From d2adf152ea5c8b38d9a7e1564c09fe77264f5df9 Mon Sep 17 00:00:00 2001
From: Curtis Rueden <ctrueden@wisc.edu>
Date: Wed, 18 Mar 2026 20:39:03 -0500
Subject: [PATCH] WIP: Add support for more builder parameters

* conda - for conda-forge packages
* pypi - for PyPI packages
* python - for Python version
---
 README.md                                     | 26 ++++++++++
 .../python/ApposePythonScriptEngine.java      | 50 ++++++++++++++++---
 2 files changed, 69 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index b55e868..725a3db 100644
--- a/README.md
+++ b/README.md
@@ -19,3 +19,29 @@ the SciJava Common wiki.
 
 See also:
 * [Python Scripting](https://imagej.net/scripting/python) on the ImageJ wiki.
+
+## Example
+
+```python
+#@script (language="appose-python", pypi=["cellcast"])
+
+#@ Img image
+
+#@ Double (value=1.0, description="minimum percentile value for normalization") pmin
+#@ Double (value=99.8, description="maximum percentile value for normalization") pmax
+#@ Double (value=0.479, description="Polygon probability threshold") prob_threshold
+#@ Double (value=0.3, description="Non-Maximum Suppression threshold") nms_threshold
+#@ Boolean (value=true, description="Set True for GPU inference via WebGPU, False for CPU inference") gpu
+
+#@output Img labels
+
+import cellcast.models.stardist_2d as stardist
+labels = stardist.predict_versatile_fluo(
+    image,
+    pmin,
+    pmax,
+    prob_threshold,
+    nms_threshold,
+    gpu,
+)
+```
diff --git a/src/main/java/org/scijava/plugins/scripting/appose/python/ApposePythonScriptEngine.java b/src/main/java/org/scijava/plugins/scripting/appose/python/ApposePythonScriptEngine.java
index 60ee909..30ee90b 100644
--- a/src/main/java/org/scijava/plugins/scripting/appose/python/ApposePythonScriptEngine.java
+++ b/src/main/java/org/scijava/plugins/scripting/appose/python/ApposePythonScriptEngine.java
@@ -237,18 +237,49 @@ private Environment buildEnvironment(final ScriptInfo info)
 		throws ScriptException
 	{
 		if (info == null) return null;
-		final String envRef = info.get("env");
-		if (envRef == null) return null;
 
-		final File envFile = resolveEnvFile(envRef, info.getPath());
+		final String envValue = info.get("env");
+		final File envFile = envValue == null ? null : resolveEnvFile(envValue, info.getPath());
 		final String envName = sanitizeEnvName(info.getPath());
 
+		final String scheme = info.get("scheme");
+		final List<String> pypi = toListOfStrings(info.get("pypi"));
+		final List<String> conda = toListOfStrings(info.get("conda"));
+		final String python = info.get("python");
+
 		log.info("Building Appose environment: " + envName);
-		try {
-			String scheme = info.get("scheme");
-			Builder<?> builder = scheme == null ?
-				Appose.file(envFile) : Appose.file(envFile).scheme(scheme);
 
+		try {
+			final Builder<?> builder;
+			if (envFile == null) {
+				// No environment file given -- use inline builder.
+				if (conda.isEmpty()) {
+					// No conda packages required -- use uv.
+					String[] pypiPkgs = pypi.toArray(new String[0]);
+					builder = python == null ?
+						Appose.uv().include(pypiPkgs) :
+						Appose.uv().python(python).include(pypiPkgs);
+				}
+				else {
+					// Conda packages specified -- use pixi.
+					List<String> condaPkgList = new ArrayList<>();
+					if (conda.stream().anyMatch(v -> v.matches("python\\b.*"))) {
+						// Python was not included in the conda package list -- add it manually.
+						// If python version value was given, use that, otherwise open-ended.
+						condaPkgList.add(python != null ? "python=" + python : "python");
+					}
+					condaPkgList.addAll(conda);
+					String[] condaPkgs = condaPkgList.toArray(new String[0]);
+					String[] pypiPkgs = pypi.toArray(new String[0]);
+					builder = Appose.pixi().conda(condaPkgs).pypi(pypiPkgs);
+				}
+			}
+			else {
+				// Build with the given environment file.
+				builder = scheme == null ?
+					Appose.file(envFile) :
+					Appose.file(envFile).scheme(scheme);
+			}
 			return builder.name(envName).build();
 		}
 		catch (final BuildException e) {
@@ -259,6 +290,11 @@ private Environment buildEnvironment(final ScriptInfo info)
 		}
 	}
 
+	private List<String> toListOfStrings(String value) {
+		// TODO Auto-generated method stub
+		throw new UnsupportedOperationException("Unimplemented method 'toListOfStrings'");
+	}
+
 	/** Resolves an (optionally relative) env file path against the script path. */
 	private static File resolveEnvFile(final String envRef,
 		final String scriptPath)