Commit Graph

17 Commits

Author SHA1 Message Date
68a3f3b982 [Feature] Alias Support (#151)
Fixes #149

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#151
2025-10-09 23:14:34 +13:00
afeb56622c [Chore] Linted Files (#150)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#150
2025-10-09 07:25:13 +13:00
22f0bbe10b [Feature] Eval package evaluation
`evaluate_model` in `PackageBasedModel` and `EnviFormer` now use evaluation packages if any are present instead of the random splits.

Co-authored-by: Liam Brydon <62733830+MyCreativityOutlet@users.noreply.github.com>
Reviewed-on: enviPath/enviPy#148
Co-authored-by: liambrydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: liambrydon <lbry121@aucklanduni.ac.nz>
2025-10-08 19:03:21 +13:00
d2f4fdc58a [Feature] Enviformer fine tuning and evaluation
## Changes
- I have finished the backend integration of EnviFormer (#19), this includes, dataset building, model finetuning, model evaluation and model prediction with the finetuned model.
- `PackageBasedModel` has been adjusted to be more abstract, this includes making the `_save_model` method and making `compute_averages` a static class function.
- I had to bump the python-version in `pyproject.toml` to >=3.12 from >=3.11 otherwise uv failed to install EnviFormer.
- The default EnviFormer loading during `settings.py` has been removed.

## Future Fix
I noticed you have a little bit of code in `PackageBasedModel` -> `evaluate_model` for using the `eval_packages` during evaluation instead of train/test splits on `data_packages`. It doesn't seem finished, I presume we want this for all models, so I will take care of that in a new branch/pullrequest after this request is merged.

Also, I haven't done anything for a POST request to finetune the model, I'm not sure if that is something we want now.

Co-authored-by: Liam Brydon <62733830+MyCreativityOutlet@users.noreply.github.com>
Reviewed-on: enviPath/enviPy#141
Reviewed-by: jebus <lorsbach@envipath.com>
Co-authored-by: liambrydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: liambrydon <lbry121@aucklanduni.ac.nz>
2025-10-07 21:14:10 +13:00
7ad4112343 [Feature] External Identifier/References
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#139
2025-10-02 00:40:00 +13:00
3f5bb76633 [Fix] Remove all Scenarios, catch empty SMILES, prevent default Package delete (#134)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#134
2025-09-30 19:10:57 +13:00
b757a07f91 [Misc] Performance improvements, SMIRKS Coverage, Minor Bugfixes (#132)
Bump Python Version to 3.12
Make use of "epauth" optional
Cache `srs` property of rules to speed up apply
Adjust view names for use of `reverse()`
Fix Views for Scenario Attachments
Added Simply Compare View/Template to identify differences between rdkit and ambit
Make migrations consistent with tests + compare
Fixes #76
Set default year for Scenario Modal
Fix html tags for package description
Added Tests for Pathway / Rule
Added remove stereo for apply

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#132
2025-09-26 19:33:03 +12:00
b5c759d74e [Feature] Register / Login / Logout View Testing (#126)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#126
2025-09-19 06:44:25 +12:00
50db2fb372 [Feature] MultiGen Eval (Backend) (#117)
Fixes #16

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#117
2025-09-18 18:40:45 +12:00
762a6b7baf [Feature] Package Export/Import (#116)
Fixes #90
Fixes #91
Fixes #115
Fixes #104

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#116
2025-09-16 02:41:10 +12:00
00d9188c0c Copy Objects between Packages (#59)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#59
2025-08-28 06:27:11 +12:00
b45c99f7d3 fixed calls to create MLRelativeReasoning during bootstrap.py and test_model.py 2025-08-22 11:28:01 +12:00
3308d47071 Fix bond breaking (#46)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#46
2025-08-15 09:06:07 +12:00
579cd519d0 Experimental App Domain (#43)
Backend App Domain done, Frontend missing

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#43
2025-08-08 20:52:21 +12:00
df896878f1 Basic System (#31)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#31
2025-07-23 06:47:07 +12:00
9323a9f7d7 Implement Compound CRUD (#22)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#22
2025-07-03 07:17:04 +12:00
ded50edaa2 Current Dev State 2025-06-23 20:13:54 +02:00