Merge pull request #1 from maflot/dev

Dev

Author: maflot

.github/workflows/release.yml

@@ -0,0 +1,73 @@
+name: Auto release on main
+
+on:
+  push:
+    branches: [main]
+
+permissions:
+  contents: write
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install package and test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e . pytest matplotlib plotly pandas numpy scipy
+      - name: Run tests
+        run: pytest tests -v
+
+  release:
+    runs-on: ubuntu-latest
+    needs: test
+    outputs:
+      released: ${{ steps.create.outputs.released }}
+      version: ${{ steps.version.outputs.version }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Read version from pyproject.toml
+        id: version
+        run: |
+          VERSION=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['project']['version'])")
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+          echo "tag=v$VERSION" >> "$GITHUB_OUTPUT"
+          echo "Detected version $VERSION"
+
+      - name: Check whether this tag already exists
+        id: check_tag
+        env:
+          TAG: ${{ steps.version.outputs.tag }}
+        run: |
+          if git rev-parse -q --verify "refs/tags/$TAG" >/dev/null; then
+            echo "exists=true" >> "$GITHUB_OUTPUT"
+            echo "Tag $TAG already exists — nothing to release."
+          else
+            echo "exists=false" >> "$GITHUB_OUTPUT"
+            echo "Tag $TAG does not exist — will create release."
+          fi
+
+      - name: Create tag and GitHub release
+        id: create
+        if: steps.check_tag.outputs.exists == 'false'
+        env:
+          GH_TOKEN: ${{ github.token }}
+          TAG: ${{ steps.version.outputs.tag }}
+          VERSION: ${{ steps.version.outputs.version }}
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git tag "$TAG"
+          git push origin "$TAG"
+          gh release create "$TAG" \
+            --title "pydiceplot $VERSION" \
+            --generate-notes
+          echo "released=true" >> "$GITHUB_OUTPUT"

.gitignore

@@ -9,12 +9,14 @@ __pycache__/
 *.mp4
 *.h5
 *.yml
+!.github/workflows/*.yml
 
 *.pth
 *.pt
 *.html
 
 *.png
+!images/domino_example.png
 
 resources/
 cmake-build-debug/
@@ -43,4 +45,6 @@ cmake-build-debug/
 *.pag
 *.brf
 /build/
+/dist/
 /pyDicePlot.egg-info/
+/pydiceplot.egg-info/

CHANGELOG.md

@@ -0,0 +1,73 @@
+# Changelog
+
+## 1.0.0 — 2026-04-15
+
+Complete rewrite of the dice-plot engine and public API, plus a full domino
+API refactor to match the new 1.0 conventions.
+
+### Breaking changes
+
+- **`dots` renamed to `pips`** throughout. The `dots` parameter, `dot_colors`,
+  and related names are gone. Use `pips`, `pip_colors`, `pip_scale`,
+  `pips_label`, `pips_order`, `max_pips` instead. ("Pip" is the correct term
+  for the marks on a die face.)
+- **Seaborn-style function signature.** `dice_plot(data, x, y, pips, ...)`
+  now takes positional `data`, `x`, `y`, `pips` followed by keyword-only
+  options. The old dict-based / mixed-positional calling convention is removed.
+- **Native return types.** matplotlib: `(Figure, Axes)` when creating a new
+  figure, just `Axes` when the caller supplies `ax=`. plotly: `go.Figure`.
+  The old wrapper return types are gone.
+- **`domino_plot` rewritten around a column-first API.** The old
+  `gene_list`/`var_id`/`logfc_col`/`pval_col`-style entry point is replaced by
+  `domino_plot(data, feature, celltype, contrast, *, fill=..., size=..., ...)`
+  with native backend returns, explicit contrast ordering, and backend-specific
+  `ax=` / `fig=` composition hooks.
+- **`n=6` uses traditional die-face layout** (two vertical columns) instead
+  of the transposed two-row layout from earlier versions. This is an
+  intentional divergence from `ggdiceplot::make_offsets`.
+
+### New features
+
+- **Up to 9 pips.** The 3×3 sub-grid now supports `max_pips=9` with
+  traditional die-face lookup for every value 1–9.
+- **Grid geometry ported from kuva.** `_layout.py` replaces the old ad-hoc
+  positioning code with a direct port of `kuva/src/plot/diceplot.rs`, ensuring
+  matplotlib and plotly produce identical pip positions and tile sizes.
+- **Per-pip continuous fill and size.** Pass `fill="col"` and/or `size="col"`
+  for numeric columns — each pip gets its own colour (colorbar) and radius
+  (size legend). Works with both backends.
+- **Per-pip discrete fill.** Pass `fill="col"` + `fill_palette={val: hex}`
+  for discrete colour encoding per pip slot.
+- **Legend stack.** A right-side legend panel stacks position legend, colorbar,
+  and size legend, matching `ggdiceplot::draw_key` semantics. Skipped when
+  the caller provides `ax=` / `fig=`.
+- **`ax=` / `fig=` composability.** Draw into an existing matplotlib `Axes`
+  or plotly `Figure` to build multi-panel layouts.
+- **Domino preprocessing rewrite.** Domino plots now validate their structural
+  columns up front, enforce exactly two contrast slots, compute shared backend
+  geometry once, and use the same color/size range semantics as `dice_plot`.
+- **Tile geometry controls.** `tile_size`, `pip_scale`, `grid_lines` parameters.
+- **Label controls.** `fill_label`, `size_label`, `pips_label` set legend
+  titles; `xlabel`, `ylabel`, `title` set axis / figure titles.
+- **pixi environment.** `pixi.toml` with `test`, `example`, `build`, `check`
+  tasks. The package is installed as an editable pypi dependency.
+
+### Example scripts
+
+- 1-to-1 ports of ggdiceplot demo plots: `oral_microbiome.py`,
+  `oral_microbiome_fill_only.py`, `mirna_direction.py`, `zebra_domino.py`.
+- Standalone `example_domino.py`: demonstrates the refactored domino API.
+- Creative `pathways_nine.py`: nine signaling pathways on a 3×3 die face.
+- Showcase `example.py`: generates all `images/dice_*.png` gallery images.
+
+### Tests
+
+- `test_dice_plot.py`: smoke tests covering all three modes (categorical,
+  continuous, discrete fill), both backends, return types, and preprocessing.
+- `test_domino_plot.py`: preprocessing, switch-axis, composition, validation,
+  and backend smoke tests for the refactored domino API.
+- `test_layout.py`: geometry unit tests for pip positions and tile sizing.
+
+## 0.0.2 — 2025
+
+Initial PyPI release with basic dice and domino plot support.

dist/pydiceplot-0.0.1-py3-none-any.whl

@@ -0,0 +1,21 @@
+"""The ggdiceplot diverging purple→white→green palette.
+
+Registered globally as `ggdiceplot_pg` so the examples can just pass
+`color_map="ggdiceplot_pg"` and get the same look as the R `scale_fill_gradient2(
+low="#40004B", high="#00441B", mid="white")`.
+"""
+
+from matplotlib import colormaps
+from matplotlib.colors import LinearSegmentedColormap
+
+
+NAME = "ggdiceplot_pg"
+
+
+def register() -> None:
+    if NAME in colormaps:
+        return
+    cmap = LinearSegmentedColormap.from_list(
+        NAME, ["#40004B", "#FFFFFF", "#00441B"],
+    )
+    colormaps.register(cmap, name=NAME)