access-moppy 1.0.0a6__tar.gz

access_moppy-1.0.0a6/LICENCE.txt

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access_moppy-1.0.0a6/PKG-INFO

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+Metadata-Version: 2.4
+Name: access_moppy
+Version: 1.0.0a6
+Summary: ACCESS Model Output Post-Processor, maps raw model output to CMIP-style defined variables and produce post-processed output using CMOR3
+Author-email: Romain Beucher <romain.beucher@anu.edu.au>
+License: Apache-2.0
+Keywords: ACCESS,post-processing
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENCE.txt
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: xarray
+Requires-Dist: netCDF4
+Requires-Dist: cftime
+Requires-Dist: dask
+Requires-Dist: pyyaml
+Requires-Dist: tqdm
+Requires-Dist: requests
+Requires-Dist: parsl
+Requires-Dist: jinja2
+Provides-Extra: dashboard
+Requires-Dist: streamlit>=1.35.0; extra == "dashboard"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-subtests; extra == "test"
+Requires-Dist: ruff; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.3.0; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=1.23.0; extra == "docs"
+Requires-Dist: myst-parser>=2.0.0; extra == "docs"
+Requires-Dist: sphinx-autoapi>=3.0.0; extra == "docs"
+Requires-Dist: nbsphinx>=0.9.0; extra == "docs"
+Requires-Dist: ipython>=8.0.0; extra == "docs"
+Requires-Dist: pygments>=2.15.0; extra == "docs"
+Dynamic: license-file
+
+<div align="center">
+  <img src="docs/images/Moppy_logo.png" alt="MOPPy Logo" width="300"/>
+</div>
+
+# ACCESS-MOPPy (Model Output Post-Processor)
+
+[![Documentation Status](https://readthedocs.org/projects/access-moppy/badge/?version=latest)](https://access-moppy.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/access_moppy.svg)](https://badge.fury.io/py/access_moppy)
+[![Conda Version](https://img.shields.io/conda/vn/accessnri/access-moppy.svg)](https://anaconda.org/accessnri/access-moppy)
+
+ACCESS-MOPPy is a CMORisation tool designed to post-process ACCESS model output and produce CMIP-compliant datasets.
+
+## Key Features
+
+- **Python API** for integration into notebooks and scripts
+- **Batch processing system** for HPC environments with PBS
+- **Real-time monitoring** with web-based dashboard
+- **Flexible CMORisation** of individual variables
+- **Dask-enabled** for scalable parallel processing
+- **Cross-platform compatibility** (not limited to NCI Gadi)
+- **CMIP6 and CMIP7 FastTrack support**
+
+## Installation
+
+ACCESS-MOPPy requires Python >= 3.11. Install with:
+
+```bash
+pip install numpy pandas xarray netCDF4 cftime dask pyyaml tqdm requests streamlit
+pip install .
+```
+
+## Quick Start
+
+### Interactive Usage (Python API)
+
+```python
+import glob
+from access_moppy import ACCESS_ESM_CMORiser
+
+# Select input files
+files = glob.glob("/path/to/model/output/*mon.nc")
+
+# Create CMORiser instance
+cmoriser = ACCESS_ESM_CMORiser(
+    input_paths=files,
+    compound_name="Amon.pr",  # table.variable format
+    experiment_id="historical",
+    source_id="ACCESS-ESM1-5",
