/api/capture.rst
new file mode 100644
index 000000000..7e0855faf
--- /dev/null
+++ b/docs/sphinx/source/api/capture.rst
@@ -0,0 +1,7 @@
+capture Module (``stx.capture``)
+================================
+
+.. automodule:: scitex.capture
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/clew.rst b/docs/sphinx/source/api/clew.rst
new file mode 100644
index 000000000..017427e08
--- /dev/null
+++ b/docs/sphinx/source/api/clew.rst
@@ -0,0 +1,94 @@
+Clew Module (``stx.clew``)
+==========================
+
+Hash-based provenance tracking for reproducible science. Clew (Ariadne's
+thread) records file hashes during ``@stx.session`` runs and traces
+dependency chains back to source.
+
+How It Works
+------------
+
+1. ``@stx.session`` starts a tracking session
+2. ``stx.io.load()`` records input file hashes
+3. ``stx.io.save()`` records output file hashes
+4. Session close computes a combined hash of all inputs/outputs
+5. Later, ``stx.clew`` can verify nothing has changed
+
+.. code-block:: python
+
+   import scitex as stx
+
+   # Automatic -- just use @stx.session + stx.io
+   @stx.session
+   def main():
+       data = stx.io.load("input.csv")      # Tracked as input
+       result = process(data)
+       stx.io.save(result, "output.png")     # Tracked as output
+       return 0
+
+   # Verify later
+   stx.clew.status()                         # Like git status
+   stx.clew.run("session_id")                # Verify by hash
+   stx.clew.chain("output.png")              # Trace to source
+
+CLI Commands
+------------
+
+.. code-block:: bash
+
+   scitex clew status                  # Show changed files
+   scitex clew list                    # List all tracked runs
+   scitex clew run <session_id>        # Verify a specific run
+   scitex clew chain <file>            # Trace dependency chain
+   scitex clew stats                   # Database statistics
+
+Verification Levels
+-------------------
+
+- **CACHE** -- Hash comparison only (fast). Checks if files match stored hashes.
+- **RERUN** -- Re-execute scripts and compare outputs (thorough). Catches logic errors.
+
+.. code-block:: python
+
+   # Fast: hash comparison
+   result = stx.clew.run("session_id")
+
+   # Thorough: re-execute and compare
+   result = stx.clew.run("session_id", from_scratch=True)
+
+Dependency Chains
+-----------------
+
+Clew traces ``parent_session`` links to build a DAG from final output
+back to original source:
+
+.. code-block:: python
+
+   chain = stx.clew.chain("final_figure.png")
+   # Shows: source.py → intermediate.csv → analysis.py → final_figure.png
+
+   # Visualize as Mermaid DAG
+   stx.clew.mermaid("session_id")
+
+Verification Statuses
+---------------------
+
+- ``VERIFIED`` -- Files match expected hashes
+- ``MISMATCH`` -- Files differ from stored hashes
+- ``MISSING`` -- Files no longer exist
+- ``UNKNOWN`` -- No prior tracking data
+
+Key Functions
+-------------
+
+- ``status()`` -- Show changed items (like ``git status``)
+- ``run(session_id)`` -- Verify a specific run
+- ``chain(target_file)`` -- Trace dependency chain
+- ``list_runs(limit, status)`` -- List tracked runs
+- ``stats()`` -- Database statistics
+
+API Reference
+-------------
+
+.. automodule:: scitex.clew
+   :members:
diff --git a/docs/sphinx/source/api/cli.rst b/docs/sphinx/source/api/cli.rst
new file mode 100644
index 000000000..c6054e8fd
--- /dev/null
+++ b/docs/sphinx/source/api/cli.rst
@@ -0,0 +1,7 @@
+cli Module (``stx.cli``)
+========================
+
+.. automodule:: scitex.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/cloud.rst b/docs/sphinx/source/api/cloud.rst
new file mode 100644
index 000000000..6980fd71e
--- /dev/null
+++ b/docs/sphinx/source/api/cloud.rst
@@ -0,0 +1,7 @@
+cloud Module (``stx.cloud``)
+============================
+
+.. automodule:: scitex.cloud
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/compat.rst b/docs/sphinx/source/api/compat.rst
new file mode 100644
index 000000000..7438ae6ca
--- /dev/null
+++ b/docs/sphinx/source/api/compat.rst
@@ -0,0 +1,7 @@
+compat Module (``stx.compat``)
+==============================
+
+.. automodule:: scitex.compat
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/config.rst b/docs/sphinx/source/api/config.rst
new file mode 100644
index 000000000..11a770d0b
--- /dev/null
+++ b/docs/sphinx/source/api/config.rst
@@ -0,0 +1,88 @@
+Config Module (``stx.config``)
+===============================
+
+YAML-based configuration with priority resolution and path management.
+
+Priority Resolution
+-------------------
+
+All config values follow the same precedence:
+
+.. code-block:: text
+
+   direct argument > config/YAML > environment variable > default
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   import scitex as stx
+
+   # Get global config (reads ~/.scitex/config.yaml)
+   config = stx.config.get_config()
+
+   # Resolve with precedence
+   log_level = config.resolve("logging.level", default="INFO")
+   # Checks: direct → YAML → SCITEX_LOGGING_LEVEL env → "INFO"
+
+   # Access nested values
+   config.get_nested("scholar", "crossref_email")
+
+   # Path management
+   paths = stx.config.get_paths()
+   paths.scholar        # ~/.scitex/scholar
+   paths.cache          # ~/.scitex/cache
+
+YAML Configuration
+------------------
+
+.. code-block:: yaml
+
+   # ~/.scitex/config.yaml (or ./config/*.yaml for projects)
+   logging:
+     level: INFO
+
+   scholar:
+     crossref_email: ${CROSSREF_EMAIL:-user@example.com}
+
+Environment variable substitution with ``${VAR:-default}`` syntax is
+supported in YAML files.
+
+Key Classes
+-----------
+
+- ``ScitexConfig`` -- YAML-based config with env var substitution and precedence resolution
+- ``PriorityConfig`` -- Dict-based config resolver for programmatic use
+- ``ScitexPaths`` -- Centralized path manager (all paths derive from ``~/.scitex/``)
+- ``EnvVar`` -- Environment variable definition dataclass
+
+Path Management
+---------------
+
+``ScitexPaths`` manages all SciTeX directories:
+
+.. code-block:: python
+
+   paths = stx.config.get_paths()
+   paths.base       # ~/.scitex (SCITEX_DIR)
+   paths.logs       # ~/.scitex/logs
+   paths.cache      # ~/.scitex/cache
+   paths.scholar    # ~/.scitex/scholar
+   paths.rng        # ~/.scitex/rng
+   paths.capture    # ~/.scitex/capture
+
+Utility Functions
+-----------------
+
+- ``get_config(path)`` -- Get singleton ScitexConfig instance
+- ``get_paths(base_dir)`` -- Get singleton ScitexPaths instance
+- ``load_yaml(path)`` -- Load YAML with env var substitution
+- ``load_dotenv(path)`` -- Load ``.env`` file
+- ``get_scitex_dir()`` -- Get SCITEX_DIR with precedence
+
+API Reference
+-------------
+
+.. automodule:: scitex.config
+   :members:
diff --git a/docs/sphinx/source/api/container.rst b/docs/sphinx/source/api/container.rst
new file mode 100644
index 000000000..6ac42573b
--- /dev/null
+++ b/docs/sphinx/source/api/container.rst
@@ -0,0 +1,7 @@
+container Module (``stx.container``)
+====================================
+
+.. automodule:: scitex.container
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/context.rst b/docs/sphinx/source/api/context.rst
new file mode 100644
index 000000000..7a7f5b8ff
--- /dev/null
+++ b/docs/sphinx/source/api/context.rst
@@ -0,0 +1,7 @@
+context Module (``stx.context``)
+================================
+
+.. automodule:: scitex.context
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/cv.rst b/docs/sphinx/source/api/cv.rst
new file mode 100644
index 000000000..e4b53ed96
--- /dev/null
+++ b/docs/sphinx/source/api/cv.rst
@@ -0,0 +1,7 @@
+cv Module (``stx.cv``)
+======================
+
+.. automodule:: scitex.cv
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/dataset.rst b/docs/sphinx/source/api/dataset.rst
new file mode 100644
index 000000000..8f600181a
--- /dev/null
+++ b/docs/sphinx/source/api/dataset.rst
@@ -0,0 +1,7 @@
+dataset Module (``stx.dataset``)
+================================
+
+.. automodule:: scitex.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/datetime.rst b/docs/sphinx/source/api/datetime.rst
new file mode 100644
index 000000000..78541bb81
--- /dev/null
+++ b/docs/sphinx/source/api/datetime.rst
@@ -0,0 +1,7 @@
+datetime Module (``stx.datetime``)
+==================================
+
+.. automodule:: scitex.datetime
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/db.rst b/docs/sphinx/source/api/db.rst
new file mode 100644
index 000000000..5945aa66d
--- /dev/null
+++ b/docs/sphinx/source/api/db.rst
@@ -0,0 +1,7 @@
+db Module (``stx.db``)
+======================
+
+.. automodule:: scitex.db
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/decorators.rst b/docs/sphinx/source/api/decorators.rst
new file mode 100644
index 000000000..b1a5f2fd0
--- /dev/null
+++ b/docs/sphinx/source/api/decorators.rst
@@ -0,0 +1,80 @@
+Decorators Module (``stx.decorators``)
+=======================================
+
+Function decorators for type conversion, batching, caching, and more.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   from scitex.decorators import torch_fn, batch_fn, cache_disk, timeout
+
+   @torch_fn
+   def process(x):
+       """Auto-converts inputs to torch tensors, outputs back."""
+       return x * 2
+
+   @batch_fn
+   def predict(data, batch_size=32):
+       """Process data in batches with progress bar."""
+       return model(data)
+
+   @cache_disk
+   def expensive_computation(params):
