CIP-000B: deprecate matplotlib visualize (warning slice)

GPy/examples/stick_explorer_spike.py

@@ -0,0 +1,30 @@
+"""Deprecated. The stick explorer moved to vidden.
+
+Install https://github.com/lawrennd/vidden and run::
+
+    from vidden.explore import stick_explorer
+    stick_explorer()
+
+or from that repository::
+
+    panel serve examples/stick.py --show
+"""
+
+from __future__ import annotations
+
+import warnings
+
+_MSG = (
+    "GPy.examples.stick_explorer_spike has moved to the vidden package. "
+    "Install vidden (https://github.com/lawrennd/vidden) and import "
+    "vidden.explore, or run `panel serve examples/stick.py --show` there."
+)
+
+warnings.warn(_MSG, DeprecationWarning, stacklevel=2)
+
+try:
+    from vidden.explore import stick_explorer
+except ImportError as exc:
+    raise ImportError(_MSG) from exc
+
+__all__ = ["stick_explorer"]

GPy/plotting/matplot_dep/visualize.py

@@ -1,7 +1,43 @@
-import numpy as np
+"""Deprecated interactive latent-space viewers (matplotlib / VPython).
+
+This module is the 2012–2015 mouse explorer for GPLVM reconstructions
+(``lvm``, ``lvm_dimselect``, ``image_show``, ``vector_show``,
+``stick_show``, ``skeleton_show``, ``data_play``). It is deprecated.
+
+Matplotlib GUI callbacks do not work reliably on macOS or Jupyter, and
+interactive visualisation does not belong in the core inference library.
+Use `vidden <https://github.com/lawrennd/vidden>`_ instead.
+
+Static GPy plots (``plot``, ``plot_latent``, ``plot_confidence``) are
+unchanged. Comments welcome on the deprecation discussion:
+https://github.com/SheffieldML/GPy/discussions/1252
+"""
+
 import time
+import warnings
+
+import numpy as np
+
 from ...core.parameterization.variational import VariationalPosterior
 
+_VISUALIZE_DEPRECATED = (
+    "GPy.plotting.matplot_dep.visualize is deprecated and will be removed. "
+    "Interactive latent-space viewers (lvm, lvm_dimselect, image_show, "
+    "vector_show, stick_show, skeleton_show, data_play) rely on matplotlib "
+    "GUI callbacks that do not work reliably on macOS or Jupyter, and "
+    "interactive visualisation does not belong in the core inference library. "
+    "Use vidden: https://github.com/lawrennd/vidden "
+    "Static GPy plots (plot, plot_latent, plot_confidence) are unchanged. "
+    "Comments welcome: https://github.com/SheffieldML/GPy/discussions/1252"
+)
+
+
+def _warn_visualize_deprecated(stacklevel=2):
+    warnings.warn(_VISUALIZE_DEPRECATED, DeprecationWarning, stacklevel=stacklevel)
+
+
+_warn_visualize_deprecated(stacklevel=2)
+
 try:
     import matplotlib.pyplot as plt
     import matplotlib as mpl
@@ -23,6 +59,7 @@ class data_show:
     """
 
     def __init__(self, vals):
+        _warn_visualize_deprecated(stacklevel=3)
         self.vals = vals.copy()
         # If no axes are defined, create some.
 
@@ -609,6 +646,9 @@ def wrap_around(self, lim, connect):
 def data_play(Y, visualizer, frame_rate=30):
     """Play a data set using the data_show object given.
 
+    Deprecated. See the module docstring and
+    https://github.com/SheffieldML/GPy/discussions/1252
+
     :Y: the data set to be visualized.
     :param visualizer: the data show objectwhether to display during optimisation
     :type visualizer: data_show
@@ -626,6 +666,7 @@ def data_play(Y, visualizer, frame_rate=30):
        GPy.util.visualize.data_play(Y, visualize)
 
     """
+    _warn_visualize_deprecated(stacklevel=2)
 
     for y in Y:
         visualizer.modify(y[None, :])

