Update README and documentation to reflect the addition of the pyzotero skill and increment skill count from 147 to 148. Bump version to 2.24.0 in marketplace.json.

.claude-plugin/marketplace.json

@@ -6,7 +6,7 @@
   },
   "metadata": {
     "description": "Claude scientific skills from K-Dense Inc",
-    "version": "2.23.0"
+    "version": "2.24.0"
   },
   "plugins": [
     {
@@ -71,6 +71,7 @@
         "./scientific-skills/pysam",
         "./scientific-skills/pytdc",
         "./scientific-skills/pytorch-lightning",
+        "./scientific-skills/pyzotero",
         "./scientific-skills/qiskit",
         "./scientific-skills/qutip",
         "./scientific-skills/rdkit",

README.md

@@ -1,11 +1,11 @@
 # Claude Scientific Skills
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE.md)
-[![Skills](https://img.shields.io/badge/Skills-147-brightgreen.svg)](#whats-included)
+[![Skills](https://img.shields.io/badge/Skills-148-brightgreen.svg)](#whats-included)
 [![Agent Skills](https://img.shields.io/badge/Standard-Agent_Skills-blueviolet.svg)](https://agentskills.io/)
 [![Works with](https://img.shields.io/badge/Works_with-Cursor_|_Claude_Code_|_Codex-blue.svg)](#getting-started)
 
-A comprehensive collection of **147+ ready-to-use scientific and research skills** (now including financial/SEC research, U.S. Treasury fiscal data, OFR Hedge Fund Monitor, and Alpha Vantage market data) for any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, created by [K-Dense](https://k-dense.ai). Works with **Cursor, Claude Code, Codex, and more**. Transform your AI agent into a research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.
+A comprehensive collection of **148+ ready-to-use scientific and research skills** (now including financial/SEC research, U.S. Treasury fiscal data, OFR Hedge Fund Monitor, and Alpha Vantage market data) for any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, created by [K-Dense](https://k-dense.ai). Works with **Cursor, Claude Code, Codex, and more**. Transform your AI agent into a research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.
 
 **Looking for the full AI co-scientist experience?** Try [K-Dense Web](https://k-dense.ai) for 200+ skills, cloud compute, and publication-ready outputs.
 
@@ -68,10 +68,10 @@ These skills enable your AI agent to seamlessly work with specialized scientific
 
 ## 📦 What's Included
 
-This repository provides **147 scientific and research skills** organized into the following categories:
+This repository provides **148 scientific and research skills** organized into the following categories:
 
 - **30+ Scientific & Financial Databases** - Direct API access to OpenAlex, PubMed, bioRxiv, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, SEC EDGAR, U.S. Treasury Fiscal Data, Alpha Vantage, and more
-- **55+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, BioServices, PennyLane, Qiskit, and others
+- **55+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, pyzotero, BioServices, PennyLane, Qiskit, and others
 - **15+ Scientific Integrations** - Benchling, DNAnexus, LatchBio, OMERO, Protocols.io, and more
 - **30+ Analysis & Communication Tools** - Literature review, scientific writing, peer review, document processing, posters, slides, schematics, and more
 - **10+ Research & Clinical Tools** - Hypothesis generation, grant writing, clinical decision support, treatment plans, regulatory compliance
@@ -113,7 +113,7 @@ Each skill includes:
 - **Multi-Step Workflows** - Execute complex pipelines with a single prompt
 
 ### 🎯 **Comprehensive Coverage**
-- **140 Skills** - Extensive coverage across all major scientific domains
+- **148 Skills** - Extensive coverage across all major scientific domains
 - **28+ Databases** - Direct access to OpenAlex, PubMed, bioRxiv, ChEMBL, UniProt, COSMIC, and more
 - **55+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioServices, PennyLane, Qiskit, and others
 

docs/scientific-skills.md

@@ -169,6 +169,7 @@
 - **HypoGeniC** - Automated hypothesis generation and testing using large language models to accelerate scientific discovery. Provides three frameworks: HypoGeniC (data-driven hypothesis generation from observational data), HypoRefine (synergistic approach combining literature insights with empirical patterns through an agentic system), and Union methods (mechanistic combination of literature and data-driven hypotheses). Features iterative refinement that improves hypotheses by learning from challenging examples, Redis caching for API cost reduction, and customizable YAML-based prompt templates. Includes command-line tools for generation (hypogenic_generation) and testing (hypogenic_inference). Research applications have demonstrated 14.19% accuracy improvement in AI-content detection and 7.44% in deception detection. Use cases: deception detection in reviews, AI-generated content identification, mental stress detection, exploratory research without existing literature, hypothesis-driven analysis in novel domains, and systematic exploration of competing explanations
 
 ### Scientific Communication & Publishing
+- **pyzotero** - Python client for the Zotero Web API v3. Programmatically manage Zotero reference libraries: retrieve, create, update, and delete items, collections, tags, and attachments. Export citations as BibTeX, CSL-JSON, and formatted bibliography HTML. Supports user and group libraries, local mode for offline access, paginated retrieval with `everything()`, full-text content indexing, saved search management, and file upload/download. Includes a CLI for searching your local Zotero library. Use cases: building research automation pipelines that integrate with Zotero, bulk importing references, exporting bibliographies programmatically, managing large reference collections, syncing library metadata, and enriching bibliographic data.
 - **Citation Management** - Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata from multiple sources (CrossRef, PubMed, arXiv), validate citations, and generate properly formatted BibTeX entries. Features include converting DOIs, PMIDs, or arXiv IDs to BibTeX, cleaning and formatting bibliography files, finding highly cited papers, checking for duplicates, and ensuring consistent citation formatting. Use cases: building bibliographies for manuscripts, verifying citation accuracy, citation deduplication, and maintaining reference databases
 - **Generate Image** - AI-powered image generation and editing for scientific illustrations, schematics, and visualizations using OpenRouter's image generation models. Supports multiple models including google/gemini-3-pro-image-preview (high quality, recommended default) and black-forest-labs/flux.2-pro (fast, high quality). Key features include: text-to-image generation from detailed prompts, image editing capabilities (modify existing images with natural language instructions), automatic base64 encoding/decoding, PNG output with configurable paths, and comprehensive error handling. Requires OpenRouter API key (via .env file or environment variable). Use cases: generating scientific diagrams and illustrations, creating publication-quality figures, editing existing images (changing colors, adding elements, removing backgrounds), producing schematics for papers and presentations, visualizing experimental setups, creating graphical abstracts, and generating conceptual illustrations for scientific communication
 - **LaTeX Posters** - Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication with layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices. Features compliance with conference size requirements (A0, A1, 36×48"), complex multi-column layouts, and integration of figures, tables, equations, and citations. Use cases: conference poster sessions, thesis defenses, symposia presentations, and research group templates

