Propagate names correctly.

lib/src/load_list.cpp

@@ -120,19 +120,14 @@ struct PythonStringVector : public uzuki2::StringVector, public PythonBase {
                 return bu.attr("StringList")(storage);
             }
         } else {
-            // Numpy arrays don't have direct support for names, so we
-            // just convert it into a dict.
-            pybind11::dict output;
-            for (size_t i = 0, end = storage.size(); i < end; ++i) {
-                output[names[i].c_str()] = storage[i];
-            }
-            return output;
+            pybind11::module bu = pybind11::module::import("biocutils");
+            using namespace pybind11::literals;
+            return bu.attr("StringList")(storage, "names"_a = names);
         }
     }
 
     pybind11::list storage;
-    std::vector<std::string> names;
-    std::vector<size_t> missing;
+    pybind11::list names;
     bool is_scalar;
 };
 
@@ -160,28 +155,17 @@ struct PythonFactor : public uzuki2::Factor, public PythonBase {
     }
 
     pybind11::object extract() const {
-        if (names.empty()) {
-            pybind11::module bu = pybind11::module::import("biocutils");
-            using namespace pybind11::literals;
+        pybind11::module bu = pybind11::module::import("biocutils");
+        using namespace pybind11::literals;
+        if (names.size() == 0) {
             return bu.attr("Factor")(storage, levels, "ordered"_a = ordered);
-
         } else {
-            // Factor doesn't have direct support for names, so we
-            // just convert it into a dict.
-            pybind11::dict output;
-            for (size_t i = 0, end = storage.size(); i < end; ++i) {
-                if (storage.at(i) >= 0) {
-                    output[names[i].c_str()] = levels[storage.at(i)];
-                } else {
-                    output[names[i].c_str()] = pybind11::none();
-                }
-            }
-            return output;
+            return bu.attr("Factor")(storage, levels, "ordered"_a = ordered, "names"_a = names);
         }
     }
 
     pybind11::array_t<int32_t> storage;
-    std::vector<std::string> names;
+    pybind11::list names;
     bool is_scalar;
     pybind11::list levels;
     bool ordered;

src/dolomite_base/save_simple_list.py

@@ -111,7 +111,7 @@ def _save_simple_list_recursive_stringlist(x: StringList, externals: list, handl
     if handle is None:
         output = { "type": "string", "values": x.as_list() }
         if nms is not None:
-            output["names"] = nms
+            output["names"] = nms.as_list()
         return output
 
     has_none = any(y is None for y in x)
@@ -125,7 +125,7 @@ def _save_simple_list_recursive_stringlist(x: StringList, externals: list, handl
     if has_none:
        dset.attrs["missing-value-placeholder"] = placeholder
     if nms is not None:
-        ut._save_fixed_length_strings(handle, "names", nms)
+        ut._save_fixed_length_strings(handle, "names", nms.as_list())
 
     return
 
@@ -335,13 +335,18 @@ def _save_simple_list_recursive_numpy_generic(x: np.generic, externals: list, ha
 
 @_save_simple_list_recursive.register
 def _save_simple_list_recursive_factor(x: Factor, externals: list, handle):
+    nms = x.get_names()
+
     if handle is None:
-        return { 
+        output = { 
             "type": "factor",
             "values": [(None if y == -1 else int(y)) for y in x.get_codes()],
             "levels": x.get_levels().as_list(),
             "ordered": x.get_ordered(),
         }
+        if not nms is None:
+            output["names"] = nms.as_list()
+        return output
 
     else:
         handle.attrs["uzuki_object"] = "vector"
@@ -354,6 +359,9 @@ def _save_simple_list_recursive_factor(x: Factor, externals: list, handle):
         ut._save_fixed_length_strings(handle, "levels", x.get_levels().as_list())
         if x.get_ordered():
             handle.create_dataset("ordered", data=x.get_ordered(), dtype="i1")
+
+        if not nms is None:
+            ut._save_fixed_length_strings(handle, "names", nms.as_list())
         return
 
 

tests/test_simple_list.py

@@ -318,3 +318,31 @@ def test_simple_list_factor():
     assert list(roundtrip["missing"]) == list(everything["missing"])
     assert list(roundtrip["ordered"]) == list(everything["ordered"])
     assert roundtrip["ordered"].get_ordered()
+
+
+def test_simple_list_named():
+    everything = {
+        "factor": Factor.from_sequence([ "sydney", "brisbane", "sydney", "melbourne"]),
+        "string": StringList(["Aria", "Akari", "Akira", "Aika"], names=["1", "2", "3", "4"])
+    }
+    everything["factor"].set_names(["A", "B", "C", "D"], in_place=True) # TODO: enable this in the constructor.
+
+    # Stage as JSON.
+    dir = os.path.join(mkdtemp(), "json")
+    meta = dl.save_object(everything, dir, simple_list_mode="json")
+
+    roundtrip = dl.read_object(dir)
+    assert list(roundtrip["factor"]) == list(everything["factor"])
+    assert roundtrip["factor"].get_names() == everything["factor"].get_names()
+    assert list(roundtrip["string"]) == list(everything["string"])
+    assert roundtrip["string"].get_names() == everything["string"].get_names()
+
+    # Stage as HDF5.
+    dir = os.path.join(mkdtemp(), "hdf5")
+    meta = dl.save_object(everything, dir, simple_list_mode="hdf5")
+
+    roundtrip = dl.read_object(dir)
+    assert list(roundtrip["factor"]) == list(everything["factor"])
+    assert roundtrip["factor"].get_names() == everything["factor"].get_names()
+    assert list(roundtrip["string"]) == list(everything["string"])
+    assert roundtrip["string"].get_names() == everything["string"].get_names()