docs: simplify README and fix mkdocs configuration

- Simplify README, move details to mkdocs site
- Add MIT license file
- Fix mkdocs emoji extension for material icons
- Remove expandable navigation

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: jayhesselberth

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 RNA Bioscience Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,141 +1,35 @@
 # charmer
 
-A terminal user interface (TUI) for monitoring Snakemake pipelines running on HPC clusters.
+A terminal user interface (TUI) for monitoring Snakemake pipelines on HPC clusters.
 
 ![Charmer Demo](docs/images/demo.gif)
 
 ## Features
 
-- **Real-time monitoring** of Snakemake pipelines on SLURM and LSF clusters
-- **Unified view** merging data from scheduler queries and Snakemake metadata
-- **Interactive TUI** with vim-style navigation
-- **Filtering & sorting** by job status, rule name, or time
-- **Log viewer** for examining job output
-- **Cross-platform** support for Linux and macOS
+- Real-time monitoring of Snakemake pipelines on SLURM and LSF clusters
+- Interactive TUI with vim-style navigation
+- Filtering, sorting, and log viewing
 
 ## Installation
 
-### From source
-
 ```bash
-# Clone the repository
-git clone https://github.com/rnabioco/charmer.git
-cd charmer
-
-# Build with cargo
-cargo build --release
-
-# Install to ~/.cargo/bin
-cargo install --path crates/charmer
+cargo install --git https://github.com/rnabioco/charmer.git
 ```
 
-### Using pixi (for development)
-
-```bash
-pixi install
-pixi run build
-```
-
-## Usage
+## Quick Start
 
 ```bash
 # Monitor current directory
 charmer
 
 # Monitor specific directory
 charmer /path/to/pipeline
-
-# With options
-charmer --poll-interval 10 --theme dark /path/to/pipeline
 ```
 
-### CLI Options
-
-| Option | Default | Description |
-|--------|---------|-------------|
-| `--poll-interval` | 5 | Seconds between scheduler queries |
-| `--run-uuid` | - | Filter to specific Snakemake run |
-| `--theme` | dark | Color theme (dark/light) |
-| `--history-hours` | 24 | Show completed jobs from last N hours |
-
-### Keyboard Shortcuts
-
-| Key | Action |
-|-----|--------|
-| `j` / `↓` | Move down |
-| `k` / `↑` | Move up |
-| `g` / `Home` | Go to first job |
-| `G` / `End` | Go to last job |
-| `f` | Cycle filter (All/Running/Failed/Pending/Completed) |
-| `s` | Cycle sort (Status/Rule/Time) |
-| `l` / `Enter` | View job logs |
-| `F` | Toggle follow mode in logs |
-| `?` | Show help |
-| `q` / `Ctrl+C` | Quit |
-
-## Supported Schedulers
-
-### SLURM
-
-Charmer queries SLURM using:
-- `squeue` for active jobs
-- `sacct` for job history
-
-Jobs are correlated with Snakemake using the comment field format:
-`rule_{rulename}_wildcards_{wildcards}`
-
-### LSF
-
-Charmer queries LSF using:
-- `bjobs` for active jobs
-- `bhist` for job history
+## Documentation
 
-## How It Works
-
-Charmer combines data from multiple sources:
-
-1. **Snakemake metadata** (`.snakemake/metadata/`) - Job inputs, outputs, shell commands
-2. **Scheduler queries** - Job status, resource usage, timing
-3. **Log files** (`.snakemake/slurm_logs/`) - Job output and errors
-
-Data is merged using rule names and timing windows to correlate jobs across sources.
-
-## Development
-
-```bash
-# Install dependencies
-pixi install
-
-# Run tests
-cargo test
-
-# Run with debug logging
-RUST_LOG=debug cargo run -- .
-
-# Build documentation
-pixi run docs
-```
-
-### Project Structure
-
-```
-charmer/
-├── crates/
-│   ├── charmer/          # Main binary
-│   ├── charmer-cli/      # CLI argument parsing
-│   ├── charmer-core/     # Snakemake metadata parsing
-│   ├── charmer-slurm/    # SLURM integration
-│   ├── charmer-lsf/      # LSF integration
-│   ├── charmer-state/    # Unified job state
-│   └── charmer-monitor/  # TUI components
-├── docs/                 # Documentation
-└── tests/                # Integration tests
-```
+Full documentation is available at **[rnabioco.github.io/charmer](https://rnabioco.github.io/charmer)**.
 
 ## License
 
 MIT License - see [LICENSE](LICENSE) for details.
-
-## Contributing
-
-Contributions welcome! Please read our [contributing guide](CONTRIBUTING.md) first.

mkdocs.yml

@@ -22,8 +22,6 @@ theme:
   features:
     - navigation.instant
     - navigation.tracking
-    - navigation.sections
-    - navigation.expand
     - toc.follow
     - content.code.copy
     - content.code.annotate
@@ -43,6 +41,9 @@ markdown_extensions:
   - pymdownx.superfences
   - pymdownx.tabbed:
       alternate_style: true
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
   - admonition
   - pymdownx.details
   - attr_list