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

scitex/writer/_compile/_runner.py

@@ -1,457 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_compile/_runner.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/_compile/_runner.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Compilation script execution.
-
-Executes LaTeX compilation scripts and captures results.
-"""
-
-from pathlib import Path
-from datetime import datetime
-from typing import Optional, Callable
-import subprocess
-import time
-import fcntl
-
-from scitex.logging import getLogger
-from scitex.sh import sh
-from scitex.writer._dataclasses.config import DOC_TYPE_DIRS
-from scitex.writer._dataclasses import CompilationResult
-from ._validator import validate_before_compile
-from ._parser import parse_output
-
-logger = getLogger(__name__)
-
-
-def _get_compile_script(project_dir: Path, doc_type: str) -> Path:
-    """
-    Get compile script path for document type.
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to project directory
-    doc_type : str
-        Document type ('manuscript', 'supplementary', 'revision')
-
-    Returns
-    -------
-    Path
-        Path to compilation script
-    """
-    script_map = {
-        "manuscript": project_dir / "scripts" / "shell" / "compile_manuscript.sh",
-        "supplementary": project_dir / "scripts" / "shell" / "compile_supplementary.sh",
-        "revision": project_dir / "scripts" / "shell" / "compile_revision.sh",
-    }
-    return script_map.get(doc_type)
-
-
-def _find_output_files(
-    project_dir: Path,
-    doc_type: str,
-) -> tuple:
-    """
-    Find generated output files after compilation.
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to project directory
-    doc_type : str
-        Document type
-
-    Returns
-    -------
-    tuple
-        (output_pdf, diff_pdf, log_file)
-    """
-    doc_dir = project_dir / DOC_TYPE_DIRS[doc_type]
-
-    # Find generated PDF
-    pdf_name = f"{doc_type}.pdf"
-    potential_pdf = doc_dir / pdf_name
-    output_pdf = potential_pdf if potential_pdf.exists() else None
-
-    # Check for diff PDF
-    diff_name = f"{doc_type}_diff.pdf"
-    potential_diff = doc_dir / diff_name
-    diff_pdf = potential_diff if potential_diff.exists() else None
-
-    # Find log file
-    log_dir = doc_dir / "logs"
-    log_file = None
-    if log_dir.exists():
-        log_files = list(log_dir.glob("*.log"))
-        if log_files:
-            log_file = max(log_files, key=lambda p: p.stat().st_mtime)
-
-    return output_pdf, diff_pdf, log_file
-
-
-def _execute_with_callbacks(
-    command: list,
-    cwd: Path,
-    timeout: int,
-    log_callback: Optional[Callable[[str], None]] = None,
-) -> dict:
-    """
-    Execute command with line-by-line output capture and callbacks.
-
-    Parameters
-    ----------
-    command : list
-        Command to execute as list
-    cwd : Path
-        Working directory
-    timeout : int
-        Timeout in seconds
-    log_callback : Optional[Callable[[str], None]]
-        Called with each output line
-
-    Returns
-    -------
-    dict
-        Dict with stdout, stderr, exit_code, success
-    """
-    # Set environment for unbuffered output
-    env = os.environ.copy()
-    env["PYTHONUNBUFFERED"] = "1"
-
-    process = subprocess.Popen(
-        command,
-        shell=False,
-        stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE,
-        bufsize=0,  # Unbuffered
-        cwd=str(cwd),
-        env=env,
-    )
-
-    stdout_lines = []
-    stderr_lines = []
-    start_time = time.time()
-
-    # Make file descriptors non-blocking
-    def make_non_blocking(fd):
-        flags = fcntl.fcntl(fd, fcntl.F_GETFL)
-        fcntl.fcntl(fd, fcntl.F_SETFL, flags | os.O_NONBLOCK)
-
-    make_non_blocking(process.stdout)
-    make_non_blocking(process.stderr)
-
-    stdout_buffer = b""
-    stderr_buffer = b""
-
-    try:
-        while True:
-            # Check timeout
-            if timeout and (time.time() - start_time) > timeout:
-                process.kill()
-                timeout_msg = f"[ERROR] Command timed out after {timeout} seconds"
-                if log_callback:
-                    log_callback(timeout_msg)
-                stderr_lines.append(timeout_msg)
-                break
-
-            # Check if process has finished
-            poll_result = process.poll()
-
-            # Read from stdout
-            try:
-                chunk = process.stdout.read()
-                if chunk:
-                    stdout_buffer += chunk