GPy/testing/test_stick_explorer_spike.py

@@ -0,0 +1,45 @@
+import importlib
+import warnings
+
+import numpy as np
+
+
+def _deprecated_visualize_warnings(caught):
+    return [
+        item
+        for item in caught
+        if issubclass(item.category, DeprecationWarning)
+        and "vidden" in str(item.message)
+        and "discussions/1252" in str(item.message)
+    ]
+
+
+def test_visualize_import_warns_and_points_at_vidden():
+    with warnings.catch_warnings(record=True) as caught:
+        warnings.simplefilter("always", DeprecationWarning)
+        mod = importlib.import_module("GPy.plotting.matplot_dep.visualize")
+        importlib.reload(mod)
+    assert _deprecated_visualize_warnings(caught)
+    message = str(_deprecated_visualize_warnings(caught)[0].message)
+    assert "macOS" in message or "macos" in message.lower()
+    assert "core inference library" in message
+
+
+def test_visualize_constructor_warns_and_points_at_discussion():
+    with warnings.catch_warnings(record=True) as caught:
+        warnings.simplefilter("always", DeprecationWarning)
+        mod = importlib.import_module("GPy.plotting.matplot_dep.visualize")
+        importlib.reload(mod)
+        mod.data_show(np.zeros((1, 3)))
+    assert _deprecated_visualize_warnings(caught)
+
+
+def test_stick_explorer_spike_warns_and_points_at_vidden():
+    with warnings.catch_warnings(record=True) as caught:
+        warnings.simplefilter("always", DeprecationWarning)
+        try:
+            importlib.import_module("GPy.examples.stick_explorer_spike")
+        except ImportError as exc:
+            assert "vidden" in str(exc)
+            return
+    assert any(issubclass(item.category, DeprecationWarning) and "vidden" in str(item.message) for item in caught)

backlog/documentation/2026-10-26_latent-explorer-example-docs.md

@@ -0,0 +1,59 @@
+---
+id: 2026-10-26_latent-explorer-example-docs
+title: Latent explorer example notebook and serve notes
+status: Ready
+priority: Low
+created: "2026-10-26"
+last_updated: "2026-10-26"
+category: documentation
+related_cips:
+- "000B"
+owner: Neil Lawrence
+dependencies:
+- 2026-10-26_explore-module-optional-extra
+tags:
+- backlog
+- documentation
+- plotting
+- jupyter
+---
+
+# Task: Latent explorer example docs
+
+> Backlog task for [CIP-000B](../../cip/cip000B.md). Informal docs only;
+> Sphinx compression waits until the CIP is Closed.
+
+## Description
+
+Add one notebook or example script that shows:
+
+- `pip install 'gpy[explore]'` (or the extra name chosen in the module task)
+- Jupyter use
+- `panel serve` for a standalone window
+
+Keep it short. Do not write a Sphinx tutorial until CIP-000B is Closed and
+compressed.
+
+The doodle notebook on `notebook-latent-doodle-space` is out of scope.
+
+## Acceptance Criteria
+
+- [ ] Example lives in `notebooks/` or `GPy/examples/` and imports the explore API
+- [ ] README or example docstring states Jupyter vs `panel serve`
+- [ ] No Sphinx page yet (compression is a later CIP-close step)
+
+## Implementation Notes
+
+- Prefer reusing the stick spike as the documented example.
+- Optional extra must be mentioned so a default GPy install is not assumed.
+
+## Related
+
+- CIP: 000B
+- Depends: 2026-10-26_explore-module-optional-extra
+
+## Progress Updates
+
+### 2026-10-26
+
+Task created when CIP-000B was Accepted.

