Merge pull request #143 from pfizer-opensource/development

Version 0.14.1.post1
pfizer-opensource · Mar 1, 2024 · 7cc8962 · 7cc8962
2 parents 5e8ba50 + 9c8b7b6
commit 7cc8962
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diff --git a/docs/conf.py b/docs/conf.py
@@ -48,7 +48,7 @@
     "sphinx.ext.autosummary",
     "numpydoc",
     "sphinx.ext.coverage",
-    "sphinx_panels",
+    "sphinx_design",
 ]
 
 # this is needed for some reason...
@@ -73,7 +73,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -243,11 +243,7 @@
     "skdh.features.lib.extensions",
     "skdh.io._extensions",
     "skdh.utility._extensions",
+    "skdh.preprocessing._extensions",
 ]
 
-# -----------------------------------------------------------------------------
-# Sphinx Panels
-# -----------------------------------------------------------------------------
-panels_add_bootstrapp_css = False
-
 # -- Extension configuration -------------------------------------------------
diff --git a/docs/index.rst b/docs/index.rst
@@ -12,91 +12,53 @@ Scikit Digital Health
 
 `SciKit-Digital-Health` is a Python package with methods for reading, pre-processing, manipulating, and analyzing Inertial Meausurement Unit data. `scikit-digital-health` contains the following sub-modules:
 
-.. panels::
-    :img-top-cls: pl-3 pr-3
-    :card: shadow
-
-    :img-top: _static/skdh_io.svg
-
-    :badge:`skdh.io,badge-primary`
-
-    +++
-    .. link-button:: skdh io
-        :type: ref
-        :text: Ingestion of common binary data files and generic data stores.
-        :classes: btn-outline-primary stretched-link btn-block
-
-    ---
-    :img-top: _static/skdh_preproc.svg
-    :badge:`skdh.preprocessing,badge-primary`
-    +++
-    .. link-button:: skdh preprocessing
-        :type: ref
-        :text: Pre-processing algorithms for inertial data.
-        :classes: btn-outline-primary stretched-link btn-block
-
-    ---
-    :img-top: _static/skdh_context.svg
-    :badge:`skdh.context,badge-primary`
-    +++
-    .. link-button:: skdh context
-        :type: ref
-        :text: Context detection methods for inertial sensor data.
-        :classes: btn-outline-primary stretched-link btn-block
-
-    ---
-    :img-top: _static/skdh_gait.svg
-    :badge:`skdh.gait,badge-primary`
-    +++
-    .. link-button:: skdh gait
-        :type: ref
-        :text: Gait detection and analysis from lumbar inertial data.
-        :classes: btn-outline-primary stretched-link btn-block
-
-    ---
-    :img-top: _static/skdh_s2s.svg
-    :badge:`skdh.sit2stand,badge-primary`
-    +++
-    .. link-button:: skdh sit2stand
-        :type: ref
-        :text: Sit-to-stand detection and analysis from lumbar inertial data.
-        :classes: btn-outline-primary stretched-link btn-block
-
-    ---
-    :img-top: _static/skdh_activity.svg
-    :badge:`skdh.activity,badge-primary`
-    +++
-    .. link-button:: skdh activity
-        :type: ref
-        :text: Actigraphy & activity analysis from inertial data.
-        :classes: btn-outline-primary stretched-link btn-block
-
-    ---
-    :img-top: _static/skdh_sleep.svg
-    :badge:`skdh.sleep,badge-primary`
-    +++
-    .. link-button:: skdh sleep
-        :type: ref
-        :text: Sleep detection and analysis from wrist inertial data.
-        :classes: btn-outline-primary stretched-link btn-block
-
-    ---
-    :img-top: _static/skdh_features.svg
-    :badge:`skdh.features,badge-primary`
-    +++
-    .. link-button:: skdh features
-        :type: ref
-        :text: Common time-series signal features.
-        :classes: btn-outline-primary stretched-link btn-block
-
-    ---
-    :img-top: _static/skdh_utility.svg
-    :badge:`skdh.utility,badge-primary`
-    +++
-    .. link-button:: skdh utility
-        :type: ref
-        :text: Utility functions for time-series analysis.
-        :classes: btn-outline-primary stretched-link btn-block
+.. grid:: 1 2 2 2
+    :gutter: 2
+
+    .. grid-item-card:: :bdg-primary:`skdh.io`
+        :img-top: _static/skdh_io.svg
+        :link: skdh-io
+        :link-type: ref
+
+    .. grid-item-card:: :bdg-primary:`skdh.preprocessing`
+        :img-top: _static/skdh_preproc.svg
+        :link: skdh-preprocessing
+        :link-type: ref
+
+    .. grid-item-card:: :bdg-primary:`skdh.context`
+        :img-top: _static/skdh_context.svg
+        :link: skdh-context
+        :link-type: ref
+
+    .. grid-item-card:: :bdg-primary:`skdh.gait`
+        :img-top: _static/skdh_gait.svg
+        :link: skdh-gait
+        :link-type: ref
+
+    .. grid-item-card:: :bdg-primary:`skdh.sit2stand`
+        :img-top: _static/skdh_s2s.svg
+        :link: skdh-sit2stand
+        :link-type: ref
+
+    .. grid-item-card:: :bdg-primary:`skdh.activity`
+        :img-top: _static/skdh_activity.svg
+        :link: skdh-activity
+        :link-type: ref
+
+    .. grid-item-card:: :bdg-primary:`skdh.sleep`
+        :img-top: _static/skdh_sleep.svg
+        :link: skdh-sleep
+        :link-type: ref
+
+    .. grid-item-card:: :bdg-primary:`skdh.features`
+        :img-top: _static/skdh_features.svg
+        :link: skdh-features
+        :link-type: ref
+
+    .. grid-item-card:: :bdg-primary:`skdh.utility`
+        :img-top: _static/skdh_utility.svg
+        :link: skdh-utility
+        :link-type: ref
 
