embodied-computation-group · LegrandNico · Dec 17, 2021 · Dec 2, 2021 · Dec 2, 2021 · Dec 2, 2021
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,7 +5,7 @@ repos:
     - id: isort
       files: ^systole/
 -   repo: https://github.com/ambv/black
-    rev: 21.9b0
+    rev: 21.12b0
     hooks:
     - id: black
       language_version: python3
@@ -16,7 +16,7 @@ repos:
     - id: flake8
       files: ^systole/
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v0.910'  # Use the sha / tag you want to point at
+    rev: 'v0.920'  # Use the sha / tag you want to point at
     hooks:
     - id: mypy 
       files: ^systole/

diff --git a/.travis.yml b/.travis.yml
diff --git a/README.rst b/README.rst
@@ -8,9 +8,6 @@
 .. image:: https://zenodo.org/badge/219720901.svg
    :target: https://zenodo.org/badge/latestdoi/219720901
 
-.. image:: https://travis-ci.org/embodied-computation-group/systole.svg?branch=master
-   :target: https://travis-ci.org/embodied-computation-group/systole
-
 .. image:: https://codecov.io/gh/embodied-computation-group/systole/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/embodied-computation-group/systole
 
@@ -66,6 +63,7 @@ The following packages are required to use Systole:
 * `pyserial <https://pyserial.readthedocs.io/en/latest/pyserial.html>`_ (>=3.4)
 * `setuptools <https://setuptools.pypa.io/en/latest/>`_ (>=38.4)
 * `requests <https://docs.python-requests.org/en/latest/>`_ (>=2.26.0)
+* `tabulate <https://github.com/astanin/python-tabulate/>`_ (>=0.8.9)
 
 
 The Python version should be 3.7 or higher.
@@ -78,6 +76,7 @@ For an introduction to Systole and cardiac signal analysis, you can refer to the
 .. list-table::
    :widths: 60 40
    :header-rows: 0
+   :align: center
 
    * - Cardiac signal analysis 
      - |Colab badge 1|
@@ -157,11 +156,11 @@ Systole implements time-domain, frequency-domain and non-linear HRV indices, as
 .. code-block:: python
 
   from bokeh.layouts import row
-  from systole.plots import plot_frequency, plot_pointcare
+  from systole.plots import plot_frequency, plot_poincare
 
   row(
       plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(300, 200)),
-      plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
+      plot_poincare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
       )
 
 .. image:: https://github.com/embodied-computation-group/systole/blob/dev/source/images/hrv.png

diff --git a/requirements-test.txt b/requirements-test.txt
@@ -11,4 +11,5 @@ numba>=0.51.2
 tqdm
 requests>=2.24.0
 papermill>=2.2.2
-pytest
+pytest
+tabulate>=0.8.9
diff --git a/requirements.txt b/requirements.txt
@@ -9,4 +9,5 @@ setuptools>=38.4
 packaging
 numba>=0.51.2
 tqdm
-requests>=2.26.0
+requests>=2.26.0
+tabulate>=0.8.9
diff --git a/setup.py b/setup.py
@@ -20,7 +20,7 @@ def get_requirements():
 DISTNAME = "systole"
 MAINTAINER = "Nicolas Legrand"
 MAINTAINER_EMAIL = "nicolas.legrand@cfin.au.dk"
-VERSION = "0.2.1"
+VERSION = "0.2.2"
 
 
 if __name__ == "__main__":

diff --git a/source/api.rst b/source/api.rst
@@ -6,7 +6,7 @@ Functions
 =========
 
 .. contents:: Table of Contents
-   :depth: 3
+   :depth: 2
 
 Correction
 ----------
@@ -37,6 +37,7 @@ Detection
 
     ppg_peaks
     ecg_peaks
+    res_peaks
     rr_artefacts
     interpolate_clipping
 
@@ -54,8 +55,13 @@ Heart Rate Variability
     pnnX
     rmssd
     time_domain
+    psd
     frequency_domain
-    nonlinear
+    nonlinear_domain
+    poincare
+    recurrence
+    recurrence_matrix
+    all_domain
 
