Fix Clustergram reordering of row and column indices.

[mkcor]

Closes #432.

About

This is a hot fix for the Clustergram component, which used to shuffle rows and/or columns (depending on whether clustering would be along rows, columns, or both) after they were reordered (as expected) from clustering (based on scipy's hierarchy submodule).

All the action is taking place at commit 611a1b3 (the rest is minor).

I included a unit test (bda8f08) using the example from the bug report (#432).

Description of changes

Before merging

• I have gone through the code review checklist
• I have completed all of the steps to take before merging
• I know how to deploy to DDS

[mkcor]

I wonder why test_dbsv004_coverage_clicked is failing for Python 3.7... 🤔

[shammamah-zz]

💃 Once we figure out what is causing that test to fail. Have you done a fresh npm ci/npm run build/pip install -e .?

[mkcor]

dancer Once we figure out what is causing that test to fail. Have you done a fresh npm ci/npm run build/pip install -e .?

@shammamah must have been that, thanks ;)

[shammamah-zz]

@mkcor Please add a CHANGELOG entry and bump the version! I can publish to npm and PyPI.

[mkcor]

Aww what's wrong with file dash_bio/async~moleculeviewer3.js? :(

[shammamah-zz]

You might have to do a full clean (rm -rf node_modules) and npm ci. :/

[mkcor]

When I clean up first, I get the same postbuild error ("postbuild": "es-check es5 dash_bio/*.js") upon running npm run build (after rm -rf node_modules and npm ci)...

[mkcor]

I'll try upating eslint.

[mkcor]

Oh dear, I went through https://flaviocopes.com/update-npm-dependencies/ but still getting this eslint postbuild error.

[shammamah-zz]

@mkcor Looking into it now!

[shammamah-zz]

@mkcor We don't want to update our npm packages here (that's why I suggested npm ci). Would you mind reverting those updates?

[mkcor]

Duh, I've been trying to run es-check es5 dash_bio/*.js while reading that I should upgrade es5 to es6! Pff, I shouldn't work when feeling sickish. Expect a new commit soon!

[mkcor]

@mkcor We don't want to update our npm packages here (that's why I suggested npm ci). Would you mind reverting those updates?

Sure. We need to update eslint though (see AtomLinter/linter-eslint#592 and apparently that's the spirit of our .eslintrc file). Is it okay if I revert all the package updates except for that of eslint?

Broader question: Why don't we want to update packages? Originally we set up #377 for this purpose.

[shammamah-zz]

Sure. We need to update eslint though (see AtomLinter/linter-eslint#592 and apparently that's the spirit of our .eslintrc file). Is it okay if I revert all the package updates except for that of eslint?

That sounds fine.

Broader question: Why don't we want to update packages? Originally we set up #377 for this purpose.

We don't want to update npm packages (that don't need to be updated) in this PR, since it only modifies one of the Python components.

[shammamah-zz]

Also, doing a clean install/build from master doesn't give the same error, so since you've only modified the Python parts, there logically shouldn't be any build issues here at all. Nothing has changed on the JS side.

This commit looks like it was the culprit: d2faa89

It seems to have changed the versions of a bunch of packages. Please check out the versions of package.json and package-lock.json that are on master, then rm -rf node_modules/npm ci/npm install.

[mkcor]

Also, doing a clean install/build from master doesn't give the same error, so since you've only modified the Python parts, there logically shouldn't be any build issues here at all. Nothing has changed on the JS side.

Right, my install/build at d2faa89 must have been messy.

This commit looks like it was the culprit: d2faa89

Thanks for looking into it! I have rebased to remove this commit and all subsequent commits. Then:

• rm -rf node_modules/
• edited package.json to bump Dash Bio's version to 0.4.6
• npm ci
• npm install
• committed (b09ff8f)

I updated the date to today's date in the changelog. Then:

• npm run build
• committed (e43023f)

Please review the visual change (Percy), thanks!

[shammamah-zz]

Thanks for taking care of this! 💃