scientific-skills/pyzotero/SKILL.md

@@ -0,0 +1,111 @@
+---
+name: pyzotero
+description: Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.
+allowed-tools: Read Write Edit Bash
+license: MIT License
+metadata:
+    skill-author: K-Dense Inc.
+---
+
+# Pyzotero
+
+Pyzotero is a Python wrapper for the [Zotero API v3](https://www.zotero.org/support/dev/web_api/v3/start). Use it to programmatically manage Zotero libraries: read items and collections, create and update references, upload attachments, manage tags, and export citations.
+
+## Authentication Setup
+
+**Required credentials** — get from https://www.zotero.org/settings/keys:
+- **User ID**: shown as "Your userID for use in API calls"
+- **API Key**: create at https://www.zotero.org/settings/keys/new
+- **Library ID**: for group libraries, the integer after `/groups/` in the group URL
+
+Store credentials in environment variables or a `.env` file:
+```
+ZOTERO_LIBRARY_ID=your_user_id
+ZOTERO_API_KEY=your_api_key
+ZOTERO_LIBRARY_TYPE=user  # or "group"
+```
+
+See [references/authentication.md](references/authentication.md) for full setup details.
+
+## Installation
+
+```bash
+uv add pyzotero
+# or with CLI support:
+uv add "pyzotero[cli]"
+```
+
+## Quick Start
+
+```python
+from pyzotero import Zotero
+
+zot = Zotero(library_id='123456', library_type='user', api_key='ABC1234XYZ')
+
+# Retrieve top-level items (returns 100 by default)
+items = zot.top(limit=10)
+for item in items:
+    print(item['data']['title'], item['data']['itemType'])
+
+# Search by keyword
+results = zot.items(q='machine learning', limit=20)
+
+# Retrieve all items (use everything() for complete results)
+all_items = zot.everything(zot.items())
+```
+
+## Core Concepts
+
+- A `Zotero` instance is bound to a single library (user or group). All methods operate on that library.
+- Item data lives in `item['data']`. Access fields like `item['data']['title']`, `item['data']['creators']`.
+- Pyzotero returns 100 items by default (API default is 25). Use `zot.everything(zot.items())` to get all items.
+- Write methods return `True` on success or raise a `ZoteroError`.
+
+## Reference Files
+
+| File | Contents |
+|------|----------|
+| [references/authentication.md](references/authentication.md) | Credentials, library types, local mode |
+| [references/read-api.md](references/read-api.md) | Retrieving items, collections, tags, groups |
+| [references/search-params.md](references/search-params.md) | Filtering, sorting, search parameters |
+| [references/write-api.md](references/write-api.md) | Creating, updating, deleting items |
+| [references/collections.md](references/collections.md) | Collection CRUD operations |
+| [references/tags.md](references/tags.md) | Tag retrieval and management |
+| [references/files-attachments.md](references/files-attachments.md) | File retrieval and attachment uploads |
+| [references/exports.md](references/exports.md) | BibTeX, CSL-JSON, bibliography export |
+| [references/pagination.md](references/pagination.md) | follow(), everything(), generators |
+| [references/full-text.md](references/full-text.md) | Full-text content indexing and retrieval |
+| [references/saved-searches.md](references/saved-searches.md) | Saved search management |
+| [references/cli.md](references/cli.md) | Command-line interface usage |
+| [references/error-handling.md](references/error-handling.md) | Errors and exception handling |
+
+## Common Patterns
+
+### Fetch and modify an item
+```python
+item = zot.item('ITEMKEY')
+item['data']['title'] = 'New Title'
+zot.update_item(item)
+```
+
+### Create an item from a template
+```python
+template = zot.item_template('journalArticle')
+template['title'] = 'My Paper'
+template['creators'][0] = {'creatorType': 'author', 'firstName': 'Jane', 'lastName': 'Doe'}
+zot.create_items([template])
+```
+
+### Export as BibTeX
+```python
+zot.add_parameters(format='bibtex')
+bibtex = zot.top(limit=50)
+# bibtex is a bibtexparser BibDatabase object
+print(bibtex.entries)
+```
+
+### Local mode (read-only, no API key needed)
+```python
+zot = Zotero(library_id='123456', library_type='user', local=True)
+items = zot.items()
+```