+       """Results cached to disk for reuse."""
+       return heavy_compute(params)
+
+   @timeout(seconds=30)
+   def risky_call():
+       """Raises TimeoutError if exceeds 30s."""
+       return external_api()
+
+Type Conversion
+---------------
+
+Auto-convert between data frameworks:
+
+- ``@torch_fn`` -- Inputs to PyTorch tensors, outputs back to original type
+- ``@numpy_fn`` -- Inputs to NumPy arrays
+- ``@pandas_fn`` -- Inputs to pandas objects
+- ``@xarray_fn`` -- Inputs to xarray objects
+
+Batch Processing
+----------------
+
+- ``@batch_fn`` -- Split input into batches with tqdm progress
+- ``@batch_numpy_fn`` -- NumPy conversion + batching
+- ``@batch_torch_fn`` -- PyTorch conversion + batching
+- ``@batch_pandas_fn`` -- Pandas conversion + batching
+
+Caching
+-------
+
+- ``@cache_mem`` -- In-memory function result caching
+- ``@cache_disk`` -- Persistent disk-based caching
+- ``@cache_disk_async`` -- Async disk caching
+
+Utilities
+---------
+
+- ``@deprecated(reason, forward_to)`` -- Mark functions as deprecated
+- ``@not_implemented`` -- Mark as not yet implemented
+- ``@timeout(seconds)`` -- Enforce execution time limits
+- ``@preserve_doc`` -- Preserve docstrings when wrapping
+
+Auto-Ordering
+-------------
+
+.. code-block:: python
+
+   from scitex.decorators import enable_auto_order
+
+   enable_auto_order()
+   # Now decorators are applied in optimal order regardless of code order
+
+API Reference
+-------------
+
+.. automodule:: scitex.decorators
+   :members:
diff --git a/docs/sphinx/source/api/dev.rst b/docs/sphinx/source/api/dev.rst
new file mode 100644
index 000000000..de05c5990
--- /dev/null
+++ b/docs/sphinx/source/api/dev.rst
@@ -0,0 +1,7 @@
+dev Module (``stx.dev``)
+========================
+
+.. automodule:: scitex.dev
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/diagram.rst b/docs/sphinx/source/api/diagram.rst
new file mode 100644
index 000000000..7e3a9f997
--- /dev/null
+++ b/docs/sphinx/source/api/diagram.rst
@@ -0,0 +1,99 @@
+Diagram Module (``stx.diagram``)
+=================================
+
+Paper-optimized diagram generation with Mermaid and Graphviz backends.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   from scitex.diagram import Diagram
+
+   # Create from Python
+   d = Diagram(type="workflow", title="Analysis Pipeline")
+   d.add_node("load", "Load Data", shape="stadium")
+   d.add_node("proc", "Process", shape="rounded", emphasis="primary")
+   d.add_node("save", "Save Results", shape="stadium", emphasis="success")
+   d.add_edge("load", "proc")
+   d.add_edge("proc", "save")
+
+   # Export
+   d.to_mermaid("pipeline.mmd")
+   d.to_graphviz("pipeline.dot")
+
+   # Or from YAML specification
+   d = Diagram.from_yaml("pipeline.diagram.yaml")
+
+YAML Specification
+------------------
+
+.. code-block:: yaml
+
+   type: workflow
+   title: SciTeX Analysis Pipeline
+
+   paper:
+     column: single          # single or double
+     mode: publication       # draft or publication
+     reading_direction: left_to_right
+
+   layout:
+     groups:
+       Input: [load, preprocess]
+       Analysis: [analyze, test]
+
+   nodes:
+     - id: load
+       label: Load Data
+       shape: stadium
+     - id: analyze
+       label: Statistical Test
+       shape: rounded
+       emphasis: primary
+
+   edges:
+     - from: load
+       to: analyze
+
+Node Shapes
+------------
+
+``box``, ``rounded``, ``stadium``, ``diamond``, ``circle``, ``codeblock``
+
+Node Emphasis
+-------------
+
+- ``normal`` -- Default (dark)
+- ``primary`` -- Key nodes (blue)
+- ``success`` -- Positive outcomes (green)
+- ``warning`` -- Issues (red)
+- ``muted`` -- Secondary (gray)
+
+Diagram Types
+-------------
+
+- ``workflow`` -- Left-to-right sequential processes
+- ``decision`` -- Top-to-bottom decision trees
+- ``pipeline`` -- Data pipeline stages
+- ``hierarchy`` -- Tree structures
+- ``comparison`` -- Side-by-side comparison
+
+Paper Modes
+-----------
+
+- **draft** -- Full arrows, medium spacing, all edges visible
+- **publication** -- Tight spacing, return edges invisible, optimized for column width
+
+Backends
+--------
+
+- **Mermaid** (``.mmd``) -- Web/markdown rendering
+- **Graphviz DOT** (``.dot``) -- Tighter layouts, render with ``dot -Tpng``
+- **YAML** (``.diagram.yaml``) -- Semantic spec, human/LLM-readable
+
+API Reference
+-------------
+
+.. automodule:: scitex.diagram
+   :members:
diff --git a/docs/sphinx/source/api/dict.rst b/docs/sphinx/source/api/dict.rst
new file mode 100644
index 000000000..7157aba95
--- /dev/null
+++ b/docs/sphinx/source/api/dict.rst
@@ -0,0 +1,7 @@
+dict Module (``stx.dict``)
+==========================
+
+.. automodule:: scitex.dict
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/dsp.rst b/docs/sphinx/source/api/dsp.rst
new file mode 100644
index 000000000..4e16f6f2d
--- /dev/null
+++ b/docs/sphinx/source/api/dsp.rst
@@ -0,0 +1,75 @@
+DSP Module (``stx.dsp``)
+========================
+
+Digital signal processing tools for filtering, spectral analysis,
+and time-frequency decomposition.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+    import scitex as stx
+    import numpy as np
+
+    # Generate test signal
+    fs = 1000  # Hz
+    t = np.arange(0, 1, 1/fs)
+    signal = np.sin(2 * np.pi * 10 * t) + 0.5 * np.sin(2 * np.pi * 50 * t)
+
+    # Filtering
+    filtered = stx.dsp.filt.bandpass(signal, fs=fs, low=5, high=30)
+    low_pass = stx.dsp.filt.lowpass(signal, fs=fs, cutoff=20)
+    high_pass = stx.dsp.filt.highpass(signal, fs=fs, cutoff=5)
+
+    # Power spectral density
+    freqs, psd = stx.dsp.psd(signal, fs=fs)
+
+    # Band powers
+    powers = stx.dsp.band_powers(signal, fs=fs, bands={
+        "delta": (1, 4),
+        "theta": (4, 8),
+        "alpha": (8, 13),
+        "beta": (13, 30),
+    })
+
+    # Hilbert transform (analytic signal)
+    analytic = stx.dsp.hilbert(signal)
+    amplitude = np.abs(analytic)
+    phase = np.angle(analytic)
+
+    # Wavelet decomposition
+    coeffs = stx.dsp.wavelet(signal, fs=fs, freqs=np.arange(1, 50))
+
+Available Functions
+-------------------
+
+**Filtering** (``stx.dsp.filt``)
+
+- ``bandpass(signal, fs, low, high)``
+- ``lowpass(signal, fs, cutoff)``
+- ``highpass(signal, fs, cutoff)``
+- ``notch(signal, fs, freq)``
+
+**Spectral Analysis**
+
+- ``psd(signal, fs)`` -- Power spectral density
+- ``band_powers(signal, fs, bands)`` -- Power in frequency bands
+- ``wavelet(signal, fs, freqs)`` -- Continuous wavelet transform
+
+**Time-Frequency**
+
+- ``hilbert(signal)`` -- Analytic signal via Hilbert transform
+- ``pac(signal, fs)`` -- Phase-amplitude coupling
+
+**Utilities**
+
+- ``demo_sig(fs, duration)`` -- Generate demo signals for testing
+- ``crop(signal, start, end, fs)`` -- Crop signal to time range
+- ``detect_ripples(signal, fs)`` -- Detect sharp-wave ripples
+
+API Reference
+-------------
+
+.. automodule:: scitex.dsp
+   :members:
diff --git a/docs/sphinx/source/api/etc.rst b/docs/sphinx/source/api/etc.rst
new file mode 100644
index 000000000..b10d3a1f4
--- /dev/null
+++ b/docs/sphinx/source/api/etc.rst
@@ -0,0 +1,7 @@
+etc Module (``stx.etc``)
+========================
+
+.. automodule:: scitex.etc
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/events.rst b/docs/sphinx/source/api/events.rst
new file mode 100644
index 000000000..2039cfecd
--- /dev/null
+++ b/docs/sphinx/source/api/events.rst
@@ -0,0 +1,7 @@
+events Module (``stx.events``)
+==============================
+
+.. automodule:: scitex.events
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/gen.rst b/docs/sphinx/source/api/gen.rst
new file mode 100644
index 000000000..4a982c9fc
--- /dev/null
+++ b/docs/sphinx/source/api/gen.rst
@@ -0,0 +1,38 @@
+Gen Module (``stx.gen``)
+========================
+
+General utilities for path management, shell commands, and system operations.
+
+.. note::
+
+   Session management has moved to ``@stx.session`` (see :doc:`/core_concepts`).
+   The ``scitex.gen.start()`` / ``scitex.gen.close()`` pattern is deprecated.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+    import scitex as stx
+
+    # Timestamped output directories
+    path = stx.gen.mk_spath("./results")
+    # → ./results/20260213_143022/
+
+    # Run shell commands
+    stx.gen.run("ls -la")
+
+    # Clipboard operations
+    stx.gen.copy("text to clipboard")
+    text = stx.gen.paste()
+
+    # String to valid path
+    stx.gen.title2path("My Experiment #1")
+    # → "my_experiment_1"
+
+API Reference
+-------------
+
+.. automodule:: scitex.gen
+   :members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/gists.rst b/docs/sphinx/source/api/gists.rst
new file mode 100644
index 000000000..b77c7eaf9
--- /dev/null
+++ b/docs/sphinx/source/api/gists.rst
@@ -0,0 +1,7 @@
+gists Module (``stx.gists``)
+============================
+
+.. automodule:: scitex.gists
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/git.rst b/docs/sphinx/source/api/git.rst
new file mode 100644
index 000000000..fcec156e3
--- /dev/null
+++ b/docs/sphinx/source/api/git.rst
@@ -0,0 +1,7 @@
+git Module (``stx.git``)
+========================
+
+.. automodule:: scitex.git
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/index.rst b/docs/sphinx/source/api/index.rst
index 6b7b42520..e8411e4f7 100644
--- a/docs/sphinx/source/api/index.rst
+++ b/docs/sphinx/source/api/index.rst
@@ -1,8 +1,113 @@
 API Reference
 =============
 