+    variant_label="r1i1p1f1",
+    grid_label="gn",
+    activity_id="CMIP",
+    output_path="/path/to/output"
+)
+
+# Run CMORisation
+cmoriser.run()
+cmoriser.write()
+```
+
+### Batch Processing (HPC/PBS)
+
+For large-scale processing on HPC systems:
+
+1. **Create a configuration file** (`batch_config.yml`):
+
+```yaml
+variables:
+  - Amon.pr
+  - Omon.tos
+  - Amon.ts
+
+experiment_id: piControl
+source_id: ACCESS-ESM1-5
+variant_label: r1i1p1f1
+grid_label: gn
+
+input_folder: "/g/data/project/model/output"
+output_folder: "/scratch/project/cmor_output"
+
+file_patterns:
+  Amon.pr: "output[0-4][0-9][0-9]/atmosphere/netCDF/*mon.nc"
+  Omon.tos: "output[0-4][0-9][0-9]/ocean/*temp*.nc"
+  Amon.ts: "output[0-4][0-9][0-9]/atmosphere/netCDF/*mon.nc"
+
+# PBS configuration
+queue: normal
+cpus_per_node: 16
+mem: 32GB
+walltime: "02:00:00"
+scheduler_options: "#PBS -P your_project"
+storage: "gdata/project+scratch/project"
+
+worker_init: |
+  module load conda
+  conda activate your_environment
+```
+
+2. **Submit batch job**:
+
+```bash
+moppy-cmorise batch_config.yml
+```
+
+3. **Monitor progress** at http://localhost:8501
+
+## Batch Processing Features
+
+The batch processing system provides:
+
+- **Parallel execution**: Each variable processed as a separate PBS job
+- **Real-time monitoring**: Web dashboard showing job status and progress
+- **Automatic tracking**: SQLite database maintains job history and status
+- **Error handling**: Failed jobs can be easily identified and resubmitted
+- **Resource optimization**: Configurable CPU, memory, and storage requirements
+- **Environment management**: Automatic setup of conda/module environments
+
+### Monitoring Tools
+
+- **Streamlit Dashboard**: Real-time web interface at http://localhost:8501
+- **Command line**: Use standard PBS commands (`qstat`, `qdel`)
+- **Database**: SQLite tracking at `{output_folder}/cmor_tasks.db`
+- **Log files**: Individual stdout/stderr for each job
+
+### File Organization
+
+```
+work_directory/
+├── batch_config.yml          # Your configuration
+├── cmor_job_scripts/          # Generated PBS scripts and logs
+│   ├── cmor_Amon_pr.sh       # PBS script
+│   ├── cmor_Amon_pr.py       # Python processing script
+│   ├── cmor_Amon_pr.out      # Job output
+│   └── cmor_Amon_pr.err      # Job errors
+└── output_folder/
+    ├── cmor_tasks.db         # Progress tracking
+    └── [CMORised files]      # Final output
+```
+
+## Documentation
+
+- **Getting Started**: `docs/source/getting_started.rst`
+- **Example Configuration**: `src/access_moppy/examples/batch_config.yml`
+- **API Reference**: [Coming soon]
+
+## Current Limitations
+
+- **Alpha version**: Intended for evaluation only
+- **Ocean variables**: Limited support in current release
+- **Variable mapping**: Under review for CMIP6/CMIP7 compliance
+
+## Support
+
+- **Issues**: Submit via GitHub Issues
+- **Questions**: Contact ACCESS-NRI support
+- **Contributions**: Welcome via Pull Requests
+
+## License
+
+ACCESS-MOPPy is licensed under the Apache-2.0 License.

