Added deprecation warnings for DeepProfiler_processing.py and cell_locations.py (cytomining#695)

* added deprecation warning for DeepProfiler_processing.py

* added deprecation warning in cell_locations.py module

* [pre-commit.ci lite] apply automatic fixes

* moved deprecation warnings to classes

* updated cell_locations warning

* added SingleCells deprecation warning

* added cmap deprecation warnings

* fixed CellLocation name and pycytominer name

* Updated deprecation warnings to point to CytoTable

---------

Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>

Author: axiomcura

pycytominer/annotate.py

@@ -2,6 +2,7 @@
 Annotates profiles with metadata information
 """
 
+import warnings
 from typing import Literal, Optional, Union
 
 import pandas as pd
@@ -116,6 +117,14 @@ def annotate(
 
     # Add specific Connectivity Map (CMAP) formatting
     if format_broad_cmap:
+        # raise deprecation warning when format_broad_cmap is set to True
+        warnings.warn(
+            "The `format_broad_cmap` parameter in annotate() is deprecated and will be "
+            "removed in a future release.",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
+
         annotated = annotate_cmap(
             annotated,
             annotate_join_on=join_on[1],

pycytominer/cyto_utils/DeepProfiler_processing.py

@@ -61,6 +61,15 @@ def __init__(
         See above for all other parameters.
         """
 
+        # setting DeepProfilerData deprecation warning
+        warnings.warn(
+            "The DeepProfilerData class is deprecated and will be removed in a future "
+            "Pycytominer release. Please use CytoTable instead: "
+            "https://github.com/cytomining/CytoTable",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
+
         self.index_df = pd.read_csv(index_file, dtype=str)
         self.profile_dir = profile_dir
         self.filename_delimiter = filename_delimiter
@@ -175,6 +184,16 @@ def __init__(
         ---------
         See above for all parameters.
         """
+
+        # setting AggregateDeepProfiler deprecation warning
+        warnings.warn(
+            "The AggregateDeepProfiler class is deprecated and will be removed in a future "
+            "Pycytominer release. Please use CytoTable instead: "
+            "https://github.com/cytomining/CytoTable",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
+
         if aggregate_operation not in [
             "median",
             "mean",
@@ -369,7 +388,14 @@ def __init__(
         ---------
         See above for all parameters.
         """
-
+        # setting SingleCellDeepProfiler deprecation warning
+        warnings.warn(
+            "The SingleCellDeepProfiler class is deprecated and will be removed in a future "
+            "Pycytominer release. Please use CytoTable instead: "
+            "https://github.com/cytomining/CytoTable",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
         self.deep_data = deep_data
 
     def get_single_cells(

pycytominer/cyto_utils/annotate_custom.py

@@ -3,6 +3,7 @@
 """
 
 import contextlib
+import warnings
 
 import numpy as np
 import pandas as pd
@@ -29,6 +30,7 @@ def prepare_external_metadata_for_annotate(
     external_metadata : pd.DataFrame
         External metadata with columns renamed to be compatible with annotate() conventions.
     """
+    # Setting deprecation warning
     # Protect certain columns with specific prefixes ("Metadata_", "Image_Metadata", and "Image_").
     # The function will protect only non-numeric columns with "Image_" prefix.
     # This prevents adding a "Metadata_" prefix, which will occur during `cp_clean`, later
@@ -92,6 +94,14 @@ def annotate_cmap(
     annotated: pd.DataFrame
         CMAP annotated data
     """
+
+    # setting deprecation warning
+    warnings.warn(
+        "annotate_cmap is deprecated and will be removed in a future release.",
+        category=DeprecationWarning,
+        stacklevel=2,
+    )
+
     pert_opts = ["none", "chemical", "genetic"]
 
     if perturbation_mode not in pert_opts:

pycytominer/cyto_utils/cell_locations.py

@@ -6,6 +6,7 @@
 import os
 import pathlib
 import tempfile
+import warnings
 from typing import Optional, Union
 
 import boto3
@@ -91,6 +92,15 @@ def __init__(
         cell_x_loc: str = "Nuclei_Location_Center_X",
         cell_y_loc: str = "Nuclei_Location_Center_Y",
     ):
+
+        # setting deprecation warning for the cell_locations module
+        warnings.warn(
+            "The CellLocation class is deprecated and will be removed in a "
+            "future Pycytominer release.",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
+
         self.metadata_input = self._expanduser(metadata_input)
         self.augmented_metadata_output = self._expanduser(augmented_metadata_output)
         self.single_cell_input = self._expanduser(single_cell_input)

pycytominer/cyto_utils/cells.py

@@ -2,6 +2,7 @@
 Class to interact with single cell morphological profiles.
 """
 
+import warnings
 from typing import Optional, Union, cast
 
 import numpy as np
@@ -136,6 +137,15 @@ def __init__(
         if not subsample_frac > 0 and subsample_frac <= 1:
             raise ValueError("subsample_frac must be between 0 and 1")
 
+        # set SingleCells deprecation warning and recommend CytoTable
+        warnings.warn(
+            "The SingleCells class is deprecated and will be removed in a future "
+            "Pycytominer release. Please use CytoTable instead: "
+            "https://github.com/cytomining/CytoTable",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
+
         self.sql_file = sql_file
         self.strata = strata
         self.load_image_data = load_image_data