diff --git a/.gitignore b/.gitignore
index e04f2a28a..493c2bf9a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -141,6 +141,8 @@ untitled*
 
 # GeoJSON schema
 packages/schema/src/schema/geojson.json
+# Schema pre-processing
+packages/schema/temp-schema
 
 # Automatically generated file for processing
 
diff --git a/packages/schema/package.json b/packages/schema/package.json
index 31c5d68c8..9a448a4c1 100644
--- a/packages/schema/package.json
+++ b/packages/schema/package.json
@@ -29,7 +29,7 @@
     "build:schema": "jlpm run build:processing && node ./cacheGeoJSONSchema.js && jlpm build:schema:js && jlpm build:schema:py",
     "build:processing": "python scripts/process.py",
     "build:schema:js": "echo 'Generating TypeScript types from schema...' && json2ts -i src/schema -o src/_interface --no-unknownAny --unreachableDefinitions --cwd ./src/schema && cd src/schema && node ../../schema.js",
-    "build:schema:py": "echo 'Generating Python types from schema...' && datamodel-codegen --input ./src/schema --output ../../python/jupytergis_core/jupytergis_core/schema/interfaces --output-model-type pydantic_v2.BaseModel --input-file-type jsonschema",
+    "build:schema:py": "echo 'Generating Python types from schema...' && node scripts/preprocess-schemas-for-python-type-generation.js && datamodel-codegen --input ./temp-schema --output ../../python/jupytergis_core/jupytergis_core/schema/interfaces --output-model-type pydantic_v2.BaseModel --input-file-type jsonschema && rm -rf ./temp-schema",
     "build:prod": "jlpm run clean && jlpm build:schema && jlpm run build:lib",
     "build:lib": "tsc -b",
     "build:dev": "jlpm run build",
diff --git a/packages/schema/scripts/preprocess-schemas-for-python-type-generation.js b/packages/schema/scripts/preprocess-schemas-for-python-type-generation.js
new file mode 100755
index 000000000..939001c5f
--- /dev/null
+++ b/packages/schema/scripts/preprocess-schemas-for-python-type-generation.js
@@ -0,0 +1,116 @@
+#!/usr/bin/env node
+
+/**
+ * Preprocesses JSON schemas for Python type generation by replacing
+ * $ref paths which are relative to the schema root directory with paths which
+ * are relative to the file containing the $ref.
+ *
+ * This is a difference between how jsonschema-to-typescript and
+ * datamodel-codegen process $refs; I believe there is no way to write a $ref
+ * containing a path which is compatible with both unless our schemas are all
+ * in a flat directory structure.
+ */
+
+const fs = require('fs');
+const path = require('path');
+
+const schemaRoot = path.join(__dirname, '..', 'src', 'schema');
+const tempDir = path.join(__dirname, '..', 'temp-schema');
+
+/*
+ * Rewrite `refValue`, if it contains a path, to be relative to `schemaDir`
+ * instead of `schemaRoot`.
+ */
+function updateRefPath(refValue, schemaDir, schemaRoot) {
+  // Handle $ref with optional fragment (e.g., "path/to/file.json#/definitions/something")
+  const [refPath, fragment] = refValue.split('#');
+
+  // Check if the referenced file exists
+  const absoluteRefPath = path.resolve(schemaRoot, refPath);
+  if (!fs.existsSync(absoluteRefPath)) {
+    throw new Error(`Referenced file does not exist: ${refPath} (resolved to ${absoluteRefPath})`);
+  }
+
+  // Convert schemaRoot-relative path to schemaDir-relative path
+  const relativeToCurrentDir = path.relative(schemaDir, absoluteRefPath);
+
+  // Just in case we're on Windows, replace backslashes.
+  const newRef = relativeToCurrentDir.replace(/\\/g, '/');
+
+  return fragment ? `${newRef}#${fragment}` : newRef;
+}
+
+/*
+ * Recursively process `schema` (JSON content) to rewrite `$ref`s containing paths.
+ *
+ * Any path will be modified to be relative to `schemaDir` instead of relative
+ * to `schemaRoot`.
+ */
+function processSchema(schema, schemaDir, schemaRoot) {
+  if (Array.isArray(schema)) {
+    // Recurse!
+    return schema.map(item => processSchema(item, schemaDir, schemaRoot));
+  }
+
+  if (Object.prototype.toString.call(schema) !== '[object Object]') {
+    return schema;
+  }
+
+  // `schema` is an "object":
+  const result = {};
+  for (const [key, value] of Object.entries(schema)) {
+    if (key === '$ref' && typeof value === 'string' && !value.startsWith('#')) {
+      result[key] = updateRefPath(value, schemaDir, schemaRoot);
+    } else {
+      // Recurse!
+      result[key] = processSchema(value, schemaDir, schemaRoot);
+    }
+  }
+
+  return result;
+}
+
+/*
+ * Recursively rewrite schema files in `src` to `dest`.
+ *
+ * For each schema, rewrite the paths in JSONSchema `$ref`s to be relative to
+ * that schema's parent directory instead of `schemaRoot`.
+ */
+function preProcessSchemaDirectory(src, dest, schemaRoot) {
+  if (!fs.existsSync(dest)) {
+    fs.mkdirSync(dest, { recursive: true });
+  }
+
+  const children = fs.readdirSync(src, { withFileTypes: true });
+
+  for (const child of children) {
+    const srcChild = path.join(src, child.name);
+    const destChild = path.join(dest, child.name);
+
+    if (child.isDirectory()) {
+      // Recurse!
+      preProcessSchemaDirectory(srcChild, destChild, schemaRoot);
+    } else if (child.isFile() && child.name.endsWith('.json')) {
+      // Process schema JSON to modify $ref paths
+      const content = fs.readFileSync(srcChild, 'utf8');
+      const schema = JSON.parse(content);
+      const processedSchema = processSchema(schema, src, schemaRoot);
+
+      fs.writeFileSync(destChild, JSON.stringify(processedSchema, null, 2));
+    } else {
+      // There should be no non-JSON files in the schema directory!
+      throw new Error(`Non-JSON file detected in schema directory: ${child.parentPath}/${child.name}`);
+    }
+  }
+}
+
+function preProcessSchemas() {
+  fs.rmSync(tempDir, { recursive: true, force: true });
+  preProcessSchemaDirectory(schemaRoot, tempDir, schemaRoot);
+}
+
+console.log(`Pre-processing JSONSchemas for Python type generation (writing to ${tempDir})...`)
+
+preProcessSchemas();
+
+console.log('Schemas pre-processed for Python type generation.');
diff --git a/packages/schema/src/interfaces.ts b/packages/schema/src/interfaces.ts
index 9249c71cd..d408c3843 100644
--- a/packages/schema/src/interfaces.ts
+++ b/packages/schema/src/interfaces.ts
@@ -27,7 +27,7 @@ import {
   SourceType,
 } from './_interface/project/jgis';
 import { IRasterSource } from './_interface/project/sources/rasterSource';
-export { IGeoJSONSource } from './_interface/geoJsonSource';
+export { IGeoJSONSource } from './_interface/project/sources/geoJsonSource';
 
