Migrate Cellpose3 environment to pixi TOML and load via ResourceUtils

Author: stefanhahmann

src/main/java/org/mastodon/mamut/detection/cellpose/Cellpose3.java

@@ -33,6 +33,7 @@
 import javax.annotation.Nullable;
 
 import org.apposed.appose.Service;
+import org.mastodon.mamut.util.ResourceUtils;
 
 /**
  * Cellpose3 is a specialized implementation of the {@link Cellpose} class, specifically
@@ -43,21 +44,10 @@ public class Cellpose3 extends Cellpose
 {
 	public static final String ENV_NAME = "cellpose3";
 
-	public static final String ENV_FILE_CONTENT = "name: " + ENV_NAME + "\n"
-			+ "channels:\n"
-			+ "  - nvidia\n"
-			+ "  - pytorch\n"
-			+ "  - conda-forge\n"
-			+ "channel_priority: strict\n"
-			+ "dependencies:\n"
-			+ "  - python=3.10\n"
-			+ "  - pip\n"
-			+ "  - pip:\n"
-			+ "    - cellpose==3.1.1.2\n"
-			+ "    - appose==" + APPOSE_PYTHON_VERSION + "\n"
-			+ "  - pytorch\n"
-			+ "  - pytorch-cuda\n"
-			+ "  - numpy\n";
+	public static final String ENV_FILE_CONTENT =
+			ResourceUtils.readResourceAsString( "org/mastodon/mamut/detection/cellpose/cellpose3.toml", Cellpose3.class )
+					.replace( "{ENV_NAME}", ENV_NAME )
+					.replace( "{APPOSE_VERSION}", APPOSE_PYTHON_VERSION );
 
 	private final ModelType modelType;
 

src/main/resources/org/mastodon/mamut/detection/cellpose/cellpose3.toml

@@ -0,0 +1,53 @@
+[workspace]
+name = 'cellpose3'
+version = '0.0.1'
+description = 'Mastodon spot detector using Cellpose 3.'
+authors = ['Stefan Hahmann']
+channels = ['conda-forge']
+platforms = ['osx-arm64', 'osx-64', 'linux-64', 'win-64']
+
+# Assume CUDA 12 is available when solving for platforms that use it (linux-64,
+# win-64). On platforms without CUDA (macOS), pixi silently ignores this at
+# runtime.
+[system-requirements]
+cuda = '12'
+
+[dependencies]
+python = '==3.10'
+numpy = '*'
+pip = '*'
+
+[pypi-dependencies]
+appose = '==0.7.2'
+cellpose = '==3.1.1.2'
+
+# ---------------------------------------------------------------------------
+# WINDOWS (GPU PyTorch by default)
+# ---------------------------------------------------------------------------
+
+[target.win-64.dependencies]
+pytorch-gpu = '*'
+
+# ---------------------------------------------------------------------------
+# LINUX (GPU PyTorch by default)
+# ---------------------------------------------------------------------------
+
+[target.linux-64.dependencies]
+pytorch-gpu = '*'
+
+# ---------------------------------------------------------------------------
+# macOS INTEL (CPU PyTorch)
+# ---------------------------------------------------------------------------
+
+[target.osx-64.dependencies]
+pytorch = '*'
+
+# ---------------------------------------------------------------------------
+# macOS Apple Silicon (MPS via PyTorch)
+# ---------------------------------------------------------------------------
+
+[target.osx-arm64.dependencies]
+pytorch = '*'
+
+[environments]
+default = { solve-group = 'default' }