scitex 2.14.0__py3-none-any.whl → 2.15.3__py3-none-any.whl

scitex/template/_templates/writer.py

@@ -0,0 +1,296 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-25
+# File: src/scitex/template/_templates/writer.py
+# ----------------------------------------
+
+"""Template for stx.writer LaTeX manuscript compilation module usage."""
+
+TEMPLATE = {
+    "name": "Writer Module",
+    "description": "stx.writer usage for LaTeX manuscript compilation and paper writing",
+    "filename": "writer_script.py",
+    "priority": 9,
+    "content": '''#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: {timestamp}
+# File: {filepath}
+
+"""
+stx.writer - LaTeX Manuscript Compilation
+=========================================
+
+stx.writer provides:
+- LaTeX to PDF compilation
+- BibTeX bibliography processing
+- Figure and table management
+- Word count and statistics
+- Manuscript structure scaffolding
+
+Usage Patterns
+--------------
+1. CLI: scitex writer <command> [options]
+2. MCP: writer_usage tool for documentation
+3. Python API: stx.writer.* functions
+
+Typical Workflow
+----------------
+1. Clone paper template: scitex template clone paper ./manuscript
+2. Write manuscript: Edit .tex files
+3. Compile: scitex writer compile ./manuscript
+4. Check: scitex writer wordcount ./manuscript
+"""
+
+import scitex as stx
+
+# ============================================================
+# Pattern 1: CLI Usage (Recommended)
+# ============================================================
+
+"""
+CLI Commands:
+-------------
+
+# Compile manuscript to PDF
+scitex writer compile ./manuscript
+scitex writer compile ./manuscript --output paper.pdf
+
+# Compile with bibliography
+scitex writer compile ./manuscript --bib
+
+# Clean auxiliary files
+scitex writer clean ./manuscript
+
+# Word count
+scitex writer wordcount ./manuscript
+
+# Check for common LaTeX errors
+scitex writer check ./manuscript
+
+# Watch for changes and auto-compile
+scitex writer watch ./manuscript
+"""
+
+# ============================================================
+# Pattern 2: Project Structure
+# ============================================================
+
+"""
+Recommended Manuscript Structure:
+---------------------------------
+
+manuscript/
+  main.tex              # Main document
+  sections/
+    abstract.tex        # Abstract
+    introduction.tex    # Introduction
+    methods.tex         # Methods
+    results.tex         # Results
+    discussion.tex      # Discussion
+    references.tex      # References section
+  figures/
+    fig1.png            # Figure files
+    fig2.pdf
+  tables/
+    table1.tex          # LaTeX tables
+  references.bib        # BibTeX bibliography
+  config/
+    preamble.tex        # Custom packages/macros
+
+Create this structure with:
+scitex template clone paper ./manuscript
+"""
+
+# ============================================================
+# Pattern 3: LaTeX Best Practices
+# ============================================================
+
+"""
+LaTeX Writing Guidelines:
+-------------------------
+
+1. Document Structure:
+   \\\\documentclass[article]
+   \\\\input[config/preamble]
+   \\\\begin[document]
+   \\\\input[sections/abstract]
+   \\\\input[sections/introduction]
+   \\\\input[sections/methods]
+   \\\\input[sections/results]
+   \\\\input[sections/discussion]
+   \\\\bibliography[references]
+   \\\\end[document]
+
+2. Figure Inclusion:
+   \\\\begin[figure][htbp]
+       \\\\centering
+       \\\\includegraphics[width=0.8\\\\linewidth][figures/fig1.png]
+       \\\\caption[Description of the figure.]
+       \\\\label[fig:main]
+   \\\\end[figure]
+
+3. Table Inclusion:
+   \\\\begin[table][htbp]
+       \\\\centering
+       \\\\caption[Description of the table.]
+       \\\\label[tab:results]
+       \\\\input[tables/table1]
+   \\\\end[table]
+
+4. Citations:
+   As shown in previous work~\\\\cite[author2023]...
