[docs] : First step for autogenerated documentation.

[CI] : Add flake8 linting.

Author: LegrandNico

.github/workflows/docs.yml

@@ -0,0 +1,35 @@
+name: Build and Deploy
+
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+    branches:
+      - master
+permissions:
+  contents: write
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.9
+
+      - name: Build
+        run: |
+          pip install .
+          pip install -r requirements-docs.txt
+          sphinx-build -b html docs docs/build/html
+
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: source/build/html
+          BRANCH: gh-pages

.github/workflows/linting.yml

@@ -30,3 +30,4 @@ jobs:
         mypy ./cardioception/ --ignore-missing-imports
         black ./cardioception/
         isort ./cardioception/
+        flake8 ./cardioception/

.isort.cfg

@@ -1,5 +1,5 @@
 [settings]
-known_third_party = numpy,pandas,papermill,pkg_resources,psychopy,serial,systole
+known_third_party = numpy,pandas,papermill,pkg_resources,psychopy,serial,sphinx_bootstrap_theme,systole
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0

.pre-commit-config.yaml

@@ -1,20 +1,24 @@
 repos:
--   repo: https://github.com/asottile/seed-isort-config
-    rev: v2.2.0
-    hooks:
-    - id: seed-isort-config
 -   repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:
     - id: isort
-      exclude: tests/
+      files: ^cardioception/
 -   repo: https://github.com/ambv/black
     rev: 22.6.0
     hooks:
     - id: black
       language_version: python3
+      files: ^cardioception/
+-   repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
+    hooks:
+    - id: flake8
+      files: ^cardioception/
+      args: [--extend-ignore=E501]
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: 'v0.971'
     hooks:
-    - id: mypy
+    - id: mypy 
+      files: ^cardioception/
       args: [--ignore-missing-imports, --follow-imports=skip]

cardioception/HBC/__init__.py

@@ -1,2 +1,4 @@
-from .parameters import *
-from .task import *
+from .parameters import getParameters
+from .task import rest, run, trial, tutorial
+
+__all__ = ["getParameters", "run", "trial", "tutorial", "rest"]

cardioception/HBC/task.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 import pandas as pd
-from psychopy import core, event, sound, visual
+from psychopy import core, event, visual
 
 
 def run(

cardioception/HRD/__init__.py

@@ -1,2 +1,19 @@
-from .parameters import *
-from .task import *
+from .parameters import getParameters
+from .task import (
+    confidenceRatingTask,
+    responseDecision,
+    run,
+    trial,
+    tutorial,
+    waitInput,
+)
+
+__all__ = [
+    "getParameters",
+    "confidenceRatingTask",
+    "responseDecision",
+    "run",
+    "trial",
+    "tutorial",
+    "waitInput",
+]

cardioception/HRD/task.py

@@ -9,7 +9,6 @@
 import pkg_resources  # type: ignore
 from psychopy import core, event, sound, visual
 from systole.detection import ppg_peaks
-from systole.recording import BrainVisionExG
 
 
 def run(
@@ -435,7 +434,9 @@ def trial(
             # You can adapt these line to work with a different setup provided that
             # it can measure and create the new variable `bpm` (the average beats per
             # minute over the 5 seconds of recording).
-            signal = parameters["oxiTask"].read(duration=5.0).recording[-75 * 6 :]
+            signal = (
+                parameters["oxiTask"].read(duration=5.0).recording[-75 * 6 :]  # noqa
+            )
             signal, peaks = ppg_peaks(signal, sfreq=75, new_sfreq=1000, clipping=True)
 
             # Get actual heart Rate

cardioception/__init__.py

@@ -1,5 +1,5 @@
 from typing import TYPE_CHECKING
 
 if not TYPE_CHECKING:
-    from .HBC import *
-    from .HRD import *
+    from .HBC import *  # noqa
+    from .HRD import *  # noqa

docs/conf.py

@@ -0,0 +1,135 @@
+# 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:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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 time
+
+import sphinx_bootstrap_theme
+
+import cardioception
+
+# -- Project information -----------------------------------------------------
+
+project = "cardioception"
+copyright = "2022-{}, Nicolas Legrand".format(time.strftime("%Y"))
+author = "Nicolas Legrand"
+release = cardioception.__version__
+
+
+image_scrapers = ("matplotlib",)
+
+sphinx_gallery_conf = {
+    "examples_dirs": "../examples/",
+    "backreferences_dir": "api",
+    "image_scrapers": image_scrapers,
+}
+
+# -- 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.mathjax",
+    "sphinx.ext.doctest",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx_gallery.gen_gallery",
+    "matplotlib.sphinxext.plot_directive",
+    "numpydoc",
+    "jupyter_sphinx",
+    "sphinx_panels",
+    "myst_nb",
+    "sphinx_gallery.load_style",
+]
+
+panels_add_bootstrap_css = False
+
+# Generate the API documentation when building
+autosummary_generate = True
+numpydoc_show_class_members = False
+
+# Include the example source for plots in API docs
+plot_include_source = True
+plot_formats = [("png", 90)]
+plot_html_show_formats = False
+plot_html_show_source_link = False
+
+source_suffix = [".rst", ".md"]
+
+# The master toctree document.
+master_doc = "index"
+
+# 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 = []
+
+# -- 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 = "pydata_sphinx_theme"
+html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+html_theme_options = {
+    "icon_links": [
+        dict(
+            name="GitHub",
+            url="https://github.com/embodied-computation-group/Cardioception",
+            icon="fab fa-github-square",
+        ),
+        dict(
+            name="Twitter",
+            url="https://twitter.com/visceral_mind",
+            icon="fab fa-twitter-square",
+        ),
+        dict(
+            name="Pypi",
+            url="https://pypi.org/project/Cardioception/",
+            icon="fas fa-box",
+        ),
+    ],
+    "logo_link": "https://embodied-computation-group.github.io/Carcioception/#",
+}
+
+html_sidebars = {"api": [], "changelog": [], "notebooks/*": []}
+
+# 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_css_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css"
+]
+html_logo = "images/logo.png"
+
+
+def setup(app):
+    app.add_css_file("style.css")
+
+
+# -- Intersphinx ------------------------------------------------
+
+intersphinx_mapping = {
+    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+    "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
+    "matplotlib": ("http://matplotlib.org/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "seaborn": ("https://seaborn.pydata.org/", None),
+    "psychopy": ("https://psychopy.org/index.html", None),
+}