dgahle / baysar Goto Github PK

Implementation of ionisation balance with a tau is currently a scalar for SCD not the factor - (1 / ne*tau). The latter needs to be added for consistency.

This contains useful supplementary functions and scripts but should not be in baysar repo.

Below is a GitHub Action to deploy PyPI releases from GitHub releases

Useful links:

• https://github.com/C-bowman/inference-tools/blob/master/.github/workflows/python_publish.yml
• https://github.com/C-bowman/inference-tools/blob/master/inference/__init__.py
• https://github.com/C-bowman/inference-tools/blob/master/pyproject.toml

Demo in very depricated and needs to be refactored

Scripts to fix:

• demo/balmer_series.py
• #20

Where to store unittest data that is open and easily accessible? Probably not in the repo.

Source: https://github.com/dgahle/mast-upgrade-baysar-analysis/tree/paper/backend/OpenADAS

Changes:

• Make main the default branch
• Merge in branches that are stale/completed tasks
• Tag/release thesis branch

API calls to the Open ADAS website should be cached to minimise URL requests. Ionisation balance output should be cached when they are evaluating the entire adf11 grids.

Template: https://github.com/dgahle/PythonRepositoryTemplate

Git hooks for automating code standardisation.

Useful link: https://rohitgupta.xyz/blog/keeping-python-code-clean-with-pre-commit-hooks-black-flake8-and-isort/

Update BaySAR to be compatible with inference.mcmc.HamiltonianChain to resolve the effective sample size in demo/balmer_series.py` flatlining at about 7.

Useful links:

• SymPy - https://python.plainenglish.io/how-is-symbolic-differentiation-done-in-python-using-sympy-6484554f25b0
• My maths notes - https://www.overleaf.com/project/64fc839f4d91b9553e1f581b

Task list

• Write out the mathematics
• Plan out the objects that require a gradient class method
• Update this list with the above and cross out as going along
• Add unit tests to verify functionality
• Update demo/balmer_series.py with the HamiltonianChain

Make saving the logger to file optional through a variable in config.json and get that to be read in logger.py and all other get_logger calls to use the default value set by the config to avoid conflict.

Move OpenADAS functionality to its own repo OpenADAS repo and integrate that into BaySAR.

(This probably needs moving into it's own milestone and making checklist a group of issues)

Todo list:

• Report OpenADAS and gcr modules into a single one
• Format OpenADAS with a doc README.md
• Get support for moving OpenADAS into it's own repo and add to PyPI
• Move OpenADAS to it's own repo
• Add OpenADAS to PyPI
• Update baysar dependencies to run in a pip install of OpenADAS

element should be passed to load_adf11 rather than having to manually run get_adf11