added deprecation warnings to pycytominer docs (cytomining#706)

Author: axiomcura

pycytominer/annotate.py

@@ -57,6 +57,10 @@ def annotate(
         Whether the plate map variables possibly need "Metadata" pre-pended
     format_broad_cmap : bool, default False
         Whether we need to add columns to make compatible with Broad CMAP naming conventions.
+
+        .. warning::
+            The ``format_broad_cmap`` parameter is deprecated and will be
+            removed in a future Pycytominer release.
     clean_cellprofiler: bool, default True
         Clean specific CellProfiler feature names by dropping
         Image_ prefix.
@@ -81,6 +85,10 @@ def annotate(
         decimal precision.
     cmap_args : dict, default None
         Potential keyword arguments for annotate_cmap(). See cyto_utils/annotate_custom.py for more details.
+
+        .. warning::
+            The ``cmap_args`` parameter is deprecated and will be
+            removed in a future Pycytominer release.
     platemap_sep : str, optional
         Column delimiter for the platemap file (e.g. ``","`` for CSV, ``"\\t"``
         for TSV). Only applies when ``platemap`` is a file path — ignored when

pycytominer/cyto_utils/DeepProfiler_processing.py

@@ -21,6 +21,11 @@
 class DeepProfilerData:
     """This class holds all functions needed to load and annotate the DeepProfiler (DP) run.
 
+    .. warning::
+        The ``DeepProfilerData`` class is deprecated and will be removed in a
+        future Pycytominer release. Please use
+        `CytoTable <https://github.com/cytomining/CytoTable>`_ instead.
+
     Attributes
     ----------
     profile_dir : str
@@ -139,6 +144,11 @@ def extract_filename_metadata(
 class AggregateDeepProfiler:
     """This class holds all functions needed to aggregate the DeepProfiler (DP) run.
 
+    .. warning::
+        The ``AggregateDeepProfiler`` class is deprecated and will be removed
+        in a future Pycytominer release. Please use
+        `CytoTable <https://github.com/cytomining/CytoTable>`_ instead.
+
     Attributes
     ----------
     deep_data : DeepProfilerData
@@ -346,6 +356,11 @@ def aggregate_deep(self):
 class SingleCellDeepProfiler:
     """This class holds functions needed to analyze single cells from the DeepProfiler (DP) run. Only pycytominer.normalization() is implemented.
 
+    .. warning::
+        The ``SingleCellDeepProfiler`` class is deprecated and will be removed
+        in a future Pycytominer release. Please use
+        `CytoTable <https://github.com/cytomining/CytoTable>`_ instead.
+
     Attributes
     ----------
     deep_data : DeepProfilerData

pycytominer/cyto_utils/annotate_custom.py

@@ -78,6 +78,10 @@ def annotate_cmap(
 ) -> pd.DataFrame:
     """Annotates data frame with custom options according to CMAP specifications
 
+    .. warning::
+        ``annotate_cmap`` is deprecated and will be removed in a future
+        Pycytominer release.
+
     Parameters
     ----------
     annotated : pd.DataFrame

pycytominer/cyto_utils/cell_locations.py

@@ -19,6 +19,10 @@ class CellLocation:
     """This class holds all the functions augment a metadata file with X,Y
     locations of cells in each image.
 
+    .. warning::
+        The ``CellLocation`` class is deprecated and will be removed in a
+        future Pycytominer release.
+
     In the metadata file, which is either a CSV or a Parquet file,
     - Each row is single multi-channel image
     - Each image is indexed by multiple columns, e.g., `Metadata_Plate`, `Metadata_Well`,`Metadata_Site`

pycytominer/cyto_utils/cells.py

@@ -35,6 +35,11 @@ class SingleCells:
     """This is a class to interact with single cell morphological profiles. Interaction
     includes aggregation, normalization, and output.
 
+    .. warning::
+        The ``SingleCells`` class is deprecated and will be removed in a
+        future Pycytominer release. Please use
+        `CytoTable <https://github.com/cytomining/CytoTable>`_ instead.
+
     Attributes
     ----------
     sql_file : str

pycytominer/cyto_utils/collate.py

@@ -46,6 +46,13 @@ def collate(
 ):
     """Collate the CellProfiler-created CSVs into a single SQLite file by calling cytominer-database
 
+    .. warning::
+        With the deprecation of cytominer-database, ``collate`` is deprecated
+        and will be removed in a future Pycytominer release. Please consider
+        using CellProfiler's ``ExportToDatabase`` module to create single-cell
+        SQLite files, or `CytoTable <https://github.com/cytomining/CytoTable>`_
+        to create single-cell Parquet files.
+
     Parameters
     ----------
     batch : str