ACCESS-NRI · minghangli-uni · Aug 25, 2025 · Aug 25, 2025 · Aug 25, 2025
diff --git a/README.md b/README.md
@@ -1,57 +1,100 @@
-# General Repository Template
+# access-experiment-runner
 
-A general template repository for default settings when creating new repositories.
+[![CI](https://github.com/ACCESS-NRI/access-experiment-runner/actions/workflows/ci.yml/badge.svg)](https://github.com/ACCESS-NRI/access-experiment-runner/actions/workflows/ci.yml)
+[![CD](https://github.com/ACCESS-NRI/access-experiment-runner/actions/workflows/cd.yml/badge.svg)](https://github.com/ACCESS-NRI/access-experiment-runner/actions/workflows/cd.yml)
+[![Coverage Status](https://codecov.io/gh/ACCESS-NRI/access-experiment-runner/branch/main/graph/badge.svg)](https://codecov.io/gh/ACCESS-NRI/access-experiment-runner)
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue?style=flat-square)](https://opensource.org/license/apache-2-0)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-This repository uses the Apache-2.0 license. `COPYRIGHT.txt` contains a current copyright statement which should be included at the top of all files.
+## About
+The main role of the ACCESS experiment runner is to manage and monitor experiment job runs on the supercomputing environment (e.g., `Gadi`). It builds on `Payu`, handling the orchestration of multiple configuration branches, experiment setup, and job lifecycle.
 
-When creating a new repository you [can use this repository as a template](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template), to automate the creation of the correct license and COPYRIGHT statement.
+## Key features
+- Leverages `Payu` and run multiple experiments from different configuration branches.
 
-## COPYRIGHT Header
+- Submits and tracks PBS jobs on `Gadi`; oversees job lifecycle from submission through completion.
+  - When a job completes within expected run times, the tool prints a confirmation and stops further submissions.
+  - If a job fails, users may choose to inspect the working directory to diagnose the root cause. The tool will detect the failure and pause further actions, giving the user control over whether to resubmit.
+  - Detects already running or queued jobs and avoids redundant submissions—quickly skips duplicates with a user notification.
 
-Best practice suggests adding a copyright statement at the top of every source code file, or text file where it is possible to add a copyright statement without interfering with the purpose of the file. The reasoning is if a file is separated from the repository in which it resides then it may not be possible to ascertain it's licensing, which may hamper re-use.
-
-Making this as short and concise as possible reduces the overhead in including such a copyright statement. To that end using [SPDX identifiers](https://spdx.dev/ids/) is simple, efficient, portable and machine-readable.
+## Installation
+### User setup
+The `experiment-runner` is installed in the `payu-dev` conda environment, hence loading `payu/dev` would directly make experiment-runner available for use.
+```
+module use /g/data/vk83/prerelease/modules && module load payu/dev
+```
 
-### Examples
+Alternatively, create and activate a python virtual environment, then install via pip,
+```
+python3 -m venv <path/to/venv> --system-site-packages
+source <path/to/venv>/bin/activate
 
-An example, short, copyright statement is reproduced below, as it might appear in different coding languages. Copy and add to files as appropriate: 
+pip install experiment-runner
+```
 
-#### plaintext
-It is common to include copyright statements at the bottom of a text document or website page
-```text
-© 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details. 
-SPDX-License-Identifier: Apache-2.0
+### Development setup
+For contributors and developers, setup a development environment,
 ```
+git clone https://github.com/ACCESS-NRI/access-experiment-runner.git
+cd access-experiment-runner
 
-#### python
-For code it is more common to include the copyright in a comment at the top
-```python
-# Copyright 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
-# SPDX-License-Identifier: Apache-2.0
+# under a virtual environment
+pip install -e .
 ```
 
-#### shell
-```bash
-# Copyright 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
-# SPDX-License-Identifier: Apache-2.0
+## Usage
 ```
+experiment-runner -i --help
 
-##### FORTRAN
-```fortran
-! Copyright 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
-! SPDX-License-Identifier: Apache-2.0
+usage: experiment-runner [-h] [-i INPUT_YAML_FILE]
+
+Manage ACCESS experiments using configurable YAML input.
+If no YAML file is specified, the tool will look for 'Experiment_runner.yaml' in the current directory.
+If that file is missing, you must specify one with -i / --input-yaml-file.
+
+options:
+  -h, --help            show this help message and exit
+  -i INPUT_YAML_FILE, --input-yaml-file INPUT_YAML_FILE
+                        Path to the YAML file specifying parameter values for experiment runs.
+                        Defaults to 'Experiment_runner.yaml' if present in the current directory.
 ```
 
-#### C/C++ 
-```c
-// Copyright 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
-// SPDX-License-Identifier: Apache-2.0
+One YAML example is provided in `example/Experiment_runner_example.yaml`
+
+```yaml
+test_path: /g/data/{PROJECT}/{USER}/prototype-0.1.0
+repository_directory: 1deg_jra55_ryf
+running_branches: [ctrl, perturb_1, perturb_2]
+keep_uuid: True
+nruns: [1,1,1]
 ```
+where,
+
+`test_path`: The base path to the experiment repository on the filesystem. In this case, it points to a prototype experiment runner checkout.
 
-### Notes
+`repository_directory`: The specific experiment configuration directory inside test_path. Here it is the `1deg_jra55_ryf` setup.
 
-Note that the date is the first time the project is created. 
+`running_branches`: A list of git branches representing experiments to run.
 
-The date signifies the year from which the copyright notice applies. **NEVER** replace with a later year, only ever add later years or a year range. 
+`keep_uuid`: Preserve unique identifiers (UUIDs) across runs.
 
-It is not necessary to include subsequent years in the copyright statement at all unless updates have been made at a later time, and even then it is largely discretionary: they are not necessary as copyright is contingent on the lifespan of copyright holder +50 years as per the [Berne Convention](https://en.wikipedia.org/wiki/Berne_Convention).
+`nruns`: A list indicating how many runs to perform for each branch listed in running_branches.
+
+## Workflow example
+1. Trigger the experiment
+```
+experiment-runner -i example/Experiment_runner_example.yaml
+```
+2. The tool then checks status:
+- Completed:
+```
+... already completed " {doneruns}, hence no new runs.
+```
+- Failed:
+```
+Clean up a failed job {work_dir} and prepare it for resubmission.
+```
+- Running/Queued: 
+```
+You have duplicated runs for in the same folder hence not submitting this job!
+```