+SciTeX is organized into focused modules.
+All modules are accessible via ``import scitex as stx`` followed by ``stx.<module>``.
+
 .. toctree::
    :maxdepth: 2
+   :caption: Core
 
-   plt
+   session
    io
+   config
+   logging
+   repro
+   clew
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Science & Analysis
+
+   stats
+   plt
+   dsp
+   diagram
+   canvas
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Literature & Writing
+
+   scholar
+   writer
+   notebook
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Machine Learning
+
+   ai
+   nn
+   torch
+   cv
+   benchmark
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Data & I/O
+
+   pd
+   db
+   dataset
+   schema
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Infrastructure
+
+   app
+   cloud
+   container
+   tunnel
+   cli
+   browser
+   capture
+   audio
+   notify
+   social
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Utilities
+
+   gen
+   template
+   decorators
+   introspect
+   str
+   dict
+   path
+   os
+   sh
+   git
+   parallel
+   linalg
+   datetime
+   types
+   rng
+   context
+   resource
+   utils
+   etc
+   web
+   msword
+   tex
+   bridge
+   compat
+   module
+   gists
+   media
+   security
+   ui
+   usage
+   dev
+   audit
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Other
+
+   events
+   linter
+   project
diff --git a/docs/sphinx/source/api/introspect.rst b/docs/sphinx/source/api/introspect.rst
new file mode 100644
index 000000000..180c1dafb
--- /dev/null
+++ b/docs/sphinx/source/api/introspect.rst
@@ -0,0 +1,71 @@
+Introspect Module (``stx.introspect``)
+=======================================
+
+IPython-like code inspection for exploring Python packages.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   import scitex as stx
+
+   # Function signature (like IPython's func?)
+   stx.introspect.q("scitex.stats.test_ttest_ind")
+   # → name, signature, parameters, return type
+
+   # Full source code (like IPython's func??)
+   stx.introspect.qq("scitex.stats.test_ttest_ind")
+   # → complete source with line numbers
+
+   # List module members (like enhanced dir())
+   stx.introspect.dir("scitex.plt", filter="public", kind="functions")
+
+   # Recursive API tree
+   df = stx.introspect.list_api("scitex", max_depth=2)
+
+IPython-Style Shortcuts
+-----------------------
+
+- ``q(dotted_path)`` -- Signature and parameters (like ``func?``)
+- ``qq(dotted_path)`` -- Full source code (like ``func??``)
+- ``dir(dotted_path, filter, kind)`` -- List members with filtering
+
+Filters: ``"public"``, ``"private"``, ``"dunder"``, ``"all"``
+
+Kinds: ``"functions"``, ``"classes"``, ``"data"``, ``"modules"``
+
+Documentation
+-------------
+
+- ``get_docstring(path, format)`` -- Extract docstrings (``"raw"``, ``"parsed"``, ``"summary"``)
+- ``get_exports(path)`` -- Get ``__all__`` exports
+- ``find_examples(path)`` -- Find usage examples in tests/examples
+
+Type Analysis
+-------------
+
+- ``get_type_hints_detailed(path)`` -- Full type annotation analysis
+- ``get_class_hierarchy(path)`` -- Inheritance tree (MRO + subclasses)
+- ``get_class_annotations(path)`` -- Class variable annotations
+
+Code Analysis
+-------------
+
+- ``get_imports(path, categorize)`` -- All imports (AST-based, grouped by stdlib/third-party/local)
+- ``get_dependencies(path, recursive)`` -- Module dependency tree
+- ``get_call_graph(path, max_depth)`` -- Function call graph (with timeout protection)
+
+API Tree
+--------
+
+.. code-block:: python
+
+   # Generate full module tree as DataFrame
+   df = stx.introspect.list_api("scitex", max_depth=3, docstring=True)
+
+API Reference
+-------------
+
+.. automodule:: scitex.introspect
+   :members:
diff --git a/docs/sphinx/source/api/linalg.rst b/docs/sphinx/source/api/linalg.rst
new file mode 100644
index 000000000..2f7ce9a85
--- /dev/null
+++ b/docs/sphinx/source/api/linalg.rst
@@ -0,0 +1,7 @@
+linalg Module (``stx.linalg``)
+==============================
+
+.. automodule:: scitex.linalg
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/linter.rst b/docs/sphinx/source/api/linter.rst
new file mode 100644
index 000000000..e061949ff
--- /dev/null
+++ b/docs/sphinx/source/api/linter.rst
@@ -0,0 +1,133 @@
+Linter Module (``stx.linter``)
+===============================
+
+AST-based Python linter enforcing SciTeX conventions for reproducible
+scientific code.
+
+.. note::
+
+   ``stx.linter`` wraps the standalone
+   `scitex-linter <https://github.com/ywatanabe1989/scitex-linter>`_ package.
+   Install with: ``pip install scitex-linter``.
+
+Quick Reference
+---------------
+
+.. code-block:: bash
+
+   # Check a file
+   scitex linter check my_script.py
+
+   # Check with specific severity
+   scitex linter check my_script.py --severity warning
+
+   # List all rules
+   scitex linter list-rules
+
+   # Filter by category
+   scitex linter list-rules --category session
+
+.. code-block:: python
+
+   from scitex_linter import check_file, list_rules
+
+   # Check a file
+   results = check_file("my_script.py")
+
+   # List available rules
+   rules = list_rules()
+
+Rule Categories
+---------------
+
+45 rules across 8 categories:
+
+.. list-table::
+   :header-rows: 1
+   :widths: 15 25 60
+
+   * - Prefix
+     - Category
+     - Examples
+   * - ``STX-S``
+     - **Session**
+     - Missing ``@stx.session``, missing ``if __name__`` guard, missing return
+   * - ``STX-I``
+     - **Import**
+     - Using ``import mngs`` instead of ``import scitex``, bare ``import numpy``
+   * - ``STX-IO``
+     - **I/O**
+     - Using ``open()`` instead of ``stx.io``, hardcoded paths
+   * - ``STX-P``
+     - **Plotting**
+     - Using ``plt.show()`` instead of ``stx.io.save``, missing ``set_xyt``
+   * - ``STX-ST``
+     - **Statistics**
+     - Using ``scipy.stats`` directly instead of ``stx.stats``
+   * - ``STX-PA``
+     - **Path**
+     - Hardcoded absolute paths, missing ``stx.gen.mk_spath``
+   * - ``STX-FM``
+     - **Format**
+     - Non-snake_case names, magic numbers, missing docstrings
+
+Severity Levels
+---------------
+
+- **error** -- Must fix (breaks reproducibility or correctness)
+- **warning** -- Should fix (best practice violations)
+- **info** -- Suggestions for improvement
+
+Interfaces
+----------
+
+The linter is available through multiple interfaces:
+
+**CLI:**
+
+.. code-block:: bash
+
+   scitex linter check script.py
+   scitex-linter check script.py    # standalone CLI
+
+**Python API:**
+
+.. code-block:: python
+
+   from scitex_linter import check_file, check_source
+
+   results = check_file("script.py")
+   results = check_source("import numpy as np\n...")
+
+**Flake8 Plugin:**
+
+.. code-block:: bash
+
+   flake8 --select=STX script.py
+
+**MCP Tools:**
+
+.. code-block:: python
+
+   # Available as MCP tools for AI agents
+   linter_check(path="script.py", severity="warning")
+   linter_list_rules(category="session")
+   linter_check_source(source="...", filepath="<stdin>")
+
+Configuration
+-------------
+
+Configure via ``pyproject.toml``:
+
+.. code-block:: toml
+
+   [tool.scitex-linter]
+   severity = "warning"
+   ignore = ["STX-S002", "STX-FM001"]
+
+API Reference
+-------------
+
+.. automodule:: scitex.linter
+   :members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/logging.rst b/docs/sphinx/source/api/logging.rst
new file mode 100644
index 000000000..f8a5512db
--- /dev/null
+++ b/docs/sphinx/source/api/logging.rst
@@ -0,0 +1,108 @@
+Logging Module (``stx.logging``)
+=================================
+
+Unified logging with file/console output, custom warnings, exception
+hierarchy, and stream redirection.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   import scitex as stx
+   from scitex import logging
+
+   # Get a logger
+   logger = logging.getLogger(__name__)
+   logger.info("Processing data")
+   logger.success("Analysis complete")   # Custom level (31)
+   logger.fail("Model diverged")         # Custom level (35)
+
+   # Configure globally
+   logging.configure(level="DEBUG", log_file="./run.log")
+   logging.set_level("WARNING")
+
+   # Temporary file logging
+   with logging.log_to_file("analysis.log"):
+       logger.info("This goes to both console and file")
+
+   # Warnings
+   logging.warn("Large dataset", category=logging.PerformanceWarning)
+   logging.warn_deprecated("old_func", "new_func", version="3.0")
+   logging.filterwarnings("ignore", category=logging.UnitWarning)
+
+Log Levels
+----------
+
+.. list-table::
+   :header-rows: 1
+   :widths: 20 15 65
+
+   * - Level
+     - Value
+     - Description
+   * - ``DEBUG``
+     - 10
+     - Detailed diagnostic information
+   * - ``INFO``
+     - 20
+     - General operational messages
+   * - ``WARNING``
+     - 30
+     - Something unexpected but not fatal
+   * - ``SUCCESS``
+     - 31
+     - Custom: operation completed successfully
+   * - ``FAIL``
+     - 35
+     - Custom: operation failed (non-fatal)
+   * - ``ERROR``
+     - 40
+     - Serious problem
+   * - ``CRITICAL``
+     - 50
+     - Program may not continue
+
+Warning Categories
+------------------
+
+- ``SciTeXWarning`` -- Base warning class
+- ``UnitWarning`` -- SI unit convention issues
+- ``StyleWarning`` -- Formatting issues
+- ``SciTeXDeprecationWarning`` -- Deprecated features
+- ``PerformanceWarning`` -- Performance issues
+- ``DataLossWarning`` -- Potential data loss
+
+Exception Hierarchy
+-------------------
+
+All inherit from ``SciTeXError``:
+
+- **I/O**: ``IOError``, ``FileFormatError``, ``SaveError``, ``LoadError``
+- **Config**: ``ConfigurationError``, ``ConfigFileNotFoundError``, ``ConfigKeyError``
+- **Path**: ``PathError``, ``InvalidPathError``, ``PathNotFoundError``
+- **Data**: ``DataError``, ``ShapeError``, ``DTypeError``
+- **Plotting**: ``PlottingError``, ``FigureNotFoundError``, ``AxisError``
+- **Stats**: ``StatsError``, ``TestError``
+- **Scholar**: ``ScholarError``, ``SearchError``, ``PDFDownloadError``, ``DOIResolutionError``
+- **NN**: ``NNError``, ``ModelError``
+- **Template**: ``TemplateError``, ``TemplateViolationError``
+
+Stream Redirection
+------------------
+
+.. code-block:: python
+
+   from scitex.logging import tee
+   import sys
+
+   # Redirect stdout/stderr to log files
+   sys.stdout, sys.stderr = tee(sys, sdir="./output")
+
+The ``@stx.session`` decorator handles this automatically.
+
+API Reference
+-------------
+
+.. automodule:: scitex.logging
+   :members:
diff --git a/docs/sphinx/source/api/media.rst b/docs/sphinx/source/api/media.rst
new file mode 100644
index 000000000..34e386c28
--- /dev/null
+++ b/docs/sphinx/source/api/media.rst
@@ -0,0 +1,7 @@
+media Module (``stx.media``)
+============================
+
+.. automodule:: scitex.media
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/module.rst b/docs/sphinx/source/api/module.rst
new file mode 100644
index 000000000..6ba06a686
--- /dev/null
+++ b/docs/sphinx/source/api/module.rst
@@ -0,0 +1,7 @@
+module Module (``stx.module``)
+==============================
+
+.. automodule:: scitex.module
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/msword.rst b/docs/sphinx/source/api/msword.rst
new file mode 100644
index 000000000..a48391fae
--- /dev/null
+++ b/docs/sphinx/source/api/msword.rst
@@ -0,0 +1,7 @@
+msword Module (``stx.msword``)
+==============================
+
+.. automodule:: scitex.msword
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/nn.rst b/docs/sphinx/source/api/nn.rst
new file mode 100644
