From c1ca60edc0fcb559a5762862e1f83233d607bb89 Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Fri, 21 Jun 2024 14:33:09 +0200
Subject: [PATCH 1/6] #64 use register_readers() to register readers

---
 docs/reader_modules.rst | 1 +
 docs/readers/mgf.rst    | 7 +++++++
 2 files changed, 8 insertions(+)
 create mode 100644 docs/readers/mgf.rst

diff --git a/docs/reader_modules.rst b/docs/reader_modules.rst
index 1a58965..79737e7 100644
--- 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
new file mode 100644
index 0000000..de1ec01
--- /dev/null
+++ b/docs/readers/mgf.rst
@@ -0,0 +1,7 @@
+alpharaw.legacy_msdata.mgf
+==========================
+
+.. automodule:: alpharaw.legacy_msdata.mgf
+   :members:
+   :undoc-members:
+   :show-inheritance:

From 73a119298869e9b06d90d34fb991d0bc7338a947 Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Fri, 21 Jun 2024 14:33:28 +0200
Subject: [PATCH 2/6] #64 use register_readers() to register readers

---
 alpharaw/__init__.py          | 22 ++++++++++------------
 alpharaw/legacy_msdata/mgf.py |  7 ++++++-
 alpharaw/ms_data_base.py      | 26 +++++++++++++++++---------
 alpharaw/mzml.py              | 13 +++++++++----
 alpharaw/sciex.py             | 15 ++++++++++-----
 alpharaw/thermo.py            | 15 ++++++++++-----
 6 files changed, 62 insertions(+), 36 deletions(-)

diff --git a/alpharaw/__init__.py b/alpharaw/__init__.py
index b19381b..de5af21 100644
--- a/alpharaw/__init__.py
+++ b/alpharaw/__init__.py
@@ -6,20 +6,18 @@
 
 
 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
-    )
+    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
index cf57c18..447ce50 100644
--- 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/ms_data_base.py b/alpharaw/ms_data_base.py
index 915ec85..3fd2546 100644
--- 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 +496,19 @@ 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)
diff --git a/alpharaw/mzml.py b/alpharaw/mzml.py
index 9ad2232..e3d5b99 100644
--- 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
index b4b4508..c14b488 100644
--- 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
index 242bed7..e32795a 100644
--- 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)

From be0cf31280cf951c7ea6778ee10c581c31401c5c Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Fri, 21 Jun 2024 14:43:56 +0200
Subject: [PATCH 3/6] #64 register_readers on __init__

---
 alpharaw/__init__.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/alpharaw/__init__.py b/alpharaw/__init__.py
index de5af21..e843c88 100644
--- a/alpharaw/__init__.py
+++ b/alpharaw/__init__.py
@@ -22,6 +22,9 @@ def register_readers():
         print("[WARN] pythonnet is not installed")
 
 
+register_readers()
+
+
 __project__ = "alpharaw"
 __version__ = "0.4.5"
 __license__ = "Apache"

From 2272dd620e002bad6898b923f7697ac5b26cfd5a Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Mon, 24 Jun 2024 08:31:25 +0200
Subject: [PATCH 4/6] #64 remove reader register call in init

---
 alpharaw/__init__.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/alpharaw/__init__.py b/alpharaw/__init__.py
index e843c88..03caef5 100644
--- a/alpharaw/__init__.py
+++ b/alpharaw/__init__.py
@@ -5,7 +5,7 @@
 warnings.filterwarnings("ignore")
 
 
-def register_readers():
+def register_all_readers():
     from .legacy_msdata.mgf import register_readers as register_mgf_readers
     from .mzml import register_readers as register_mzml_readers
 
@@ -22,9 +22,6 @@ def register_readers():
         print("[WARN] pythonnet is not installed")
 
 
-register_readers()
-
-
 __project__ = "alpharaw"
 __version__ = "0.4.5"
 __license__ = "Apache"

From c320b12fd9d530acba6abf945bed8abb9b21a0d6 Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Mon, 24 Jun 2024 10:13:28 +0200
Subject: [PATCH 5/6] #64 FIX side effects of using register_readers()

---
 alpharaw/match/psm_match.py                | 4 ++--
 nbs_tests/legacy_msdata/mgf.ipynb          | 5 ++++-
 nbs_tests/match/psm_match.ipynb            | 5 ++++-
 nbs_tests/wrappers/alphatims_wrapper.ipynb | 5 ++++-
 4 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/alpharaw/match/psm_match.py b/alpharaw/match/psm_match.py
index 0f5572c..be8b5d8 100644
--- 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/nbs_tests/legacy_msdata/mgf.ipynb b/nbs_tests/legacy_msdata/mgf.ipynb
index adf706d..4c2e4cc 100644
--- 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
index 5b7ad77..7f872c4 100644
--- 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
index 42eb351..0df8f1d 100644
--- 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()"
    ]
   },
   {

From 6b8156c1db7150a3afdf8ed9a36cfdff9dc04cda Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Thu, 27 Jun 2024 15:53:20 +0200
Subject: [PATCH 6/6] ADD register MSData_HDF by default

---
 alpharaw/ms_data_base.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/alpharaw/ms_data_base.py b/alpharaw/ms_data_base.py
index 3fd2546..4b09aac 100644
--- a/alpharaw/ms_data_base.py
+++ b/alpharaw/ms_data_base.py
@@ -512,3 +512,6 @@ def register_readers():
     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()