Add CLI to run WSIMOD #38
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AdrianDAlessandro
requested changes
Nov 17, 2023
| run: python -m pip install -r requirements-dev.txt | ||
| run: | | ||
| python -m pip install -r requirements-dev.txt | ||
| python -m pip install . |
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You are not currently installing the pinned versions of the main packages here because they are not specified in the requirements-dev.txt. You can see that pandas etc is being installed at the python -m pip install . step in the CI https://github.com/ImperialCollegeLondon/wsi/actions/runs/6875139142/job/18698156546
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Just to check, are you intentionally not updating the |
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No, that's just me being dumb... updated now. |
AdrianDAlessandro
approved these changes
Nov 21, 2023
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Adds a CLI for using WSIMOD directly from the terminal.
The main work here has been coming up with an input file structure and processing that can provide enough flexibility to create the appropriate inputs for WSIMOD in a sort of declarative way without becoming too complicated. The chosen format has been YAML, as TOML was looking really odd. The data processing let us run the quickstart demo directly from an input file. An example settings file has been provided.
The most difficult part has been the data processing. Some manipulation has been included which, hopefully, covers many use cases, but ultimately is up to the user to provide input files simple and clean enough such that can be used directly by WSIMOD without too much processing. It is simply not possible to provide custom pre-processing scripts.
TODO