Merge pull request #67 from MannLabs/64-register-readers

64 register readers
MannLabs · Jun 28, 2024 · 1fdcde7 · 1fdcde7
2 parents efdb5fe + 6b8156c
commit 1fdcde7
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Showing 12 changed files with 88 additions and 42 deletions.
diff --git a/alpharaw/__init__.py b/alpharaw/__init__.py
@@ -5,21 +5,19 @@
 warnings.filterwarnings("ignore")
 
 
-def register_readers():
-    from .legacy_msdata import mgf  # noqa: F401  # TODO remove import side effect
-    from .ms_data_base import (
-        ms_reader_provider,  # noqa: F401  # TODO remove import side effect
-    )
-    from .mzml import MzMLReader  # noqa: F401  # TODO remove import side effect
-    from .wrappers import (
-        alphapept_wrapper,  # noqa: F401  # TODO remove import side effect
-    )
+def register_all_readers():
+    from .legacy_msdata.mgf import register_readers as register_mgf_readers
+    from .mzml import register_readers as register_mzml_readers
+
+    register_mzml_readers()
+    register_mgf_readers()
 
     try:
-        from .sciex import SciexWiffData  # noqa: F401  # TODO remove import side effect
-        from .thermo import (
-            ThermoRawData,  # noqa: F401  # TODO remove import side effect
-        )
+        from .sciex import register_readers as register_wiff_readers
+        from .thermo import register_readers as register_raw_readers
+
+        register_wiff_readers()
+        register_raw_readers()
     except (RuntimeError, ImportError):
         print("[WARN] pythonnet is not installed")
 

diff --git a/alpharaw/legacy_msdata/mgf.py b/alpharaw/legacy_msdata/mgf.py
@@ -146,4 +146,9 @@ def _set_dataframes(self, raw_data: dict):
         )
 
 
-ms_reader_provider.register_reader("mgf", MGFReader)
+def register_readers():
+    """
+    Register :class:`MGFReader` for file format "mgf" in
+    :obj:`alpharaw.ms_data_base.ms_reader_provider`.
+    """
+    ms_reader_provider.register_reader("mgf", MGFReader)
diff --git a/alpharaw/match/psm_match.py b/alpharaw/match/psm_match.py
@@ -9,7 +9,7 @@
     get_charged_frag_types,
 )
 
-from alpharaw import register_readers
+from alpharaw import register_all_readers
 from alpharaw.dia.normal_dia import NormalDIAGrouper
 from alpharaw.match.match_utils import (
     match_closest_peaks,
@@ -24,7 +24,7 @@
 )
 from alpharaw.utils.ms_path_utils import parse_ms_files_to_dict
 
-register_readers()  # TODO remove this import side effect
+register_all_readers()  # TODO remove this import side effect
 
 
 class PepSpecMatch:

diff --git a/alpharaw/ms_data_base.py b/alpharaw/ms_data_base.py
@@ -440,8 +440,9 @@ def index_ragged_list(ragged_list: list) -> np.ndarray:
 class MSData_HDF(MSData_Base):
     """
     Wrapper of reader for alpharaw's HDF5 spectrum file.
-    This class is registered as "alpharaw", "raw.hdf", "alpharaw_hdf", "hdf" and "hdf5"
-    in :obj:`ms_reader_provider` instance.
+    This class will be registered as file formats (types)
+    "alpharaw", "raw.hdf", "alpharaw_hdf", "hdf" and "hdf5"
+    in :obj:`ms_reader_provider` instance by :func:`register_readers`.
     """
 
     def import_raw(self, _path: str):
@@ -495,12 +496,22 @@ def get_reader(
 
 ms_reader_provider = MSReaderProvider()
 """
-MS data register (:class:`.MSReaderProvider`) performs as a factory to
-produce different readers for different file formats.
+MS data register (:class:`MSReaderProvider`) performs as a factory to
+produce different readers for given file formats.
 """
 
-ms_reader_provider.register_reader("alpharaw", MSData_HDF)
-ms_reader_provider.register_reader("raw.hdf", MSData_HDF)
-ms_reader_provider.register_reader("alpharaw_hdf", MSData_HDF)
-ms_reader_provider.register_reader("hdf", MSData_HDF)
-ms_reader_provider.register_reader("hdf5", MSData_HDF)
+
+def register_readers():
+    """
+    Register :class:`MSData_HDF` for file formats (types):
+    "alpharaw", "raw.hdf", "alpharaw_hdf", "hdf", "hdf5"
+    in :obj:`ms_reader_provider`.
+    """
+    ms_reader_provider.register_reader("alpharaw", MSData_HDF)
+    ms_reader_provider.register_reader("raw.hdf", MSData_HDF)
+    ms_reader_provider.register_reader("alpharaw_hdf", MSData_HDF)
+    ms_reader_provider.register_reader("hdf", MSData_HDF)
+    ms_reader_provider.register_reader("hdf5", MSData_HDF)
+
+
+register_readers()
diff --git a/alpharaw/mzml.py b/alpharaw/mzml.py
@@ -11,9 +11,9 @@
 
 class MzMLReader(MSData_Base):
     """
-    Load mzml file as `:class:`MSData_Base` structure.
-    This reader will be registered as "mzml"
-    in :obj:`alphraw.ms_data_base.ms_reader_provider`.
+    Load mzml file as `:class:`alpharaw.ms_data_base.MSData_Base` structure.
+    This reader will be registered as "mzml" in
+    :obj:`alphraw.ms_data_base.ms_reader_provider` by :func:`register_readers`
     """
 
     def __init__(self, centroided: bool = True, save_as_hdf: bool = False, **kwargs):
@@ -222,4 +222,9 @@ def parse_mzml_entry(item_dict: dict) -> tuple:
     )
 
