sciwrite-lint 0.2.0__py3-none-any.whl

sciwrite_lint/__init__.py

@@ -0,0 +1,3 @@
+"""sciwrite-lint: a linter for scientific manuscripts."""
+
+__version__ = "0.2.0"

sciwrite_lint/__main__.py

@@ -0,0 +1,527 @@
+"""CLI entry point: sciwrite-lint check paper.tex
+
+Command implementations live in sciwrite_lint.cli submodules:
+- cli.check: check, checks
+- cli.verify: verify, verify-claims, status
+- cli.fetch: fetch
+- cli.rank: contributions
+- cli.misc: init, parse, override, dismiss-claim, grobid, vllm, vision
+"""
+
+from __future__ import annotations
+
+import argparse
+import sys
+from pathlib import Path
+
+from loguru import logger
+
+from sciwrite_lint import __version__
+from sciwrite_lint.config import LintConfig, PaperConfig, load_config
+
+
+# ---------------------------------------------------------------------------
+# Helpers (used by CLI submodules)
+# ---------------------------------------------------------------------------
+
+
+def _load_config(args: argparse.Namespace) -> LintConfig:
+    """Load config from --config flag or auto-discovery."""
+    if getattr(args, "config", None):
+        return load_config(Path(args.config))
+
+    config = load_config(None)
+    if config.config_path is None:
+        from sciwrite_lint.config import _detect_papers
+
+        logger.error("No .sciwrite-lint.toml found.")
+        detected = _detect_papers()
+        if detected:
+            logger.error("  Detected .tex files:")
+            for p in detected:
+                bib = f" (bib: {p['bib']})" if p.get("bib") else ""
+                logger.error(f"    {p['file_path']}{bib}")
+        logger.error("  Run: sciwrite-lint init")
+        logger.error("  Then review .sciwrite-lint.toml before running checks.")
+    return config
+
+
+def _resolve_paper(config: LintConfig, name: str) -> PaperConfig | None:
+    """Resolve a paper name to its config. Print error if not found."""
+    pc = config.get_paper(name)
+    if not pc:
+        if config.papers:
+            names = ", ".join(p.name for p in config.papers)
+            logger.error(f"Unknown paper '{name}'. Registered: {names}")
+        else:
+            logger.error(f"Unknown paper '{name}'. No papers registered.")
+            logger.error(
+                f"  Add [[papers]] to {config.config_path or '.sciwrite-lint.toml'}"
+            )
+    return pc
+
+
+def _paper_names(config: LintConfig) -> list[str]:
+    return [p.name for p in config.papers]
+
+
+def _resolve_input_files(
+    args: argparse.Namespace, config: LintConfig
+) -> list[tuple[str, Path]]:
+    """Resolve which files to check (.tex or .pdf).
+
+    Priority: positional file > --paper (from config) > all papers in config.
+    Returns list of (name, path) pairs.
+    """
+    if hasattr(args, "file") and args.file:
+        p = Path(args.file)
+        return [(p.stem, p)]
+
+    paper_filter = getattr(args, "paper", None)
+    if paper_filter:
+        pc = _resolve_paper(config, paper_filter)
+        if not pc:
+            return []
+        return [(pc.name, pc.file_path)]
+
+    if config.papers:
+        return [(pc.name, pc.file_path) for pc in config.papers]
+
+    logger.error("No papers registered. Either:")
+    logger.error("  sciwrite-lint check <file.tex|file.pdf> — check a specific file")
+    logger.error(
+        "  sciwrite-lint init                      — set up project with [[papers]]"
+    )
+    return []
+
+
+def _classify_verify_issue(issue: str) -> tuple[str, str]:
+    """Classify a verify issue string into (level, rule_id) for findings."""
+    from sciwrite_lint.pipeline import _classify_verify_issue as _classify
+
+    return _classify(issue)
+
+
+def _setup_logging(config: LintConfig) -> None:
+    """Configure loguru rotating file sink from config."""
