OpenFreeEnergy / OpenFreeEnergy/ExampleNotebooks

Make cookbook materials fetchables

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Dominant language
Jupyter Notebook
Stars
70
Forks
15
Avg merge
10h 42m
Merged PRs (30d)
2

Description

Follow-up on #84: There should be a single source of truth for cookbook input files (SDFs, PDBs, etc.) instead of having a copy in, e.g., the OpenFE test suite, with a duplicate stored here.

We could then make the first line of each notebook be ! openfe fetch cookbook-files — this could be either a fetchable per-notebook or a single fetchable to download all cookbook notebooks.

This would have the advantage that even a download of a single notebook would be self-contained, instead of requiring users to download a tarball/clone of the repo.

Steps to make this happen:

  1. Create the fetchables in the OpenFE CLI. See fetchables.py for examples
  2. Cut a release of OpenFE, update ExampleNotebooks to use that OpenFE version.
  3. Update the cookbook notebooks here to download the required files.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with openfecli/fetchables.py for existing fetchable patterns, then inspect the cookbook notebooks and the duplicate input files mentioned in the issue. Coordinate the OpenFE release and version update in ExampleNotebooks before changing notebook setup lines. Done means the required cookbook inputs download through OpenFE and a single notebook works without a repository clone or tarball.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook
Domain
cli, documentation
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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