-                    # Process complete lines
-                    while b"\n" in stdout_buffer:
-                        line, stdout_buffer = stdout_buffer.split(b"\n", 1)
-                        line_str = line.decode("utf-8", errors="replace")
-                        stdout_lines.append(line_str)
-                        if log_callback:
-                            log_callback(line_str)
-            except (IOError, BlockingIOError):
-                pass
-
-            # Read from stderr
-            try:
-                chunk = process.stderr.read()
-                if chunk:
-                    stderr_buffer += chunk
-                    # Process complete lines
-                    while b"\n" in stderr_buffer:
-                        line, stderr_buffer = stderr_buffer.split(b"\n", 1)
-                        line_str = line.decode("utf-8", errors="replace")
-                        stderr_lines.append(line_str)
-                        if log_callback:
-                            log_callback(f"[STDERR] {line_str}")
-            except (IOError, BlockingIOError):
-                pass
-
-            # If process finished, do final read and break
-            if poll_result is not None:
-                # Process remaining buffer content
-                if stdout_buffer:
-                    line_str = stdout_buffer.decode("utf-8", errors="replace")
-                    stdout_lines.append(line_str)
-                    if log_callback:
-                        log_callback(line_str)
-
-                if stderr_buffer:
-                    line_str = stderr_buffer.decode("utf-8", errors="replace")
-                    stderr_lines.append(line_str)
-                    if log_callback:
-                        log_callback(f"[STDERR] {line_str}")
-
-                break
-
-            # Small sleep to prevent CPU spinning
-            time.sleep(0.05)
-
-    except Exception as e:
-        process.kill()
-        raise
-
-    return {
-        "stdout": "\n".join(stdout_lines),
-        "stderr": "\n".join(stderr_lines),
-        "exit_code": process.returncode,
-        "success": process.returncode == 0,
-    }
-
-
-def run_compile(
-    doc_type: str,
-    project_dir: Path,
-    timeout: int = 300,
-    track_changes: bool = False,
-    no_figs: bool = False,
-    ppt2tif: bool = False,
-    crop_tif: bool = False,
-    quiet: bool = False,
-    verbose: bool = False,
-    force: bool = False,
-    log_callback: Optional[Callable[[str], None]] = None,
-    progress_callback: Optional[Callable[[int, str], None]] = None,
-) -> CompilationResult:
-    """
-    Run compilation script and parse results with optional callbacks.
-
-    Parameters
-    ----------
-    doc_type : str
-        Document type ('manuscript', 'supplementary', 'revision')
-    project_dir : Path
-        Path to project directory (containing 01_manuscript/, etc.)
-    timeout : int
-        Timeout in seconds
-    track_changes : bool
-        Enable change tracking (revision only)
-    no_figs : bool
-        Exclude figures for quick compilation (manuscript only)
-    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
-    verbose : bool
-        Show detailed logs for LaTeX compilation
-    force : bool
-        Force full recompilation, ignore cache (manuscript only)
-    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
-    """
-    start_time = datetime.now()
-    project_dir = Path(project_dir).absolute()
-
-    # Helper for progress tracking
-    def progress(percent: int, step: str):
-        if progress_callback:
-            progress_callback(percent, step)
-        logger.info(f"Progress: {percent}% - {step}")
-
-    # Helper for logging
-    def log(message: str):
-        if log_callback:
-            log_callback(message)
-        logger.info(message)
-
-    # Progress: Starting
-    progress(0, "Starting compilation...")
-    log("[INFO] Starting LaTeX compilation...")
-
-    # Validate project structure before compilation
-    try:
-        progress(5, "Validating project structure...")
-        validate_before_compile(project_dir)
-        log("[INFO] Project structure validated")
-    except Exception as e:
-        error_msg = f"[ERROR] Validation failed: {e}"
-        log(error_msg)
-        return CompilationResult(
-            success=False,
-            exit_code=1,
-            stdout="",
-            stderr=str(e),
-            duration=0.0,
-        )
-
-    # Get compile script
-    compile_script = _get_compile_script(project_dir, doc_type)
