scitex 2.14.0__py3-none-any.whl → 2.15.2__py3-none-any.whl

scitex/cli/scholar/_crossref_scitex.py

@@ -0,0 +1,296 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-24
+# File: src/scitex/cli/scholar/_crossref_scitex.py
+"""CrossRef-SciTeX CLI commands for scitex scholar.
+
+Provides access to the local CrossRef database (167M+ papers) via crossref-local.
+Branded as crossref-scitex to distinguish from official CrossRef API.
+"""
+
+from __future__ import annotations
+
+import json
+import sys
+
+import click
+
+
+@click.group("crossref-scitex")
+def crossref_scitex():
+    """
+    CrossRef-SciTeX database search (167M+ papers)
+
+    \b
+    Search and query the local CrossRef database via crossref-local.
+    Supports both direct DB access and HTTP API mode.
+
+    \b
+    Examples:
+        scitex scholar crossref-scitex search "deep learning"
+        scitex scholar crossref-scitex get 10.1038/nature12373
+        scitex scholar crossref-scitex count "epilepsy seizure"
+        scitex scholar crossref-scitex info
+    """
+    pass
+
+
+@crossref_scitex.command("search")
+@click.argument("query")
+@click.option("-n", "--limit", default=20, help="Maximum results (default: 20)")
+@click.option("--offset", default=0, help="Skip N results for pagination")
+@click.option("--year-min", type=int, help="Minimum publication year")
+@click.option("--year-max", type=int, help="Maximum publication year")
+@click.option("--enrich", is_flag=True, help="Add citation counts and references")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def search_cmd(query, limit, offset, year_min, year_max, enrich, as_json):
+    """
+    Search for papers in CrossRef database.
+
+    \b
+    Examples:
+        scitex scholar crossref-scitex search "hippocampal sharp wave ripples"
+        scitex scholar crossref search "deep learning" --limit 50
+        scitex scholar crossref search "CRISPR" --year-min 2020 --enrich
+    """
+    try:
+        from scitex.scholar import crossref_scitex as crossref
+    except ImportError:
+        click.secho(
+            "crossref-local not installed. Install with: pip install crossref-local",
+            fg="red",
+        )
+        sys.exit(1)
+
+    try:
+        results = crossref.search(query, limit=limit, offset=offset)
+
+        if enrich:
+            results = crossref.enrich(results)
+
+        papers = []
+        for work in results:
+            if year_min and work.year and work.year < year_min:
+                continue
+            if year_max and work.year and work.year > year_max:
+                continue
+            papers.append(work)
+            if len(papers) >= limit:
+                break
+
+        if as_json:
+            output = {
+                "query": query,
+                "total": results.total,
+                "count": len(papers),
+                "papers": [
+                    {
+                        "doi": p.doi,
+                        "title": p.title,
+                        "authors": p.authors,
+                        "year": p.year,
+                        "journal": p.journal,
+                        "citation_count": p.citation_count,
+                    }
+                    for p in papers
+                ],
+            }
+            click.echo(json.dumps(output, indent=2))
+        else:
+            click.secho(
+                f"Found {results.total} papers for: {query}", fg="green", bold=True
+            )
+            click.echo()
+
+            for i, paper in enumerate(papers, 1):
+                authors = ", ".join(paper.authors[:3]) if paper.authors else "Unknown"
+                if paper.authors and len(paper.authors) > 3:
+                    authors += " et al."
+
+                click.secho(f"{i}. {paper.title}", fg="cyan", bold=True)
+                click.echo(f"   Authors: {authors}")
+                click.echo(
+                    f"   Year: {paper.year or 'N/A'} | Journal: {paper.journal or 'N/A'}"
+                )
+                click.echo(f"   DOI: {paper.doi}")
+                if paper.citation_count:
+                    click.echo(f"   Citations: {paper.citation_count}")
+                click.echo()
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red")
+        sys.exit(1)
+
+
+@crossref_scitex.command("get")
+@click.argument("doi")
+@click.option("--citations", is_flag=True, help="Include citing papers")
+@click.option("--references", is_flag=True, help="Include referenced papers")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def get_cmd(doi, citations, references, as_json):
+    """
+    Get paper details by DOI.
+
+    \b
+    Examples:
+        scitex scholar crossref get 10.1038/nature12373
+        scitex scholar crossref get 10.1126/science.aax0758 --citations
+    """
+    try:
+        from scitex.scholar import crossref_scitex as crossref
+    except ImportError:
+        click.secho(
+            "crossref-local not installed. Install with: pip install crossref-local",
+            fg="red",
+        )
+        sys.exit(1)
+
+    try:
+        work = crossref.get(doi)
+
+        if work is None:
+            click.secho(f"DOI not found: {doi}", fg="red")
+            sys.exit(1)
+
+        if as_json:
+            output = {
+                "doi": work.doi,
+                "title": work.title,
+                "authors": work.authors,
+                "year": work.year,
+                "journal": work.journal,
+                "abstract": work.abstract,
+                "citation_count": work.citation_count,
+                "reference_count": work.reference_count,
+                "type": work.type,
+                "publisher": work.publisher,
+            }
+            if citations:
+                output["citing_dois"] = crossref.get_citing(doi)
+            if references:
+                output["referenced_dois"] = crossref.get_cited(doi)
+            click.echo(json.dumps(output, indent=2))
+        else:
+            click.secho(work.title, fg="cyan", bold=True)
+            click.echo()
+
+            if work.authors:
+                click.echo(f"Authors: {', '.join(work.authors)}")
+            click.echo(f"Year: {work.year or 'N/A'}")
+            click.echo(f"Journal: {work.journal or 'N/A'}")
+            click.echo(f"DOI: {work.doi}")
+            click.echo(f"Type: {work.type or 'N/A'}")
+            click.echo(f"Publisher: {work.publisher or 'N/A'}")
+            click.echo(f"Citations: {work.citation_count or 0}")
+            click.echo(f"References: {work.reference_count or 0}")
+
+            if work.abstract:
+                click.echo()
+                click.secho("Abstract:", bold=True)
+                click.echo(
+                    work.abstract[:500] + "..."
+                    if len(work.abstract) > 500
+                    else work.abstract
+                )
+
+            if citations:
+                citing = crossref.get_citing(doi)
+                click.echo()
+                click.secho(f"Citing papers ({len(citing)}):", bold=True)
+                for c_doi in citing[:10]:
+                    click.echo(f"  - {c_doi}")
+                if len(citing) > 10:
+                    click.echo(f"  ... and {len(citing) - 10} more")
+
+            if references:
+                cited = crossref.get_cited(doi)
+                click.echo()
+                click.secho(f"References ({len(cited)}):", bold=True)
+                for r_doi in cited[:10]:
+                    click.echo(f"  - {r_doi}")
+                if len(cited) > 10:
+                    click.echo(f"  ... and {len(cited) - 10} more")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red")
+        sys.exit(1)
+
+
+@crossref_scitex.command("count")
+@click.argument("query")
+def count_cmd(query):
+    """
+    Count papers matching a query.
+
+    \b
+    Examples:
+        scitex scholar crossref count "machine learning"
+        scitex scholar crossref count "CRISPR gene editing"
+    """
+    try:
+        from scitex.scholar import crossref_scitex as crossref
+    except ImportError:
+        click.secho(
+            "crossref-local not installed. Install with: pip install crossref-local",
+            fg="red",
+        )
+        sys.exit(1)
+
+    try:
+        count = crossref.count(query)
+        click.echo(f"{count:,} papers match: {query}")
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red")
+        sys.exit(1)
+
+
+@crossref_scitex.command("info")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def info_cmd(as_json):
+    """
+    Show CrossRef database configuration and status.
+
+    \b
+    Examples:
+        scitex scholar crossref info
+        scitex scholar crossref info --json
+    """
+    try:
+        from scitex.scholar import crossref_scitex as crossref
+    except ImportError:
+        click.secho(
+            "crossref-local not installed. Install with: pip install crossref-local",
+            fg="red",
+        )
+        sys.exit(1)
+
+    try:
+        info = crossref.info()
+        mode = crossref.get_mode()
+
+        if as_json:
+            info["mode"] = mode
+            click.echo(json.dumps(info, indent=2))
+        else:
+            click.secho("CrossRef Database Status", fg="cyan", bold=True)
+            click.echo()
+            click.echo(f"Mode: {mode}")
+            click.echo(f"Status: {info.get('status', 'unknown')}")
+
+            if "version" in info:
+                click.echo(f"Version: {info['version']}")
+
+            if "work_count" in info:
+                click.echo(f"Papers: {info['work_count']:,}")
+
+            if "db_path" in info:
+                click.echo(f"Database: {info['db_path']}")
+
+            if "api_url" in info:
+                click.echo(f"API URL: {info['api_url']}")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red")
+        sys.exit(1)
+
+
+# EOF

scitex/cli/scholar/_fetch.py

@@ -219,13 +219,35 @@ def _add_single(
             project=project,
             force=force,
         )
+
+        # Granular success flags
+        has_doi = bool(paper and paper.metadata.id.doi)
+        has_metadata = bool(paper and paper.metadata.basic.title)
+        has_pdf = bool(symlink_path)
+        has_content = bool(
+            paper
+            and hasattr(paper, "container")
+            and paper.container.pdf_size_bytes
+            and paper.container.pdf_size_bytes > 0
+        )
+        pdf_method = None
+        if paper and paper.metadata.path.pdfs_engines:
+            pdf_method = paper.metadata.path.pdfs_engines[0]
+
         return {
-            "success": True,
-            "message": "Paper fetched",
+            "success": has_pdf,  # Overall success = PDF obtained
+            "success_doi": has_doi,
+            "success_metadata": has_metadata,
+            "success_pdf": has_pdf,
+            "success_content": has_content,
+            "pdf_method": pdf_method,
+            "message": "Paper fetched"
+            if has_pdf
+            else "Metadata fetched but PDF not downloaded",
             "doi": paper.metadata.id.doi if paper else None,
             "title": paper.metadata.basic.title if paper else None,
             "path": str(symlink_path) if symlink_path else None,
-            "has_pdf": bool(symlink_path),
+            "has_pdf": has_pdf,
             "timestamp": datetime.now().isoformat(),
         }
 

