scitex 2.16.0__py3-none-any.whl → 2.16.1__py3-none-any.whl

scitex/writer/_compile/supplementary.py

@@ -1,100 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-11-08 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_compile/supplementary.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/_compile/supplementary.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Supplementary materials compilation function.
-
-Provides supplementary-specific compilation with options for:
-- Figure inclusion (default)
-- PowerPoint to TIF conversion
-- TIF cropping
-- Quiet mode
-"""
-
-from pathlib import Path
-from typing import Optional, Callable
-from ._runner import run_compile
-from .._dataclasses import CompilationResult
-
-
-def compile_supplementary(
-    project_dir: Path,
-    timeout: int = 300,
-    no_figs: bool = False,
-    ppt2tif: bool = False,
-    crop_tif: bool = False,
-    quiet: bool = False,
-    log_callback: Optional[Callable[[str], None]] = None,
-    progress_callback: Optional[Callable[[int, str], None]] = None,
-) -> CompilationResult:
-    """
-    Compile supplementary materials with optional callbacks.
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to writer project directory
-    timeout : int
-        Timeout in seconds
-    no_figs : bool
-        Exclude figures (default includes figures)
-    ppt2tif : bool
-        Convert PowerPoint to TIF on WSL
-    crop_tif : bool
-        Crop TIF images to remove excess whitespace
-    quiet : bool
-        Suppress detailed logs for LaTeX compilation
-    log_callback : Optional[Callable[[str], None]]
-        Called with each log line
-    progress_callback : Optional[Callable[[int, str], None]]
-        Called with progress updates (percent, step)
-
-    Returns
-    -------
-    CompilationResult
-        Compilation status and outputs
-
-    Examples
-    --------
-    >>> from pathlib import Path
-    >>> from scitex.writer._compile import compile_supplementary
-    >>>
-    >>> # Standard compilation with figures
-    >>> result = compile_supplementary(
-    ...     project_dir=Path("~/my-paper"),
-    ...     ppt2tif=True,
-    ...     quiet=False
-    ... )
-    >>>
-    >>> # Quick compilation without figures
-    >>> result = compile_supplementary(
-    ...     project_dir=Path("~/my-paper"),
-    ...     no_figs=True,
-    ...     quiet=True
-    ... )
-    """
-    return run_compile(
-        "supplementary",
-        project_dir,
-        timeout=timeout,
-        no_figs=no_figs,
-        ppt2tif=ppt2tif,
-        crop_tif=crop_tif,
-        quiet=quiet,
-        log_callback=log_callback,
-        progress_callback=progress_callback,
-    )
-
-
-__all__ = ["compile_supplementary"]
-
-# EOF

scitex/writer/_dataclasses/__init__.py

@@ -1,44 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/dataclasses/__init__.py
-
-"""
-Type definitions for Writer module.
-
-Provides dataclasses for document structures with clear separation of concerns.
-Each document type includes:
-- Typed access to sections and files
-- Nested Contents dataclass for content/ subdirectory
-- verify_structure() method for validation
-"""
-
-from .core import Document, DocumentSection
-from .contents import ManuscriptContents, SupplementaryContents, RevisionContents
-from .config import WriterConfig
-from .results import CompilationResult, LaTeXIssue
-
-# Tree structures (internal use)
-from .tree import (
-    ConfigTree,
-    SharedTree,
-    ScriptsTree,
-    ManuscriptTree,
-    SupplementaryTree,
-    RevisionTree,
-)
-
-__all__ = [
-    # Core document dataclasses
-    "DocumentSection",
-    "Document",
-    # Document contents
-    "ManuscriptContents",
-    "SupplementaryContents",
-    "RevisionContents",
-    # Configuration and results
-    "CompilationResult",
-    "WriterConfig",
-    "LaTeXIssue",
-]
-
-# EOF

