Linting vi

alphabase/psm_reader/alphapept_reader.py

@@ -1,3 +1,5 @@
+"""Reader for AlphaPept's *.ms_data.hdf files."""
+
 from pathlib import Path
 from typing import Optional, Tuple
 
@@ -48,6 +50,8 @@ def parse_ap(precursor: str) -> Tuple[str, str, str, str, int]:
 
 
 class AlphaPeptReader(PSMReaderBase):
+    """Reader for AlphaPept's *.ms_data.hdf files."""
+
     def __init__(
         self,
         *,
@@ -105,4 +109,5 @@ def _load_modifications(self, df: pd.DataFrame) -> None:
 
 
 def register_readers() -> None:
+    """Register readers for AlphaPept's *.ms_data.hdf files."""
     psm_reader_provider.register_reader("alphapept", AlphaPeptReader)

alphabase/psm_reader/dia_psm_reader.py

@@ -1,3 +1,5 @@
+"""Readers for Spectronaut's output library and reports, Swath data and DIANN data."""
+
 from typing import List, Optional
 
 import numpy as np
@@ -33,6 +35,7 @@ def __init__(  # noqa: PLR0913 many arguments in function definition
         rt_unit: str = "minute",
         **kwargs,
     ):
+        """Initialize SpectronautReader."""
         if mod_seq_columns is None:
             mod_seq_columns = psm_reader_yaml["spectronaut"]["mod_seq_columns"]
 
@@ -69,6 +72,8 @@ def _load_file(self, filename: str) -> pd.DataFrame:
 
 
 class SwathReader(SpectronautReader):
+    """Reader for SWATH or OpenSWATH library TSV/CSV."""
+
     def __init__(  # noqa: PLR0913 many arguments in function definition
         self,
         *,
@@ -96,6 +101,8 @@ def __init__(  # noqa: PLR0913 many arguments in function definition
 
 
 class DiannReader(SpectronautReader):
+    """Reader for DIANN data."""
+
     def __init__(  # noqa: PLR0913 many arguments in function definition
         self,
         *,
@@ -107,9 +114,7 @@ def __init__(  # noqa: PLR0913 many arguments in function definition
         rt_unit: str = "minute",
         **kwargs,
     ):
-        """Also similar to `MaxQuantReader`,
-        but different in column_mapping and modification_mapping.
-        """
+        """Similar to `SpectronautReader` but different in column_mapping and modification_mapping."""
         super().__init__(
             column_mapping=column_mapping,
             modification_mapping=modification_mapping,
@@ -161,6 +166,7 @@ def __init__(  # noqa: PLR0913 many arguments in function definition
         rt_unit: str = "minute",
         **kwargs,
     ):
+        """Initialize SpectronautReportReader."""
         super().__init__(
             column_mapping=column_mapping,
             modification_mapping=modification_mapping,
@@ -190,6 +196,7 @@ def _load_file(self, filename: str) -> pd.DataFrame:
 
 
 def register_readers() -> None:
+    """Register readers for Spectronaut's output library and reports, Swath data and DIANN data."""
     psm_reader_provider.register_reader("spectronaut", SpectronautReader)
     psm_reader_provider.register_reader("speclib_tsv", SpectronautReader)
     psm_reader_provider.register_reader("openswath", SwathReader)

alphabase/psm_reader/keys.py

@@ -1,10 +1,13 @@
+"""Constants for accessing the columns of a PSM dataframe."""
+
 from typing import Any, List, NoReturn
 
 
 class ConstantsClass(type):
     """A metaclass for classes that should only contain string constants."""
 
     def __setattr__(cls, name: Any, value: Any) -> NoReturn:  # noqa: ANN401
+        """Raise an error when trying to set an attribute."""
         raise TypeError("Constants class cannot be modified")
 
     def get_values(cls) -> List[str]:

alphabase/psm_reader/maxquant_reader.py

@@ -1,3 +1,5 @@
+"""Reader for MaxQuant data."""
+
 import copy
 import warnings
 from typing import List, Optional
@@ -32,6 +34,7 @@
 def replace_parentheses_with_brackets(
     modseq: str,
 ) -> str:
+    """Replace parentheses with brackets in the modified sequence."""
     mod_depth = 0
     for i, aa in enumerate(modseq):
         if aa == "(":
@@ -66,9 +69,9 @@ def parse_mod_seq(
         separator to indicate the modification section.
         Defaults to '()'
 
-    fixed_C : bool
+    fixed_C57 : bool
         If Carbamidomethyl@C is a fixed modification
-        and not displayed in the sequence. Defaults to True for MaxQuant.
+        and not displayed in the sequence. Defaults to True.
 
