Fix (Windows) Cellpose 3/4 issues by migrating environments to TOML#154
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stefanhahmann wants to merge 5 commits into
Open
Fix (Windows) Cellpose 3/4 issues by migrating environments to TOML#154stefanhahmann wants to merge 5 commits into
stefanhahmann wants to merge 5 commits into
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* Add a toml file for env configuration
* Add a toml file for env configuration
…nment configuration
…ers for environment configuration * This is to reflect cellpose3, cellpose4 and stardist use pixi and trackastra uses mamba
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This pull request updates the way Python environments for Cellpose 3 and 4 detectors are defined and installed, moving from hardcoded YAML strings (and using micromamba) to TOML resource files. It also generalizes the environment installation logic to allow for different builders (e.g., Pixi or Mamba).
Environment definition and installation improvements:
Cellpose3andCellpose4are now loaded from TOML resource files (cellpose3.toml,cellpose4.toml), allowing for platform-specific dependencies. Placeholders for environment name and Appose version are dynamically replaced at runtime.ApposeUtils.installEnvironment) is refactored to accept aBuilder<?>parameter, making it possible to use either Pixi or Mamba for environment setup. All relevant calls and tests are updated to use this new signature.UI and builder selection updates:
PythonEnvironmentManagerUIand itsEnvironmentPanelnow require and use a specific builder for each environment, enabling the use of Pixi for Cellpose and StarDist, and Mamba for Trackastra. This ensures the correct tool is used for each environment type.StarDist environment and config adjustments:
ENV_NAME) instead of a hardcoded string, both for the model path and for extracting configuration from the Bioimage.io model descriptor.