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

scitex/writer/_project/__init__.py

@@ -1,29 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_project/__init__.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/_project/__init__.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Project initialization helpers for writer module.
-
-Handles project creation, attachment, and validation.
-"""
-
-from ._create import ensure_project_exists
-from ._validate import validate_structure
-from ._trees import create_document_trees
-
-__all__ = [
-    "ensure_project_exists",
-    "validate_structure",
-    "create_document_trees",
-]
-
-# EOF

scitex/writer/_project/_create.py

@@ -1,89 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_project/_create.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/_project/_create.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Project creation logic for writer module.
-
-Handles creating new writer projects from template.
-"""
-
-from pathlib import Path
-from typing import Optional
-
-from scitex.logging import getLogger
-from scitex.writer._clone_writer_project import (
-    clone_writer_project as _clone_writer_project,
-)
-
-logger = getLogger(__name__)
-
-
-def ensure_project_exists(
-    project_dir: Path,
-    project_name: str,
-    git_strategy: Optional[str] = "child",
-    branch: Optional[str] = None,
-    tag: Optional[str] = None,
-) -> Path:
-    """
-    Ensure project directory exists, creating it if necessary.
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to project directory
-    project_name : str
-        Name of the project
-    git_strategy : str or None
-        Git initialization strategy
-    branch : str, optional
-        Specific branch of template repository to clone. If None, clones the default branch.
-        Mutually exclusive with tag parameter.
-    tag : str, optional
-        Specific tag/release of template repository to clone. If None, clones the default branch.
-        Mutually exclusive with branch parameter.
-
-    Returns
-    -------
-    Path
-        Path to the project directory
-
-    Raises
-    ------
-    RuntimeError
-        If project creation fails
-    """
-    if project_dir.exists():
-        logger.info(f"Attached to existing project at {project_dir.absolute()}")
-        return project_dir
-
-    logger.info(f"Creating new project '{project_name}' at {project_dir.absolute()}")
-
-    # Initialize project directory structure
-    success = _clone_writer_project(str(project_dir), git_strategy, branch, tag)
-
-    if not success:
-        logger.error(f"Failed to initialize project directory for {project_name}")
-        raise RuntimeError(f"Could not create project directory at {project_dir}")
-
-    # Verify project directory was created
-    if not project_dir.exists():
-        logger.error(f"Project directory {project_dir} was not created")
-        raise RuntimeError(f"Project directory {project_dir} was not created")
-
-    logger.success(f"Successfully created project at {project_dir.absolute()}")
-    return project_dir
-
-
-__all__ = ["ensure_project_exists"]
-
-# EOF

scitex/writer/_project/_trees.py

@@ -1,63 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_project/_trees.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/_project/_trees.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Document tree creation for writer module.
-
-Creates and initializes document tree objects for manuscript, supplementary,
-revision, and scripts.
-"""
-
-from pathlib import Path
-from typing import Optional, Tuple
-
-from scitex.logging import getLogger
-from scitex.writer._dataclasses import ManuscriptTree, SupplementaryTree, RevisionTree
-from scitex.writer._dataclasses.tree import ScriptsTree
-
-logger = getLogger(__name__)
-
-
-def create_document_trees(
-    project_dir: Path,
-    git_root: Optional[Path],
-) -> Tuple[ManuscriptTree, SupplementaryTree, RevisionTree, ScriptsTree]:
-    """
-    Create document tree objects for writer project.
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to project directory
-    git_root : Path or None
-        Path to git root (for efficiency)
-
-    Returns
-    -------
-    tuple
-        (manuscript, supplementary, revision, scripts) tree objects
-    """
-    manuscript = ManuscriptTree(project_dir / "01_manuscript", git_root=git_root)
-    supplementary = SupplementaryTree(
-        project_dir / "02_supplementary", git_root=git_root
-    )
-    revision = RevisionTree(project_dir / "03_revision", git_root=git_root)
-    scripts = ScriptsTree(project_dir / "scripts", git_root=git_root)
-
-    logger.success("Document trees initialized")
-
-    return manuscript, supplementary, revision, scripts
-
-
-__all__ = ["create_document_trees"]
-
-# EOF

