scitex 2.11.0__py3-none-any.whl → 2.13.0__py3-none-any.whl

scitex/cli/template.py

@@ -0,0 +1,236 @@
+#!/usr/bin/env python3
+"""
+SciTeX CLI - Template Commands (Project Scaffolding)
+
+Provides project template cloning and management.
+"""
+
+import sys
+from pathlib import Path
+
+import click
+
+
+@click.group(context_settings={"help_option_names": ["-h", "--help"]})
+def template():
+    """
+    Project template scaffolding
+
+    \b
+    Available templates:
+      research      - Full scientific workflow structure
+      pip-project   - Pip-installable Python package
+      singularity   - Container-based project
+      paper         - Academic paper writing template
+
+    \b
+    Examples:
+      scitex template list                        # Show available templates
+      scitex template clone research ./my-project # Clone research template
+      scitex template clone pip-project ./my-pkg  # Clone package template
+    """
+    pass
+
+
+@template.command(name="list")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def list_templates(as_json):
+    """
+    List available project templates
+
+    \b
+    Example:
+      scitex template list
+      scitex template list --json
+    """
+    try:
+        from scitex.template import get_available_templates_info
+
+        templates = get_available_templates_info()
+
+        if as_json:
+            import json
+
+            click.echo(json.dumps(templates, indent=2))
+        else:
+            click.secho("Available SciTeX Templates", fg="cyan", bold=True)
+            click.echo("=" * 60)
+
+            for tmpl in templates:
+                click.echo()
+                click.secho(f"{tmpl['name']} ({tmpl['id']})", fg="green", bold=True)
+                click.echo(f"  {tmpl['description']}")
+                click.echo(f"  Use case: {tmpl['use_case']}")
+                click.echo(f"  GitHub: {tmpl['github_url']}")
+                if tmpl.get("features"):
+                    click.echo("  Features:")
+                    for feature in tmpl["features"][:3]:  # Show first 3
+                        click.echo(f"    - {feature}")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@template.command()
+@click.argument(
+    "template_type",
+    type=click.Choice(["research", "pip-project", "singularity", "paper"]),
+)
+@click.argument("destination", type=click.Path())
+@click.option(
+    "--git-strategy",
+    "-g",
+    type=click.Choice(["child", "parent", "origin", "none"]),
+    default="child",
+    help="Git initialization strategy (default: child)",
+)
+@click.option("--branch", "-b", help="Specific branch to clone")
+@click.option("--tag", "-t", help="Specific tag/release to clone")
+def clone(template_type, destination, git_strategy, branch, tag):
+    """
+    Clone a project template
+
+    \b
+    Template Types:
+      research    - Full scientific workflow (scripts, data, docs, results)
+      pip-project - Python package (src, tests, docs, CI/CD)
+      singularity - Container-based (definition files, build scripts)
+      paper       - Academic paper (LaTeX, BibTeX, figures)
+
+    \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 template clone research ./my-research
+      scitex template clone pip-project ./my-package --git-strategy parent
+      scitex template clone paper ./manuscript --branch develop
+    """
+    try:
+        # Validate mutual exclusivity
+        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 == "none":
+            git_strategy = None
+
+        # Map template types to clone functions
+        clone_funcs = {
+            "research": "clone_research",
+            "pip-project": "clone_pip_project",
+            "singularity": "clone_singularity",
+            "paper": "clone_writer_directory",
+        }
+
+        func_name = clone_funcs[template_type]
+
+        # Import the appropriate function
+        from scitex import template as tmpl_module
+
+        clone_func = getattr(tmpl_module, func_name)
+
+        click.echo(f"Cloning {template_type} template to {destination}...")
+
+        # Call clone function
+        kwargs = {"path": destination}
+        if git_strategy is not None:
+            kwargs["git_strategy"] = git_strategy
+        if branch:
+            kwargs["branch"] = branch
+        if tag:
+            kwargs["tag"] = tag
+
+        result = clone_func(**kwargs)
+
+        if result:
+            dest_path = Path(destination).absolute()
+            click.secho("Successfully cloned template!", fg="green")
+            click.echo()
+            click.echo(f"Location: {dest_path}")
+            click.echo()
+            click.echo("Next steps:")
+            click.echo(f"  cd {destination}")
+
+            if template_type == "research":
+                click.echo("  # Start your research project")
+                click.echo("  # Edit scripts/, data/, docs/")
+            elif template_type == "pip-project":
+                click.echo("  # Develop your package")
+                click.echo("  pip install -e .")
+                click.echo("  pytest")
+            elif template_type == "singularity":
+                click.echo("  # Build your container")
+                click.echo("  singularity build container.sif Singularity.def")
+            elif template_type == "paper":
+                click.echo("  # Write your paper")
+                click.echo("  scitex writer compile manuscript")
+        else:
+            click.secho("Failed to clone template", fg="red", err=True)
+            sys.exit(1)
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@template.command()
+@click.argument("template_id")
+def info(template_id):
+    """
+    Show detailed information about a template
+
+    \b
+    Example:
+      scitex template info research
+      scitex template info pip-project
+    """
+    try:
+        from scitex.template import get_available_templates_info
+
+        templates = get_available_templates_info()
+
+        # Find matching template
+        template_info = None
+        for tmpl in templates:
+            if tmpl["id"] == template_id or tmpl["name"].lower() == template_id.lower():
+                template_info = tmpl
+                break
+
+        if not template_info:
+            click.secho(f"Template '{template_id}' not found", fg="red", err=True)
+            click.echo("Available templates:")
+            for tmpl in templates:
+                click.echo(f"  - {tmpl['id']}")
+            sys.exit(1)
+
+        click.secho(f"Template: {template_info['name']}", fg="cyan", bold=True)
+        click.echo("=" * 50)
+        click.echo()
+        click.echo(f"ID: {template_info['id']}")
+        click.echo(f"Description: {template_info['description']}")
+        click.echo(f"Use case: {template_info['use_case']}")
+        click.echo(f"GitHub: {template_info['github_url']}")
+        click.echo()
+        click.secho("Features:", fg="yellow")
+        for feature in template_info.get("features", []):
+            click.echo(f"  - {feature}")
+        click.echo()
+        click.echo("Clone with:")
+        click.secho(
+            f"  scitex template clone {template_info['id']} ./my-project", fg="green"
+        )
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    template()

