scitex 2.5.0__py3-none-any.whl → 2.7.3__py3-none-any.whl

scitex/cli/config.py

@@ -0,0 +1,224 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-12-09 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/cli/config.py
+
+"""
+SciTeX Configuration CLI Commands
+
+Commands for managing SciTeX configuration and paths.
+"""
+
+import os
+import click
+
+
+@click.group()
+def config():
+    """
+    Configuration management commands.
+
+    \b
+    Examples:
+      scitex config list          # Show all configured paths
+      scitex config list --env    # Show environment variables
+      scitex config init          # Initialize all directories
+    """
+    pass
+
+
+@config.command("list")
+@click.option(
+    "--env",
+    is_flag=True,
+    help="Show relevant environment variables",
+)
+@click.option(
+    "--exists",
+    is_flag=True,
+    help="Only show paths that exist",
+)
+@click.option(
+    "--json",
+    "as_json",
+    is_flag=True,
+    help="Output as JSON",
+)
+def list_config(env, exists, as_json):
+    """
+    List all configured paths and settings.
+
+    \b
+    Examples:
+      scitex config list            # Show all paths
+      scitex config list --env      # Include environment variables
+      scitex config list --exists   # Only show existing directories
+      scitex config list --json     # Output as JSON
+    """
+    from scitex.config import ScitexPaths, get_scitex_dir
+
+    paths = ScitexPaths()
+    all_paths = paths.list_all()
+
+    if as_json:
+        import json
+
+        output = {}
+        if env:
+            output["environment"] = {
+                "SCITEX_DIR": os.getenv("SCITEX_DIR", "(not set)"),
+            }
+        output["paths"] = {k: str(v) for k, v in all_paths.items()}
+        if exists:
+            output["paths"] = {
+                k: v for k, v in output["paths"].items() if all_paths[k].exists()
+            }
+        click.echo(json.dumps(output, indent=2))
+        return
+
+    # Header
+    click.secho("SciTeX Configuration", fg="cyan", bold=True)
+    click.echo("=" * 50)
+    click.echo()
+
+    # Environment variables
+    if env:
+        click.secho("Environment Variables:", fg="yellow", bold=True)
+        scitex_dir = os.getenv("SCITEX_DIR")
+        if scitex_dir:
+            click.echo(f"  SCITEX_DIR = {scitex_dir}")
+        else:
+            click.echo(f"  SCITEX_DIR = (not set, using default: ~/.scitex)")
+        click.echo()
+
+    # Base directory
+    click.secho("Base Directory:", fg="yellow", bold=True)
+    base = paths.base
+    exists_mark = (
+        click.style("✓", fg="green") if base.exists() else click.style("✗", fg="red")
+    )
+    click.echo(f"  {exists_mark} {base}")
+    click.echo()
+
+    # All paths
+    click.secho("Configured Paths:", fg="yellow", bold=True)
+
+    # Group paths by category
+    categories = {
+        "Core": ["logs", "cache", "function_cache", "capture", "screenshots", "rng"],
+        "Browser": [
+            "browser",
+            "browser_screenshots",
+            "browser_sessions",
+            "browser_persistent",
+            "test_monitor",
+        ],
+        "Cache": ["impact_factor_cache", "openathens_cache"],
+        "Scholar": ["scholar", "scholar_cache", "scholar_library"],
+        "Other": ["writer"],
+    }
+
+    for category, path_names in categories.items():
+        click.secho(f"\n  {category}:", fg="blue")
+        for name in path_names:
+            if name not in all_paths:
+                continue
+            path = all_paths[name]
+            if exists and not path.exists():
+                continue
+            exists_mark = (
+                click.style("✓", fg="green")
+                if path.exists()
+                else click.style("✗", fg="red")
+            )
+            # Show relative to base if under base
+            try:
+                rel_path = path.relative_to(paths.base)
+                display_path = f"$SCITEX_DIR/{rel_path}"
+            except ValueError:
+                display_path = str(path)
+            click.echo(f"    {exists_mark} {name:<22} {display_path}")
+
+    click.echo()
+
+
+@config.command("init")
+@click.option(
+    "--dry-run",
+    is_flag=True,
+    help="Show what would be created without creating",
+)
+def init_config(dry_run):
+    """
+    Initialize all SciTeX directories.
+
+    Creates all standard directories if they don't exist.
+
+    \b
+    Examples:
+      scitex config init            # Create all directories
+      scitex config init --dry-run  # Show what would be created
+    """
+    from scitex.config import ScitexPaths
+
+    paths = ScitexPaths()
+    all_paths = paths.list_all()
+
+    click.secho("Initializing SciTeX directories...", fg="cyan", bold=True)
+    click.echo()
+
+    created = 0
+    existed = 0
+
+    for name, path in all_paths.items():
+        if path.exists():
+            existed += 1
+            click.echo(f"  {click.style('EXISTS', fg='yellow')}: {path}")
+        else:
+            if dry_run:
+                click.echo(f"  {click.style('WOULD CREATE', fg='blue')}: {path}")
+            else:
+                path.mkdir(parents=True, exist_ok=True)
+                click.echo(f"  {click.style('CREATED', fg='green')}: {path}")
+            created += 1
+
+    click.echo()
+    if dry_run:
+        click.echo(f"Would create {created} directories ({existed} already exist)")
+    else:
+        click.echo(f"Created {created} directories ({existed} already existed)")
+
+
+@config.command("show")
+@click.argument("path_name")
+def show_path(path_name):
+    """
+    Show a specific configured path.
+
+    \b
+    PATH_NAME can be one of:
+      base, logs, cache, function_cache, capture, screenshots,
+      browser, browser_screenshots, browser_sessions, browser_persistent,
+      test_monitor, impact_factor_cache, openathens_cache,
+      scholar, scholar_cache, scholar_library, writer, rng
+
+    \b
+    Examples:
+      scitex config show logs
+      scitex config show scholar_library
+    """
+    from scitex.config import ScitexPaths
+
+    paths = ScitexPaths()
+
+    if hasattr(paths, path_name):
+        path = getattr(paths, path_name)
+        click.echo(str(path))
+    else:
+        available = list(paths.list_all().keys())
+        click.secho(f"Unknown path: {path_name}", fg="red", err=True)
+        click.echo(f"Available paths: {', '.join(available)}", err=True)
+        raise SystemExit(1)
+
+
+# EOF

