[feat] real readme

README.md

@@ -1,38 +1,73 @@
-<!-- # Bio-Image Archive Kubernetes analysis platform -->
+# BIA Binder Deployment
 
-<!-- - [`setup.md`](docs/setup.md) If you are setting this up from scratch follow these instructions to setup GitLab CI/CD.
-- [`deployment.md`](docs/deployment.md) If you wish to change the deployment read this.
- -->
+This repository contains the materials for deploying the BIA Binder, including the codebase and relevant supplementary files. The repository is currently aimed at deploying to Embassy Cloud and has historically also worked with DeNBI Cloud.
 
-## Quick start
+## Usage
 
-Install minikube and helmfile
+### Installation
 
-    https://kubernetes.io/docs/tasks/tools/install-minikube/
-    https://github.com/roboll/helmfile#installation
+1. **Clone the repository**:
+    ```bash
+    git clone https://github.com/yourusername/bia-binder.git
+    cd bia-binder
+    ```
 
-Add the secrets to your local environment
+2. **Install Helmsman**: Follow the instructions on the [Helmsman GitHub page](https://github.com/Praqma/helmsman) to install Helmsman on your system.
 
-    source secrets.env
+### Deployment
 
-<!-- Create a namespace, role, account and additional token for the Gitlab runner -->
+To deploy the application to different environments, you can use the Makefile. The Makefile supports deployment to `prod`, `dev`, and `local` environments for different variants: `embassy`, `denbi`, and `minikube`.
 
-<!-- 
-https://kubernetes.io/docs/admin/service-accounts-admin/
+1. **Deploy to production**:
+    ```bash
+    make embassy.prod
+    make denbi.prod
+    make minikube.prod
+    ```
 
-    kubectl apply -f ./k8s-clusterrole/
+2. **Deploy to development**:
+    ```bash
+    make embassy.dev
+    make denbi.dev
+    make minikube.dev
+    ```
 
-This will give the GitLab runner almost full administrative access to the cluster.
+3. **Deploy to local environment**:
+    ```bash
+    make embassy.local
+    make denbi.local
+    make minikube.local
+    ```
 
-    bash gitlab-ci/install-helm.sh
-    helmfile -e minikube sync
+4. **Generate htpassword file**:
+    ```bash
+    make htpassword
+    ```
 
-For prod
+### Example `.env` File
 
-    helmfile -e default sync -->
+Create a `.env` file in the root directory of the repository with the following structure:
 
-## TODO
+```env
+# Generic .env file example
 
-- Continuous integration
-- Elixir login portal
-- Speed up image pull
+# CI/CD Configuration
+CI_REGISTRY_IMAGE="bioimagearchive/binder-"
+CI_REGISTRY_URL="https://registry.binder.bioimagearchive.org"
+HOST_NAME="binder.bioimagearchive.org"
+KUBECONFIG="kube/embassy.config"
+CI_REGISTRY_USER=ctr26
+CI_REGISTRY_PASSWORD=4c16f763-****-****-****-80ec19d2f840
+
+# Secret keys (values obfuscated for security)
+SECRET_ELIXIR_CLIENTID=********-****-****-****-************
+SECRET_ELIXIR_CLIENTSECRET=********-****-****-****-************
+SECRET_HUB_PASSWORD=1e54cdb91f9c78d3f93a577b90567771ad076424ab24470192cc0776a3d45bd5
+SECRET_JUPYTERHUB_PROXY_TOKEN=1e54cdb91f9c78d3f93a577b90567771ad076424ab24470192cc0776a3d45bd5
+SECRET_BINDERHUB_SERVICE=569d94fdabd71bf88452db33782e4fa1881241764226e3038aedf6ec2cce1aa1
+SECRET_GITHUBREPOPROVIDER=ghp_************-**********
+SECRET_PROMETHEUS_AUTH_HTPASSWD=
+
+# AAI Configuration
+AAI_CLIENT_ID="cfac1c45-ab70-4596-b5b6-d1d92cf8ce3b"
+AAI_CLIENT_SECRET="c064871e-****-****-****-f82b1ad6e2c6"