mirror of
https://github.com/lllin000/PaperForge.git
synced 2026-07-22 06:50:53 +00:00
style: ruff format pass across paperforge/
This commit is contained in:
Research Assistant
parent
9a3cdaa3b8
commit
e9a31705d3
16 changed files with 284 additions and 177 deletions
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@ -25,6 +25,7 @@ def obsidian_wikilink_for_pdf(pdf_path: str, vault_dir: Path, zotero_dir: Path |
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if zotero_dir is not None and zotero_dir.exists():
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try:
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from paperforge.pdf_resolver import resolve_junction
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real_zotero = resolve_junction(zotero_dir)
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if real_zotero != zotero_dir:
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rel_to_zotero = absolute_path.relative_to(real_zotero)
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@ -153,12 +153,7 @@ def run(args: argparse.Namespace) -> int:
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elif collection:
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# Collection filter: prefix match on any element in "collections" list
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filtered = [
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e
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for e in items
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if any(
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isinstance(c, str) and c.startswith(collection)
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for c in e.get("collections", [])
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)
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e for e in items if any(isinstance(c, str) and c.startswith(collection) for c in e.get("collections", []))
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]
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elif all_mode:
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@ -69,9 +69,7 @@ def _gather_dashboard_data(vault: Path) -> dict:
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if paths["literature"].exists():
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for domain_dir in sorted(paths["literature"].iterdir()):
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if domain_dir.is_dir():
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count = sum(
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1 for p in domain_dir.rglob("*.md") if p.name not in _skip_names
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)
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count = sum(1 for p in domain_dir.rglob("*.md") if p.name not in _skip_names)
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if count > 0:
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domain_counts[domain_dir.name] = count
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@ -85,8 +83,8 @@ def _gather_dashboard_data(vault: Path) -> dict:
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_path_error_pat = re.compile(r'^path_error:\s*"(.+?)"\s*$', re.MULTILINE)
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_pdf_path_pat = re.compile(r'^pdf_path:\s*".*?"\s*$', re.MULTILINE)
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_ocr_status_pat = re.compile(r'^ocr_status:\s*(\S+)', re.MULTILINE)
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_do_ocr_pat = re.compile(r'^do_ocr:\s*true\s*$', re.MULTILINE)
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_ocr_status_pat = re.compile(r"^ocr_status:\s*(\S+)", re.MULTILINE)
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_do_ocr_pat = re.compile(r"^do_ocr:\s*true\s*$", re.MULTILINE)
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if paths["literature"].exists():
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for note_path in paths["literature"].rglob("*.md"):
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@ -126,9 +124,7 @@ def _gather_dashboard_data(vault: Path) -> dict:
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can_sync = len(export_files) > 0
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paddle_token = (
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os.environ.get("PADDLEOCR_API_TOKEN")
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or os.environ.get("PADDLEOCR_API_KEY")
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or os.environ.get("OCR_TOKEN")
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os.environ.get("PADDLEOCR_API_TOKEN") or os.environ.get("PADDLEOCR_API_KEY") or os.environ.get("OCR_TOKEN")
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)
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can_ocr = bool(paddle_token)
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@ -29,32 +29,38 @@ def validate_entry_fields(
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# Check 1: Required fields present
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for field_name, meta in owner_fields.items():
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if meta.get("required", False) and field_name not in entry:
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issues.append({
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"severity": "error",
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"code": "MISSING_REQUIRED",
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"field": field_name,
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"message": f"Missing required field '{field_name}' in {owner} entry{(' (' + entry_label + ')') if entry_label else ''}",
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"suggestion": f"Add '{field_name}' to the entry with appropriate value ({meta.get('type', 'str')})",
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})
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issues.append(
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{
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"severity": "error",
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"code": "MISSING_REQUIRED",
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"field": field_name,
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"message": f"Missing required field '{field_name}' in {owner} entry{(' (' + entry_label + ')') if entry_label else ''}",
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"suggestion": f"Add '{field_name}' to the entry with appropriate value ({meta.get('type', 'str')})",
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}
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)
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elif not meta.get("required", True) and field_name not in entry:
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issues.append({
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"severity": "info",
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"code": "MISSING_OPTIONAL",
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"field": field_name,
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"message": f"Missing optional field '{field_name}' in {owner} entry{(' (' + entry_label + ')') if entry_label else ''}",
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})
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issues.append(
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{
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"severity": "info",
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"code": "MISSING_OPTIONAL",
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"field": field_name,
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"message": f"Missing optional field '{field_name}' in {owner} entry{(' (' + entry_label + ')') if entry_label else ''}",
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}
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)
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# Check 2: Unknown fields (drift detection)
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known_fields = set(owner_fields.keys())
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for key in entry:
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if key not in known_fields:
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issues.append({
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"severity": "warning",
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"code": "DRIFT",
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"field": key,
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"message": f"Unknown field '{key}' in {owner} entry{(' (' + entry_label + ')') if entry_label else ''} — not in field registry",
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"suggestion": f"Either remove '{key}' or add it to field_registry.yaml under '{owner}'",
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})
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issues.append(
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{
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"severity": "warning",
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"code": "DRIFT",
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"field": key,
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"message": f"Unknown field '{key}' in {owner} entry{(' (' + entry_label + ')') if entry_label else ''} — not in field registry",
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"suggestion": f"Either remove '{key}' or add it to field_registry.yaml under '{owner}'",
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}
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)
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return issues
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@ -143,9 +149,17 @@ def validate_frontmatter_from_file(
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# Parse frontmatter
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import re
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fm_match = re.match(r"^---\s*\n(.*?)\n---", text, re.DOTALL)
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if not fm_match:
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return [{"severity": "warning", "code": "NO_FRONTMATTER", "field": "", "message": f"No frontmatter found in {file_path.name}"}]
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return [
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{
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"severity": "warning",
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"code": "NO_FRONTMATTER",
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"field": "",
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"message": f"No frontmatter found in {file_path.name}",
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}
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]
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frontmatter = {}
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for line in fm_match.group(1).splitlines():
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@ -9,6 +9,7 @@ from typing import Any
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@dataclass
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class SetupStepResult:
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"""Result of a single setup step."""