scitex/cli/main.py

@@ -7,10 +7,10 @@ SciTeX CLI Main Entry Point
 import os
 import sys
 import click
-from . import cloud, scholar, security, web, writer
+from . import cloud, config, scholar, security, web, writer
 
 
-@click.group(context_settings={'help_option_names': ['-h', '--help']})
+@click.group(context_settings={"help_option_names": ["-h", "--help"]})
 @click.version_option()
 def cli():
     """
@@ -18,6 +18,8 @@ def cli():
 
     \b
     Examples:
+      scitex config list                    # Show all configured paths
+      scitex config init                    # Initialize directories
       scitex cloud login
       scitex cloud clone ywatanabe/my-project
       scitex scholar bibtex papers.bib --project myresearch
@@ -36,6 +38,7 @@ def cli():
 
 # Add command groups
 cli.add_command(cloud.cloud)
+cli.add_command(config.config)
 cli.add_command(scholar.scholar)
 cli.add_command(security.security)
 cli.add_command(web.web)
@@ -44,14 +47,12 @@ cli.add_command(writer.writer)
 
 @cli.command()
 @click.option(
-    '--shell',
-    type=click.Choice(['bash', 'zsh', 'fish'], case_sensitive=False),
-    help='Shell type (auto-detected if not provided)'
+    "--shell",
+    type=click.Choice(["bash", "zsh", "fish"], case_sensitive=False),
+    help="Shell type (auto-detected if not provided)",
 )
 @click.option(
-    '--show',
-    is_flag=True,
-    help='Show completion script instead of installing'
+    "--show", is_flag=True, help="Show completion script instead of installing"
 )
 def completion(shell, show):
     """
@@ -79,18 +80,18 @@ def completion(shell, show):
     """
     # Auto-detect shell if not provided
     if not shell:
-        shell_env = os.environ.get('SHELL', '')
-        if 'bash' in shell_env:
-            shell = 'bash'
-        elif 'zsh' in shell_env:
-            shell = 'zsh'
-        elif 'fish' in shell_env:
-            shell = 'fish'
+        shell_env = os.environ.get("SHELL", "")
+        if "bash" in shell_env:
+            shell = "bash"
+        elif "zsh" in shell_env:
+            shell = "zsh"
+        elif "fish" in shell_env:
+            shell = "fish"
         else:
             click.secho(
                 "Could not auto-detect shell. Please specify with --shell option.",
-                fg='red',
-                err=True
+                fg="red",
+                err=True,
             )
             sys.exit(1)
 
