chromosomix 0.4.0

What changed in chromosomix 0.4.0, released on 4 August 2026.

Added

• Three named panels — General, Annotations, Aesthetics — all foldable and all resizable. They had grown into three unrelated things: a sidebar with a fold button, a column added beside it with a fold button copied from it, and a controls column with no button and no name at all. They are the same object, so they are now one; what differs is a name, a side and a default width. Drag a panel’s inner edge to resize it, double-click the edge to reset it, and both the width and the fold are remembered. b, a and m fold them. A card too wide for the column it is in scrolls inside it rather than spilling out of it.

• The tracks pan and zoom the map. A lane is a picture of the same window the map shows, drawn through the same scales, so dragging one and dragging the map are the same gesture on the same data — and a track you could read but not move was an exception a reader had to discover. Dragging a bottom lane scrolls the columns, dragging a right lane scrolls the rows, and a wheel over either zooms exactly as a wheel over the map does. The lanes carry the map’s arrowhead cursor for the same reason.

• An annotations panel of its own, between the file sidebar and the map. The three annotation cards used to live in the file sidebar, folded in under the record card, and shared its scroll box: a growing list of tracks bought its height by pushing the file’s own identity off the top of the screen, and folding the sidebar to get the room back took the annotations with it. They are now a column with its own fold (a layers button beside the sidebar’s, or a) and its own scroll. The two left columns are ordered outward from the map by how often they are touched.

• The colour and the name are edited where they are shown. Clicking the swatch in a row opens the colour picker; clicking the name edits it in place. Both were fields behind the settings disclosure, which made the two commonest changes to an annotation among the most expensive. They are no longer offered in the settings, because they are no longer hidden.

• Rows can be reordered, by dragging the grip or by focusing it and pressing the arrow keys. The order is the order the lanes are stacked in beside the map, so this replaces removing three tracks and dropping them again in the order you wanted.

• One hairline, and every value at once, when you point at a track. Hovering a lane draws a single line — not a crosshair — across the lane stack and the map, at the position under the pointer, and the tooltip reads out every value track on that edge at that position rather than only the lane being pointed at. The lane the pointer is in is marked. A gene or peak under the pointer is described underneath.

• Placing marks by clicking the map is a mode, not a single shot. “Pick on map” stays on and becomes Done; every click places a mark until Done or Esc. Marking up a figure is eight gestures, not one, and the trip back to the sidebar between each was the whole cost of the feature.

• Autoscale groups are a picker. A group is only a group once two tracks are in it, so the second track has to be given the same name as the first — and the free-text box gave no way to find out what that was. A misremembered name raised nothing; it quietly made a group of one. The list is now the memory, and new group… is where a name is coined.

Changed

• The centre column stays light in the dark theme. A contact map is a figure: its colormaps are built for ink on white, its labels and frame are drawn in the greys ops/show.py uses, and what leaves as a PNG or a PDF is light whatever the screen was. Letting the theme through meant the picture on screen was not the picture exported — and the halo behind every label, which is the page background, turned black behind dark grey text on a white plot. Everything around it — header, panels, status bar — is dark as before.

• The lane tooltip names the position, not the lane. The lane is the one the pointer is on, which the pointer already says and the marked row repeats; the heading is now the coordinate alone. Values read name: number.

• The auto limit is a button, bordered while it is on, rather than a tick box — and typing either bound turns it off, which is the only thing typing a bound can mean. The tick box was a third control on a row that already held two number boxes, and it took the width that made them overflow their card.

• The annotation cards have lost their subtitles. Each drop area under the heading already says what it takes and how it is drawn.

• A new annotation is drawn on the right edge, not the bottom. The bottom already carries the coordinate axis, the block labels and the colourbar caption, and a stack of tracks there pushes the map up the page; the space beside it is empty in every view. Both tick boxes still work as before.

• Lane height is typed in pixels, with the drawing style beside it, in place of a slider. A slider is for a quantity with no natural unit, and this one has the most natural unit there is.

• Track limits are trimmed the way the colour clip’s boxes already were, and capped at three decimals. A bigWig header stores float32, so the faithful seed for a limit was 0.03999999910593033.

• Loop calls are ringed once, on the upper side of the diagonal, instead of on both. The matrix is symmetric, so ringing both said the same thing twice — and on a set of any size the second ring was a few hundred circles the reader has to check against the diagonal to know they are not a second set. A view whose two axes are different blocks still shows the one placement it can.

• A track’s summary no longer counts the file’s zoom levels. That is a fact about how the bigWig was built rather than about what is in it, and it pushed the value range — the number a reader can act on — onto a second line.

Removed

• The per-track linear/log2 scaling option. It was a dropdown whose effect on a lane forty pixels tall was hard to read and easy to forget having set, and it put a lane on a different value axis from the one beside it, which is the opposite of what the autoscale group next to it is for. A ratio that wants a log axis is better written that way by the tool that made the bigWig, where the axis label can say so. A stored session that had log2 set comes back linear.

Fixed

• The colourbar no longer disappears when tracks are shown. Assigning canvas.width clears a canvas, and the legend’s redraw was guarded on the colour scale having changed — which a resize does not change. Adding a track was enough to trigger it: the lanes relayout the plot, the resize observer fires, the bar is cleared, the guard says the scale is the same, and the legend is gone for as long as the view lasts. The invariant now lives inside resize, where a third caller cannot forget it.

• A right-hand lane stack no longer overflows the column it is in. The map’s height budget accounted for the tracks stacked under it but its width accounted for nothing stacked beside it, so nine tracks on the right edge ran out under the view controls — where the far half of the stack was not merely off-screen but could not be hovered at all. Unreachable before this release because the bottom edge was the default; the default is now the right one.