scientific-skills/pyzotero/references/authentication.md

@@ -0,0 +1,90 @@
+# Authentication & Setup
+
+## Credentials
+
+Obtain from https://www.zotero.org/settings/keys:
+
+| Credential | Where to Find |
+|-----------|---------------|
+| **User ID** | "Your userID for use in API calls" section |
+| **API Key** | Create new key at /settings/keys/new |
+| **Group Library ID** | Integer after `/groups/` in group URL (e.g. `https://www.zotero.org/groups/169947`) |
+
+## Environment Variables
+
+Store in `.env` or export in shell:
+```
+ZOTERO_LIBRARY_ID=436
+ZOTERO_API_KEY=ABC1234XYZ
+ZOTERO_LIBRARY_TYPE=user
+```
+
+Load in Python:
+```python
+import os
+from dotenv import load_dotenv
+from pyzotero import Zotero
+
+load_dotenv()
+
+zot = Zotero(
+    library_id=os.environ['ZOTERO_LIBRARY_ID'],
+    library_type=os.environ['ZOTERO_LIBRARY_TYPE'],
+    api_key=os.environ['ZOTERO_API_KEY']
+)
+```
+
+## Library Types
+
+```python
+# Personal library
+zot = Zotero('436', 'user', 'ABC1234XYZ')
+
+# Group library
+zot = Zotero('169947', 'group', 'ABC1234XYZ')
+```
+
+**Important**: A `Zotero` instance is bound to a single library. To access multiple libraries, create multiple instances.
+
+## Local Mode (Read-Only)
+
+Connect to your local Zotero installation without an API key. Only supports read requests.
+
+```python
+zot = Zotero(library_id='436', library_type='user', local=True)
+items = zot.items(limit=10)  # reads from local Zotero
+```
+
+## Optional Parameters
+
+```python
+zot = Zotero(
+    library_id='436',
+    library_type='user',
+    api_key='ABC1234XYZ',
+    preserve_json_order=True,   # use OrderedDict for JSON responses
+    locale='en-US',             # localise field names (e.g. 'fr-FR' for French)
+)
+```
+
+## Key Permissions
+
+Check what the current API key can access:
+```python
+info = zot.key_info()
+# Returns dict with user info and group access permissions
+```
+
+Check accessible groups:
+```python
+groups = zot.groups()
+# Returns list of group libraries accessible to the current key
+```
+
+## API Key Scopes
+
+When creating an API key at https://www.zotero.org/settings/keys/new, choose appropriate permissions:
+- **Read Only**: For retrieving items and collections
+- **Write Access**: For creating, updating, and deleting items
+- **Notes Access**: To include notes in read/write operations
+- **Files Access**: Required for uploading attachments

scientific-skills/pyzotero/references/cli.md

@@ -0,0 +1,100 @@
+# Command-Line Interface
+
+The pyzotero CLI connects to your **local Zotero installation** (not the remote API). It requires a running local Zotero desktop app.
+
+## Installation
+
+```bash
+uv add "pyzotero[cli]"
+# or run without installing:
+uvx --from "pyzotero[cli]" pyzotero search -q "your query"
+```
+
+## Searching
+
+```bash
+# Search titles and metadata
+pyzotero search -q "machine learning"
+
+# Full-text search (includes PDF content)
+pyzotero search -q "climate change" --fulltext
+
+# Filter by item type
+pyzotero search -q "methodology" --itemtype journalArticle --itemtype book
+
+# Filter by tags (AND logic)
+pyzotero search -q "evolution" --tag "reviewed" --tag "high-priority"
+
+# Search within a collection
+pyzotero search --collection ABC123 -q "test"
+
+# Paginate results
+pyzotero search -q "deep learning" --limit 20 --offset 40
+
+# Output as JSON (for machine processing)
+pyzotero search -q "protein" --json
+```
+
+## Getting Individual Items
+
+```bash
+# Get a single item by key
+pyzotero item ABC123
+
+# Get as JSON
+pyzotero item ABC123 --json
+
+# Get child items (attachments, notes)
+pyzotero children ABC123 --json
+
+# Get multiple items at once (up to 50)
+pyzotero subset ABC123 DEF456 GHI789 --json
+```
+
+## Collections & Tags
+
+```bash
+# List all collections
+pyzotero listcollections
+
+# List all tags
+pyzotero tags
+
+# Tags in a specific collection
+pyzotero tags --collection ABC123
+```
+
+## Full-Text Content
+
+```bash
+# Get full-text content of an attachment
+pyzotero fulltext ABC123
+```
+
+## Item Types
+
+```bash
+# List all available item types
+pyzotero itemtypes
+```
+
+## DOI Index
+
+```bash
+# Get complete DOI-to-key mapping (useful for caching)
+pyzotero doiindex > doi_cache.json
+# Returns JSON: {"10.1038/s41592-024-02233-6": {"key": "ABC123", "doi": "..."}}
+```
+
+## Output Format
+
+By default the CLI outputs human-readable text including title, authors, date, publication, volume, issue, DOI, URL, and PDF attachment paths.
+
+Use `--json` for structured JSON output suitable for piping to other tools.
+
+## Search Behaviour Notes
+
+- Default search covers top-level item titles and metadata fields only
+- `--fulltext` expands search to PDF content; results show parent bibliographic items (not raw attachments)
+- Multiple `--tag` flags use AND logic
+- Multiple `--itemtype` flags use OR logic

scientific-skills/pyzotero/references/collections.md

@@ -0,0 +1,113 @@
+# Collection Management
+
+## Reading Collections
+
+```python
+# All collections (flat list including nested)
+all_cols = zot.collections()
+
+# Only top-level collections
+top_cols = zot.collections_top()
+
+# Specific collection
+col = zot.collection('COLKEY')
+
+# Sub-collections of a collection
+sub_cols = zot.collections_sub('COLKEY')
+
+# All collections under a given collection (recursive)
+tree = zot.all_collections('COLKEY')
+# Or all collections in the library:
+tree = zot.all_collections()
+```
+
+## Collection Data Structure
+
+```python
+col = zot.collection('5TSDXJG6')
+name = col['data']['name']
+key = col['data']['key']
+parent = col['data']['parentCollection']  # False if top-level, else parent key
+version = col['data']['version']
+n_items = col['meta']['numItems']
+n_sub_collections = col['meta']['numCollections']
+```
+
+## Creating Collections
+
+```python
+# Create a top-level collection
+zot.create_collections([{'name': 'My New Collection'}])
+
+# Create a nested collection
+zot.create_collections([{
+    'name': 'Sub-Collection',
+    'parentCollection': 'PARENTCOLKEY'
+}])
+
+# Create multiple at once
+zot.create_collections([
+    {'name': 'Collection A'},
+    {'name': 'Collection B'},
+    {'name': 'Sub-B', 'parentCollection': 'BKEY'},
+])
+```
+
+## Updating Collections
+
+```python
+cols = zot.collections()
+# Rename the first collection
+cols[0]['data']['name'] = 'Renamed Collection'
+zot.update_collection(cols[0])
+
+# Update multiple collections (auto-chunked at 50)
+zot.update_collections(cols)
+```
+
+## Deleting Collections
+
+```python
+# Delete a single collection
+col = zot.collection('COLKEY')
+zot.delete_collection(col)
+
+# Delete multiple collections
+cols = zot.collections()
+zot.delete_collection(cols)  # pass a list of dicts
+```
+
+## Managing Items in Collections
+
+```python
+# Add an item to a collection
+item = zot.item('ITEMKEY')
+zot.addto_collection('COLKEY', item)
+
+# Remove an item from a collection
+zot.deletefrom_collection('COLKEY', item)
+
+# Get all items in a collection
+items = zot.collection_items('COLKEY')
+
+# Get only top-level items in a collection
+top_items = zot.collection_items_top('COLKEY')
+
+# Count items in a collection
+n = zot.num_collectionitems('COLKEY')
+
+# Get tags in a collection
+tags = zot.collection_tags('COLKEY')
+```
+
+## Find Collection Key by Name
+
+```python
+def find_collection(zot, name):
+    for col in zot.everything(zot.collections()):
+        if col['data']['name'] == name:
+            return col['data']['key']
+    return None
+
+key = find_collection(zot, 'Machine Learning Papers')
+```