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step: str
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ok: bool = True
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message: str = ""
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@ -31,9 +31,7 @@ class RuntimeInstaller:
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if self.progress_callback:
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self.progress_callback(message)
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def _pip_install(
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self, package_spec: str
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) -> tuple[bool, str, str]:
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def _pip_install(self, package_spec: str) -> tuple[bool, str, str]:
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"""Run pip install and return (ok, stdout, stderr)."""
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try:
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result = subprocess.run(
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@ -53,9 +51,7 @@ class RuntimeInstaller:
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self._log("Installing PaperForge...")
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if self.version:
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package_spec = (
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f"git+https://github.com/LLLin000/PaperForge.git@{self.version}"
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)
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package_spec = f"git+https://github.com/LLLin000/PaperForge.git@{self.version}"
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else:
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package_spec = "git+https://github.com/LLLin000/PaperForge.git"
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@ -65,9 +61,7 @@ class RuntimeInstaller:
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return SetupStepResult(
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step="runtime_installer",
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ok=True,
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message=(
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f"PaperForge installed successfully{(' (' + self.version + ')') if self.version else ''}"
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),
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message=(f"PaperForge installed successfully{(' (' + self.version + ')') if self.version else ''}"),
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details={"version": self.version or "latest", "stdout": stdout[:500]},
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)
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else:
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@ -55,9 +55,7 @@ class VaultInitializer:
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def create_zotero_junction(self, zotero_path: str | None = None) -> SetupStepResult:
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"""Create Zotero junction/symlink to vault."""
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system_dir = self.vault / self.config.get(
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"system_dir", self.DEFAULT_DIRS["system_dir"]
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)
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system_dir = self.vault / self.config.get("system_dir", self.DEFAULT_DIRS["system_dir"])
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zotero_link = system_dir / "Zotero"
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if zotero_link.exists() or zotero_link.is_symlink():
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@ -499,11 +499,7 @@ def _merge_env_incremental(env_path: Path, values: dict[str, str]) -> str:
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for line in existing_text.splitlines()
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if line.strip() and not line.lstrip().startswith("#") and "=" in line
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}
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missing_lines = [
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f"{key}={value}"
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for key, value in values.items()
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if key not in existing_keys
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]
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missing_lines = [f"{key}={value}" for key, value in values.items() if key not in existing_keys]
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if not missing_lines:
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return "preserved"
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@ -546,7 +542,9 @@ def _deploy_skill_directory(
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skill_dst = vault / skill_dir / skill_name
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skill_dst.mkdir(parents=True, exist_ok=True)
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text = skill_file.read_text(encoding="utf-8")
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text = _substitute_vars(text, system_dir, resources_dir, literature_dir, control_dir, base_dir, skill_dir, prefix)
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text = _substitute_vars(
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text, system_dir, resources_dir, literature_dir, control_dir, base_dir, skill_dir, prefix
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)
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_write_text_incremental(skill_dst / "SKILL.md", text)
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imported.append(skill_name)
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@ -673,7 +671,7 @@ def headless_setup(
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# Determine repo_root (where paperforge package sources live)
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if repo_root is None:
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wizard_dir = Path(__file__).parent.resolve()
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if (wizard_dir / "paperforge" if wizard_dir.name != "paperforge" else False):
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if wizard_dir / "paperforge" if wizard_dir.name != "paperforge" else False:
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_repo = wizard_dir
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elif (wizard_dir.parent / "paperforge").exists():
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_repo = wizard_dir.parent
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@ -749,7 +747,9 @@ def headless_setup(
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if sys.platform == "win32":
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result = subprocess.run(
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["cmd", "/c", "mklink", "/J", str(zotero_link_path), str(zotero_data)],
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capture_output=True, text=True, timeout=30,
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capture_output=True,
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text=True,
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timeout=30,
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)
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if result.returncode != 0:
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print(f" [WARN] Zotero junction failed: {result.stderr.strip()}")
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@ -837,9 +837,18 @@ def headless_setup(
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return 4
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_copy_file_incremental(worker_src, worker_dst)
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for mod in ["ocr.py", "repair.py", "status.py", "deep_reading.py",
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"update.py", "base_views.py", "__init__.py",
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"_utils.py", "_progress.py", "_retry.py"]:
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for mod in [
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"ocr.py",
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"repair.py",
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"status.py",
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"deep_reading.py",
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"update.py",
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"base_views.py",
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"__init__.py",
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"_utils.py",
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"_progress.py",
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"_retry.py",
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]:
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mod_src = repo_root / "paperforge/worker" / mod
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if mod_src.exists():
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_copy_file_incremental(mod_src, pf_path / "worker/scripts" / mod)
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@ -852,24 +861,52 @@ def headless_setup(
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if fmt == "flat_command":
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imported_skills = _deploy_flat_command(
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vault, agent_config["command_dir"], repo_root,
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system_dir, resources_dir, literature_dir, control_dir, base_dir, skill_dir,
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vault,
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agent_config["command_dir"],
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repo_root,
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system_dir,
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resources_dir,
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literature_dir,
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control_dir,
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base_dir,
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skill_dir,
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)
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# OpenCode also needs the skill directory (ld_deep.py, prompt, chart-reading)
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imported_skills += _deploy_skill_directory(
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vault, skill_dir, repo_root,
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system_dir, resources_dir, literature_dir, control_dir, base_dir, prefix,
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vault,
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skill_dir,
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repo_root,
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system_dir,
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resources_dir,
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literature_dir,
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control_dir,
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base_dir,
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prefix,
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)
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elif fmt == "rules_file":
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imported_skills = _deploy_rules_file(
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vault, agent_config["skill_dir"], repo_root,
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system_dir, resources_dir, literature_dir, control_dir, base_dir, skill_dir,
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vault,
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agent_config["skill_dir"],
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repo_root,
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system_dir,
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resources_dir,
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literature_dir,
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control_dir,
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base_dir,
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skill_dir,
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)
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else:
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# skill_directory (default)
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imported_skills = _deploy_skill_directory(
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vault, skill_dir, repo_root,
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system_dir, resources_dir, literature_dir, control_dir, base_dir, prefix,
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vault,
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skill_dir,
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repo_root,
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system_dir,
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resources_dir,
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literature_dir,
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control_dir,
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base_dir,
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prefix,
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)
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if imported_skills:
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@ -997,26 +1034,32 @@ def headless_setup(
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try:
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try:
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import paperforge as _pf
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current_ver = getattr(_pf, '__version__', '?')
