Merge branch 'v2' into batch_cmoriser

Author: rbeucher

.gitignore

@@ -3,3 +3,4 @@ docs/build
 src/access_mopper.egg-info
 # pixi environments
 .pixi
+notebooks/.ipynb_checkpoints

.zenodo.json

@@ -0,0 +1,39 @@
+{
+    "creators": [
+        {
+            "orcid": "0000-0003-3891-5444",
+            "affiliation": "ACCESS-NRI",
+            "name": "Beucher, Romain"
+        }
+    ],
+    "contributors": [
+        {
+            "name": "Paola Petrellui",
+            "affiliation": "University of Tasmania",
+            "orcid": "0000-0002-0164-5105",
+            "type": "Version 1 developer"
+        },
+        {
+            "name": "Samuel Green",
+            "affiliation": "ARC Centre of Excellence for the Weather of the 21st Century",
+            "orcid": "0000-0003-1129-4676",
+            "type": "Version 1 developer"
+        },
+        {
+            "name": "Chloe Mackallah",
+            "affiliation": "CSIRO",
+            "orcid": "0000-0003-4989-5530",
+            "type": "APP4 developer"
+        }
+    ],
+
+    "license": "Apache-2.0",
+
+    "title": "ACCESS-MOPPeR",
+
+    "keywords": ["Climate", "Science", "Model Evaluation", "CMOR", "CMIP", "ACCESS", "ACCESS-NRI", "NCI"],
+
+    "communities": [
+        {"identifier": "access-nri"}
+    ]
+}

README.md

@@ -1,7 +1,7 @@
-# ACCESS-MOPPeR v2.1.0a (Alpha Version)
+# ACCESS Model Output Post-Processor (ACCESS-MOPPeR) v2.1.0a (Alpha Version)
 
 ## Overview
-ACCESS-MOPPeR v2.0.0a is a CMORisation tool designed to post-process ACCESS model output. This version represents a significant rewrite of the original MOPPeR, focusing on usability rather than raw performance. It introduces a more flexible and user-friendly Python API that can be integrated into Jupyter notebooks and other workflows.
+ACCESS-MOPPeR v2.1.0a is a CMORisation tool designed to post-process ACCESS model output. This version represents a significant rewrite of the original MOPPeR, focusing on usability rather than raw performance. It introduces a more flexible and user-friendly Python API that can be integrated into Jupyter notebooks and other workflows.
 
 ACCESS-MOPPeR allows for targeted CMORisation of individual variables and is specifically designed to support the ACCESS-ESM1.6 configuration prepared for CMIP7 FastTrack. However, ocean variable support remains limited in this alpha release.
 
@@ -15,23 +15,52 @@ ACCESS-MOPPeR allows for targeted CMORisation of individual variables and is spe
 
 ## Current Limitations
 - **Alpha Version**: Intended for evaluation purposes only; not recommended for data publication.
-- **Limited Ocean Variable Support**: Further development is needed to support ocean-related variables fully.
+
+> **⚠️ Variable Mapping Under Review**
+>
+> We are currently reviewing the mapping of ACCESS variables to their CMIP6 and CMIP7 equivalents. Some variables that require derivation may not be available yet, or their calculation may need further verification.
+> **If you notice any major issues or missing variables, please submit an issue!**
+
 
 ## Background
-ACCESS-MOPPeR builds upon the original APP4 and MOPPeR frameworks, which were initially developed for CMIP5 and later extended for CMIP6. These tools leveraged CMOR3 and CMIP6 data request files to produce CF-compliant datasets aligned with ESGF standards. MOPPeR introduced the **mopdb** tool, allowing users to create custom mappings and CMOR table definitions.
+ACCESS-MOPPeR v2 is a complete rewrite of the original APP4 and MOPPeR frameworks. Unlike previous versions, it does **not** depend on CMOR; instead, it leverages modern Python libraries such as **xarray** and **dask** for efficient processing of NETCDF files. This approach streamlines the workflow, improves flexibility, and enhances integration with contemporary data science tools.
+
+While retaining the core concepts of "custom" and "cmip" modes, ACCESS-MOPPeR v2 unifies these workflows within a single configuration file, focusing on usability and extensibility for current and future CMIP projects.
+
+---
+
+## Installation
+
+
+```sh
+pip install numpy pandas xarray netCDF4 cftime dask pyyaml tqdm requests
+pip install .
+```
+
+---
+
+## Documentation
+
+See the [Getting Started notebook](notebooks/Getting_started.ipynb) and the [docs](docs/) folder for detailed usage and API documentation.
+
+---
+
+## Testing
+
+To run tests:
+
+```sh
+pytest
+```
+
+---
 
-This rewrite retains key features of the original MOPPeR while enhancing usability. The differentiation between "custom" and "cmip" modes remains, but both modes now follow a unified workflow defined in a single configuration file.
+## License
 
-## Usage
-ACCESS-MOPPeR v2.0.0a is best suited for users interested in evaluating outputs from ACCESS-ESM1.6 development releases. Full documentation is not available yet.
-Please refer to the [Getting Started Notebook](https://github.com/ACCESS-NRI/ACCESS-MOPPeR/blob/v2/notebooks/Getting_started.ipynb):
+ACCESS-MOPPeR is licensed under the Apache-2.0 License.
 
-## Future Development
-- **Optimised Multi-CPU Execution**: Parallel processing support will be introduced in later versions.
-- **Enhanced Ocean Variable Support**: Expansion of CMORisation capabilities for ocean-related data.
-- **Expanded CMORisation Standards**: Continued flexibility in defining custom post-processing standards beyond CMIP6.
+---
 
-## Disclaimer
-This is an **alpha release** and should not be used for official data publications. Users should expect potential changes in future versions that may affect workflow compatibility.
+## Contact
 
-For feedback or issues, please submit your contributions via the project's repository or contact the development team.
+Author: Romain Beucher