386098b8a6
[Feature] EnzymeLink Annotations ( #152 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#152
2025-10-15 19:35:26 +13:00
afeb56622c
[Chore] Linted Files ( #150 )
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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
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`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
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## 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
3f2b046bd6
[Feature] More on Legacy API ( #142 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#142
2025-10-03 00:07:30 +13:00
7ad4112343
[Feature] External Identifier/References
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#139
2025-10-02 00:40:00 +13:00
b757a07f91
[Misc] Performance improvements, SMIRKS Coverage, Minor Bugfixes ( #132 )
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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
50db2fb372
[Feature] MultiGen Eval (Backend) ( #117 )
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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 )
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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
7905a8c2c1
[Bug] Fixes for Group handling, Load all objects only if necessary ( #113 )
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Fixes #109
Fixes #110
Fixes #111
Fixes #112
Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#113
2025-09-11 18:19:27 +12:00
31783306e2
[Feature] Pathway SVG Export ( #102 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#102
2025-09-10 18:44:18 +12:00
3453a169e1
[Feature] Async Prediction Status Poll ( #93 )
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Fixed #81
Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#93
2025-09-09 20:39:26 +12:00
5477b5b3d4
[Feature] Rule Based Model ( #92 )
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Fixes #89
Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#92
2025-09-09 19:32:12 +12:00
4158bd36cb
[Feature] Legacy API Layer ( #80 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#80
2025-09-03 01:35:51 +12:00
2babe7f7e2
[Feature] Scenario Creation ( #78 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#78
2025-09-02 08:06:18 +12:00
00d9188c0c
Copy Objects between Packages ( #59 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#59
2025-08-28 06:27:11 +12:00
13816ecaf3
Make URL a Field instead a property ( #63 )
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This PR adds a new Field to all existing Models.
As its a data migrations the Migration is added.
Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#63
2025-08-27 06:46:09 +12:00
6e6b394289
Cleanup ( #52 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#52
2025-08-22 06:36:22 +12:00
ec387cc12e
Added UI elements to add/remove Scenarios to various objects ( #51 )
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Fixes #23
Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#51
2025-08-21 07:56:44 +12:00
a7637d046a
External References ( #50 )
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Fix for #24
Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#50
2025-08-21 06:11:05 +12:00
fc8192fb0d
Fix App Domain Bug when a Rule can be applied more than once ( #49 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#49
2025-08-19 22:10:18 +12:00
c3c1d4f5cf
App Domain Pathway Prediction ( #47 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#47
2025-08-19 02:53:56 +12:00
1267ca8ace
Enable App Domain Assessment on Model Page ( #45 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#45
2025-08-12 09:02:11 +12:00
ec52b8872d
Functional Group Calculation ( #44 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#44
2025-08-11 09:07:07 +12:00
579cd519d0
Experimental App Domain ( #43 )
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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
c9d6d8b024
Delete Stale Edges when removing a Node from a Pathway ( #41 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#41
2025-07-31 07:50:50 +12:00
79b4b1586c
Download Pathway Functionality ( #38 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#38
2025-07-31 01:30:16 +12:00
aec61151ce
Correct Label assignment ( #37 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#37
2025-07-31 00:43:28 +12:00
df896878f1
Basic System ( #31 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#31
2025-07-23 06:47:07 +12:00
49e02ed97d
feature/additional_information ( #30 )
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Fixes #12
Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#30
2025-07-19 08:10:40 +12:00
9323a9f7d7
Implement Compound CRUD ( #22 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#22
2025-07-03 07:17:04 +12:00
4e58a1fad7
Implement functionality to assigne Licenses to Packages and show existing Licenses ( #17 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#17
2025-07-03 06:28:49 +12:00
9950112311
Implemented Reaction Page ( #5 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#5
2025-06-28 06:40:58 +12:00
bcd9451450
Implement basic Group handling ( #3 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#3
2025-06-26 00:18:40 +12:00
844d0708c9
Granting/Updating Permission for Packages ( #2 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#2
2025-06-25 08:49:58 +12:00
7c3bc69b38
Scenario Import + Gitea PR Test ( #1 )
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Co-authored-by: Tim Lorsbach <tim@lorsba.ch >
Reviewed-on: enviPath/enviPy#1
2025-06-24 23:56:45 +12:00
ded50edaa2
Current Dev State
2025-06-23 20:13:54 +02:00