scientific-skills/pyzotero/references/error-handling.md

@@ -0,0 +1,103 @@
+# Error Handling
+
+## Exception Types
+
+Pyzotero raises `ZoteroError` subclasses for API errors. Import from `pyzotero.zotero_errors`:
+
+```python
+from pyzotero import zotero_errors
+```
+
+Common exceptions:
+
+| Exception | Cause |
+|-----------|-------|
+| `UserNotAuthorised` | Invalid or missing API key |
+| `HTTPError` | Generic HTTP error |
+| `ParamNotPassed` | Required parameter missing |
+| `CallDoesNotExist` | Invalid API method for library type |
+| `ResourceNotFound` | Item/collection key not found |
+| `Conflict` | Version conflict (optimistic locking) |
+| `PreConditionFailed` | `If-Unmodified-Since-Version` check failed |
+| `TooManyItems` | Batch exceeds 50-item limit |
+| `TooManyRequests` | API rate limit exceeded |
+| `InvalidItemFields` | Item dict contains unknown fields |
+
+## Basic Error Handling
+
+```python
+from pyzotero import Zotero
+from pyzotero import zotero_errors
+
+zot = Zotero('123456', 'user', 'APIKEY')
+
+try:
+    item = zot.item('BADKEY')
+except zotero_errors.ResourceNotFound:
+    print('Item not found')
+except zotero_errors.UserNotAuthorised:
+    print('Invalid API key')
+except Exception as e:
+    print(f'Unexpected error: {e}')
+    if hasattr(e, '__cause__'):
+        print(f'Caused by: {e.__cause__}')
+```
+
+## Version Conflict Handling
+
+```python
+try:
+    zot.update_item(item)
+except zotero_errors.PreConditionFailed:
+    # Item was modified since you retrieved it — re-fetch and retry
+    fresh_item = zot.item(item['data']['key'])
+    fresh_item['data']['title'] = new_title
+    zot.update_item(fresh_item)
+```
+
+## Checking for Invalid Fields
+
+```python
+from pyzotero import zotero_errors
+
+template = zot.item_template('journalArticle')
+template['badField'] = 'bad value'
+
+try:
+    zot.check_items([template])
+except zotero_errors.InvalidItemFields as e:
+    print(f'Invalid fields: {e}')
+    # Fix fields before calling create_items
+```
+
+## Rate Limiting
+
+The Zotero API rate-limits requests. If you receive `TooManyRequests`:
+
+```python
+import time
+from pyzotero import zotero_errors
+
+def safe_request(func, *args, **kwargs):
+    retries = 3
+    for attempt in range(retries):
+        try:
+            return func(*args, **kwargs)
+        except zotero_errors.TooManyRequests:
+            wait = 2 ** attempt
+            print(f'Rate limited, waiting {wait}s...')
+            time.sleep(wait)
+    raise RuntimeError('Max retries exceeded')
+
+items = safe_request(zot.items, limit=100)
+```
+
+## Accessing Underlying Error
+
+```python
+try:
+    zot.item('BADKEY')
+except Exception as e:
+    print(e.__cause__)    # original HTTP error
+    print(e.__context__)  # exception context
+```

scientific-skills/pyzotero/references/exports.md

@@ -0,0 +1,102 @@
+# Export Formats
+
+## BibTeX
+
+```python
+zot.add_parameters(format='bibtex')
+bibtex_db = zot.top(limit=50)
+# Returns a bibtexparser BibDatabase object
+
+# Access entries as list of dicts
+entries = bibtex_db.entries
+for entry in entries:
+    print(entry.get('title'), entry.get('author'))
+
+# Write to .bib file
+import bibtexparser
+with open('library.bib', 'w') as f:
+    bibtexparser.dump(bibtex_db, f)
+```
+
+## CSL-JSON
+
+```python
+zot.add_parameters(content='csljson', limit=50)
+csl_items = zot.items()
+# Returns a list of dicts in CSL-JSON format
+```
+
+## Bibliography HTML (formatted citations)
+
+```python
+# APA style bibliography
+zot.add_parameters(content='bib', style='apa')
+bib_entries = zot.items(limit=50)
+# Returns list of HTML <div> strings
+
+for entry in bib_entries:
+    print(entry)  # e.g. '<div>Smith, J. (2024). Title. <i>Journal</i>...</div>'
+```
+
+**Note**: `format='bib'` removes the `limit` parameter. The API enforces a max of 150 items.
+
+### Available Citation Styles
+
+Pass any valid CSL style name from the [Zotero style repository](https://www.zotero.org/styles):
+- `'apa'`
+- `'chicago-author-date'`
+- `'chicago-note-bibliography'`
+- `'mla'`
+- `'vancouver'`
+- `'ieee'`
+- `'harvard-cite-them-right'`
+- `'nature'`
+
+## In-Text Citations
+
+```python
+zot.add_parameters(content='citation', style='apa')
+citations = zot.items(limit=50)
+# Returns list of HTML <span> elements: ['<span>(Smith, 2024)</span>', ...]
+```
+
+## Other Formats
+
+Set `content` to any Zotero export format:
+
+| Format | `content` value | Returns |
+|--------|----------------|---------|
+| BibTeX | `'bibtex'` | via `format='bibtex'` |
+| CSL-JSON | `'csljson'` | list of dicts |
+| RIS | `'ris'` | list of unicode strings |
+| RDF (Dublin Core) | `'rdf_dc'` | list of unicode strings |
+| Zotero RDF | `'rdf_zotero'` | list of unicode strings |
+| BibLaTeX | `'biblatex'` | list of unicode strings |
+| Wikipedia Citation Templates | `'wikipedia'` | list of unicode strings |
+
+**Note**: When using an export format as `content`, you must provide a `limit` parameter. Multiple simultaneous format retrieval is not supported.
+
+```python
+# Export as RIS
+zot.add_parameters(content='ris', limit=50)
+ris_data = zot.items()
+with open('library.ris', 'w', encoding='utf-8') as f:
+    f.write('\n'.join(ris_data))
+```
+
+## Keys Only
+
+```python
+# Get item keys as a newline-delimited string
+zot.add_parameters(format='keys')
+keys_str = zot.items()
+keys = keys_str.strip().split('\n')
+```
+
+## Version Information (for syncing)
+
+```python
+# Dict of {key: version} for all items
+zot.add_parameters(format='versions')
+versions = zot.items()
+```