@@ -101,45 +102,45 @@ def completion(shell, show):
     if not os.path.isabs(scitex_path):
         # If relative path, find the full path
         import shutil
-        scitex_full = shutil.which('scitex') or scitex_path
+
+        scitex_full = shutil.which("scitex") or scitex_path
     else:
         scitex_full = scitex_path
 
     # Generate completion script
-    if shell == 'bash':
-        completion_script = f'_SCITEX_COMPLETE=bash_source {scitex_full}'
-        rc_file = os.path.expanduser('~/.bashrc')
+    if shell == "bash":
+        completion_script = f"_SCITEX_COMPLETE=bash_source {scitex_full}"
+        rc_file = os.path.expanduser("~/.bashrc")
         eval_line = f'eval "$(_SCITEX_COMPLETE=bash_source {scitex_full})"'
-    elif shell == 'zsh':
-        completion_script = f'_SCITEX_COMPLETE=zsh_source {scitex_full}'
-        rc_file = os.path.expanduser('~/.zshrc')
+    elif shell == "zsh":
+        completion_script = f"_SCITEX_COMPLETE=zsh_source {scitex_full}"
+        rc_file = os.path.expanduser("~/.zshrc")
         eval_line = f'eval "$(_SCITEX_COMPLETE=zsh_source {scitex_full})"'
-    elif shell == 'fish':
-        completion_script = f'_SCITEX_COMPLETE=fish_source {scitex_full}'
-        rc_file = os.path.expanduser('~/.config/fish/config.fish')
-        eval_line = f'eval (env _SCITEX_COMPLETE=fish_source {scitex_full})'
+    elif shell == "fish":
+        completion_script = f"_SCITEX_COMPLETE=fish_source {scitex_full}"
+        rc_file = os.path.expanduser("~/.config/fish/config.fish")
+        eval_line = f"eval (env _SCITEX_COMPLETE=fish_source {scitex_full})"
 
     if show:
         # Just show the completion script
         click.echo(f"Add this line to your {rc_file}:")
         click.echo()
-        click.secho(eval_line, fg='green')
+        click.secho(eval_line, fg="green")
         sys.exit(0)
 
     # Check if already installed (and not commented out)
     if os.path.exists(rc_file):
-        with open(rc_file, 'r') as f:
+        with open(rc_file, "r") as f:
             for line in f:
                 # Check if the line exists and is not commented
                 stripped = line.strip()
-                if stripped == eval_line and not stripped.startswith('#'):
+                if stripped == eval_line and not stripped.startswith("#"):
                     click.secho(
-                        f"Tab completion is already installed in {rc_file}",
-                        fg='yellow'
+                        f"Tab completion is already installed in {rc_file}", fg="yellow"
                     )
                     click.echo()
                     click.echo("To reload, run:")
-                    click.secho(f"  source {rc_file}", fg='cyan')
+                    click.secho(f"  source {rc_file}", fg="cyan")
                     sys.exit(0)
 
     # Install completion
@@ -147,25 +148,25 @@ def completion(shell, show):
         # Create config directory if it doesn't exist (for fish)
         os.makedirs(os.path.dirname(rc_file), exist_ok=True)
 
-        with open(rc_file, 'a') as f:
+        with open(rc_file, "a") as f:
             f.write(f"\n# SciTeX tab completion\n")
             f.write(f"{eval_line}\n")
 
-        click.secho(f"Successfully installed tab completion to {rc_file}", fg='green')
+        click.secho(f"Successfully installed tab completion to {rc_file}", fg="green")
         click.echo()
         click.echo("To activate completion in current shell, run:")
-        click.secho(f"  source {rc_file}", fg='cyan')
+        click.secho(f"  source {rc_file}", fg="cyan")
         click.echo()
         click.echo("Or restart your shell.")
         sys.exit(0)
 
     except Exception as e:
-        click.secho(f"ERROR: Failed to install completion: {e}", fg='red', err=True)
+        click.secho(f"ERROR: Failed to install completion: {e}", fg="red", err=True)
         click.echo()
         click.echo("You can manually add this line to your shell config:")
-        click.secho(eval_line, fg='green')
+        click.secho(eval_line, fg="green")
         sys.exit(1)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     cli()

scitex/cli/scholar.py

@@ -12,8 +12,10 @@ import sys
 import asyncio
 from pathlib import Path
 
+from scitex.config import get_paths
 
-@click.group(context_settings={'help_option_names': ['-h', '--help']})
+
+@click.group(context_settings={"help_option_names": ["-h", "--help"]})
 def scholar():
     """
     Literature management with browser automation
@@ -26,19 +28,26 @@ def scholar():
     - OpenAthens/institutional access support
 