+    logger.add(
+        "logs/sciwrite-lint.log",
+        rotation="10 MB",
+        retention="30 days",
+        compression="gz",
+        level=config.log_level,
+        format="{time:YYYY-MM-DD HH:mm:ss} | {level:<8} | {name}:{function}:{line} | {message}",
+    )
+
+
+# ---------------------------------------------------------------------------
+# Main parser
+# ---------------------------------------------------------------------------
+
+
+def main(argv: list[str] | None = None) -> int:
+    from sciwrite_lint.cli.check import run_check, run_checks_list
+    from sciwrite_lint.cli.config import run_config
+    from sciwrite_lint.cli.fetch import run_fetch
+    from sciwrite_lint.cli.misc import (
+        run_containers,
+        run_dismiss_claim,
+        run_grobid,
+        run_init,
+        run_override,
+        run_parse,
+        run_vision,
+        run_vllm,
+    )
+    from sciwrite_lint.cli.rank import run_contributions
+    from sciwrite_lint.cli.verify import (
+        run_ref_health,
+        run_status,
+        run_verify,
+        run_verify_claims,
+    )
+
+    parser = argparse.ArgumentParser(
+        prog="sciwrite-lint",
+        description="A linter for scientific manuscripts.",
+    )
+    parser.add_argument(
+        "--version", action="version", version=f"sciwrite-lint {__version__}"
+    )
+    sub = parser.add_subparsers(dest="command")
+
+    # --- check ---
+    p_check = sub.add_parser(
+        "check",
+        help="Full pipeline: verify references, check claims, assess reliability → SciLint Score",
+    )
+    p_check.add_argument(
+        "file",
+        nargs="?",
+        default=None,
+        help="Path to .tex or .pdf file (.tex: text + LLM rules, .pdf: GROBID parse + checks)",
+    )
+    p_check.add_argument("--paper", help="Paper name from [[papers]] in config")
+    p_check.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_check.add_argument("--format", choices=["terminal", "json"], default=None)
+    p_check.add_argument(
+        "--fresh",
+        action="store_true",
+        help="Start from scratch: re-verify references, re-fetch, re-parse, re-run claims (ignore all caches)",
+    )
+    p_check.add_argument(
+        "--concurrency",
+        type=int,
+        default=2,
+        help="Max papers in concurrent stages when checking 2+ papers "
+        "(default: 2, validated up to 4). GPU stages always batched into one "
+        "subprocess; vLLM and network stages run concurrently up to this "
+        "limit. Above 4, the live monitor may fail to track progress and "
+        "vLLM/API throughput plateaus.",
+    )
+    p_check.set_defaults(func=run_check)
+
+    # --- checks ---
+    p_checks = sub.add_parser("checks", help="List all registered checks")
+    p_checks.set_defaults(func=run_checks_list)
+
+    # --- init ---
+    p_init = sub.add_parser(
+        "init", help="Initialize project: config + references directory"
+    )
+    p_init.add_argument(
+        "--force", action="store_true", help="Overwrite existing config"
+    )
+    p_init.set_defaults(func=run_init)
+
+    # --- config ---
+    p_config = sub.add_parser("config", help="Manage polite email and API keys")
+    config_sub = p_config.add_subparsers(dest="config_action")
+
+    p_config_show = config_sub.add_parser(
+        "show", help="Show current email and API key status"
+    )
+    p_config_show.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_config_show.set_defaults(func=run_config)
+
+    p_config_email = config_sub.add_parser(
+        "set-email", help="Set polite email (for CrossRef, Unpaywall, Retraction Watch)"
+    )
+    p_config_email.add_argument("email", help="Your email address")
+    p_config_email.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_config_email.set_defaults(func=run_config)
+
+    p_config_set_key = config_sub.add_parser(
+        "set-key", help="Save an API key for a service"
+    )