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current_ver = getattr(_pf, "__version__", "?")
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except ImportError:
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current_ver = 'not installed'
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current_ver = "not installed"
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# If repo_root is the source repository (has pyproject.toml), install from it.
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# Otherwise (site-packages copy) install from GitHub tagged release.
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if (repo_root / "pyproject.toml").exists():
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install_target = [str(repo_root)]
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else:
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from paperforge import __version__ as _pv
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install_target = [f"git+https://github.com/LLLin000/PaperForge.git@{_pv}"]
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result = subprocess.run(
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[sys.executable, "-m", "pip", "install", "--upgrade"] + install_target,
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capture_output=True, text=True, timeout=120,
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capture_output=True,
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text=True,
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timeout=120,
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)
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if result.returncode == 0:
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_new = subprocess.run(
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[sys.executable, "-c", "import paperforge; print(getattr(paperforge, '__version__', '?'))"],
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capture_output=True, text=True, timeout=15,
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capture_output=True,
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text=True,
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timeout=15,
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)
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new_ver = _new.stdout.strip() or '?'
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new_ver = _new.stdout.strip() or "?"
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print(f" [OK] paperforge {current_ver} -> {new_ver}")
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else:
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stderr_short = result.stderr[:200] if result.stderr else ""
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|
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@ -1057,7 +1100,9 @@ def headless_setup(
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print(" Existing files in the target vault were preserved; setup only created missing files and folders.")
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print()
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print("Next steps:")
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print(f" 1. In Zotero, export the library or a collection as Better BibTeX JSON into: {vault / system_dir / 'PaperForge' / 'exports'}")
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print(
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f" 1. In Zotero, export the library or a collection as Better BibTeX JSON into: {vault / system_dir / 'PaperForge' / 'exports'}"
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)
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print(" Enable 'Keep updated' so Zotero keeps the JSON in sync.")
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print(" 2. Open Obsidian → Settings → Community Plugins → Enable 'PaperForge'")
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print(" 3. Press Ctrl+P and type 'PaperForge' to open the dashboard")
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|
|
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|
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@ -86,11 +86,7 @@ def compute_health(entry: dict) -> dict[str, str]:
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ocr_health = ocr_messages.get(ocr_status, "OCR pending: run `paperforge ocr`")
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# Note health
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note_health = (
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"Formal note missing: run `paperforge sync` to regenerate"
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if not note_path
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else "healthy"
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)
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note_health = "Formal note missing: run `paperforge sync` to regenerate" if not note_path else "healthy"
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# Asset health — check three workspace paths (deep reading lives in main note)
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workspace_paths = {
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|
|
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|
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@ -104,17 +104,46 @@ def build_base_views(domain: str) -> list[dict]:
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},
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{
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"name": "待深度阅读",
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"order": ["year", "first_author", "title", "has_pdf", "do_ocr", "analyze", "ocr_status", "deep_reading_status", "pdf_path"],
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"order": [
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"year",
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"first_author",
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"title",
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"has_pdf",
|
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"do_ocr",
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"analyze",
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"ocr_status",
|
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"deep_reading_status",
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"pdf_path",
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],
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"filter": "analyze = true AND ocr_status = 'done' AND deep_reading_status = 'pending'",
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},
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{
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"name": "深度阅读完成",
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"order": ["year", "first_author", "title", "has_pdf", "do_ocr", "analyze", "ocr_status", "deep_reading_status", "pdf_path"],
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"order": [
|
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"year",
|
||||
"first_author",
|
||||
"title",
|
||||
"has_pdf",
|
||||
"do_ocr",
|
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"analyze",
|
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"ocr_status",
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"deep_reading_status",
|
||||
"pdf_path",
|
||||
],
|
||||
"filter": "deep_reading_status = 'done'",
|
||||
},
|
||||
{
|
||||
"name": "正式卡片",
|
||||
"order": ["title", "year", "first_author", "journal", "impact_factor", "has_pdf", "deep_reading_status", "pdf_path"],
|
||||
"order": [
|
||||
"title",
|
||||
"year",
|
||||
"first_author",
|
||||
"journal",
|
||||
"impact_factor",
|
||||
"has_pdf",
|
||||
"deep_reading_status",
|
||||
"pdf_path",
|
||||
],
|
||||
"filter": "deep_reading_status = 'done'",
|
||||
},
|
||||
{
|
||||
|
|
@ -334,6 +363,7 @@ views:
|
|||
def _update_folder_filter(content: str, new_filter: str) -> str:
|
||||
"""Update the folder filter in a .base file if it changed."""
