Draft: Summer placement 2024

.gitignore

@@ -1,160 +1,16 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
 
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
+.vscode/
+__pycache__/
+.pyvale
+pyvale
+examples/2d_thermal_dataset/sim-workdir-1/*
+examples/monoblock_dataset/sim-workdir-1/*
+.ipynb_checkpoints/
+.test-env
+notebook_dataset_generator.ipynb
+best_model.pth
 *.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+dist/
+model_training.log
+.package-testing
+.testing-env/

README.md

@@ -1,2 +1,108 @@
-# icarus
-Machine learning for fusion simulation validation.
+# Icarus
+Machine learning for simulation validation. Icarus provide a set of machine learning tools that engineers can use to assess the agreement between an experiment and simulation; that is, to validate the simulation with experimental data.
+
+
+## Installation
+
+
+### Standard Installation (PyPI) 
+
+You can install icarus from PyPi as follows:
+
+```
+pip install icarus-fusion
+```
+
+### Developer Installation
+
+Clone `icarus` to your local system and `cd` to the root directory of `icarus`. Ensure that your virtual environment is activated and run from the `icarus` root directory:
+
+```
+pip install -e .
+```
+
+
+### PyTorch
+
+Icarus requires the latest stable version of PyTorch. The installation process varies depending on your hardware and operating system. Please follow the appropriate instructions below:
+
+#### CPU Installation:
+
+If you do not have access to NVIDIA GPUs, install the CPU version of PyTorch. Use the following commands based on your operating system:
+
+- Windows/macOS:
+
+```
+pip3 install torch
+```
+
+- Linux: 
+
+```
+pip3 install torch --index-url https://download.pytorch.org/whl/cpu
+```
+
+#### GPU Installation (NVIDIA CUDA):
+
+If you have access to NVIDIA GPUs and want to leverage CUDA for faster computation, use these commands (note: CUDA is not available on MacOS):
+
+- Linux:
+
+```
+pip3 install torch
+```
+
+- Windows:
+```
+pip3 install torch --index-url https://download.pytorch.org/whl/cu121
+```
+
+*Note: The CUDA version (`cu121` in this example) may change. Always check the official [PyTorch](https://pytorch.org/get-started/locally/) website for the most up-to-date installation instructions and CUDA version compatibility.*
+
+
+#### Verifying Installation:
+
+After installation, you can verify that PyTorch is installed correctly by running:
+
+```python
+import torch
+
+print(torch.__version__)
+print(torch.cuda.is_available())  # returns True if CUDA available and properly installed
+```
+
+## Getting Started
+
+The examples folder includes a sequence of examples using `icarus` : to generate the dataset and train an ml model from the suite available on the generated data.
+
+#### Moose Config File
+
+here are instructions for hoe to setup the moose config file.
+
+```python
+from pathlib import Path
+from mooseherder import MooseConfig
+
+
+def main() -> None:
+    """main: create moose config json
+    """
+    config = {'main_path': Path.home()/ 'moose',
+            'app_path': Path.home() / 'proteus',
+            'app_name': 'proteus-opt'}
+
+    moose_config = MooseConfig(config)
+
+    save_path = Path.cwd() / 'example-moose-config.json'
+    moose_config.save_config(save_path)
+
+
+if __name__ == "__main__":
+    main()
+```
+
+## Contributors
+
+- Arjav Poudel, UK Atomic Energy Authority, (arjavp-ukaea)
+- Baris Cavusoglu, UK Atomic Energy Authority, (barisc-ukaea)
+- Luke Humphrey, UK Atomic Energy Authority, (lukethehuman)

moose-config.json

@@ -0,0 +1,5 @@
+{
+    "main_path": "/path/to/moose",
+    "app_path": "/path/to/proteus",
+    "app_name": "proteus-opt"
+}

pyproject.toml

@@ -3,8 +3,8 @@ requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "icarus"
-version = "0.1.0"
+name = "icarus-fusion"
+version = "0.1.2"
 description = "A machine learning tool for fusion simulation validation."
 authors = [
   { name = "arjavp-ukaea", email = "[email protected]" },
@@ -21,11 +21,22 @@ classifiers = [
 requires-python = ">=3.11"
 dependencies = [
   "numpy>=1.26.0",
+  "netCDF4>=1.6.5",
+  "scikit-learn>=1.5.0",
+  "scikit-optimize>=0.10.2",
+  "mooseherder>=0.1.0",
+  "matplotlib>=3.8.0",
+  "tqdm>=4.66.4",
+  "scipy==1.11.3",
 ]
 
 [project.urls]
 "Repository" = "https://github.com/aurora-multiphysics/icarus"
 "Issue Tracker" = "https://github.com/aurora-multiphysics/icarus/issues"
 
 [tool.setuptools.packages.find]
-where = ["src"]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"icarus" = ["data/*.npz"]
+where = ["src"]

src/icarus/__init__.py

@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+"""
+icarus
+"""
+
+from icarus.sample_generator import CreateThermalDataset, SimulationParameters
+from icarus.dataloader import ThermalModelDataset
+from icarus.model import IcarusModel, NNParameters
+from icarus.datasets import load_2d_thermal_dataset, load_monoblock_thermal_dataset

src/icarus/create_moose_config.py

@@ -0,0 +1,19 @@
+from pathlib import Path
+from mooseherder import MooseConfig
+
+
+def main() -> None:
+    """main: create moose config json
+    """
+    config = {'main_path': Path.home()/ 'moose',
+            'app_path': Path.home() / 'proteus',
+            'app_name': 'proteus-opt'}
+
+    moose_config = MooseConfig(config)
+
+    save_path = Path.cwd() / 'moose-config.json'
+    moose_config.save_config(save_path)
+
+
+if __name__ == "__main__":
+    main()