MannLabs · jalew188 · Jun 24, 2024 · Jun 17, 2024 · Jun 17, 2024 · Jun 17, 2024
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,25 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+# formats: all
+
+# conda:
+#   environment: misc/conda_dev_env.yaml
+
+# # Optionally set the version of Python and requirements required to build your docs
+python:
+  install:
+    - requirements: extra_requirements/development.txt
diff --git a/alpharaw/ms_data_base.py b/alpharaw/ms_data_base.py
@@ -440,7 +440,7 @@ 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 :data:`ms_reader_provider` instance.
+    in :obj:`ms_reader_provider` instance.
     """
 
     def import_raw(self, _path: str):

diff --git a/alpharaw/thermo.py b/alpharaw/thermo.py
@@ -26,8 +26,7 @@
     "faims_cv",
 ]
 
-#: The auxiliary items and types that can be accessed from thermo RawFileReader.
-__auxiliary_item_dtypes__ = {
+auxiliary_item_dtypes: dict = {
     "injection_time": np.float32,
     "cv": np.float32,
     "max_ion_time": np.float32,
@@ -45,27 +44,31 @@
     "scan_event_string": "U",
     "multinotch": "O",
 }
+"""
+The auxiliary items and types that can be accessed from thermo RawFileReader.
+"""
 
 
 class ThermoRawData(MSData_Base):
     """
     Loading Thermo Raw data as MSData_Base data structure.
-    This class is registered "thermo" and "thermo_raw" in :data:`ms_reader_provider`.
+    This class is registered "thermo" and "thermo_raw" in
+    :obj:`alpharaw.ms_data_base.ms_reader_provider`.
 
     Parameters
     ----------
     centroided : bool, optional
         If peaks will be centroided after loading. By defaults True.
     process_count : int, optional
-        number of spectra to load in each batch, by default 10.
+        Number of processes to load RAW data, by default 10.
     mp_batch_size : int, optional
-        automatically save hdf after load raw data, by default 5000.
+        Number of spectra to load in each batch, by default 5000.
     save_as_hdf : bool, optional
-        is DDA data, by default False.
+        Automatically save hdf after load raw data, by default False.
     dda : bool, optional
-        _description_, by default False.
+        Is DDA data, by default False.
     auxiliary_items : list, optional
-        Additional spectrum items, candidates are in :data:`__auxiliary_item_dtypes__`.
+        Additional spectrum items, candidates are in :data:`auxiliary_item_dtypes`.
         By default [].
     """
 
@@ -85,7 +88,7 @@ def __init__(
         self.mp_batch_size = mp_batch_size
         self.dda = dda
         self.auxiliary_items = auxiliary_items
-        self.column_dtypes.update(__auxiliary_item_dtypes__)
+        self.column_dtypes.update(auxiliary_item_dtypes)
 
     def _import(
         self,
@@ -190,7 +193,7 @@ def _import_batch(
         is dda data.
 
     auxiliary_items : list
-        Candidates are in :data:`__auxiliary_item_dtypes__`.
+        Candidates are in :data:`auxiliary_item_dtypes`.
 
     Returns
     -------
@@ -357,7 +360,7 @@ def _import_batch(
         "nce": np.array(ce_list, dtype=np.float32).copy(),
     }
     for key, val in list(auxiliary_dict.items()):
-        auxiliary_dict[key] = np.array(val, dtype=__auxiliary_item_dtypes__[key]).copy()
+        auxiliary_dict[key] = np.array(val, dtype=auxiliary_item_dtypes[key]).copy()
     spec_dict.update(auxiliary_dict)
     return spec_dict
 

diff --git a/docs/build_docs.sh b/docs/build_docs.sh
@@ -1,8 +1,8 @@
-rm -rf build
-conda env remove -n alphabasedocs
-conda create -n alphabasedocs python=3.9 -y
-# conda create -n alphatimsinstaller python=3.9
-conda activate alphabasedocs
+rm -rf _build
+conda env remove -n alpharawdocs
+conda create -n alpharawdocs python=3.10 -y
+# conda create -n alphatimsinstaller python=3.10
+conda activate alpharawdocs
 # call conda install git -y
 # call pip install 'git+https://github.com/MannLabs/alphatims.git#egg=alphatims[gui]' --use-feature=2020-resolver
 # brew install freetype

diff --git a/docs/conf.py b/docs/conf.py
@@ -36,6 +36,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.linkcode",
     "sphinx.ext.viewcode",
+    # 'sphinx.ext.autodoc',
     "autodocsumm",
     "nbsphinx",
     "myst_parser",
@@ -80,7 +81,7 @@ def linkcode_resolve(domain, info):
         # e.g. object is a typing.Union
         return None
     file = os.path.relpath(file, os.path.abspath(".."))
-    if not file.startswith("peptdeep"):
+    if not file.startswith("alpharaw"):
         # e.g. object is a typing.NewType
         return None
     start, end = lines[1], lines[1] + len(lines[0]) - 1
@@ -100,6 +101,10 @@ def linkcode_resolve(domain, info):
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
+html_css_files = [
+    "css/custom.css",
+]
+
 autodoc_default_options = {
     "autosummary": True,
     "special-members": "__init__",  # Include __init__ methods.

