Fix whitelists on windows

[vadimpiven]

Fixing errors of https://github.com/platforma-open/runenv-python-3/actions/runs/27696123144/job/81934866371 build

Greptile Summary

This PR updates the Windows x64 import-error whitelists for three Python 3.12.10 environment variants to fix a failing CI build. The old entries whitelisted 8 matplotlib submodule failures all attributed to "Could not determine home directory"; the new entries replace them with a single matplotlib.backends._tkagg failure whose actual error is "Failed to load Tcl_SetVar or Tcl_SetVar2".

• Whitelist narrowing: 7 previously-whitelisted matplotlib import errors (_c_internal_utils, _image, _path, _qhull, _tri, _backend_agg, ft2font) are removed. These were likely cascade failures triggered by the missing-home-directory condition, which has since been resolved in the CI environment.
• Remaining exception: Only matplotlib.backends._tkagg stays whitelisted, now with the more precise Tcl/Tk DLL error that reflects the actual runtime environment on Windows.
• Changeset: A patch bump is recorded for all three packages (python-3.12.10, python-3.12.10-h5ad, python-3.12.10-sccoda).

Confidence Score: 5/5

Safe to merge — the whitelist files now accurately reflect the actual import errors observed in the Windows CI environment.

The change removes 7 matplotlib whitelist entries whose root cause ("Could not determine home directory") no longer occurs in the CI environment, and replaces them with the one entry that does: a Tcl/Tk DLL load failure for matplotlib.backends._tkagg. The narrower whitelist is strictly more correct — it no longer silently accepts errors that are no longer expected. All three environment variants (base, h5ad, sccoda) are updated consistently, and the changeset bumps each package at patch level.

No files require special attention. All three whitelist JSON files make the same targeted change and the changeset covers them all.

Important Files Changed

Filename	Overview
checker/whitelists/python-3.12.10/windows-x64.json	Replaces 8 "Could not determine home directory" matplotlib entries with a single tkagg Tcl error; all other entries unchanged.
checker/whitelists/python-3.12.10-h5ad/windows-x64.json	Same matplotlib whitelist narrowing as the base variant; numba and scipy entries retained.
checker/whitelists/python-3.12.10-sccoda/windows-x64.json	Same matplotlib whitelist narrowing as the base variant; numpy, numba, rpy2, and scipy entries retained.
.changeset/all-candies-repeat.md	Patch-level changeset correctly covering all three affected packages.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[CI: Import checker runs on Windows x64] --> B{matplotlib wheel imports}
    B -->|Before PR| C["8 modules fail\n'Could not determine home directory'"]
    B -->|After PR| D["1 module fails\nmatplotlib.backends._tkagg\n'Failed to load Tcl_SetVar or Tcl_SetVar2'"]
    C --> E[All 8 whitelisted\nin windows-x64.json]
    D --> F[Only tkagg whitelisted\nin windows-x64.json]
    E --> G["CI passes\n(but whitelist is over-broad)"]
    F --> H["CI passes\n(whitelist matches actual errors)"]
    C -->|Home directory issue resolved| D

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%%{init: {'theme': 'base', 'themeVariables': {"darkMode": true, "background": "#0d1117", "primaryColor": "#21262d", "primaryTextColor": "#e6edf3", "primaryBorderColor": "#8b949e", "lineColor": "#8b949e", "textColor": "#e6edf3", "edgeLabelBackground": "#161b22", "actorBkg": "#21262d", "actorBorder": "#8b949e", "actorTextColor": "#e6edf3", "actorLineColor": "#8b949e", "signalColor": "#8b949e", "signalTextColor": "#e6edf3", "noteBkgColor": "#373320", "noteBorderColor": "#d4a72c", "noteTextColor": "#f0e6c0", "labelBoxBkgColor": "#21262d", "labelBoxBorderColor": "#8b949e", "labelTextColor": "#e6edf3", "loopTextColor": "#e6edf3", "activationBkgColor": "#30363d", "activationBorderColor": "#8b949e"}}}%%
flowchart TD
    A[CI: Import checker runs on Windows x64] --> B{matplotlib wheel imports}
    B -->|Before PR| C["8 modules fail\n'Could not determine home directory'"]
    B -->|After PR| D["1 module fails\nmatplotlib.backends._tkagg\n'Failed to load Tcl_SetVar or Tcl_SetVar2'"]
    C --> E[All 8 whitelisted\nin windows-x64.json]
    D --> F[Only tkagg whitelisted\nin windows-x64.json]
    E --> G["CI passes\n(but whitelist is over-broad)"]
    F --> H["CI passes\n(whitelist matches actual errors)"]
    C -->|Home directory issue resolved| D

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[gemini-code-assist]

Code Review

This pull request updates the Windows-x64 whitelists for Python 3.12.10 environments (including h5ad and sccoda variants) by removing several obsolete matplotlib home directory warnings and updating the expected error for the matplotlib TkAgg backend. A changeset has also been added to document these changes. I have no further feedback to provide as there are no review comments.

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