-    if not compile_script or not compile_script.exists():
-        error_msg = f"[ERROR] Compilation script not found: {compile_script}"
-        log(error_msg)
-        return CompilationResult(
-            success=False,
-            exit_code=127,
-            stdout="",
-            stderr=error_msg,
-            duration=0.0,
-        )
-
-    # Build command
-    progress(10, "Preparing compilation command...")
-    script_path = compile_script.absolute()
-    cmd = [str(script_path)]
-
-    # Add document-specific options
-    if doc_type == "revision":
-        if track_changes:
-            cmd.append("--track-changes")
-
-    elif doc_type == "manuscript":
-        if no_figs:
-            cmd.append("--no_figs")
-        if ppt2tif:
-            cmd.append("--ppt2tif")
-        if crop_tif:
-            cmd.append("--crop_tif")
-        if quiet:
-            cmd.append("--quiet")
-        elif verbose:
-            cmd.append("--verbose")
-        if force:
-            cmd.append("--force")
-
-    elif doc_type == "supplementary":
-        if not no_figs:  # For supplementary, --figs means include figures (default)
-            cmd.append("--figs")
-        if ppt2tif:
-            cmd.append("--ppt2tif")
-        if crop_tif:
-            cmd.append("--crop_tif")
-        if quiet:
-            cmd.append("--quiet")
-
-    log(f"[INFO] Running: {' '.join(cmd)}")
-    log(f"[INFO] Working directory: {project_dir}")
-
-    try:
-        cwd_original = Path.cwd()
-        os.chdir(project_dir)
-
-        try:
-            progress(15, "Executing LaTeX compilation...")
-
-            # Use callbacks version if callbacks provided
-            if log_callback:
-                result_dict = _execute_with_callbacks(
-                    command=cmd,
-                    cwd=project_dir,
-                    timeout=timeout,
-                    log_callback=log_callback,
-                )
-            else:
-                # Fallback to original sh() implementation
-                result_dict = sh(
-                    cmd,
-                    verbose=True,
-                    return_as="dict",
-                    timeout=timeout,
-                    stream_output=True,
-                )
-
-            result = type(
-                "Result",
-                (),
-                {
-                    "returncode": result_dict["exit_code"],
-                    "stdout": result_dict["stdout"],
-                    "stderr": result_dict["stderr"],
-                },
-            )()
-
-            duration = (datetime.now() - start_time).total_seconds()
-        finally:
-            os.chdir(cwd_original)
-
-        # Find output files
-        if result.returncode == 0:
-            progress(90, "Compilation successful, locating output files...")
-            log("[INFO] Compilation succeeded, checking output files...")
-            output_pdf, diff_pdf, log_file = _find_output_files(project_dir, doc_type)
-            if output_pdf:
-                log(f"[SUCCESS] PDF generated: {output_pdf}")
-        else:
-            output_pdf, diff_pdf, log_file = None, None, None
-            log(f"[ERROR] Compilation failed with exit code {result.returncode}")
-
-        # Parse errors and warnings
-        progress(95, "Parsing compilation logs...")
-        errors, warnings = parse_output(result.stdout, result.stderr, log_file=log_file)
-
-        compilation_result = CompilationResult(
-            success=(result.returncode == 0),
-            exit_code=result.returncode,
-            stdout=result.stdout,
-            stderr=result.stderr,
-            output_pdf=output_pdf,
-            diff_pdf=diff_pdf,
-            log_file=log_file,
-            duration=duration,
-            errors=errors,
-            warnings=warnings,
-        )
-
-        if compilation_result.success:
-            progress(100, "Complete!")
-            log(f"[SUCCESS] Compilation succeeded in {duration:.2f}s")
-        else:
-            progress(100, "Compilation failed")
-            if errors:
-                log(f"[ERROR] Found {len(errors)} errors")
-
-        return compilation_result
-
-    except Exception as e:
-        duration = (datetime.now() - start_time).total_seconds()
-        logger.error(f"Compilation error: {e}")
-        return CompilationResult(
-            success=False,
-            exit_code=1,
-            stdout="",
-            stderr=str(e),
-            duration=duration,
-        )
-
-
-__all__ = ["run_compile"]
-
-# EOF