+    p_config_set_key.add_argument(
+        "service",
+        choices=["semantic-scholar", "ncbi", "core"],
+        help="Service name",
+    )
+    p_config_set_key.add_argument("key", help="API key value")
+    p_config_set_key.set_defaults(func=run_config)
+
+    p_config_rm_key = config_sub.add_parser(
+        "remove-key", help="Remove a stored API key"
+    )
+    p_config_rm_key.add_argument(
+        "service",
+        choices=["semantic-scholar", "ncbi", "core"],
+        help="Service to remove key for",
+    )
+    p_config_rm_key.set_defaults(func=run_config)
+
+    # --- verify ---
+    p_verify = sub.add_parser("verify", help="Verify citations against APIs (slow)")
+    p_verify.add_argument("--paper", required=True, help="Paper to verify")
+    p_verify.add_argument("--key", help="Verify a single citation key")
+    p_verify.add_argument(
+        "--fetch", action="store_true", help="Also attempt full-text download"
+    )
+    p_verify.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_verify.add_argument("--format", choices=["terminal", "json"], default=None)
+    p_verify.set_defaults(func=run_verify)
+
+    # --- status ---
+    p_status = sub.add_parser("status", help="Show citation verification status")
+    p_status.add_argument("--paper", required=True, help="Paper to show")
+    p_status.add_argument("--tier", choices=["T1", "T2", "T3"], help="Filter by tier")
+    p_status.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_status.set_defaults(func=run_status)
+
+    # --- ref-health ---
+    p_rh = sub.add_parser(
+        "ref-health",
+        help="Fast deterministic reference health check (no API calls)",
+    )
+    p_rh.add_argument("file", nargs="?", help=".tex file to check")
+    p_rh.add_argument("--paper", help="Paper name from config")
+    p_rh.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_rh.set_defaults(func=run_ref_health)
+
+    # --- fetch ---
+    p_fetch = sub.add_parser("fetch", help="Download full text for T2 citations")
+    p_fetch.add_argument("--paper", required=True, help="Paper to fetch for")
+    p_fetch.add_argument("--key", help="Fetch for a single citation key")
+    p_fetch.add_argument(
+        "--all-missing", action="store_true", help="Fetch all T2 citations"
+    )
+    p_fetch.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_fetch.set_defaults(func=run_fetch)
+
+    # --- parse ---
+    p_parse = sub.add_parser(
+        "parse", help="Parse T1 PDFs via GROBID and compute embeddings"
+    )
+    p_parse.add_argument("--paper", required=True, help="Paper name from [[papers]]")
+    p_parse.add_argument("--key", help="Parse a single citation key")
+    p_parse.add_argument(
+        "--fresh", action="store_true", help="Ignore cached results, re-parse all"
+    )
+    p_parse.add_argument(
+        "--no-embed", action="store_true", help="Skip embedding computation"
+    )
+    p_parse.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_parse.set_defaults(func=run_parse)
+
+    # --- verify-claims ---
+    p_vc = sub.add_parser("verify-claims", help="Verify claims against cited sources")
+    p_vc.add_argument("--paper", required=True, help="Paper to verify")
+    p_vc.add_argument(
+        "--backend",
+        choices=["vllm", "claude"],
+        default="vllm",
+        help="vllm (local LLM, fast) or claude (Claude CLI, deep)",
+    )
+    p_vc.add_argument(
+        "--model",
+        choices=["qwen3", "gemma3"],
+        default="",
+        help="vLLM model preset (default: qwen3)",
+    )
+    p_vc.add_argument("--key", help="Verify only claims citing this key")
+    p_vc.add_argument("--limit", type=int, help="Max claims to verify")
+    p_vc.add_argument(
+        "--fresh",
+        action="store_true",
+        help="Ignore cached results, re-verify all claims",
+    )
+    p_vc.add_argument("--output-dir", default=None, help="Output directory")