+   Multiple citations~\\\\cite[ref1,ref2,ref3]...
+
+5. Cross-references:
+   See Figure~\\\\ref[fig:main]...
+   Table~\\\\ref[tab:results] shows...
+   Section~\\\\ref[sec:methods] describes...
+
+Note: Replace [] with curly braces in actual LaTeX code.
+"""
+
+# ============================================================
+# Pattern 4: BibTeX Management
+# ============================================================
+
+"""
+BibTeX Best Practices:
+----------------------
+
+# references.bib structure
+@article key=author2023,
+  author  = Smith, John and Doe, Jane,
+  title   = Title of the Paper,
+  journal = Journal Name,
+  year    = 2023,
+  volume  = 10,
+  pages   = 1--15,
+  doi     = 10.1000/example
+
+
+# Enrich with scitex scholar
+scitex scholar enrich --bibtex references.bib
+
+# This adds:
+# - Missing DOIs
+# - Abstracts
+# - Citation counts
+# - Impact factors
+"""
+
+# ============================================================
+# Pattern 5: Integration with SciTeX
+# ============================================================
+
+@stx.session
+def main(
+    manuscript_dir="./manuscript",
+    CONFIG=stx.INJECTED,
+    logger=stx.INJECTED,
+):
+    """Manuscript preparation workflow."""
+    from pathlib import Path
+
+    ms_dir = Path(manuscript_dir)
+
+    # 1. Generate figures from analysis
+    logger.info("Generating figures...")
+    # (figures created with stx.plt would go in ms_dir/figures/)
+
+    # 2. Generate tables from data
+    logger.info("Generating tables...")
+    # (tables created with stx.io.save() in LaTeX format)
+
+    # 3. Copy to manuscript directory
+    import shutil
+    if (CONFIG.SDIR_OUT / "figures").exists():
+        for fig in (CONFIG.SDIR_OUT / "figures").glob("*.png"):
+            shutil.copy(fig, ms_dir / "figures" / fig.name)
+            logger.info("Copied figure to manuscript")
+
+    logger.info("Figures ready in manuscript/figures/")
+    return 0
+
+# ============================================================
+# Pattern 6: Python API
+# ============================================================
+
+def python_api_example():
+    """Direct Python API for writer."""
+    from scitex.writer import (
+        compile_manuscript,
+        clean_auxiliary,
+        word_count,
+        check_manuscript,
+    )
+
+    # Compile
+    result = compile_manuscript(
+        manuscript_dir="./manuscript",
+        output="paper.pdf",
+        bibliography=True
+    )
+    print("Compilation complete")
+
+    # Word count
+    stats = word_count("./manuscript")
+    print("Word count complete")
+
+    # Check for issues
+    issues = check_manuscript("./manuscript")
+    for issue in issues:
+        print("Warning found")
+
+    # Clean
+    clean_auxiliary("./manuscript")
+
+# ============================================================
+# Pattern 7: Automated Paper Generation
+# ============================================================
+
+"""
+Automated Workflow:
+-------------------
+
+1. Run analysis scripts:
+   python scripts/analysis.py
+
+2. Figures auto-generated to:
+   script_out/FINISHED_SUCCESS/<session>/
+
+3. Copy figures to manuscript:
+   cp script_out/FINISHED_SUCCESS/*/figures/* manuscript/figures/
+
+4. Compile manuscript:
+   scitex writer compile ./manuscript
+
+5. Check word count:
+   scitex writer wordcount ./manuscript
+"""
+
+# ============================================================
+# MCP Tools Reference
+# ============================================================
+
+"""
+MCP Tools:
+----------
+
+Documentation:
+- writer_usage()  # Get complete usage guide
+
+Note: Most writer operations are done via CLI:
+- scitex writer compile <dir>
+- scitex writer clean <dir>
+- scitex writer wordcount <dir>
+- scitex writer check <dir>
+- scitex writer watch <dir>
+"""
+
+if __name__ == "__main__":
+    main()
+''',
+}
+
+__all__ = ["TEMPLATE"]
+
+# EOF

