scitex 2.15.2__py3-none-any.whl → 2.15.4__py3-none-any.whl

scitex/cli/writer.py

@@ -1,453 +1,79 @@
 #!/usr/bin/env python3
 """
-SciTeX Writer Commands - LaTeX Manuscript Management
+SciTeX Writer CLI - Thin wrapper delegating to scitex-writer package.
 
-Provides manuscript project initialization and compilation.
+All commands are delegated to scitex-writer CLI for maintainability.
 """
 
+import subprocess
 import sys
-from pathlib import Path
 
 import click
 
+# Check if scitex-writer package is available
+try:
+    import scitex_writer
 
-@click.group(
-    context_settings={"help_option_names": ["-h", "--help"]},
-    invoke_without_command=True,
-)
-@click.option("--help-recursive", is_flag=True, help="Show help for all subcommands")
-@click.pass_context
-def writer(ctx, help_recursive):
-    """
-    Manuscript writing and LaTeX compilation
-
-    \b
-    Provides manuscript project management:
-    - Initialize new manuscript projects
-    - Compile manuscript, supplementary, and revision documents
-    - Watch mode for auto-recompilation
-    - Project structure management
-    """
-    if help_recursive:
-        _print_help_recursive(ctx)
-        ctx.exit(0)
-    elif ctx.invoked_subcommand is None:
-        click.echo(ctx.get_help())
-
-
-def _print_help_recursive(ctx):
-    """Print help for all commands recursively."""
-    fake_parent = click.Context(click.Group(), info_name="scitex")
-    parent_ctx = click.Context(writer, info_name="writer", parent=fake_parent)
-
-    click.secho("━━━ scitex writer ━━━", fg="cyan", bold=True)
-    click.echo(writer.get_help(parent_ctx))
-
-    for name in sorted(writer.list_commands(ctx) or []):
-        cmd = writer.get_command(ctx, name)
-        if cmd is None:
-            continue
-        click.echo()
-        click.secho(f"━━━ scitex writer {name} ━━━", fg="cyan", bold=True)
-        with click.Context(cmd, info_name=name, parent=parent_ctx) as sub_ctx:
-            click.echo(cmd.get_help(sub_ctx))
-
-
-@writer.command()
-@click.argument("project_dir", type=click.Path())
-@click.option(
-    "--git-strategy",
-    "-g",
-    type=click.Choice(["child", "parent", "origin", "none"], case_sensitive=False),
-    default="child",
-    help="Git initialization strategy (default: child)",
-)
-@click.option("--branch", "-b", help="Specific branch of template to clone")
-@click.option("--tag", "-t", help="Specific tag/release of template to clone")
-def clone(project_dir, git_strategy, branch, tag):
-    """
-    Clone a new writer project from template
-
-    \b
-    Arguments:
-        PROJECT_DIR  Path to project directory (will be created)
+    HAS_WRITER_PKG = True
+except ImportError:
+    HAS_WRITER_PKG = False
 
-    \b
-    Git Strategies:
-        child   - Create isolated git in project directory (default)
-        parent  - Use parent git repository
-        origin  - Preserve template's original git history
-        none    - Disable git initialization
 
