feat(scholar): Citation graph visualization + Flask GUI + API cleanup#163
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ywatanabe1989 merged 11 commits intomainfrom Feb 18, 2026
Merged
feat(scholar): Citation graph visualization + Flask GUI + API cleanup#163ywatanabe1989 merged 11 commits intomainfrom
ywatanabe1989 merged 11 commits intomainfrom
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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Use XARRAY_AVAILABLE flag pattern (consistent with TORCH_AVAILABLE, CATBOOST_AVAILABLE, etc.) to avoid ModuleNotFoundError when xarray is not installed. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…t-local symlinks, and normalized search filenames
- SearchQueryParser.from_shell_syntax(): parses -t/-a/-j/-ymin/-ymax/-cmin/-cmax/-ifmin/-ifmax operators
- scitex.scholar.filters: apply_filters() for plain-dict paper filtering (no Django ORM)
- normalize_search_filename(): timestamped YYYYMMDD-HHMMSS-keyword-keyword.bib naming
- LibraryManager.project_dir: mirrors paper symlinks into {project_dir}/scitex/scholar/library/{project}/
- SymlinkHandlersMixin._create_project_local_symlink(): absolute-path symlinks in project tree
- scitex.writer: re-export export module from scitex_writer
- fix: metadata_engines/utils broken import scitex.scholar.utils → scitex.scholar._utils
- fix: test__describe.py stat names nanmean/nanstd → mean/std/median
- fix: pre-commit config empty YAML → repos: []
- tests: 42 tests for normalize_search_filename and _create_project_local_symlink (42/42 pass)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…_key, sanitize_filename Three new public helpers extracted from scitex-cloud to scitex.scholar as single source of truth: - paper_from_search_result(result): normalises raw search-API dicts (handles externalUrl, snippet aliases) - make_citation_key(last_name, year): citation key generation from author/year components - sanitize_filename(filename, max_length=50): safe download filename generation Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Fix circular import: import ScholarConfig before Scholar/Paper/Papers (ScholarPDFDownloader imports ScholarConfig from scitex.scholar) - Remove ensure_workspace from delattr list (function same name as module) - Hide local_dbs exports with underscore prefix (_crossref_scitex, _openalex_scitex) - Use delattr loop to remove leaked submodule attributes from namespace - Power-user classes accessible but excluded from __all__ Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Read papers directly from Zotero's SQLite database without API key. Auto-detects Linux (~/Zotero/) and Windows WSL (/mnt/c/Users/*/Zotero/) installations. Reuses existing ZoteroMapper for data conversion. - ZoteroLocalReader: read_all(), read_by_tags(), read_by_collection() - export_for_zotero(): write BibTeX/RIS for Zotero > File > Import - Batch SQL queries (4 queries total, no N+1) - 16 tests, all passing against actual ~/Zotero/zotero.sqlite Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add to_networkx() to CitationGraph model and create visualization.py with 4 backends (figrecipe > scitex.plt > matplotlib > pyvis) using _XXX_AVAILABLE flags for graceful degradation. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Hide power-user classes and internal helpers via __getattr__ with backward compatibility. Expose CitationGraphBuilder and plot_citation_graph. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Ported from scitex-cloud's scholar_app to standalone Flask app. Includes force-directed SVG graph visualization, dark theme, 4 API endpoints, and CLI command (scitex scholar gui). Library, Search, and Enrichment tabs are placeholders for future phases. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
_XXX_AVAILABLEflags for graceful degradation. Addedto_networkx()to CitationGraph model.scitex scholar guicommand launches interactive web app with Citation Graph tab (force-directed SVG). Ported from scitex-cloud's scholar_app. Library/Search/Enrichment tabs as placeholders.__getattr__with backward compatibility.list_collections()andlist_tags()methods.Test plan
scitex scholar gui --helpshows optionsscitex scholar list-python-apisshows 14 clean public namesscitex scholar mcp list-tools -vshows 22 tools (consistent with main command)🤖 Generated with Claude Code