Update readme

Author: steriva

README.md

@@ -1,30 +1,83 @@
-# Papers with code
+# Papers with code — ERMETE-Lab
 
-This repository is a lightweight wrapper for journal papers that link to code
-hosted in other repositories in the `ERMETE-Lab` organization.
+[![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Browse%20paper%20index-blue?logo=github)](https://ermete-lab.github.io/Papers-with-code/)
+
+This repository is a lightweight wrapper that indexes journal papers published by
+the [ERMETE-Lab](https://github.com/ERMETE-Lab) group **that have companion
+code** — not every group paper, only those accompanied by a public code
+repository.
+
+Each entry in the index links out to a dedicated repository in the ERMETE-Lab
+organization. Those repositories are also tracked as git submodules under
+`repositories/` so the code can be fetched alongside this wrapper in one step.
+
+---
 
 ## Repository layout
 
-- `index.html` renders a simple browser-based index of papers and linked code
-  repositories.
-- `papers.json` stores the paper metadata that drives the index.
-- `repositories/` is reserved for the git submodules that mirror the linked
-  repositories inside this wrapper repository.
+| Path                   | Purpose                                                  |
+| ---------------------- | -------------------------------------------------------- |
+| `index.html`           | Static browser-based paper index (the GitHub Pages site) |
+| `papers.json`          | Paper metadata that drives the index                     |
+| `repositories/<name>/` | Git submodules — one per companion code repository       |
+
+---
+
+## Adding a new paper
+
+### 1. Add the companion repository as a submodule
+
+```bash
+git submodule add https://github.com/ERMETE-Lab/<repo-name> repositories/<repo-name>
+git commit -m "Add <repo-name> submodule"
+```
+
+Replace `<repo-name>` with the repository name in the ERMETE-Lab organization
+(e.g. `NuSHRED`).
+
+### 2. Add an entry to `papers.json`
+
+Open `papers.json` and append a new object inside the `"papers"` array:
+
+```jsonc
+{
+  "title": "Full paper title",
+  "authors": "Author One; Author Two; Author Three",
+  "journal": "Journal Name",
+  "year": 2025,
+  "volume": "1",           // optional
+  "pages": "100000",       // optional
+  "repository": "<repo-name>",
+  "repository_url": "https://github.com/ERMETE-Lab/<repo-name>",
+  "submodule_path": "repositories/<repo-name>",
+  "doi": "10.xxxx/xxxxx",  // optional
+  "paper_url": "https://doi.org/10.xxxx/xxxxx", // optional
+  "notes": "One-sentence summary shown in the index." // optional
+}
+```
+
+Required fields: `title`, `repository`, `repository_url`, `submodule_path`.
+
+### 3. Push — the site updates automatically
+
+A GitHub Actions workflow publishes `index.html` and `papers.json` to GitHub
+Pages on every push to `main`. Once the workflow completes the new paper will
+appear at
+[ermete-lab.github.io/Papers-with-code](https://ermete-lab.github.io/Papers-with-code/).
+
+---
 
-## Adding a paper entry
+## Cloning with submodules
 
-1. Add the target repository as a git submodule under `repositories/<name>`.
-2. Add a matching entry to `papers.json` with:
-   - `title`
-   - `repository`
-   - `repository_url`
-   - `submodule_path`
-   - optional `authors`, `journal`, `year`, `doi`, `paper_url`, and `notes`
+To clone this repository and also fetch all companion code repositories in one
+command:
 
-Until entries are added, the wrapper renders an empty-state message instead of
-an empty table.
+```bash
+git clone --recurse-submodules https://github.com/ERMETE-Lab/Papers-with-code.git
+```
 
-## GitHub Pages
+If you already cloned without `--recurse-submodules`:
 
-The repository includes a workflow that publishes the static site (`index.html`
-and `papers.json`) to GitHub Pages on pushes to `main`.
+```bash
+git submodule update --init --recursive
+```