jebus/enviPy-bayer
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d8741c537525106aae18023af14542c5378cdc01
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Tim Lorsbach d8741c5375 wip
CI / test (pull_request) Failing after 29s
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API CI / api-tests (pull_request) Failing after 42s
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2026-09-02 21:34:26 +02:00
Tim Lorsbach 887de03a19 reactionSmarts 2026-09-02 21:30:53 +02:00
Tim Lorsbach b54c8eaab6 minor
CI / test (pull_request) Failing after 28s
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API CI / api-tests (pull_request) Failing after 44s
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2026-08-28 13:14:43 +02:00
Tim Lorsbach f885745127 Fix import
CI / test (pull_request) Failing after 27s
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API CI / api-tests (pull_request) Failing after 41s
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2026-08-27 11:46:08 +02:00
Tim Lorsbach 48d2bce52a minor 2026-08-20 09:28:23 +02:00
Tim Lorsbach 67aa3731cb PES Adjustments, Check is User is in enviPath Entra Group
CI / test (pull_request) Failing after 28s
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API CI / api-tests (pull_request) Failing after 42s
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2026-08-20 08:59:24 +02:00
Tim Lorsbach 0033513d99 adjusted migration
CI / test (pull_request) Failing after 27s
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API CI / api-tests (pull_request) Failing after 40s
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Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

Make PES Link clickable

Return proper http response instead of error

Fixed error return, removed unused options

Fix PES Link HTML for other entities

Fixed molfile assignment, adjusted Export

Package Export/Import cycle

highlight Description links

implemented non persistent

Harmonised proposed field in Json output

Added pesLink field to PW Api output

PES Fields in API Output

removed debug

Fix Classification import, Fix PES Deserialization

underline pes link in templates

Fix alter name/desc for node, make /node /edge funcitonal

provide setting link and copy button

Implemented Compound Names / Reaction Names View Option

Unconnected Nodes

Make links thicker, reduce timeout trigger time

Show proposed info in popover

Pathway Build no stereo removal

Include probs in reaction name option viz

Detect clicks outside nodes/edges

Provide proper Error Pages

View Package Perm

wip

sync

Auth log

auth log leftovers

...

secret packs viz

auth log for api

model stats

Fix Package Adjustment

Adjust Group Auth Log

Fix Secret image size in Navbar

leftover

...

minor
 2026-08-19 21:05:40 +02:00
jebusandTim Lorsbach fedd1b5280 [Feature] Management Command to Compute and Store Reaction <-> Rule Associations (#453) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#453
 2026-08-14 20:45:12 +12:00
jebusandTim Lorsbach 2d3dca6a75 [Fix] Adjust Rules according to manual QA, Add missing Rule (#452) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#452
 2026-08-13 17:37:38 +12:00
jebusandTim Lorsbach ada270aa3c [Fix] Canonicalize SMILES when checking overlaps in smiles_covered_by (#443) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#443
 2026-08-12 21:01:41 +12:00
jebusandTim Lorsbach 093daa5ecf [Fix] 'Object of type ConfidenceLevel is not JSON serializable' in Pathway.d3_json (#450) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#450
 2026-08-07 19:58:36 +12:00
jebusandTim Lorsbach f4f284925a [Fix] Entrypoint Location (#446) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#446
 2026-08-05 09:15:09 +12:00
jebusandTim Lorsbach ca6e926b30 [Fix] Fix Image Tags (#445) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#445
 2026-08-05 08:55:35 +12:00
jebusandTim Lorsbach 2504d7045b [Chore] Build Docker Images on pushes to develop, main (#444) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#444
 2026-08-05 08:36:24 +12:00
jebusandTim Lorsbach 032ebc30a2 [Fix] Return a File instead of raw text for new export endpoint (#442) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#442
 2026-07-31 08:24:14 +12:00
jebusandTim Lorsbach 703f377b7f [Fix] Export IUCLID Properties, Show Model Params and Statistics, Adjust Batch Prediction Settings (#434) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#434
 2026-07-30 08:30:18 +12:00
jebusandTim Lorsbach 7639b23e4e [Feature] Package Pathway Export to CSV (#439) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#439
 2026-07-30 08:03:01 +12:00
jebusandTim Lorsbach 7632b3a029 [Fix] All thresholds, Increase Batch Predict Limit, Make "Back" Button on error page trigger a new pageload. (#432) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#432
 2026-07-24 09:29:05 +12:00
jebusandTim Lorsbach d657c0285a [Fix] Catch invalid reactions smiles on reaction creation (#431) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#431
 2026-07-23 07:45:36 +12:00
jebusandTim Lorsbach f4c198981b [Feature] SPathway to_json outputs Bayes Probabilities (#430) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#430
 2026-07-23 07:20:26 +12:00
t03i cdd51fc7aa [Fix] Iuclid export produce only one root substance (#429) 
Reviewed-on: enviPath/enviPy#429
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
 2026-07-23 06:37:02 +12:00
jebusandTim Lorsbach ac8df05913 [Feature] Attach AdditionalInformation to Nodes (#428) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#428
 2026-07-20 09:32:28 +12:00
jebusandTim Lorsbach 31c57299e4 [Feature] Ketcher V3 (#427) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#427
 2026-07-17 08:16:09 +12:00
jebusandTim Lorsbach 3566571b42 [Chore] Leftovers (#426) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#426
 2026-07-16 21:33:12 +12:00
jebusandTim Lorsbach 72a63b4876 [Feature] Sync Features from Client Repo (#425) 
- New PackageImporter
- Fix persisting Molfile on Structure creation
- Add NonPersistent Prediction
- Pathway View Options
- Edit Node Fix

