@gair/codex-med 0.1.0 → 0.1.1

package/README.md

@@ -1,71 +1,63 @@
-<p align="center"><strong>Codex CLI</strong> is a coding agent from OpenAI that runs locally on your computer.
+<p align="center"><strong>codex-med</strong> — a medical-domain coding agent built on top of OpenAI's Codex CLI.</p>
+
 <p align="center">
-  <img src="https://github.com/openai/codex/blob/main/.github/codex-cli-splash.png" alt="Codex CLI splash" width="80%" />
+  Adds biomedical tools (UniProt / GenBank / PDB lookup, antibody training database queries, planned external model gateway) on top of the upstream Codex CLI.
 </p>
-</br>
-If you want Codex in your code editor (VS Code, Cursor, Windsurf), <a href="https://developers.openai.com/codex/ide">install in your IDE.</a>
-</br>If you want the desktop app experience, run <code>codex app</code> or visit <a href="https://chatgpt.com/codex?app-landing-page=true">the Codex App page</a>.
-</br>If you are looking for the <em>cloud-based agent</em> from OpenAI, <strong>Codex Web</strong>, go to <a href="https://chatgpt.com/codex">chatgpt.com/codex</a>.</p>
 
 ---
 
 ## Quickstart
 
-### Installing and running Codex CLI
-
-Run the following on Mac or Linux to install Codex CLI:
+### Install via npm (Linux x64)
 
 ```shell
-curl -fsSL https://chatgpt.com/codex/install.sh | sh
+npm install -g @gair/codex-med
 ```
 
-Run the following on Windows to install Codex CLI:
-
-```
-powershell -ExecutionPolicy ByPass -c "irm https://chatgpt.com/codex/install.ps1 | iex"
-```
+Currently only `linux-x64` (glibc) prebuilt binaries are published. Other platforms can build from source — see [Building from source](#building-from-source).
 
-Codex CLI can also be installed via the following package managers:
+Then run:
 
 ```shell
-# Install using npm
-npm install -g @openai/codex
+codex-med
 ```
 
-```shell
-# Install using Homebrew
-brew install --cask codex
-```
+### Sign in
+
+Inside the TUI, follow the prompts to sign in with your ChatGPT account or paste an API key. See `docs/config.md` for full configuration reference.
 
-Then simply run `codex` to get started.
+---
+
+## What's different from upstream Codex
 
-<details>
-<summary>You can also go to the <a href="https://github.com/openai/codex/releases/latest">latest GitHub Release</a> and download the appropriate binary for your platform.</summary>
+This is a fork; everything in the upstream README about agents, sandboxing, MCP support, etc. still applies. The medical-fork-specific additions:
 
-Each GitHub Release contains many executables, but in practice, you likely want one of these:
+- **Built-in biomedical lookup tools** — fetch UniProt entries, GenBank records, PDB structures, and search UniProt directly from the agent loop
+- **Antibody training database tool** — read-only SQL queries over a local SQLite database (`training_ready_v1.sqlite`); see `docs/` for schema
+- **External model gateway integration** *(planned)* — see [docs/model-integration.md](docs/model-integration.md) for the design and onboarding guide for connecting self-hosted models (affinity prediction, structure prediction, ADMET, etc.) via MCP
 
-- macOS
-  - Apple Silicon/arm64: `codex-aarch64-apple-darwin.tar.gz`
-  - x86_64 (older Mac hardware): `codex-x86_64-apple-darwin.tar.gz`
-- Linux
-  - x86_64: `codex-x86_64-unknown-linux-musl.tar.gz`
-  - arm64: `codex-aarch64-unknown-linux-musl.tar.gz`
+---
 
-Each archive contains a single entry with the platform baked into the name (e.g., `codex-x86_64-unknown-linux-musl`), so you likely want to rename it to `codex` after extracting it.
+## Building from source
 
-</details>
+Requires Rust 1.95+ and Node 16+.
 
-### Using Codex with your ChatGPT plan
+```shell
+git clone https://github.com/openai/codex.git codex-med
+cd codex-med/codex-rs
+cargo build --release -p codex-cli --bin codex
+```
 
-Run `codex` and select **Sign in with ChatGPT**. We recommend signing into your ChatGPT account to use Codex as part of your Plus, Pro, Business, Edu, or Enterprise plan. [Learn more about what's included in your ChatGPT plan](https://help.openai.com/en/articles/11369540-codex-in-chatgpt).
+The binary lands at `codex-rs/target/release/codex`. To package it as an npm tarball locally, see `codex-cli/scripts/build_npm_package.py` and `scripts/stage_npm_packages.py`.
 
-You can also use Codex with an API key, but this requires [additional setup](https://developers.openai.com/codex/auth#sign-in-with-an-api-key).
+---
 
 ## Docs
 
-- [**Codex Documentation**](https://developers.openai.com/codex)
-- [**Contributing**](./docs/contributing.md)
-- [**Installing & building**](./docs/install.md)
-- [**Open source fund**](./docs/open-source-fund.md)
+- [Model integration guide](docs/model-integration.md) — how to plug self-hosted prediction models into the agent
+- [Configuration](docs/config.md)
+- [Contributing](docs/contributing.md)
+
+---
 
 This repository is licensed under the [Apache-2.0 License](LICENSE).

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gair/codex-med",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "Codex CLI for medical domain agents (fork of OpenAI Codex CLI).",
   "license": "Apache-2.0",
   "bin": {
@@ -20,6 +20,6 @@
   },
   "packageManager": "pnpm@10.33.0+sha512.10568bb4a6afb58c9eb3630da90cc9516417abebd3fabbe6739f0ae795728da1491e9db5a544c76ad8eb7570f5c4bb3d6c637b2cb41bfdcdb47fa823c8649319",
   "optionalDependencies": {
-    "@gair/codex-med-linux-x64": "npm:@gair/codex-med@0.1.0-linux-x64"
+    "@gair/codex-med-linux-x64": "npm:@gair/codex-med@0.1.1-linux-x64"
   }
 }