scitex/template/clone_writer_directory.py

@@ -25,8 +25,8 @@ TEMPLATE_REPO_URL = "https://github.com/ywatanabe1989/scitex-writer.git"
 def clone_writer_directory(
     project_dir: str,
     git_strategy: Optional[str] = "child",
-    branch: Optional[str] = None,
-    tag: Optional[str] = "v2.0.0",
+    branch: Optional[str] = "main",
+    tag: Optional[str] = None,
 ) -> bool:
     """
     Create a new paper directory from the scitex-writer template repository.
@@ -39,10 +39,10 @@ def clone_writer_directory(
     git_strategy : str, optional
         Git initialization strategy ('child', 'parent', None). Default is 'child'.
     branch : str, optional
-        Specific branch of the template repository to clone. If None, clones the default branch.
+        Specific branch of the template repository to clone. Default is 'main'.
         Mutually exclusive with tag parameter.
     tag : str, optional
-        Specific tag/release of the template repository to clone. Default is 'v2.0.0'.
+        Specific tag/release of the template repository to clone. If None, uses the branch.
         Mutually exclusive with branch parameter.
 
     Returns
@@ -53,7 +53,7 @@ def clone_writer_directory(
     Example
     -------
     >>> from scitex.template import clone_writer_directory
-    >>> clone_writer_directory("my_paper")  # Uses v2.0.0
+    >>> clone_writer_directory("my_paper")  # Uses main branch
     >>> clone_writer_directory("./papers/my_paper")
     >>> clone_writer_directory("my_paper", branch="develop")
     >>> clone_writer_directory("my_paper", tag="v2.0.0")

scitex/ui/_backends/_email.py

@@ -24,8 +24,16 @@ class EmailBackend(BaseNotifyBackend):
         recipient: Optional[str] = None,
         sender: Optional[str] = None,
     ):
-        self.recipient = recipient or os.getenv("SCITEX_NOTIFY_EMAIL_TO")
-        self.sender = sender or os.getenv("SCITEX_NOTIFY_EMAIL_FROM")
+        self.recipient = (
+            recipient
+            or os.getenv("SCITEX_UI_EMAIL_NOTIFICATION_TO")
+            or os.getenv("SCITEX_NOTIFY_EMAIL_TO")
+        )
+        self.sender = (
+            sender
+            or os.getenv("SCITEX_UI_EMAIL_NOTIFICATION_FROM")
+            or os.getenv("SCITEX_NOTIFY_EMAIL_FROM")
+        )
 
     def is_available(self) -> bool:
         return bool(

scitex/ui/_backends/_webhook.py

@@ -22,7 +22,11 @@ class WebhookBackend(BaseNotifyBackend):
     name = "webhook"
 
     def __init__(self, url: Optional[str] = None):
-        self.url = url or os.getenv("SCITEX_NOTIFY_WEBHOOK_URL")
+        self.url = (
+            url
+            or os.getenv("SCITEX_UI_WEBHOOK_URL")
+            or os.getenv("SCITEX_NOTIFY_WEBHOOK_URL")
+        )
 
     def is_available(self) -> bool:
         return bool(self.url)

scitex/web/_search_pubmed.py

@@ -179,9 +179,11 @@ def get_crossref_metrics(
 
     # Use provided email or fallback to environment variables
     if not email:
-        email = os.getenv(
-            "SCITEX_CROSSREF_EMAIL",
-            os.getenv("SCITEX_PUBMED_EMAIL", "research@example.com"),
+        email = (
+            os.getenv("SCITEX_SCHOLAR_CROSSREF_EMAIL")
+            or os.getenv("SCITEX_CROSSREF_EMAIL")
+            or os.getenv("SCITEX_SCHOLAR_PUBMED_EMAIL")
+            or os.getenv("SCITEX_PUBMED_EMAIL", "research@example.com")
         )
     headers = {"User-Agent": f"SciTeX/1.0 (mailto:{email})"}
 