index 000000000..a4f886c7d
--- /dev/null
+++ b/docs/sphinx/source/api/nn.rst
@@ -0,0 +1,80 @@
+NN Module (``stx.nn``)
+======================
+
+PyTorch neural network layers for signal processing and neuroscience
+applications.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   import scitex as stx
+   import torch
+
+   # Bandpass filtering as a differentiable layer
+   bpf = stx.nn.BandPassFilter(
+       bands=[[4, 8], [8, 13], [13, 30]],  # theta, alpha, beta
+       fs=256, seq_len=1024
+   )
+   filtered = bpf(signal)  # (batch, channels, 3, 1024)
+
+   # Power spectral density
+   psd = stx.nn.PSD(sample_rate=256)
+   power, freqs = psd(signal)
+
+   # Phase-amplitude coupling
+   pac = stx.nn.PAC(seq_len=1024, fs=256)
+   coupling = pac(signal)
+
+Signal Processing Layers
+-------------------------
+
+**Filtering** (all differentiable):
+
+- ``BandPassFilter(bands, fs, seq_len)`` -- Multi-band frequency filtering
+- ``BandStopFilter(bands, fs, seq_len)`` -- Reject frequency bands
+- ``LowPassFilter(cutoffs_hz, fs, seq_len)`` -- Anti-aliasing / smoothing
+- ``HighPassFilter(cutoffs_hz, fs, seq_len)`` -- High-frequency emphasis
+- ``GaussianFilter(sigma)`` -- Gaussian kernel smoothing
+- ``DifferentiableBandPassFilter(...)`` -- Learnable bandpass parameters
+
+**Spectral Analysis**:
+
+- ``Spectrogram(sampling_rate, n_fft)`` -- STFT-based magnitude spectrogram
+- ``PSD(sample_rate, prob)`` -- FFT-based power spectral density
+- ``Wavelet(samp_rate, freq_scale)`` -- Continuous wavelet transform
+
+**Phase & Coupling**:
+
+- ``Hilbert(seq_len)`` -- Analytic signal (phase + amplitude)
+- ``ModulationIndex(n_bins)`` -- Phase-amplitude coupling metric
+- ``PAC(seq_len, fs, ...)`` -- Complete PAC analysis pipeline
+
+Channel Manipulation
+--------------------
+
+- ``SwapChannels()`` -- Random channel permutation (training augmentation)
+- ``DropoutChannels(dropout)`` -- Drop entire channels
+- ``ChannelGainChanger(n_chs)`` -- Learnable per-channel scaling
+- ``FreqGainChanger(n_bands, fs)`` -- Learnable per-band scaling
+
+Attention & Shape
+-----------------
+
+- ``SpatialAttention(n_chs_in)`` -- Adaptive channel weighting
+- ``TransposeLayer(axis1, axis2)`` -- Dimension permutation
+- ``AxiswiseDropout(dropout_prob, dim)`` -- Drop entire axis
+
+Architectures
+-------------
+
+- ``ResNet1D(n_chs, n_out, n_blks)`` -- 1D residual network
+- ``BNet`` / ``BNet_Res`` -- Multi-head EEG classifier
+- ``MNet1000`` -- 2D CNN feature extractor
+
+API Reference
+-------------
+
+.. automodule:: scitex.nn
+   :members:
diff --git a/docs/sphinx/source/api/notebook.rst b/docs/sphinx/source/api/notebook.rst
new file mode 100644
index 000000000..b66a0a1c0
--- /dev/null
+++ b/docs/sphinx/source/api/notebook.rst
@@ -0,0 +1,7 @@
+notebook Module (``stx.notebook``)
+==================================
+
+.. automodule:: scitex.notebook
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/notify.rst b/docs/sphinx/source/api/notify.rst
new file mode 100644
index 000000000..4dfc60e3a
--- /dev/null
+++ b/docs/sphinx/source/api/notify.rst
@@ -0,0 +1,7 @@
+notify Module (``stx.notify``)
+==============================
+
+.. automodule:: scitex.notify
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/os.rst b/docs/sphinx/source/api/os.rst
new file mode 100644
index 000000000..be2fda313
--- /dev/null
+++ b/docs/sphinx/source/api/os.rst
@@ -0,0 +1,7 @@
+os Module (``stx.os``)
+======================
+
+.. automodule:: scitex.os
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/parallel.rst b/docs/sphinx/source/api/parallel.rst
new file mode 100644
index 000000000..620d8333d
--- /dev/null
+++ b/docs/sphinx/source/api/parallel.rst
@@ -0,0 +1,7 @@
+parallel Module (``stx.parallel``)
+==================================
+
+.. automodule:: scitex.parallel
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/path.rst b/docs/sphinx/source/api/path.rst
new file mode 100644
index 000000000..672ff6967
--- /dev/null
+++ b/docs/sphinx/source/api/path.rst
@@ -0,0 +1,7 @@
+path Module (``stx.path``)
+==========================
+
+.. automodule:: scitex.path
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/pd.rst b/docs/sphinx/source/api/pd.rst
new file mode 100644
index 000000000..9a34275d0
--- /dev/null
+++ b/docs/sphinx/source/api/pd.rst
@@ -0,0 +1,46 @@
+PD Module (``stx.pd``)
+======================
+
+Pandas DataFrame helper functions for common transformations.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+    import scitex as stx
+    import pandas as pd
+
+    df = pd.DataFrame({
+        "subject": ["A", "A", "B", "B"],
+        "condition": ["ctrl", "exp", "ctrl", "exp"],
+        "score": [10, 15, 12, 18],
+    })
+
+    # Find individual (unique) values
+    subjects = stx.pd.find_indi(df, "subject")
+
+    # Convert to long format
+    melted = stx.pd.melt_cols(df, id_vars=["subject"])
+
+    # Merge columns
+    merged = stx.pd.merge_cols(df, cols=["subject", "condition"], sep="_")
+
+    # Force to DataFrame
+    stx.pd.force_df({"a": [1, 2], "b": [3, 4]})
+
+Available Functions
+-------------------
+
+- ``find_indi(df, col)`` -- Find unique individual identifiers
+- ``find_pval(df)`` -- Find p-value columns in a DataFrame
+- ``force_df(data)`` -- Convert any data to a DataFrame
+- ``melt_cols(df, id_vars)`` -- Melt columns to long format
+- ``merge_cols(df, cols, sep)`` -- Merge multiple columns into one
+- ``to_xyz(df, x, y, z)`` -- Reshape to x, y, z pivot format
+
+API Reference
+-------------
+
+.. automodule:: scitex.pd
+   :members:
diff --git a/docs/sphinx/source/api/project.rst b/docs/sphinx/source/api/project.rst
new file mode 100644
index 000000000..b0440a59f
--- /dev/null
+++ b/docs/sphinx/source/api/project.rst
@@ -0,0 +1,7 @@
+project Module (``stx.project``)
+================================
+
+.. automodule:: scitex.project
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/repro.rst b/docs/sphinx/source/api/repro.rst
new file mode 100644
index 000000000..0e8dc4fea
--- /dev/null
+++ b/docs/sphinx/source/api/repro.rst
@@ -0,0 +1,71 @@
+Repro Module (``stx.repro``)
+============================
+
+Reproducibility utilities: random state management, ID generation,
+timestamps, and array hashing.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   import scitex as stx
+
+   # Fix all random seeds (numpy, torch, random, ...)
+   rng = stx.repro.get()           # Global manager (seed=42)
+   rng = stx.repro.reset(seed=123) # Reset with new seed
+
+   # Named generators for deterministic results
+   data_gen = rng.get_np_generator("data")
+   data = data_gen.random(100)  # Same seed+name = same result
+
+   # Unique identifiers
+   stx.repro.gen_id()
+   # → "2026Y-02M-13D-14h30m15s_a3Bc9xY2"
+
+   stx.repro.gen_timestamp()
+   # → "2026-0213-1430"
+
+   # Verify reproducibility
+   rng.verify(data, "train_data")  # First: caches hash
+   rng.verify(data, "train_data")  # Later: verifies match
+
+RandomStateManager
+------------------
+
+Central class for managing random states across libraries.
+
+.. code-block:: python
+
+   rng = stx.repro.RandomStateManager(seed=42)
+
+   # Named generators (same name + seed = deterministic)
+   np_gen = rng.get_np_generator("experiment")
+   torch_gen = rng.get_torch_generator("model")
+
+   # Checkpoint and restore
+   rng.checkpoint("before_training")
+   rng.restore("before_training.pkl")
+
+   # Temporary seed change
+   with rng.temporary_seed(999):
+       noise = rng.get_np_generator("noise").random(10)
+
+Automatically fixes seeds for: ``random``, ``numpy``, ``torch`` (+ CUDA),
+``tensorflow``, ``jax``.
+
+Available Functions
+-------------------
+
+- ``get(verbose)`` -- Get or create global RandomStateManager singleton
+- ``reset(seed, verbose)`` -- Reset global instance with new seed
+- ``fix_seeds(seed, ...)`` -- Legacy function (use RandomStateManager instead)
+- ``gen_id(time_format, N)`` -- Generate unique timestamp + random ID
+- ``gen_timestamp()`` -- Generate timestamp string for file naming
+- ``hash_array(array_data)`` -- SHA256 hash of numpy array (16 chars)
+
+API Reference
+-------------
+
+.. automodule:: scitex.repro
+   :members:
diff --git a/docs/sphinx/source/api/resource.rst b/docs/sphinx/source/api/resource.rst
new file mode 100644
index 000000000..d4fbcc001
--- /dev/null
+++ b/docs/sphinx/source/api/resource.rst
@@ -0,0 +1,7 @@
+resource Module (``stx.resource``)
+==================================
+
+.. automodule:: scitex.resource
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/rng.rst b/docs/sphinx/source/api/rng.rst
new file mode 100644
index 000000000..a6ab74def
--- /dev/null
+++ b/docs/sphinx/source/api/rng.rst
@@ -0,0 +1,7 @@
+rng Module (``stx.rng``)
+========================
+
+.. automodule:: scitex.rng
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/schema.rst b/docs/sphinx/source/api/schema.rst
new file mode 100644
index 000000000..919582dbf
--- /dev/null
+++ b/docs/sphinx/source/api/schema.rst
@@ -0,0 +1,7 @@
+schema Module (``stx.schema``)
+==============================
+
+.. automodule:: scitex.schema
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/scholar.rst b/docs/sphinx/source/api/scholar.rst
new file mode 100644
index 000000000..2be71119e
--- /dev/null
+++ b/docs/sphinx/source/api/scholar.rst
@@ -0,0 +1,133 @@
+Scholar Module (``stx.scholar``)
+=================================
+
+Literature management: search papers, download PDFs, enrich BibTeX,
+and organize a local library across multiple projects.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   from scitex.scholar import Scholar
+
+   scholar = Scholar(project="my_research")
+
+   # Load and enrich BibTeX
+   papers = scholar.load_bibtex("references.bib")
+   enriched = scholar.enrich_papers(papers)
+   # Adds: DOIs, abstracts, citation counts, impact factors
+
+   # Save to library and export
+   scholar.save_papers_to_library(enriched)
+   scholar.save_papers_as_bibtex(enriched, "enriched.bib")
+
+   # Search your library
+   results = scholar.search_library("neural oscillations")
+
+   # Download PDFs
+   scholar.download_pdfs(dois, output_dir)
+
+CLI Usage
+---------
+
+.. code-block:: bash
+
+   # Full pipeline from BibTeX
+   scitex scholar bibtex refs.bib --project myresearch --num-workers 8
+
+   # Search papers
+   scitex scholar search "deep learning EEG"
+
+   # Download PDFs
+   scitex scholar download --doi 10.1038/nature12373
+
+   # Institutional authentication
+   scitex scholar auth --method openathens
+   scitex scholar auth --method shibboleth --institution "MIT"
+
+Data Sources
+------------
+
+Searches and enriches from:
+
+- **CrossRef** (167M+ papers) -- DOI resolution, citation counts
+- **Semantic Scholar** -- Abstracts, references, influence scores
+- **PubMed** -- Biomedical literature
+- **arXiv** -- Preprints
+- **OpenAlex** (284M+ works) -- Open metadata
+
+Key Classes
+-----------
+
+- ``Scholar`` -- Main entry point (search, enrich, download, organize)
+- ``Paper`` -- Type-safe metadata container (Pydantic model)
+- ``Papers`` -- Collection with filtering, sorting, and export
+- ``ScholarConfig`` -- YAML-based configuration
+- ``ScholarLibrary`` -- Local library storage and caching
+
+Paper Metadata
+--------------
+
+Each ``Paper`` contains structured metadata sections:
+
+.. code-block:: python
+
+   paper.metadata.basic          # title, authors, year, abstract, keywords
+   paper.metadata.id             # DOI, arXiv, PMID, Semantic Scholar ID