|
||||
import re
|
||||
|
||||
old_match = re.search(r'file\.inFolder\("([^"]+)"\)', content)
|
||||
if not old_match or old_match.group(1) == new_filter:
|
||||
return content
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ logger = logging.getLogger(__name__)
|
|||
_SCHEMA_VERSION = "1"
|
||||
_ISO_FORMAT = "%Y-%m-%dT%H:%M:%S%z"
|
||||
_MD_SEPARATOR = "---"
|
||||
_MD_SPECIAL_CHARS = re.compile(r'([*#\[\]_`])')
|
||||
_MD_SPECIAL_CHARS = re.compile(r"([*#\[\]_`])")
|
||||
"""Regex for markdown special characters that must be escaped in QA text fields."""
|
||||
|
||||
LOCK_TIMEOUT = 10
|
||||
|
|
@ -63,7 +63,7 @@ def _escape_md(text: str) -> str:
|
|||
when user questions or AI answers contain these characters.
|
||||
Does not double-escape already-escaped characters.
|
||||
"""
|
||||
return _MD_SPECIAL_CHARS.sub(r'\\\1', text)
|
||||
return _MD_SPECIAL_CHARS.sub(r"\\\1", text)
|
||||
|
||||
|
||||
def _today_str(iso_stamp: str) -> str:
|
||||
|
|
@ -333,12 +333,10 @@ def record_session(
|
|||
_atomic_write_md(md_path, content)
|
||||
except filelock.Timeout:
|
||||
logger.warning("Could not acquire lock for discussion files: %s", lock_path)
|
||||
return {"status": "error",
|
||||
"message": "Concurrent access conflict. Please try again."}
|
||||
return {"status": "error", "message": "Concurrent access conflict. Please try again."}
|
||||
except Exception as exc:
|
||||
logger.warning("Failed to write discussion files: %s", exc)
|
||||
return {"status": "error",
|
||||
"message": f"Failed to write discussion files: {exc}"}
|
||||
return {"status": "error", "message": f"Failed to write discussion files: {exc}"}
|
||||
|
||||
return {
|
||||
"status": "ok",
|
||||
|
|
@ -368,7 +366,7 @@ def _build_cli_parser() -> argparse.ArgumentParser:
|
|||
record_p.add_argument(
|
||||
"--qa-pairs",
|
||||
default="[]",
|
||||
help='JSON array of Q&A pairs',
|
||||
help="JSON array of Q&A pairs",
|
||||
)
|
||||
return parser
|
||||
|
||||
|
|
|
|||
|
|
@ -33,6 +33,8 @@ def _read_dotenv(vault: Path, key: str) -> str:
|
|||
except (OSError, UnicodeDecodeError):
|
||||
continue
|
||||
return ""
|
||||
|
||||
|
||||
from paperforge.worker.asset_index import refresh_index_entry
|
||||
from paperforge.worker._retry import retry_with_meta
|
||||
from paperforge.worker._utils import (
|
||||
|
|
@ -282,11 +284,7 @@ def normalize_obsidian_markdown(text: str) -> str:
|
|||
)
|
||||
normalized = re.sub(
|
||||
r"(?<!\$)\bp\s*<\s*[\d]+(?:\.[\d]+)?",
|
||||
lambda m: (
|
||||
f"${m.group(0).strip()}$"
|
||||
if normalized[: m.start()].count("$") % 2 == 0
|
||||
else m.group(0)
|
||||
),
|
||||
lambda m: f"${m.group(0).strip()}$" if normalized[: m.start()].count("$") % 2 == 0 else m.group(0),
|
||||
normalized,
|
||||
)
|
||||
normalized = re.sub("([A-Za-z])(\\$[^$\\n]+\\$)", "\\1 \\2", normalized)
|
||||
|
|
@ -1677,7 +1675,9 @@ def run_ocr(vault: Path, verbose: bool = False, no_progress: bool = False) -> in
|
|||
for line in lines:
|
||||
page_payload = json.loads(line)["result"]
|
||||
all_results.append(page_payload)
|
||||
page_num, markdown_path, json_path, fulltext_md_path = postprocess_ocr_result(vault, key, all_results)
|
||||
page_num, markdown_path, json_path, fulltext_md_path = postprocess_ocr_result(
|
||||
vault, key, all_results
|
||||
)
|
||||
except Exception as e:
|
||||
meta["ocr_status"] = "pending"
|
||||
meta["error"] = str(e)
|
||||
|
|
@ -1725,21 +1725,23 @@ def run_ocr(vault: Path, verbose: bool = False, no_progress: bool = False) -> in
|
|||
active_submitted = max(0, active_submitted - 1)
|
||||
write_json(paths["ocr"] / key / "meta.json", meta)
|
||||
changed += 1
|
||||
|
||||
# Upload pending items in batches until none remain (processes all do_ocr items, not just max_items)
|
||||
def _do_upload(token_val: str, pdf_path: Path) -> requests.Response:
|
||||
with open(pdf_path, "rb") as file_handle:
|
||||
resp = requests.post(
|
||||
job_url,
|
||||
headers={"Authorization": f"bearer {token_val}"},
|
||||
data={"model": model, "optionalPayload": json.dumps(optional_payload)},
|
||||
files={"file": file_handle},
|
||||
timeout=120,
|
||||
)
|
||||
resp.raise_for_status()
|
||||
return resp
|
||||
with open(pdf_path, "rb") as file_handle:
|
||||
resp = requests.post(
|
||||
job_url,
|
||||
headers={"Authorization": f"bearer {token_val}"},
|
||||
data={"model": model, "optionalPayload": json.dumps(optional_payload)},
|
||||
files={"file": file_handle},
|
||||
timeout=120,
|
||||
)
|
||||
resp.raise_for_status()
|
||||
return resp
|
||||
|
||||
# Combined upload + poll loop: process all items in batches up to max_items concurrency
|
||||
import time as _time
|
||||
|
||||
poll_interval = int(os.environ.get("PAPERFORGE_POLL_INTERVAL", "15"))
