sdevenes · spanoamara · Oct 6, 2020 · Oct 5, 2020 · Oct 5, 2020 · Oct 5, 2020
diff --git a/.gitignore b/.gitignore
@@ -3,8 +3,9 @@ data/
 
 ### Sphinx Doc ###
 docs/build/*
-public/*
+docs/source/api/
 
 ### Python execution ###
 scripts/__pycache__/
 tests/output/
+
diff --git a/.travis.yml b/.travis.yml
@@ -18,15 +18,21 @@ install:
 
 script:
   # Run phase of our CI pipeline
-  - make unitTests
-  - make doc
+  # Run unitTests
+  - nosetests --nocapture -v tests/test.py
+
+  # Generate rst files from docstring
+  - sphinx-apidoc -fMeT -o docs/source/api scripts
+  # Build documentation
+  - sphinx-build docs/source docs/build
+  - touch docs/build/.nojekyll
 
 deploy:
   - provider: pages:git
     verbose: true
     edge: true
     token: $GITHUB_TOKEN
-    local_dir: ./public/
+    local_dir: ./docs/build
     on:
         branch: master
         condition: $TRAVIS_PYTHON_VERSION = 3.8
diff --git a/README.rst b/README.rst
@@ -12,8 +12,21 @@
 This mini project was developed during the M05 course "reproducibility and open science"
 taught by Idiap as part of the AI master 2020-2021.
 
-.. topic:: Working hypothesis
+Working hypothesis
+------------------
 
-    It is possible to perform human activity recognition using data from continuous ambient sensors
+It is possible to perform human activity recognition using data from continuous ambient sensors
 
+Dataset
+-------
 
+The dataset that was used for this project is the following: https://archive.ics.uci.edu/ml/datasets/Human+Activity+Recognition+from+Continuous+Ambient+Sensor+Data.
+It represents ambient data collected in 30 homes with volunteer residents.
+Data are collected continuously while residents perform their normal routines.
+It contains 36 features measured plus one output for the classification label of the activity, for
+a total of 13956534 entries.
+
+Machine learning
+----------------
+
+Random forest classifiers from scikit-learn were used to obtains the results presented in this project.
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/source/algorithm.rst b/docs/source/algorithm.rst
diff --git a/docs/source/analysis.rst b/docs/source/analysis.rst
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -0,0 +1,9 @@
+API Documentation
+=================
+
+Information on specific functions, classes, and methods.
+
+.. toctree::
+   :glob:
+
+   api/*
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -18,11 +18,11 @@
 
 # -- Project information -----------------------------------------------------
 AUTHOR='Spano Amara, Devènes Steve'
-VERSION = "0.1.0"  # subprocess.check_output(["git", "describe"]).decode('UTF-8')
+VERSION = "0.2.0"
 
 project = 'M05 miniProject'
-copyright = '2020'
-author = 'Spano Amara, Devènes Steve'
+import time
+copyright = u"%s" % time.strftime("%Y")
 
 author = AUTHOR
 
@@ -37,23 +37,35 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    #'sphinx.ext.autodoc',
+    "sphinx.ext.doctest",
     'sphinx.ext.napoleon',
+    'sphinx.ext.intersphinx',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
 ]
 
+intersphinx_mapping = dict(
+    python=('https://docs.python.org/3', None),
+    numpy=("https://numpy.org/doc/stable/", None),
+    scipy=("https://docs.scipy.org/doc/scipy/reference", None)
+)
+
+# Generates auto-summary automatically
+autosummary_generate = True
+
 # Also document special classes like __init__
 autoclass_content = 'both'
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+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 = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'pastie'
+pygments_style = 'sphinx'
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -71,7 +83,7 @@
 # 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']
+#html_static_path = ['_static']
 
 
 # -- Extension configuration -------------------------------------------------
@@ -95,15 +107,6 @@
     'titles_only': False,
 }
 
-# html_context = {
-#     "display_gitlab": True,
-#     "gitlab_user": "",
-#     "gitlab_repo": "",
-#     "gitlab_version": "master",
-#     "conf_py_path": "/docs/source/",
-#     "gitlab_host": "",
-#      }
-
 # html_logo = '../../img/****.svg'
 html_title = 'M05 MiniProject docs'
 

diff --git a/docs/source/database.rst b/docs/source/database.rst
diff --git a/docs/source/download_data.rst b/docs/source/download_data.rst
diff --git a/docs/source/guide.rst b/docs/source/guide.rst
@@ -1,6 +1,6 @@
-============
+===========
  User Guide
-============
+===========
 
 This guide explains how to use this package and obtain results published in our
 paper.  Results can be re-generated automatically by executing the following

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,5 +1,5 @@
-Welcome to M05 miniProject's documentation!
-===========================================
+Human Activity Recognition from Continuous Ambient Sensor Data
+==============================================================
 
 Documentation
 -------------
@@ -9,7 +9,7 @@ Documentation
    installation
    guide
    troubleshooting
-   modules
+   api
 
 
 Authors

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -2,9 +2,9 @@
 Installation
 ------------
 
-This package depends on the python libraries listed in requirements.txt to run properly. 
+This package depends on the python libraries listed in `requirements.txt <https://github.com/sdevenes/M05_MiniProject/blob/master/requirements.txt>`_  to run properly. 
 Please install a modern version of these packages before trying to run the code examples.
-Or create directly a conda virtual environment using the conda.yml file as in the following
+Or create directly a conda virtual environment using the requirements.txt file as in the following
 exemple.
 
 To download a copy of this package, clone it from its repository in GitHub:
@@ -21,11 +21,14 @@ To download a copy of this package, clone it from its repository in GitHub:
 Building the documentation
 --------------------------
 
-The project documentation is generated with sphinx and can simply be build using the command:
+The project documentation is generated with sphinx and can simply be build using these two commands:
 
 .. code:: sh
 
-   $ make doc
+   $ sphinx-apidoc -fMeT -o docs/source/api scripts
+   $ sphinx-build docs/source docs/build
 
-The python API documentation will be automatically generated for all the python modules located
-in `scripts <https://github.com/sdevenes/M05_MiniProject/tree/feature/documentation/scripts>`_, as long as their docstring is completed.
+The first command will generates restructured files containing API documentation for all the python 
+modules located in `scripts <https://github.com/sdevenes/M05_MiniProject/tree/master/scripts>`_ 
+based on their docstring. And the second command will packages all the rst files together and build this
+html doc.
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
diff --git a/docs/source/paper.rst b/docs/source/paper.rst
diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
@@ -5,7 +5,7 @@ Unit tests are available for the project and can be run simply with the followin
 
 .. code-block:: shell
 
-   (project) $ make unitTests
+   (project) $ nosetests --nocapture -v tests/test.py
 
 .. note::
    the tests are implemented using `nose <https://pypi.org/project/nose/>`_ python package, it needs to be installed beforhand

diff --git a/makefile b/makefile