 
 ..

diff --git a/docs/ref/activity.rst b/docs/ref/activity.rst
@@ -1,4 +1,4 @@
-.. _skdh activity:
+.. _skdh-activity:
 
 .. automodule:: skdh.activity
     :ignore-module-all:
diff --git a/docs/ref/context.rst b/docs/ref/context.rst
@@ -1,4 +1,4 @@
-.. _skdh context:
+.. _skdh-context:
 
 .. automodule:: skdh.context
     :ignore-module-all:
diff --git a/docs/ref/features.rst b/docs/ref/features.rst
@@ -1,4 +1,4 @@
-.. _skdh features:
+.. _skdh-features:
 
 .. automodule:: skdh.features
     :ignore-module-all:
diff --git a/docs/ref/gait.rst b/docs/ref/gait.rst
@@ -1,4 +1,4 @@
-.. _skdh gait:
+.. _skdh-gait:
 
 .. automodule:: skdh.gait
     :ignore-module-all:
diff --git a/docs/ref/gait_old.rst b/docs/ref/gait_old.rst
@@ -1,4 +1,4 @@
-.. _skdh gait_old:
+.. _skdh-gait_old:
 
 .. automodule:: skdh.gait_old
     :ignore-module-all:
diff --git a/docs/ref/io.rst b/docs/ref/io.rst
@@ -1,4 +1,4 @@
-.. _skdh io:
+.. _skdh-io:
 
 .. automodule:: skdh.io
     :ignore-module-all:
diff --git a/docs/ref/preprocessing.rst b/docs/ref/preprocessing.rst
@@ -1,4 +1,4 @@
-.. _skdh preprocessing:
+.. _skdh-preprocessing:
 
 .. automodule:: skdh.preprocessing
     :ignore-module-all:
diff --git a/docs/ref/sit2stand.rst b/docs/ref/sit2stand.rst
@@ -1,4 +1,4 @@
-.. _skdh sit2stand:
+.. _skdh-sit2stand:
 
 .. automodule:: skdh.sit2stand
     :ignore-module-all:
diff --git a/docs/ref/skdh.rst b/docs/ref/skdh.rst
@@ -1,4 +1,4 @@
-.. _skdh base:
+.. _skdh-base:
 
 .. automodule:: skdh
     :ignore-module-all:
diff --git a/docs/ref/sleep.rst b/docs/ref/sleep.rst
@@ -1,4 +1,4 @@
-.. _skdh sleep:
+.. _skdh-sleep:
 
 .. automodule:: skdh.sleep
     :ignore-module-all:
diff --git a/docs/ref/utility.rst b/docs/ref/utility.rst
@@ -1,4 +1,4 @@
-.. _skdh utility:
+.. _skdh-utility:
 
 .. automodule:: skdh.utility
     :ignore-module-all:
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -5,4 +5,4 @@ matplotlib
 numpydoc
 sphinx>=2.2.0
 pydata-sphinx-theme
-sphinx-panels
+sphinx-design
diff --git a/docs/src/dev/adding_documentation.rst b/docs/src/dev/adding_documentation.rst
@@ -19,69 +19,71 @@ Other than this, the docstrings will be automatically scanned and generated, wit
 
 Documentation of the your new module occurs almost fully in the ``__init__.py`` file
 for the module. This will contain any information on the module, how it works, as
-well as any relevant background information (e.g. :ref:`Gait <skdh gait>`). For
+well as any relevant background information (e.g. :ref:`Gait <skdh-gait>`). For
 another good reference from NumPy, see the
 `numpy.fft <https://numpy.org/doc/stable/reference/routines.fft.html>`_ page.
 