|
||||
max_poll_cycles = int(os.environ.get("PAPERFORGE_POLL_MAX_CYCLES", "60"))
|
||||
for _cycle in range(max_poll_cycles):
|
||||
|
|
@ -1748,11 +1750,9 @@ def run_ocr(vault: Path, verbose: bool = False, no_progress: bool = False) -> in
|
|||
break
|
||||
available_slots = max(0, max_items - active_submitted)
|
||||
if available_slots > 0:
|
||||
upload_items = [
|
||||
r
|
||||
for r in remaining
|
||||
if r.get("queue_status", "") not in ("queued", "running")
|
||||
][:available_slots]
|
||||
upload_items = [r for r in remaining if r.get("queue_status", "") not in ("queued", "running")][
|
||||
:available_slots
|
||||
]
|
||||
for queue_row in upload_items:
|
||||
key = queue_row["zotero_key"]
|
||||
meta = ensure_ocr_meta(vault, queue_row)
|
||||
|
|
@ -1782,6 +1782,7 @@ def run_ocr(vault: Path, verbose: bool = False, no_progress: bool = False) -> in
|
|||
if meta.get("needs_sanitize"):
|
||||
try:
|
||||
import tempfile
|
||||
|
||||
doc = fitz.open(str(resolved_pdf))
|
||||
_sanitized_temp = Path(tempfile.mktemp(suffix=".pdf"))
|
||||
doc.save(str(_sanitized_temp), garbage=4, deflate=True, clean=True)
|
||||
|
|
@ -1804,8 +1805,9 @@ def run_ocr(vault: Path, verbose: bool = False, no_progress: bool = False) -> in
|
|||
if _sanitized_temp is not None and _sanitized_temp.exists():
|
||||
_sanitized_temp.unlink(missing_ok=True)
|
||||
import requests as _requests
|
||||
|
||||
if isinstance(e, _requests.exceptions.HTTPError):
|
||||
_status = getattr(getattr(e, 'response', None), 'status_code', 0)
|
||||
_status = getattr(getattr(e, "response", None), "status_code", 0)
|
||||
if _status == 401:
|
||||
meta["ocr_status"] = "blocked"
|
||||
meta["error"] = "PaddleOCR token invalid"
|
||||
|
|
@ -1896,9 +1898,7 @@ def run_ocr(vault: Path, verbose: bool = False, no_progress: bool = False) -> in
|
|||
_time.sleep(poll_interval)
|
||||
# Collect completed OCR keys for incremental index refresh (before filtering)
|
||||
_done_ocr_keys = (
|
||||
[r.get("zotero_key", "") for r in ocr_queue if r.get("queue_status") == "done"]
|
||||
if queue_changed
|
||||
else []
|
||||
[r.get("zotero_key", "") for r in ocr_queue if r.get("queue_status") == "done"] if queue_changed else []
|
||||
)
|
||||
if queue_changed:
|
||||
ocr_queue = [row for row in ocr_queue if str(row.get("queue_status", "")).lower() != "done"]
|
||||
|
|
|
|||
|
|
@ -69,9 +69,7 @@ def write_paper_meta(
|
|||
elif "migrated_from" in existing:
|
||||
meta["migrated_from"] = existing["migrated_from"]
|
||||
|
||||
meta_path.write_text(
|
||||
json.dumps(meta, ensure_ascii=False, indent=2), encoding="utf-8"
|
||||
)
|
||||
meta_path.write_text(json.dumps(meta, ensure_ascii=False, indent=2), encoding="utf-8")
|
||||
return meta_path
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -191,7 +191,11 @@ def run_repair(vault: Path, paths: dict, verbose: bool = False, fix: bool = Fals
|
|||
dict with scanned, divergent, fixed, errors counts
|
||||
"""
|
||||
result = {"scanned": 0, "divergent": [], "fixed": 0, "errors": [], "rebuilt": 0}
|
||||
record_paths = [p for p in paths["literature"].rglob("*.md") if p.name not in ("fulltext.md", "deep-reading.md", "discussion.md")]
|
||||
record_paths = [
|
||||
p
|
||||
for p in paths["literature"].rglob("*.md")
|
||||
if p.name not in ("fulltext.md", "deep-reading.md", "discussion.md")
|
||||
]
|
||||
for record_path in record_paths:
|
||||
try:
|
||||
record_text = record_path.read_text(encoding="utf-8")
|
||||
|
|
@ -256,10 +260,7 @@ def run_repair(vault: Path, paths: dict, verbose: bool = False, fix: bool = Fals
|
|||
meta_ocr_status is not None
|
||||
and meta_validated_status is not None
|
||||
and note_ocr_status != meta_validated_status
|
||||
and not (
|
||||
note_ocr_status == "pending"
|
||||
and meta_validated_status == "pending"
|
||||
)
|
||||
and not (note_ocr_status == "pending" and meta_validated_status == "pending")
|
||||
):
|
||||
is_divergent = True
|
||||
div_reason = f"formal_note={note_ocr_status} vs meta post-validation={meta_validated_status}"
|
||||
|
|
|
|||
|
|
@ -216,7 +216,7 @@ _MODULE_MANIFEST = [
|
|||
|
||||
def _read_plugin_data(vault: Path) -> dict:
|
||||
"""Read Obsidian plugin's data.json to get the user's python_path override.
|
||||
|
||||
|
||||
Returns empty dict if file not found, invalid, or not a dict.
|
||||
"""
|
||||
plugin_data_path = vault / ".obsidian" / "plugins" / "paperforge" / "data.json"
|
||||
|
|
@ -233,13 +233,13 @@ def _read_plugin_data(vault: Path) -> dict:
|
|||
|
||||
def _resolve_plugin_interpreter(vault: Path, plugin_data: dict) -> tuple[str, str, list[str]]:
|
||||
"""Replicate the plugin's resolvePythonExecutable() logic in pure Python.
