Update docs for nested namespace (#30)

* Update docs for nested namespace

* Fix failed docs

Author: superstar54

.readthedocs.yml

@@ -12,6 +12,7 @@ build:
       - rabbitmq-server -detached
       - sleep 5
       - rabbitmq-diagnostics status
+      - pip list
       - verdi presto
       - verdi daemon start
       - verdi status

docs/environment.yml

@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - aiida-core
+  - aiida-core~=2.6.3
   - aiida-core.services

docs/gallery/autogen/pythonjob.py

@@ -279,6 +279,51 @@ def generate_structures(structure: Atoms, factor_lst: list) -> dict:
     print(key, value)
 
 
+######################################################################
+# --------------------------
+# Nested Namespace
+# --------------------------
+#
+# One can also define nested namespace outputs by specifying the "ports" parameter.
+
+
+def generate_structures(structure: Atoms, factor_lst: list) -> dict:
+    """Scale the structure by the given factor_lst."""
+    scaled_structures = {}
+    volumes = {}
+    for i in range(len(factor_lst)):
+        atoms = structure.copy()
+        atoms.set_cell(atoms.cell * factor_lst[i], scale_atoms=True)
+        scaled_structures[f"s_{i}"] = atoms
+        volumes[f"v_{i}"] = atoms.get_volume()
+    return {
+        "outputs": {
+            "scaled_structures": scaled_structures,
+            "volume": volumes,
+        }
+    }
+
+
+inputs = prepare_pythonjob_inputs(
+    generate_structures,
+    function_inputs={"structure": bulk("Al"), "factor_lst": [0.95, 1.0, 1.05]},
+    output_ports=[
+        {
+            "name": "outputs",
+            "identifier": "namespace",
+            "ports": [
+                {"name": "scaled_structures", "identifier": "namespace"},
+                {"name": "volume", "identifier": "namespace"},
+            ],
+        }
+    ],
+)
+
+result, node = run_get_node(PythonJob, inputs=inputs)
+print("result: ", result["outputs"]["scaled_structures"])
+print("volumes: ", result["outputs"]["volume"])
+
+
 ######################################################################
 # What if my calculation fails?
 # --------------------------------

docs/requirements.txt

@@ -1,4 +1,6 @@
-sphinx_rtd_theme==1.2.2
+sphinx_rtd_theme~=3.0
+click~=8.1.0
+pydantic~=2.11.0
 sphinx-gallery
 nbsphinx==0.9.2
 ipython

src/aiida_pythonjob/utils.py

@@ -476,6 +476,7 @@ def parse_outputs(
             for output in output_ports["ports"]:
                 if output["name"] not in results:
                     if output.get("required", True):
+                        logger.warning(f"Found output: {output['name']} not in results, but it is required.")
                         return exit_codes.ERROR_MISSING_OUTPUT
                 else:
                     output["value"] = serialize_ports(