+    p_vc.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_vc.add_argument("--format", choices=["terminal", "json"], default=None)
+    p_vc.set_defaults(func=run_verify_claims)
+
+    # --- override ---
+    p_override = sub.add_parser(
+        "override", help="Manually override a citation's verification tier"
+    )
+    p_override.add_argument("--paper", required=True, help="Paper name from [[papers]]")
+    p_override.add_argument("--key", required=True, help="Citation key to override")
+    p_override.add_argument(
+        "--tier",
+        choices=["T1", "T2"],
+        required=True,
+        help="Target tier (T1 if you have full text, T2 if confirmed real)",
+    )
+    p_override.add_argument(
+        "--reason", required=True, help="Why you're overriding (stored in metadata)"
+    )
+    p_override.add_argument(
+        "--clear", action="store_true", help="Remove an existing override"
+    )
+    p_override.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_override.set_defaults(func=run_override)
+
+    # --- dismiss-claim ---
+    p_dismiss = sub.add_parser(
+        "dismiss-claim", help="Dismiss a claim finding as false positive"
+    )
+    p_dismiss.add_argument("--paper", required=True, help="Paper the claim belongs to")
+    p_dismiss.add_argument("--key", required=True, help="Citation key")
+    p_dismiss.add_argument(
+        "--line", type=int, required=True, help="Line number of the claim"
+    )
+    p_dismiss.add_argument(
+        "--reason", required=True, help="Why this is a false positive"
+    )
+    p_dismiss.add_argument("--clear", action="store_true", help="Remove dismissal")
+    p_dismiss.add_argument("--output-dir", default=None, help="Output directory")
+    p_dismiss.set_defaults(func=run_dismiss_claim)
+
+    # --- contributions ---
+    p_score = sub.add_parser(
+        "contributions",
+        help="Compute contribution axes and update SciLint Score. Requires vLLM.",
+    )
+    p_score.add_argument(
+        "file",
+        nargs="?",
+        default=None,
+        help="Path to .tex or .pdf file (standalone scoring, no check needed)",
+    )
+    p_score.add_argument("--paper", default=None, help="Paper to score")
+    p_score.add_argument("--output-dir", default=None, help="Output directory")
+    p_score.add_argument(
+        "--findings", help="Path to check findings JSON (for internal score)"
+    )
+    p_score.add_argument(
+        "--model", default="", help="vLLM model preset (default: from config)"
+    )
+    p_score.add_argument(
+        "--format",
+        choices=["terminal", "json"],
+        default="terminal",
+        help="Output format (default: terminal)",
+        dest="format",
+    )
+    p_score.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_score.set_defaults(func=run_contributions)
+
+    # --- vision ---
+    p_vision = sub.add_parser(
+        "vision",
+        help="Extract and describe manuscript figures via Qwen3-VL-2B (also runs automatically in check pipeline).",
+    )
+    p_vision.add_argument("--paper", required=True, help="Paper name from [[papers]]")
+    p_vision.add_argument(
+        "--device",
+        choices=["auto", "cpu", "cuda"],
+        default="auto",
+        help="Device for VL inference (default: auto — CUDA if available)",
+    )
+    p_vision.add_argument(
+        "--fresh",
+        action="store_true",
+        help="Ignore vision cache and re-describe all figures",
+    )
+    p_vision.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_vision.set_defaults(func=run_vision)
+
+    # --- containers (grobid + vllm together) ---
+    p_containers = sub.add_parser(
+        "containers", help="Manage GROBID and vLLM containers together"
+    )
+    p_containers.add_argument(
+        "action",
+        choices=["start", "stop", "restart", "status", "monitor"],
+        help="start/stop/restart/status/monitor of all containers",
+    )
+    p_containers.add_argument(
+        "--model", choices=["qwen3", "gemma3"], help="vLLM model to use"