scientific-skills/pyzotero/references/files-attachments.md

@@ -0,0 +1,97 @@
+# Files & Attachments
+
+## Downloading Files
+
+```python
+# Get raw binary content of an attachment
+raw = zot.file('ATTACHMENTKEY')
+with open('paper.pdf', 'wb') as f:
+    f.write(raw)
+
+# Convenient wrapper: dump file to disk
+# Uses stored filename, saves to current directory
+zot.dump('ATTACHMENTKEY')
+
+# Dump to a specific path and filename
+zot.dump('ATTACHMENTKEY', 'renamed_paper.pdf', '/home/user/papers/')
+# Returns the full file path on success
+```
+
+**Note**: HTML snapshots are dumped as `.zip` files named with the item key.
+
+## Finding Attachments
+
+```python
+# Get child items (attachments, notes) of a parent item
+children = zot.children('PARENTKEY')
+attachments = [c for c in children if c['data']['itemType'] == 'attachment']
+
+# Get the attachment key
+for att in attachments:
+    key = att['data']['key']
+    filename = att['data']['filename']
+    content_type = att['data']['contentType']
+    link_mode = att['data']['linkMode']  # 'imported_file', 'linked_file', 'imported_url', 'linked_url'
+```
+
+## Uploading Attachments
+
+**Note**: Attachment upload methods are in beta.
+
+```python
+# Simple upload: one or more files by path
+result = zot.attachment_simple(['/path/to/paper.pdf', '/path/to/notes.docx'])
+
+# Upload as child items of a parent
+result = zot.attachment_simple(['/path/to/paper.pdf'], parentid='PARENTKEY')
+
+# Upload with custom filenames: list of (name, path) tuples
+result = zot.attachment_both([
+    ('Paper 2024.pdf', '/path/to/paper.pdf'),
+    ('Supplementary.pdf', '/path/to/supp.pdf'),
+], parentid='PARENTKEY')
+
+# Upload files to existing attachment items
+result = zot.upload_attachments(attachment_items, basedir='/path/to/files/')
+```
+
+Upload result structure:
+```python
+{
+    'success': [attachment_item1, ...],
+    'failure': [attachment_item2, ...],
+    'unchanged': [attachment_item3, ...]
+}
+```
+
+## Attachment Templates
+
+```python
+# Get template for a file attachment
+template = zot.item_template('attachment', linkmode='imported_file')
+# linkmode options: 'imported_file', 'linked_file', 'imported_url', 'linked_url'
+
+# Available link modes
+modes = zot.item_attachment_link_modes()
+```
+
+## Downloading All PDFs from a Collection
+
+```python
+import os
+
+collection_key = 'COLKEY'
+output_dir = '/path/to/output/'
+os.makedirs(output_dir, exist_ok=True)
+
+items = zot.everything(zot.collection_items(collection_key))
+for item in items:
+    children = zot.children(item['data']['key'])
+    for child in children:
+        if child['data']['itemType'] == 'attachment' and \
+           child['data'].get('contentType') == 'application/pdf':
+            try:
+                zot.dump(child['data']['key'], path=output_dir)
+            except Exception as e:
+                print(f"Failed to download {child['data']['key']}: {e}")
+```

scientific-skills/pyzotero/references/full-text.md

@@ -0,0 +1,68 @@
+# Full-Text Content
+
+Pyzotero can retrieve and set full-text index content for attachment items.
+
+## Retrieving Full-Text Content
+
+```python
+# Get full-text content for a specific attachment item
+data = zot.fulltext_item('ATTACHMENTKEY')
+# Returns:
+# {
+#   "content": "Full text of the document...",
+#   "indexedPages": 50,
+#   "totalPages": 50
+# }
+# For text docs: indexedChars/totalChars instead of pages
+
+text = data['content']
+coverage = data['indexedPages'] / data['totalPages']
+```
+
+## Finding Items with New Full-Text Content
+
+```python
+# Get item keys with full-text updated since a library version
+new_fulltext = zot.new_fulltext(since='1085')
+# Returns dict: {'KEY1': 1090, 'KEY2': 1095, ...}
+# Values are the library version at which full-text was indexed
+```
+
+## Setting Full-Text Content
+
+```python
+# Set full-text for a PDF attachment
+payload = {
+    'content': 'The full text content of the document.',
+    'indexedPages': 50,
+    'totalPages': 50
+}
+zot.set_fulltext('ATTACHMENTKEY', payload)
+
+# For text documents use indexedChars/totalChars
+payload = {
+    'content': 'Full text here.',
+    'indexedChars': 15000,
+    'totalChars': 15000
+}
+zot.set_fulltext('ATTACHMENTKEY', payload)
+```
+
+## Full-Text Search via CLI
+
+The CLI provides full-text search across locally indexed PDFs:
+
+```bash
+# Search full-text content
+pyzotero search -q "CRISPR gene editing" --fulltext
+
+# Output as JSON (retrieves parent bibliographic items for attachments)
+pyzotero search -q "climate tipping points" --fulltext --json
+```
+
+## Search in API (qmode=everything)
+
+```python
+# Search in titles/creators + full-text content
+results = zot.items(q='protein folding', qmode='everything', limit=20)
+```