 Plots
 -----
@@ -72,7 +78,7 @@ Plots
     plot_events
     plot_evoked
     plot_frequency
-    plot_pointcare
+    plot_poincare
     plot_raw
     plot_rr
     plot_shortlong

diff --git a/source/api/systole.detection.res_peaks.examples b/source/api/systole.detection.res_peaks.examples
diff --git a/source/api/systole.hrv.all_domain.examples b/source/api/systole.hrv.all_domain.examples
diff --git a/source/api/systole.hrv.nonlinear_domain.examples b/source/api/systole.hrv.nonlinear_domain.examples
diff --git a/source/api/systole.hrv.poincare.examples b/source/api/systole.hrv.poincare.examples
diff --git a/source/api/systole.hrv.psd.examples b/source/api/systole.hrv.psd.examples
diff --git a/source/api/systole.hrv.recurrence.examples b/source/api/systole.hrv.recurrence.examples
diff --git a/source/api/systole.hrv.recurrence_matrix.examples b/source/api/systole.hrv.recurrence_matrix.examples
diff --git a/source/api/systole.plots.plot_poincare.examples b/source/api/systole.plots.plot_poincare.examples
diff --git a/source/changelog.rst b/source/changelog.rst
@@ -24,6 +24,10 @@ This page contains information about what has changed in each new version of ``s
 
    <div class="col-md-9">
 
+.. include:: releases/v0.2.2.txt
+
+.. include:: releases/v0.2.1.txt
+
 .. include:: releases/v0.2.0.txt
 
 .. include:: releases/v0.1.3.txt

diff --git a/source/conf.py b/source/conf.py
@@ -106,16 +106,24 @@
     "logo_link": "https://systole-docs.github.io/",
 }
 
+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 = {

diff --git a/source/getting_started.rst b/source/getting_started.rst
@@ -20,6 +20,7 @@ The following packages are required to use Systole:
 * `pyserial <https://pyserial.readthedocs.io/en/latest/pyserial.html>`_ (>=3.4)
 * `setuptools <https://setuptools.pypa.io/en/latest/>`_ (>=38.4)
 * `requests <https://docs.python-requests.org/en/latest/>`_ (>=2.26.0)
+* `tabulate <https://github.com/astanin/python-tabulate/>`_ (>=0.8.9)
 
 
 The Python version should be 3.7 or higher.
@@ -76,11 +77,11 @@ Systole implements time-domain, frequency-domain and non-linear HRV indices, as
 .. code-block:: python
 
   from bokeh.layouts import row
-  from systole.plots plot_frequency, plot_pointcare
+  from systole.plots plot_frequency, plot_poincare
 
   row(
       plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(300, 200)),
-      plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
+      plot_poincare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
       )
 
 .. raw:: html

diff --git a/source/images/create_figures.py b/source/images/create_figures.py
@@ -4,7 +4,7 @@
 
 from systole import import_dataset1
 from systole.detection import ecg_peaks
-from systole.plots import plot_frequency, plot_pointcare, plot_raw, plot_subspaces
+from systole.plots import plot_frequency, plot_poincare, plot_raw, plot_subspaces
 from bokeh.io import export_png, save
 from bokeh.layouts import row
 # Import ECg recording
@@ -39,15 +39,15 @@
 export_png(
     row(
         plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(600, 400)),
-        plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(400, 400)),
+        plot_poincare(peaks, input_type="peaks", backend="bokeh", figsize=(400, 400)),
     ),filename="hrv.png"
 )
 
 #%% As HTML
 save(
     row(
         plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(300, 200)),
-        plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
+        plot_poincare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
     ),filename="hrv.html"
 )
 

diff --git a/source/index.rst b/source/index.rst
@@ -8,9 +8,6 @@
 .. image:: https://zenodo.org/badge/219720901.svg
    :target: https://zenodo.org/badge/latestdoi/219720901
 
-.. image:: https://travis-ci.org/embodied-computation-group/systole.svg?branch=master
-   :target: https://travis-ci.org/embodied-computation-group/systole
-
 .. image:: https://codecov.io/gh/embodied-computation-group/systole/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/embodied-computation-group/systole
 
@@ -149,6 +146,8 @@ Contributors
 - Jan C. Brammer (jan.c.brammer@gmail.com)
 - Gidon Levakov (gidonlevakov@gmail.com)
 - Peter Doggart (peter.doggart@pulseai.io)
+- Dominique Makowski (https://github.com/DominiqueMakowski)
+- Bertrand Hermann (bertrand.hermann@ghu-paris.fr)
 
 ================