Write inline pyproject.toml with table headers

Jackson's TomlMapper writes nested tables as dotted keys, e.g.
tool.pixi.workspace.channels = [...]. That is valid TOML, but pixi 0.58
(the version Appose pins) does not then recognize the file as a pixi
manifest, failing with "Missing table in manifest pyproject.toml".
Newer pixi versions accept either form.

So we now emit an explicit [header] per table, which all pixi versions
understand, still letting TomlMapper serialize the leaf values.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Author: ctrueden

src/main/java/org/scijava/plugins/scripting/appose/python/_internal/InlineMetadata.java

@@ -40,6 +40,7 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import com.fasterxml.jackson.core.io.JsonStringEncoder;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.fasterxml.jackson.dataformat.toml.TomlMapper;
@@ -175,7 +176,9 @@ else if ("tool".equals(key)) {
 		}
 
 		try {
-			return mapper.writeValueAsString(pyproject);
+			final StringBuilder sb = new StringBuilder();
+			writeTable(mapper, pyproject, null, sb);
+			return sb.toString();
 		}
 		catch (final IOException e) {
 			throw new IllegalArgumentException(
@@ -249,6 +252,40 @@ private static void unsupported(final JsonNode table, final String prefix,
 		});
 	}
 
+	/**
+	 * Writes the given table as TOML, using a {@code [header]} per table rather
+	 * than the dotted keys that {@link TomlMapper} would produce, since some
+	 * pixi versions (e.g. 0.58) do not recognize {@code tool.pixi.workspace}
+	 * written in dotted form.
+	 */
+	private static void writeTable(final TomlMapper mapper, final JsonNode table,
+		final String path, final StringBuilder sb) throws IOException
+	{
+		final List<Map.Entry<String, JsonNode>> subtables = new ArrayList<>();
+		final ObjectNode values = mapper.createObjectNode();
+		table.fields().forEachRemaining(field -> {
+			if (field.getValue().isObject()) subtables.add(field);
+			else values.set(field.getKey(), field.getValue());
+		});
+		if (path != null && (!values.isEmpty() || subtables.isEmpty())) {
+			if (sb.length() > 0) sb.append('\n');
+			sb.append('[').append(path).append("]\n");
+		}
+		if (!values.isEmpty()) sb.append(mapper.writeValueAsString(values));
+		for (final Map.Entry<String, JsonNode> subtable : subtables) {
+			final String key = tomlKey(subtable.getKey());
+			writeTable(mapper, subtable.getValue(),
+				path == null ? key : path + "." + key, sb);
+		}
+	}
+
+	/** Quotes the given key if it is not a valid TOML bare key. */
+	private static String tomlKey(final String key) {
+		if (key.matches("[A-Za-z0-9_-]+")) return key;
+		return '"' + new String(JsonStringEncoder.getInstance().quoteAsString(
+			key)) + '"';
+	}
+
 	/** Removes the comment prefix from each line, as the specification says. */
 	private static String uncomment(final String content) {
 		final StringBuilder sb = new StringBuilder();

src/test/java/org/scijava/plugins/scripting/appose/python/_internal/InlineMetadataTest.java

@@ -36,6 +36,10 @@
 import static org.junit.Assert.assertThrows;
 import static org.junit.Assert.assertTrue;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.dataformat.toml.TomlMapper;
 
@@ -125,6 +129,26 @@ public void testToPyProject() throws Exception {
 			pixi.get("workspace").get("platforms").get(0).asText());
 	}
 
+	@Test
+	public void testToPyProjectUsesTableHeaders() {
+		// Older pixi versions (e.g. 0.58) do not recognize a pixi manifest
+		// written with dotted keys, such as tool.pixi.workspace.channels.
+		final String toml = InlineMetadata.toPyProject(String.join("\n", //
+			"[tool.pixi.dependencies]", //
+			"numpy = \"*\"", //
+			"[tool.pixi.pypi-dependencies.\"my.pkg\"]", //
+			"path = \".\"", //
+			""), "my-env");
+		final List<String> headers = new ArrayList<>();
+		for (final String line : toml.split("\n")) {
+			if (line.startsWith("[")) headers.add(line);
+			else if (!line.isEmpty()) assertFalse(line, line.split(" = ")[0].contains("."));
+		}
+		assertEquals(Arrays.asList("[project]", "[tool.pixi.dependencies]",
+			"[tool.pixi.pypi-dependencies.\"my.pkg\"]", "[tool.pixi.workspace]"),
+			headers);
+	}
+
 	@Test
 	public void testToPyProjectKeepsDeclaredWorkspace() throws Exception {
 		final JsonNode pyproject = pyproject(String.join("\n", //