+   paper.metadata.publication    # journal, impact factor, volume, issue
+   paper.metadata.citation_count # total + yearly breakdown (2015--2024)
+   paper.metadata.url            # DOI URL, publisher, arXiv, PDFs
+   paper.metadata.access         # open access status, license
+
+Filtering and Sorting
+---------------------
+
+.. code-block:: python
+
+   # Criteria-based filtering
+   recent = papers.filter(year_min=2020, has_doi=True)
+   elite = papers.filter(min_impact_factor=10, min_citations=500)
+
+   # Lambda filtering
+   custom = papers.filter(lambda p: "EEG" in (p.metadata.basic.title or ""))
+
+   # Sorting
+   papers.sort_by("year", reverse=True)
+   papers.sort_by("citation_count", reverse=True)
+
+   # Chaining
+   top_recent = papers.filter(year_min=2020).sort_by("citation_count", reverse=True)
+
+Project Organization
+--------------------
+
+.. code-block:: python
+
+   scholar = Scholar(project="review_paper")
+   scholar.list_projects()
+   papers = scholar.load_project()
+
+   # Export to multiple formats
+   scholar.save_papers_as_bibtex(papers, "output.bib")
+   papers.to_dataframe()  # pandas DataFrame
+
+Storage Architecture
+--------------------
+
+.. code-block:: text
+
+   ~/.scitex/scholar/library/
+   +-- MASTER/                     # Centralized master storage
+   |   +-- 8DIGIT01/              # Hash-based unique ID from DOI
+   |   |   +-- metadata.json
+   |   |   +-- paper.pdf
+   +-- project_name/               # Project-specific symlinks
+       +-- Author-Year-Journal -> ../MASTER/8DIGIT01
+
+API Reference
+-------------
+
+.. automodule:: scitex.scholar
+   :members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/security.rst b/docs/sphinx/source/api/security.rst
new file mode 100644
index 000000000..232a5da7f
--- /dev/null
+++ b/docs/sphinx/source/api/security.rst
@@ -0,0 +1,7 @@
+security Module (``stx.security``)
+==================================
+
+.. automodule:: scitex.security
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/session.rst b/docs/sphinx/source/api/session.rst
new file mode 100644
index 000000000..8f16f4670
--- /dev/null
+++ b/docs/sphinx/source/api/session.rst
@@ -0,0 +1,213 @@
+Session Decorator (``@stx.session``)
+=====================================
+
+The ``@stx.session`` decorator is the primary entry point for SciTeX
+scripts. It wraps a function to provide automatic CLI generation,
+output directory management, configuration injection, and provenance tracking.
+
+Basic Usage
+-----------
+
+.. code-block:: python
+
+   import scitex as stx
+
+   @stx.session
+   def main(
+       data_path="data.csv",       # CLI: --data-path data.csv
+       threshold=0.5,              # CLI: --threshold 0.7
+       CONFIG=stx.INJECTED,        # Auto-injected session config
+       plt=stx.INJECTED,           # Pre-configured matplotlib
+       logger=stx.INJECTED,        # Session logger
+   ):
+       """Analyze experimental data."""
+       data = stx.io.load(data_path)
+       result = process(data, threshold)
+       stx.io.save(result, "output.csv")
+       return 0  # exit code (0 = success)
+
+   if __name__ == "__main__":
+       main()  # No arguments triggers CLI mode
+
+Run from the command line:
+
+.. code-block:: bash
+
+   python my_script.py --data-path experiment.csv --threshold 0.3
+   python my_script.py --help  # Shows all parameters with defaults
+
+How It Works
+------------
+
+.. image:: ../_static/session_lifecycle.png
+   :width: 60%
+   :align: center
+   :alt: Session lifecycle: main() → Parse CLI → Create dir → Load config → Execute → SUCCESS or ERROR
+
+When ``main()`` is called **without arguments**, the decorator:
+
+1. **Parses CLI arguments** from the function signature (type hints and defaults become ``argparse`` options)
+2. **Creates a session directory** under ``script_out/RUNNING/{session_id}/``
+3. **Loads configuration** from ``./config/*.yaml`` files into ``CONFIG``
+4. **Injects globals** (``CONFIG``, ``plt``, ``COLORS``, ``logger``, ``rngg``) into the function
+5. **Redirects stdout/stderr** to log files
+6. **Executes the function** with parsed arguments
+7. **Moves output** from ``RUNNING/`` to ``FINISHED_SUCCESS/`` (or ``FINISHED_ERROR/``)
+
+When called **with arguments** (e.g., ``main(data_path="x.csv")``), the decorator
+is bypassed and the function runs directly -- useful for testing and notebooks.
+
+Output Directory Structure
+--------------------------
+
+Each run produces a self-contained output directory:
+
+.. code-block:: text
+
+   my_script_out/
+   +-- FINISHED_SUCCESS/
+   |   +-- 2026Y-02M-13D-14h30m15s_Z5MR/
+   |       +-- CONFIGS/
+   |       |   +-- CONFIG.yaml     # Frozen configuration
+   |       |   +-- CONFIG.pkl      # Pickled config
+   |       +-- logs/
+   |       |   +-- stdout.log      # Captured stdout
+   |       |   +-- stderr.log      # Captured stderr
+   |       +-- output.csv          # Your saved files
+   |       +-- sine.png            # Your saved figures
+   |       +-- sine.csv            # Auto-exported figure data
+   +-- FINISHED_ERROR/
+   |   +-- ...                     # Runs that returned non-zero
+   +-- RUNNING/
+       +-- ...                     # Currently active sessions
+
+The session ID format is ``YYYY-MM-DD-HH:MM:SS_XXXX`` where ``XXXX`` is
+a random 4-character suffix for uniqueness.
+
+Injected Parameters
+-------------------
+
+Use ``stx.INJECTED`` as the default value to receive auto-injected objects:
+
+.. list-table::
+   :header-rows: 1
+   :widths: 20 20 60
+
+   * - Parameter Name
+     - Type
+     - Description
+   * - ``CONFIG``
+     - ``DotDict``
+     - Session config with ``ID``, ``SDIR_RUN``, ``FILE``, ``ARGS``, plus all ``./config/*.yaml`` values
+   * - ``plt``
+     - module
+     - ``matplotlib.pyplot`` configured for the session (Agg backend, style settings)
+   * - ``COLORS``
+     - ``DotDict``
+     - Color palette for consistent plotting
+   * - ``logger``
+     - Logger
+     - SciTeX logger writing to session log files
+   * - ``rngg``
+     - ``RandomStateManager``
+     - Reproducibility manager (seeds fixed by default)
+
+Only request the parameters you need:
+
+.. code-block:: python
+
+   @stx.session
+   def main(n=100, CONFIG=stx.INJECTED):
+       """Minimal example -- only CONFIG injected."""
+       print(f"Session ID: {CONFIG.ID}")
+       print(f"Output dir: {CONFIG.SDIR_RUN}")
+       return 0
+
+CONFIG Object
+-------------
+
+The injected ``CONFIG`` is a ``DotDict`` supporting both dictionary and
+dot-notation access:
+
+.. code-block:: python
+
+   CONFIG["MODEL"]["hidden_size"]   # dict-style
+   CONFIG.MODEL.hidden_size         # dot-style (equivalent)
+
+It contains:
+
+.. code-block:: python
+
+   CONFIG.ID             # "2026Y-02M-13D-14h30m15s_Z5MR"
+   CONFIG.PID            # Process ID
+   CONFIG.FILE           # Path to the script
+   CONFIG.SDIR_OUT       # Base output directory
+   CONFIG.SDIR_RUN       # Current session's output directory
+   CONFIG.START_DATETIME # When the session started
+   CONFIG.ARGS           # Parsed CLI arguments as dict
+   CONFIG.EXIT_STATUS    # 0 (success), 1 (error), or None
+
+Any YAML files in ``./config/`` are merged into CONFIG:
+
+.. code-block:: yaml
+
+   # ./config/EXPERIMENT.yaml
+   learning_rate: 0.001
+   batch_size: 32
+
+.. code-block:: python
+
+   # Accessible as:
+   CONFIG.EXPERIMENT.learning_rate  # 0.001
+   CONFIG.EXPERIMENT.batch_size     # 32
+
+Decorator Options
+-----------------
+
+.. code-block:: python
+
+   @stx.session(verbose=True, agg=False, notify=True, sdir_suffix="v2")
+   def main(...):
+       ...
+
+.. list-table::
+   :header-rows: 1
+   :widths: 20 15 15 50
+
+   * - Option
+     - Type
+     - Default
+     - Description
+   * - ``verbose``
+     - bool
+     - ``False``
+     - Enable verbose logging
+   * - ``agg``
+     - bool
+     - ``True``
+     - Use matplotlib Agg backend (set ``False`` for interactive plots)
+   * - ``notify``
+     - bool
+     - ``False``
+     - Send notification when session completes
+   * - ``sdir_suffix``
+     - str
+     - ``None``
+     - Append suffix to output directory name
+
+Best Practices
+--------------
+
+1. **One session per script** -- each ``.py`` file should have one ``@stx.session`` function
+2. **Return 0 for success** -- the return value becomes the exit status
+3. **Save outputs with** ``stx.io.save`` -- files go into the session directory and are provenance-tracked
+4. **Put config in YAML** -- use ``./config/*.yaml`` instead of hardcoding parameters
+5. **Use** ``stx.repro.fix_seeds()`` -- already called by default via ``rngg``
+
+API Reference
+-------------
+
+.. automodule:: scitex.session
+   :members:
+   :no-undoc-members:
+   :exclude-members: _InjectedSentinel
diff --git a/docs/sphinx/source/api/sh.rst b/docs/sphinx/source/api/sh.rst
new file mode 100644
index 000000000..7c4694af6
--- /dev/null
+++ b/docs/sphinx/source/api/sh.rst
@@ -0,0 +1,7 @@
+sh Module (``stx.sh``)
+======================
+
+.. automodule:: scitex.sh
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/social.rst b/docs/sphinx/source/api/social.rst
new file mode 100644
index 000000000..cc82af401
--- /dev/null
+++ b/docs/sphinx/source/api/social.rst
@@ -0,0 +1,7 @@
+social Module (``stx.social``)
+==============================
+
+.. automodule:: scitex.social
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/stats.rst b/docs/sphinx/source/api/stats.rst
new file mode 100644
index 000000000..17ca488dd
--- /dev/null
+++ b/docs/sphinx/source/api/stats.rst
@@ -0,0 +1,153 @@
+Stats Module (``stx.stats``)
+============================
+
+23 statistical tests with effect sizes, confidence intervals, and
+publication-ready formatting.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+    import scitex as stx
+    import numpy as np
+
+    g1 = np.random.normal(0, 1, 50)
+    g2 = np.random.normal(0.5, 1, 50)
+
+    # Run a test
+    result = stx.stats.test_ttest_ind(g1, g2)
+
+    # Result is a flat dict with all details
+    print(result["statistic"])     # t-statistic
+    print(result["pvalue"])        # p-value
+    print(result["effect_size"])   # Cohen's d
+    print(result["stars"])         # Significance stars
+
+    # Get as DataFrame or LaTeX
+    df = stx.stats.test_ttest_ind(g1, g2, return_as="dataframe")
+    tex = stx.stats.test_ttest_ind(g1, g2, return_as="latex")
+
+Available Tests
+---------------
+
+**Parametric**
+
+- ``test_ttest_1samp(data, popmean)`` -- One-sample t-test
+- ``test_ttest_ind(g1, g2)`` -- Independent two-sample t-test
+- ``test_ttest_rel(g1, g2)`` -- Paired t-test
+- ``test_anova(*groups)`` -- One-way ANOVA
+- ``test_anova_2way(data, factor1, factor2)`` -- Two-way ANOVA
+- ``test_anova_rm(data, groups)`` -- Repeated measures ANOVA
+
+**Non-parametric**
+
+- ``test_mannwhitneyu(g1, g2)`` -- Mann-Whitney U test
+- ``test_wilcoxon(g1, g2)`` -- Wilcoxon signed-rank test
+- ``test_kruskal(*groups)`` -- Kruskal-Wallis H test
+- ``test_friedman(*groups)`` -- Friedman test
+- ``test_brunner_munzel(g1, g2)`` -- Brunner-Munzel test
+
+**Correlation**
+
+- ``test_pearson(x, y)`` -- Pearson correlation
+- ``test_spearman(x, y)`` -- Spearman rank correlation
+- ``test_kendall(x, y)`` -- Kendall tau correlation
+- ``test_theilsen(x, y)`` -- Theil-Sen robust regression
+
+**Categorical**
+
+- ``test_chi2(observed)`` -- Chi-squared test
+- ``test_fisher(table)`` -- Fisher's exact test
+- ``test_mcnemar(table)`` -- McNemar test
