Merge pull request #16 from PfizerRD/development

Update to version 0.2.0

.coveragerc

@@ -0,0 +1,21 @@
+[run]
+data_file = coverage/.coverage
+omit =
+    # setup files
+    *setup.py
+    # init files
+    *__init__.py
+    # version file
+    *version.py
+source = src/
+
+[report]
+# regexes for lines to exclude from consideration
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    def __str__
+    if version_info
+
+[html]
+directory = coverage

.gitignore

@@ -3,6 +3,9 @@
 .idea/*
 .idea*
 
+# other
+.DS_Store
+
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -138,3 +141,4 @@ dmypy.json
 !src/skimu/features/lib/
 /docs/ref/gait/generated/
 /docs/**/generated/
+/coverage/

docs/conf.py

@@ -194,7 +194,7 @@
 # -----------------------------------------------------------------------------
 intersphinx_mapping = {
     'python': ('https://docs.python.org/dev', None),
-    'numpy': ('https://numpy.org/doc/stable/reference/index.html', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable', None),
 }

docs/index.rst

@@ -4,12 +4,12 @@
    contain the root `toctree` directive.
 
 Welcome to SciKit-IMU's documentation!
-=================================
+======================================
 
-.. image:: https://github.com/PfizerRD/scikit-imu/workflows/skimu/badge.svg)
+.. image:: https://github.com/PfizerRD/scikit-imu/workflows/skimu/badge.svg
    :alt: GitHub Actions Badge
 
-`Scikit-IMU` is a Python package with methods for reading, pre-processing, manipulating, and analyzing Inertial Meausurement Unit data. `SciKit-IMU` contains the following sub-modules:
+`SciKit-IMU` is a Python package with methods for reading, pre-processing, manipulating, and analyzing Inertial Meausurement Unit data. `scikit-imu` contains the following sub-modules:
 
 sit2stand
 ---------

docs/ref/index.rst

@@ -1,10 +1,13 @@
 .. _skimu api reference
 
 API Reference
-================
+=============
 
 .. toctree::
     :maxdepth: 2
 
+    skimu
+    read
+    features
     gait
-    features
+    sit2stand

docs/ref/read.rst

@@ -0,0 +1,2 @@
+.. automodule:: skimu.read
+    :ignore-module-all:

docs/ref/sit2stand.rst

@@ -0,0 +1,2 @@
+.. automodule:: skimu.sit2stand
+    :ignore-module-all:

docs/ref/skimu.rst

@@ -0,0 +1,2 @@
+.. automodule:: skimu
+    :ignore-module-all:

setup.py

@@ -149,7 +149,8 @@ def parse_setuppy_commands():
     'scipy>=1.3.1',
     'pandas>=0.23.4',
     'lightgbm>=2.3.0',
-    'pywavelets'
+    'pywavelets',
+    'scikit-learn'  # needed for lightgbm
 ]
 
 if sys.version_info < (3, 7):
@@ -204,7 +205,8 @@ def configuration(parent_package='', top_path=None):
     # ========================
     config.add_data_files(
         ('skimu/gait/model', 'src/skimu/gait/model/final_features.json'),
-        ('skimu/gait/model', 'src/skimu/gait/model/lgbm_gait_classifier_no-stairs.lgbm')
+        ('skimu/gait/model', 'src/skimu/gait/model/lgbm_gait_classifier_no-stairs_50hz.lgbm'),
+        ('skimu/gait/model', 'src/skimu/gait/model/lgbm_gait_classifier_no-stairs_20hz.lgbm')
     )
     # ========================
 

src/skimu/__init__.py

@@ -1,8 +1,35 @@
+"""
+Scikit IMU (:mod:`skimu`)
+=======================================
+
+.. currentmodule:: skimu
+
+Pipeline Processing
+-------------------
+
+.. autosummary::
+    :toctree: generated/
+
+    Pipeline
+
+Utility Functions
+-----------------
+
+.. autosummary::
+    :toctree: generated/
+
+    utility.compute_window_samples
+    utility.get_windowed_view
+"""
 from skimu.version import __version__
 
+from skimu.pipeline import Pipeline
+from skimu import utility
+
 from skimu import gait
 from skimu import sit2stand
 from skimu import features
+from skimu import read
 
 __skimu_version__ = __version__
-__all__ = ['gait', 'sit2stand', 'features', '__skimu_version__']
+__all__ = ['Pipeline', 'gait', 'sit2stand', 'read', 'features', 'utility', '__skimu_version__']