feat(workflow-operator): volcano plot significance cut-offs - #9041

What changes were proposed in this PR?

The Volcano Plot draws a plain scatter of effect size vs -log10(p), colored by effect size, which is already the x axis. Nothing shows where the significance bar is or which points clear it. This PR adds three optional properties, all off by default, so saved workflows render as before.

Before:  px.scatter(color=<effect column>, color_continuous_scale="RdBu")
After:   same by default
         + fig.add_hline(...)                        when a significance threshold is set
         + fig.add_vline(+eff) / fig.add_vline(-eff) when an effect-size threshold is set
         + color="Significance", 3-color map         when the toggle is on and both thresholds are set

Categories use strict comparisons on the selected p-value column: Up = p < sig and effect > eff, Down = p < sig and effect < -eff, everything else Not significant. The category is written to a column named Significance (also the legend title); an input column of that name would be shadowed inside the operator only. Colors are ColorBrewer RdBu end points #B2182B / #2166AC plus grey #9E9E9E.

Validation: the JSON schema bounds above stop bad values in the property panel. For hand-edited JSON the operator also ignores a threshold it cannot draw (NaN, infinite, <= 0, or a p cut-off > 1) and falls back to the continuous coloring if the toggle is on but a threshold is missing. A cut-off of exactly 1 is allowed and draws its line at y = 0. If the cut-off's -log10 is beyond the data range the line may fall outside the auto-ranged axis; extending the range is left for a follow-up.

Since #8504 merged, the operator also exports a standalone script through generateStandaloneCode(). This PR adds the cut-off lines, the Significance column and the three-color map there too, from the same helpers where possible: the color map and category order are one shared literal, the threshold lines come from the same builder, and only the column names differ (Python literals instead of decoded strings). A spec checks that both paths make the same line and coloring decisions for eight threshold shapes, so the exported figure cannot drift from the engine's.

Independent of the label-fix (#9037) and hover-column (#9038) PRs; all three touch neighbouring lines of VolcanoPlotOpDesc.scala, so whichever lands second needs a small rebase.

Figures below are the operator's generated Python from main and from this branch, run on the 430-gene example workflow from the issue, with thresholds 0.05 and 1.

Before	After (lines only)	After (lines + Color by significance)

Any related issues, documentation, discussions?

Closes #9039

PR #8504 (merged) added the generateStandaloneCode() export path; the mirroring described above is the follow-up it needed.

How was this PR tested?

New tests in VolcanoPlotOpDescSpec, written before the source change:

• defaults: no lines, continuous coloring; each threshold alone emits only its own line(s); both with the toggle off keep the continuous coloring
• toggle on with both thresholds: strict comparisons, np.select column, exact color map and category order, no color_continuous_scale
• toggle on with one or no threshold: continuous fallback
• zero / negative thresholds and a p cut-off above 1 emit no line of their own; Infinity, -Infinity, NaN from JSON never reach the Python
• a cut-off of exactly 1 draws its line and still colors by category
• thresholds are emitted as valid Python floats, checked for 1e-300, Double.MIN_VALUE and 1e21 in every site they appear
• the generated JSON schema carries exclusiveMinimum / maximum on the two thresholds
• JSON deserialization: numbers, numeric strings, null, blank, absent, and the boolean toggle
• a workflow JSON saved before this change generates byte-for-byte the same code as a default-constructed operator
• generateStandaloneCode: defaults draw no line and keep the continuous coloring; thresholds with the toggle off draw the dashed lines only; the toggle on colors Up / Down / Not significant with the column names as literals; a cross-path test checks that the exported script makes the same cut-off and coloring decisions as the engine for eight threshold shapes (unset, one side only, zero, p cut-off above 1, non-finite, exactly 1); a saved workflow renders as a default-constructed operator

sbt -Dsbt.server.forcestart=true "WorkflowOperator/testOnly *VolcanoPlotOpDescSpec"
# Tests: succeeded 30, failed 0, canceled 0, ignored 0, pending 1   (the pending one is pre-existing)

sbt -Dsbt.server.forcestart=true "WorkflowOperator/scalafmtAll" "WorkflowOperator/Test/scalafmtAll"
sbt -Dsbt.server.forcestart=true "WorkflowOperator/scalafixAll --check"
# success

Smoke run outside Texera (pytexera stubbed, pandas + plotly 5.24.1) on the 430-gene mock table, 420 rows after the operator drops zero and missing p-values:

The exponent-form dumps pass python -m py_compile. The exported script for the default, lines-only and colored configurations parses with ast.parse.

Was this PR authored or co-authored using generative AI tooling?

Yes. Generated-by: Claude Code (claude-fable-5-1). Co-authored with Claude; the author reviewed the change before submission.