refactor: move io, logger and parser modules to new mip_dmp.utils subpackage

mip_dmp/cli/mip_dataset_mapper_cli.py

@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 """Standalone script which runs the MIP Dataset Mapper from the terminal."""
 
 import sys
@@ -21,15 +20,15 @@
 # import logging
 from mip_dmp.process.mapping import map_dataset
 
-from mip_dmp.io import (
+from mip_dmp.utils.io import (
     load_csv,
     load_excel,
     # load_excel,
     load_json,
 )
-from mip_dmp.parser import create_parser
+from mip_dmp.utils.parser import create_parser
 
-# from mip_dmp.logger import setup_logging
+# from mip_dmp.utils.logger import setup_logging
 
 
 def main():

mip_dmp/process/embedding.py

@@ -21,7 +21,7 @@
 from sklearn.decomposition import PCA
 
 # Internal imports
-from mip_dmp.io import load_glove_model, load_c2v_model
+from mip_dmp.utils.io import load_glove_model, load_c2v_model
 
 
 def glove_embedding(text, glove_model):

mip_dmp/qt5/components/dataset_mapper_window.py

@@ -48,7 +48,7 @@
 import pkg_resources
 
 # Internal imports
-from mip_dmp.io import load_mapping_json
+from mip_dmp.utils.io import load_mapping_json
 from mip_dmp.process.mapping import (
     map_dataset,
     MAPPING_TABLE_COLUMNS,

mip_dmp/utils/__init__.py

@@ -0,0 +1,15 @@
+# Copyright 2023 The HIP team, University Hospital of Lausanne (CHUV), Switzerland & Contributors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Sub-package that contains modules with utility functions for i/o, logging, and script argument parsing."""