access_moppy-1.0.0a6/README.md

@@ -0,0 +1,159 @@
+<div align="center">
+  <img src="docs/images/Moppy_logo.png" alt="MOPPy Logo" width="300"/>
+</div>
+
+# ACCESS-MOPPy (Model Output Post-Processor)
+
+[![Documentation Status](https://readthedocs.org/projects/access-moppy/badge/?version=latest)](https://access-moppy.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/access_moppy.svg)](https://badge.fury.io/py/access_moppy)
+[![Conda Version](https://img.shields.io/conda/vn/accessnri/access-moppy.svg)](https://anaconda.org/accessnri/access-moppy)
+
+ACCESS-MOPPy is a CMORisation tool designed to post-process ACCESS model output and produce CMIP-compliant datasets.
+
+## Key Features
+
+- **Python API** for integration into notebooks and scripts
+- **Batch processing system** for HPC environments with PBS
+- **Real-time monitoring** with web-based dashboard
+- **Flexible CMORisation** of individual variables
+- **Dask-enabled** for scalable parallel processing
+- **Cross-platform compatibility** (not limited to NCI Gadi)
+- **CMIP6 and CMIP7 FastTrack support**
+
+## Installation
+
+ACCESS-MOPPy requires Python >= 3.11. Install with:
+
+```bash
+pip install numpy pandas xarray netCDF4 cftime dask pyyaml tqdm requests streamlit
+pip install .
+```
+
+## Quick Start
+
+### Interactive Usage (Python API)
+
+```python
+import glob
+from access_moppy import ACCESS_ESM_CMORiser
+
+# Select input files
+files = glob.glob("/path/to/model/output/*mon.nc")
+
+# Create CMORiser instance
+cmoriser = ACCESS_ESM_CMORiser(
+    input_paths=files,
+    compound_name="Amon.pr",  # table.variable format
+    experiment_id="historical",
+    source_id="ACCESS-ESM1-5",
+    variant_label="r1i1p1f1",
+    grid_label="gn",
+    activity_id="CMIP",
+    output_path="/path/to/output"
+)
+
+# Run CMORisation
+cmoriser.run()
+cmoriser.write()
+```
+
+### Batch Processing (HPC/PBS)
+
+For large-scale processing on HPC systems:
+
+1. **Create a configuration file** (`batch_config.yml`):
+
+```yaml
+variables:
+  - Amon.pr
+  - Omon.tos
+  - Amon.ts
+
+experiment_id: piControl
+source_id: ACCESS-ESM1-5
+variant_label: r1i1p1f1
+grid_label: gn
+
+input_folder: "/g/data/project/model/output"
+output_folder: "/scratch/project/cmor_output"
+
+file_patterns:
+  Amon.pr: "output[0-4][0-9][0-9]/atmosphere/netCDF/*mon.nc"
+  Omon.tos: "output[0-4][0-9][0-9]/ocean/*temp*.nc"
+  Amon.ts: "output[0-4][0-9][0-9]/atmosphere/netCDF/*mon.nc"
+
+# PBS configuration
+queue: normal
+cpus_per_node: 16
+mem: 32GB
+walltime: "02:00:00"
+scheduler_options: "#PBS -P your_project"
+storage: "gdata/project+scratch/project"
+
+worker_init: |
+  module load conda
+  conda activate your_environment
+```
+
+2. **Submit batch job**:
+
+```bash
+moppy-cmorise batch_config.yml
+```
+
+3. **Monitor progress** at http://localhost:8501
+
+## Batch Processing Features
+
+The batch processing system provides:
+
+- **Parallel execution**: Each variable processed as a separate PBS job
+- **Real-time monitoring**: Web dashboard showing job status and progress
+- **Automatic tracking**: SQLite database maintains job history and status
+- **Error handling**: Failed jobs can be easily identified and resubmitted
+- **Resource optimization**: Configurable CPU, memory, and storage requirements
+- **Environment management**: Automatic setup of conda/module environments
+
+### Monitoring Tools
+
+- **Streamlit Dashboard**: Real-time web interface at http://localhost:8501
+- **Command line**: Use standard PBS commands (`qstat`, `qdel`)
+- **Database**: SQLite tracking at `{output_folder}/cmor_tasks.db`
+- **Log files**: Individual stdout/stderr for each job
+
+### File Organization
+
+```
+work_directory/
+├── batch_config.yml          # Your configuration
+├── cmor_job_scripts/          # Generated PBS scripts and logs
+│   ├── cmor_Amon_pr.sh       # PBS script
+│   ├── cmor_Amon_pr.py       # Python processing script
+│   ├── cmor_Amon_pr.out      # Job output
+│   └── cmor_Amon_pr.err      # Job errors
+└── output_folder/
+    ├── cmor_tasks.db         # Progress tracking
+    └── [CMORised files]      # Final output
+```
+
+## Documentation
+
+- **Getting Started**: `docs/source/getting_started.rst`
+- **Example Configuration**: `src/access_moppy/examples/batch_config.yml`
+- **API Reference**: [Coming soon]
+
+## Current Limitations
+
+- **Alpha version**: Intended for evaluation only
+- **Ocean variables**: Limited support in current release
+- **Variable mapping**: Under review for CMIP6/CMIP7 compliance
+
+## Support
+
+- **Issues**: Submit via GitHub Issues
+- **Questions**: Contact ACCESS-NRI support
+- **Contributions**: Welcome via Pull Requests
+
+## License
+
+ACCESS-MOPPy is licensed under the Apache-2.0 License.