-    \b
-    Examples:
-        scitex writer clone my_paper
-        scitex writer clone ./papers/my_paper
-        scitex writer clone my_paper --git-strategy parent
-        scitex writer clone my_paper --branch develop
-        scitex writer clone my_paper --tag v1.0.0
-    """
-    try:
-        from scitex.writer._clone_writer_project import clone_writer_project
-
-        # Validate mutual exclusivity of branch and tag
-        if branch and tag:
-            click.echo("Error: Cannot specify both --branch and --tag", err=True)
-            sys.exit(1)
-
-        # Convert git_strategy 'none' to None
-        if git_strategy and git_strategy.lower() == "none":
-            git_strategy = None
-
-        click.echo(f"Cloning writer project: {project_dir}")
-
-        # Clone writer project
-        result = clone_writer_project(
-            project_dir=project_dir,
-            git_strategy=git_strategy,
-            branch=branch,
-            tag=tag,
+def _require_writer_pkg():
+    """Check if scitex-writer package is available."""
+    if not HAS_WRITER_PKG:
+        click.secho(
+            "scitex-writer package not installed. "
+            "Install with: pip install scitex-writer",
+            fg="red",
+            err=True,
         )
-
-        if result:
-            project_path = Path(project_dir)
-            click.echo()
-            click.secho(
-                f"✓ Successfully cloned project at {project_path.absolute()}",
-                fg="green",
-            )
-            click.echo()
-            click.echo("Project structure:")
-            click.echo(f"  {project_dir}/")
-            click.echo(
-                "    ├── 00_shared/          # Shared resources (figures, bibliography)"
-            )
-            click.echo("    ├── 01_manuscript/      # Main manuscript")
-            click.echo("    ├── 02_supplementary/   # Supplementary materials")
-            click.echo("    ├── 03_revision/        # Revision documents")
-            click.echo("    └── scripts/            # Compilation scripts")
-            click.echo()
-            click.echo("Next steps:")
-            click.echo(f"  cd {project_dir}")
-            click.echo("  # Edit your manuscript in 01_manuscript/contents/")
-            click.echo("  scitex writer compile manuscript")
-        else:
-            click.secho("✗ Failed to clone project", fg="red", err=True)
-            sys.exit(1)
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red", err=True)
-        sys.exit(1)
-
-
-@writer.command()
-@click.argument(
-    "document",
-    type=click.Choice(
-        ["manuscript", "supplementary", "revision"], case_sensitive=False
-    ),
-    default="manuscript",
-)
-@click.option(
-    "--dir",
-    "-d",
-    type=click.Path(exists=True),
-    help="Project directory (defaults to current directory)",
-)
-@click.option(
-    "--track-changes", is_flag=True, help="Enable change tracking (revision only)"
-)
-@click.option(
-    "--timeout",
-    type=int,
-    default=300,
-    help="Compilation timeout in seconds (default: 300)",
-)
-def compile(document, dir, track_changes, timeout):
-    """
-    Compile LaTeX document to PDF
-
-    \b
-    Arguments:
-        DOCUMENT  Document type to compile (manuscript|supplementary|revision)
-
-    \b
-    Examples:
-        scitex writer compile manuscript
-        scitex writer compile manuscript --dir ./my_paper
-        scitex writer compile revision --track-changes
-        scitex writer compile supplementary --timeout 600
-    """
-    from scitex.writer import Writer
-
-    project_dir = Path(dir) if dir else Path.cwd()
-
-    # Check if this is a Writer project before trying to attach
-    required_dirs = ["01_manuscript", "02_supplementary", "03_revision"]
-    missing = [d for d in required_dirs if not (project_dir / d).exists()]
-
-    if missing:
-        click.echo(f"Not a Writer project: {project_dir.absolute()}")
-        click.echo(f"Missing directories: {', '.join(missing)}")
-        click.echo()
-        click.echo("To create a new project, run:")
-        click.echo("  scitex writer clone <project-name>")
-        return  # Exit gracefully with code 0
-
-    try:
-        writer = Writer(project_dir)
-
-        click.echo(f"Compiling {document} in {project_dir}...")
-        click.echo()
-
-        # Compile based on document type
-        if document == "manuscript":
-            result = writer.compile_manuscript(timeout=timeout)
-        elif document == "supplementary":
-            result = writer.compile_supplementary(timeout=timeout)
-        elif document == "revision":
-            result = writer.compile_revision(
-                track_changes=track_changes, timeout=timeout
-            )
-
-        if result.success:
-            click.secho("✓ Compilation successful!", fg="green")
-            click.echo(f"PDF: {result.output_pdf}")
-        else:
-            click.secho(
-                f"✗ Compilation failed (exit code {result.exit_code})",
-                fg="red",
-                err=True,
-            )
-            if result.errors:
-                click.echo()
-                click.echo("Errors:")
-                for error in result.errors[:10]:  # Show first 10 errors
-                    click.echo(f"  - {error}")
-            sys.exit(result.exit_code)
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red", err=True)
         sys.exit(1)
 
