refine packaging process

[geoHeil]

achievements:

• should simplify windows support (How to get it to work on windows? #17)
• should upgrade pytorch and paddle to recent versions (upgrade pytorch #14)
• should simplify the development of cpu/gpu environments

missing items

• port over all the metadata from the old setup.py file

up for discussion

• should code linters like ruff which I use internally be added as well?

usage

# download model files
pxi run setup

pixi shell -e molgrapher-cpu
# if you want gpu support
# pixi shell -e molgrapher-gpu

./molgrapher/scripts/annotate/run.sh

./molgrapher/scripts/annotate/docling/docling_convert_and_enrich.sh ./data/pdfs/US9259003_page_4.pdf ./data/docling_documents/US9259003_page_4/

advantages

• neat lockfiles - reproducibility
• easy packaging no fiddling with dependencies
• upgraded versions of pytorch/paddlepaddle

[geoHeil]

TODO add missing metadata from setup.py (if there is interest in getting this merged)