scitex/writer/_compile/_validator.py

@@ -1,46 +0,0 @@
-#!/usr/bin/env python3
-# Timestamp: "2025-10-29 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_compile/_validator.py
-# ----------------------------------------
-from __future__ import annotations
-
-import os
-
-__FILE__ = "./src/scitex/writer/_compile/_validator.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Pre-compile validation for writer projects.
-
-Validates project structure before attempting compilation.
-"""
-
-from pathlib import Path
-
-from scitex.logging import getLogger
-from scitex.writer.utils._verify_tree_structure import verify_tree_structure
-
-logger = getLogger(__name__)
-
-
-def validate_before_compile(project_dir: Path) -> None:
-    """
-    Validate project structure before compilation.
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to project directory
-
-    Raises
-    ------
-    RuntimeError
-        If validation fails
-    """
-    verify_tree_structure(project_dir)
-
-
-__all__ = ["validate_before_compile"]
-
-# EOF

scitex/writer/_compile/manuscript.py

@@ -1,110 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-11-08 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_compile/manuscript.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/_compile/manuscript.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Manuscript compilation function.
-
-Provides manuscript-specific compilation with options for:
-- Figure exclusion for quick compilation
-- PowerPoint to TIF conversion
-- TIF cropping
-- Verbose/quiet modes
-- Force recompilation
-"""
-
-from pathlib import Path
-from typing import Optional, Callable
-from ._runner import run_compile
-from .._dataclasses import CompilationResult
-
-
-def compile_manuscript(
-    project_dir: Path,
-    timeout: int = 300,
-    no_figs: bool = False,
-    ppt2tif: bool = False,
-    crop_tif: bool = False,
-    quiet: bool = False,
-    verbose: bool = False,
-    force: bool = False,
-    log_callback: Optional[Callable[[str], None]] = None,
-    progress_callback: Optional[Callable[[int, str], None]] = None,
-) -> CompilationResult:
-    """
-    Compile manuscript document with optional callbacks.
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to writer project directory
-    timeout : int
-        Timeout in seconds
-    no_figs : bool
-        Exclude figures for quick compilation
-    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
-    verbose : bool
-        Show detailed logs for LaTeX compilation
-    force : bool
-        Force full recompilation, ignore cache
-    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_manuscript
-    >>>
-    >>> # Quick compilation without figures
-    >>> result = compile_manuscript(
-    ...     project_dir=Path("~/my-paper"),
-    ...     no_figs=True,
-    ...     quiet=True
-    ... )
-    >>>
-    >>> # Full compilation with PowerPoint conversion
-    >>> result = compile_manuscript(
-    ...     project_dir=Path("~/my-paper"),
-    ...     ppt2tif=True,
-    ...     crop_tif=True,
-    ...     verbose=True
-    ... )
-    """
-    return run_compile(
-        "manuscript",
-        project_dir,
-        timeout=timeout,
-        no_figs=no_figs,
-        ppt2tif=ppt2tif,
-        crop_tif=crop_tif,
-        quiet=quiet,
-        verbose=verbose,
-        force=force,
-        log_callback=log_callback,
-        progress_callback=progress_callback,
-    )
-
-
-__all__ = ["compile_manuscript"]
-
-# EOF

scitex/writer/_compile/revision.py

@@ -1,82 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-11-08 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/_compile/revision.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/_compile/revision.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Revision response compilation function.
-
-Provides revision-specific compilation with options for:
-- Change tracking (diff highlighting)
-"""
-
-from pathlib import Path
-from typing import Optional, Callable
-from ._runner import run_compile
-from .._dataclasses import CompilationResult
-
-
-def compile_revision(
-    project_dir: Path,
-    track_changes: bool = False,
-    timeout: int = 300,
-    log_callback: Optional[Callable[[str], None]] = None,
-    progress_callback: Optional[Callable[[int, str], None]] = None,
-) -> CompilationResult:
-    """
-    Compile revision responses with optional callbacks.
-
-    Parameters
-    ----------
-    project_dir : Path
-        Path to writer project directory
-    track_changes : bool
-        Whether to enable change tracking (diff highlighting)
-    timeout : int
-        Timeout in seconds
-    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_revision
-    >>>
-    >>> # Standard revision compilation
-    >>> result = compile_revision(
-    ...     project_dir=Path("~/my-paper")
-    ... )
-    >>>
-    >>> # Compilation with change tracking
-    >>> result = compile_revision(
-    ...     project_dir=Path("~/my-paper"),
-    ...     track_changes=True
-    ... )
-    """
-    return run_compile(
-        "revision",
-        project_dir,
-        timeout=timeout,
-        track_changes=track_changes,
-        log_callback=log_callback,
-        progress_callback=progress_callback,
-    )
-
-
-__all__ = ["compile_revision"]
-
-# EOF