scitex/writer/_dataclasses/config/_CONSTANTS.py

@@ -1,46 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 06:08:36 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/dataclasses/_CONSTANTS.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/dataclasses/_CONSTANTS.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Constants for writer module.
-
-Centralized definitions for document dataclasses and directory mappings.
-"""
-
-# Document type to directory mapping
-DOC_TYPE_DIRS = {
-    "manuscript": "01_manuscript",
-    "supplementary": "02_supplementary",
-    "revision": "03_revision",
-}
-
-# Document type to command-line flag mapping
-DOC_TYPE_FLAGS = {
-    "manuscript": "-m",
-    "supplementary": "-s",
-    "revision": "-r",
-}
-
-# Document type to PDF filename mapping
-DOC_TYPE_PDFS = {
-    "manuscript": "manuscript.pdf",
-    "supplementary": "supplementary.pdf",
-    "revision": "revision.pdf",
-}
-
-__all__ = [
-    "DOC_TYPE_DIRS",
-    "DOC_TYPE_FLAGS",
-    "DOC_TYPE_PDFS",
-]
-
-# EOF

scitex/writer/_dataclasses/config/_WriterConfig.py

@@ -1,175 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 06:08:47 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/dataclasses/_WriterConfig.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/dataclasses/_WriterConfig.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-WriterConfig - dataclass for writer configuration.
-"""
-
-from dataclasses import dataclass
-from pathlib import Path
-from typing import Optional
-
-
-@dataclass
-class WriterConfig:
-    """Configuration for scitex.writer."""
-
-    project_dir: Path
-    """Root directory of writer project"""
-
-    manuscript_dir: Path
-    """Directory for manuscript (01_manuscript/)"""
-
-    supplementary_dir: Path
-    """Directory for supplementary (02_supplementary/)"""
-
-    revision_dir: Path
-    """Directory for revision (03_revision/)"""
-
-    shared_dir: Path
-    """Directory for shared resources (00_shared/)"""
-
-    compile_script: Optional[Path] = None
-    """Path to compile script (auto-detected if None)"""
-
-    @classmethod
-    def from_directory(cls, project_dir: Path) -> "WriterConfig":
-        """
-        Create config from project directory.
-
-        Args:
-            project_dir: Path to writer project root
-
-        Returns:
-            WriterConfig instance
-
-        Examples:
-            >>> config = WriterConfig.from_directory(Path("/path/to/project"))
-            >>> print(config.manuscript_dir)
-        """
-        project_dir = Path(project_dir)
-
-        return cls(
-            project_dir=project_dir,
-            manuscript_dir=project_dir / "01_manuscript",
-            supplementary_dir=project_dir / "02_supplementary",
-            revision_dir=project_dir / "03_revision",
-            shared_dir=project_dir / "00_shared",
-        )
-
-    def validate(self) -> bool:
-        """
-        Validate that required directories exist.
-
-        Returns:
-            True if valid writer project structure
-
-        Raises:
-            ValueError: If invalid structure
-        """
-        if not self.project_dir.exists():
-            raise ValueError(f"Project directory not found: {self.project_dir}")
-
-        # Check for at least one document directory
-        doc_dirs = [
-            self.manuscript_dir,
-            self.supplementary_dir,
-            self.revision_dir,
-        ]
-
-        if not any(d.exists() for d in doc_dirs):
-            raise ValueError(
-                f"No document directories found in {self.project_dir}. "
-                "Expected: 01_manuscript/, 02_supplementary/, or 03_revision/"
-            )
-
-        return True
-
-
-def run_session() -> None:
-    """Initialize scitex framework, run main function, and cleanup."""
-    global CONFIG, CC, sys, plt, rng
-    import sys
-    import matplotlib.pyplot as plt
-    import scitex as stx
-
-    args = parse_args()
-
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
-        sys,
-        plt,
-        args=args,
-        file=__FILE__,
-        sdir_suffix=None,
-        verbose=False,
-        agg=True,
-    )
-
-    exit_status = main(args)
-
-    stx.session.close(
-        CONFIG,
-        verbose=False,
-        notify=False,
-        message="",
-        exit_status=exit_status,
-    )
-
-
-def main(args):
-    config = WriterConfig.from_directory(Path(args.dir))
-
-    print(f"Project dir: {config.project_dir}")
-    print(f"Manuscript dir: {config.manuscript_dir}")
-    print(f"Supplementary dir: {config.supplementary_dir}")
-    print(f"Revision dir: {config.revision_dir}")
-    print(f"Shared dir: {config.shared_dir}")
-
-    if args.validate:
-        try:
-            config.validate()
-            print("\nValidation: PASSED")
-        except ValueError as ee:
-            print(f"\nValidation: FAILED - {ee}")
-            return 1
-
-    return 0
-
-
-def parse_args():
-    import argparse
-
-    parser = argparse.ArgumentParser(description="Demonstrate WriterConfig dataclass")
-    parser.add_argument(
-        "--dir",
-        type=str,
-        default="./my_paper",
-        help="Project directory (default: ./my_paper)",
-    )
-    parser.add_argument(
-        "--validate",
-        action="store_true",
-        help="Validate directory structure",
-    )
-
-    return parser.parse_args()
-
-
-if __name__ == "__main__":
-    run_session()
-
-
-__all__ = ["WriterConfig"]
-
-# python -m scitex.writer._dataclasses.config._WriterConfig --dir ./my_paper --validate
-
-# EOF

