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
## Summary
This PR improves the local development setup experience by adding Docker Compose and Makefile for streamlined setup.
## Changes
- **Added `docker-compose.yml`**: for one-command PostgreSQL database setup
- **Added `Makefile`**: Convenient shortcuts for common dev tasks (\`make setup\`, \`make dev\`, etc.)
- **Updated `README.md`**: Quick development setup instructions using Make
-
- **Added**: RDkit installation pain point documentation
- **Fixed**: Made Java feature properly dependent
## Why these changes?
The application uses PostgreSQL-specific features (\`ArrayField\`) and requires an anonymous user created by the bootstrap command. This PR makes the setup process trivial for new developers:
```bash
cp .env.local.example .env
make setup # Starts DB, runs migrations, bootstraps data
make dev # Starts development server
```
Java fix:
Moved global Java import to inline to avoid everyone having to configure the Java path.
Numerous changes to view and settings.
- Applied ruff-formatting
## Testing
Verified complete setup from scratch works with:
- PostgreSQL running in Docker
- All migrations applied
- Bootstrap data loaded successfully
- Anonymous user created
- The development server starts correctly.
Co-authored-by: Tobias O <tobias.olenyi@tum.de>
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-authored-by: Liam <62733830+limmooo@users.noreply.github.com>
Reviewed-on: enviPath/enviPy#143
Reviewed-by: jebus <lorsbach@envipath.com>
Reviewed-by: liambrydon <lbry121@aucklanduni.ac.nz>
Co-authored-by: t03i <mail+envipath@t03i.net>
Co-committed-by: t03i <mail+envipath@t03i.net>