     \b
-    Storage: ~/.scitex/scholar/library/
+    Storage: $SCITEX_DIR/scholar/library/
     Backend: Browser automation + metadata APIs
     """
     pass
 
 
 @scholar.command()
-@click.option('--doi', help='DOI of the paper (e.g., "10.1038/nature12373")')
-@click.option('--title', help='Paper title (will resolve DOI automatically)')
-@click.option('--project', help='Project name for organizing papers')
-@click.option('--browser-mode', type=click.Choice(['stealth', 'interactive']), default='stealth', help='Browser mode for PDF download')
-@click.option('--chrome-profile', default='system', help='Chrome profile name')
-@click.option('--force', '-f', is_flag=True, help='Force re-download even if files exist')
+@click.option("--doi", help='DOI of the paper (e.g., "10.1038/nature12373")')
+@click.option("--title", help="Paper title (will resolve DOI automatically)")
+@click.option("--project", help="Project name for organizing papers")
+@click.option(
+    "--browser-mode",
+    type=click.Choice(["stealth", "interactive"]),
+    default="stealth",
+    help="Browser mode for PDF download",
+)
+@click.option("--chrome-profile", default="system", help="Chrome profile name")
+@click.option(
+    "--force", "-f", is_flag=True, help="Force re-download even if files exist"
+)
 def single(doi, title, project, browser_mode, chrome_profile, force):
     """
     Process a single paper (DOI or title)
@@ -89,12 +98,25 @@ def single(doi, title, project, browser_mode, chrome_profile, force):
 
 
 @scholar.command()
-@click.option('--dois', multiple=True, help='DOIs to process (can be specified multiple times)')
-@click.option('--titles', multiple=True, help='Paper titles to process (can be specified multiple times)')
-@click.option('--project', help='Project name for organizing papers')
-@click.option('--num-workers', type=int, default=4, help='Number of parallel workers')
-@click.option('--browser-mode', type=click.Choice(['stealth', 'interactive']), default='stealth', help='Browser mode for all workers')
-@click.option('--chrome-profile', default='system', help='Base Chrome profile to sync from')
+@click.option(
+    "--dois", multiple=True, help="DOIs to process (can be specified multiple times)"
+)
+@click.option(
+    "--titles",
+    multiple=True,
+    help="Paper titles to process (can be specified multiple times)",
+)
+@click.option("--project", help="Project name for organizing papers")
+@click.option("--num-workers", type=int, default=4, help="Number of parallel workers")
+@click.option(
+    "--browser-mode",
+    type=click.Choice(["stealth", "interactive"]),
+    default="stealth",
+    help="Browser mode for all workers",
+)
+@click.option(
+    "--chrome-profile", default="system", help="Base Chrome profile to sync from"
+)
 def parallel(dois, titles, project, num_workers, browser_mode, chrome_profile):
     """
     Process multiple papers in parallel
@@ -144,12 +166,21 @@ def parallel(dois, titles, project, num_workers, browser_mode, chrome_profile):
 
 
 @scholar.command()
-@click.argument('bibtex_file', type=click.Path(exists=True))
-@click.option('--project', help='Project name for organizing papers')
-@click.option('--output', help='Output path for enriched BibTeX (default: {input}_processed.bib)')
-@click.option('--num-workers', type=int, default=4, help='Number of parallel workers')
-@click.option('--browser-mode', type=click.Choice(['stealth', 'interactive']), default='stealth', help='Browser mode for all workers')
-@click.option('--chrome-profile', default='system', help='Base Chrome profile to sync from')
+@click.argument("bibtex_file", type=click.Path(exists=True))
+@click.option("--project", help="Project name for organizing papers")
+@click.option(
+    "--output", help="Output path for enriched BibTeX (default: {input}_processed.bib)"
+)
+@click.option("--num-workers", type=int, default=4, help="Number of parallel workers")
+@click.option(
+    "--browser-mode",
+    type=click.Choice(["stealth", "interactive"]),
+    default="stealth",
+    help="Browser mode for all workers",
+)
+@click.option(
+    "--chrome-profile", default="system", help="Base Chrome profile to sync from"
+)
 def bibtex(bibtex_file, project, output, num_workers, browser_mode, chrome_profile):
     """
     Process papers from BibTeX file
@@ -201,7 +232,7 @@ def bibtex(bibtex_file, project, output, num_workers, browser_mode, chrome_profi
 
