Add sphinx docs.

.gitignore

@@ -142,3 +142,4 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
+/docs/generated/

README.md

@@ -1,6 +1,6 @@
 # eeglabio
 
-Python I/O support for EEGLAB files
+I/O support for EEGLAB files in Python.
 
 ### Installation
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_templates/autosummary/class.rst

@@ -0,0 +1,9 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :special-members: __contains__,__getitem__,__iter__,__len__,__add__,__sub__,__mul__,__div__,__neg__,__hash__
+   :members:
+
+.. _sphx_glr_backreferences_{{ fullname }}:

docs/_templates/autosummary/function.rst

@@ -0,0 +1,7 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ objname }}
+
+.. _sphx_glr_backreferences_{{ fullname }}:

docs/api.rst

@@ -0,0 +1,21 @@
+=============
+API Reference
+=============
+
+This is the reference for classes (``CamelCase`` names) and functions
+(``underscore_case`` names) of eeglabio.
+
+.. container:: d-none
+
+   :py:mod:`eeglabio`:
+
+   .. automodule:: eeglabio
+      :no-members:
+      :no-inherited-members:
+
+.. toctree::
+    :maxdepth: 2
+
+    raw
+    epochs
+    utils

docs/conf.py

@@ -0,0 +1,78 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+currdir = os.path.dirname(__file__)
+sys.path.append(os.path.abspath(os.path.join(currdir, '..')))
+
+import eeglabio
+
+# -- Project information -----------------------------------------------------
+
+project = 'eeglabio'
+copyright = '2021, Jack Zhang'
+author = 'Jack Zhang'
+
+# The full version, including alpha/beta/rc tags
+release = eeglabio.__version__
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'numpydoc',
+    'sphinx_copybutton',
+]
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://numpy.org/devdocs', None),
+    'scipy': ('https://scipy.github.io/devdocs', None),
+    'mne': ('https://mne.tools/dev', None)
+}
+
+numpydoc_attributes_as_param_list = True
+numpydoc_xref_param_type = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+autosummary_generate = True
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+html_theme = "pydata_sphinx_theme"
+html_theme_options = {
+    "github_url": "https://github.com/jackz314/eeglabio",
+    "show_prev_next": True,
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/epochs.rst

@@ -0,0 +1,17 @@
+
+Epochs
+======
+
+
+:py:mod:`eeglabio.epochs`:
+
+.. automodule:: eeglabio.epochs
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: eeglabio.epochs
+
+.. autosummary::
+   :toctree: generated/
+
+   export_set

docs/examples.rst

@@ -0,0 +1,20 @@
+Example Usage with `MNE <http://mne.tools/>`_
+=============================================
+
+Export from :class:`mne.Epochs` to EEGLAB (``.set``):
+
+    .. code-block:: python
+
+        import mne
+        from eeglabio.utils import export_mne_epochs
+        epochs = mne.Epochs(...)
+        export_mne_epochs(epochs, "file_name.set")
+
+Export from :class:`mne.io.Raw` to EEGLAB (``.set``):
+
+    .. code-block:: python
+
+        import mne
+        from eeglabio.utils import export_mne_raw
+        raw = mne.io.read_raw(...)
+        export_mne_raw(raw, "file_name.set")

docs/index.rst

@@ -0,0 +1,23 @@
+.. eeglabio documentation master file, created by
+   sphinx-quickstart on Tue Apr 13 18:47:08 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+I/O support for `EEGLAB <https://eeglab.org/>`_ files in Python
+===============================================================
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   Installation <install>
+   Examples <examples>
+   API Reference <api>
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/install.rst

@@ -0,0 +1,15 @@
+Installation
+============
+
+eeglabio requires Python version 3.6 or higher.
+You can install MNE-Python using ``pip`` from `PyPI <http://pypi.org/project/eeglabio>`_:
+
+  .. code-block:: console
+
+      pip install eeglabio  # dependencies are numpy, scipy
+
+Alternatively, from `Test PyPI <http://test.pypi.org/project/eeglabio>`_:
+
+  .. code-block:: console
+
+      pip install -i https://test.pypi.org/simple/ eeglabio

