From 8bde7b9a0faf7e74620bb8dd02dac22971a11578 Mon Sep 17 00:00:00 2001
From: RalfG <ralfg@hotmail.be>
Date: Mon, 6 May 2024 17:46:52 +0200
Subject: [PATCH] Add io.parquet module to docs

---
 docs/source/api/psm_utils.io.rst | 23 ++++++++++++++++-------
 psm_utils/io/__init__.py         | 12 ++++++------
 psm_utils/io/sage.py             |  6 +++---
 3 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/docs/source/api/psm_utils.io.rst b/docs/source/api/psm_utils.io.rst
index 40e42d7..d858997 100644
--- a/docs/source/api/psm_utils.io.rst
+++ b/docs/source/api/psm_utils.io.rst
@@ -6,19 +6,19 @@ psm_utils.io
    :members:
 
 
-psm_utils.io.ionbot
-##########################
 
-.. automodule:: psm_utils.io.ionbot
+psm_utils.io.idxml
+##################
+
+.. automodule:: psm_utils.io.idxml
    :members:
    :inherited-members:
 
 
+psm_utils.io.ionbot
+##########################
 
-psm_utils.io.idxml
-##################
-
-.. automodule:: psm_utils.io.idxml
+.. automodule:: psm_utils.io.ionbot
    :members:
    :inherited-members:
 
@@ -51,6 +51,15 @@ psm_utils.io.mzid
 
 
 
+psm_utils.io.parquet
+#################
+
+.. automodule:: psm_utils.io.parquet
+   :members:
+   :inherited-members:
+
+
+
 psm_utils.io.peptide_record
 ###########################
 
diff --git a/psm_utils/io/__init__.py b/psm_utils/io/__init__.py
index 45b3d7a..79f09ac 100644
--- a/psm_utils/io/__init__.py
+++ b/psm_utils/io/__init__.py
@@ -28,6 +28,12 @@
 from psm_utils.psm_list import PSMList
 
 FILETYPES = {
+    "ionbot": {
+        "reader": ionbot.IonbotReader,
+        "writer": None,
+        "extension": "ionbot.first.csv",
+        "filename_pattern": r"^ionbot.first.csv$",
+    },
     "idxml": {
         "reader": idxml.IdXMLReader,
         "writer": idxml.IdXMLWriter,
@@ -100,12 +106,6 @@
         "extension": ".parquet",
         "filename_pattern": r"^.*(?:_|\.).sage.parquet$",
     },
-    "ionbot": {
-        "reader": ionbot.IonbotReader,
-        "writer": None,
-        "extension": "ionbot.first.csv",
-        "filename_pattern": r"^ionbot.first.csv$",
-    },
     "parquet": {  # List after proteoscape and sage to avoid extension matching conflicts
         "reader": parquet.ParquetReader,
         "writer": parquet.ParquetWriter,
diff --git a/psm_utils/io/sage.py b/psm_utils/io/sage.py
index 4cc23e3..eb1fae9 100644
--- a/psm_utils/io/sage.py
+++ b/psm_utils/io/sage.py
@@ -24,7 +24,7 @@
 set_csv_field_size_limit()
 
 
-class SageReaderBase(ReaderBase, ABC):
+class _SageReaderBase(ReaderBase, ABC):
     def __init__(
         self, filename, score_column: str = "sage_discriminant_score", *args, **kwargs
     ) -> None:
@@ -104,7 +104,7 @@ def from_dataframe(cls, dataframe) -> PSMList:
         )
 
 
-class SageTSVReader(SageReaderBase):
+class SageTSVReader(_SageReaderBase):
     def __iter__(self) -> Iterable[PSM]:
         """Iterate over file and return PSMs one-by-one."""
         with open(self.filename, "r") as open_file:
@@ -119,7 +119,7 @@ def __iter__(self) -> Iterable[PSM]:
 SageReader = SageTSVReader  # Alias for backwards compatibility
 
 
-class SageParquetReader(SageReaderBase):
+class SageParquetReader(_SageReaderBase):
     def __iter__(self) -> Iterable[PSM]:
         """Iterate over file and return PSMs one-by-one."""
         with pq.ParquetFile(self.filename) as pq_file: