Merge pull request #31 from yutanagano/improve_docs

Improve docs
yutanagano · Aug 21, 2024 · 037027d · 037027d
2 parents 3fb49d3 + 9ed6793
commit 037027d
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Showing 2 changed files with 24 additions and 10 deletions.
diff --git a/src/sceptr/__init__.py b/src/sceptr/__init__.py
@@ -20,9 +20,12 @@ def calc_cdist_matrix(anchors: DataFrame, comparisons: DataFrame) -> ndarray:
     Parameters
     ----------
     anchors : DataFrame
-        DataFrame in the :ref:`prescribed format <data_format>`.
+        DataFrame specifying the first (anchor) collection of input TCRs.
+        It must be in the :ref:`prescribed format <data_format>`.
+
     comparisons : DataFrame
-        DataFrame in the :ref:`prescribed format <data_format>`.
+        DataFrame specifying the second (comparison) collection of input TCRs.
+        It must be in the :ref:`prescribed format <data_format>`.
 
     Returns
     -------
@@ -40,7 +43,8 @@ def calc_pdist_vector(instances: DataFrame) -> ndarray:
     Parameters
     ----------
     instances : DataFrame
-        DataFrame in the :ref:`prescribed format <data_format>`.
+        DataFrame specifying the input TCRs.
+        It must be in the :ref:`prescribed format <data_format>`.
 
     Returns
     -------
@@ -58,7 +62,8 @@ def calc_vector_representations(instances: DataFrame) -> ndarray:
     Parameters
     ----------
     instances : DataFrame
-        DataFrame in the :ref:`prescribed format <data_format>`.
+        DataFrame specifying the input TCRs.
+        It must be in the :ref:`prescribed format <data_format>`.
 
     Returns
     -------
@@ -77,11 +82,13 @@ def calc_residue_representations(instances: DataFrame) -> ResidueRepresentations
     Parameters
     ----------
     instances : DataFrame
-        DataFrame in the :ref:`prescribed format <data_format>`.
+        DataFrame specifying the input TCRs.
+        It must be in the :ref:`prescribed format <data_format>`.
 
     Returns
     -------
     :py:class:`~sceptr.model.ResidueRepresentations`
+        An array of representation vectors for each amino acid residue in the tokenised forms of the input TCRs.
         For details on how to interpret/use this output, please refer to the documentation for :py:class:`~sceptr.model.ResidueRepresentations`.
     """
     return get_default_model().calc_residue_representations(instances)

diff --git a/src/sceptr/model.py b/src/sceptr/model.py
@@ -137,7 +137,8 @@ def calc_vector_representations(self, instances: DataFrame) -> ndarray:
         Parameters
         ----------
         instances : DataFrame
-            DataFrame in the :ref:`prescribed format <data_format>`.
+            DataFrame specifying the input TCRs.
+            It must be in the :ref:`prescribed format <data_format>`.
 
         Returns
         -------
@@ -160,11 +161,13 @@ def calc_residue_representations(self, instances: DataFrame) -> ResidueRepresent
         Parameters
         ----------
         instances : DataFrame
-            DataFrame in the :ref:`prescribed format <data_format>`.
+            DataFrame specifying the input TCRs.
+            It must be in the :ref:`prescribed format <data_format>`.
 
         Returns
         -------
         :py:class:`~sceptr.model.ResidueRepresentations`
+            An array of representation vectors for each amino acid residue in the tokenised forms of the input TCRs.
             For details on how to interpret/use this output, please refer to the documentation for :py:class:`~sceptr.model.ResidueRepresentations`.
         """
         if not isinstance(self._tokeniser, CdrTokeniser):
@@ -239,9 +242,12 @@ def calc_cdist_matrix(self, anchors: DataFrame, comparisons: DataFrame) -> ndarr
         Parameters
         ----------
         anchors : DataFrame
-            DataFrame in the :ref:`prescribed format <data_format>`.
+            DataFrame specifying the first (anchor) collection of input TCRs.
+            It must be in the :ref:`prescribed format <data_format>`.
+
         comparisons : DataFrame
-            DataFrame in the :ref:`prescribed format <data_format>`.
+            DataFrame specifying the second (comparison) collection of input TCRs.
+            It must be in the :ref:`prescribed format <data_format>`.
 
         Returns
         -------
@@ -263,7 +269,8 @@ def calc_pdist_vector(self, instances: DataFrame) -> ndarray:
         Parameters
         ----------
         instances : DataFrame
-            DataFrame in the :ref:`prescribed format <data_format>`.
+            DataFrame specifying the input TCRs.
+            It must be in the :ref:`prescribed format <data_format>`.
 
         Returns
         -------