+- ``test_cochran_q(*groups)`` -- Cochran's Q test
+
+**Normality**
+
+- ``test_shapiro(data)`` -- Shapiro-Wilk test
+- ``test_ks_1samp(data)`` -- One-sample Kolmogorov-Smirnov test
+- ``test_ks_2samp(x, y)`` -- Two-sample Kolmogorov-Smirnov test
+- ``test_normality(*samples)`` -- Multi-sample normality check
+
+Seaborn-Style Data Parameter
+----------------------------
+
+All two-sample and one-sample tests accept an optional ``data`` parameter
+for DataFrame/CSV column resolution (like seaborn):
+
+.. code-block:: python
+
+   import pandas as pd
+
+   df = pd.read_csv("experiment.csv")
+
+   # Two-sample: column names as x/y
+   result = stx.stats.test_ttest_ind(x="before", y="after", data=df)
+
+   # One-sample: column name as x
+   result = stx.stats.test_shapiro(x="scores", data=df)
+
+   # Multi-group: value + group columns
+   result = stx.stats.test_anova(data=df, value_col="score", group_col="treatment")
+
+   # Also works with CSV path
+   result = stx.stats.test_ttest_ind(x="col1", y="col2", data="data.csv")
+
+Test Recommendation
+-------------------
+
+Not sure which test to use? Let SciTeX recommend:
+
+.. code-block:: python
+
+    recommendations = stx.stats.recommend_tests(
+        n_groups=2,
+        sample_sizes=[30, 35],
+        outcome_type="continuous",
+        paired=False,
+    )
+
+Output Formats
+--------------
+
+Every test supports ``return_as`` parameter:
+
+- ``"dict"`` (default) -- Returns plain dict with all results
+- ``"dataframe"`` -- Returns pandas DataFrame
+
+Descriptive Statistics
+----------------------
+
+.. code-block:: python
+
+    stx.stats.describe(data)                    # mean, std, median, IQR, etc.
+    stx.stats.effect_sizes.cohens_d(g1, g2)     # Cohen's d
+    stx.stats.test_normality(g1, g2)            # Multi-sample normality
+    stx.stats.p_to_stars(0.003)                 # "**"
+
+Multiple Comparison Correction
+------------------------------
+
+.. code-block:: python
+
+    corrected = stx.stats.correct_pvalues(
+        [0.01, 0.03, 0.05, 0.001],
+        method="fdr_bh",
+    )
+
+Post-hoc Tests
+--------------
+
+.. code-block:: python
+
+    stx.stats.posthoc_test(
+        [g1, g2, g3],
+        group_names=["Control", "Treatment A", "Treatment B"],
+        method="tukey",
+    )
+
+API Reference
+-------------
+
+.. automodule:: scitex.stats
+   :members:
diff --git a/docs/sphinx/source/api/str.rst b/docs/sphinx/source/api/str.rst
new file mode 100644
index 000000000..b29b4f485
--- /dev/null
+++ b/docs/sphinx/source/api/str.rst
@@ -0,0 +1,7 @@
+str Module (``stx.str``)
+========================
+
+.. automodule:: scitex.str
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/template.rst b/docs/sphinx/source/api/template.rst
new file mode 100644
index 000000000..44b943dd2
--- /dev/null
+++ b/docs/sphinx/source/api/template.rst
@@ -0,0 +1,86 @@
+Template Module (``stx.template``)
+====================================
+
+Project scaffolding and code snippet templates for quick starts.
+
+Project Templates
+-----------------
+
+.. code-block:: bash
+
+   # Clone a project template
+   scitex template clone research my_project
+   scitex template clone pip_project my_package
+   scitex template clone paper my_paper
+
+.. list-table::
+   :header-rows: 1
+   :widths: 20 80
+
+   * - Template
+     - Description
+   * - ``research``
+     - Full scientific workflow (scripts, data, docs, config)
+   * - ``research_minimal``
+     - Essential modules only
+   * - ``pip_project``
+     - Distributable Python package for PyPI
+   * - ``singularity``
+     - Reproducible containerized environment
+   * - ``paper_directory``
+     - Academic paper with LaTeX/BibTeX structure
+
+Git Strategies
+--------------
+
+.. list-table::
+   :header-rows: 1
+   :widths: 20 80
+
+   * - Strategy
+     - Behavior
+   * - ``child`` (default)
+     - Fresh git repo, isolated from template
+   * - ``parent``
+     - Use parent repo if available
+   * - ``origin``
+     - Preserve template's git history
+   * - ``None``
+     - No git initialization
+
+Code Templates
+--------------
+
+.. code-block:: bash
+
+   # List available code templates
+   scitex template code list
+
+   # Get a template
+   scitex template code session           # Full @stx.session script
+   scitex template code session-minimal   # Lightweight session
+   scitex template code session-plot      # Figure-focused session
+   scitex template code session-stats     # Statistics-focused session
+   scitex template code io                # I/O operations
+   scitex template code plt               # Plotting patterns
+   scitex template code stats             # Statistical analysis
+   scitex template code scholar           # Literature management
+
+Python API
+----------
+
+.. code-block:: python
+
+   from scitex.template import clone_template, get_code_template
+
+   # Clone project
+   clone_template("research", "my_experiment", git_strategy="child")
+
+   # Get code snippet
+   code = get_code_template("session", filepath="analyze.py")
+
+API Reference
+-------------
+
+.. automodule:: scitex.template
+   :members:
diff --git a/docs/sphinx/source/api/tex.rst b/docs/sphinx/source/api/tex.rst
new file mode 100644
index 000000000..e0f775bd9
--- /dev/null
+++ b/docs/sphinx/source/api/tex.rst
@@ -0,0 +1,7 @@
+tex Module (``stx.tex``)
+========================
+
+.. automodule:: scitex.tex
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/torch.rst b/docs/sphinx/source/api/torch.rst
new file mode 100644
index 000000000..1a11fe241
--- /dev/null
+++ b/docs/sphinx/source/api/torch.rst
@@ -0,0 +1,7 @@
+torch Module (``stx.torch``)
+============================
+
+.. automodule:: scitex.torch
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/tunnel.rst b/docs/sphinx/source/api/tunnel.rst
new file mode 100644
index 000000000..e28928527
--- /dev/null
+++ b/docs/sphinx/source/api/tunnel.rst
@@ -0,0 +1,7 @@
+tunnel Module (``stx.tunnel``)
+==============================
+
+.. automodule:: scitex.tunnel
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/types.rst b/docs/sphinx/source/api/types.rst
new file mode 100644
index 000000000..f4f1e1031
--- /dev/null
+++ b/docs/sphinx/source/api/types.rst
@@ -0,0 +1,7 @@
+types Module (``stx.types``)
+============================
+
+.. automodule:: scitex.types
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/ui.rst b/docs/sphinx/source/api/ui.rst
new file mode 100644
index 000000000..2a8a65a64
--- /dev/null
+++ b/docs/sphinx/source/api/ui.rst
@@ -0,0 +1,7 @@
+ui Module (``stx.ui``)
+======================
+
+.. automodule:: scitex.ui
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/utils.rst b/docs/sphinx/source/api/utils.rst
new file mode 100644
index 000000000..9b893ac20
--- /dev/null
+++ b/docs/sphinx/source/api/utils.rst
@@ -0,0 +1,7 @@
+utils Module (``stx.utils``)
+============================
+
+.. automodule:: scitex.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/web.rst b/docs/sphinx/source/api/web.rst
new file mode 100644
index 000000000..5b6589d9d
--- /dev/null
+++ b/docs/sphinx/source/api/web.rst
@@ -0,0 +1,7 @@
+web Module (``stx.web``)
+========================
+
+.. automodule:: scitex.web
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sphinx/source/api/writer.rst b/docs/sphinx/source/api/writer.rst
new file mode 100644
index 000000000..c03eaeee1
--- /dev/null
+++ b/docs/sphinx/source/api/writer.rst
@@ -0,0 +1,166 @@
+Writer Module (``stx.writer``)
+==============================
+
+LaTeX manuscript compilation, figure/table management, bibliography
+handling, and IMRAD writing guidelines.
+
+.. note::
+
+   ``stx.writer`` wraps the standalone
+   `scitex-writer <https://github.com/ywatanabe1989/scitex-writer>`_ package.
+   Install with: ``pip install scitex-writer``.
+
+Quick Reference
+---------------
+
+.. code-block:: python
+
+   from scitex.writer import Writer
+   from pathlib import Path
+
+   writer = Writer(Path("my_paper"))
+
+   # Compile manuscript → PDF
+   result = writer.compile_manuscript()
+   if result.success:
+       print(f"PDF: {result.output_pdf}")
+
+   # Compile supplementary materials
+   result = writer.compile_supplementary()
+
+   # Compile revision with change tracking
+   result = writer.compile_revision(track_changes=True)
+
+CLI Usage
+---------
+
+.. code-block:: bash
+
+   # Compile
+   scitex writer compile manuscript ./my-paper
+   scitex writer compile supplementary ./my-paper
+   scitex writer compile revision ./my-paper --track-changes
+
+   # Bibliography
+   scitex writer bib list ./my-paper
+   scitex writer bib add ./my-paper "@article{...}"
+
+   # Tables and figures
+   scitex writer tables add ./my-paper data.csv
+   scitex writer figures list ./my-paper
+
+   # Writing guidelines
+   scitex writer guidelines get abstract
+
+Project Structure
+-----------------
+
+A writer project follows this layout:
+
+.. code-block:: text
+
+   my_paper/
+   +-- 00_shared/
+   |   +-- bibliography.bib
+   |   +-- figures/
+   |   +-- tables/
+   +-- 01_manuscript/
+   |   +-- main.tex
+   |   +-- sections/
+   +-- 02_supplementary/
+   |   +-- main.tex
+   +-- 03_revision/
+       +-- main.tex
+
+Create a new project:
+
+.. code-block:: bash
+
+   scitex template clone paper my_paper
+
+Key Classes
+-----------
+
+- ``Writer`` -- Main entry point for compilation and project management
+- ``CompilationResult`` -- Compilation outcome (success, output path, logs)
+- ``ManuscriptTree`` -- Document tree for the main manuscript
+- ``SupplementaryTree`` -- Document tree for supplementary materials
+- ``RevisionTree`` -- Document tree for revision responses
+
+Document Management
+-------------------
+
+**Figures:**
+
+.. code-block:: python
+
+   # Add figure (copies image + creates caption file)
+   writer.add_figure("fig1", "plot.png", caption="Results")
+
+   # List figures
+   writer.list_figures()
+
+   # Convert between formats
+   writer.convert_figure("figure.pdf", "figure.png", dpi=300)
+
+**Tables:**
+
+.. code-block:: python
+
+   # Add table from CSV
+   writer.add_table("tab1", csv_content, caption="Demographics")
+
+   # CSV ↔ LaTeX conversion
+   writer.csv_to_latex("data.csv", "table.tex")
+   writer.latex_to_csv("table.tex", "data.csv")
+
+**Bibliography:**
+
+.. code-block:: python
+
+   # Add BibTeX entry
+   writer.add_bibentry('@article{key, title={...}, ...}')
+
+   # Merge multiple .bib files
+   writer.merge_bibfiles(output_file="bibliography.bib")
+
+Writing Guidelines
+------------------
+
+IMRAD guidelines for each manuscript section:
+
+.. code-block:: bash
+
+   scitex writer guidelines list
+   scitex writer guidelines get introduction
+
+.. code-block:: python
+
+   from scitex.writer import guidelines
+
+   # Get guideline for a section
+   guide = guidelines.get("methods")
+
+   # Build editing prompt: guideline + draft
+   prompt = guidelines.build("discussion", draft_text)
+
+Compilation Options
+-------------------
+
+.. code-block:: python
+
+   result = writer.compile_manuscript(
+       timeout=300,        # Max compilation time (seconds)
+       no_figs=False,      # Exclude figures
+       no_tables=False,    # Exclude tables
+       draft=False,        # Draft mode (fast, lower quality)
+       dark_mode=False,    # Dark color scheme
+       quiet=False,        # Suppress output
+   )
+
+API Reference
+-------------
+
+.. automodule:: scitex.writer
+   :members:
+   :show-inheritance:

From 5ce05b9089b179052b12e2233326ad5fccfa383c Mon Sep 17 00:00:00 2001
From: Yusuke Watanabe <ywatanabe@scitex.ai>
Date: Sun, 15 Mar 2026 10:28:48 +1100
Subject: [PATCH 3/5] fix(notify): pass kwargs through notify_handler to
 backends

notify_call MCP tool was failing because repeat, to_number, and
flow_sid were rejected by notify_handler. Add **kwargs passthrough
to get_backend() and b.send().

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 src/scitex/notify/_mcp/handlers.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/scitex/notify/_mcp/handlers.py b/src/scitex/notify/_mcp/handlers.py
index b5e40e772..a4a56ed2d 100755
--- a/src/scitex/notify/_mcp/handlers.py
+++ b/src/scitex/notify/_mcp/handlers.py
@@ -25,6 +25,7 @@ async def notify_handler(
     backend: Optional[str] = None,
     backends: Optional[list[str]] = None,
     timeout: float = 5.0,
+    **kwargs,
 ) -> dict:
     """Send notification via specified backend(s)."""
     from .._backends import BACKENDS, NotifyLevel, get_backend
@@ -61,12 +62,13 @@ async def notify_handler(
                     )
                     continue
 
-                b = get_backend(backend_name)
+                b = get_backend(backend_name, **kwargs)
                 result = await b.send(
                     message,
                     title=title,
                     level=notify_level,
                     timeout=timeout,
+                    **kwargs,
                 )
 
                 results.append(

From fa0e12d480401fa0cb5c2cb0998f2ba68a45e04c Mon Sep 17 00:00:00 2001
From: Yusuke Watanabe <ywatanabe@scitex.ai>
Date: Mon, 16 Mar 2026 06:57:11 +1100
Subject: [PATCH 4/5] refactor(notify): delegate to standalone
 scitex-notification package

- Add scitex-notification>=0.1.0 dependency
- Replace notify/__init__.py with thin re-export wrapper
- Update _mcp_tools/notify.py imports to scitex_notification
- Update cli/notify.py imports to scitex_notification
- Add scitex-notification to ecosystem registry

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 pyproject.toml                  |   1 +
 src/scitex/_dev/_ecosystem.py   |   6 +
 src/scitex/_mcp_tools/notify.py |  15 +-
 src/scitex/cli/notify.py        |  10 +-
 src/scitex/notify/__init__.py   | 297 ++------------------------------
 5 files changed, 34 insertions(+), 295 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5165ad869..ba4fbff68 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -69,6 +69,7 @@ dependencies = [
     "scitex-io>=0.2.0",
     "scitex-stats>=0.2.0",
     "scitex-audio>=0.1.0",
+    "scitex-notification>=0.1.0",
 ]
 
 [project.urls]
diff --git a/src/scitex/_dev/_ecosystem.py b/src/scitex/_dev/_ecosystem.py
index c6270861d..04eae4f2b 100755
--- a/src/scitex/_dev/_ecosystem.py
+++ b/src/scitex/_dev/_ecosystem.py
@@ -43,6 +43,12 @@ class PackageInfo(TypedDict, total=False):
         "github_repo": "ywatanabe1989/scitex-clew",
         "import_name": "scitex_clew",
     },
+    "scitex-notification": {
+        "local_path": "~/proj/scitex-notification",
+        "pypi_name": "scitex-notification",
+        "github_repo": "ywatanabe1989/scitex-notification",
+        "import_name": "scitex_notification",
+    },
     "scitex-cloud": {
         "local_path": "~/proj/scitex-cloud",
         "pypi_name": "scitex-cloud",
diff --git a/src/scitex/_mcp_tools/notify.py b/src/scitex/_mcp_tools/notify.py
index ed7cbc832..1da7855f3 100755
--- a/src/scitex/_mcp_tools/notify.py
+++ b/src/scitex/_mcp_tools/notify.py
@@ -18,8 +18,7 @@ async def notify_send(
     ) -> str:
         """Send a notification via configured backends."""
         from scitex_dev.mcp_utils import async_wrap_as_mcp
-
-        from scitex.notify._mcp.handlers import notify_handler
+        from scitex_notification._mcp.handlers import notify_handler
 
         return await async_wrap_as_mcp(
             notify_handler,
@@ -46,8 +45,7 @@ async def notify_call(
         Use repeat=2 to bypass iOS silent/manner mode (calls 30s apart).
         """
         from scitex_dev.mcp_utils import async_wrap_as_mcp
-
-        from scitex.notify._mcp.handlers import notify_handler
+        from scitex_notification._mcp.handlers import notify_handler
 
         kwargs = {"repeat": repeat}
         if to_number:
@@ -74,8 +72,7 @@ async def notify_sms(
     ) -> str:
         """Send an SMS via Twilio."""
         from scitex_dev.mcp_utils import async_wrap_as_mcp
-
-        from scitex.notify._backends._twilio import send_sms
+        from scitex_notification._backends._twilio import send_sms
 
         kwargs = {}
         if to_number:
@@ -93,8 +90,7 @@ async def notify_sms(
     async def notify_backends() -> str:
         """List all notification backends and their availability."""
         from scitex_dev.mcp_utils import async_wrap_as_mcp
-
-        from scitex.notify._mcp.handlers import list_backends_handler
+        from scitex_notification._mcp.handlers import list_backends_handler
 
         return await async_wrap_as_mcp(
             list_backends_handler,
@@ -105,8 +101,7 @@ async def notify_backends() -> str:
     async def notify_config() -> str:
         """Get current notification configuration."""
         from scitex_dev.mcp_utils import async_wrap_as_mcp
-
-        from scitex.notify._mcp.handlers import get_config_handler
+        from scitex_notification._mcp.handlers import get_config_handler
 
         return await async_wrap_as_mcp(
             get_config_handler,
diff --git a/src/scitex/cli/notify.py b/src/scitex/cli/notify.py
index d2c2d6579..73dfac3d3 100755
--- a/src/scitex/cli/notify.py
+++ b/src/scitex/cli/notify.py
@@ -307,8 +307,12 @@ def list_backends(as_json):
       scitex notify backends --json
     """
     try:
-        from scitex.notify import DEFAULT_FALLBACK_ORDER, available_backends
-        from scitex.notify._backends import BACKENDS
+        from scitex_notification._backends import BACKENDS  # noqa: E402
+
+        from scitex.notify import (  # noqa: E402
+            DEFAULT_FALLBACK_ORDER,
+            available_backends,
+        )
 
         available = available_backends()
 
@@ -363,7 +367,7 @@ def config(as_json):
       scitex notify config --json
     """
     try:
-        from scitex.notify._backends._config import get_config
+        from scitex_notification._backends._config import get_config
 
         cfg = get_config()
 
diff --git a/src/scitex/notify/__init__.py b/src/scitex/notify/__init__.py
index 41c3076af..219e1ac88 100755
--- a/src/scitex/notify/__init__.py
+++ b/src/scitex/notify/__init__.py
@@ -1,297 +1,30 @@
 #!/usr/bin/env python3
-# Timestamp: "2026-01-13 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/ui/__init__.py
+"""SciTeX Notify — thin wrapper delegating to scitex-notification package.
 