scientific-skills/pyzotero/references/pagination.md

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+# Pagination: follow(), everything(), Generators
+
+Pyzotero returns 100 items by default. Use these methods to retrieve more.
+
+## everything() — Retrieve All Results
+
+The simplest way to get all items:
+
+```python
+# All items in the library
+all_items = zot.everything(zot.items())
+
+# All top-level items
+all_top = zot.everything(zot.top())
+
+# All items in a collection
+all_col = zot.everything(zot.collection_items('COLKEY'))
+
+# All items matching a search
+all_results = zot.everything(zot.items(q='machine learning', itemType='journalArticle'))
+```
+
+`everything()` works with all Read API calls that can return multiple items.
+
+## follow() — Sequential Pagination
+
+```python
+# Retrieve items in batches, manually advancing the page
+first_batch = zot.top(limit=25)
+second_batch = zot.follow()   # next 25 items
+third_batch = zot.follow()    # next 25 items
+```
+
+**Warning**: `follow()` raises `StopIteration` when no more items are available. Not valid after single-item calls like `zot.item()`.
+
+## iterfollow() — Generator
+
+```python
+# Create a generator over follow()
+first = zot.top(limit=10)
+lazy = zot.iterfollow()
+
+# Retrieve subsequent pages
+second = next(lazy)
+third = next(lazy)
+```
+
+## makeiter() — Generator over Any Method
+
+```python
+# Create a generator directly from a method call
+gen = zot.makeiter(zot.top(limit=25))
+
+page1 = next(gen)  # first 25 items
+page2 = next(gen)  # next 25 items
+# Raises StopIteration when exhausted
+```
+
+## Manual start/limit Pagination
+
+```python
+page_size = 50
+offset = 0
+
+while True:
+    batch = zot.items(limit=page_size, start=offset)
+    if not batch:
+        break
+    # process batch
+    for item in batch:
+        process(item)
+    offset += page_size
+```
+
+## Performance Notes
+
+- `everything()` makes multiple API calls sequentially; large libraries may take time.
+- For libraries with thousands of items, use `since=version` to retrieve only changed items (useful for sync workflows).
+- All of `follow()`, `everything()`, and `makeiter()` are only valid for methods that return multiple items.

scientific-skills/pyzotero/references/read-api.md

@@ -0,0 +1,137 @@
+# Read API Methods
+
+## Retrieving Items
+
+```python
+# All items in library (100 per call by default)
+items = zot.items()
+
+# Top-level items only (excludes attachments/notes that are children)
+top = zot.top(limit=25)
+
+# A specific item by key
+item = zot.item('ITEMKEY')
+
+# Multiple specific items (up to 50 per call)
+subset = zot.get_subset(['KEY1', 'KEY2', 'KEY3'])
+
+# Items from trash
+trash = zot.trash()
+
+# Deleted items (requires 'since' parameter)
+deleted = zot.deleted(since=1000)
+
+# Items from "My Publications"
+pubs = zot.publications()  # user libraries only
+
+# Count all items
+count = zot.count_items()
+
+# Count top-level items
+n = zot.num_items()
+```
+
+## Item Data Structure
+
+Items are returned as dicts. Data lives in `item['data']`:
+
+```python
+item = zot.item('VDNIEAPH')[0]
+title = item['data']['title']
+item_type = item['data']['itemType']
+creators = item['data']['creators']
+tags = item['data']['tags']
+key = item['data']['key']
+version = item['data']['version']
+collections = item['data']['collections']
+doi = item['data'].get('DOI', '')
+```
+
+## Child Items
+
+```python
+# Get child items (notes, attachments) of a parent
+children = zot.children('PARENTKEY')
+```
+
+## Retrieving Collections
+
+```python
+# All collections (including subcollections)
+collections = zot.collections()
+
+# Top-level collections only
+top_collections = zot.collections_top()
+
+# A specific collection
+collection = zot.collection('COLLECTIONKEY')
+
+# Sub-collections of a collection
+sub = zot.collections_sub('COLLECTIONKEY')
+
+# All collections and sub-collections in a flat list
+all_cols = zot.all_collections()
+# Or from a specific collection down:
+all_cols = zot.all_collections('COLLECTIONKEY')
+
+# Items in a specific collection (not sub-collections)
+col_items = zot.collection_items('COLLECTIONKEY')
+
+# Top-level items in a specific collection
+col_top = zot.collection_items_top('COLLECTIONKEY')
+
+# Count items in a collection
+n = zot.num_collectionitems('COLLECTIONKEY')
+```
+
+## Retrieving Tags
+
+```python
+# All tags in the library
+tags = zot.tags()
+
+# Tags from a specific item
+item_tags = zot.item_tags('ITEMKEY')
+
+# Tags in a collection
+col_tags = zot.collection_tags('COLLECTIONKEY')
+```
+
+## Retrieving Groups
+
+```python
+groups = zot.groups()
+# Returns list of group libraries accessible to current key
+```
+
+## Version Information
+
+```python
+# Last modified version of the library
+version = zot.last_modified_version()
+
+# Item versions dict {key: version}
+item_versions = zot.item_versions()
+
+# Collection versions dict {key: version}
+col_versions = zot.collection_versions()
+
+# Changes since a known version (for syncing)
+changed_items = zot.item_versions(since=1000)
+```
+
+## Library Settings
+
+```python
+settings = zot.settings()
+# Returns synced settings (feeds, PDF reading progress, etc.)
+# Use 'since' to get only changes:
+new_settings = zot.settings(since=500)
+```
+
+## Saved Searches
+
+```python
+searches = zot.searches()
+# Retrieves saved search metadata (not results)
+```