 export type JgisCoordinates = { x: number; y: number };
 
diff --git a/packages/schema/src/schema/geoJsonSource.json b/packages/schema/src/schema/project/sources/geoJsonSource.json
similarity index 100%
rename from packages/schema/src/schema/geoJsonSource.json
rename to packages/schema/src/schema/project/sources/geoJsonSource.json
diff --git a/packages/schema/src/types.ts b/packages/schema/src/types.ts
index 6a59a4c3c..b48a35312 100644
--- a/packages/schema/src/types.ts
+++ b/packages/schema/src/types.ts
@@ -1,7 +1,7 @@
 export * from './_interface/project/jgis';
 
 // Sources
-export * from './_interface/geoJsonSource';
+export * from './_interface/project/sources/geoJsonSource';
 export * from './_interface/project/sources/geoTiffSource';
 export * from './_interface/project/sources/imageSource';
 export * from './_interface/project/sources/rasterDemSource';
diff --git a/python/jupytergis_core/jupytergis_core/schema/__init__.py b/python/jupytergis_core/jupytergis_core/schema/__init__.py
index 31ff42e2f..f25a838d9 100644
--- a/python/jupytergis_core/jupytergis_core/schema/__init__.py
+++ b/python/jupytergis_core/jupytergis_core/schema/__init__.py
@@ -10,7 +10,7 @@
 
 from .interfaces.project.sources.vectorTileSource import IVectorTileSource  # noqa
 from .interfaces.project.sources.rasterSource import IRasterSource  # noqa
-from .interfaces.geoJsonSource import IGeoJSONSource  # noqa
+from .interfaces.project.sources.geoJsonSource import IGeoJSONSource  # noqa
 from .interfaces.project.sources.videoSource import IVideoSource  # noqa
 from .interfaces.project.sources.imageSource import IImageSource  # noqa
 from .interfaces.project.sources.geoTiffSource import IGeoTiffSource  # noqa