Merge pull request #54 from maestroque/integrate-physutils

Integrate physutils - Physio object usage

.all-contributorsrc

@@ -110,6 +110,20 @@
         "review",
         "userTesting"
       ]
+    },
+    {
+      "login": "maestroque",
+      "name": "George Kikas",
+      "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4",
+      "profile": "https://github.com/maestroque",
+      "contributions": [
+        "code",
+        "ideas",
+        "infra",
+        "docs",
+        "bug",
+        "review"
+      ]
     }
   ],
   "contributorsPerLine": 8,

.circleci/config.yml

@@ -15,14 +15,14 @@ orbs:
 # Define a job to be invoked later in a workflow.
 # See: https://circleci.com/docs/2.0/configuration-reference/#jobs
 jobs:
-  test37: # This is the name of the job, feel free to change it to better match what you're trying to do!
+  test39: # This is the name of the job, feel free to change it to better match what you're trying to do!
     # These next lines defines a Docker executors: https://circleci.com/docs/2.0/executor-types/
     # You can specify an image from Dockerhub or use one of the convenience images from CircleCI's Developer Hub
     # A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
     # The executor is the environment in which the steps below will be executed - below will use a python 3.6.14 container
     # Change the version below to your required version of python
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.9
     working_directory: /tmp/src/phys2denoise
     resource_class: medium
     # Checkout the code as the first step. This is a dedicated CircleCI step.
@@ -46,7 +46,7 @@ jobs:
           command: |
             pytest --cov=./phys2denoise
             mkdir /tmp/src/coverage
-            mv ./.coverage /tmp/src/coverage/.coverage.py37
+            mv ./.coverage /tmp/src/coverage/.coverage.py39
       - store_artifacts:
           path: /tmp/src/coverage
       # Persist the specified paths (workspace/echo-output) into the workspace for use in downstream job.
@@ -56,11 +56,11 @@ jobs:
           root: /tmp
           # Must be relative path from root
           paths:
-            - src/coverage/.coverage.py37
+            - src/coverage/.coverage.py39
 
-  test310:
+  test311:
     docker:
-      - image: cimg/python:3.10
+      - image: cimg/python:3.11
     working_directory: /tmp/src/phys2denoise
     resource_class: medium
     steps:
@@ -75,17 +75,17 @@ jobs:
           command: |
             pytest --cov=./phys2denoise
             mkdir /tmp/src/coverage
-            mv ./.coverage /tmp/src/coverage/.coverage.py310
+            mv ./.coverage /tmp/src/coverage/.coverage.py311
       - store_artifacts:
           path: /tmp/src/coverage
       - persist_to_workspace:
           root: /tmp
           paths:
-            - src/coverage/.coverage.py310
+            - src/coverage/.coverage.py311
 
   style_check:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.9
     working_directory: /tmp/src/phys2denoise
     resource_class: small
     steps:
@@ -105,7 +105,7 @@ jobs:
   merge_coverage:
     working_directory: /tmp/src/phys2denoise
     docker:
-      - image: cimg/python:3.10
+      - image: cimg/python:3.11
     resource_class: small
     steps:
       - attach_workspace:
@@ -133,13 +133,13 @@ workflows:
     # Inside the workflow, you define the jobs you want to run.
     jobs:
       - style_check
-      - test37:
+      - test39:
           requires:
             - style_check
-      - test310:
+      - test311:
           requires:
             - style_check
       - merge_coverage:
           requires:
-            - test37
-            - test310
+            - test39
+            - test311

docs/user_guide/metrics.rst

@@ -71,6 +71,10 @@ example shows how to compute the heart rate and the heart rate variability using
 
     from phys2denoise.metrics.chest_belt import respiratory_variance_time
 
-    # Given that the respiratory signal is stored in `data`, the peaks in `peaks`, the troughs in `troughs`
+    # Given that the respiratory signal is stored in `data` (which is not a physio.Physio instance), the peaks in `peaks`, the troughs in `troughs`
     # and the sample rate in `sample_rate`
-    _, rvt = respiratory_variance_time(data, peaks, troughs, sample_rate)
+    rvt = respiratory_variance_time(data, peaks, troughs, sample_rate)
+
+The computed respiratory variance time is stored in the variable ``rvt``. An internal check is performed to verify if the input data is a Physio object or not
+determining the appropriate output format. If the input is not a ``Physio`` object, the output will be a numpy array only containing the computed metric. Otherwise,
+the output will be a tuple with the updated Physio object and the computed metric.