docs: update README with project overview, features, installation instructions, and usage examples; add logo image

Author: matisiekpl

README.md

@@ -1,135 +1,84 @@
-# kubefold
-// TODO(user): Add simple overview of use/purpose
+<div align="center">
+  <img src="assets/logo.png" alt="Kubefold Logo" />
+</div>
 
-## Description
-// TODO(user): An in-depth paragraph about your project and overview of use
+# 🧬 Kubefold
 
-## Getting Started
+Kubefold is a Kubernetes operator for managing protein structure prediction workflows. It provides a declarative way to handle protein databases and run conformation predictions in a Kubernetes cluster.
 
-### Prerequisites
-- go version v1.23.0+
-- docker version 17.03+.
-- kubectl version v1.11.3+.
-- Access to a Kubernetes v1.11.3+ cluster.
+## 🚀 Features
 
-### To Deploy on the cluster
-**Build and push your image to the location specified by `IMG`:**
+- **Protein Database Management** - Download and manage various protein databases (UniProt, PDB, BFD, etc.)
+- **Conformation Prediction** - Run protein structure predictions with configurable parameters
+- **Cloud Integration** - Store results in S3 and receive notifications via SMS
+- **Scalable Architecture** - Built on Kubernetes for horizontal scaling and resource management
 
-```sh
-make docker-build docker-push IMG=<some-registry>/kubefold:tag
-```
-
-**NOTE:** This image ought to be published in the personal registry you specified.
-And it is required to have access to pull the image from the working environment.
-Make sure you have the proper permission to the registry if the above commands don’t work.
-
-**Install the CRDs into the cluster:**
-
-```sh
-make install
-```
-
-**Deploy the Manager to the cluster with the image specified by `IMG`:**
-
-```sh
-make deploy IMG=<some-registry>/kubefold:tag
-```
-
-> **NOTE**: If you encounter RBAC errors, you may need to grant yourself cluster-admin
-privileges or be logged in as admin.
-
-**Create instances of your solution**
-You can apply the samples (examples) from the config/sample:
-
-```sh
-kubectl apply -k config/samples/
-```
-
->**NOTE**: Ensure that the samples has default values to test it out.
-
-### To Uninstall
-**Delete the instances (CRs) from the cluster:**
-
-```sh
-kubectl delete -k config/samples/
-```
+## 📋 Prerequisites
 
-**Delete the APIs(CRDs) from the cluster:**
+- Kubernetes cluster (v1.11.3+)
+- kubectl (v1.11.3+)
+- Access to an S3 bucket for storing results
+- AWS credentials for S3 and SMS notifications (if using these features)
 
-```sh
-make uninstall
-```
-
-**UnDeploy the controller from the cluster:**
+## 🛠️ Installation
 
 ```sh
-make undeploy
+kubectl apply -f https://raw.githubusercontent.com/kubefold/operator/main/dist/install.yaml
 ```
 
-## Project Distribution
-
-Following the options to release and provide this solution to the users.
+## 📝 Usage
 
-### By providing a bundle with all YAML files
+### Protein Database
 
-1. Build the installer for the image built and published in the registry:
+Create a ProteinDatabase resource to download and manage protein databases:
 
-```sh
-make build-installer IMG=<some-registry>/kubefold:tag
+```yaml
+apiVersion: data.kubefold.io/v1
+kind: ProteinDatabase
+metadata:
+  name: my-database
+spec:
+  datasets:
+    uniprot: true
+    pdb: true
+  volume:
+    storageClassName: fsx-sc
 ```
 
-**NOTE:** The makefile target mentioned above generates an 'install.yaml'
-file in the dist directory. This file contains all the resources built
-with Kustomize, which are necessary to install this project without its
-dependencies.
-
-2. Using the installer
-
-Users can just run 'kubectl apply -f <URL for YAML BUNDLE>' to install
-the project, i.e.:
-
-```sh
-kubectl apply -f https://raw.githubusercontent.com/<org>/kubefold/<tag or branch>/dist/install.yaml
+### Protein Conformation Prediction
+
+Run a protein structure prediction:
+
+```yaml
+apiVersion: data.kubefold.io/v1
+kind: ProteinConformationPrediction
+metadata:
+  name: my-prediction
+spec:
+  database: my-database
+  protein:
+    id: ['A']
+    sequence: "YOUR_PROTEIN_SEQUENCE"
+  model:
+    volume:
+      storageClassName: fsx-sc
+    weights:
+      http: "https://your-model-weights.bin.zst"
+  destination:
+    s3:
+      bucket: your-bucket
+      region: your-region
+  notify:
+    region: your-region
+    sms:
+      - "+1234567890"
 ```
 
-### By providing a Helm Chart
+## 🧹 Cleanup
 
-1. Build the chart using the optional helm plugin
+To uninstall the operator:
 
 ```sh
-kubebuilder edit --plugins=helm/v1-alpha
+kubectl delete -f https://raw.githubusercontent.com/kubefold/operator/main/dist/install.yaml
 ```
 
-2. See that a chart was generated under 'dist/chart', and users
-can obtain this solution from there.
-
-**NOTE:** If you change the project, you need to update the Helm Chart
-using the same command above to sync the latest changes. Furthermore,
-if you create webhooks, you need to use the above command with
-the '--force' flag and manually ensure that any custom configuration
-previously added to 'dist/chart/values.yaml' or 'dist/chart/manager/manager.yaml'
-is manually re-applied afterwards.
-
-## Contributing
-// TODO(user): Add detailed information on how you would like others to contribute to this project
-
-**NOTE:** Run `make help` for more information on all potential `make` targets
-
-More information can be found via the [Kubebuilder Documentation](https://book.kubebuilder.io/introduction.html)
-
-## License
-
-Copyright 2025 Mateusz Woźniak <wozniakmat@student.agh.edu.pl>.
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-    http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-