Merge 'algae' branch into 'main' branch

GaYeongKim commented 8 months ago

pm2_batch: calibration of pm2 model with batch experiment data
pm2_ecorecover: calibration and validation of pm2 model with continuous online monitoring data obtained from EcoRecover plant

GaYeongKim commented 8 months ago

@yalinli2 @joyxyz1994 The errors seem to occur due to 'optuna', a new optimizer package I used..... Should we include 'optuna' package into Exposan?

yalinli2 commented 8 months ago

Thanks @GaYeongKim ! Let me think of/take a look at this in the next couple of days (or during Thanksgiving if I can't get to it over the weekend...), I've been thinking of cutting down dependencies that are not core to QSDsan so that the environment is easier to build on the cloud, maybe I should get back to have separate config files for installation and testing

yalinli2 commented 8 months ago

Oh and does this need to use the algae branch of QSDsan?

GaYeongKim commented 8 months ago

Not necessarily? There are no changes in 'algae' branch. It is rather 87 commits behind 'main' branch. I was afraid that modeling would fail due to the new qsdsan updates, so I left the 'algae' branch. I will merge it too sooner or later after checking everything is okay!

yalinli2 commented 8 months ago

Ohhh I see, sounds good and thanks!

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Not necessarily? There are no changes in 'algae' branch. It is rather 87 commits behind 'main' branch. I was afraid that modeling would fail due to the new qsdsan updates, so I left the 'algae' branch. I will merge it too sooner or later after checking everything is okay!

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yalinli2 commented 8 months ago

@GaYeongKim , thanks so much for the contribution (and having the README)! I made the following changes:

Updated algae with main (otherwise tests in other modules won't pass), none of those changes should affect PM2 modules since the modules are compartmentalized.
Added codes (based on the ones in READMEs) for testing, they will make sure the systems can be loaded and simulated, but won't check for results. You can add the number checks if you want.
Updated README to include a note on optuna, I didn't include it in the dependency at the current stage, maybe one day when we include an optimization module in QSDsan we should/will optuna as a dependency.
Since all the remote tests are run using the main branch of QSDsan and they passed, you can get the algae branch updated, but I'm not sure if this will affect any of your numbers. However not updating for a really long time could also be a problem... As sometimes there are bug fixes that should be merged in (Jianan had a bad experience...)

Anyway, I'm good with merging in this PR if you think it's OK!

GaYeongKim commented 8 months ago

@yalinli2 I have checked a few key simulations with QSDsan main branch, and it seems to be working! I guess this is ready to merge! (I'm not authorized to merge, plz merge this!)

QSD-Group / EXPOsan

Merge 'algae' branch into 'main' branch #43