 
-@writer.command()
-@click.option(
-    "--dir",
-    "-d",
-    type=click.Path(exists=True),
-    help="Project directory (defaults to current directory)",
+@click.command(
+    context_settings={
+        "help_option_names": ["-h", "--help"],
+        "ignore_unknown_options": True,
+        "allow_extra_args": True,
+        "allow_interspersed_args": False,
+    },
 )
-def info(dir):
-    """
-    Show project information
-
-    \b
-    Examples:
-        scitex writer info
-        scitex writer info --dir ./my_paper
-    """
-    from scitex.writer import Writer
-
-    project_dir = Path(dir) if dir else Path.cwd()
-
-    # Check if this is a Writer project before trying to attach
-    required_dirs = ["01_manuscript", "02_supplementary", "03_revision"]
-    missing = [d for d in required_dirs if not (project_dir / d).exists()]
-
-    if missing:
-        click.echo(f"Not a Writer project: {project_dir.absolute()}")
-        click.echo(f"Missing directories: {', '.join(missing)}")
-        return  # Exit gracefully with code 0
-
-    try:
-        writer = Writer(project_dir)
-
-        click.echo(f"Project: {writer.project_name}")
-        click.echo(f"Location: {writer.project_dir.absolute()}")
-        click.echo(f"Git root: {writer.git_root}")
-        click.echo()
-        click.echo("Documents:")
-        click.echo(f"  - Manuscript: {writer.manuscript.root}")
-        click.echo(f"  - Supplementary: {writer.supplementary.root}")
-        click.echo(f"  - Revision: {writer.revision.root}")
-        click.echo()
-
-        # Check for compiled PDFs
-        click.echo("Compiled PDFs:")
-        for doc_type in ["manuscript", "supplementary", "revision"]:
-            pdf = writer.get_pdf(doc_type)
-            if pdf:
-                click.secho(f"  ✓ {doc_type}: {pdf}", fg="green")
-            else:
-                click.echo(f"  - {doc_type}: not compiled")
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red", err=True)
-        sys.exit(1)
-
-
-@writer.group()
-def mcp():
+@click.argument("args", nargs=-1, type=click.UNPROCESSED)
+@click.pass_context
+def writer(ctx, args):
     """
-    MCP (Model Context Protocol) tools for writer module.
+    Manuscript writing and LaTeX compilation (delegates to scitex-writer)
 
     \b
-    Examples:
-      scitex writer mcp list-tools      # List available MCP tools
-      scitex writer mcp usage           # Show tool usage and parameters
-    """
-    pass
-
-
-@mcp.command("list-tools")
-@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
-def list_tools(as_json: bool):
-    """
-    List available MCP tools for writer module.
+    Commands (from scitex-writer):
+      compile     Compile LaTeX to PDF
+      bib         Bibliography management
+      tables      Table management
+      figures     Figure management
+      guidelines  IMRAD writing guidelines
+      prompts     AI prompts (Asta integration)
+      mcp         MCP server commands
 