|
||||
|
||||
|
||||
Detection order:
|
||||
1. Manual override: plugin_data["python_path"] if set and on disk
|
||||
2. Venv candidates: .paperforge-test-venv, .venv, venv (Scripts/ on Windows, bin/ on POSIX)
|
||||
3. System candidates: py -3, python, python3 (tested via --version)
|
||||
4. Fallback: python
|
||||
|
||||
|
||||
Returns (interpreter_path, source, extra_args).
|
||||
"""
|
||||
# 1. Manual override
|
||||
|
|
@ -288,11 +288,9 @@ def _resolve_plugin_interpreter(vault: Path, plugin_data: dict) -> tuple[str, st
|
|||
return ("python", "auto-detected", [])
|
||||
|
||||
|
||||
def _query_resolved_version(
|
||||
interp: str, extra_args: list[str]
|
||||
) -> tuple[str | None, tuple[int, int, int] | None]:
|
||||
def _query_resolved_version(interp: str, extra_args: list[str]) -> tuple[str | None, tuple[int, int, int] | None]:
|
||||
"""Run interpreter --version, parse and return version info.
|
||||
|
||||
|
||||
Returns (version_string, (major, minor, micro)) or (None, None) on failure.
|
||||
"""
|
||||
try:
|
||||
|
|
@ -312,11 +310,9 @@ def _query_resolved_version(
|
|||
return (None, None)
|
||||
|
||||
|
||||
def _query_resolved_package(
|
||||
interp: str, extra_args: list[str], package_name: str
|
||||
) -> dict | None:
|
||||
def _query_resolved_package(interp: str, extra_args: list[str], package_name: str) -> dict | None:
|
||||
"""Run pip show for a package under the resolved interpreter.
|
||||
|
||||
|
||||
Returns dict with keys Name, Version, Location, etc., or None if not found.
|
||||
"""
|
||||
try:
|
||||
|
|
@ -390,20 +386,24 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
)
|
||||
|
||||
# --- Plugin-resolved interpreter checks ---
|
||||
add_check("Python 环境 (插件)", "pass",
|
||||
f"已解析解释器: {interp} (来源: {source})")
|
||||
add_check("Python 环境 (插件)", "pass", f"已解析解释器: {interp} (来源: {source})")
|
||||
|
||||
if version_tuple is not None and version_tuple >= (3, 10, 0):
|
||||
add_check("Python 环境 (插件)", "pass",
|
||||
f"Python {version_str}")
|
||||
add_check("Python 环境 (插件)", "pass", f"Python {version_str}")
|
||||
elif version_tuple is not None:
|
||||
add_check("Python 环境 (插件)", "fail",
|
||||
add_check(
|
||||
"Python 环境 (插件)",
|
||||
"fail",
|
||||
f"Python {version_str} (需要 3.10+)",
|
||||
f"升级解释器 {interp} 到 Python 3.10 或更高版本")
|
||||
f"升级解释器 {interp} 到 Python 3.10 或更高版本",
|
||||
)
|
||||
else:
|
||||
add_check("Python 环境 (插件)", "fail",
|
||||
add_check(
|
||||
"Python 环境 (插件)",
|
||||
"fail",
|
||||
f"无法获取 {interp} 的 Python 版本",
|
||||
f"验证 {interp} 是一个有效的 Python 解释器")
|
||||
f"验证 {interp} 是一个有效的 Python 解释器",
|
||||
)
|
||||
|
||||
resolved_pf_module = _query_resolved_module(interp, extra_args, "paperforge")
|
||||
|
||||
|
|
@ -412,17 +412,22 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
pkg_location = pf_pkg_info.get("Location", "?")
|
||||
expected_version = __import__("paperforge").__version__
|
||||
if pkg_version == expected_version:
|
||||
add_check("PaperForge 包", "pass",
|
||||
f"v{pkg_version} 已安装 -> {pkg_location}")
|
||||
add_check("PaperForge 包", "pass", f"v{pkg_version} 已安装 -> {pkg_location}")
|
||||
else:
|
||||
add_check("PaperForge 包", "warn",
|
||||
add_check(
|
||||
"PaperForge 包",
|
||||
"warn",
|
||||
f"v{pkg_version} 已安装 (插件版本 v{expected_version}) - 版本不匹配",
|
||||
f"运行: {interp} -m pip install --upgrade git+https://github.com/LLLin000/PaperForge.git@{expected_version}")
|
||||
f"运行: {interp} -m pip install --upgrade git+https://github.com/LLLin000/PaperForge.git@{expected_version}",
|
||||
)
|
||||
else:
|
||||
expected_version = __import__("paperforge").__version__
|
||||
add_check("PaperForge 包", "fail",
|
||||
add_check(
|
||||
"PaperForge 包",
|
||||
"fail",
|
||||
f"PaperForge 未安装在 {interp} 中",
|
||||
f"运行: {interp} -m pip install --upgrade git+https://github.com/LLLin000/PaperForge.git@{expected_version}")
|
||||
f"运行: {interp} -m pip install --upgrade git+https://github.com/LLLin000/PaperForge.git@{expected_version}",
|
||||
)
|
||||
|
||||
# Wrong-environment detection
|
||||
current_package_file = os.path.normcase(os.path.abspath(__import__("paperforge").__file__))
|
||||
|
|
@ -430,18 +435,21 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
if resolved_pf_module and resolved_pf_module.get("file"):
|
||||
resolved_package_file = os.path.normcase(os.path.abspath(str(resolved_pf_module["file"])))
|
||||
if resolved_package_file and resolved_package_file != current_package_file:
|
||||
add_check("PaperForge 包", "warn",
|
||||
f"包路径不一致: 已解析解释器 -> {resolved_package_file} | 当前诊断进程 -> {current_package_file}",
|
||||
"建议: 使用已解析解释器运行 doctor，或统一 Python 环境")
|
||||
add_check(
|
||||
"PaperForge 包",
|
||||
"warn",
|
||||
f"包路径不一致: 已解析解释器 -> {resolved_package_file} | 当前诊断进程 -> {current_package_file}",
|
||||
"建议: 使用已解析解释器运行 doctor，或统一 Python 环境",
|
||||
)
|
||||
|
||||
# --- Per-module dependency checks (Phase 53: DOCTOR-03) ---
|
||||
for mod_info in _MODULE_MANIFEST:
|
||||
mod_name = mod_info["import"]
|
||||
mod_info_resolved = _query_resolved_module(interp, extra_args, mod_name)
|
||||
if mod_info_resolved is None:
|
||||
add_check("Python 环境", "fail",
|
||||
f"{mod_info['label']} 缺失",
|
||||
f"运行: {interp} -m pip install {mod_info['pip']}")
|
||||
add_check(
|
||||
"Python 环境", "fail", f"{mod_info['label']} 缺失", f"运行: {interp} -m pip install {mod_info['pip']}"
|
||||
)
|
||||
continue
|
||||
|
||||
ver = mod_info_resolved.get("version")
|
||||
|
|
@ -452,15 +460,17 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
try:
|
||||
ver_parts = str(ver).split(".")
