todo (before merging webmap code into main ?)

[turbomam]

@cmungall

• [x] remove all research-project specific files
• [ ] remove mentions of research-project specific files from READMEs
• [ ] move research-project specific files to their own repos
  • they're currently in a local, .gitignored folder on @turbomam 's laptop
• [ ] create tabular output in SSSOM format
  • [ ] confidence = 1 - cosine distance between query and matched term?

Makefile:

include a simpler example within this repo e.g

• [ ] mixs
• [x] a fake simple example

mapping code in general

• [ ] minor: some of this belongs in git commit messages
• [x] in general no need to retain commented out code, git takes care of history
• [ ] in general most docs should go in docstrings so they are visible at IDE/RTD level
• [ ] we may want to think about a yaml config file in the future
  • (the config file would be described using linkml)
• [ ] consider using rtd to document this repo

@wdduncan

You may want to consider

• [ ] creating a pypi package for this
• [ ] attaching command-line utils to the package. I have examples of this in nmdc-schema.

[turbomam]

@wdduncan can you elaborate on what a CLI utility for the webmapping would look like? I am already using a click CLI.

[wdduncan]

In the setup.py on nmdc-schema you will see the validate-nmdc-json and nmdc-version entry points.

This allows to run the associated python files from any directory just like other command line tools. E.g., after installing nmdc-schema (i.e., pip install nmdc-schema) you can find out the version of the schema by executing nmdc-version.

To accomplish the same thing with a .py file you need to 1) clone the repo and 2) modify your path to include the .py file.

[sierra-moxon]

I am going to close for now; I think a lot of this functionality is in place. Please reopen if needed.