-"""SciTeX UI Module - User alerts and feedback.
-
-Usage:
-    import scitex
-
-    # Simple alert - uses fallback priority (audio → emacs → desktop → ...)
-    scitex.notify.alert("2FA required!")
-
-    # Specify backend (no fallback)
-    scitex.notify.alert("Error", backend="email")
-
-    # Multiple backends (tries all)
-    scitex.notify.alert("Critical", backend=["audio", "email"])
-
-    # Use fallback explicitly
-    scitex.notify.alert("Important", fallback=True)
-
-    # Make a phone call via Twilio
-    scitex.notify.call("Critical alert!")
-
-Environment Variables:
-    SCITEX_NOTIFY_DEFAULT_BACKEND: audio, email, desktop, webhook
-    SCITEX_UI_DEFAULT_BACKEND: (deprecated) use SCITEX_NOTIFY_DEFAULT_BACKEND
+All notification logic lives in the standalone scitex-notification package.
+This module re-exports the public API for backward compatibility.
 """
 
-from __future__ import annotations
-
-import asyncio
-import os
-from typing import Optional, Union
-
-from ._backends import NotifyLevel as _AlertLevel
-from ._backends import available_backends as _available_backends
-from ._backends import get_backend as _get_backend
+from scitex_notification import (
+    DEFAULT_FALLBACK_ORDER,
+    alert,
+    alert_async,
+    available_backends,
+    call,
+    call_async,
+    sms,
+    sms_async,
+)
 
 __all__ = [
     "alert",
     "alert_async",
-    "available_backends",
     "call",
     "call_async",
     "sms",
     "sms_async",
+    "available_backends",
+    "DEFAULT_FALLBACK_ORDER",
 ]
 
-# Default fallback priority order
-DEFAULT_FALLBACK_ORDER = [
-    "audio",  # 1st: TTS audio (non-blocking, immediate)
-    "emacs",  # 2nd: Emacs minibuffer (if in Emacs)
-    "matplotlib",  # 3rd: Visual popup
-    "playwright",  # 4th: Browser popup
-    "email",  # 5th: Email (slowest, most reliable)
-]
-
-
-def available_backends() -> list[str]:
-    """Return list of available alert backends."""
-    return _available_backends()
-
-
-async def alert_async(
-    message: str,
-    title: Optional[str] = None,
-    backend: Optional[Union[str, list[str]]] = None,
-    level: str = "info",
-    fallback: bool = True,
-    **kwargs,
-) -> bool:
-    """Send alert asynchronously.
-
-    Parameters
-    ----------
-    message : str
-        Alert message
-    title : str, optional
-        Alert title
-    backend : str or list[str], optional
-        Backend(s) to use. If None, uses default with fallback.
-    level : str
-        Alert level: info, warning, error, critical
-    fallback : bool
-        If True and backend fails, try next in priority order.
-        Default True when backend=None, False when backend specified.
-
-    Returns
-    -------
-    bool
-        True if any backend succeeded
-    """
-    try:
-        lvl = _AlertLevel(level.lower())
-    except ValueError:
-        lvl = _AlertLevel.INFO
-
-    # Determine backends to try
-    if backend is None:
-        # No backend specified: use fallback priority
-        default = os.getenv("SCITEX_NOTIFY_DEFAULT_BACKEND") or os.getenv(
-            "SCITEX_UI_DEFAULT_BACKEND", "audio"
-        )
-        if fallback:
-            # Start with default, then try others in priority order
-            backends = [default] + [b for b in DEFAULT_FALLBACK_ORDER if b != default]
-        else:
-            backends = [default]
-    else:
-        # Backend specified: use it (with optional fallback)
-        backends = [backend] if isinstance(backend, str) else list(backend)
-        if fallback and len(backends) == 1:
-            # Add fallback backends after the specified one
-            backends = backends + [
-                b for b in DEFAULT_FALLBACK_ORDER if b not in backends
-            ]
-
-    # Try backends until one succeeds
-    available = _available_backends()
-    for name in backends:
-        if name not in available:
-            continue
-        try:
-            b = _get_backend(name)
-            result = await b.send(message, title=title, level=lvl, **kwargs)
-            if result.success:
-                return True
-        except Exception:
-            pass
-
-    return False
-
-
-def alert(
-    message: str,
-    title: Optional[str] = None,
-    backend: Optional[Union[str, list[str]]] = None,
-    level: str = "info",
-    fallback: bool = True,
-    **kwargs,
-) -> bool:
-    """Send alert synchronously.
-
-    Parameters
-    ----------
-    message : str
-        Alert message
-    title : str, optional
-        Alert title
-    backend : str or list[str], optional
-        Backend(s) to use. If None, uses fallback priority order.
-    level : str
-        Alert level: info, warning, error, critical
-    fallback : bool
-        If True and backend fails, try next in priority order.
-
-    Returns
-    -------
-    bool
-        True if any backend succeeded
-
-    Fallback Order
-    --------------
-    1. audio      - TTS (fast, non-blocking)
-    2. emacs      - Minibuffer message
-    3. matplotlib - Visual popup
-    4. playwright - Browser popup
-    5. email      - Email (slowest)
-    """
-    try:
-        asyncio.get_running_loop()
-        import concurrent.futures
-
-        with concurrent.futures.ThreadPoolExecutor() as executor:
-            future = executor.submit(
-                asyncio.run,
-                alert_async(message, title, backend, level, fallback, **kwargs),
-            )
-            return future.result(timeout=30)
-    except RuntimeError:
-        return asyncio.run(
-            alert_async(message, title, backend, level, fallback, **kwargs)
-        )
-
-
-def call(
-    message: str,
-    title: Optional[str] = None,
-    level: str = "info",
-    to_number: Optional[str] = None,
-    **kwargs,
-) -> bool:
-    """Make a phone call via Twilio.
-
-    Convenience wrapper for alert(backend="twilio").
-    """
-    return alert(
-        message,
-        title=title,
-        backend="twilio",
-        level=level,
-        fallback=False,
-        to_number=to_number,
-        **kwargs,
-    )
-
-
-async def call_async(
-    message: str,
-    title: Optional[str] = None,
-    level: str = "info",
-    to_number: Optional[str] = None,
-    **kwargs,
-) -> bool:
-    """Make a phone call via Twilio (async)."""
-    return await alert_async(
-        message,
-        title=title,
-        backend="twilio",
-        level=level,
-        fallback=False,
-        to_number=to_number,
-        **kwargs,
-    )
-
-
-async def sms_async(
-    message: str,
-    title: Optional[str] = None,
-    to_number: Optional[str] = None,
-    **kwargs,
-) -> bool:
-    """Send an SMS via Twilio (async).
-
-    Parameters
-    ----------
-    message : str
-        SMS body text
-    title : str, optional
-        Prepended to message if provided
-    to_number : str, optional
-        Override SCITEX_NOTIFY_TWILIO_TO
-
-    Returns
-    -------
-    bool
-        True if SMS sent successfully
-    """
-    from ._backends._twilio import send_sms as _send_sms
-
-    result = await _send_sms(
-        message,
-        title=title,
-        to_number=to_number,
-        **kwargs,
-    )
-    return result.success
-
-
-def sms(
-    message: str,
-    title: Optional[str] = None,
-    to_number: Optional[str] = None,
-    **kwargs,
-) -> bool:
-    """Send an SMS via Twilio.
-
-    Parameters
-    ----------
-    message : str
-        SMS body text
-    title : str, optional
-        Prepended to message if provided
-    to_number : str, optional
-        Override SCITEX_NOTIFY_TWILIO_TO
-
-    Returns
-    -------
-    bool
-        True if SMS sent successfully
-    """
-    try:
-        asyncio.get_running_loop()
-        import concurrent.futures
-
-        with concurrent.futures.ThreadPoolExecutor() as executor:
-            future = executor.submit(
-                asyncio.run,
-                sms_async(message, title, to_number, **kwargs),
-            )
-            return future.result(timeout=30)
-    except RuntimeError:
-        return asyncio.run(sms_async(message, title, to_number, **kwargs))
-
-
 # EOF

From 3751bb51dd05e6582b860a8a9f07cd6ac00f334a Mon Sep 17 00:00:00 2001
From: Yusuke Watanabe <ywatanabe@scitex.ai>
Date: Mon, 16 Mar 2026 17:15:03 +1100
Subject: [PATCH 5/5] docs: add Star History chart to README

Dark/light mode compatible via <picture> element.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 README.md | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index c1a25c4ca..0eaca42ec 100755
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 <!-- ---
-!-- Timestamp: 2026-02-16 10:13:53
+!-- Timestamp: 2026-03-16 17:14:33
 !-- Author: ywatanabe
 !-- File: /home/ywatanabe/proj/scitex-python/README.md
 !-- --- -->
@@ -43,7 +43,7 @@ SciTeX provides a **modular Python toolkit** that unifies the research workflow
 
 ## Demo
 
-**40 min, zero human intervention** — AI agent conducts full research pipeline:
+**40 min, minimal human intervention** — AI agent conducts full research pipeline:
 
 > Literature search → Data analysis → Statistics → Figures → 21-page manuscript → Peer review simulation
 
@@ -304,8 +304,20 @@ The SciTeX system follows the Four Freedoms for Research below, inspired by [the
 
 ---
 
+## Star History
+
+<a href="https://star-history.com/#ywatanabe1989/scitex-python&Date">
+ <picture>
+   <source media="(prefers-color-scheme: dark)" srcset="https://api.star-history.com/svg?repos=ywatanabe1989/scitex-python&type=Date&theme=dark" />
+   <source media="(prefers-color-scheme: light)" srcset="https://api.star-history.com/svg?repos=ywatanabe1989/scitex-python&type=Date" />
+   <img alt="Star History Chart" src="https://api.star-history.com/svg?repos=ywatanabe1989/scitex-python&type=Date" />
+ </picture>
+</a>
+
+---
+
 <p align="center">
   <a href="https://scitex.ai" target="_blank"><img src="docs/assets/images/scitex-icon-navy-inverted.png" alt="SciTeX" width="40"/></a>
 </p>
 
-<!-- EOF -->
+<!-- EOF -->
\ No newline at end of file