scitex/cli/social.py

@@ -0,0 +1,314 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-22
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/cli/social.py
+
+"""
+SciTeX CLI - Social Media Commands
+
+Thin wrapper around socialia CLI with SCITEX_ environment variable prefix.
+All commands delegate to socialia for reproducibility.
+"""
+
+import subprocess
+import sys
+
+import click
+
+
+def _run_socialia(*args, json_output: bool = False) -> int:
+    """Run socialia CLI command."""
+    cmd = [sys.executable, "-m", "socialia"]
+    if json_output:
+        cmd.append("--json")
+    cmd.extend(args)
+
+    result = subprocess.run(cmd)
+    return result.returncode
+
+
+def _check_socialia() -> bool:
+    """Check if socialia is available."""
+    try:
+        import socialia  # noqa: F401
+
+        return True
+    except ImportError:
+        return False
+
+
+@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 social(ctx, help_recursive):
+    """
+    Social media management (powered by socialia)
+
+    \b
+    Platforms:
+      twitter   - Twitter/X posting and management
+      linkedin  - LinkedIn posting
+      reddit    - Reddit posting
+      youtube   - YouTube video uploads
+
+    \b
+    Examples:
+      scitex social post twitter "Hello from SciTeX!"
+      scitex social post linkedin "Research update"
+      scitex social status
+      scitex social analytics twitter
+
+    \b
+    Environment Variables (SCITEX_SOCIAL_ prefix):
+      SCITEX_SOCIAL_X_CONSUMER_KEY          Twitter API keys
+      SCITEX_SOCIAL_LINKEDIN_ACCESS_TOKEN   LinkedIn OAuth token
+      SCITEX_SOCIAL_REDDIT_CLIENT_ID        Reddit app credentials
+      SCITEX_SOCIAL_YOUTUBE_API_KEY         YouTube API key
+
+    Note: Falls back to SOCIALIA_ prefix if SCITEX_SOCIAL_ not set.
+    """
+    if not _check_socialia():
+        click.secho("Error: socialia not installed", fg="red", err=True)
+        click.echo("\nInstall with: pip install socialia")
+        ctx.exit(1)
+
+    if help_recursive:
+        from . import print_help_recursive
+
+        print_help_recursive(ctx, social)
+        ctx.exit(0)
+    elif ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
+
+
+@social.command()
+@click.argument(
+    "platform", type=click.Choice(["twitter", "linkedin", "reddit", "youtube"])
+)
+@click.argument("text", required=False)
+@click.option(
+    "-f", "--file", type=click.Path(exists=True), help="Read content from file"
+)
+@click.option("--reply-to", help="Post ID to reply to (Twitter)")
+@click.option("--quote", help="Post ID to quote (Twitter)")
+@click.option("-s", "--subreddit", default="test", help="Target subreddit (Reddit)")
+@click.option("-t", "--title", help="Post title (Reddit/YouTube)")
+@click.option("--dry-run", is_flag=True, help="Preview without posting")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def post(platform, text, file, reply_to, quote, subreddit, title, dry_run, as_json):
+    """
+    Post content to a social platform
+
+    \b
+    Examples:
+      scitex social post twitter "Hello world!"
+      scitex social post twitter --file tweet.txt
+      scitex social post reddit "Check this out" -s python -t "Cool project"
+      scitex social post linkedin "Professional update"
+      scitex social post twitter "Test" --dry-run
+    """
+    args = ["post", platform]
+
+    if text:
+        args.append(text)
+    if file:
+        args.extend(["--file", file])
+    if reply_to:
+        args.extend(["--reply-to", reply_to])
+    if quote:
+        args.extend(["--quote", quote])
+    if subreddit and platform == "reddit":
+        args.extend(["--subreddit", subreddit])
+    if title:
+        args.extend(["--title", title])
+    if dry_run:
+        args.append("--dry-run")
+
+    sys.exit(_run_socialia(*args, json_output=as_json))
+
+
+@social.command()
+@click.argument("platform", type=click.Choice(["twitter", "linkedin", "reddit"]))
+@click.argument("post_id")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def delete(platform, post_id, as_json):
+    """
+    Delete a post from a platform
+
+    \b
+    Examples:
+      scitex social delete twitter 1234567890
+      scitex social delete reddit abc123
+    """
+    sys.exit(_run_socialia("delete", platform, post_id, json_output=as_json))
+
+
+@social.command()
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def status(as_json):
+    """
+    Check configuration and authentication status
+
+    \b
+    Example:
+      scitex social status
+      scitex social status --json
+    """
+    sys.exit(_run_socialia("status", json_output=as_json))
+