|
||||
if int(ver_parts[0]) < 6:
|
||||
add_check("Python 环境", "fail",
|
||||
add_check(
|
||||
"Python 环境",
|
||||
"fail",
|
||||
f"{mod_info['label']} {ver} (需要 >=6.0)",
|
||||
f"运行: {interp} -m pip install {mod_info['pip']}")
|
||||
f"运行: {interp} -m pip install {mod_info['pip']}",
|
||||
)
|
||||
continue
|
||||
except (ValueError, IndexError):
|
||||
pass
|
||||
|
||||
add_check("Python 环境", "pass",
|
||||
f"{mod_info['label']} 已安装{ver_str}")
|
||||
add_check("Python 环境", "pass", f"{mod_info['label']} 已安装{ver_str}")
|
||||
|
||||
if (vault / "paperforge.json").exists():
|
||||
add_check("Vault 结构", "pass", "paperforge.json 存在")
|
||||
|
|
@ -612,7 +622,11 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
total_issues += 1
|
||||
add_check(
|
||||
"字段注册表",
|
||||
"fail" if issue["severity"] == "error" else "warn" if issue["severity"] == "warning" else "pass",
|
||||
"fail"
|
||||
if issue["severity"] == "error"
|
||||
else "warn"
|
||||
if issue["severity"] == "warning"
|
||||
else "pass",
|
||||
issue["message"],
|
||||
issue.get("suggestion", ""),
|
||||
)
|
||||
|
|
@ -692,7 +706,8 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
try:
|
||||
if int(_sv) < 2:
|
||||
add_check(
|
||||
"Index Health", "warn",
|
||||
"Index Health",
|
||||
"warn",
|
||||
f"Legacy index schema v{_sv} -- consider rebuild to v2",
|
||||
"Run `paperforge sync --rebuild-index`",
|
||||
)
|
||||
|
|
@ -712,7 +727,8 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
continue
|
||||
if _legacy > 0:
|
||||
add_check(
|
||||
"Index Health", "warn",
|
||||
"Index Health",
|
||||
"warn",
|
||||
f"{_legacy} Base file(s) use legacy columns (has_pdf, do_ocr) instead of lifecycle",
|
||||
"Run `paperforge sync` to regenerate Base views",
|
||||
)
|
||||
|
|
@ -731,7 +747,8 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
continue
|
||||
if _partial > 0:
|
||||
add_check(
|
||||
"Index Health", "warn",
|
||||
"Index Health",
|
||||
"warn",
|
||||
f"{_partial} partial OCR asset(s) found",
|
||||
"Re-run `paperforge ocr` on affected items",
|
||||
)
|
||||
|
|
@ -739,6 +756,7 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
# WS-05: Workspace integrity checks
|
||||
try:
|
||||
from paperforge.worker.asset_index import read_index as _ws_read_idx
|
||||
|
||||
_idx_content = _ws_read_idx(vault)
|
||||
_items = _idx_content.get("items", []) if isinstance(_idx_content, dict) else []
|
||||
_missing_workspace = 0
|
||||
|
|
@ -751,6 +769,7 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
if not _key or not _dom:
|
||||
continue
|
||||
from paperforge.worker._utils import slugify_filename
|
||||
|
||||
_slug = slugify_filename(_title or _key)
|
||||
_ws_dir = _ws_literature / _dom / f"{_key} - {_slug}"
|
||||
if not _ws_dir.exists():
|
||||
|
|
@ -762,13 +781,15 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
_missing_fulltext += 1
|
||||
if _missing_workspace > 0:
|
||||
add_check(
|
||||
"Index Health", "warn",
|
||||
"Index Health",
|
||||
"warn",
|
||||
f"{_missing_workspace} paper(s) missing workspace directories",
|
||||
"Run `paperforge sync` to create workspace folders",
|
||||
)
|
||||
if _missing_fulltext > 0:
|
||||
add_check(
|
||||
"Index Health", "warn",
|
||||
"Index Health",
|
||||
"warn",
|
||||
f"{_missing_fulltext} paper(s) missing fulltext.md in workspace",
|
||||
"Re-run OCR or run `paperforge sync` to bridge fulltext",
|
||||
)
|
||||
|
|
@ -783,7 +804,8 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
_stale_count = sum(1 for _ in _lr_dir.rglob("*.md"))
|
||||
if _stale_count > 0:
|
||||
add_check(
|
||||
"Index Health", "warn",
|
||||
"Index Health",
|
||||
"warn",
|
||||
f"{_stale_count} stale record(s) found in control directory",
|
||||
"Review and remove stale files from the control directory",
|
||||
)
|
||||
|
|
@ -791,10 +813,7 @@ def run_doctor(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
add_check("Index Health", "info", "No canonical index -- run `paperforge sync` to generate")
|
||||
|
||||
if json_output:
|
||||
checklist_data = [
|
||||
{"category": cat, "status": st, "message": msg, "fix": fx}
|
||||
for cat, st, msg, fx in checks
|
||||
]
|
||||
checklist_data = [{"category": cat, "status": st, "message": msg, "fix": fx} for cat, st, msg, fx in checks]
