From 0da9c3b3cb5eebcb768884bdc7f452aa68bbaf43 Mon Sep 17 00:00:00 2001
From: Yan Lin <github@yanlincs.com>
Date: Tue, 29 Jul 2025 15:49:49 +0200
Subject: [PATCH] Add papis reference manager configuration
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- Add papis.nix module with embedded configuration
- Configure library at ~/Documents/Library/papis
- Set up nvim editor and fzf picker integration
- Add comprehensive papis documentation to README

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 README.md         | 64 +++++++++++++++++++++++++++++++++++++++++++++++
 modules/papis.nix | 46 ++++++++++++++++++++++++++++++++++
 2 files changed, 110 insertions(+)
 create mode 100644 modules/papis.nix

diff --git a/README.md b/README.md
index 1076807..dd898f0 100644
--- a/README.md
+++ b/README.md
@@ -400,6 +400,70 @@ rsync -avh --progress --exclude-from=~/.rsync-exclude source/ dest/
 - Safety options including partial transfers and dry-run capability
 - Preserves extended attributes and ACLs on macOS
 
+### 🌟 Reference Management
+
+**Tool**: papis
+**Purpose**: Command-line reference manager for academic papers and documents
+
+A powerful bibliography manager that stores documents and metadata in a human-readable format:
+
+#### Key Features:
+- **Document Library**: Centralized storage at `~/Documents/Library/papis`
+- **BibTeX Integration**: Import/export references in standard academic formats
+- **PDF Management**: Automatic file organization and retrieval
+- **Search & Filter**: Fast document discovery with fuzzy finding (fzf)
+- **Metadata Storage**: Human-readable YAML files for bibliographic data
+- **Editor Integration**: Configured with nvim for editing document metadata
+
+#### Usage Examples:
+
+**Adding documents:**
+```bash
+# Add a paper from DOI
+papis add --from doi 10.1000/example.doi
+
+# Add a PDF file with interactive metadata entry
+papis add paper.pdf
+
+# Add from arXiv
+papis add --from arxiv 2301.12345
+
+# Add from URL
+papis add --from url https://example.com/paper.pdf
+```
+
+**Searching and browsing:**
+```bash
+# Search documents (uses fzf picker)
+papis open
+papis search "machine learning"
+papis search author:smith year:2023
+
+# List all documents
+papis list
+
+# Open specific document
+papis open smith2023
+```
+
+**Document management:**
+```bash
+# Edit document metadata
+papis edit
+
+# Export to BibTeX
+papis export --all --format bibtex > references.bib
+papis export search_term --format bibtex
+
+# Show document information
+papis show document_key
+```
+
+**Configuration location**: `modules/papis.nix` with embedded configuration
+**Main library**: `~/Documents/Library/papis`
+**Editor**: nvim (configured automatically)
+**Picker**: fzf for interactive document selection
+
 ### 🌟 Python Development & Package Management
 
 **Tool**: uv
diff --git a/modules/papis.nix b/modules/papis.nix
new file mode 100644
index 0000000..58ee628
--- /dev/null
+++ b/modules/papis.nix
@@ -0,0 +1,46 @@
+{ pkgs, ... }:
+
+{
+  # Install papis package
+  home.packages = with pkgs; [
+    papis
+  ];
+
+  # Papis configuration
+  home.file.".config/papis/config".text = ''
+    [settings]
+    default-library = main
+    editor = nvim
+    opentool = open
+    file-browser = open
+    
+    # Document management
+    add-folder-name = {doc[author]}-{doc[year]}-{doc[title]}
+    add-file-name = {doc[author]}-{doc[year]}-{doc[title]}
+    ref-format = {doc[author]}{doc[year]}
+    
+    # Search and display
+    sort-field = year
+    sort-reverse = True
+    match-format = {doc[tags]}{doc[author]}{doc[title]}{doc[year]}
+    
+    # Database and storage
+    database-backend = papis
+    use-git = False
+    
+    # Interface
+    fzf-binary = fzf
+    picktool = fzf
+    
+    [main]
+    dir = ~/Documents/Library/papis
+    
+    # Local configuration for the main library
+    local-config-file = .papisrc
+  '';
+
+  # Create the papis library directory
+  home.activation.createPapisDir = ''
+    mkdir -p ~/Documents/Library/papis
+  '';
+}