Update installation instructions and make the README more markdowny - #17
Update installation instructions and make the README more markdowny#17habi wants to merge 8 commits into
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I had to `touch vesselfm/__init__.py`, too to make it work. The init file is added in commit 93c9df5
Already mentioned in bwittmann#15
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The more markdowny README is added as bonus. |
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Pull request overview
This PR aims to resolve Linux installation/import issues (Issue #16) by updating the README installation/run instructions and by adding a package initializer so vesselfm can be installed/imported as a Python package.
Changes:
- Reworked
README.mdto use standard Markdown formatting and clearer installation steps (clone +pip install -e .) and inference invocation. - Added
vesselfm/__init__.pyto makevesselfma package for setuptools discovery.
Reviewed changes
Copilot reviewed 1 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
vesselfm/__init__.py |
Marks vesselfm as a package to support installation/import. |
README.md |
Improves Markdown formatting and updates installation + inference run instructions to address Issue #16. |
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| Additional information on inference, pre-training, and fine-tuning are available [here](./vesselfm/seg). Checkpoints will be downloaded automatically and are also available on [Hugging Face 🤗](https://huggingface.co/bwittmann/vesselFM). | ||
| ```bash | ||
| python vesselfm/seg/inference.py |
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The README suggests running python vesselfm/seg/inference.py, but the package layout currently won’t install/import vesselfm.seg... with setup.py using find_packages() because vesselfm/seg/ (and vesselfm/seg/utils/) have no __init__.py. After adding vesselfm/__init__.py this becomes a hard import error (No module named 'vesselfm.seg'). Consider (a) adding __init__.py files to the subpackages (seg, seg/utils, etc.) or switching to find_namespace_packages, and (b) documenting python -m vesselfm.seg.inference as the invocation to avoid sys.path issues when running from source.
| python vesselfm/seg/inference.py | |
| python -m vesselfm.seg.inference |
With the updated installation instructions and the added init.py file I was able to install vesselFM on my system.
Fixes #16