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/raw.rst

@@ -0,0 +1,17 @@
+
+Raw
+===
+
+
+:py:mod:`eeglabio.raw`:
+
+.. automodule:: eeglabio.raw
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: eeglabio.raw
+
+.. autosummary::
+   :toctree: generated/
+
+   export_set

docs/utils.rst

@@ -0,0 +1,20 @@
+
+Utils
+=====
+
+
+:py:mod:`eeglabio.utils`:
+
+.. automodule:: eeglabio.utils
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: eeglabio.utils
+
+.. autosummary::
+   :toctree: generated/
+
+   cart_to_eeglab
+   cart_to_eeglab_sph
+   export_mne_epochs
+   export_mne_raw

eeglabio/__init__.py

@@ -1,5 +1,6 @@
 from ._version import __version__
 from . import epochs
 from . import raw
+from . import utils
 
-__all__ = [epochs, raw]
+__all__ = ['epochs', 'raw', 'utils']

eeglabio/epochs.py

@@ -13,12 +13,12 @@ def export_set(fname, data, sfreq, events, tmin, tmax, ch_names,
     ----------
     fname : str
         Name of the export file.
-    data : np.ndarray, shape (n_epochs, n_channels, n_samples)
+    data : numpy.ndarray, shape (n_epochs, n_channels, n_samples)
         Data array containing epochs. Follows the same format as
         MNE Epochs' data array.
     sfreq : int
         sample frequency of data
-    events : np.ndarray, shape (n_events, 3)
+    events : numpy.ndarray, shape (n_events, 3)
         Event array, the first column contains the event time in samples,
         the second column contains the value of the stim channel immediately
         before the event/step, and the third column contains the event id.
@@ -32,13 +32,17 @@ def export_set(fname, data, sfreq, events, tmin, tmax, ch_names,
     event_id : dict
         Names of conditions corresponding to event ids (last column of events).
         If None, event names will default to string versions of the event ids.
-    ch_locs : np.ndarray, shape (n_channels, 3)
+    ch_locs : numpy.ndarray, shape (n_channels, 3)
         Array containing channel locations in Cartesian coordinates (x, y, z)
 
+    See Also
+    --------
+    .raw.export_set
+
     Notes
     -----
-    Channel locations are expanded to the full EEGLAB format
-    For more details see .io.utils.cart_to_eeglab_full_coords
+    Channel locations are expanded to the full EEGLAB format.
+    For more details see :func:`.utils.cart_to_eeglab_sph`.
     """
 
     data = data * 1e6  # convert to microvolts

eeglabio/raw.py

@@ -12,14 +12,14 @@ def export_set(fname, data, sfreq, ch_names, ch_locs=None, annotations=None):
     ----------
     fname : str
         Name of the export file.
-    data : np.ndarray, shape (n_epochs, n_channels, n_samples)
+    data : numpy.ndarray, shape (n_epochs, n_channels, n_samples)
         Data array containing epochs. Follows the same format as
         MNE Epochs' data array.
     sfreq : int
         sample frequency of data
     ch_names : list of str
         Channel names.
-    ch_locs : np.ndarray, shape (n_channels, 3)
+    ch_locs : numpy.ndarray, shape (n_channels, 3)
         Array containing channel locations in Cartesian coordinates (x, y, z)
     annotations : list, shape (3, n_annotations)
         List containing three annotation subarrays:
@@ -28,10 +28,14 @@ def export_set(fname, data, sfreq, ch_names, ch_locs=None, annotations=None):
         third array (float) is duration (in seconds)
         This roughly follows MNE's Annotations structure.
 
+    See Also
+    --------
+    .epochs.export_set
+
     Notes
     -----
-    Channel locations are expanded to the full EEGLAB format
-    For more details see .utils.cart_to_eeglab_full_coords
+    Channel locations are expanded to the full EEGLAB format.
+    For more details see :func:`.utils.cart_to_eeglab_sph`.
     """
 
     data = data * 1e6  # convert to microvolts