     Returns
     -------
@@ -132,6 +135,8 @@ def parse_mod_seq(
 
 
 class MaxQuantReader(PSMReaderBase):
+    """Reader for MaxQuant data."""
+
     def __init__(  # noqa: PLR0913 many arguments in function definition
         self,
         *,
@@ -172,6 +177,9 @@ def __init__(  # noqa: PLR0913 many arguments in function definition
             The columns to find modified sequences,
             by default ['Modified sequence']
 
+        **kwargs : dict
+            deprecated
+
         """
         if mod_seq_columns is None:
             mod_seq_columns = [
@@ -205,6 +213,7 @@ def _init_modification_mapping(self) -> None:
     def set_modification_mapping(
         self, modification_mapping: Optional[dict] = None
     ) -> None:
+        """Set modification mapping."""
         super().set_modification_mapping(modification_mapping)
         self._add_all_unimod()
         self._extend_mod_brackets()
@@ -300,4 +309,5 @@ def _load_modifications(self, origin_df: pd.DataFrame) -> None:
 
 
 def register_readers() -> None:
+    """Register MaxQuant reader."""
     psm_reader_provider.register_reader("maxquant", MaxQuantReader)

alphabase/psm_reader/msfragger_reader.py

@@ -1,3 +1,5 @@
+"""MSFragger reader."""
+
 from typing import List, Optional, Tuple
 
 import numpy as np
@@ -81,14 +83,19 @@ def _get_mods_from_masses(  # noqa: PLR0912, C901 too many branches, too complex
 
 
 class MSFragger_PSM_TSV_Reader(PSMReaderBase):  # noqa: N801 name should use CapWords convention TODO: refactor
+    """Reader for MSFragger's psm.tsv file."""
+
     def __init__(
         self,
         **kwargs,
     ):
+        """Constructor."""
         raise NotImplementedError("MSFragger_PSM_TSV_Reader for psm.tsv")
 
 
 class MSFraggerPepXML(PSMReaderBase):
+    """Reader for MSFragger's pep.xml file."""
+
     def __init__(  # noqa: PLR0913 many arguments in function definition
         self,
         *,
@@ -182,6 +189,7 @@ def _post_process(self) -> None:
 
 
 def register_readers() -> None:
+    """Register MSFragger readers."""
     psm_reader_provider.register_reader("msfragger_psm_tsv", MSFragger_PSM_TSV_Reader)
     psm_reader_provider.register_reader("msfragger", MSFragger_PSM_TSV_Reader)
     psm_reader_provider.register_reader("msfragger_pepxml", MSFraggerPepXML)

alphabase/psm_reader/pfind_reader.py

@@ -1,3 +1,5 @@
+"""pFind reader."""
+
 from typing import Optional, Tuple, Union
 
 import numpy as np
@@ -49,6 +51,7 @@ def _convert_one_pfind_mod(mod: str) -> Optional[str]:  # noqa:  C901 too comple
 
 
 def translate_pFind_mod(mod_str: str) -> Union[str, NAType]:  # noqa: N802 name `get_pFind_mods` should be lowercase TODO: used by peptdeep
+    """Translate pFind modification string."""
     if not mod_str:
         return ""
     ret_mods = []
@@ -61,6 +64,7 @@ def translate_pFind_mod(mod_str: str) -> Union[str, NAType]:  # noqa: N802 name
 
 
 def get_pFind_mods(pfind_mod_str: str) -> Tuple[str, str]:  # noqa: N802 name `get_pFind_mods` should be lowercase TODO: used by peptdeep
+    """Parse pFind modification string."""
     pfind_mod_str = pfind_mod_str.strip(";")
     if not pfind_mod_str:
         return "", ""
@@ -79,6 +83,7 @@ def get_pFind_mods(pfind_mod_str: str) -> Tuple[str, str]:  # noqa: N802 name `g
 
 
 def parse_pfind_protein(protein: str, *, keep_reverse: bool = True) -> str:
+    """Parse pFind protein string."""
     proteins = protein.strip("/").split("/")
     return ";".join(
         [
@@ -90,6 +95,8 @@ def parse_pfind_protein(protein: str, *, keep_reverse: bool = True) -> str:
 
 
 class pFindReader(PSMReaderBase):  # noqa: N801 name `pFindReader` should use CapWords convention TODO: used by peptdeep, alpharaw
+    """Reader for pFind's *.txt files."""
+
     def __init__(
         self,
         *,
@@ -99,6 +106,7 @@ def __init__(
         keep_decoy: bool = False,
         **kwargs,
     ):
+        """Reading PSMs from pFind's *.txt."""
         super().__init__(
             column_mapping=column_mapping,
             modification_mapping=modification_mapping,
@@ -151,5 +159,6 @@ def _load_modifications(self, pfind_df: pd.DataFrame) -> None:
 
 
 def register_readers() -> None:
+    """Register pFind readers."""
     psm_reader_provider.register_reader("pfind", pFindReader)
     psm_reader_provider.register_reader("pfind3", pFindReader)