scitex/cli/tex.py

@@ -0,0 +1,286 @@
+#!/usr/bin/env python3
+"""
+SciTeX CLI - TeX Commands (LaTeX Operations)
+
+Provides LaTeX compilation and preview utilities.
+"""
+
+import sys
+from pathlib import Path
+
+import click
+
+
+@click.group(context_settings={"help_option_names": ["-h", "--help"]})
+def tex():
+    """
+    LaTeX compilation and utilities
+
+    \b
+    Commands:
+      compile    Compile LaTeX document to PDF
+      preview    Preview LaTeX document
+      to-vec     Convert to vector format (SVG/PDF)
+
+    \b
+    Examples:
+      scitex tex compile paper.tex
+      scitex tex preview paper.tex
+      scitex tex to-vec figure.tex --format svg
+    """
+    pass
+
+
+@tex.command()
+@click.argument("tex_file", type=click.Path(exists=True))
+@click.option("--output", "-o", type=click.Path(), help="Output PDF path")
+@click.option(
+    "--engine",
+    "-e",
+    type=click.Choice(["pdflatex", "xelatex", "lualatex"]),
+    default="pdflatex",
+    help="LaTeX engine (default: pdflatex)",
+)
+@click.option(
+    "--clean", "-c", is_flag=True, help="Clean auxiliary files after compilation"
+)
+@click.option(
+    "--timeout",
+    type=int,
+    default=300,
+    help="Compilation timeout in seconds (default: 300)",
+)
+@click.option("--verbose", "-v", is_flag=True, help="Show detailed compilation output")
+def compile(tex_file, output, engine, clean, timeout, verbose):
+    """
+    Compile LaTeX document to PDF
+
+    \b
+    Examples:
+      scitex tex compile paper.tex
+      scitex tex compile paper.tex --output ./output/paper.pdf
+      scitex tex compile paper.tex --engine xelatex
+      scitex tex compile paper.tex --clean --verbose
+    """
+    try:
+        from scitex.tex import compile_tex
+
+        path = Path(tex_file)
+        click.echo(f"Compiling: {path.name}")
+
+        result = compile_tex(
+            tex_path=path,
+            output_path=output,
+            engine=engine,
+            timeout=timeout,
+        )
+
+        if result.success:
+            click.secho("Compilation successful!", fg="green")
+            click.echo(f"PDF: {result.output_pdf}")
+
+            if clean:
+                # Clean auxiliary files
+                aux_extensions = [
+                    ".aux",
+                    ".log",
+                    ".out",
+                    ".toc",
+                    ".bbl",
+                    ".blg",
+                    ".fls",
+                    ".fdb_latexmk",
+                ]
+                for ext in aux_extensions:
+                    aux_file = path.with_suffix(ext)
+                    if aux_file.exists():
+                        aux_file.unlink()
+                click.echo("Auxiliary files cleaned")
+        else:
+            click.secho(
+                f"Compilation failed (exit code {result.exit_code})", fg="red", err=True
+            )
+            if result.errors and verbose:
+                click.echo("\nErrors:")
+                for error in result.errors[:10]:
+                    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)
+
+
+@tex.command()
+@click.argument("tex_file", type=click.Path(exists=True))
+@click.option("--viewer", "-v", help="PDF viewer to use (default: system default)")
+def preview(tex_file, viewer):
+    """
+    Preview LaTeX document (compile and open)
+
+    \b
+    Examples:
+      scitex tex preview paper.tex
+      scitex tex preview paper.tex --viewer evince
+    """
+    try:
+        from scitex.tex import preview as tex_preview
+
+        path = Path(tex_file)
+        click.echo(f"Previewing: {path.name}")
+
+        tex_preview(path, viewer=viewer)
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@tex.command("to-vec")
+@click.argument("tex_file", type=click.Path(exists=True))
+@click.option(
+    "--format",
+    "-f",
+    "fmt",
+    type=click.Choice(["svg", "pdf", "eps"]),
+    default="svg",
+    help="Output format (default: svg)",
+)
+@click.option("--output", "-o", type=click.Path(), help="Output file path")
+def to_vec(tex_file, fmt, output):
+    """
+    Convert LaTeX to vector format