+    )
+    p_containers.add_argument(
+        "--update",
+        action="store_true",
+        help="Pull latest container images before starting",
+    )
+    p_containers.add_argument(
+        "-i",
+        "--interval",
+        type=float,
+        default=2,
+        help="Monitor refresh interval in seconds (default: 2)",
+    )
+    p_containers.add_argument(
+        "--recreate",
+        action="store_true",
+        help="Remove and recreate containers (applies config changes like memory limits)",
+    )
+    p_containers.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_containers.set_defaults(func=run_containers)
+
+    # --- grobid ---
+    p_grobid = sub.add_parser("grobid", help="Manage GROBID container")
+    p_grobid.add_argument(
+        "action",
+        choices=["start", "stop", "status"],
+        help="start/stop/status of GROBID container",
+    )
+    p_grobid.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_grobid.set_defaults(func=run_grobid)
+
+    # --- vllm ---
+    p_vllm = sub.add_parser(
+        "vllm", help="Manage local vLLM server for LLM-engine rules"
+    )
+    vllm_sub = p_vllm.add_subparsers(dest="vllm_action")
+
+    p_vllm_status = vllm_sub.add_parser(
+        "status", help="Show vLLM status and API health"
+    )
+    p_vllm_status.set_defaults(func=run_vllm)
+
+    p_vllm_start = vllm_sub.add_parser("start", help="Start vLLM server")
+    p_vllm_start.add_argument(
+        "--model", choices=["qwen3", "gemma3"], help="Model to serve"
+    )
+    p_vllm_start.add_argument(
+        "--update",
+        action="store_true",
+        help="Pull latest vLLM image before starting",
+    )
+    p_vllm_start.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_vllm_start.set_defaults(func=run_vllm)
+
+    p_vllm_stop = vllm_sub.add_parser("stop", help="Stop vLLM server")
+    p_vllm_stop.add_argument(
+        "--model", choices=["qwen3", "gemma3"], help="Model to stop"
+    )
+    p_vllm_stop.set_defaults(func=run_vllm)
+
+    p_vllm_logs = vllm_sub.add_parser("logs", help="Show vLLM container logs")
+    p_vllm_logs.add_argument("--model", choices=["qwen3", "gemma3"])
+    p_vllm_logs.add_argument(
+        "-f", "--follow", action="store_true", help="Follow log output"
+    )
+    p_vllm_logs.add_argument("-n", "--tail", type=int, default=50, help="Lines to show")
+    p_vllm_logs.set_defaults(func=run_vllm)
+
+    p_vllm_rm = vllm_sub.add_parser("rm", help="Remove vLLM container")
+    p_vllm_rm.add_argument("--model", choices=["qwen3", "gemma3"])
+    p_vllm_rm.add_argument(
+        "--force", action="store_true", help="Force remove even if running"
+    )
+    p_vllm_rm.set_defaults(func=run_vllm)
+
+    p_vllm_monitor = vllm_sub.add_parser(
+        "monitor", help="Live terminal monitor for vLLM server"
+    )
+    p_vllm_monitor.add_argument(
+        "-i",
+        "--interval",
+        type=float,
+        default=2,
+        help="Refresh interval in seconds (default: 2)",
+    )
+    p_vllm_monitor.add_argument("--config", help="Path to .sciwrite-lint.toml")
+    p_vllm_monitor.set_defaults(func=run_vllm)
+
+    args = parser.parse_args(argv)
+    if not args.command:
+        parser.print_help()
+        return 0
+
+    if args.command == "config" and not getattr(args, "config_action", None):
+        p_config.print_help()
+        return 0
+
+    if args.command == "vllm" and not getattr(args, "vllm_action", None):
+        p_vllm.print_help()
+        return 0
+
+    # Set up file logging from config (stderr sink stays at INFO by default)
+    try:
+        config = load_config(
+            Path(args.config) if getattr(args, "config", None) else None
+        )
+    except Exception as e:
+        logger.debug("Config load failed, using defaults: {}", e)
+        config = LintConfig()
+    _setup_logging(config)
+
+    return args.func(args)
+
+
+if __name__ == "__main__":
+    sys.exit(main())