Prepare 0.30.0 for release - #430
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Aratz
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There are a lot of changes in this release, some being more relevant to users than others. Perhaps you could squash and highlight the most important ones (default min_allowed_nodes_pct, changes in single-cell-pna graph, signed plot color scales)?
In general, I've started thinking if it wouldn't be better to group the changes into categories from semantic versioning, i.e. something like
### Major updates
#### Added
#### Changed
#### Fixed
### Minor updates
#### Added
...
### Patches
...
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| - `pixelator.pna.analysis.comparison.compare_sample_pairs` to check that pairs of PNA samples are | ||
| similar in terms of abundance (mean marker CLR) and proximity (mean marker-pair proximity score) | ||
| patterns, reporting the correlation between each pair. | ||
| - `pixelator.pna.analysis.compare_sample_pairs_by_gate` to run the same comparison restricted to | ||
| components matching a cell-type gate (e.g. `["+CD3e", "+CD4", "-CD19"]`), with positive/negative | ||
| thresholds determined automatically from each marker's CLR distribution. |
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Maybe these two items could be squashed together?
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| (`PIXELGEN_ACCENT_COLORS`, `PIXELGEN_CELL_PALETTE`, `pixelgen_gradient`, `pixelgen_palette`, | ||
| `pixelgen_accent_colors`, `pixelgen_discrete_colors`, `create_discrete_palette`, | ||
| `pixelgen_colorscale`/`pixelgen_sequential_colormap`/`pixelgen_divergent_colormap`/`pixelgen_colormap`, | ||
| `set_pixelgen_theme`/`pixelgen_theme`, `style_facet_strips`), ported from the internal |
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| (`PIXELGEN_ACCENT_COLORS`, `PIXELGEN_CELL_PALETTE`, `pixelgen_gradient`, `pixelgen_palette`, | |
| `pixelgen_accent_colors`, `pixelgen_discrete_colors`, `create_discrete_palette`, | |
| `pixelgen_colorscale`/`pixelgen_sequential_colormap`/`pixelgen_divergent_colormap`/`pixelgen_colormap`, | |
| `set_pixelgen_theme`/`pixelgen_theme`, `style_facet_strips`), ported from the internal | |
| , ported from the internal |
Alternatively, we could link to the original PR
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| - `pixelgen_divergent_colormap` and the `plot_colocalization_heatmap`/ | ||
| `plot_colocalization_diff_volcano`/`plot_polarity_diff_volcano` plots that use it now center on a | ||
| light Pixelgen grey rather than white, and use a `min_level` floor on both hues, so values near | ||
| zero stay visible against a white background instead of fading out. | ||
| - Color scales for signed metrics (`abundance_colocalization_plot`'s hue mapping, | ||
| `plot_colocalization_heatmap`'s `center=0`, and the `CenteredNorm` used by the volcano plots) are | ||
| now correctly centered on zero, instead of on the (potentially skewed) 10th-90th percentile midpoint | ||
| or raw data min/max. |
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Description
Prepare 0.30.0 for release.
Note
Low Risk
Documentation-only changelog edit with no runtime or dependency changes.
Overview
Finalizes the 0.30.0 release notes by replacing the
[Unreleased]heading with[0.30.0] - 2026-08-04and publishing the accumulated feature, behavior, and fix entries under that version.The listed changes cover PNA sample-pair comparison and gating APIs, docs build/deploy setup, Pixelgen plotting theme defaults, ACE/graph/denoise reporting tweaks, and several
single-cell-pna graphrobustness fixes. This PR only updatesCHANGELOG.md(including minor line wrapping and grouping the Fixed bullets separately from Changed); it does not modify application code.Reviewed by Cursor Bugbot for commit 3a01443. Bugbot is set up for automated code reviews on this repo. Configure here.