     \b
     Examples:
-      scitex writer mcp list-tools
-      scitex writer mcp list-tools --json
-    """
-    from scitex.writer._mcp.tool_schemas import get_tool_schemas
-
-    tools = get_tool_schemas()
-
-    if as_json:
-        import json
-
-        output = {
-            "module": "writer",
-            "count": len(tools),
-            "tools": [
-                {
-                    "name": t.name,
-                    "description": t.description,
-                    "parameters": list(t.inputSchema.get("properties", {}).keys()),
-                    "required": t.inputSchema.get("required", []),
-                }
-                for t in tools
-            ],
-        }
-        click.echo(json.dumps(output, indent=2))
-    else:
-        click.secho(
-            f"SciTeX Writer MCP Tools ({len(tools)} total)", fg="cyan", bold=True
-        )
-        click.echo()
-
-        for tool in tools:
-            click.secho(f"  {tool.name}", fg="green", bold=True)
-            # First line of description
-            desc = tool.description.split("\n")[0] if tool.description else ""
-            click.echo(f"    {desc}")
-
-            # Parameters
-            props = tool.inputSchema.get("properties", {})
-            required = tool.inputSchema.get("required", [])
-            if props:
-                params = []
-                for pname, pinfo in props.items():
-                    req_marker = "*" if pname in required else ""
-                    params.append(f"{pname}{req_marker}")
-                click.echo(f"    Parameters: {', '.join(params)}")
-            click.echo()
-
-
-@mcp.command("usage")
-@click.argument("tool_name", required=False)
-def usage(tool_name: str):
-    """
-    Show detailed usage for writer MCP tools.
+      scitex writer compile manuscript ./my-paper
+      scitex writer bib list ./my-paper
+      scitex writer tables add ./my-paper data.csv
+      scitex writer figures list ./my-paper
+      scitex writer guidelines get abstract
+      scitex writer prompts asta ./my-paper --section introduction
 
     \b
-    Examples:
-      scitex writer mcp usage                    # Show all tools
-      scitex writer mcp usage compile_manuscript # Show specific tool
+    For full help:
+      scitex writer --help
+      scitex-writer --help
     """
-    from scitex.writer._mcp.tool_schemas import get_tool_schemas
-
-    tools = get_tool_schemas()
-
-    if tool_name:
-        # Find specific tool
-        tool = next((t for t in tools if t.name == tool_name), None)
-        if not tool:
-            click.secho(f"Tool '{tool_name}' not found", fg="red", err=True)
-            click.echo(f"Available tools: {', '.join(t.name for t in tools)}")
-            raise SystemExit(1)
-        tools = [tool]
-
-    for tool in tools:
-        click.secho(f"━━━ {tool.name} ━━━", fg="cyan", bold=True)
-        click.echo()
-        click.echo(f"Description: {tool.description}")
-        click.echo()
+    _require_writer_pkg()
 
-        props = tool.inputSchema.get("properties", {})
-        required = tool.inputSchema.get("required", [])
-
-        if props:
-            click.secho("Parameters:", bold=True)
-            for pname, pinfo in props.items():
-                req = " (required)" if pname in required else ""
-                ptype = pinfo.get("type", "any")
-                pdesc = pinfo.get("description", "")
-                default = pinfo.get("default")
-                default_str = f" [default: {default}]" if default is not None else ""
-
-                click.echo(f"  {pname}: {ptype}{req}{default_str}")
-                if pdesc:
-                    click.echo(f"    {pdesc}")
-        click.echo()
-
-
-@writer.command()
-@click.option(
-    "--dir",
-    "-d",
-    type=click.Path(exists=True),
-    help="Project directory (defaults to current directory)",
-)
-def watch(dir):
-    """
-    Watch for file changes and auto-recompile
-
-    \b
-    Examples:
-        scitex writer watch
-        scitex writer watch --dir ./my_paper
-    """
-    from scitex.writer import Writer
-
-    project_dir = Path(dir) if dir else Path.cwd()
-
-    # Check if this is a Writer project before trying to attach
-    required_dirs = ["01_manuscript", "02_supplementary", "03_revision"]
-    missing = [d for d in required_dirs if not (project_dir / d).exists()]
-
-    if missing:
-        click.echo(f"Not a Writer project: {project_dir.absolute()}")
-        click.echo(f"Missing directories: {', '.join(missing)}")
-        return  # Exit gracefully with code 0
-
-    try:
-        writer = Writer(project_dir)
-
-        click.echo(f"Watching {project_dir} for changes...")
-        click.echo("Press Ctrl+C to stop")
-        click.echo()
-
-        writer.watch()
-
-    except KeyboardInterrupt:
-        click.echo()
-        click.echo("Stopped watching")
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red", err=True)
-        sys.exit(1)
+    # Delegate to scitex-writer CLI
+    cmd = ["scitex-writer"] + list(args)
+    sys.exit(subprocess.call(cmd))
 
