fix docstrings after review

cytomining · Feb 4, 2022 · 442219e · 442219e
1 parent 92da3a0
commit 442219e
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Showing 4 changed files with 31 additions and 9 deletions.
diff --git a/pycytominer/cyto_utils/load.py b/pycytominer/cyto_utils/load.py
@@ -8,8 +8,8 @@ def infer_delim(file):
     """
     Sniff the delimiter in the given file
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     file : str
         File name
 
@@ -33,8 +33,8 @@ def load_profiles(profiles):
     """
     Unless a dataframe is provided, load the given profile dataframe from path or string
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     profiles : {str, pandas.DataFrame}
         file location or actual pandas dataframe of profiles
 
@@ -55,8 +55,8 @@ def load_platemap(platemap, add_metadata_id=True):
     """
     Unless a dataframe is provided, load the given platemap dataframe from path or string
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     platemap : pandas dataframe
         location or actual pandas dataframe of platemap file
 
@@ -65,7 +65,7 @@ def load_platemap(platemap, add_metadata_id=True):
 
     Return
     ------
-    platemap : pandas DataFrame
+    platemap : pandas.core.frame.DataFrame
         pandas DataFrame of profiles
     """
     if not isinstance(platemap, pd.DataFrame):
@@ -93,12 +93,17 @@ def load_npz(npz_file, fallback_feature_prefix="DP"):
 
     If the npz file does not exist, this function returns an empty dataframe.
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     npz_file : str
         file path to the compressed output (typically DeepProfiler output)
     fallback_feature_prefix :str
         a string to prefix all features [default: "DP"].
+
+    Return
+    ------
+    df : pandas.core.frame.DataFrame
+        pandas DataFrame of profiles
     """
     try:
         npz = np.load(npz_file, allow_pickle=True)

diff --git a/pycytominer/cyto_utils/output.py b/pycytominer/cyto_utils/output.py
@@ -118,6 +118,11 @@ def check_compression_method(compression):
     ----------
     compression : str
         The category of compression options available
+
+    Returns
+    -------
+    None
+        Asserts available options
     """
     assert (
         compression in compress_options

diff --git a/pycytominer/cyto_utils/single_cell_ingest_utils.py b/pycytominer/cyto_utils/single_cell_ingest_utils.py
@@ -35,6 +35,11 @@ def assert_linking_cols_complete(linking_cols="default", compartments="default")
     compartments : str or list, default "default"
         Which compartments used in the experiment.
 
+    Returns
+    -------
+    None
+        Asserts linking columns are appropriately defined
+
     .. note::
         assert_linking_cols_complete() does not check if columns are present
     """

diff --git a/pycytominer/operations/transform.py b/pycytominer/operations/transform.py
@@ -125,6 +125,13 @@ def fit(self, X, y=None):
     def transform(self, X, y=None):
         """Perform the sphering transform
 
+        Parameters
+        ----------
+        X : pd.core.frame.DataFrame
+            Profile dataframe to be transformed using the precompiled weights
+        y : None
+            Has no effect; only used for consistency in sklearn transform API
+
         Returns
         -------
         pandas.core.frame.DataFrame