FEAT: cooccurence network integration, github action docker image build and deployment

[Mariuuus]

FEAT: integrating co-occurrence networks

Summary

Adjusts dependencies and imports to allow for an integration of the (previously) separated co-occurrence network analysis.

Changes

• Added .gitignore
• Downgraded numpy and pandas due to the compatibility with grakel
• Added missing dependency for openpyxl
• Added Dockerfile (uv-based) and adjust workflow (build and deploy image)

How to Test

1. Check out this branch
2. Run uv run westerfeld/cooccurence.py (make sure you provided the input files)

Results are located at out

Docker

1. Check out this branch
2. (Manual build) docker build -t westerfeld-analyses -f docker/Dockerfile .
3. Run docker container (mounting data & output folder):

   sudo docker run \
         -v ../data:/app/input \
         -v .out:/app/out \
         westerfeld-analyses  westerfeld/cooccurence.py
   

Notes

The downgrade of numpy and pandas due to the compatibility with grakel may come with some downsides.
Currently there is no (official) newer grakel version that supports modern numpy and the PR targeting this issue is on open for 8 months.

[laschuet]

LGTM. I'll add a few changes myself later on. Thank you very much for this PR!