Merge branch 'main' into test_modules

Author: toqduj

src/modacor/dataclasses/process_step_describer.py

@@ -54,14 +54,14 @@ class ProcessStepDescriber:
     step_doc: str = field(default="")  # documentation for the process
     step_reference: NXCite = field(default="")  # NXCite to the paper describing the process
     step_note: str | None = field(default=None)
-    use_frames_cache: list[str] = field(factory=list)
-    # for produced_values dictionary key names in this list, the produced_values are cached
-    # on first run, and reused on subsequent runs. Maybe two chaches, one for per-file and
-    # one for per-execution.
-    use_overall_cache: list[str] = field(factory=list)
-    # for produced_values dictionary key names in this list, the produced_values are cached
-    # on first run, and reused on subsequent runs. Maybe two chaches, one for per-file and
-    # one for per-execution.
+    # use_frames_cache: list[str] = field(factory=list)
+    # # for produced_values dictionary key names in this list, the produced_values are cached
+    # # on first run, and reused on subsequent runs. Maybe two chaches, one for per-file and
+    # # one for per-execution.
+    # use_overall_cache: list[str] = field(factory=list)
+    # # for produced_values dictionary key names in this list, the produced_values are cached
+    # # on first run, and reused on subsequent runs. Maybe two chaches, one for per-file and
+    # # one for per-execution.
 
     def copy(self) -> ProcessStepDescriber:
         raise NotImplementedError()

src/modacor/io/hdf/hdf_loader.py

@@ -39,10 +39,10 @@
 from ..io_sources import IoSources
 
 
-class HDFLoader(IoSources):
-    def __init__(self, source_reference: str, source: IoSource, logging_level=WARNING):
-        super().__init__(source_reference, source)
-        self.hdf_logger = MessageHandler("hdf5logger", logging_level)
+class HDFLoader(IoSource):
+    def __init__(self, source_reference: str, logging_level = WARNING):
+        super().__init__(source_reference)
+        self.hdf_logger = MessageHandler(level = logging_level, name = 'hdf5logger')
         self._file_path = None
         self._file_reference = None
         self._file_datasets = []
@@ -59,12 +59,12 @@ def _open_file(self, file_path=None):
             self._file_path = abspath(file_path)
             self._file_reference.visititems(self._find_datasets)
         except OSError as error:
-            self.hdf_logger.log.error(error)
+            self.hdf_logger.logger.error(error)
             raise OSError(error)
 
     def _close_file(self):
         try:
-            self.file_reference.close()
+            self._file_reference.close()
             self._file_path = None
             self._file_reference = None
             self._file_datasets.clear()

src/modacor/modules/base_modules/poisson_uncertainties.py

@@ -1,5 +1,5 @@
-# src/modacor/dataclasses/processingdata.py
-# -*- coding: utf-8 -*-
+__coding__ = "utf-8"
+__file__ = "src/modacor/dataclasses/processingdata.py"
 __author__ = "Brian R. Pauw"
 __copyright__ = "MoDaCor team"
 __license__ = "BSD3"
@@ -8,6 +8,7 @@
 __status__ = "Development"  # "Development", "Production"
 
 
+from pathlib import Path
 from typing import Any
 
 import numpy as np
@@ -25,7 +26,7 @@ class PoissonUncertainties(ProcessStep):
     documentation = ProcessStepDescriber(
         calling_name="Add Poisson Uncertainties",
         calling_id="PoissonUncertainties",
-        calling_module_path=__file__,
+        calling_module_path=Path(__file__),
         calling_version=__version__,
         required_data_keys=["signal"],
         works_on={"variances": ["Poisson"]},

src/modacor/tests/io/hdf/test_hdf_loader.py

@@ -29,7 +29,10 @@
 import unittest
 from logging import WARNING
 from os.path import abspath
-
+from os import unlink
+import numpy as np
+import tempfile
+import unittest
 import h5py
 import numpy as np
 
@@ -40,33 +43,34 @@ class TestHDFLoader(unittest.TestCase):
     """Testing class for modacor/io/hdf/hdf_loader.py"""
 
     def setUp(self):
-        self.test_hdf_loader = HDFLoader()
-        self.test_file_path = "tbd - some form of temp file"
-        self.test_dataset_name = "dataset"
-        self.test_dataset_shape = (10, 2)
+        self.test_hdf_loader = HDFLoader(source_reference = 'Test Data')
+        self.temp_file_handle = tempfile.NamedTemporaryFile(delete=False, delete_on_close=False)
+        self.temp_file_path = self.temp_file_handle.name
+        self.temp_file_handle.close()
+        self.temp_dataset_name = "dataset"
+        self.temp_dataset_shape = (10, 2)
+        self.temp_hdf_file = h5py.File(self.temp_file_path, 'w')
+        self.temp_hdf_file[self.temp_dataset_name] = np.zeros(self.temp_dataset_shape)
+        self.temp_file_handle.close()
 
     def tearDown(self):
         self.test_h5_loader = None
         self.test_file_path = None
         self.test_dataset_name = None
         self.test_dataset_shape = None
+        unlink(self.temp_file_path)
 
     def test_open_file(self):
-        absolute_test_file_path = abspath(self.test_file_path)
-        self.test_h5_loader._open_file(self.test_file_path)
-
-        self.assertEqual(absolute_test_file_path, self.test_h5_loader._file_path)
-        self.assertEqual(self.test_dataset_name, self.test_h5_loader._file_datasets[0])
-        self.assertEqual(
-            self.test_dataset_shape,
-            self.test_h5_loader._file_datasets_shapes[self.test_dataset_name],
-        )
+        self.test_hdf_loader._open_file(self.temp_file_path)
+        self.assertEqual(self.temp_file_path, self.test_hdf_loader._file_path)
+        self.assertEqual(self.temp_dataset_name, self.test_hdf_loader._file_datasets[0])
+        self.assertEqual(self.temp_dataset_shape, self.test_hdf_loader._file_datasets_shapes[self.temp_dataset_name])
 
     def test_close_file(self):
         self.test_open_file()
-        self.test_h5_loader._close_file()
+        self.test_hdf_loader._close_file()
 
-        self.assertEqual(None, self.test_h5_loader._file_path)
-        self.assertEqual(None, self.test_h5_loader._file_reference)
-        self.assertEqual([], self.test_h5_loader._file_datasets)
-        self.assertEqual({}, self.test_h5_loader._file_datasets_shapes)
+        self.assertEqual(None, self.test_hdf_loader._file_path)
+        self.assertEqual(None, self.test_hdf_loader._file_reference)
+        self.assertEqual([], self.test_hdf_loader._file_datasets)
+        self.assertEqual({}, self.test_hdf_loader._file_datasets_shapes)