|
||||
status_counts: dict[str, int] = {}
|
||||
for _, st, _, _ in checks:
|
||||
status_counts[st] = status_counts.get(st, 0) + 1
|
||||
|
|
@ -961,7 +980,11 @@ def run_status(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
ensure_base_views(vault, paths, config)
|
||||
export_files = sorted(paths["exports"].glob("*.json"))
|
||||
record_count = (
|
||||
sum(1 for p in paths["literature"].rglob("*.md") if p.name not in ("fulltext.md", "deep-reading.md", "discussion.md"))
|
||||
sum(
|
||||
1
|
||||
for p in paths["literature"].rglob("*.md")
|
||||
if p.name not in ("fulltext.md", "deep-reading.md", "discussion.md")
|
||||
)
|
||||
if paths["literature"].exists()
|
||||
else 0
|
||||
)
|
||||
|
|
@ -1101,15 +1124,21 @@ def run_status(vault: Path, verbose: bool = False, json_output: bool = False) ->
|
|||
if summary is not None:
|
||||
lc = lifecycle_level_counts
|
||||
print(f"- index: {summary['paper_count']} papers")
|
||||
print(f" lifecycle: indexed={lc['indexed']} pdf_ready={lc['pdf_ready']} "
|
||||
f"fulltext_ready={lc['fulltext_ready']} deep_read={lc['deep_read_done']} "
|
||||
f"ai_ready={lc['ai_context_ready']}")
|
||||
print(
|
||||
f" lifecycle: indexed={lc['indexed']} pdf_ready={lc['pdf_ready']} "
|
||||
f"fulltext_ready={lc['fulltext_ready']} deep_read={lc['deep_read_done']} "
|
||||
f"ai_ready={lc['ai_context_ready']}"
|
||||
)
|
||||
ha = health_aggregate
|
||||
print(f" health: pdf={ha['pdf_health']['healthy']}/{ha['pdf_health']['unhealthy']} "
|
||||
f"ocr={ha['ocr_health']['healthy']}/{ha['ocr_health']['unhealthy']} "
|
||||
f"note={ha['note_health']['healthy']}/{ha['note_health']['unhealthy']} "
|
||||
f"asset={ha['asset_health']['healthy']}/{ha['asset_health']['unhealthy']}")
|
||||
print(f"- ocr: {ocr_done}/{ocr_total} done (pending: {ocr_pending}, processing: {ocr_processing}, failed: {ocr_failed})")
|
||||
print(
|
||||
f" health: pdf={ha['pdf_health']['healthy']}/{ha['pdf_health']['unhealthy']} "
|
||||
f"ocr={ha['ocr_health']['healthy']}/{ha['ocr_health']['unhealthy']} "
|
||||
f"note={ha['note_health']['healthy']}/{ha['note_health']['unhealthy']} "
|
||||
f"asset={ha['asset_health']['healthy']}/{ha['asset_health']['unhealthy']}"
|
||||
)
|
||||
print(
|
||||
f"- ocr: {ocr_done}/{ocr_total} done (pending: {ocr_pending}, processing: {ocr_processing}, failed: {ocr_failed})"
|
||||
)
|
||||
print(f"- path_errors: {path_error_count}")
|
||||
if path_error_count > 0:
|
||||
print(" Tip: Run `paperforge repair --fix-paths` to attempt resolution")
|
||||
|
|
|
|||
|
|
@ -52,6 +52,7 @@ def protected_paths(vault: Path) -> set[str]:
|
|||
def _remote_version() -> str | None:
|
||||
"""Read version from __init__.py on GitHub (single source of truth)."""
|
||||
import re
|
||||
|
||||
try:
|
||||
api = f"https://api.github.com/repos/{GITHUB_REPO}/contents/paperforge/__init__.py"
|
||||
req = urllib.request.Request(
|
||||
|
|
@ -176,12 +177,21 @@ def _update_via_git(vault: Path) -> bool:
|
|||
if not (vault / ".git").is_dir():
|
||||
logger.error("不是 git 仓库")
|
||||
return False
|
||||
r = subprocess.run(["git", "status", "--short"], cwd=vault, capture_output=True, text=True, encoding="utf-8", errors="replace")
|
||||
r = subprocess.run(
|
||||
["git", "status", "--short"], cwd=vault, capture_output=True, text=True, encoding="utf-8", errors="replace"
|
||||
)
|
||||
if r.stdout.strip():
|
||||
logger.warning("有未提交的更改，请先提交或储藏")
|
||||
return False
|
||||
logger.info("执行 git pull...")
|
||||
r = subprocess.run(["git", "pull", "origin", "master"], cwd=vault, capture_output=True, text=True, encoding="utf-8", errors="replace")
|
||||
r = subprocess.run(
|
||||
["git", "pull", "origin", "master"],
|
||||
cwd=vault,
|
||||
capture_output=True,
|
||||
text=True,
|
||||
encoding="utf-8",
|
||||
errors="replace",
|
||||
)
|
||||
if r.returncode != 0:
|
||||
logger.error("git pull 失败: %s", r.stderr)
|
||||
return False
|
||||
|
|
@ -231,6 +241,7 @@ def run_update(vault: Path) -> int:
|
|||
"""运行更新检查与安装"""
|
||||
try:
|
||||
import paperforge
|
||||
|
||||
local = paperforge.__version__
|
||||
except Exception:
|
||||
local = "unknown"
|
||||
|
|
|
|||
Loading…
Reference in a new issue