backlog/features/2026-10-26_explore-module-optional-extra.md

@@ -0,0 +1,67 @@
+---
+id: 2026-10-26_explore-module-optional-extra
+title: Add GPy.plotting.explore module and optional extra
+status: Abandoned
+priority: High
+created: "2026-10-26"
+last_updated: "2026-10-27"
+category: features
+related_cips:
+- "000B"
+owner: Neil Lawrence
+dependencies:
+- 2026-10-26_panel-stick-explorer-spike
+tags:
+- backlog
+- plotting
+- packaging
+- holoviews
+---
+
+# Task: Explore module and optional extra
+
+> Backlog task for [CIP-000B](../../cip/cip000B.md). Depends on the Panel spike.
+
+## Description
+
+Extract the spike into a small public module so demos share one explorer.
+Keep GPy models ignorant of the UI: latent point in, `predict` out, viewer
+pane for `Y`.
+
+Provisional names (lock them here if the spike suggests better ones):
+
+- `GPy.plotting.explore.latent_explorer`
+- `image_view`, `vector_view`, `stick_view`
+
+Add a Poetry extra (e.g. `gpy[explore]`) for HoloViews and Panel. Default
+`pip install gpy` must not pull them.
+
+## Acceptance Criteria
+
+- [ ] Module importable when the extra is installed
+- [ ] Import of `GPy` and `GPy.plotting` succeeds without HoloViews/Panel
+- [ ] Unit tests for reconstruct helpers on `Agg` with a tiny GPLVM
+- [ ] Explorer tests skip via `pytest.importorskip` when the extra is absent
+- [ ] Extra declared in `pyproject.toml`
+
+## Implementation Notes
+
+- Do not add HoloViews/Panel to core or to `gpy[plotting]` (matplotlib/plotly).
+- Tests must not start a GUI or a browser driver.
+- Stick view can live here; Plotly 3D skeleton is a later task.
+
+## Related
+
+- CIP: 000B
+- Depends: 2026-10-26_panel-stick-explorer-spike
+
+## Progress Updates
+
+### 2026-10-26
+
+Task created when CIP-000B was Accepted.
+
+### 2026-10-27
+
+Abandoned. The explorer is not a GPy extra. It lives in
+https://github.com/lawrennd/vidden (vidden CIP-0001).

backlog/features/2026-10-26_panel-stick-explorer-spike.md

@@ -0,0 +1,75 @@
+---
+id: 2026-10-26_panel-stick-explorer-spike
+title: Panel spike for stick_bgplvm latent explorer
+status: Completed
+priority: High
+created: "2026-10-26"
+last_updated: "2026-10-27"
+category: features
+related_cips:
+- "000B"
+owner: Neil Lawrence
+dependencies: []
+tags:
+- backlog
+- plotting
+- panel
+- holoviews
+- gplvm
+---
+
+# Task: Panel spike for stick_bgplvm
+
+> Backlog task for [CIP-000B](../../cip/cip000B.md). No public API yet.
+
+## Description
+
+Prove that a browser explorer can replace matplotlib `lvm_dimselect` on macOS.
+Build a Panel app around `stick_bgplvm(optimize=False)`: latent scatter, stick
+reconstruction from `model.predict`, and two widgets to choose which latent
+axes to plot. Other latent dimensions stay at the posterior mean.
+
+Do this in an example or notebook on this branch. Do not add
+`GPy.plotting.explore` or a Poetry extra until the spike works.
+
+## Acceptance Criteria
+
+- [x] Pointer (or tap) in the latent scatter updates the stick figure via `predict`
+- [x] Two dim selectors change which latent axes are plotted
+- [ ] Works in Jupyter on macOS without the matplotlib `macosx` GUI backend
+- [x] Same app runs with `panel serve`
+- [x] No new core GPy dependency
+
+## Implementation Notes
+
+- HoloViews `PointerXY` / `Tap` plus Panel layout, as sketched in CIP-000B.
+- BayesianGPLVM latents are `m.X.mean`; copy to a writable `(1, Q)` array
+  before writing the two active coordinates.
+- Reuse stick connectivity from `pods.datasets.osu_run1()["connect"]`.
+- Keep the spike throwaway-friendly; the next task extracts the module.
+
+## Related
+
+- CIP: 000B
+- Demo: `GPy.examples.dimensionality_reduction.stick_bgplvm`
+
+## Progress Updates
+
+### 2026-10-26
+
+Task created when CIP-000B was Accepted.
+
+Spike app in `GPy/examples/stick_explorer_spike.py`. `panel serve` on macOS shows
+the latent scatter, Plotly stick reconstruction, and dim selectors. Changing the
+y-axis from 1 to 2 updates the scatter. Pointer position is written into
+`predict`. Jupyter still needs a manual check:
+
+```python
+from GPy.examples.stick_explorer_spike import stick_explorer
+stick_explorer()
+```
+
+### 2026-10-27
+
+Completed by moving the spike to vidden (`vidden.explore`,
+`examples/stick.py`). GPy's file is a deprecation stub.