scitex/writer/_project/_validate.py

@@ -1,61 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_project/_validate.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/_project/_validate.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Project structure validation for writer module.
-
-Verifies that writer projects have expected directory structure.
-"""
-
-from pathlib import Path
-
-from scitex.logging import getLogger
-
-logger = getLogger(__name__)
-
-
-def validate_structure(project_dir: Path) -> None:
-    """
-    Verify attached project has expected structure.
-
-    Checks:
-    - Required directories exist (01_manuscript, 02_supplementary, 03_revision)
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to project directory
-
-    Raises
-    ------
-    RuntimeError
-        If structure is invalid
-    """
-    required_dirs = [
-        project_dir / "01_manuscript",
-        project_dir / "02_supplementary",
-        project_dir / "03_revision",
-    ]
-
-    for dir_path in required_dirs:
-        if not dir_path.exists():
-            logger.error(f"Expected directory missing: {dir_path}")
-            raise RuntimeError(
-                f"Project structure invalid: missing {dir_path.name} directory (expected at: {dir_path})"
-            )
-
-    logger.success(f"Project structure verified at {project_dir.absolute()}")
-
-
-__all__ = ["validate_structure"]
-
-# EOF

scitex/writer/utils/.legacy_git_retry.py

@@ -1,164 +0,0 @@
-#!/usr/bin/env python3
-# Timestamp: "2025-10-28 17:10:52 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/git_utils.py
-# ----------------------------------------
-from __future__ import annotations
-
-import os
-
-__FILE__ = "./src/scitex/writer/git_utils.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Git utilities for Writer.
-
-Provides git lock handling and retry logic for concurrent access.
-"""
-
-import subprocess
-import time
-from typing import Callable, TypeVar
-
-from scitex.logging import getLogger
-
-logger = getLogger(__name__)
-
-T = TypeVar("T")
-
-
-def git_retry(
-    operation: Callable[[], T],
-    max_retries: int = 5,
-    initial_delay: float = 0.1,
-    max_delay: float = 2.0,
-    backoff_factor: float = 2.0,
-) -> T:
-    """
-    Retry git operations with exponential backoff.
-
-    Handles git index.lock conflicts when multiple processes access git.
-
-    Args:
-        operation: Function to retry
-        max_retries: Maximum number of retry attempts
-        initial_delay: Initial delay in seconds
-        max_delay: Maximum delay between retries
-        backoff_factor: Exponential backoff multiplier
-
-    Returns:
-        Result of operation
-
-    Raises:
-        TimeoutError: If all retries exhausted due to lock
-        Exception: Original exception if not a lock error
-
-    Example:
-        >>> def commit_file():
-        ...     subprocess.run(["git", "commit", "-m", "msg"], check=True)
-        >>> git_retry(commit_file)
-    """
-    delay = initial_delay
-    last_exception = None
-
-    for attempt in range(max_retries):
-        try:
-            return operation()
-        except subprocess.CalledProcessError as e:
-            # Check if it's a lock error
-            stderr = (
-                e.stderr
-                if isinstance(e.stderr, str)
-                else (e.stderr.decode("utf-8", errors="ignore") if e.stderr else "")
-            )
-
-            if "index.lock" in stderr and attempt < max_retries - 1:
-                logger.debug(
-                    f"Git lock detected, retrying in {delay:.2f}s "
-                    f"(attempt {attempt + 1}/{max_retries})"
-                )
-                time.sleep(delay)
-                delay = min(delay * backoff_factor, max_delay)
-                last_exception = e
-                continue
-
-            # Not a lock error, or retries exhausted
-            raise
-        except Exception:
-            # Non-git errors: don't retry
-            raise
-
-    # All retries exhausted
-    if last_exception:
-        raise TimeoutError(
-            f"Could not acquire git lock after {max_retries} attempts"
-        ) from last_exception
-
-
-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):
-    def demo_operation():
-        print("Simulating git operation...")
-        return "Success"
-
-    result = git_retry(demo_operation, max_retries=args.max_retries)
-    print(f"Result: {result}")
-    return 0
-
-
-def parse_args():
-    import argparse
-
-    parser = argparse.ArgumentParser(
-        description="Demonstrate git retry with exponential backoff"
-    )
-    parser.add_argument(
-        "--max-retries",
-        type=int,
-        default=5,
-        help="Maximum retry attempts (default: 5)",
-    )
-
-    return parser.parse_args()
-
-
-if __name__ == "__main__":
-    run_session()
-
-
-__all__ = ["git_retry"]
-
-# python -m scitex.writer.utils._git_retry --max-retries 3
-
-# EOF

scitex/writer/utils/__init__.py

@@ -1,24 +0,0 @@
-#!/usr/bin/env python3
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/utils/__init__.py
-
-"""Utility functions for writer module."""
-
-from scitex.writer.utils._converters import (
-    convert_figure,
-    csv2latex,
-    latex2csv,
-    list_figures,
-    pdf_to_images,
-)
-from scitex.writer.utils._verify_tree_structure import verify_tree_structure
-
-__all__ = [
-    "convert_figure",
-    "csv2latex",
-    "latex2csv",
-    "list_figures",
-    "pdf_to_images",
-    "verify_tree_structure",
-]
-
-# EOF