Move save/load code to a new location to avoid circular references

demos/demo_save_load.ipynb

@@ -18,7 +18,7 @@
     "from tempfile import NamedTemporaryFile\n",
     "\n",
     "from kymata.datasets.sample import KymataMirror2023Q3Dataset, TVLInsLoudnessOnlyDataset, TVLDeltaInsTC1LoudnessOnlyDataset\n",
-    "from kymata.entities.expression import HexelExpressionSet"
+    "from kymata.io.nkg import save_expression_set, load_expression_set"
    ]
   },
   {
@@ -77,7 +77,7 @@
    "outputs": [],
    "source": [
     "# Let's load the KymataMirror2023Q3 .nkg file. This contains around 30 functions.\n",
-    "expression_data_kymata_mirror = HexelExpressionSet.load(from_path_or_file=nkg_path)"
+    "expression_data_kymata_mirror = load_expression_set(from_path_or_file=nkg_path)"
    ],
    "metadata": {
     "collapsed": false,
@@ -95,8 +95,8 @@
    "source": [
     "# Let's seperately load the 'ins_loudness' .nkg file, and then load and add the\n",
     "# d_ins_tc1_loudness to it using '+='. 'expression_data_new_results' now contains two functions.\n",
-    "expression_data_new_results = HexelExpressionSet.load(from_path_or_file=ins_loudness_path)\n",
-    "expression_data_new_results += HexelExpressionSet.load(from_path_or_file=d_ins_tc1_loudness_path)"
+    "expression_data_new_results = load_expression_set(from_path_or_file=ins_loudness_path)\n",
+    "expression_data_new_results += load_expression_set(from_path_or_file=d_ins_tc1_loudness_path)"
    ],
    "metadata": {
     "collapsed": false,
@@ -126,7 +126,7 @@
     "\n",
     "# Save new expressionSet for use again in the future.\n",
     "with NamedTemporaryFile() as tf:\n",
-    "    expression_data_extended.save(tf)"
+    "    save_expression_set(expression_data_extended, tf)"
    ],
    "metadata": {
     "collapsed": false,

kymata/datasets/sample.py

@@ -6,6 +6,7 @@
 
 from kymata.entities.expression import HexelExpressionSet
 from kymata.io.file import path_type
+from kymata.io.nkg import load_expression_set
 
 _DATA_PATH_ENVIRONMENT_VAR_NAME = "KYMATA_DATA_ROOT"
 _DATA_DIR_NAME = "kymata-toolbox-data"
@@ -78,7 +79,9 @@ def __init__(self, data_root: Optional[path_type] = None, download: bool = True)
         )
 
     def to_expressionset(self) -> HexelExpressionSet:
-        return HexelExpressionSet.load(from_path_or_file=Path(self.path, self.filenames[0]))
+        es = load_expression_set(from_path_or_file=Path(self.path, self.filenames[0]))
+        assert isinstance(es, HexelExpressionSet)
+        return es
 
 
 class TVLInsLoudnessOnlyDataset(SampleDataset):
@@ -95,7 +98,9 @@ def __init__(self, data_root: Optional[path_type] = None, download: bool = True)
         )
 
     def to_expressionset(self) -> HexelExpressionSet:
-        return HexelExpressionSet.load(from_path_or_file=Path(self.path, self.filenames[0]))
+        es = load_expression_set(from_path_or_file=Path(self.path, self.filenames[0]))
+        assert isinstance(es, HexelExpressionSet)
+        return es
 
 
 class TVLDeltaInsTC1LoudnessOnlyDataset(SampleDataset):
@@ -112,7 +117,9 @@ def __init__(self, data_root: Optional[path_type] = None, download: bool = True)
         )
 
     def to_expressionset(self) -> HexelExpressionSet:
-        return HexelExpressionSet.load(from_path_or_file=Path(self.path, self.filenames[0]))
+        es = load_expression_set(from_path_or_file=Path(self.path, self.filenames[0]))
+        assert isinstance(es, HexelExpressionSet)
+        return es
 
 
 def data_root_path(data_root: Optional[path_type] = None) -> Path:

kymata/entities/datatypes.py

@@ -0,0 +1,12 @@
+from numpy import int_, str_, float_
+
+
+Hexel = int  # Todo: change this and others to `type Hexel = int` on dropping support for python <3.12
+Sensor = str
+Latency = float
+
+# Set consistent dtypes for use in arrays
+HexelDType = int_
+SensorDType = str_
+LatencyDType = float_
+FunctionNameDType = str_