+
+@social.command()
+@click.argument(
+    "platform",
+    type=click.Choice(["twitter", "linkedin", "reddit", "youtube"]),
+    required=False,
+)
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def check(platform, as_json):
+    """
+    Check platform connection status.
+
+    \b
+    Examples:
+      scitex social check              # Check all platforms
+      scitex social check twitter      # Check specific platform
+    """
+    args = ["check"]
+    if platform:
+        args.append(platform)
+    sys.exit(_run_socialia(*args, json_output=as_json))
+
+
+@social.command()
+@click.argument(
+    "platform",
+    type=click.Choice(["twitter", "linkedin", "reddit"]),
+    required=False,
+)
+@click.option("--limit", "-l", type=int, default=10, help="Number of posts to fetch")
+@click.option("--mentions", is_flag=True, help="Get mentions/notifications instead")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def feed(platform, limit, mentions, as_json):
+    """
+    Get recent posts from platform feeds.
+
+    \b
+    Examples:
+      scitex social feed                    # All platforms
+      scitex social feed twitter --limit 5  # Specific platform
+      scitex social feed --mentions         # Get mentions
+    """
+    args = ["feed"]
+    if platform:
+        args.append(platform)
+    args.extend(["--limit", str(limit)])
+    if mentions:
+        args.append("--mentions")
+    sys.exit(_run_socialia(*args, json_output=as_json))
+
+
+@social.command()
+@click.argument("platform", type=click.Choice(["twitter", "linkedin", "reddit"]))
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def me(platform, as_json):
+    """
+    Get user profile information.
+
+    \b
+    Examples:
+      scitex social me twitter
+      scitex social me linkedin --json
+    """
+    sys.exit(_run_socialia("me", platform, json_output=as_json))
+
+
+@social.command()
+@click.argument("platform", type=click.Choice(["twitter", "youtube", "ga"]))
+@click.option("--days", "-d", type=int, default=7, help="Number of days to analyze")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def analytics(platform, days, as_json):
+    """
+    Get analytics for a platform
+
+    \b
+    Platforms:
+      twitter  - Tweet engagement metrics
+      youtube  - Channel and video statistics
+      ga       - Google Analytics reports
+
+    \b
+    Examples:
+      scitex social analytics twitter
+      scitex social analytics youtube --days 30
+      scitex social analytics ga --json
+    """
+    args = ["analytics", platform, "--days", str(days)]
+    sys.exit(_run_socialia(*args, json_output=as_json))
+
+
+@social.command()
+@click.argument("platform", type=click.Choice(["twitter"]))
+@click.option(
+    "-f", "--file", type=click.Path(exists=True), required=True, help="Thread file"
+)
+@click.option("--delay", type=int, default=2, help="Delay between posts (seconds)")
+@click.option("--dry-run", is_flag=True, help="Preview without posting")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def thread(platform, file, delay, dry_run, as_json):
+    """
+    Post a thread (multiple connected posts)
+
+    \b
+    Thread file format (--- separates posts):
+      First tweet in the thread
+      ---
+      Second tweet, replying to first
+      ---
+      Third tweet, and so on...
+
+    \b
+    Example:
+      scitex social thread twitter --file thread.txt
+      scitex social thread twitter --file thread.txt --dry-run
+    """
+    args = ["thread", platform, "--file", file, "--delay", str(delay)]
+    if dry_run:
+        args.append("--dry-run")
+    sys.exit(_run_socialia(*args, json_output=as_json))
+
+
+@social.command()
+@click.option(
+    "-t",
+    "--transport",
+    type=click.Choice(["stdio", "sse", "http"]),
+    default="stdio",
+    help="Transport protocol",
+)
+@click.option("--host", default="0.0.0.0", help="Host for HTTP/SSE transport")
+@click.option("--port", default=8086, type=int, help="Port for HTTP/SSE transport")
+def serve(transport, host, port):
+    """
+    Run socialia MCP server
+
+    \b
+    Examples:
+      scitex social serve                    # stdio for Claude Desktop
+      scitex social serve -t http --port 8086
+    """
+    args = ["mcp", "run", "--transport", transport]
+    if transport != "stdio":
+        args.extend(["--host", host, "--port", str(port)])
+        click.secho(f"Starting socialia MCP server ({transport})", fg="cyan")
+        click.echo(f"  Host: {host}")
+        click.echo(f"  Port: {port}")
+
+    sys.exit(_run_socialia(*args))
+
+
+if __name__ == "__main__":
+    social()
+
+# EOF