+
+    \b
+    Useful for embedding equations and figures in other documents.
+
+    \b
+    Examples:
+      scitex tex to-vec equation.tex
+      scitex tex to-vec equation.tex --format pdf
+      scitex tex to-vec figure.tex --output ./vectors/fig.svg
+    """
+    try:
+        from scitex.tex import to_vec as convert_to_vec
+
+        path = Path(tex_file)
+        click.echo(f"Converting: {path.name} -> {fmt.upper()}")
+
+        if output:
+            output_path = Path(output)
+        else:
+            output_path = path.with_suffix(f".{fmt}")
+
+        result = convert_to_vec(path, output_path, format=fmt)
+
+        if result:
+            click.secho("Conversion successful!", fg="green")
+            click.echo(f"Output: {result}")
+        else:
+            click.secho("Conversion failed", fg="red", err=True)
+            sys.exit(1)
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@tex.command()
+@click.argument("tex_file", type=click.Path(exists=True))
+def check(tex_file):
+    """
+    Check LaTeX document for common issues
+
+    \b
+    Checks:
+      - Missing packages
+      - Undefined references
+      - Overfull/underfull boxes
+      - Citation warnings
+
+    \b
+    Example:
+      scitex tex check paper.tex
+    """
+    try:
+        import subprocess
+        from pathlib import Path
+
+        path = Path(tex_file)
+        click.echo(f"Checking: {path.name}")
+
+        # Run LaTeX in draft mode to check
+        result = subprocess.run(
+            ["pdflatex", "-draftmode", "-interaction=nonstopmode", str(path)],
+            capture_output=True,
+            text=True,
+            cwd=path.parent,
+            timeout=60,
+        )
+
+        # Parse log for issues
+        log_file = path.with_suffix(".log")
+        issues = {
+            "warnings": [],
+            "errors": [],
+            "overfull": [],
+            "undefined": [],
+        }
+
+        if log_file.exists():
+            with open(log_file) as f:
+                for line in f:
+                    if "Warning:" in line:
+                        issues["warnings"].append(line.strip())
+                    elif "Error:" in line or "!" in line[:2]:
+                        issues["errors"].append(line.strip())
+                    elif "Overfull" in line or "Underfull" in line:
+                        issues["overfull"].append(line.strip())
+                    elif "undefined" in line.lower():
+                        issues["undefined"].append(line.strip())
+
+        # Report
+        total_issues = sum(len(v) for v in issues.values())
+
+        if total_issues == 0:
+            click.secho("No issues found!", fg="green")
+        else:
+            click.secho(f"Found {total_issues} issue(s):", fg="yellow")
+
+            if issues["errors"]:
+                click.secho(f"\nErrors ({len(issues['errors'])}):", fg="red")
+                for err in issues["errors"][:5]:
+                    click.echo(f"  {err}")
+
+            if issues["undefined"]:
+                click.secho(
+                    f"\nUndefined References ({len(issues['undefined'])}):", fg="yellow"
+                )
+                for ref in issues["undefined"][:5]:
+                    click.echo(f"  {ref}")
+
+            if issues["overfull"]:
+                click.secho(
+                    f"\nOverfull/Underfull Boxes ({len(issues['overfull'])}):",
+                    fg="yellow",
+                )
+                for box in issues["overfull"][:5]:
+                    click.echo(f"  {box}")
+
+            if issues["warnings"]:
+                click.secho(f"\nWarnings ({len(issues['warnings'])}):", fg="yellow")
+                for warn in issues["warnings"][:5]:
+                    click.echo(f"  {warn}")
+
+    except subprocess.TimeoutExpired:
+        click.secho("Check timed out", fg="yellow")
+    except FileNotFoundError:
+        click.secho("Error: pdflatex not found. Install TeX Live.", fg="red", err=True)
+        sys.exit(1)
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    tex()