scientific-skills/pyzotero/references/saved-searches.md

@@ -0,0 +1,77 @@
+# Saved Searches
+
+## Retrieving Saved Searches
+
+```python
+# Get all saved search metadata (not results)
+searches = zot.searches()
+# Returns list of dicts with name, key, conditions, version
+
+for search in searches:
+    print(search['data']['name'], search['data']['key'])
+```
+
+**Note**: Saved search *results* cannot be retrieved via the API (as of 2025). Only metadata is returned.
+
+## Creating Saved Searches
+
+Each condition dict must have `condition`, `operator`, and `value`:
+
+```python
+conditions = [
+    {
+        'condition': 'title',
+        'operator': 'contains',
+        'value': 'machine learning'
+    }
+]
+zot.saved_search('ML Papers', conditions)
+```
+
+### Multiple Conditions (AND logic)
+
+```python
+conditions = [
+    {'condition': 'itemType', 'operator': 'is', 'value': 'journalArticle'},
+    {'condition': 'tag', 'operator': 'is', 'value': 'unread'},
+    {'condition': 'date', 'operator': 'isAfter', 'value': '2023-01-01'},
+]
+zot.saved_search('Recent Unread Articles', conditions)
+```
+
+## Deleting Saved Searches
+
+```python
+# Get search keys first
+searches = zot.searches()
+keys = [s['data']['key'] for s in searches if s['data']['name'] == 'Old Search']
+zot.delete_saved_search(keys)
+```
+
+## Discovering Valid Operators and Conditions
+
+```python
+# All available operators
+operators = zot.show_operators()
+
+# All available conditions
+conditions = zot.show_conditions()
+
+# Operators valid for a specific condition
+title_operators = zot.show_condition_operators('title')
+# e.g. ['is', 'isNot', 'contains', 'doesNotContain', 'beginsWith']
+```
+
+## Common Condition/Operator Combinations
+
+| Condition | Common Operators |
+|-----------|-----------------|
+| `title` | `contains`, `doesNotContain`, `is`, `beginsWith` |
+| `tag` | `is`, `isNot` |
+| `itemType` | `is`, `isNot` |
+| `date` | `isBefore`, `isAfter`, `is` |
+| `creator` | `contains`, `is` |
+| `publicationTitle` | `contains`, `is` |
+| `year` | `is`, `isBefore`, `isAfter` |
+| `collection` | `is`, `isNot` |
+| `fulltextContent` | `contains` |

scientific-skills/pyzotero/references/search-params.md

@@ -0,0 +1,90 @@
+# Search & Request Parameters
+
+Parameters can be passed directly to any Read API call, or set globally with `add_parameters()`.
+
+```python
+# Inline parameters (valid for one call only)
+results = zot.items(q='climate change', limit=50, sort='date', direction='desc')
+
+# Set globally (overridden by inline params on the next call)
+zot.add_parameters(limit=50, sort='dateAdded')
+results = zot.items()
+```
+
+## Available Parameters
+
+| Parameter | Type | Description |
+|-----------|------|-------------|
+| `q` | str | Quick search — titles and creator fields by default |
+| `qmode` | str | `'titleCreatorYear'` (default) or `'everything'` (full-text) |
+| `itemType` | str | Filter by item type. See search syntax for operators |
+| `tag` | str or list | Filter by tag(s). Multiple tags = AND logic |
+| `since` | int | Return only objects modified after this library version |
+| `sort` | str | Sort field (see below) |
+| `direction` | str | `'asc'` or `'desc'` |
+| `limit` | int | 1–100, or `None` |
+| `start` | int | Offset into result set |
+| `format` | str | Response format (see exports.md) |
+| `itemKey` | str | Comma-separated item keys (up to 50) |
+| `content` | str | `'bib'`, `'html'`, `'citation'`, or export format |
+| `style` | str | CSL style name (used with `content='bib'`) |
+| `linkwrap` | str | `'1'` to wrap URLs in `<a>` tags in bibliography output |
+
+## Sort Fields
+
+`dateAdded`, `dateModified`, `title`, `creator`, `type`, `date`, `publisher`,
+`publicationTitle`, `journalAbbreviation`, `language`, `accessDate`,
+`libraryCatalog`, `callNumber`, `rights`, `addedBy`, `numItems`, `tags`
+
+## Tag Search Syntax
+
+```python
+# Single tag
+zot.items(tag='machine learning')
+
+# Multiple tags — AND logic (items must have all tags)
+zot.items(tag=['climate', 'adaptation'])
+
+# OR logic (items with any tag)
+zot.items(tag='climate OR adaptation')
+
+# Exclude a tag
+zot.items(tag='-retracted')
+```
+
+## Item Type Filtering
+
+```python
+# Single type
+zot.items(itemType='journalArticle')
+
+# OR multiple types
+zot.items(itemType='journalArticle || book')
+
+# Exclude a type
+zot.items(itemType='-note')
+```
+
+Common item types: `journalArticle`, `book`, `bookSection`, `conferencePaper`,
+`thesis`, `report`, `dataset`, `preprint`, `note`, `attachment`, `webpage`,
+`patent`, `statute`, `case`, `hearing`, `interview`, `letter`, `manuscript`,
+`map`, `artwork`, `audioRecording`, `videoRecording`, `podcast`, `film`,
+`radioBroadcast`, `tvBroadcast`, `presentation`, `encyclopediaArticle`,
+`dictionaryEntry`, `forumPost`, `blogPost`, `instantMessage`, `email`,
+`document`, `computerProgram`, `bill`, `newspaperArticle`, `magazineArticle`
+
+## Examples
+
+```python
+# Recent journal articles matching query, sorted by date
+zot.items(q='CRISPR', itemType='journalArticle', sort='date', direction='desc', limit=20)
+
+# Items added since a known library version
+zot.items(since=4000)
+
+# Items with a specific tag, offset for pagination
+zot.items(tag='to-read', limit=25, start=25)
+
+# Full-text search
+zot.items(q='gene editing', qmode='everything', limit=10)
+```