scitex/cli/stats.py

@@ -11,8 +11,13 @@ from pathlib import Path
 import click
 
 
-@click.group(context_settings={"help_option_names": ["-h", "--help"]})
-def stats():
+@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 stats(ctx, help_recursive):
     """
     Statistical analysis and testing utilities
 
@@ -29,20 +34,22 @@ def stats():
       scitex stats describe data.csv
       scitex stats save results.json --output analysis.stats
     """
-    pass
+    if help_recursive:
+        _print_help_recursive(ctx)
+        ctx.exit(0)
+    elif ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
 
 
-@stats.command("help-recursive")
-@click.pass_context
-def help_recursive(ctx):
-    """Show help for all commands recursively."""
+def _print_help_recursive(ctx):
+    """Print help for all commands recursively."""
     fake_parent = click.Context(click.Group(), info_name="scitex")
     parent_ctx = click.Context(stats, info_name="stats", parent=fake_parent)
     click.secho("━━━ scitex stats ━━━", fg="cyan", bold=True)
     click.echo(stats.get_help(parent_ctx))
     for name in sorted(stats.list_commands(ctx) or []):
         cmd = stats.get_command(ctx, name)
-        if cmd is None or name == "help-recursive":
+        if cmd is None:
             continue
         click.echo()
         click.secho(f"━━━ scitex stats {name} ━━━", fg="cyan", bold=True)