 
-ms_reader_provider.register_reader("mzml", MzMLReader)
+def register_readers():
+    """
+    Register :class:`MzMLReader` for file format "mzml" in
+    :obj:`alpharaw.ms_data_base.ms_reader_provider`.
+    """
+    ms_reader_provider.register_reader("mzml", MzMLReader)
diff --git a/alpharaw/sciex.py b/alpharaw/sciex.py
@@ -7,9 +7,9 @@
 
 class SciexWiffData(MSData_Base):
     """
-    Load Sciex Wiff data as :class:`MSData_Base` data structure.
+    Load Sciex Wiff data as :class:`alpharaw.ms_data_base.MSData_Base` data structure.
     This reader will be registered as "sciex", "sciex_wiff", and "sciex_raw"
-    in :obj:`alpharaw.ms_data_base.ms_reader_provider`.
+    in :obj:`alpharaw.ms_data_base.ms_reader_provider` by :func:`register_readers()`.
     """
 
     def __init__(self, centroided: bool = True, save_as_hdf: bool = False, **kwargs):
@@ -62,6 +62,11 @@ def _import(self, _wiff_file_path: str) -> dict:
         return data_dict
 
 
-ms_reader_provider.register_reader("sciex", SciexWiffData)
-ms_reader_provider.register_reader("sciex_wiff", SciexWiffData)
-ms_reader_provider.register_reader("sciex_raw", SciexWiffData)
+def register_readers():
+    """
+    Register :class:`SciexWiffData` for file formats (types):
+    "sciex", "sciex_wiff", and "sciex_raw" in :obj:`alpharaw.ms_data_base.ms_reader_provider`.
+    """
+    ms_reader_provider.register_reader("sciex", SciexWiffData)
+    ms_reader_provider.register_reader("sciex_wiff", SciexWiffData)
+    ms_reader_provider.register_reader("sciex_raw", SciexWiffData)
diff --git a/alpharaw/thermo.py b/alpharaw/thermo.py
@@ -51,9 +51,9 @@
 
 class ThermoRawData(MSData_Base):
     """
-    Loading Thermo Raw data as MSData_Base data structure.
-    This class is registered "thermo" and "thermo_raw" in
-    :obj:`alpharaw.ms_data_base.ms_reader_provider`.
+    Loading Thermo Raw data as :class:`alpharaw.ms_data_base.MSData_Base` data structure.
+    This class will be registered as file formats "thermo" and "thermo_raw" in
+    :obj:`alpharaw.ms_data_base.ms_reader_provider` by :func:`register_readers`.
     """
 
     def __init__(
@@ -372,5 +372,10 @@ def _get_mono_and_charge(trailer_data, scan_event):
     return mono, charge
 
 
-ms_reader_provider.register_reader("thermo", ThermoRawData)
-ms_reader_provider.register_reader("thermo_raw", ThermoRawData)
+def register_readers():
+    """
+    Register :class:`ThermoRawData` for file formats (types):
+    "thermo" and "thermo_raw" in :obj:`alpharaw.ms_data_base.ms_reader_provider`.
+    """
+    ms_reader_provider.register_reader("thermo", ThermoRawData)
+    ms_reader_provider.register_reader("thermo_raw", ThermoRawData)
diff --git a/docs/reader_modules.rst b/docs/reader_modules.rst
@@ -8,3 +8,4 @@ readers modules
    readers/thermo
    readers/sciex
    readers/mzml
+   readers/mgf
diff --git a/docs/readers/mgf.rst b/docs/readers/mgf.rst
@@ -0,0 +1,7 @@
+alpharaw.legacy_msdata.mgf
+==========================
+
+.. automodule:: alpharaw.legacy_msdata.mgf
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/nbs_tests/legacy_msdata/mgf.ipynb b/nbs_tests/legacy_msdata/mgf.ipynb
@@ -22,7 +22,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from alpharaw.legacy_msdata.mgf import *"
+    "from alpharaw import register_all_readers\n",
+    "from alpharaw.legacy_msdata.mgf import *\n",
+    "\n",
+    "register_all_readers()"
    ]
   },
   {

diff --git a/nbs_tests/match/psm_match.ipynb b/nbs_tests/match/psm_match.ipynb
@@ -29,7 +29,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from alpharaw.match.psm_match import *"
+    "from alpharaw import register_all_readers\n",
+    "from alpharaw.match.psm_match import *\n",
+    "\n",
+    "register_all_readers()"
    ]
   },
   {

diff --git a/nbs_tests/wrappers/alphatims_wrapper.ipynb b/nbs_tests/wrappers/alphatims_wrapper.ipynb
@@ -22,7 +22,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from alpharaw.wrappers.alphatims_wrapper import *"
+    "from alpharaw import register_all_readers\n",
+    "from alpharaw.wrappers.alphatims_wrapper import *\n",
+    "\n",
+    "register_all_readers()"
    ]
   },
   {