scitex/writer/_dataclasses/config/__init__.py

@@ -1,9 +0,0 @@
-from ._WriterConfig import WriterConfig
-from ._CONSTANTS import DOC_TYPE_DIRS, DOC_TYPE_FLAGS, DOC_TYPE_PDFS
-
-__all__ = [
-    "WriterConfig",
-    "DOC_TYPE_DIRS",
-    "DOC_TYPE_FLAGS",
-    "DOC_TYPE_PDFS",
-]

scitex/writer/_dataclasses/contents/_ManuscriptContents.py

@@ -1,236 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 06:08:43 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/dataclasses/_ManuscriptContents.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/dataclasses/_ManuscriptContents.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-ManuscriptContents - dataclass for manuscript contents structure.
-
-Represents the 01_manuscript/contents/ directory structure with all files.
-"""
-
-from pathlib import Path
-from typing import Optional
-from dataclasses import dataclass
-
-from ..core import DocumentSection
-
-
-@dataclass
-class ManuscriptContents:
-    """Contents subdirectory of manuscript (01_manuscript/contents/)."""
-
-    root: Path
-    git_root: Optional[Path] = None
-
-    # Core sections
-    abstract: DocumentSection = None
-    introduction: DocumentSection = None
-    methods: DocumentSection = None
-    results: DocumentSection = None
-    discussion: DocumentSection = None
-
-    # Metadata
-    title: DocumentSection = None
-    authors: DocumentSection = None
-    keywords: DocumentSection = None
-    journal_name: DocumentSection = None
-
-    # Optional sections
-    graphical_abstract: DocumentSection = None
-    highlights: DocumentSection = None
-    data_availability: DocumentSection = None
-    additional_info: DocumentSection = None
-    wordcount: DocumentSection = None
-
-    # Files/directories
-    figures: Path = None
-    tables: Path = None
-    bibliography: DocumentSection = None
-    latex_styles: Path = None
-
-    def __post_init__(self):
-        """Initialize all DocumentSection instances."""
-        if self.abstract is None:
-            self.abstract = DocumentSection(self.root / "abstract.tex", self.git_root)
-        if self.introduction is None:
-            self.introduction = DocumentSection(
-                self.root / "introduction.tex", self.git_root
-            )
-        if self.methods is None:
-            self.methods = DocumentSection(self.root / "methods.tex", self.git_root)
-        if self.results is None:
-            self.results = DocumentSection(self.root / "results.tex", self.git_root)
-        if self.discussion is None:
-            self.discussion = DocumentSection(
-                self.root / "discussion.tex", self.git_root
-            )
-        if self.title is None:
-            self.title = DocumentSection(self.root / "title.tex", self.git_root)
-        if self.authors is None:
-            self.authors = DocumentSection(self.root / "authors.tex", self.git_root)
-        if self.keywords is None:
-            self.keywords = DocumentSection(self.root / "keywords.tex", self.git_root)
-        if self.journal_name is None:
-            self.journal_name = DocumentSection(
-                self.root / "journal_name.tex", self.git_root
-            )
-        if self.graphical_abstract is None:
-            self.graphical_abstract = DocumentSection(
-                self.root / "graphical_abstract.tex", self.git_root
-            )
-        if self.highlights is None:
-            self.highlights = DocumentSection(
-                self.root / "highlights.tex", self.git_root
-            )
-        if self.data_availability is None:
-            self.data_availability = DocumentSection(
-                self.root / "data_availability.tex", self.git_root
-            )
-        if self.additional_info is None:
-            self.additional_info = DocumentSection(
-                self.root / "additional_info.tex", self.git_root
-            )