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#425
 2026-07-16 07:50:46 +12:00
jebusandTim Lorsbach 2c2437e3f5 [Feature] Generate Compounds by Molfile (#423) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#423
 2026-07-15 23:56:24 +12:00
jebusandTim Lorsbach 9bc9f86ff1 [Fix] Pathway SVG Export has Edges again, Fix In/Out Edge coloring (#422) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#422
 2026-07-03 07:24:02 +12:00
jebusandTim Lorsbach dba6514013 [Chore] Package Export, Blanks for fields, Styling (#421) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#421
 2026-07-02 20:12:26 +12:00
jebusandTim Lorsbach a092d4a558 [Chore] Updated Dockerfile (#418) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#418
 2026-06-17 08:33:02 +12:00
jebusandTim Lorsbach 2502c020f7 [Fix] Collection of minor Bugfixes (#417) 
User feedback from on-prem installation

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#417
 2026-06-17 07:56:32 +12:00
jebusandTim Lorsbach 6ab9180291 [Feature] Vizualize Reaction Circles (#410) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#410
 2026-06-11 02:07:49 +12:00
jebusandTim Lorsbach 3657d14659 [Fix] Cascade deletion of Reactions to Edges (#409) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#409
 2026-06-11 00:24:06 +12:00
jebusandTim Lorsbach ef6091d416 [Fix] Set depth to -1 when adding a Node via Pathway.add_node to be in sync with legacy_api (#408) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#408
 2026-06-09 23:55:16 +12:00
jebusandTim Lorsbach 14cfc1e4d7 [Feature] Integrate DOI Links, Handle Cycles in Pathway Viz (#407) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#407
 2026-06-03 06:00:38 +12:00
jebusandTim Lorsbach 868bbf5c05 [Fix] False as multi_step default in legacy API (#406) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#406
 2026-05-29 08:12:52 +12:00
jebusandTim Lorsbach be5ee1d1d7 [Fix] Propagate multi_step in Edge.create to Reaction.create to ensure deduplication is working (#405) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#405
 2026-05-29 07:39:32 +12:00
jebusandTim Lorsbach 20fd949dfd [Fix] Implement legacy PFASConfidence object construction (#404) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#404
 2026-05-28 23:57:34 +12:00
jebusandTim Lorsbach c9b643fe6e [Feature] Make JobLog Page Paginated (#403) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#403
 2026-05-28 23:01:27 +12:00
jebusandTim Lorsbach 1a9f1cf9af [Fix] Legacy API Node Depth Parsing, description validation in Reaction.create (#402) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#402
 2026-05-28 09:53:39 +12:00
jebusandTim Lorsbach c7c7e17e43 [Feature] Implement legacy endpoints to enable copy via python client (#400) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#400
 2026-05-28 01:41:28 +12:00
jebusandTim Lorsbach 674e10c7fa [Fix] Legacy API Package Endpoint, Pepper Unit in Pathway View (#399) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#399
 2026-05-27 21:09:17 +12:00
jebusandTim Lorsbach 8079b80d57 [Fix] Fix Typo in multi_step assignment (#397) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#397
 2026-05-21 09:56:21 +12:00
jebusandTim Lorsbach 76e63fda2c [Fix] Fix BART Upload (#396) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#396
 2026-05-21 03:16:02 +12:00
jebusandTim Lorsbach 1e43c298d2 [Fix] Simplify Depth adjustment (#386) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#386
 2026-05-12 21:04:56 +12:00
jebusandTim Lorsbach b39fc7eaf8 [Fix] Update Node depth when adding new Edges to a Pathway (#384) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#384
 2026-05-12 09:40:35 +12:00
jebusandTim Lorsbach a2fc9f72cb [Feature] Make use of HalfLifeModel Enum (#383) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#383
 2026-05-12 09:23:56 +12:00
t03i 734b02767e [Fix] Update plotting imports and thread handling in Pepper class (#382) 
- plt.subplot does not work reliably with async/ threads.
- Bug in thread run that would fail with env set (string to number)

Reviewed-on: enviPath/enviPy#382
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
 2026-05-12 06:43:26 +12:00
jebusandTim Lorsbach 9d70db2ca2 [Fix] Wrong indentation in welcome mail (#373) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#373
 2026-04-22 08:47:05 +12:00
jebusandTim Lorsbach fec26d0233 [Feature] Admin Actions for Activation and Affiliation Request (#372) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#372
 2026-04-22 08:36:31 +12:00
jebusandTim Lorsbach 689f7998eb [Dep] Updated enviFormer, additional information lib, aiohttp, fsspec (#371) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#371
 2026-04-22 06:38:31 +12:00