 
 @scholar.command()
-@click.option('--project', help='Show library for specific project')
+@click.option("--project", help="Show library for specific project")
 def library(project):
     """
     Show your Scholar library
@@ -211,7 +242,7 @@ def library(project):
         scitex scholar library
         scitex scholar library --project neuroscience
     """
-    library_path = Path.home() / '.scitex' / 'scholar' / 'library'
+    library_path = get_paths().scholar_library
 
     if not library_path.exists():
         click.echo("No library found. Process some papers first!")
@@ -233,8 +264,10 @@ def library(project):
                 click.echo(f"  - {item.name}")
     else:
         # List all projects
-        master_path = library_path / 'MASTER'
-        project_dirs = [d for d in library_path.iterdir() if d.is_dir() and d.name != 'MASTER']
+        master_path = library_path / "MASTER"
+        project_dirs = [
+            d for d in library_path.iterdir() if d.is_dir() and d.name != "MASTER"
+        ]
 
         if master_path.exists():
             num_papers = len(list(master_path.iterdir()))
@@ -256,20 +289,20 @@ def config():
 
     Displays library location, browser settings, and authentication status.
     """
-    library_path = Path.home() / '.scitex' / 'scholar' / 'library'
+    library_path = get_paths().scholar_library
 
     click.echo("\n=== SciTeX Scholar Configuration ===\n")
     click.echo(f"Library location: {library_path}")
     click.echo(f"Library exists: {'Yes' if library_path.exists() else 'No'}")
 
     if library_path.exists():
-        master_path = library_path / 'MASTER'
+        master_path = library_path / "MASTER"
         if master_path.exists():
             num_papers = len(list(master_path.iterdir()))
             click.echo(f"Papers in library: {num_papers}")
 
     # Check for Chrome profiles
-    chrome_config_path = Path.home() / '.config' / 'google-chrome'
+    chrome_config_path = Path.home() / ".config" / "google-chrome"
     click.echo(f"\nChrome config: {chrome_config_path}")
     click.echo(f"Chrome available: {'Yes' if chrome_config_path.exists() else 'No'}")
 

scitex/cli/security.py

@@ -34,18 +34,13 @@ def security():
 
 @security.command()
 @click.option(
-    '--repo',
-    help='Repository in format "owner/repo" (default: current repo)'
+    "--repo", help='Repository in format "owner/repo" (default: current repo)'
 )
+@click.option("--save", is_flag=True, help="Save report to file")
 @click.option(
-    '--save',
-    is_flag=True,
-    help='Save report to file'
-)
-@click.option(
-    '--output-dir',
+    "--output-dir",
     type=click.Path(),
-    help='Output directory (default: ./logs/security)'
+    help="Output directory (default: ./logs/security)",
 )
 def check(repo, save, output_dir):
     """Check GitHub security alerts."""
@@ -55,8 +50,7 @@ def check(repo, save, output_dir):
 
         # Count open alerts
         total = sum(
-            len([a for a in alerts[key] if a.get("state") == "open"])
-            for key in alerts
+            len([a for a in alerts[key] if a.get("state") == "open"]) for key in alerts
         )
 
         if save:
@@ -70,23 +64,23 @@ def check(repo, save, output_dir):
 
         # Exit with error code if alerts found
         if total > 0:
-            click.secho(f"\n❌ Found {total} open security alert(s)", fg='red')
+            click.secho(f"\n❌ Found {total} open security alert(s)", fg="red")
             sys.exit(1)
         else:
-            click.secho("\n✓ No security alerts found", fg='green')
+            click.secho("\n✓ No security alerts found", fg="green")
             sys.exit(0)
 
     except GitHubSecurityError as e:
-        click.secho(f"ERROR: {e}", fg='red', err=True)
+        click.secho(f"ERROR: {e}", fg="red", err=True)
         sys.exit(1)
 
 
 @security.command()
 @click.option(
-    '--dir',
-    'security_dir',
+    "--dir",
+    "security_dir",
     type=click.Path(),
-    help='Security directory (default: ./logs/security)'
+    help="Security directory (default: ./logs/security)",
 )
 def latest(security_dir):
     """Show the latest security alerts file."""
@@ -97,13 +91,13 @@ def latest(security_dir):
         if latest_file:
             click.echo(latest_file.read_text())
         else:
-            click.secho("No security alerts files found", fg='yellow')
+            click.secho("No security alerts files found", fg="yellow")
             sys.exit(1)
 
     except Exception as e:
-        click.secho(f"ERROR: {e}", fg='red', err=True)
+        click.secho(f"ERROR: {e}", fg="red", err=True)
         sys.exit(1)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     security()