@@ -218,9 +220,11 @@ async def get_crossref_metrics_async(
 
     # Use provided email or fallback to environment variables
     if not email:
-        email = os.getenv(
-            "SCITEX_CROSSREF_EMAIL",
-            os.getenv("SCITEX_PUBMED_EMAIL", "research@example.com"),
+        email = (
+            os.getenv("SCITEX_SCHOLAR_CROSSREF_EMAIL")
+            or os.getenv("SCITEX_CROSSREF_EMAIL")
+            or os.getenv("SCITEX_SCHOLAR_PUBMED_EMAIL")
+            or os.getenv("SCITEX_PUBMED_EMAIL", "research@example.com")
         )
     headers = {"User-Agent": f"SciTeX/1.0 (mailto:{email})"}
 

scitex/writer/README.md

@@ -1,7 +1,7 @@
 <!-- ---
 !-- Timestamp: 2025-10-29 17:33:34
 !-- Author: ywatanabe
-!-- File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/README.md
+!-- File: /home/ywatanabe/proj/scitex-python/src/scitex/writer/README.md
 !-- --- -->
 
 # SciTeX Writer

scitex/writer/__init__.py

@@ -1,46 +1,55 @@
 #!/usr/bin/env python3
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/__init__.py
-
 """
-SciTeX Writer - LaTeX Compilation System
-
-Python wrapper around scitex-writer shell scripts for LaTeX compilation.
+SciTeX Writer - Thin wrapper delegating to scitex-writer package.
 
-Examples:
-    >>> from scitex.writer import Writer, compile
+Single source of truth: scitex-writer package
+This module re-exports scitex-writer as-is, without modifications.
 
-    # Using Writer class
-    >>> writer = Writer(project_dir=Path("."))
-    >>> result = writer.compile_manuscript()
-
-    # Using unified compile function
-    >>> result = compile("manuscript", project_dir=Path("."))
-    >>> results = compile("manuscript", "supplementary", project_dir=Path("."))
-    >>> results = await compile("all", project_dir=Path("."), async_=True)
+Install: pip install scitex-writer
 """
 
-from . import utils
-from ._compile import compile
-from .Writer import Writer
+import os as _os
+
+# Set branding environment variables BEFORE importing scitex-writer
+_os.environ.setdefault("SCITEX_WRITER_BRAND", "scitex.writer")
+_os.environ.setdefault("SCITEX_WRITER_ALIAS", "sw")
+
+# Re-export from scitex-writer package (single source of truth)
+try:
+    from scitex_writer import __version__ as writer_version
+    from scitex_writer import (
+        bib,
+        compile,
+        figures,
+        guidelines,
+        project,
+        prompts,
+        tables,
+    )
+
+    HAS_WRITER_PKG = True
+
+except ImportError:
+    HAS_WRITER_PKG = False
+    writer_version = None
+    bib = None
+    compile = None
+    figures = None
+    guidelines = None
+    project = None
+    prompts = None
+    tables = None
 
 __all__ = [
-    "Writer",
+    "HAS_WRITER_PKG",
+    "writer_version",
+    "bib",
     "compile",
-    "utils",
+    "figures",
+    "guidelines",
+    "project",
+    "prompts",
+    "tables",
 ]
 
-
-# Clean up namespace - hide internal submodules
-def _cleanup():
-    import sys
-
-    _this = sys.modules[__name__]
-    for _attr in list(vars(_this).keys()):
-        if _attr in ("_dataclasses",):
-            delattr(_this, _attr)
-
-
-_cleanup()
-del _cleanup
-
 # EOF