scitex/cli/web.py

@@ -1,20 +1,18 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 """
 SciTeX CLI - Web Scraping Commands
 """
 
-import os
+import subprocess
 import sys
-import click
+from datetime import datetime
 from pathlib import Path
 
-from scitex.web import get_urls, download_images, get_image_urls
-from scitex.web._scraping import _get_default_download_dir
+import click
+
 from scitex.logging import getLogger
-import subprocess
-import json
-from datetime import datetime
+from scitex.web import download_images, get_image_urls, get_urls
+from scitex.web.download_images import _get_default_download_dir
 
 logger = getLogger(__name__)
 
@@ -34,7 +32,7 @@ def web():
     \b
     Examples:
       scitex web get-urls https://example.com
-      scitex web get-urls https://example.com --pattern "\.pdf$"
+      scitex web get-urls https://example.com --pattern "\\.pdf$"
       scitex web get-image-urls https://example.com
       scitex web download-images https://example.com --output ./downloads
       scitex web download-images https://example.com --min-size 100x100
@@ -195,7 +193,7 @@ def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers
                 min_size_tuple = (width, height)
             except ValueError:
                 click.secho(
-                    f"ERROR: Invalid min-size format. Use WIDTHxHEIGHT (e.g., '100x100')",
+                    "ERROR: Invalid min-size format. Use WIDTHxHEIGHT (e.g., '100x100')",
                     fg="red",
                     err=True,
                 )
@@ -301,6 +299,7 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
         try:
             # For now, we'll use a simpler approach with playwright directly
             import asyncio
+
             from playwright.async_api import async_playwright
 
             async def capture():
@@ -322,7 +321,7 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
             asyncio.run(capture())
 
             if output_file.exists():
-                click.secho(f"Screenshot saved successfully", fg="green")
+                click.secho("Screenshot saved successfully", fg="green")
                 click.echo(f"Location: {output_file}")
                 sys.exit(0)
             else:
@@ -340,7 +339,7 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
             )
 
             if result.returncode == 0 and output_file.exists():
-                click.secho(f"Screenshot saved successfully", fg="green")
+                click.secho("Screenshot saved successfully", fg="green")
                 click.echo(f"Location: {output_file}")
                 sys.exit(0)
             else:

scitex/dev/__init__.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 """Scitex dev module."""
 
+# Pyproject utilities (lazy import to avoid tomlkit dependency)
+from . import _pyproject as pyproject
 from ._analyze_code_flow import CodeFlowAnalyzer, analyze_code_flow, main, parse_args
 from ._reload import reload, reload_auto, reload_stop
 
@@ -12,4 +14,5 @@ __all__ = [
     "reload",
     "reload_auto",
     "reload_stop",
+    "pyproject",
 ]