scientific-skills/pyzotero/references/tags.md

@@ -0,0 +1,87 @@
+# Tag Management
+
+## Retrieving Tags
+
+```python
+# All tags in the library
+tags = zot.tags()
+# Returns list of strings: ['climate change', 'machine learning', ...]
+
+# Tags for a specific item
+item_tags = zot.item_tags('ITEMKEY')
+
+# Tags in a specific collection
+col_tags = zot.collection_tags('COLKEY')
+
+# Filter tags by prefix (e.g. all tags starting with 'bio')
+filtered = zot.tags(q='bio')
+```
+
+## Adding Tags to Items
+
+```python
+# Add one or more tags to an item (retrieves item first)
+item = zot.item('ITEMKEY')
+updated = zot.add_tags(item, 'tag1', 'tag2', 'tag3')
+
+# Add a list of tags
+tag_list = ['reviewed', 'high-priority', '2024']
+updated = zot.add_tags(item, *tag_list)
+```
+
+## Deleting Tags
+
+```python
+# Delete specific tags from the library
+zot.delete_tags('old-tag', 'unused-tag')
+
+# Delete a list of tags
+tags_to_remove = ['deprecated', 'temp']
+zot.delete_tags(*tags_to_remove)
+```
+
+## Searching Items by Tag
+
+```python
+# Items with a single tag
+items = zot.items(tag='machine learning')
+
+# Items with multiple tags (AND logic)
+items = zot.items(tag=['climate', 'adaptation'])
+
+# Items with any of these tags (OR logic)
+items = zot.items(tag='climate OR sea level')
+
+# Items NOT having a tag
+items = zot.items(tag='-retracted')
+```
+
+## Batch Tag Operations
+
+```python
+# Add a tag to all items in a collection
+items = zot.everything(zot.collection_items('COLKEY'))
+for item in items:
+    zot.add_tags(item, 'collection-reviewed')
+
+# Find all items with a specific tag and retag them
+old_tag_items = zot.everything(zot.items(tag='old-name'))
+for item in old_tag_items:
+    # Add new tag
+    item['data']['tags'].append({'tag': 'new-name'})
+    # Remove old tag
+    item['data']['tags'] = [t for t in item['data']['tags'] if t['tag'] != 'old-name']
+zot.update_items(old_tag_items)
+```
+
+## Tag Types
+
+Zotero has two tag types stored in `tag['type']`:
+- `0` — User-added tags (default)
+- `1` — Automatically imported tags (from bibliographic databases)
+
+```python
+item = zot.item('ITEMKEY')
+for tag in item['data']['tags']:
+    print(tag['tag'], tag.get('type', 0))
+```

scientific-skills/pyzotero/references/write-api.md

@@ -0,0 +1,123 @@
+# Write API Methods
+
+## Creating Items
+
+Always use `item_template()` to get a valid template before creating items.
+
+```python
+# Get a template for a specific item type
+template = zot.item_template('journalArticle')
+
+# Fill in fields
+template['title'] = 'Deep Learning for Genomics'
+template['date'] = '2024'
+template['publicationTitle'] = 'Nature Methods'
+template['volume'] = '21'
+template['DOI'] = '10.1038/s41592-024-02233-6'
+template['creators'] = [
+    {'creatorType': 'author', 'firstName': 'Jane', 'lastName': 'Doe'},
+    {'creatorType': 'author', 'firstName': 'John', 'lastName': 'Smith'},
+]
+
+# Validate fields before creating (raises InvalidItemFields if invalid)
+zot.check_items([template])
+
+# Create the item
+resp = zot.create_items([template])
+# resp: {'success': {'0': 'NEWITEMKEY'}, 'failed': {}, 'unchanged': {}}
+new_key = resp['success']['0']
+```
+
+### Create Multiple Items at Once
+
+```python
+templates = []
+for data in paper_data_list:
+    t = zot.item_template('journalArticle')
+    t['title'] = data['title']
+    t['DOI'] = data['doi']
+    templates.append(t)
+
+resp = zot.create_items(templates)
+```
+
+### Create Child Items
+
+```python
+# Create a note as a child of an existing item
+note_template = zot.item_template('note')
+note_template['note'] = '<p>My annotation here</p>'
+zot.create_items([note_template], parentid='PARENTKEY')
+```
+
+## Updating Items
+
+```python
+# Retrieve, modify, update
+item = zot.item('ITEMKEY')
+item['data']['title'] = 'Updated Title'
+item['data']['abstractNote'] = 'New abstract text.'
+success = zot.update_item(item)  # returns True or raises error
+
+# Update many items at once (auto-chunked at 50)
+items = zot.items(limit=10)
+for item in items:
+    item['data']['extra'] += '\nProcessed'
+zot.update_items(items)
+```
+
+## Deleting Items
+
+```python
+# Must retrieve item first (version field is required)
+item = zot.item('ITEMKEY')
+zot.delete_item([item])
+
+# Delete multiple items
+items = zot.items(tag='to-delete')
+zot.delete_item(items)
+```
+
+## Item Types and Fields
+
+```python
+# All available item types
+item_types = zot.item_types()
+# [{'itemType': 'artwork', 'localized': 'Artwork'}, ...]
+
+# All available fields
+fields = zot.item_fields()
+
+# Valid fields for a specific item type
+journal_fields = zot.item_type_fields('journalArticle')
+
+# Valid creator types for an item type
+creator_types = zot.item_creator_types('journalArticle')
+# [{'creatorType': 'author', 'localized': 'Author'}, ...]
+
+# All localised creator field names
+creator_fields = zot.creator_fields()
+
+# Attachment link modes (needed for attachment templates)
+link_modes = zot.item_attachment_link_modes()
+
+# Template for an attachment
+attach_template = zot.item_template('attachment', linkmode='imported_file')
+```
+
+## Optimistic Locking
+
+Use `last_modified` to prevent overwriting concurrent changes:
+
+```python
+# Only update if library version matches
+zot.update_item(item, last_modified=4025)
+# Raises an error if the server version differs
+```
+
+## Notes
+
+- `create_items()` accepts up to 50 items per call; batch if needed.
+- `update_items()` auto-chunks at 50 items.
+- If a dict passed to `create_items()` contains a `key` matching an existing item, it will be updated rather than created.
+- Always call `check_items()` before `create_items()` to catch field errors early.