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,10 +1,13 @@
 Documentation for AlphaRaw
 =====================================
 
-The deep learning framework MS proteomics.
-For more information, see AlphaPeptDeep on `GitHub <https://github.com/MannLabs/alpharaw/>`_.
+AlphaRaw is a pure Python package which is designed to load MS data of different formats
+(Thermo, Sciex, mzml, ...) into a standard DataFrame (tabular) format.
+For more information, see AlphaRaw on `GitHub <https://github.com/MannLabs/alpharaw/>`_.
 
 .. toctree::
    :maxdepth: 2
 
-   notebooks
+   reader_modules
+   match_modules
+   viz_modules
diff --git a/docs/match/match_utils.rst b/docs/match/match_utils.rst
@@ -0,0 +1,7 @@
+alpharaw.match.match_utils
+==========================
+
+.. automodule:: alpharaw.match.match_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/match/psm_match.rst b/docs/match/psm_match.rst
@@ -0,0 +1,7 @@
+alpharaw.match.psm_match
+==========================
+
+.. automodule:: alpharaw.match.psm_match
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/match/spec_finder.rst b/docs/match/spec_finder.rst
@@ -0,0 +1,7 @@
+alpharaw.match.spec_finder
+==========================
+
+.. automodule:: alpharaw.match.spec_finder
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/match_modules.rst b/docs/match_modules.rst
@@ -0,0 +1,9 @@
+match functionalities
+===========================
+
+.. toctree::
+   :maxdepth: 1
+
+   match/match_utils
+   match/psm_match
+   match/spec_finder
diff --git a/docs/reader_modules.rst b/docs/reader_modules.rst
@@ -0,0 +1,10 @@
+readers modules
+===========================
+
+.. toctree::
+   :maxdepth: 1
+
+   readers/ms_data_base
+   readers/thermo
+   readers/sciex
+   readers/mzml
diff --git a/docs/readers/ms_data_base.rst b/docs/readers/ms_data_base.rst
@@ -0,0 +1,7 @@
+alpharaw.ms_data_base
+==========================
+
+.. automodule:: alpharaw.ms_data_base
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/readers/mzml.rst b/docs/readers/mzml.rst
@@ -0,0 +1,7 @@
+alpharaw.mzml
+==========================
+
+.. automodule:: alpharaw.mzml
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/readers/sciex.rst b/docs/readers/sciex.rst
@@ -0,0 +1,7 @@
+alpharaw.sciex
+==========================
+
+.. automodule:: alpharaw.sciex
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/readers/thermo.rst b/docs/readers/thermo.rst
@@ -0,0 +1,7 @@
+alpharaw.thermo
+==========================
+
+.. automodule:: alpharaw.thermo
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/viz/df_utils.rst b/docs/viz/df_utils.rst
@@ -0,0 +1,7 @@
+alpharaw.viz.df_utils
+==========================
+
+.. automodule:: alpharaw.viz.df_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/viz/plot_utils.rst b/docs/viz/plot_utils.rst
@@ -0,0 +1,7 @@
+alpharaw.viz.plot_utils
+==========================
+
+.. automodule:: alpharaw.viz.plot_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/viz/psm_plot.rst b/docs/viz/psm_plot.rst
@@ -0,0 +1,7 @@
+alpharaw.viz.psm_plot
+==========================
+
+.. automodule:: alpharaw.viz.psm_plot
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/viz/xic_plot.rst b/docs/viz/xic_plot.rst
@@ -0,0 +1,7 @@
+alpharaw.viz.xic_plot
+==========================
+
+.. automodule:: alpharaw.viz.xic_plot
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/viz_modules.rst b/docs/viz_modules.rst
@@ -0,0 +1,10 @@
+visualization
+===========================
+
+.. toctree::
+   :maxdepth: 1
+
+   viz/df_utils
+   viz/plot_utils
+   viz/psm_plot
+   viz/xic_plot