 Next is the file directing Sphinx to automatically find and document the custom
 module, ``docs/ref/custom_module.rst``. Finally, to make the new module show up
 in the API reference, add it to the ``docs/ref/index.rst`` toctree!
 
-.. tabbed:: src/skdh/custom_module/\_\_init\_\_.py
-    :selected:
+.. tab-set::
 
-    .. code-block:: python
+    .. tab-item:: src/skdh/custom_module/\_\_init\_\_.py
+        :selected:
 
-        """
-        IMU <Custom Module> (:mod:`skdh.custom_module`)
-        ===============================================
+        .. code-block:: python
 
-        .. currentmodule:: skdh.custom_module
+            """
+            IMU <Custom Module> (:mod:`skdh.custom_module`)
+            ===============================================
 
-        Inertial sensor <custom module>
-        -------------------------------
+            .. currentmodule:: skdh.custom_module
 
-        .. _Remove the `` below
+            Inertial sensor <custom module>
+            -------------------------------
 
-        .. ``autosummary``::
-            :toctree: generated/
+            .. _Remove the `` below
 
-            CustomClass  .. _this is the name of your class
+            .. ``autosummary``::
+                :toctree: generated/
 
-        Headline 2
-        ----------
-        content
-        """
-        from skdh.custom_module.custom_module import CustomModule
+                CustomClass  .. _this is the name of your class
 
-.. tabbed:: docs/ref/custom_module.rst
+            Headline 2
+            ----------
+            content
+            """
+            from skdh.custom_module.custom_module import CustomModule
 
-    .. code:: rst
+    .. tab-item:: docs/ref/custom_module.rst
 
-        ..
-            _Give it a custom explicit reference label
+        .. code:: rst
 
-        .. _skdh custom-module:
+            ..
+                _Give it a custom explicit reference label
 
-        .. automodule:: skdh.custom_module
-            :ignore-module-all:
+            .. _skdh custom-module:
 
-.. tabbed:: docs/ref/index.rst
+            .. automodule:: skdh.custom_module
+                :ignore-module-all:
 
-    .. code:: rst
+    .. tab-item:: docs/ref/index.rst
 
-        .. _skdh api reference:
+        .. code:: rst
 
-        API Reference
-        =============
+            .. _skdh api reference:
 
-        .. toctree::
-            :maxdepth: 2
+            API Reference
+            =============
 
-            gait
-            sit2stand
-            read
-            custom_module
+            .. toctree::
+                :maxdepth: 2
+
+                gait
+                sit2stand
+                read
+                custom_module
 
 And thats it! Before pushing and creating a pull request, make sure that the documentation builds properly:
 

diff --git a/docs/src/installation.rst b/docs/src/installation.rst
@@ -3,28 +3,30 @@ Installation
 
 Both PyPI and Conda-Forge should have pre-built wheels for major distributions.
 
-.. tabbed:: conda
+.. tab-set::
 
-    ::
+    .. tab-item:: conda
 
-        conda install -c conda-forge scikit-digital-health
+        ::
 
-.. tabbed:: pip
-    :selected:
+            conda install -c conda-forge scikit-digital-health
 
-    ::
+    .. tab-item:: pip
+        :selected:
 
-        pip install scikit-digital-health
+        ::
 
-.. tabbed:: pip from GitHub
+            pip install scikit-digital-health
 
-    ::
+    .. tab-item:: pip from GitHub
 
-        pip install git+ssh://[email protected]/PfizerRD/scikit-digital-health.git
-        # install from a specific tag
-        pip install git+ssh://[email protected]/PfizerRD/[email protected]
-        # install from a specific branch
-        pip install git+ssh://[email protected]/PfizerRD/scikit-digital-health@development
+        ::
+
+            pip install git+ssh://[email protected]/PfizerRD/scikit-digital-health.git
+            # install from a specific tag
+            pip install git+ssh://[email protected]/PfizerRD/[email protected]
+            # install from a specific branch
+            pip install git+ssh://[email protected]/PfizerRD/scikit-digital-health@development
 
 Run-time requirements
 ^^^^^^^^^^^^^^^^^^^^^