Change import statements with try except to enable explicit import of submodules from import to avoid conflicts with parent project.

instruments/readers/acsm_tofware_reader.py

@@ -6,6 +6,9 @@ import yaml
 
 #root_dir = os.path.abspath(os.curdir)
 #sys.path.append(root_dir)
+try:
+    from dima.utils import g5505_utils as utils
+except ModuleNotFoundError:
     import utils.g5505_utils as utils
 
 

instruments/readers/filereader_registry.py

@@ -3,10 +3,14 @@ import sys
 #root_dir = os.path.abspath(os.curdir)
 #sys.path.append(root_dir)
 
+try:
+    from dima.instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict
+    from dima.instruments.readers.g5505_text_reader import read_txt_files_as_dict
+    
+except ModuleNotFoundError:
     from instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict
     from instruments.readers.g5505_text_reader import read_txt_files_as_dict
 
-
 file_extensions = ['.ibw','.txt','.dat','.h5','.TXT','.csv','.pkl','.json','.yaml']
 
 # Define the instruments directory (modify this as needed or set to None)

instruments/readers/flag_reader.py

@@ -8,7 +8,10 @@ import json
 #from instruments.readers import set_dima_path as configpath
 #configpath.set_dima_path()
 
-from utils import g5505_utils
+try:
+    from dima.utils import g5505_utils as utils
+except ModuleNotFoundError:
+    import utils.g5505_utils as utils
 
 
 def read_jsonflag_as_dict(path_to_file):

pipelines/data_integration.py

@@ -22,6 +22,12 @@ from datetime import datetime
 from itertools import chain 
 
 # Import DIMA modules
+try:
+    from dima.src import hdf5_writer as hdf5_lib
+    from dima.utils import g5505_utils as utils
+    from dima.instruments.readers import filereader_registry
+except ModuleNotFoundError:
+    print(':)')
     import src.hdf5_writer as hdf5_lib
     import utils.g5505_utils as utils
     from instruments.readers import filereader_registry

pipelines/metadata_revision.py

@@ -15,9 +15,14 @@ if dimaPath not in sys.path:  # Avoid duplicate entries
 
 import h5py
 import yaml
+
+try:
+    from dima.src import hdf5_ops as hdf5_ops
+except ModuleNotFoundError:
     import src.hdf5_ops as hdf5_ops
 
 
+
 def load_yaml(review_yaml_file):
     with open(review_yaml_file, 'r') as stream:
         try:

src/git_ops.py

@@ -1,5 +1,10 @@
 import subprocess
 import os
+
+try: 
+    from dima.utils import g5505_utils as utils
+    from dima.pipelines.metadata_revision import update_hdf5_file_with_review
+except ModuleNotFoundError:
     import utils.g5505_utils as utils
     from pipelines.metadata_revision import update_hdf5_file_with_review
 

src/hdf5_ops.py

@@ -17,9 +17,6 @@ if dimaPath not in sys.path:  # Avoid duplicate entries
 import h5py
 import pandas as pd
 import numpy as np
-
-import utils.g5505_utils as utils
-import src.hdf5_writer as hdf5_lib
 import logging
 import datetime
 
@@ -29,6 +26,13 @@ import yaml
 import json
 import copy
 
+try:
+    from dima.utils import g5505_utils as utils
+    from dima.src import hdf5_writer as hdf5_lib
+except ModuleNotFoundError:
+    import utils.g5505_utils as utils
+    import src.hdf5_writer as hdf5_lib
+
 class HDF5DataOpsManager():
 
     """

src/hdf5_writer.py

@@ -1,13 +1,17 @@
 import sys
 import os
-root_dir = os.path.abspath(os.curdir)
+#root_dir = os.path.abspath(os.curdir)
-sys.path.append(root_dir)
+#sys.path.append(root_dir)
 
 import pandas as pd
 import numpy as np
 import h5py
 import logging
 
+try:
+    from dima.utils import g5505_utils as utils
+    from dima.instruments.readers import filereader_registry as filereader_registry
+except ModuleNotFoundError:
     import utils.g5505_utils as utils
     import instruments.readers.filereader_registry as filereader_registry
 

visualization/hdf5_vis.py

@@ -13,8 +13,11 @@ from plotly.subplots import make_subplots
 import plotly.graph_objects as go
 import plotly.express as px
 #import plotly.io as pio
-from src.hdf5_ops import get_parent_child_relationships
 
+try:
+    from dima.src.hdf5_ops import get_parent_child_relationships
+except ModuleNotFoundError:
+    from src.hdf5_ops import get_parent_child_relationships
  
 
 def display_group_hierarchy_on_a_treemap(filename: str):