#1387 Correctly branching from beta

[jiacelyne]

Pull Request Checklist

• GitHub Actions C.I. build passes
• All five Demos look as expected when loaded
• Reload works as expected
• Load an Excel file (GRN and PPI)
• Load a SIF file (GRN and PPI)
• Load a GraphML file (GRN)
• Loading file with Error brings up error modal, and it looks as expected
• Loading file with Warning brings up warnings modal
• Loading a network from the database looks as expected when loaded (GRN and PPI)
• Network can be exported to SIF (GRN and PPI) and GraphML (GRN-only)
• Network, Expression data, and Additional Sheets can be exported to Excel
• Image can be exported to PNG, SVG and PDF
• Print works as expected
• Restrict graph to viewport works as expected (check/uncheck)
• Viewport Size Changing works as expected (small/medium/large/fit)
• Toggle between Grid Layout and Force Graph Layout works as expected
• Force Graph Parameter Sliders change the number above them and have an effect on the graph
• Locking/Unlocking/Resetting/Undo Resetting the force graph parameters works as expected
• Enabling and disabling node coloring works as expected
• Node coloring options work as expected (selection top/bottom dataset, averaging values, changing max value)
• Weighted graph loaded with the "Enable Edge Coloring" option checked appears as expected
• Hide/Show Weights works as expected (always/never/upon mouseover)
• Edge Weight Normalization Factor can be changed (set/reset)
• Gray Edge Threshold can be changed, slider changes the number and has an effect on the graph
• Checking Show Gray Edges as Dashed works as expected (check/uncheck)
• D-pad left/right/top/bottom/center works as expected
• Zoom slider changes number and has effect on graph (viewport and menu)
• Right click on a node opens gene page, page is populated with correct data (currently broken, though)

[dondi]

OK, things are definitely cleaner here but there appears to be one last loose end (database/schema/README.md). See if you can produce one last instance of this branch that is 100% just your intended change for #1387

[dondi]

The provenance of the branch looks good now, but it looks like your first commit (0793d5e) piggy-backed this file unintentionally. We can talk about how that might have happened this time and what can be done to avoid it, but in terms of finalizing this PR, can you redo the branch one more time and make sure that your committed changes have just your intended changes exclusively. The redo will also help you determine how/why this file found its way to your commit

[dondi]

For now, we can keep this code as-is. But for future reference—and we’ll see if there’s time to discuss this at the meeting—what the code is doing here represents a higher-level programming pattern of imperative code whose sole result is the value of a single variable (source). When you have code that does this, there is an alternative approach that does not rely on side effects (and again if you’re unfamiliar with the term, we can discuss that)

In broader practice, this latter alternative (which will also be good for Alex to know) is generally considered safer and more robust, so even though what you have here is functionally equivalent, in terms of programming craft, the alternative is recommended. We can discuss this at some future juncture; it doesn’t need to block this PR

[dondi]

OK, so I see now what happened, which is that you did a cherry-pick of commit 7a235b8—and yes, this was the instruction from last time ✅

But also stepping back, note the context of the instruction: the purpose was to produce a clean jia-1387 branch that exclusively includes just your work. So in a broader sense, upon following the instruction, spotted the oversight, and either addressed it beforehand or asked a question on how to resolve it. On the one hand, I could have looked at my directive more closely to be more precise about what to do…and yep, sorry, I own that miss 😕

On the other hand, you also have agency here and can continue to hold your own counsel as you follow steps. This summer work is a great opportunity for you to advance in that regard

[dondi]

This has been superseded by #1609, so closing this one directly