 
 # EOF

scitex/dev/plt/data/mpl/PLOTTING_FUNCTIONS.yaml

@@ -0,0 +1,90 @@
+# Timestamp: "2025-12-21 12:37:14 (ywatanabe)"
+# File: ./src/scitex/dev/plt/data/mpl/PLOTTING_FUNCTIONS.yaml
+
+basic:
+  - plot           # Line/marker plots
+  - scatter        # Scatter plots
+  - bar            # Vertical bar charts
+  - barh           # Horizontal bar charts
+  - stem           # Stem plots
+  - step           # Step plots
+  - fill           # Filled polygons
+  - fill_between   # Fill between y-values
+  - fill_betweenx  # Fill between x-values
+
+statistical:
+  - hist           # Histogram
+  - hist2d         # 2D histogram
+  - boxplot        # Box and whisker plots
+  - bxp            # Box plot from precomputed stats
+  - violinplot     # Violin plots
+  - violin         # Single violin
+  - errorbar       # Error bar plots
+  - pie            # Pie charts
+  - ecdf           # Empirical cumulative distribution
+
+image:
+  - imshow         # Display image/array
+  - matshow        # Display matrix
+  - pcolor         # Pseudocolor plot
+  - pcolormesh     # Pseudocolor mesh (faster)
+  - pcolorfast     # Pseudocolor (fastest)
+  - contour        # Contour lines
+  - contourf       # Filled contours
+  - hexbin         # Hexagonal binning
+  - spy            # Sparsity pattern
+
+vector:
+  - quiver         # Arrow/vector field
+  - streamplot     # Streamlines
+  - barbs          # Wind barbs
+
+spectral:
+  - specgram           # Spectrogram
+  - psd                # Power spectral density
+  - csd                # Cross spectral density
+  - cohere             # Coherence
+  - acorr              # Autocorrelation
+  - xcorr              # Cross-correlation
+  - angle_spectrum     # Phase angle spectrum
+  - magnitude_spectrum # Magnitude spectrum
+  - phase_spectrum     # Phase spectrum
+
+triangulation:
+  - tricontour   # Triangular contour lines
+  - tricontourf  # Triangular filled contours
+  - tripcolor    # Triangular pseudocolor
+  - triplot      # Triangular grid lines
+
+composite:
+  - stackplot    # Stacked area plots
+  - stairs       # Stair/step plots
+  - eventplot    # Event sequence plots
+  - broken_barh  # Broken horizontal bars
+
+log_scale:
+  - loglog       # Log-log scale plot
+  - semilogx     # Semi-log x scale
+  - semilogy     # Semi-log y scale
+
+annotation:
+  - annotate     # Text with arrow annotation
+  - text         # Text at position
+  - arrow        # Arrow patch
+  - axhline      # Horizontal line across axes
+  - axvline      # Vertical line across axes
+  - hlines       # Horizontal lines at y positions
+  - vlines       # Vertical lines at x positions
+  - axhspan      # Horizontal span (shaded region)
+  - axvspan      # Vertical span (shaded region)
+  - axline       # Infinite line
+
+decoration:
+  - legend       # Add legend
+  - grid         # Add grid
+  - table        # Add table
+  - clabel       # Contour labels
+  - bar_label    # Bar chart labels
+  - quiverkey    # Quiver key/legend
+
+# EOF