Add pixi support#22
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CellposeCLIBase now extends EnvCLIConfigurator instead of CondaCLIConfigurator, giving all cellpose/omnipose detectors a dual-mode conda/pixi launcher selector in the config panel. ICellposeCLI and ICellposeSAMCLI interfaces are extracted so CellposeDetector and CellposeSAMDetector can accept both the original concrete class and future pixi-aware subclasses without casting. CommandBuilder.build() is called with an explicit (CLIConfigurator) cast since the interface no longer extends CLIConfigurator directly. Info text in all detector factories updated to mention pixi setup. TrackMate dependency bumped to 8.1.7-SNAPSHOT (adds EnvCLIConfigurator). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Previously the non-omnipose cellpose process (i.e. the pixi/conda execution path) redirected both stdout and stderr to INHERIT and ignored the exit code, so a failed run silently reported 0 spots. Fixes: - stdout is now redirected to the cellpose log file (already tailed to the TrackMate logger for live progress output) - stderr is drained in a background thread to prevent pipe-buffer blocking - non-zero exit code causes detection to fail with an error message that includes the captured stderr, making the cause visible in the TrackMate info window Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ound Aligns with upstream 8.1.7: bump pom-scijava 43→44, replace enforcer.skip with legacyMode workaround for JPMS javadoc failure, fix contributor indentation and trailing whitespace. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
RequireReproducibleBuilds blocks builds with SNAPSHOT deps. Skip enforcer while developing against TrackMate 8.1.7-SNAPSHOT; remove once 8.1.7 releases. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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This pull request refactors the Cellpose and Cellpose-SAM CLI integration in TrackMate to improve extensibility and support both Conda and Pixi environments. The main changes include introducing new interfaces for CLI configurators, updating class hierarchies, and improving process management and user documentation.
CLI Refactoring and Extensibility
ICellposeCLIandICellposeSAMCLIto abstract CLI configuration, making it easier to support multiple launchers and extend functionality. (src/main/java/fiji/plugin/trackmate/cellpose/ICellposeCLI.java[1]src/main/java/fiji/plugin/trackmate/cellpose/sam/ICellposeSAMCLI.java[2]CellposeCLIBaseto extendEnvCLIConfigurator(instead ofCondaCLIConfigurator) and implementICellposeCLI, allowing runtime selection between Conda and Pixi launchers. (src/main/java/fiji/plugin/trackmate/cellpose/CellposeCLIBase.java[1] [2] [3]CellposeSAMCLIto implementICellposeSAMCLIfor consistency with the new interface-based design. (src/main/java/fiji/plugin/trackmate/cellpose/sam/CellposeSAMCLI.javasrc/main/java/fiji/plugin/trackmate/cellpose/sam/CellposeSAMCLI.javaL30-R30)Detector and Factory Updates
CellposeDetectorandCellposeSAMDetectorto depend on the new CLI interfaces, improving decoupling and flexibility. (src/main/java/fiji/plugin/trackmate/cellpose/CellposeDetector.java[1]src/main/java/fiji/plugin/trackmate/cellpose/sam/CellposeSAMDetector.java[2]src/main/java/fiji/plugin/trackmate/cellpose/advanced/AdvancedCellposeDetectorFactory.javasrc/main/java/fiji/plugin/trackmate/cellpose/advanced/AdvancedCellposeDetectorFactory.javaL87-R88)Process Management and Logging
CellposeDetectorto redirect stdout to a log file (for live output) and capture stderr in a background thread, enabling better error reporting and avoiding buffer blocking. (src/main/java/fiji/plugin/trackmate/cellpose/CellposeDetector.java[1] [2]User Documentation
src/main/java/fiji/plugin/trackmate/cellpose/CellposeDetectorFactory.java[1]src/main/java/fiji/plugin/trackmate/cellpose/sam/CellposeSAMDetectorFactory.java[2]src/main/java/fiji/plugin/trackmate/omnipose/OmniposeDetectorFactory.java[3]Dependency Management
TrackMate.versionto8.1.7-SNAPSHOTand added a property to skip reproducible-builds enforcement during development with SNAPSHOT dependencies. (pom.xmlpom.xmlL96-R99)