-        if self.wordcount is None:
-            self.wordcount = DocumentSection(self.root / "wordcount.tex", self.git_root)
-        if self.figures is None:
-            self.figures = self.root / "figures"
-        if self.tables is None:
-            self.tables = self.root / "tables"
-        if self.bibliography is None:
-            self.bibliography = DocumentSection(
-                self.root / "bibliography.bib", self.git_root
-            )
-        if self.latex_styles is None:
-            self.latex_styles = self.root / "latex_styles"
-
-    def verify_structure(self) -> tuple[bool, list[str]]:
-        """
-        Verify manuscript structure has required files.
-
-        Returns:
-            (is_valid, list_of_missing_files_with_paths)
-        """
-        required = [
-            ("abstract.tex", self.abstract),
-            ("introduction.tex", self.introduction),
-            ("methods.tex", self.methods),
-            ("results.tex", self.results),
-            ("discussion.tex", self.discussion),
-        ]
-
-        missing = []
-        for name, section in required:
-            if not section.path.exists():
-                expected_path = (
-                    section.path.relative_to(self.git_root)
-                    if self.git_root
-                    else section.path
-                )
-                missing.append(f"{name} (expected at: {expected_path})")
-
-        return len(missing) == 0, missing
-
-
-def run_session() -> None:
-    """Initialize scitex framework, run main function, and cleanup."""
-    global CONFIG, CC, sys, plt, rng
-    import sys
-    import matplotlib.pyplot as plt
-    import scitex as stx
-
-    args = parse_args()
-
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
-        sys,
-        plt,
-        args=args,
-        file=__FILE__,
-        sdir_suffix=None,
-        verbose=False,
-        agg=True,
-    )
-
-    exit_status = main(args)
-
-    stx.session.close(
-        CONFIG,
-        verbose=False,
-        notify=False,
-        message="",
-        exit_status=exit_status,
-    )
-
-
-def main(args):
-    contents_path = Path(args.dir) / "01_manuscript" / "contents"
-    git_root = Path(args.dir) if args.git_root else None
-
-    contents = ManuscriptContents(
-        root=contents_path,
-        git_root=git_root,
-    )
-
-    print(f"Root: {contents.root}")
-    print(f"Git root: {contents.git_root}")
-    print(f"\nCore sections:")
-    print(f"  Abstract: {contents.abstract.path}")
-    print(f"  Introduction: {contents.introduction.path}")
-    print(f"  Methods: {contents.methods.path}")
-    print(f"  Results: {contents.results.path}")
-    print(f"  Discussion: {contents.discussion.path}")
-
-    if args.verify:
-        is_valid, missing = contents.verify_structure()
-        if is_valid:
-            print("\nStructure verification: PASSED")
-        else:
-            print(f"\nStructure verification: FAILED")
-            print(f"Missing files: {', '.join(missing)}")
-            return 1
-
-    return 0
-
-
-def parse_args():
-    import argparse
-
-    parser = argparse.ArgumentParser(
-        description="Demonstrate ManuscriptContents dataclass"
-    )
-    parser.add_argument(
-        "--dir",
-        type=str,
-        default="./my_paper",
-        help="Project directory (default: ./my_paper)",
-    )
-    parser.add_argument(
-        "--git-root",
-        action="store_true",
-        help="Use project dir as git root",
-    )
-    parser.add_argument(
-        "--verify",
-        action="store_true",
-        help="Verify structure has required files",
-    )
-
-    return parser.parse_args()
-
-
-if __name__ == "__main__":
-    run_session()
-
-
-__all__ = ["ManuscriptContents"]
-
-# python -m scitex.writer._dataclasses.contents._ManuscriptContents --dir ./my_paper --verify
-
-# EOF